A Parsimony Approach to Biological Pathway Reconstruction Inference for Genomes and Metagenomes

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Talanta79(2009)768–774Contents lists available at ScienceDirectTalantaj o u r n a l h o m e p a g e:w w w.e l s e v i e r.c o m/l o c a t e/t a l a n taSimultaneous voltammetric determination of prednisone and prednisolone in human bodyﬂuidsRajendra N.Goyal∗,Sunita BishnoiDepartment of Chemistry,Indian Institute of Technology Roorkee,Roorkee247667,Indiaa r t i c l e i n f oArticle history:Received1April2009Received in revised form29April2009 Accepted30April2009Available online9May2009Keywords:PrednisonePrednisoloneVoltammetryDopingBiologicalﬂuids a b s t r a c tA sensitive,rapid and reliable electrochemical method based on voltammetry at single wall carbon nan-otube(SWNT)modiﬁed edge plane pyrolytic graphite electrode(EPPGE)is proposed for the simultaneous determination of prednisolone and prednisone in human bodyﬂuids and pharmaceutical preparations. The electrochemical response of both the drugs was evaluated by osteryoung square wave voltammetry (OSWV)in phosphate buffer medium of pH7.2.The modiﬁed electrode exhibited good electrocat-alytic properties towards prednisone and prednisolone reduction with a peak potential of∼−1230and ∼−1332mV respectively.The concentration versus peak current plots were linear for both the analytes in the range0.01–100␮M and the detection limit(3 /slope)observed for prednisone and prednisolone were0.45×10−8,0.90×10−8M,respectively.The results of the quantitative estimation of prednisone and prednisolone in biologicalﬂuids were also compared with HPLC and the results were in good agreement.©2009Elsevier B.V.All rights reserved.1.IntroductionCorticosteroids affect biochemical events and cellular processes in tissues and organ of the body,hence,play a crucial role in human physiology[1].Synthetic corticosteroids also have important physi-ological activities,such as anti-inﬂammatory and anti-stress action and are regarded as the most effective treatment for topical dis-eases[2,3]and these drugs also have the potential positive effects on sports performance.Hence,synthetic corticoids are extensively abused by athletes in competitive games and their use has been forbidden by the International Olympic Committee and World Anti-Doping Agency[4–6].Prednisone(I)and prednisolone(II)are synthetic corticosteroids usually prescribed in the treatment of a wide variety of inﬂammatory diseases such as asthma,rheumatoid arthritis,various kidney diseases including nephritic syndrome, allergies and cluster headache[7–11].These are available in market in the form of tablets,capsules,injections,ointments and creams and the use of both the compounds is banned in sports under anti-doping rules[12–14].Simultaneous determination of prednisolone and prednisone has great signiﬁcance to bioscience and clinical diagnosis since prednisone is a biologically inactive11-dehydro metabolite of prednisolone.In human system prednisone is con-verted to the bioactive moiety prednisolone,via reduction of the 11-oxo group by the liver enzyme,11-␤-hydroxydehydrogenase ∗Corresponding author.Tel.:+911332285794;fax:+911332273560.E-mail addresses:rngcyfcy@iitr.ernet.in,rngcyfcy@(R.N.Goyal).[15,16].In mammals including humans interconversion of pred-nisone to prednisolone was found after oral administration of either of them with somewhat favoured prednisolone[17–19].In view of the clinical importance and increased abuse of prednisolone and prednisone by athletes,it is considered desirable to analyze their concentrations in bodyﬂuids as well as in pharmaceutical formu-lations.In view of the importance of corticosteroids in human physi-ology many methods such as spectroscopy and chromatographic methods coupled with spectroscopy or diode array detector and chemiluminescence have been developed for the simultaneous or individual determination of prednisone and prednisolone in biolog-icalﬂuids[20–23].However,inspite of the fact that above methods are sensitive and widely used,they require special sample prepa-ration,time consuming extraction steps and long derivatization procedures.Polarography has also been attempted for determi-nation of prednisone and prednisolone,however,the two peaks were found to be seriously overlapping[24].In view of the increas-ing cases of doping by the athletes,simple,efﬁcient,sensitive and reproducible analytical technique is needed to detect such cases at the site of games.Osteryoung square wave voltammetry has been used for the sensitive determination of large number of anabolic steroids[25,26].However,the determination in these studies is based on oxidation of steroids.Since blood and urine possess uric acid,dopamine,xanthine and ascorbic acid,etc.,a major problem is encountered due to interference of their oxidation signals with ana-lyte signal.Hence,attempts in the present method are focused on determination based on reduction of prednisone and prednisolone.0039-9140/$–see front matter©2009Elsevier B.V.All rights reserved. doi:10.1016/j.talanta.2009.04.067R.N.Goyal,S.Bishnoi /Talanta 79(2009)768–774769The present paper presents determination of prednisone and pred-nisolone in biological ﬂuids using edge plane pyrolytic graphite electrode after modiﬁcation with single wall carbonnanotube.2.Materials and methods 2.1.InstrumentationVoltammetric experiments were carried out using a comput-erized BAS (Bioanalytical Systems,West Lafayette,USA)CV-50W analyzer.A three-electrode single compartment cell system was employed,with a platinum wire as counter electrode and Ag/AgCl electrode (3M NaCl)as reference (Model MF-2052RB-5B).The edge plane pyrolytic graphite electrode (∼6mm 2)used as the working electrode was prepared in the laboratory by the reported method [27].The pH of the buffers was measured using a Century India Ltd.,digital pH meter (Model CP-901).All potentials reported are referred to Ag/AgCl electrode at an ambient temperature of 27±2◦C.High performance liquid chromatography (HPLC)experi-ments were performed on Agilent 1100series system with reverse phase column RP-18e (5␮M).The mobile phase used for HPLC experiments was a mixture of water:methanol (60:40)at a ﬂow rate of 1.4ml min −1and absorbance of the eluent was monitored at 254nm.The JEOL JSM-7400F ﬁeld emission scanning electron microscopy (FE-SEM)instrument was used to study the surface morphology of SWNT modiﬁed EPPGE.2.2.Chemicals and reagentsPrednisone and prednisolone were obtained from Sigma (St.Louis,MO,USA).Prednisolone containing tablets manufactured by different pharmaceutical companies were purchased from the local market.Single-wall carbon nanotube (SWNT)of purity >95%was purchased from Bucky,USA.Phosphate buffers of desired pH and ionic strength (0.5M)were prepared according to the method of Christian and Purdy [28]using analytical grade chemicals from Merck.The stock solutions of desired concentration of prednisone and prednisolone were prepared in methanol (A.R.).Other solvents and chemicals used were of analytical grade.2.3.ProcedureVoltammograms were recorded after mixing 2mL of the stock solution of appropriate compound with 2mL of phosphate buffer.The solution was deoxygenated by bubbling nitrogen for 8–10min before recording the voltammograms.The optimized operating parameters to record osteryoung square voltammograms (OSWVs)were:initial E :0.0mV and ﬁnal E :−1600mV,square wave fre-quency (f ):15Hz,square wave amplitude (E SW ):25mV and potential step (E ):4mV.Control urine sample were received from healthy laboratory personnel and urine samples of patients undergoing treatment with prednisolone were obtained from the Institute Hospital.The samples were obtained after 4h of administration of prednisolonetablet (Nucort Forte 10mg).The human blood samples from three healthy volunteers were obtained from the Institute Hospital.The blood with EDTA as anticoagulant was ultra-centrifuged and the supernatant blood plasma obtained was taken for the analysis of prednisone and prednisolone.Urine and blood plasma samples were used for voltammetric analysis without any dilution since bio-logical samples did not show any reduction peak on scanning from 0.0to −1600mV.2.4.Fabrication of SWNT modiﬁed PGEThe bare edge plane pyrolytic graphite electrode was rubbed on an emery paper and washed with double distilled water and then touched softly onto tissue paper.The electrode was then ready for modiﬁcation.A 0.05mg mL −1suspension of SWNT was prepared by dispersing 0.05mg SWNT in 1.0mL N,N-dimethylformamide (DMF)by ultrasonic agitation.Initially 10–100␮L of the solution was casted at the surface of EPPGE using a microsyringe and dried in a stream of hot air.It was found that the peak current for pred-nisone as well as prednisolone did not increase after 40␮L.Hence,for further studies 40␮L of this solution was coated onto the sur-face of the clean pyrolytic graphite electrode.The electrode was then kept in air for 8–10h and now the working electrode with a well-coated layer of SWNT on its surface was ready for experi-mental purpose.Initially the response of modiﬁed electrode was recorded in a solution containing 2mL phosphate buffer solution of pH 7.2and 2mL methanol,which was previously de-oxygenated with nitrogen for at least 10min.The absence of peak in voltammo-gram in the region 0.0to −1.6V versus Ag/AgCl and very low current values indicate that the modiﬁed electrode can be safely used for experimental purposes.A comparison of typical FE-SEM images of bare edge plane PGE with SWNT modiﬁed EPPGE is presented in Fig.1.3.Results and discussion3.1.Electrochemical behaviour of prednisone and prednisolone Fig.2presents a comparison of typical osteryoung square wave voltammograms of 10␮M of prednisolone and prednisone at the bare and modiﬁed edge plane pyrolytic graphite electrodes in phosphate buffer of pH 7.2.Well deﬁned peaks for the reduc-tion of prednisone and prednisolone were observed at potentials ∼−1299and ∼−1412mV respectively at the bare electrode.The peak obtained for both the compounds is rather broad,suggesting slow electron transfer kinetics.However,with increase in concen-tration of prednisolone the second peak merged with background,hence,the attempts to use bare EPPGE for determination of the two steroids failed.At the SWNT modiﬁed electrode,well-deﬁned reduction peaks were obtained,where,the reduction peak potential of prednisone and prednisolone shifted to less negative potentials,∼−1230and ∼−1332mV respectively and the peak current also increased.The above results suggested that the SWNT modiﬁed electrode promoted the electrochemical reduction of prednisone and prednisolone by considerably accelerating the rate of elec-tron transfer.One of the reasons for this catalysis is that metallic impurities in nanotubes act as a promoter by increasing the rate of electron transfer,thus,a negative shift in their reduction poten-tials is observed.The electrocatalytic activity of SWNT has been assigned by many workers to entrapped metals in the cavity [29,30].3.2.Effect of pH and square wave frequencyThe effect of pH on the reduction of both the drugs was studied in the pH range 2.4–10.0.The peak potential (E p )of both the drugs770R.N.Goyal,S.Bishnoi /Talanta 79(2009)768–774Fig.1.A comparison of typical FE-SEM image of (A)bare edge plane PGE and (B)SWNT modiﬁed edge plane pyrolytic graphiteelectrode.Fig.2.Observed osteryoung square wave voltammograms for the reduction of 10␮M of prednisolone and prednisone at bare EPPGE (—–),SWCNT modiﬁed EPPGE (—)and background PBS (pH 7.2)at SWNT modiﬁed EPPGE (......).Fig.3.(A)Observed dependence of peak potential (−E p )on pH for 10␮M prednisone ( )and 10␮M prednisolone ( )at SWNT modiﬁed EPPGE.(B)Plot of −E p versus logarithm of frequency (log f )of 10␮M prednisone ( )and 10␮M prednisolone ( )at SWNT modiﬁed EPPGE.(C)Calibration plot observed for prednisone ( )and prednisolone ( )at SWNT modiﬁed EPPGE at pH 7.2.was found to shift towards more negative potentials with increase in pH (Fig.3A).The variation of peak potential (E p )with pH was linear for both the analytes and the dependence of E p on pH obey the relations:−E p (pH 2.4−10.0)=[825.52+54.53pH]versus Ag/AgCl for prednisone−E p (pH 2.4−10.0)=[944.52+54.58pH]versus Ag/AgCl for prednisolonehaving correlation coefﬁcients 0.9973and 0.9968respectively.The slope of the −E p versus pH curves was ∼55mV/pH for both the analytes,indicating that equal number of protons and electrons are involved in the electrode reaction.The inﬂuence of square wave frequency (f )on the peak current (i p )of both analytes was examined in the range of 5–75Hz.At fre-quency higher than 75Hz,the peaks merged with the background.The peak current (i p )of both the analytes was found to increase with increase in square wave frequency (f ).The dependence of peak cur-rent on square wave frequency was linear suggesting thereby that the electrode reaction for both the compounds is adsorption con-trolled [31,32].The variation of i p with f can be expressed by theR.N.Goyal,S.Bishnoi/Talanta79(2009)768–774771equations:i p(␮A)=0.2268f+0.4283for prednisonei p(␮A)=0.2215f+0.1444for prednisolonehaving correlation coefﬁcients0.9958and0.9991respectively.The peak potential of prednisone and prednisolone were also found to shift towards more negative potentials with increase in square wave frequency and the plots of E p versus log f were linear in the frequency range5–75Hz(Fig.3B).The variation of E p with log f can be expressed by the equations:−E p(mV)=103.22log f+1107.4for prednisone−E p(mV)=98.775log f+1212.6for prednisolonewith correlation coefﬁcients0.9988and0.9929respectively.Sucha behaviour indicates the nature of redox reaction as reversible[32].3.3.Individual determination of prednisone and prednisoloneThe square wave voltammograms were recorded for prednisone as well as prednisolone at different concentrations in the range 0.01–100␮M.It was found that the peak currents increased lin-early with increasing concentration(Fig.3C).The graphs between peak current(i p)and concentration from the data generated during OSWV studies were linear and the relation can be represented by the equations:i p(␮A)=0.3233C(␮M)+0.8415for prednisonei p(␮A)=0.1897C(␮M)+0.5815for prednisolonewith correlation coefﬁcients0.9993and0.9945respectively,where i p is current in␮A and C is concentration in␮M.The observed sensi-tivities for prednisone and prednisolone are0.33and0.19␮A␮M−1 respectively,indicating that both analytes can be safely estimated in the given concentration range.The detection limit of pred-nisone and prednisolone was calculated by using the formula3 /b, where is standard deviation of the blank and b is slope of the calibration curve,and found to be0.45×10−8and0.90×10−8M respectively.3.4.Simultaneous determination of prednisone and prednisoloneThe main aim of the present study was to simultaneously investi-gate the electrochemical response of prednisone and prednisolone in human bodyﬂuids,as metabolism of prednisolone in human system proceeds through prednisone.The main problem encoun-tered with simultaneous determination in earlier reports was close reduction potentials due to which it was difﬁcult to resolve the overlapped voltammograms[33].This problem was resolved in the present studies using SWNT modiﬁed edge plane pyrolytic graphite electrode.The simultaneous determination of prednisone and pred-nisolone at modiﬁed EPPGE was carried out byﬁxing the concentration of one compound and varying the concentration of other at pH7.2.Fig.4A shows square wave voltammograms for different concentration of prednisone keeping the concentration of prednisolone constant(10␮M).Theﬁgure clearly depicts that the voltammetric peak of prednisolone remains unaltered and the peak current remained practically constant.The peak current of prednisone increased with increase in its concentration.Similarly, Fig.4B shows square wave voltammograms obtained by varying the concentration of prednisolone keeping the concentration of pred-nisone constant(10␮M).The prednisolone signal increaseswith Fig.4.(A)Square wave voltammograms of mixture of prednisolone and prednisone at modiﬁed electrodes in0.1M phosphate buffer(pH7.2);(A)prednisone at a ﬁxed concentration of prednisolone10␮M;[prednisone]:a=5,b=10,c=30,d=40, e=60␮M and(B)prednisolone at aﬁxed concentration of prednisone;[prednisone] 10␮M;[prednisolone]:a=5,b=10,c=30,d=40,e=60␮M.increase in its concentration without affecting the prednisone sig-nal,which remains almost constant.Currents observed in both the cases for the varied component were essentially same as observed during the individual determination and obeyed the relation for the calibration plot.It was found that the reduction peak of nei-ther prednisone nor prednisolone interferes with each other in the studied concentration range and thus,the proposed method can be safely applied for their simultaneous determination.3.5.Interference studyIt was considered necessary to evaluate the inﬂuence of some electroactive interferents such as,uric acid,ascorbic acid,xanthine, albumin and hypoxanthine in the determination of prednisone and prednisolone,since these are common biological compounds present in noticeable amount in living systems.Study of their inﬂu-ence on voltammetric response of prednisone and prednisolone was carried out by recording voltammograms for mixtures con-tainingﬁxed quantity(10␮M)of the analytes(prednisone or prednisolone)and varying concentration of each interferent in the range10–1000␮M.The addition of these interferents did not affect the peak current of prednisone or prednisolone and no new reduc-tion peaks were observed in the range0to−1.6V.This behaviour suggested that prednisone and prednisolone can be safely deter-mined in biologicalﬂuids.As determination is based on reduction of prednisone and prednisolone,it is understandable that common metabolites present in biologicalﬂuids do not interfere because none of them are reducible.772R.N.Goyal,S.Bishnoi /Talanta 79(2009)768–774Fig.5.Square wave voltammograms of control urine sample (a),urine sample after administration of prednisolone tablet (b),control urine spiked with 30␮M pred-nisolone (c)and control urine spiked with 30␮M prednisone (d)at SWNT modiﬁed EPPGE.3.6.Analytical applications3.6.1.Real sample analysisTo establish the utility of the developed method,prednisone and prednisolone was determined in human urine samples.In mammals including humans,interconversion of prednisolone to prednisone,has been reported,hence,residues of both steroids are found after oral administration of either of them [17–19].Square wave voltammograms of control urine sample from healthy volunteer (a),urine sample (sample 1)from patient undergoing treatment with prednisolone after 4h of administration of sin-gle dose of 10mg prednisolone tablet (Nucort Forte)(b),control urine sample spiked with 30␮M of prednisolone (c)and con-trol urine sample spiked with 30␮M of prednisone (d)at SWNT modiﬁed edge plane pyrolytic graphite electrode are depicted in Fig.5.As can be seen,two clear peaks at −1230and −1332mV are observed in voltammograms (c)and (d),which are due to reduction of prednisone and prednisolone respectively.Curve (a)presents voltammogram of control urine and does not exhibit peaks corre-sponding to prednisone and prednisolone,however,peaks at same potentials in curve (b)indicate that both these steroids are excreted in urine sample (sample 1)from the patient undergoing treatment with prednisolone.The concentrations of both the compounds in urine sample 1were determined using developed method and were found as 12.48and 7.12␮M for prednisolone and prednisone respectively.Three urine samples were analyzed and the results obtained are presented in Table 1.The concentrations of prednisone and prednisolone in human urine samples were also determined using HPLC and the results were compared with the ones observed by present method.For this purpose,various concentrations of prednisone and prednisolone standards were analyzed using HPLC and the calibration curves were obtained by plotting the peak area of the analytes peaks against concentrations.Typical HPLC chromatograms of prednisoneTable 1A comparison of prednisone and prednisolone concentration determined by SWNT modiﬁed EPPGE and HPLC in human urine after 4h of administration of 10mg of prednisolone tablet.SamplePrednisolone Prednisone Modiﬁed EPPGEHPLC Modiﬁed EPPGE HPLC 112.4812.007.127.20212.0612.207.447.80312.8012.607.606.60Fig.6.A comparison of typical HPLC chromatograms observed for (A)standard solu-tion of prednisone,(B)standard solution of prednisolone,(C)control urine sample,(D)urine sample obtained from patient undergoing treatment with prednisolone after 4h of administration of 10mg prednisolone tablet.and prednisolone are presented by curves A and B in Fig.6and exhibit peaks at retention time ∼7.990and ∼9.432min respectively.Urine samples were diluted 6times prior to analysis to minimize the complexity of matrix.Curve C in Fig.6presents chromatogram of control urine and does not exhibit peaks corresponding to pred-nisone and prednisolone.The urine samples obtained from patients undergoing treatment with prednisolone after 4h of administration of prednisolone tablet were then injected.Samples were then ana-lyzed using HPLC method and a typical chromatogram observed for sample 1is presented by curve D.Two well-deﬁned peaks at reten-tion time ∼7.990and ∼9.432min were noticed corresponding to prednisone and prednisolone respectively.Other prominent peaks in chromatogram were observed at R t ∼1.090and ∼1.223min,most probably due to the presence of major urine metabolites like uric acid,xanthine,etc.,however,no attempts were made to identify them.Finally,the concentrations of prednisolone and prednisone in human urine samples were determined using calibration curves and found as 2.00and 1.2␮M respectively.As urine sample was diluted 6times before injection in HPLC,the concentration of pred-nisone and prednisolone in urine (sample 1)was determined as 12.0and 7.2␮M respectively.A comparison of prednisone and prednisolone determined by the developed method and HPLC is presented in Table 1and clearly indicates that the proposed method is in good agreement with those obtained by HPLC method.3.6.2.Analysis of prednisolone in pharmaceutical preparationsPrednisolone is normally prescribed for the treatment of vari-ous diseases,hence,the modiﬁed EPPGE was also used to analyze the prednisolone content in three common commercial medicinal samples,viz.Nucort Forte (Unimax Laboratories,Mfg.Lic.No.;32-B (H)),Omnacortil –10(Macleods Pharmaceuticals Ltd.,Mfg.Lic.No.;DD/313)and Wysolone*10,(Wyeth Ltd.,Mfg.Lic.No.;545).The tablets were grounded to powder,dissolved in methanol and then diluted so that the concentration of prednisolone falls in theR.N.Goyal,S.Bishnoi/Talanta79(2009)768–774773Table2Determination of prednisolone in commercial tablets using SWNT modiﬁed edgeplane pyrolytic graphite electrode.Sample Stated content(mg/tablet)Detected content(mg/tablet)Error(%)Nucort Forte109.83−1.7 Wysolone109.94−0.6 Omnacortil-10109.62−3.8working range.Following the proposed method the concentration of prednisolone in three commercial samples was determined using modiﬁed EPPGE.The results are summarized in Table2and clearly indicate that the prednisolone content determined by the proposed method is in good agreement with the claimed prednisolone con-tent in pharmaceutical preparations.It is also expected that the SWNT modiﬁed EPPGE has great potential for the determination of prednisone and prednisolone in pharmaceutical sample analysis.3.6.3.Recovery testRecovery experiments were also performed using standard addition method to evaluate the accuracy of the proposed method. The recovery tests of both drugs ranging from10to50␮M were carried out utilizing SWNT modiﬁed EPPGE.Three human plasma samples obtained from healthy volunteers were spiked with known amounts of standard prednisone and prednisolone subsequently followed by recording their voltammograms.In all the cases two separate well-deﬁned peaks were observed with E p−1230and −1332mV corresponding to prednisone and prednisolone respec-tively.The concentration of the two compounds was calculated using calibration plots and the results observed are listed in Table3. The recoveries varied in the range from97.60%to101.50%in the case of prednisolone and from96.60%to103.28%in case of pred-nisone.The recoveries indicate that the accuracy of the proposed voltammetric method is good.3.7.Stability and reproducibility of modiﬁed EPPGEThe stability and reproducibility of the modiﬁed electrode was evaluated by monitoring the peak current responses daily at a con-stant prednisolone or prednisone concentration over a period of15 days.The experimental results indicated that the current responses showed a relative standard deviation of3.24%and4.12%for pred-nisone and prednisolone respectively.After15days,reduction peak potentials shifted towards more negative potentials and current values were also decreased.These results suggest that the modi-ﬁed electrode can be safely used up to15days of its preparation, hence,possesses good stability.Table3Recovery results obtained for prednisone and prednisolone in human plasma sam-ples at the modiﬁed electrode.Prednisolone PrednisoneSpiked(␮M)Detected(␮M)Recovery(%)Detected(␮M)Recovery(%) Sample110.010.15101.509.8898.8030.029.8499.4730.24100.8050.050.60101.2051.64103.28Sample210.09.7697.609.6696.6030.030.34101.1330.96103.2050.049.9599.9051.08102.16 Sample310.010.00100.009.7697.6030.030.09100.3030.16100.5350.049.5099.0050.0100.00To examine the intraday reproducibility,repetitive measure-ments were carried out in a solution ofﬁxed concentration of either prednisolone or prednisone.The results of seven successive scans show a relative standard deviation of1.06%and1.64%respectively for prednisone and prednisolone.To ascertain the reproducibility of the results further,four electrodes with almost same area were modiﬁed with the same volume of SWNT solution in DMF and their response towards the reduction ofﬁxed concentration of pred-nisolone and prednisone was observed.The current obtained for the four independent electrodes showed a relative standard devi-ation of2.08%and1.84%respectively,conﬁrming thereby that the results are reproducible.Thus,the modiﬁed electrode exhibits good reproducibility and stability for the determination of prednisone and prednisolone.4.ConclusionsThe results presented above clearly demonstrate that pred-nisone and prednisolone can be simultaneously determined using square wave voltammetric technique at SWNT modiﬁed edge plane pyrolytic graphite electrode.The most promising result of the proposed method is the use of pyrolytic graphite electrode.The modiﬁed electrode not only exhibited strong catalytic activity towards the simultaneous reduction of prednisone and pred-nisolone,but also increased the peak currents.Several studies have been devoted to investigate the reason of electrocatalytic activity of SWNT.It is now generally accepted that embedded metals present in SWNT and accessible toﬂuids are responsible for such catalysis. The impurity of metals in SWNT has been assigned to cause elec-trocatalysis[29].Hurt et al.[34]and Liu et al.[35]have reported that metal which is completely encapsulated in impermeable car-bon shells and not in contact withﬂuid does not play any role during bioavailability studies of nickel in SWNT.It is also reported that with puriﬁcation of carbon nanotubes,the peak potential of dopamine shifts to more negative potential[30].Hence,such a metal is expected not to be electrochemically active.Thus,the “ﬂuid accessible metal”is probably an important property of car-bon nanotubes(rather than total metal present)and is believed to be responsible for electrocatalytic activity of CNT.The method has been successfully applied for the determina-tion of prednisolone in commercial preparations.Both the steroids have also been determined in human blood and urine samples with adequate reproducibility and sensitivity.As both drugs are exten-sively abused by athletes for doping and both are interconvertable to each other,therefore,it is expected that the simultaneous deter-mination of these corticosteroids in bodyﬂuids would provide a simple and fast method for detecting the cases of doping at the site of competitive games.Thus,the proposed method is a fast, sensitive and reliable approach for simultaneous determination of both synthetic corticosteroids and a promising substitute to other reported methods owing to its simplicity,rapidity and lowﬁnancial input.The available sites for reduction in prednisolone are the keto groups at positions3and20and in prednisone the keto groups at positions3,11and20.Ketosteroid having a carbonyl group con-jugated with a double bond has been reported to undergo easier reduction in comparison to isolated keto groups[36].In prednisone reduction at carbonyl group,C-11has been reported to be hindered due to the presence of methyl group at position10[23,37].Thus,the probable active site for reduction in both ketosteroids is carbonyl groups at position3.Therefore,peaks at−1230and−1332mV are assigned to the reduction of carbonyl groups at position3to give corresponding hydroxyl groups in a2H+,2e−reaction.Their inter-conversion in liver indicates that carbonyl group at position11is reduced to CHOH group[17–19]in prednisone and hydroxyl group in prednisolone is oxidized to C O.。

2017年全国医学博士英语统一考试试题

2017年全国医学博士英语统一考试试题2017年全国医学博士英语统一考试试题Part I Listening Comprehension(30%)略Part II Vocabulary(10%)Section ADirections:In this section,all the sentences are incomplete.Four words or phrases marked A,B,C and D are given beneath each of them.You are to choose the word or phrase that best completes the sentence,then mark your answer on the ANSWER SHEET.31.Chronic high-dose intake of vitamin A has been shown to have____effects on bones.A.adverseB.prevalentC.instantD.purposeful32.Drinking more water is good for the rest of your body,helping to lubricate joints and___toxinsand impurities.A.screen outB.knock outC.flush outD.rule out33.Rheumatologist advises that those with ongoing aches and pains first seek medical helpto____the problem.A.affiliateB.alleviateC.aggravateD.accelerate34.Generally,vaccine makers_____the virus in fertilized chicken eggs in a process that can takefour to six months.A.penetrateB.designateC.generateD.exaggerate35.Danish research shows that the increase in obese people in Denmark is roughly____to theincrease of carbon dioxide in the atmosphere.A.equivalentB.temporaryC.permanentD.relevant36.Ted was felled by a massive stroke that affected his balance and left him barely able tospeak____.A.bluntlyB.intelligiblyC.reluctantlyD.ironically37.In a technology-intensive enterprise,computers____all processes of the production andmanagement.A.dominateB.overwhelmC.substituteD.imitate38.Although most dreams apparently happen____,dream activity may be provoked by externalinfluences.A.homogeneouslyB.instantaneouslyC.spontaneouslyD.simultaneously39.We are much quicker to respond,and we respond far too quickly by giving____to our anger.A.ventB.impulseC.temperD.offence40.By maintaining a strong family_____,they are also maintaining the infrastructure of society.A.biasB.honorC.estateD.bondSection BDirections:Each of the following sentences has a word or phrase underlined.There are four words or phrases beneath each sentence.Choose the word or phrase which can best keep the meaning of the original sentence if it is substituted for the underlined part.Mark your answer on the ANSWER SHEET.rm the manager if you are on medication that makes you drowsy.A.uneasyB.sleepyC.guiltyD.fiery42.Diabetes is one of the most prevalent and potentially dangerous diseases in the world.A.crucialB.virulentC.colossalD.widespread43.Likewise,soot and smoke from fire contain a multitude of carcinogens.A.a matter ofB.a body ofC.plenty ofD.sort of44.Many questions about estrogen’s effects remain to be elucidated,and investigations areseeking answers through ongoing laboratory and clinical studies.A.implicatedB.impliedC.illuminatedD.initiated45.A network chatting is a limp substitute for meeting friends over coffee.A.accomplishmentB.refreshmentplementD.replacement46.When patients spend extended periods in hospital,they tend to become overly dependent andlose interest in taking care of themselves.A.extremelyB.exclusivelyC.exactlyD.explicitly47.Attempts to restrict parking in the city centre have further aggravated the problem of trafficcongestion.A.AmelioratedB.aggregatedC.deterioratedD.duplicated48.It was reported that bacteria contaminated up to80%of domestic retail raw chicken in theUnited States.A.inflamedB.inflictedC.infectedD.infiltrated49.Researchers recently ran the numbers on gun violence in the United States and reported thatright-to-carry-gun laws do not inhibit violent crime.A.curbB.induceC.lessenD.impel50.Regardless of our uneasiness about stereotypes,numerous studies have shown clear differencebetween Chinese and western parenting.A.specificationsB.sensationsC.conventionsD.conservations PartⅢCloze(10%)Directions:In this section there is a passage with ten numbered blanks.For each blank,there are four choices marked A,B,C and D on the right side.Choose the best answer and mark the letter of your choice on the ANSWER SHEET.It was the kind of research that gave insight into how flu strains could mutate so quickly.The same branch of research concluded in2005that the1918flu started in birds before passing to humans.Parsing this animal-human51could provide clues to52the next potential super flu,whichalready has a name:H5N1,also known as avian flu or bird flu.This potential killer also has a number:59%.According to the WHO,nearly three-fifths of the people who53H5NI since2003died from the virus,which was first reported54humans in Hong Kong in1997before a more serious55occurred in Southeast Asia between2003and2004.(It has since spread to Africa and Europe.)Some researchers argue that those mortality numbers are exaggerated because WHO only56cases in which victims are sick enough to go to the hospitals for treatment.57,compare that to the worldwide mortality rate of the1918pandemic;it may have killed roughly50million people,but that was only10%of the number of people infected,according to a2006estimate.H5NI’s saving grace—and the only reason we’re not running around masked up in public right now—is that the strain doesn’t jump from birds to humans,or from humans to humans,easily. There have been just over600cases(and359deaths)since2003.But58its lethality,and the chance it could turn into something far more transmissible,one might expect H5NI research to be exploding,with labs59the virus’s molecular components to understand how it spreads between animals and60to humans,and hoping to discover a vaccine that could head off a pandemic.51.A.rejection B.interface plement D.contamination52.A.be stopped B.stopping C.being stopped D.having stopped53.A.mutated B.effected C.infected D.contracted54.A.in B.on C.with D.from55.A.trigger unch C.outbreak D.outcome56.A.counts B.amounts to C.accounts for D.accumulates57.A.Thereafter B.Thereby C.Furthermore D.Still58.A.given B.regarding C.in spite of D.speaking of59.A.parses B.parsed C.parsing D.to parse60.A.potently B.absolutely C.potentially D.importantlyPart IV Reading Comprehension(30%)Directions:In this part,there are six passages,each of which is followed by five questions.For each question,there are four possible answers marked A,B,C,and D.Choose the best answer and mark the letter of your choice on the ANSWER SHEET.Passage OneIf you are reading this article,antibiotics have probably saved your life—and not once but several times.A rotten tooth,a knee operation,a brush with pneumonia;any number of minor infections that never turned nasty.You may not remember taking the pills,so unremarkable have these one-time wonder drugs become.Modern medicine relies on antibiotics—not just to cure diseases,but to augment the success of surgery,childbirth and cancer treatments.Yet now health authorities are warning,in uncharacteristically apocalyptic terms,that the era of antibiotics is about to end.In some ways,bacteria are continually evolving to resist the drugs.But in the past we’ve always developed new ones that killed them again.Not this time.Infections that once succumbed to everyday antibiotics now require last-resort drugs with unpleasant side effects.Others have become so difficult to treat that they kill some 25,000Europeans yearly.And some bacteria now resist every known antibiotic.Regular readers will know why:New Scientist has reported warnings about this for years.We have misused antibiotics appallingly,handing them out to humans like medicinal candy and feeding them to livestock by the tonne,mostly not for health reasons but to make meat cheaper.Now antibiotic-resistant bacteria can be found all over the world—not just in medical facilities,but everywhere from muddy puddles in India to the snows of Antarctica（南极洲）.How did we reach this point without viable successors to today’s increasingly ineffectual drugs? The answer lies not in evolution but economics.Over the past20years,nearly every major pharmaceutical company has abandoned panies must make money,and there isn’t much in short-term drugs that should be used sparingly.So researchers have discovered promising candidates,but can’t reach into the deep pockets needed to develop them.This can be fixed.As we report this week,regulatory agencies,worried medical bodies and Big Pharma are finally hatching ways to remedy this market failure.Delinking profits from the volume of drug sold(by adjusting patent rights,say,or offering prizes for innovation)has worked for other drugs,and should work for antibiotics—although there may be a worryingly long wait before they reach the market.One day,though,these will all to resistance too.Ultimately,we need,evolution-proof cures for bacterial infection:treatments that stop bacteria from causing disease,but don’t otherwise inconvenience the little blighters.When resisting drugs confers no selective advantage,drugs will stop breeding resistance.Researchers have a couple of candidates for such treatment.But they fear regulators will drag their feet over such radical approaches.That,too,can be fixed.We must not neglect development of the sustainable medicine we need,the way we have neglected simple antibiotic R&D.If we do,one day another top doctor will be telling us that the drugs no longer work—and there really will be no help on the way.61.In the first paragraph,the author is tying to_____.A.warn us against the rampant abuse of antibiotics everywhereB.suggest a course of action to reduce antibiotic resistanceC.tell us a time race between humans and bacteriaD.remind us of the universal benefit of antibiotics62.The warning from health authorities implies that_____.A.the pre-antibiotic era will returnB.the antibiotic crisis is about to repeatC.the wonder drugs are a double-edged swordD.the development of new antibiotics is too slow63.The appalling misuse of antibiotics,according to the passage,_____.A.has developed resistant bacteria worldwideB.has been mainly practiced for health reasonsC.has been seldom reported as a warning in the worldD.has been particularly worsened in the developing countries64.The market failure refers to____.A.the inability to develop more powerful antibioticsB.the existing increasingly ineffectual drugs in the marketC.the poor management of the major pharmaceutical companiesD.the deprived investment in developing new classes of antibiotics65.During the presentation of the two solutions,the author carries a tone of_____.A.doubtB.urgencyC.indifferenceD.helplessness Passage TwoThis issue of Science contains announcements for more than100different Gorgon Research Conferences，on topics that range from atomic physics to developmental biology.The brainchild（某人的主意）of Neil Gordon of Johns Hopkins University,these week-long meetings are designed to promote intimate,informal discussions of frontier science.Often confined to fewer than125 attendees,they have traditionally been held in remote places with minimal distractions.Beginning in the early1960s,I attended the summer Nucleic Acids Gordon Conference in rural New Hampshire，sharing austere（简朴的）dorm facilities in a private boy’s school with randomly assigned roommates.As a beginning scientist,I found the question period after each talk especially fascinating,providing valuable insights into the personalities and ways of thinking of many senior scientists whom I had not encountered previously.Back then,there were no cellphones and no internet,and all of the speakers seemed to stay for the entire week.During the long,session-free afternoons,graduate students mingled freely with professors.Many lifelong friendships were begun, and—as Gordon intended—new scientific collaborations began.Leap forward to today,and every scientist can gain immediate access to a vast store of scientific thought and to millions of other scientists via the Internet.Why,nevertheless,do in-person scientific meetings remain so valuable for a life in science?Part of the answer is that science works best when there is a deep mutual trust and understanding between the collaborators,which is hard to develop from a distance.But most important is the critical role that face-to-face scientific meetings play in stimulating a random collision of ideas and approaches.The best science occurs when someone combines the knowledge gained by other scientists in non-obvious ways to create a new understanding of how the world works.A successful scientist needs to deeply believe,whatever the problem being tackled,that there is always a better way to approach that problem than the path currently being taken.The scientist is then constantly on the alert for new paths to take in his or her work,which is essential for makingbreakthroughs.Thus,as much as possible,scientific meetings should be designed to expose the attendees to ways of thinking and techniques that are different from the ones that they already know.66.Assembled at Gordon Research Conference are those who____.A.are physicists and biologistsB.just start doing their sciencesC.stay in the forefront of scienceD.are accomplished senior scientists67.Speaking of the summer Nucleic Acids Gordon Conference,the author thinks highly of____.A.the personalities of senior scientistsB.the question period after each talkC.the austere facilities aroundD.the week-long duration68.It can be inferred from the author that the value of the in-person scientific conference_____.A.does not change with timesB.can be explored online exclusivelyC.lies in exchanging the advances in lie scienceD.is questioned in establishing a vast store of ideas69.The author believes that the face-to-face scientific conferences can help the attendeesbetter_____.A.understand what making a breakthrough means to themB.expose themselves to novel ideas and new approachesC.foster the passion for doing scienceD.tackle the same problem in science70.What would the author most probably talk about in the following paragraphs?A.How to explore scientific collaborations.B.How to make scientific breakthroughs.C.How to design scientific meetings.D.How to think like a genius.Passage ThreeBack in1896,the Swedish scientist Svante Arrhenius realized that by burning coal we were adding carbon dioxide to the air,and that this would warm the Earth.But he mentioned the issue only in passing（顺便地），for his calculations suggested it would not become a problem for thousands of years.Others thought that the oceans would soak up any extra CO2,so there was nothing much to worry about.That this latter argument has persisted to this day in some quarters highlights our species’propensity（倾向）to underestimate the scale of our impact on the planet.Even the Earth’s vast oceans cannot suck up CO2as quickly as we can produce it,and we now know the stored CO2is acidifying the oceans,a problem in itself.Now a handful of researchers are warning that energy sources we normally think of as innocuous could affect the planet’s climate too.If we start to extract immense amounts of power from the wind,for instance,it will have an impact on how warmth and water move around the planet,and thus on temperatures and rainfall.Just to be clear,no one is suggesting we should stop building wind farms on the basis of this risk.Aside from the huge uncertainties about the climatic effects of extracting power from the wind,our present and near-term usage is far too tiny to make any difference.For the moment,any negative consequences on the climate are massively outweighed by the effects of pumping out even more CO2.That poses by far the greater environmental threat;weaning ourselves off fossil fuels should remain the priority.Even so,now it is the time to start thinking about the long-term effects of the alternative energy sources we are turning to.Those who have already started to look at these issues report weary, indifferent or even hostile reactions to their work.That’s understandable,but disappointing.These effects may be inconsequential,in which case all that will have been wasted is some research time that may well yield interesting insights anyway. Or they may turn out to be sharply negative,in which case the more notice we have,the better.It would be unfortunate to put it mildly,to spend countless trillions replacing fossil-fuel energy infrastructure（基础建设）only to discover that its successor（替代物）is also more damaging than it need be.These climatic effects may even be beneficial.The first,tentative models suggest that extracting large amounts of energy from high-altitude jet streams would cool the planet, counteracting the effects of rising greenhouse gases.It might even be possible to build an energy infrastructure that gives us a degree of control over the weather:turning off wind turbines here, capturing more of the sun’s energy there.We may also need to rethink our long-term research priorities.The sun is ultimately the only source of energy that doesn’t end up altering the planet’s energy balance.So the best bet might be invest heavily in improving solar technology and energy storage—rather than in efforts to harness, say,nuclear fusion.For the moment,all of this remains supposition（推测）.But our species has a tendency to myopia.We have nothing to lose,and everything to gain by taking the long view for a change.71.In the first two paragraphs,the author is trying to draw our attention to____.A.the escalating scale of the global warmingB.the division of scientists over the issue of global warmingC.reasons for us to worry about extra CO2for the oceansD.the human tendency to underestimate the harmful effects on the planet72.The author’s illustration of wind-power extraction reflects____.A.the priority of protecting the environmentB.the same human propensity as mentioned previouslyC.the best strategy of reducing the environmental threatD.the definite huge uncertainties about the climatic effects73.The author argues that it would be unfortunate to replace fossil fuels only to find out that____.A.the successors are also damagingB.the countless trillions spent are wastedC.the alternative energy sources don’t workD.the research invites indifferent or even hostile reactions74.According to the author,the best strategy is____.A.to counteract the effects of rising greenhouse gasesB.to develop a degree of control over the weatherC.to extract large amounts of energy from windD.to explore solar energy and its storage75.It can be concluded from the passage that we need to take the long view on____.A.human existence on the planetB.humanity’s energy suppliesC.our environmental threatsD.our tendency to myopiaPassage FourOptical illusions are like magic,thrilling us because of their capacity to reveal the fallibility of our senses But there’s more to them than that,according to Dr.Beau Lotto,who is wowing the scientific world with work that crosses the boundaries of art,neurology,natural history and philosophy.What they reveal,he says,is that the whole world is the creation of our brain.What we see, what we hear,feel and what we think we know is not a photographic reflection of the word,but an instantaneous unthinking calculation as to what is the most useful way of seeing the world.It’s a best guess based on the past experience of the individual,a long evolutionary past that has shaped the structure of our brains.The world is literally shaped by our pasts.Dr.Lotto,40,an American who is a reader in neuroscience at University College London,has set out to prove it in stunning visual illusions,sculptures and installations,which have been included in art-science exhibitions.He explains his complex ideas from the starting point of visual illusions,which far from revealing how fragile our senses are show how remarkably robust they are at providing a picture of the world that serves a purpose to us.For centuries,artists and scientists have noted that a grey dot looks lighter against a dark background than being against a light background.The conventional belief was that it was because of some way the brain and eye is intrinsically wired.But Dr.Lotto believes it’s a learnt response;in other words,we see the world not as it is but as it is useful to us.“Context is everything,because our brains have evolved to constantly re-define normality,”says Dr.Lotto.“What we see is defined by our own experiences of the past,but also by what the human race has experienced through its history.”This is illustrated by the fact that different cultures and communities have different viewpoints of the world,conditioned over generations.For example,Japanese people have a famous inability to distinguish between the“R”and the“L”sound.This arises because in Japanese the sounds are totally interchangeable.“Differentiating between them has never been useful,so the brain has never learnt to do it.It’s not just that Japanese people find it hard to tell the difference.They literally cannot hear the difference.”Dr.Lotto’s experiments are grounding more and more hypotheses in hard science.“Yes,mywork is idea-driven,”he says.“But lots of research,such as MRI brain scanning,is technique-driven.I don’t believe you can understand the brain by taking it out of its natural environment and looking at it in a laboratory.You have to look at what it evolved to do,and look at it in relationship to its ecology.”76.What does the word“them”in the first paragraph refer to?A.Human senses.B.The fallibility of senses.C.Revealing capacity.D.Optical illusions.77.According to the passage,what is known about Dr.Beau Lotto?A.Though he is a neuroscientist,he has shocked the scientific world with his extensiveresearch in art,neurology,natural history and philosophy.B.Dr.Lotto is a professor at University College Landon who is specialized in a number ofdisciplines such as art,neurology,natural history and philosophy.C.Dr.Lotto has been attempting to exhibit his creative productions in art-science exhibitionsin the hope of proving his idea on optical illusions.D.Dr.Lotto has set out to create visual illusions,sculptures and installations which wellcombined the knowledge of art,neurology,natural history and philosophy.78.Which of the following statements can be inferred from Dr.Lotto’s study?A.People should believe their brains rather than their eyes as the world,to a great measure,iscreated and shaped by human brain.B.People should never believe their senses for what they see,hear,feel,and the truth may becontrary to the photographic image of the world.C.People should never believe their eyes for what they see are only accidental and temporaryforms of the world,which varies in accordance with contexts.D.People should be aware that their eyes can play tricks on them as what they see is actuallycreated by their brains which are shaped by their past experiences.79.According to Dr.Lotto,what is the reason for the fact that a grey dot looks lighter against adark background than being against a light background?A.It is a fact that the dot emerged to be lighter against a dark background than being against alight one.B.Human senses are remarkably robust at providing a picture of the world that serves apurpose to us through what they have learnt from past experiences.C.It is because of some way the brain and eye is intrinsically wired.D.Because the context in which the little dot placed has changed to be lighter.80.Which of the following statements is true about the research in neuroscience?A.Investigation on the brain involves scrutinizing a network in which both environment andthe brain itself function together.B.Both idea-driven and technique-driven are popular research methods in research study inneuroscience.C.People cannot carry out research study on brain in laboratory where it is isolated fromhuman body.D.Brain can be investigated in isolation with other faculties and organs as long as the researchis carried out in proper natural context.Passage FiveThe biggest thing in operating rooms these days is a million-dollar,multi-armed robot named da Vinci,used in nearly400,000surgeries nationwide last year—triple the number just four years earlier.But now the high-tech helper is under scrutiny over reports of problems,including several deaths that may be linked with it and the high cost of using the robotic system.There also have been a few disturbing,freak incidents:a robotic hand that wouldn’t let go of tissue grasped during surgery and a robotic arm hit-ting a patient in the face as she lay on the operating table.Is it time to curb the robot enthusiasm?Some doctors say yes,concerned that the“wow”factor and heavy marketing have boosted use. They argue that there is not enough robust research showing that robotic surgery is at least as good or better than conventional surgeries.Many U.S.hospitals promote robotic surgery in patient brochures,online and even on highway billboards.Their aim is partly to attract business that helps pay for the costly robot.The da Vinci is used for operations that include removing prostates,gallbladders and wombs, repairing heart valves,shrinking stomachs and transplanting organs.Its use has increased worldwide, but the system is most popular in the United States.For surgeons,who control the robot while sitting at a computer screen rather than standing over the patient,these operations can be less tiring.Plus robot hands don’t shake.Advocates say patients sometimes have less bleeding and often are sent home sooner than with conventional laparoscopic surgeries and operations involving large incisions.But the Food and Drug Administration is looking into a spike in reported problems during robotic surgeries.Earlier this year,the FDA began a survey of surgeons using the robotic system. The agency conducts such surveys of devices routinely,but FDA spokeswoman Synim Rivers said the reason for it now“is the increase in number of reports received”about da Vinci.Reports filed since early last year include at least five deaths.Whether there truly are more problems recently is uncertain.Rivers said she couldn’t quantify the increase and that it may simply reflect more awareness among doctors and hospitals about the need to report problems.Doctors aren’t required to report such things;device makers and hospitals are.Company spokesman Geoff Curtis said Intuitive Surgical has physician-educators and other trainers who teach surgeons how to use the robot.But they don’t train them how to do specific procedures robotically,he said,and that it’s up to hospitals and surgeons to decide“if and when a surgeon is ready to perform robotic cases.”A2010New England Journal of Medicine essay by a doctor and a health policy analyst said surgeons must do at least150procedures to become adept at using the robotic system.But there is no expert consensus on how much training is needed.New Jersey banker Alexis Grattan did a lot of online research before her gallbladder was removed last month at Hackensack University Medical Center.She said the surgeon’s many years of experience with robotic operations was an important factor.She also had heard that the surgeon was among the first to do the robotic operation with just one small incision in the belly button,instead of four cuts in conventional keyhole surgery.81.Why did FDA begin to scrutinize da Vinci?A.The number used in operation has been tripled.B.It is too expensive.C.It is reported to have frequent mechanical breakdown.wsuits increase with death case reports.82.According to some doctors,which of the following is NOT the reason to curb the enthusiasmfor da Vinci?A.The high cost causes unreasonable marketing.B.It is not as good as traditional surgeries.C.It needs more statistics to prove its value.D.It is necessary for doctors to consider some problems.83.What does FDA spokeswoman Synim Rivers mean?A.Doctors and hospitals should be responsible for those problems.B.It is doctors that think da Vinci robots are problematic.C.There are so many problems reports that FDA has to do an enquiry.D.FDA hasn’t finished the previous enquiry about the surgeons who used robots.84.What is correct about training according to the Geoff Curtis?A.A lack of sufficient training on the part of surgeons.B.A lack of sufficient training an the part of company.C.Doctors and hospitals are not sufficiently trained on specific procedures.D.Doctors and hospitals are not sufficiently trained on how to use robots.85.What is the best title for this passage?A.Four Hands Better than Two?B.Too Good to Be TrueC.Smart RobotsD.Who Is the Killer?Passage SixIn a poor,inland,gang-infested part of Los Angeles,there is a clinic for people with type1 diabetes.As part of the country health care system,it serves persons who have fallen through all other safety-net options,the poorest of the poor.Although type2diabetes is rampant in this part of。

担子果边缘担子果的边缘有两类一类...

中国隔担菌属的分类研究摘要隔担菌属真菌是一种植物病原菌，与蚧虫共生，可引起植物的膏药病。

在中国一般分布在黄河流域上游以南及长江流域各省，以云南、海南和台湾三省的种类最为丰富。

隔担菌属在很多植物上引起膏药病，但是一般在经济作物上引起病害时才会引起较多关注。

在板栗种植大省安徽，膏药病已经成为板栗主要病害之一，病害严重时可导致板栗树势极度衰弱，甚至枯死，严重影响了板栗产量和品质，给当地的栗农带来了较大的经济损失1，2。

一般条件下，我国隔担菌属真菌的生长和繁殖期为每年的3月至10月，即早春至晚秋，11月至来年2月处于休眠期。

隔担菌属的寄主植物涉及56个科，其中蔷薇科、芸香科和桑科居多。

寄主蚧虫涉及蚧总科盾蚧科下的8个属，其中拟白轮盾蚧属和白轮盾蚧属最为常见。

本论文研究了馆藏和野外新鲜采集的隔担菌属标本共200多号，描述了9个已知种，15个新种和6个中国新记录种。

首先，研究确认我国HMAS馆藏的2号隔担菌属标本，从中发现了一个新种（Septobasidium. yunnanense S.Z. Chen & L. Guo)3，纠正了一个错误鉴定的种(原定为S. leucostemum Pat.)，并发现其为中国新记录种(S. septobasidioides (Henn.) Höhn. & Litsch.)3。

其次，研究自海南、广西、西藏、四川等省新鲜采集的200多号标本，从中发现了5个中国新记录种S. atropunctum Couch3、S. conidiophorum Couch ex L.D. Gómez & Henk3、S. henningsii Pat.4、S. pseudopedicellatum Burt5和S. rhabarbarinum (Mont.) Bres.，还从中发现了14个新种。

已发表的11个新种包括S. albiziae6、S. atalantiae4、S. glycosmidis6、S. saurauiae5、S. elaeagni3、S. hydrangeae3、S. yunnanense3、S. capparis7、S. reevesiae7、S. dacrydii7和S.sichuanens8，待发表的4个新种包括S. cotoneaster、S. euonymi、S. symploci和S. hoveniae。

中国云南及西藏水生环境中的新种——棕孢香港霉(英文)

Hongkongmyces C.C.C. Tsang et ol., was introduced with a single species Hongkongmyces pedis, which is a human pathogen found from
菌物学报 1275
BAO Dan-Feng et al. /Hongkongmyces brunneisporus sp. nov. (Lindgomycetaceae) from...
摘要：在大湄公河次区域的水生真菌调查中Байду номын сангаас从中国云南和西藏的沉水腐木中分离得到4 个菌株。基
于 LSU、SSU、ITS、TEFl-cx和 RPB2 序列进行多基因系统发育分析，表明 4 个菌株属于菩提科香港霉属真
菌。系统发育分析结果显示4 个菌株聚集在一起，并与泰国香港霉形成姐妹支。基于形态学及分子系统学研究，将这 4 个菌株鉴定为新种棕孢香港霉。棕孢香港霉是香港霉属的第二个有性型物种，它因子囊果的孔口处有棕色至黑色的刚毛，且子囊孢子呈梭形，孢子两端逐渐变窄且钝圆，红棕色至暗棕色，具有多个隔膜而区别于另一个有性型物种泰国香港霉。本研究提供了该真菌新种的描述及图版并比较了该种与其他物种的形态差异。关键词：新种，形态学，系统发育，有性型，分类
Supported by the National Natural Science Foundation of China (31860006, 31970021) and Fungal Diversity Conservation and Utilization Innovation Team of Dali University (ZKLX2019213). o Corresponding author. E-mail: suhongyanl6@ Received: 2020-09-23, accepted: 2020-10-29

适配体在生物毒素检测中的应用进展

河南农业科学，2018，47(2):1-6Journal of Henan Agricultural Sciences d〇i：10. 15933/ki. 1004-3268.2018.02.001适配体在生物毒素检测中的应用进展王耀#，2,李少珍#，2,游一3,王珊4,李志娟4,胡骁飞2,王方雨2!(1.河南科技大学食品与生物工程学院/食品加工与安全国家实验教学示范中心，河南洛阳471023;2.河南省农业科学院河南省动物免疫学重点实验室，河南郑州450002;3.河南省农业科学院畜牧兽医研究所，河南郑州450002; 4.河南安必诺检测技术有限公司，河南郑州450001)摘要：食物中毒是一类重要的食源性疾病，近年来由生物毒素引起的食物中毒事件频繁出现，引起了社会广泛关注，对于食品中生物毒素的快速、高效检测提出了更高要求。

在众多快速检测技术中，基于适配体的检测方法是目前的研究热点之一。

作为新型识别工具，适配体具有特异性强、亲和力高、制备成本低等明显优势，已被应用于食品中危害物质的识别检测。

对适配体及其在各类生物毒素检测中的应用进行综述，并对该技术存在的问题及其发展方向进行探讨，以期促进基于适配体的检测方法在生物毒素快速检测中得到进一步的推广和应用。

关键词：适配体；生物毒素；检测中图分类号：S859.84 文献标志码：A文章编号：1004 -3268(2018)02 -0001 -06Application Progress of Aptamer in Biotoxin DetectionWANG Yao1，2,L I Shaozhen1,2,YOU Y i3,WANG Shan4,L I Zhijuan4,HU Xiaofei2,WANG Fan(1. College of Food and B io e n g in e e rin g，H enan U n ive rsity of Science and T e ch n o lo g y/N a tio n a l D em onstration C enter forE xperim enta l Food Processing and Safety E d u c a tio n，Luoyang 471023，C h in a；2. Henan Key Laboratory of A n im a lIm m u n o lo g y，H enan A cadem y of A g ric u ltu ra l S ciences，Zhengzhou 450002, C hina; 3. A n im a l H usbandry and V eterinaryResearch In s titu te，H enan Academ y of A g ric u ltu ra l Sciences, Zhengzhou 450002, C hina;4. Henan A n b in u o Inspection Technology Co. L td. ，Zhengzhou 450001，C hina)Abstract&Food poisoning is an important foodborne disease.In recent years，food poisoning caused bybiotoxins has been aroused the social widespread interest，thus the rapid and efficient detection of biotoxins in food has raised higher requirements.In man/ rapid detection techniques，the detection methodbased on the a ptamer is one of the research focus.As a new recognition tool，aptamer has the advantagesof strong specificity，high a fin it/ and low cost of preparation.In this paper，the aptam in various biological t oxin detection were reviewed，and the existing problems and development direction ofthe technology were discussed，so as t o promote the application aptamer-based method in the rapid detection of bio t oxins.Key words:Aptamer；Biotoxins;Detection生物毒素是动物、植物、微生物分泌代谢或半生物合成产生的、不可自复制的有毒化学物质，对其他生物物种具有毒害作用，按其来源可以将其分为微生物毒素、植物毒素和动物毒素。

2005年03月考博英语试题及答案

中国科学院博士研究生入学考试英语试卷2005年3月考生须知：一、本试卷由试卷一(PAPER ONE)和试卷二(PAPER TWO)两部分组成。

试卷一为客观题，答卷使用标准化机读答题纸；试卷二为主观题，答卷使用普通答题纸。

二、请考生一律用HB或2B铅笔填涂标准化机读答题纸，画线不得过细或过短。

修改时请用橡皮擦拭干净。

若因填涂不符合要求而导致计算机无法识别，责任由考生自负。

请保持机读答题纸清洁、无折皱。

三、全部考试时间总计180分钟，满分为100分。

时间及分值分布如下：试卷一：Ⅰ听力20分钟20分Ⅱ词汇15分钟10分Ⅲ完形填空15分钟15分Ⅳ阅读60分钟30分小计110分钟75分试卷二：Ⅴ英译汉30分钟10分Ⅵ写作40分钟15分小计70分钟25分CHINESE ACADEMY OF SCIENCESENGLISH ENTRANCE EXAMINATIONFORDOCTORAL CANDIDATESMarch 2005PAPER ONEPART Ⅰ LISTENING COMPREHENSION (20 minutes, 20 points)Directions:In this section, you will hear ten short conversations between two speakers. At the end of each conversation, a question will be asked about what was said. The question will be spoken only once. Choose the best answer from the four choices given by marking the corresponding letter with a single bar across the square brackets on your Machine-scoring Answer Sheet.1. A. He needs more fresh air. B. He is willing to go out.C. He is too sick to go out.D. He opened the window.2. A. Their friemts. B. Daily activities.C. Past experiences.D. Historical events.3. A. To buy a ticket. B. To pay a fee.C. To pay back a debt.D. To buy a gift.4. A. Give information. B. State preferences.C. Ask permission.D. Attract attention.5. A. In a gymnasium. B. In an art exhibition.C. In a shop.D. In a hotel.6. A. 19 dollars each. B. 38 dollars each.C. 30 dollars altogether.D. 36 dollars altogether.7. A. Jack is a gentleman. B. Jack does everything right.C. Jack is a desirable husband.D. Jack behaves immaturely sometimes.8. A. It was remarkable to both the man and the woman.B. It was not suitable for the woman.C. The man hated this kind of movie.D. The woman complained about its quality.9. A. See how much the jacket is.B. See if the jacket there is blue.C. See if there is a cell phone in the jacket.D. See if there was anything turned in this morning.10. A. The man has caught a cold. B. The woman was caught in a rainstorm.C. The weather forecast was inaccurate.D. It rained very heavily.Directions:In this section, you will hear three short talks. At the end of each talk, there will be a few questions. Both the talk and the questions will be read to you only once. After each question, there will be a pause. During the pause, you must choose the best answer fromthe four choices given by marking the corresponding letter with a single bar across the square brackets on your Machine-scoring Answer Sheet.Questions 11-13 are based on Talk 1.11. A. Language comes from physical labor.B. Language learning is a long-term endeavor.C. Language reflects history.D. Language study is very important.12. A. Constructing a wheel. B. Making a choice.C. Coming back.D. Turning around.13. A. The overthrow of a class. B. The overthrow of a tyrant.C. The overthrow of a belief.D. The overthrow of an act.Questions 14-17 are based on Talk 2.14. A. It‟s a wonderful idea.B. It‟s not a smart thing to do.C. It‟s too difficult to put into practice.D. It‟s interesting to the decision maker.15. A. Telling people about your degrees.B. Promising that you will make good achievements.C. Introducing your job responsibilities.D. Talking about the needs of the potential employer.16. A. The results which your potential boss wants to gain with your assistance.B. The results of making more money on an international market.C. The results that the employer has seen in the past.D. The results that your potential boss does not want to see.17. A. Proving that you are capable of doing the job.B. Seeking the position that is not too high or too low for you.C. Insisting that experience is more important than knowledge.D. Claiming that you are better than any other applicant.Questions 18-20 are based on Talk 3.18. A. They exercise dogs twice a day.B. They learn how to be responsible for dogs.C. They encourage dogs to go for long walks.D. They like dogs too much to care about other things.19. A. Working for the police.B. Relaxing with other dogs.C. Protecting businesses.D. Guiding the blind.20. A. Dogs ride in public transport.B. Dogs bite their owners when in a rage.C. Vehicles run over stray dogs.D. People always keep dogs on leads.PART ⅡVOCABULARY (15 minutes, 10 points, 0.5 point each)Directions: Choose the word or expression below each sentence that best completes the statement, and mark the corresponding letter of your choice with a single bar across the square brackets on your Machine-scoring Answer Sheet.21. Giorgio, now fifteen, and Lucia, also in her teens, were reaching the of their adolescence.A. crisisB. criterionC. causalityD. credibility22. At first Jackie prayed, frozen in fear, but gradually his terror curiosity.A. put up withB. lived up toC. did away withD. gave way to23. The International Olympic Committee rejects the accusations that Beijing‟s budget-cutting move might its preparation for the games.A. degradeB. deliberateC. deployD. defend24. You are not allowed to take a second job your employer gives you permission.A. so long asB. otherwiseC. unlessD. whereas25. They continued to about and enjoy themselves until they became tired.A. strokeB. strollC. stammerD. string26. The survey asked 750 school children about the values and beliefs they from television.A. pick upB. take upC. put upD. make up27. I am grateful for your invitation, and I‟d like to accept your offer with pleasure.A. delightedB. innocentC. graciousD. prestigious28. I must you farewell right now, but on some future occasion, I hope to see you again.A. relayB. bidC. sendD. deliver29. Perhaps my dishes will not be as delicious as those which you are accustomed to eating, but I beg you to grant my and have dinner with me.A. resentmentB. requirementC. requestD. reservation30. That singular ach ievement was not just about Korea‟s arrival as a football force but as a self-confident mature nation to be seriously.A. copedB. shownC. establishedD. taken31. Europe as a unit did little by itself; it either sent for US help, or each European government acted on its own.A. incidentalB. apparentC. cohesiveD. descendent32. On 9 December, James Joyce experienced one of those coincidences which affected him at the time and which later became material for his books.A. inadequatelyB. systematicallyC. profoundlyD. simultaneously33. Embarrassed, I nodded, trying to think of some way to my error.A. make do withB. make up forC. go in forD. go along with34. Furthermore, if I were to leave him, he would , for he cannot endure to be separated from me for more than one hour.A. prevailB. presideC. perishD. persecute35. With high hopes, the company sent samples of the substance to scientists, but theycouldn‟t any practical uses for it.A. come up withB. do justice toC. get even withD. look up to36. He signed a new contract with the Dublin firm, Maunsel & Company, on more favorable than those Grant Richards had given him.A. itemsB. termsC. articlesD. specifications37. Most scientists agree this outpouring contributes to global warming, which could eventually lead to coastal flooding, weather, and widespread crop loss.A. intensiveB. extremeC. unpleasedD. unique38. There was a quick turnover of staff in the department as the manager treated his employees with contempt.A. utterB. soleC. intimateD. corresponding39. The source, who spoke on condition of anonymity, to discuss the implication of that conclusion.A. recededB. impliedC. compliedD. declined40. Childhood can be a time of great insecurity and loneliness, during which the need to be accepted by peers great significance.A. takes onB. works outC. brings aboutD. gives inPART ⅢCLOZE TEST (is minutes, 15 points)Directions: There are 15 blanks in the following passage. Read the passage through. Then, go back and choose the most suitable of the words or phrases marked A, B, C, and D for each blank in the passage. Mark the corresponding letter of the word or phrase you have chosen with a single bar across the square brackets on your Machine-scoring Answer Sheet.Can exercise be a bad thing? Sudden death during or soon after strenuous exertion on the squash court or on the army training grounds, is not unheard of. 41 trained marathon runners are not immune to fatal heart attacks. But no one knows just 42 common these sudden deaths linked to exercise are. The registration and investigation of such 43 is very patchy; only a national survey could determine the true 44 of sudden deaths in sports. But the climate ofmedical opinion is shifting in 45 of exercise, for the person recovering from a heart attack as 46 as the average lazy individual. Training can help the victim of a heart attack by lowering the 47 of oxygen the heart needs at any given level of work 48 the patient can do more before reaching the point where chest pains indicate a heart starved of oxygen. The question is, should middle-aged people, 49 particular, be screened for signs of heart disease before 50 vigorous exercise?Most cases of sudden death in sport are caused by lethal arrhythmias in the beating of the heart, often in people 51 undiagnosed coronary heart disease. In North America 52 over 35 is advised to have a physical check-up and even an exercise electrocardiogram. The British, on the whole, think all this testing is unnecessary. Not many people die from exercise, 53 , and ECGs(心电图)are notoriously inaccurate. However, two medical cardiologists at the Victoria Infirmary in Glasgow, advocate screening by exercise ECG for people over 40, or younger people 54 at risk of developing coronary heart disease. Individuals showing a particular abnormality in their ECGs 55 , they say, a 10 to 20 times greater risk of subsequently developing signs of coronary heart disease, or of sudden death.41. A. Then B. Though C. Since D. Even42. A. why B. how C. if D. what43. A. runners B. exercises C. patients D. cases44. A. initiation B. evidence C. incidence D. indication45. A. favor B. positive C. inclination D. bias46. A. good B. well C. much D. far47. A. weight B. amount C. degree D. quality48. A. however B. because C. but D. so49. A. at B. to C. for D. in50. A. taking up B. trying on C. getting over D. doing with51. A. beyond B. by C. with D. of52. A. anyone B. none C. some D. nobody53. A. of course B. at all C. after all D. by far54. A. readily B. suddenly C. already D. ready55. A. having B. had C. having been D. havePART ⅣREADING COMPREHENSION (60 minutes, 30 points)Directions: You will read five passages in this part of the test. Below each passage there are some questions or incomplete statements. Each question or statement is followed by four choices marked A, B, C, and D. Read the passage carefully, and then select the choice that best answers the question or completes the statement. Mark the letter of your choice with a single bar across the square brackets on your Machine-scoring Answer Sheet.Passage 1I myself first saw Samarkand from a rise across a wilderness of crumbling ruins and great graveyards which lie between it and the airport. Suddenly we caught a glimpse of painted towers and the great blue domes of mosques and tombs shouldering the full weight of the sky among bright green trees and gardens. Beyond the gardens and the glittering domes still were those watchful mountains and their evocative snow. I found myself thinking of the thrill I had on catching my first sight of Damascus after crossing the desert from Syria. The light, the orchards and many of the trees were the same but deeper still was the sense of coming into contact with one of the most astonishing cultures in history, the world of the one and only Allah and his prophet Muhammad. It was a world that completely overawed me.Yet the memory of Samarkand which stays with me most clearly is quite a humble one. Coming back to the city from the country on my last evening we passed some unusual elm trees and I stopped to have a look at them. They were, my guide told me, perhaps a thousand years old, older certainly than Genghis Khan. A flock of fat-tailed sheep (the same kind of sheep that my own ancestors saw a Hottentot keeping when they landed at the Cape of Good Hope 321 years ago), tended by some Tadshik children, moved slowly home in the distance. Then from the city came quite clearly the call to prayer from mosque and minaret. I had not expected any calls at all and it made no difference that some of the calls came over loud-speakers. Then beyond the trees an old manappeared on a donkey, dismounted, spread a prayer mat on the ground, and kneeling towards Mecca, he began to pray.From Samarkand I journeyed on to Bokhara which was once the holiest city in Central Asia. At one time it possessed over a hundred religious colleges and close to four hundred mosques. It drew adventurers of all races towards it as it did Marco Polo. Not many of them reached their destination. These days at what used to be one of the richest market places in the world, one buys ice-cream instead of slaves; watches and mass-produced trinkets and fizzy drinks instead of gold, silks and turquoise jewellery. Few of the four hundred mosques remain and most have vanished without even leavinga trace.56. Samarkand lies .A. in a desertB. high in the mountainsC. in front of DamascusD. between the mountains and the airport57. The author said that he was overawed by .A. the beauty of the sceneB. the sight of DamascusC. the age of the placeD. the world of Allah and Muhammad58. The author refers to his clearest memory of Samarkand as “humble” because .A. it was an ordinary scene that he rememberedB. it was his last night in the city and his last memoryC. the elm trees were older than Genghis KhanD. the trees looked impressive in the evening light59. The author says that the sheep he saw were similar to .A. the ones his ancestors had keptB. the ones that lived in his own countryC. those his ancestors had seen at the Cape of Good HopeD. those his ancestors had taken to the Cape of Good Hope60. The author was surprised to hear the calls to prayer because .A. he was far away from the city, yet he could hear them clearlyB. he did not think there would be any callsC. the calls came from the mosquesD. the calls were no different over loud-speakers61. The market has changed in character because now .A. it does sell jewelleryB. the holy men do not sell thereC. it sells goods for tourists and items of little valueD. the traders have disappeared because it is too dangerous to sell therePassage 2The component of the healthy personality that is the first to develop is the sense of trust. As with other personality components, the sense of trust is not something that develops independent of other manifestations of growth. It is not that infants learn how to use their bodies for purposeful movement, learn to recognize people and objects around them, and also develop a sense of trust. Rather, the concept “sense of trust” is a shortcut expression intended to convey the characteristic flavor of all the child‟s satisfying experiences at this early age.Studies of mentally ill individuals and observations of infants who have been grossly deprived of affection suggest that trust is an early-formed and important element in the healthy personality. Psychiatrists find again and again that the most serious illnesses occur in patients who have been sorely neglected or abused or otherwise deprived of love in infancy.Observations of infants brought up in emotionally unfavorable institutions or moved to hospitals with inadequate facilities for psychological care support these findings. A recent report says that “Infants under 5 months of age who have been in an institution for some time present a well-defined picture. The outstanding features are listlessness, relative immobility, quietness, poor sleep, an appearance of unhappiness, etc.”Another investigation of children separated from their mothers at 6 to 12 months and not provided with an adequate substitute comes to much the same conclusion.Most significant for our present point, these reactions are most likely to occur in children who, up to the time of separation at 6 to 9 months of age, had a happy relation with their mothers, while those whose relations were unhappy are relatively unaffected.It is at about this age that the struggle between trusting and mistrusting the world comes to a climax, for it is then that children first perceive clearly that they and their environment are things apart. That at this point formerly happy infants should react so badly to separation suggests, indeed, that they had a faith that now has been shattered. In most primitive societies and in some sections of our own society, the attention accorded infants is more in line with natural processes. Throughout infancy the baby is surrounded by people who are ready to feed it, fondle it, and otherwise comfort it at a moment‟s notice. Moreover, these ministrations are given spontaneously and wholeheartedly, and without that element of nervous concern that may characterize the efforts of young mothers made self-conscious and insecure by our scientific age.We must not exaggerate, however. Most infants in our society too find smiles and comfort. As their own bodies come to be more dependable, there is added to the pleasures of increasing sensory response and motor control the pleasure of the mothers‟ encouragement. Then, too, psychologists tell us that mothers create a sense of trust in their children not by the particular techniques they employ but by the sensitiveness with which they respond to the children‟s needs and by their overall attitude.62. The sense of trust in an infant is under development when .A. the infant experiences some satisfactionB. adults‟ trust is adequateC. the infant learns how to moveD. the infant is surrounded by people he can recognize63. The author raises evidence of mental illness and other disorders in children .A. to introduce a discussion of the effect of institutions on childrenB. to show the effect on children of an unhappy relation with their mothers during infancyC. to warn parents of the dangers of neglecting and abusing their childrenD. to support the point that trust is an early formed and important element of a healthy personality64. Babies might mistrust the world if .A. they did not receive food when they were hungryB. they mastered their body movements too quicklyC. someone came too close to themD. they saw an object disappear65. The climax in the development of a sense of trust occurs .A. before maternal affection is providedB. when a child perceives that he or she is separate from the environmentC. when a child successfully controls his or her muscular coordinationD. as a result of maternal separation66. A possible reason that a child having an unhappy relation with his/her mother will not be affected by maternal separation at 6 to 9 months is that .A. the struggle between trusting and mistrusting has reached a climaxB. the child sees himself/herself as being separate from the environmentC. the child‟s sense of trust is destroyedD. no sense of trust has ever developed67. According to this passage, the most important factor in developing a sense of trust is .A. the type of techniques used by the motherB. the sensitivity of the childC. maternal loveD. the combined effect of natural feeling and cultural attitudes68. How can mothers create a sense of trust in a child?A. By showing confidence and experience in front of the child.B. By applying techniques taught by psychologists.C. By showing the child that the mother is understanding of his/her wants.D. By offering smiles and comforts.Passage 3I saw a television advertisement recently for a new product called an air sanitizer. A woman stood in her kitchen, spraying the empty space in front of her as though using Mace against an imaginary assailant. She appeared very determined. Where others aresatisfied with antibacterial-laced sponges, dish soaps, hand sanitizers and telephone wipes, here was a woman who sought to sterilize the air itself.As a casual student of microbiology, I find it hard to escape the absurdity here. This woman is, like any human being, home to hundreds of trillions of bacteria. Bacteria make up a solid third, by weight, of the contents of her intestines. If you were to sneak into her bathroom while she was showering—and based on my general impression of this woman from the advertisement, I don‟t recommend this—and secret away a teaspoon of the water at her feet, you would find some 820 billion bacteria. Bacteria are unavoidably, inevitably—and, usually, utterly benignly—a part of our world.The fantasy of a germ-free home is not only absurd, but it is also largely pointless. Unless you share your home with someone very old, very young (under 6 months) or very ill, the few hundred bacteria on a countertop, doorknob or spoon pose no threat. The bacteria that cause food poisoning, the only significant rational bacterial worry in the average home, need to multiply into the thousands or millions before they can overwhelm your immune system and cause symptoms.The only way common food poisoning bacteria can manage this is to spend four or five hours reproducing at room temperature in something moist that you then eat. If you are worried about food poisoning, the best defense is the refrigerator. If you don‟t make a habit of eating perishable food that has been left out too long, don‟t worry about bacteria.Viruses are slightly different. You need only pick up a few virus particles to infect yourself with a cold or flu, and virus particles can survive on surfaces for days. So disinfecting the surfaces in the home should, in theory, reduce the chances of picking up a bug.In practice, the issue is less clear. A study by Dr. Elaine Larson at the Columbia School of Nursing called into question the usefulness of antibacterial products for the home. In New York, 224 households, each with at least one preschooler, were randomly assigned to two groups. One group used antibacterial cleaning, laundry and hand-washing products. The other used ordinary products. For 48 weeks, the groups were monitored for seven symptoms of colds, flu and food poisoning—and found to be essentially thesame. A ccording to Dr. Gerba‟s research, an active adult touches an average of 300 surfaces every 30 minutes. You cannot win at this. You will become obsessive-compulsive. Just wash your hands with soap and water a few times a day, and leave it at that.69. What is the main idea of this passage？A. We don‟t need to worry too much about bacteria everywhere in our life.B. Antibacterial products for the home are found to be effective.C. The TV advertisement the writer mentioned is a total failure.D. The existent bacteria pose a threat only to the very young and very old.70. We can infer from Paragraph 3 that .A. healthy people should live separately from unhealthy members of the familyB. a germ-free home is not only possible, but significantC. unless you live with the vulnerable, it is pointless to sterilize the airD. our immune systems are too weak to fight against the food poisoning bacteria71. In the first sentence of Paragraph 4, “... manage this” means “to manage the process of .A. killing the bacteria in your bodyB. multiplying to a significantly large numberC. raising the room temperatureD. sterilizing the perishable food72. According to the author, if you want to keep healthy, you had better .A. make the room dryB. keep the food in the refrigeratorC. wash your hands as much as possibleD. clean the surfaces with anti-bacterial products73. From Paragraph 5 the author emphasizes .A. the danger of virusesB. the common existence of virus particlesC. the short life span of virusesD. the difficulty in killing viruses74. The word “bug” used in Paragraph 5 means .A. a bacteriumB. a coldC. a fluD. a virus75. According to the author, one will become obsessive-compulsive .A. if he washes his hands every time he touches a surfaceB. if he only washes his hands with soap and waterC. if he could not win over the bacteria in his homeD. if he does not fight against the bacteria at homePassage 4Until recently the halls of North High in Minneapolis were lined with vending machines where students could buy soda pop and other sugary drinks, as they can in most other high schools in the nation. But with rates of childhood obesity sky-rocketing, the Minneapolis school district worried about pushing pop. The district needed a way to keep its lucrative vending contract with Coca-Cola while steering kids toward more healthful beverages.Bryan Bass, North‟s assistant principal, took the challenge. He stocked 12 of North‟s 16 vending machines only with water, priced at 75 cents a bottle. Three machines dispensed juice and sports drinks for $1. Only one sold soft drinks, at $1.25 per can. “We located the water machines strategically outside our buildings, so when you come out of a classroom what you see is a water machine,” says Bass. “We also decided to allow water in classrooms but not juice or pop.” The result? Profits from the vending machines nearly tripled, from $ 4,500 to $11,000 in two years. They‟re now in their third year, and says Bass:“Water has become …cool.‟”North‟s suc cess demonstrates what many obesity experts and parents believe: Kids will learn to make healthful food and drink choices if they have access to them and are motivated to do so. “Price is a powerful motivator,” says Simone French of the University of Minnesota, an expert on school-based obesity prevention. She‟s impressed with North‟s efforts, but she says the problem is implementing these strategiesthroughout society. “Obesity is the biggest health issue facing kids,and we‟ve got to do more.”How to do mo re was outlined last week in the Institute of Medicine‟s 460-page action plan, mandated by Congress, on “Preventing Childhood Obesity.” Chaired by Emory University‟s Jeffrey Koplan, the plan is the first comprehensive look at childhood obesity and what government, industry, schools, communities, families, and medical professionals can do to reduce its impact. “I think this is similar in importance to the first Surgeon General‟s Report on Smoking and Health in 1964,” Koplan says. That landmark document led to the health warning on cigarette packages and a ban on cigarette advertising on TV.76. In most American high schools, selling soft drinks is .A. encouragedB. allowedC. unlawfulD. unprofitable77. Water has become “cool” in the Minneapol is school district partly because .A. water is provided freeB. most kids can afford nothing but waterC. water machines are put in noticeable positionsD. children have realized the harm of sugary drinks78. We can infer that in terms of healthful drinks for kids, Simone French and some other experts are .A. confident about children‟s choicesB. pessimistic about the futureC. puzzled about which approach to takeD. worried about how to motivate children79. By mentioning the 1964 report on smoking, Jeffrey Koplan implied that .A. more children tend to smoke today than yesterdayB. both obesity and smoking require the attention of schools and society.C. the present plan on obesity would function similarly as a landmark.D. obesity and smoking are both health problems.80. The primary purpose of this passage is to .。

系统发生分析软件PAUP和TreePuzzle使用方法介绍

基金项目国家自然科学基金资助项目（３０３７０７７３）。

作者简介王勇（１９６５－），男，浙江衢州人，在读博士，副研究员，从事昆虫生物信息学研究。

＊通讯作者，研究员，博士生导师，Ｅ!ｍａｉｌ：ｋｐｃｈｅｎ＠ｕｊｓ．ｅｄｕ．ｃｎ收稿日期２００７!０９!０３近年来，系统发生分析被广泛应用于研究不同生物ＤＮＡ、蛋白质序列的进化关系［１－３］，但由于系统发生分析是对过去已经发生的进化事件进行模拟，任何软件都不能保证所得出的结论就是真实的进化历史。

因此，在进行系统发生分析时，往往需要采用不同的分析方法同时进行。

而只有当多种分析方法获得的结果一致时，才可得出一个较为可靠的结论［４］。

ＰＡＵＰ和ＴｒｅｅＰｕｚｚｌｅ是目前使用较多的系统发生分析软件，其中ＰＡＵＰ更是国内外不少科技期刊都指定使用的。

ＰＡＵＰ（ｐｈｙｌｏｇｅｎｅｔｉｃａｎａｌｙｓｉｓｕｓｉｎｇｐａｒｓｉｍｏｎｙ，用最大简约法做系统发生分析）既能对ＤＮＡ序列做邻近归并法（ｎｅｉｇｈｂｏｒｊｏｉｎｉｎｇ，ＮＪ）、最大简约法（ｍａｘｉｍｕｍｐａｒｓｉｍｏｎｙ，ＭＰ）和最大相似法（ｍａｘｉｍｕｍｌｉｋｅｌｉｈｏｏｄ，ＭＬ）分析，又能对蛋白质序列做ＮＪ和ＭＰ分析［５］。

ＴｒｅｅＰｕｚｚｌｅ则是专门用于构建ＭＬ进化树的软件。

然而，ＰＡＵＰ软件使用方法比较复杂，特别是Ｗｉｎｄｏｗｓ版，不能进行菜单操作而需要自己输入命令。

ＴｒｅｅＰｕｚｚｌｅ则是一个ＤＯＳ版本的软件，使用上有较大的不便之处［６］。

初学者在没人指点的情况下，往往感觉一筹莫展。

为此，笔者通过研读软件的使用手册和有关资料［７］从序列信息模块、序列参数模块、运算命令模块３个方面介绍ＰＡＵＰ软件的使用方法，之后对ＴｒｅｅＰｕｚｚｌｅ软件的使用和进化树的编辑与注释方法做一简要说明。

１序列信息模块要做ＰＡＵＰ分析，首先必须建立Ｎｅｘｕｓ文件。

Ｎｅｘｕｓ文件是ＰＡＵＰ软件的可执行文件，后缀名为．ｎｅｘ。

一般来说，Ｎｅｘｕｓ文件包含以下３个模块：序列信息模块、参数设定模块、运算命令模块。

2011年3月中科院考博英语真题及答案详解免费版

GRADUATE UNIVERSITY, CHINESE ACADEMYOF SCIENCES ENGLISH ENTRANCEEXAMINATIONFORDOCTORAL CANDIDA TESMarch 2011PAPER ONEPART ⅠVOCABULARY(15 minutes, 10points, 0. 5point each)Directions: Choose the word or expression below each sentence that best completes the statement, and mark the corresponding letter of your choice with a single bar across the square bracket on your Machine-scoring Answer Sheet.1. My father was a nuclear engineer, a very academically _________ Man with multiple degrees from prestigious institutions.A. promotedB. activatedC. orientedD. functioned2. Public _________ for the usually low-budget, high-quality films has enabled the independent film industry to grow and thrive.A. appreciationB. recognitionC. gratitudeD. tolerance3. Dirty Jobs on the Discovery Channel, an unlikely television program, has become a surprising success with a _________ fan base.A. contributedB. devotedC. reveredD. scared4. Pop culture doesn't _________ to strict rules; it enjoys being jazzy, unpredictable, chaotic.A. adhereB. lendC. exposeD. commit5. Intellectual property is a kind of _________ monopoly, which should be used properly or else would disrupt healthy competition order.A. legibleB. legendaryC. lenientD. legitimate6. I am thankful to the company for giving me such a chance, and I earnestly hope that I will _________ everyone’s expectations.A. boil down toB. look forward toC. live up toD. catch on to7. The image of an unfortunate resident having to climb 20 flights of stairs because the lift is _________ is now a common one.A. out of the wayB. on orderC. out of orderD. in no way8. My eyes had become _________ to the now semi-darkness, so I could pick out shapes about seventy-five yards away.A. inclinedB. accustomedC. vulnerableD. sensitive9. Despite what I’d been told about the local people’s attitude to strangers, _________ did I encounter any rudeness.A. at no timeB. in no timeC. at any timeD. at some time10. In times of severe _________ companies are often forced to make massive job cuts in order to survive.A. retreat B, retrospect C. reduction D. recession11. Sport was integral to the national and local press, TV and, to a diminishing _________ , to radio.A. extentB. scopeC. scaleD. range12. Unless your handwriting is _________ , or the form specifically asks for typewriting, the form should be neatly handwritten.A. illegitimate B, illegal C. illegible D. illiterate13. The profession fell into , with some physicists sticking to existing theories, while others came up with the big-bang theory.A. harmonyB. turmoilC. distortionD. accord14. With the purchasing power of many middle-class households _________ behind the cost of living, there was an urgent demand for credit.A. leavingB. leveringC. lackingD. lagging15. Frank stormed into the room and _________ the door, but it wasn’t that easy to close the door on what Jack had said.A. slashedB. slammedC. slippedD. slapped16. When I was having dinner with you and Edward at his apartment, I sensed a certain _________ between the two of you.A. intimacyB. proximityC. discrepancyD. diversity17. I decided to _________ between Ralph and his brother, who were arguing endlessly.A. interfereB. interveneC. interruptD. interact18. “I mean Gildas and Ludens are both wise, reasonable and tactful; but naturally they’re _________ , they want to know what’s happening, and make judgments on it all. ”A. indifferentB. innocentC. inquisitiveD. instinctive19. In Africa HIV and AIDS continue to _________ the population; nearly 60 percent of those infected are women.A. alleviateB. boostC. captureD. ravage20. By the end of the Spring and Autumn Period slave society was _________ disintegration.A. on the ground ofB. on the top ofC. in the light ofD. on the verge ofPART ⅡCLOZE TEST(15 minutes, 15 points)Directions: For each blank in the following passage, choose the best answer from the four choices given below. Mark the corresponding letter of your choice with a single bar across the square bracket on your Machine-scoring Answer Sheet.Tomorrow Japan and South Korea will celebrate White Day, an annual event when men are expected to buy a gift for the adored women in their lives. It is a relatively new 21 that was commercially created as payback for V alentine’s Day. That’s 22 in both countries, 14 February is all about the man.On V alentine’s Day, women are expected to buy all the important male 23 in their lives a token gift; not just their partners, 24 their bosses or older relatives too.This seems 25 enough. Surely it’s reasonable for men to be indulged on one day of the year, 26 the number of times they’re expected to produce bouquets of flowers and 27 their woman with perfume or pearls.But the idea of a woman 28 a man didn’t sit easily with people. In 1978, the NationalConfectionery Industry Association(糖果业协会) 29 an idea to solve this problem. They started to market white chocolate that men could give to women on 14 March, as 30 for the male-oriented V alentine’s Day.It started with a handful of sweet-makers’producing candy 31 a simple gift idea. The day 32 the public imagination, and is now a nationally 33 date in the diary-and one where men are 34 to whip out their credit cards. In fact, men are now expected to give gifts worth 35 the value of those they received. What a complication: not only do men have to remember who bought them what, they have to estimate the value and multiply it by three.21. A. copy B. concept C. choice D. belief22. A. because B. as C. so D. why23. A. clients B. friends C. figures D. colleagues24. A. but B. and C. instead of D. rather than25. A. odd B. good C. fair D. rare26. A. given B. if C. but D. though27. A. attract B. frustrate C. surprise D. touch28. A. supporting B. spoiling C. comforting D. fooling29. A. came up with B. come out of C. came up toD. came along with30. A. companion B. compromise C. competence D. compensation31. A. via B. as C. with D. for32. A. captured B. appealed C. favored D. held33. A. documented B. recognized C. illustrated D. scheduled34. A. volunteered B. embarrassed C. sponsoredD. obliged35. A. triple B. double C. fourfold D. equalPART ⅢREADING COMPREHENSIONSection A(60 minutes, 30 points)Directions: Below each of the following passages you will find some questions or incomplete statements. Each question or statement is followed by four choices marked A, B, C, and D. Read each passage carefully, and then select the choice that best answers the question or completes the statement. Mark the letter of your choice with a single bar across the square bracket on your Machine-scoring Answer Sheet.Passage OneAt many colleges, smokers are being run not just out of school buildings but off the premises. On Nov. 19 , the University of Kentucky, the tobacco state’s flagship public institution, Launched a campus wide ban on cigarettes and all other forms of tobacco on school grounds and parking areas. Pro-nicotine students staged a “smoke-out”to protest the new policy, which even rules out smoking inside cars if they’re on school property.Kentucky joins more than 365 U. S. colleges and universities that in recent years have instituted antismoking rules both indoors and out. In most places, the issue doesn’t seem to be secondhand smoke. Rather, the rationale for going smoke-free in wide open spaces is a desire to model healthy behavior.Purdue University, which has 30-ft. buffer zones, recently considered adopting a campuswide ban but tempered its proposal after receiving campus input. Smoking will now be restricted tolimited outdoor areas.One big problem with a total ban is enforcing it. Take the University of Iowa. In July 2008, the school went smoke-free in accordance with the Iowa Smokefree Air Act, violations of which can result in a $50 fine. But so far, the university has ticketed only about 25 offenders. “Our campus is about 1, 800 acres, so to think that we could keep track of who is smoking on campus at any given time isn’t really feasible, ”says Joni Troester, director of the university’s campus wellness program. Instead, the school helps those trying to kick the habit by offering smoking-cessation programs and providing reimbursement for nicotine patches, gum and prescription medications like Zyban.The University of Michigan will probably take a similar approach when its ban takes effect in July 2011. “We don’t have a desire to give tickets or levy punishments, ”says Robert Winfield, the school’s chief health officer. “We want to encourage people to stop smoking, set a good example for students and make this a healthier community. ”Naturally, there has been pushback from students. “Where do we draw the line between a culture of health and individual choice?”asks Jnathan Slemrod, a University of Michigan senior and president of the school’s College Libertarians. “If they truly want a culture of health, I expect them to go through all our cafeterias and get rid of all our Taco Bells, all our pizza places. ”Students might want to enjoy those Burrito Supremes while they can. In today’s health-obsessed culture, those may be next.36. We can infer that the “newness”of the antismoking policy at the University of Kentucky lies in _________ .A. its extended scope of no-smoking placesB. its prohibition of cigarette sales on campusC. its penalty for bringing tobacco to schoolD. its ban on smoke when people are driving37. By setting the antismoking rules the University of Kentucky mainly aims for _________ .A. protecting students against passive smokingB. modeling itself on many other universitiesC. promoting the students’ health awarenessD. punishing those who dare smoke on campus38. One of the problems enforcing the ban on smoking at the University of Iows is _________ .A. limiting the smoke-free areasB. tracing smokers on campusC. forcing smokers to give up smokingD. providing alternative ways for smokers39. The word “levy”(in Paragraph 5)most probably means_________ .A. imposeB. avoidC. deserveD. receive40. According to Jonathan Slemrod, Taco Bell is _________ .A. a tobacco shopB. a school cafeteriaC. an organic food storeD. an unhealthy food chain41. The author’s tone in the essay is _________ .A. radicalB. optimisticC. objectiveD. criticalPassage T woThe familiar sounds of an early English summer are with us once again. Millions of children sit down to SA Ts, GCSEs, AS-levels, A-levels and a host of lesser exams, and the argument over educational standards starts. Depending on whom you listen to, we should either be letting up on over-examined pupils by abolishing SA Ts, and even GCSEs, or else making exams far more rigorous.The chorus will reach a peak when GCSE and A-level results are published in August. If pass rates rise again, commentators will say that standards are falling because exams are getting easier. If pass rates drop, they will say that standards are falling because children are getting lower marks. Parents like myself try to ignore this and base our judgments on what our children are learning. But it’s not easy given how much education has changed since we were at school.Some trends are encouraging-education has been made more relevant and enthuses many children that it would have previously bored. My sons’ A-level French revision involved listening to radio debates on current affairs, whereas mine involved rereading Moliere. And among their peers, a far greater proportion stayed in education for longer.On the other hand, some aspects of schooling today are incomprehensible to my generation, such as gaps in general knowledge and the hand-holding that goes with ensuring that students leave with good grades. Even when we parents resist the temptation to help with GCSE or A-level coursework, a teacher with the child’s interests at heart may send a draft piece of work back several times with pointers to how it can be improved before the examiners see it.The debate about standards persists because there is no single objective answer to the question: “Are standards better or worse than they were a generation ago?”Each side points to indicators that favor them, in the knowledge that there is no authoritative definition, let alone a measure that has been consistently applied over the decades. But the annual soul-searching over exams is about more than student assessment. It reveals a national insecurity about whether our education system is teaching the right things. It is also fed by an anxiety about whether, in a country with a history of upholding standards by ensuring that plenty of students fail, we can attain the more modern objective of ensuring that every child leaves school with something to show for it.42. It can be concluded from Paragraph 1 that _________ .A. SA Ts is one of the most rigorous exams mentionedB. it has been debated if children should b given examsC. few parents approve of the exam systems in EnglandD. each year children have to face up to some new exams43. Parents try to judge the educational standards by _________ .A. whether their children have passed the examsB. what knowledge their children have acquiredC. what educators say about curriculum planningD. whether their children’s school scores are stable44. To the author, the rereading of Moliere was _________ .A. drearyB. routineC. outmodedD. arduous45. To the author’s generation, it is beyond understanding today why _________ .A. teachers lay great stress on helping students obtain good gradesB. teachers show much concern for students’ futureC. parents help little with their children’s courseworkD. parents focus on their children’s general knowledge46. According to the passage, with respect to educational standards in Britain, _________ .A. no authorities have ever made a commentB. no one has ever tried to give them a definitionC. no effective ways have been taken to apply themD. no consistent yardstick has ever been used47. In the author’s opinion, the school education in Britain has been _________ .A. inflexibleB. irresponsibleC. unsuccessfulD. unforgivablePassage ThreeSuzan Fellman had a hard time with Laura Bush’s redo of the famed guest quarters named for President Lincoln: “Looking at it , I thought I was in a Radisson lobby somewhere in the Midwest long ago. I could not imagine spending a night in that space. ”Done up with Victorian furnishings, the Lincoln Bedroom is one of the residence’s least-changed spaces, said Betty Monkman, formerly chief curator of the White House for nearly 40 years. “It’s a quasi-museum room, ”she said, “with a lot of objects, such as the bed , that have symbolic importance. ”The elaborately carved bed bought for Lincoln is the centerpiece of the room.According to historian William Seale, the president was furious that his wife, Mary, spent so much money redecorating the White House during a time of war. He never slept in the bed , and the ornate piece eventually was moved to a spare room.Los Angeles designer Fellman saw parallels, calling the Obama era a period of“pulling back on extravagance. ”It is a good time, she said, to revisit pieces in storage, to rearrange old furniture in a new fashion, and use paint and fabrics to bring life and fun into a room without spending a fortune.In this re-imagining of the Lincoln Bedroom, Fellman would retain the legendary bed but paint the ceiling a sky blue and use a Cecil Beaton rose-print fabric for curtains. “Lincoln loved roses, ”Fellman said, “and this beige and ivory version keeps it from being too bold, modern or feminine. ”At a time when Americana is expected to stage a strong revival, Fellman said traditional styles such as Colonial and Federal can co-exist with European antiques if they are balanced in scale.Mindful of the recession, the designer advocated selecting furniture with longevity in mind. “If you are going to spend money, buy quality things that you never want to get rid of, ”she said. “A couple of really good things can make all the difference in a room. ”Her splurges would include a camel-hair sofa, which Fellman said was long-lasting and timeless. As a Pop Art-influenced statement about thrift, a custom rug woven with a 6-foot-diameter medallion replicates the penny’s image of Lincoln in subtle shades of ivory and copper.In bad times as in good, spare rooms don’t have to be grand to be effective, Fellman said. “A guest room should feel inviting and intimate, ”she said. “It has to exude serenity. ”48. To Suzan Fellman, Laura Bush’s redecoration of the Lincoln Bedroom could hardly be _________ .A. evaluatedB. imaginedC. understoodD. praised49. The Lincoln Bedroom in White House is a place for_________ .A. the president to have a restB. visitors to stay overnightC. storing Victorian furnishingsD. exhibiting classic objects50. According to Fellman, the Obama era is similar to the Lincoln era in _________ .A. decorating housesB. respecting the pastC. protecting the classicD. encouraging thrift51. The way Fellman would rearrange the Lincoln Bedroom includes _________ .A. putting some roses on the tableB. omitting some European antiquesC. adding to it some Federal stylesD. giving it the look of a strong America52. In choosing the new furniture for the room, Fellman would give top priority to _________ .A. its durabilityB. its simplic ityC. its priceD. its color53. Fellman would avoid making the Lincoln Bedroom look_________ .A. tranquilB. luxuriousC. hospitableD. fascinatingPassage FourLaurance Rockefeller, the middle brother of the five prominent and benevolent grandsons of John D. Rockefeller, who concentrated his own particular generosity on conservation, recreation, ecological concerns and medical research, particularly the treatment of cancer, died of pulmonary fibrosis at his home in Manhattan.His career began on Wall Street almost 70 years ago, where he became a pioneer of modern venture capitalism, compounding his inherited wealth many times over. In the decades since he first took his seat on the New Y ork Stock Exchange, he often used his native instinct for identifying the next big thing, not content simply to make more money but to make the money produce something of lasting value.Less sociable than his older brother Nelson, who was a four-term governor of New Y ork and the country’s vice president under Gerald R. Ford, Laurance Spelman Rockefeller was also more reserved and private than his flamboyant younger brother Winthrop who was the governor of Arkansas. A philosophy major at Princeton he had long wrestled with the question of how he might most efficiently and satisfyingly use the great wealth to which he was born and which he later kept compounding as a successful pioneer of modern venture capitalism.Using significant amounts of his money as well as his connections and prestige and negotiating skills he was instrumental in establishing and enlarging National Parks in Wyoming, California, the V irgin Islands, V ermont, Maine and Hawaii. As an active member of the Palisade Interstate Parkway Commission, he helped create a chain of parks that blocked the advance of sprawl, thus maintaining the majestic view that he first saw as a child looking out from Kykuit, the Rockefeller country home in Pocantico.His commitment to wilderness, recreation and environmental conservation had many roots.Since childhood he liked to ride hrses through unspoiled terrain. He was a passionate photographer in search of new landscapes. Even before Laurance reached adulthood the Rockefellers had included parks among their many philanthropic projects.Laurance was born on May 26, 1910. As Laurance matured he came to more closely resemble his grandfather than did any other family member, having the same pursed and seemingly serious expression that John D. Rockefeller often showed in photographs. According to family accounts he was also the one who most closely revealed his grandfather’s ability for profitable deals.54. Paragraph 1 suggests that Laurance Rockefeller was a man who is _________ .A. full of social responsibilityB. famous but short-livedC. successful in many fieldsD. zealous in social activities55. We can learn that, in making investments, Laurance Rockefeller was very _________ .A. cold-heartedB. close-fistedC. far-sightedD. half-witted56. Compared with his two brothers, Laurance _________ .A. often relied on himselfB. rarely appeared in publicC. rarely voiced his opinionsD. often worried about his wealth57. The word“instrumental”(boldfaced in Para 4)in this context can be replaced by “_________ . ”A. generousB. strategicC. resoluteD. important58. Laurance’s childhood experience led him later to make significant contributions to _________ .A. the building of national parksB. the enlargement of urban areasC. the perfection of his hometownD. the popularization of horse riding59. According to the passage, Laurance resembled his grandfather in having _________ .A. a contribution to public goodB. a talent of making moneyC. a passion for wildernessD. a bias against political affairsPassage FiveThe first three days of July 1863 saw the bloodiest hours of the Civil War, in a battle that spilled across the fields and hills surrounding Gettysburg, Pa. The fighting climaxed in the bright, hot afternoon of the third day, when more than 11, 000 Confederate soldiers mounted a disastrous assault on the heart of the Union line. That assault marked the farthest the South would penetrate into Union territory. In a much larger sense, it marked the turning point of the war.No surprise, then, than the Battle of Gettysburg would become the subject of songs, poems, funeral monuments and, ultimately, some of the biggest paintings ever displayed on this continent. Paul Philippoteaux, famed for his massive360-degree cyclorama paintings, painted four versions of the battle in the 1880s. Cycloramas were hugely popular in the United States in the last decades ofthe 19th century, before movies displaced them in the public’s affection. Conceived on a mammoth scale, a cyclorama painting was longer than a football field and almost 50 feet tall. Little thought was given to preserving these enormous works of art. They were commercial ventures, and when they stopped earning they were tossed. Most were ultimately lost-victims of water damage or fire. One of Philippoteaux’s Gettysburg renderings was cut up and hung in panels in a Newark, N. J. , department store before finding its way back to Gettysburg, where it has been displayed off and on since1913. Along the way, the painting lost most of its sky and a few feet off the bottom. Sections since 1913. Along the way, the painting lost most of its sky and a few feet off the bottom. Sections were cut and moved to patch holes in other sections. And some of the restorative efforts proved almost as crippling to the original as outright neglect. Since 2003, a team of conservators has labored in a $12million effort to restore Philippoteaux’s masterwork. They have cleaned it front and back, patched it , added canvas for a new shy and returned the painting to its original shape-a key part of a cyclorama’s optical illusion was its hyperbolic shape: it bellies out at its central point, thrusting the image toward the viewer.When restoration is completed later this year, the painting will be the centerpiece of the new Gettysburg battlefield visitors’ center, which opens to the public on April 14. Much work remains to be done. But even partially restored, the painting seethes with life-and death.60. With respect to the Battle of Gettysburg, Paragraph 1 mainly emphasizes _________ .A. the reason for its occurrenceB. the significance of the battleC. the place where it broke outD. the bloodiness of the battle61. To the author, that Gettysburg Battle got reflected in many art works is _________ .A. reasonableB. meaningfulC. necessaryD. impressive62. We can infer that cyclorama paintings _________ .A. has regained their popularity since 1913B. were mostly destroyed by the Civil WarC. more often than not lost than gained moneyD. had been popular before movies came in63. Work done to restore the Philippoteaux’s painting already began _________ .A. before 1900B. after 1913C. in 2003D. at its birth64. According to the author, some previous efforts to restore the Philippoteaux’s painting turned out to be _________ .A. time consumingB. fruitlessC. destructiveD. a waste of money65. What is true of the present state of the Philippoteaux’s Gettysburg rendering?A. It is illusory in depiction.B. It is a perfect restoration.C. It is a modified version.D. It is incredibly lifelike.Section B(20 minutes, 10 points)Directions: In each of the following passages, five sentences have been removed from theoriginal text. They are listed from A to F and put below the passage. Choose the most suitable sentence from the list to fill in each of the blanks(numbered 66 to 75). For each passage, there is one sentence that does not fit in any of the blanks. Mark your answers on your Machine-scoring Answer Sheet.Passage OneAdvertising is paid, nonpersonal communication that is designed to communicate in a creative manner, through the use of mass or information-directed media, the nature of products, services, and ideas. It is a form of persuasive communication that offers information about products, ideas, and services that serves the objectives determined by the advertiser. 66 Thus, the ultimate objective of advertising is to sell things persuasively and creatively. Advertising is used by commercial firms trying to sell products and services; by politicians and political interest groups to sell ideas or persuade voters; by not-for-profit organizations to raise funds, solicit volunteers, or influence the actions of viewers; and by governments seeking to encourage or discourage particular activities, such as wearing seatbelts, participating in the census, or ceasing to smoke. 67 The visual and verbal commercial messages that are a part of advertising are intended to attract attention and produce some response by the viewer. Advertising is pervasive and virtually impossible to escape. Newspapers and magazines often have more advertisements than copy; radio and television provide entertainment but are also laden with advertisements; advertisements pop up on Internet sites; and the mail brings a variety of advertisements. 68 In shopping malls, there are prominent logos on designer clothes, moviegoers regularly view advertisements for local restaurants, hair salons, and so on, and live sporting and cultural events often include signage, logos, products, and related information about the event sponsors. 69Although the primary objective of advertising is to persuade, it may achieve this objective in many different ways. An important function of advertising is the identification function, that is, to identify a product and differentiate it from others; this creates an awareness of the product and provides a basis for consumers to choose the advertised product over other products. 70 The third function of advertising is to induce consumers to try new products and to suggest reuse of the product as well as new uses; this is the persuasion function.A. Another function of advertising is to communicate information about the product, its attributes, and its location of sale; this is the information function.B. The forms that advertising takes and the media in which advertisements appear are as varied as the advertisers themselves and the messages that they wish to deliver.C. An especially important issue in the creation of advertising is related to understanding how much information consumers want about a given product.D. Advertising may influence consumers in many different ways, but the primary goal of advertising is to increase the probability that consumers exposed to an advertisement will behave or believe as the advertiser wishes.E. Advertising also exists on billboards along the freeway, in subway and train stations, on benches at bus stops, and on the frames around car license plates.F. The pervasiveness of advertising and its creative elements are designed to cause viewers to take note.Passage T woFew numbers tell a happier story than those that measure life expectancy. An American born in 1900 could expect to live 47 years. Thanks to colossal improvements in sanitation and medic ine,。

贵州芒果炭疽菌种类鉴定及表型特征分析

2023年第16期现代园艺贵州芒果炭疽菌种类鉴定及表型特征分析姚令1，吴石平1，陈小均1，黄海2，陈文1*（1贵州省农业科学院植物保护研究所，贵州贵阳550006；2贵州省农业科学院亚热带作物研究所，贵州兴义562400）摘要:为明确贵州芒果叶斑病病原炭疽菌（）的种类及表型特征，在贵州芒果主产区望谟县、安龙县和贞丰县等地采集芒果叶斑病标样及分离菌株，对其内转录间隔区、机动蛋白、β-微管蛋白、几丁质合成酶1、3-磷酸甘油醛脱氢酶等多个基因的序列进行系统学分析，测定不同炭疽菌的菌落形态、分生孢子大小、菌丝生长速率等特征。

结果表明，引起贵州芒果叶斑病的病原炭疽菌种类有和，其中和为主要为害种类，的菌丝生长速率和分生孢子长度均显著大于和，侵染叶片造成病斑扩展速度最快。

关键词:芒果炭疽病；炭疽菌；系统发育学分析；表型特征；鉴定芒果以其色、香、味俱佳而享有“热带果王”之美誉，是世界第二大热带水果。

贵州芒果集中种植在南、北盘江及红水干热河谷地区，拟规划种植3.33万hm2[1-2]，截至2021年，种植约1.33万hm2。

炭疽病是芒果生产中发生最普遍、为害性最重的一种真菌病害，在世界各芒果产区均有分布，其可为害芒果的新梢、嫩叶、花和果实，一般造成芒果减产30%~60%，严重的为100%[3]。

炭疽菌引起的芒果叶斑病，常引起中后期花穗和果实炭疽病的频生，造成严重的经济损失[4]。

目前，国内外报道为害芒果的炭疽菌种类多样，分布于不同种植区域[5-11]。

贵州田间芒果炭疽病的为害问题日趋凸显，病原种类不明，制约其有效防治。

因此，本研究拟采用传统生物学和分子生物学手段，鉴定为害贵州芒果的病原炭疽菌的种类，测定病原菌的生长速率、病斑的扩展速率等表型特征，以为贵州芒果炭疽病的防治提供依据。

1材料与方法1.1标样采集及菌株分离2020年2月在贵州望谟县（2个果园）、贞丰县（1个果园）、安龙县（2个果园）等地芒果园采集芒果叶斑病病叶，每个果园随机采集来自5株果树的叶斑病标样9~10个，带回实验室对标样进行编号、记录和拍照。

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1AaA ViÕt t¾t cña adenineAb kh¸ng thÓ ViÕt t¾t cña antibody. ABC model Widely accepted model of flower organ identity that appears generally applicable to distantly related dicotyledonous, although less well to monocotyledon ous plants.The model incorporates the Arabidopsis genes required for flower organ identity.m« h×nh ABC M« h×nh ®-îc chÊp nhËn réng r·i vÒ sù nhËn biÕt c¬ quan hoa thùc vËt mμ xuÊt hiÖn thÝch hîp chung víi c¸c c©y hai l¸ mÇm quan hÖ xa, tuy vËy Ýt thÝch hîp víi c©y mét l¸ mÇm. M« h×nh hîp nhÊt c¸c gen Arabidopsis cÇn thiÕt ®Ó nhËn biÕt c¬ quan hoa.abiotic Absence of living organisms.v« sinh V¾ng mÆt sinh vËt sèng. abscisic acid A phytohormone implicated in the control of many plant responses to abiotic stress, such as extent of stomatal opening under water deficit (i.e. drought) conditions.axit abscisic Hãc m«n thùc vËt liªn quan ®Õn ®iÒu khiÓn ph¶n øng thùc vËt víi c¨ng th¼ng v« sinh, nh- phÇn më réng khÝ khæng trong ®iÒu kiÖn thiÕu n-íc (nghÜa lμ h¹n h¸n)abzyme Xem: catalytic antibody. acaricide A pesticide used to kill or control mites or ticks.thuèc diÖt ve N«ng d-îc ®-îc dïng ®ÓdiÖt hoÆc h¹n chÕ ve hoÆc bÐt.ACC synthase Abbreviation for 1-aminocyclopropane-1-carboxylase. The enzyme catalyses the rate limiting step in the ethylene biosynthetic pathway, and is particularly significant in the fruit ripening process. Plants typically carry a number of distinct ACC synthase genes, which are differentially regulated in response to a variety of developmental, environmental and chemical factors.enzim tæng hîp ACC ViÕt t¾t cña: 1-aminocyclopropane-1-carboxylaza. Enzim xóc t¸c ph¹m vi giíi h¹n nhÞp ®é cña ®-êng mßn sinh tæng hîp ª-ti-len, vμ ®Æc biÖt quan träng khi xö lý lμm chÝn qu¶. Thùc vËt tiªu biÓu mang mét sè l-îng gen tæng hîp ACC riªng biÖt, chóng ®-îc ®iÒu chØnh kh¸c nhau ®Ó ph¶n øng l¹i sù ®a d¹ng cña c¸c t¸c nh©n ho¸ häc, m«i tr-êng vμ ph¸t triÓn.acceptor control The regulation of the rate of respiration by the availability of ADP as a phosphate acceptor.®iÒu khiÓn chÊt nhËn §iÒu khiÓn nhÞp ®éh« hÊp do cã s½n ADP lμm chÊt nhËn phèt ph¸t.acceptor junction site The junction between the 3' end of an intron and the 5' end of an exon. See: donor junction site. vÞ trÝ nèi thÓ nhËn VÞ trÝnèi gi÷a mót 3' tr×nh tù kh«ng m· ho¸ vμ mót 5' tr×nh tùm· ho¸. Xem: donor junction site. accessory bud A lateral bud occurring at the base of a terminal bud or at the side of an axillary bud.mÇm phô MÇm bªn n¶y në t¹i gèc mÇm ngän hoÆc ë c¹nh mÇm n¸ch. acclimatization The adaptation of a living organism (plant, animal or micro-organism) to a changed environment that subjects it to physiological stress. Acclimatization should not be confused with adaptation.thuÇn ho¸ ThÝch nghi cña sinh vËt sèng (thùc vËt, ®éng vËt hoÆc vi sinh vËt) víi m«i tr-êng thay ®æi vèn g©y c¨ng th¼ng sinh lý. ThuÇn ho¸ kh«ng nªn nhÇm lÉn víi thÝch øng.acellular Tissues or organisms that are not made up of separate cells but often have more than one nucleus.phi tÕ bμo C¸c m« hoÆc sinh vËt kh«ng ®-îc t¹o ra tõ nh÷ng tÕ bμo riªng biÖt nh-ng th-êng cã h¬n mét nh©n.2acentric chromosome Chromosome fragment lacking a centromere .nhiÔm s¾c thÓ kh«ng t©m §o¹n nhiÔm s¾c thÓ thiÕu t©m ®éng.acetyl CoA ViÕt t¾t cña acetyl co-enzyme A.acetyl co-enzyme A (Abbreviation t: acetyl CoA) A compound formed in the mitochondria when an acetyl group (CH 3CO-) - derived from breakdown of fats,proteins , or carbohydrates - combines with the thiol group (-SH) of co-enzyme A .acetyl co-enzim A Hîp chÊt h×nh thμnh trong ty thÓ khi gèc axetyl (CH3CO-) - b¾t nguån tõ ph©n huû chÊt bÐo, protein, hoÆc hydrat cacbon - kÕt hîp víi gèc thiol (-SH)cña co-enzyme A.ACP ViÕt t¾t cña acyl carrier protein .acquired Developed in response to the environment, not inherited, such as a character trait (acquired characteristic)resulting from environmental effect(s). cf acclimatization .tËp nhiÔm Ph¸t triÓn ®Ó ph¶n øng l¹i m«i tr-êng, kh«ng di truyÒn, nh- mét tÝnh tr¹ng riªng (®Æc tÝnh tËp nhiÔm) do ¶nh h-ëng m«i tr-êng. So s¸nh víi: acclimatization acridine dyes A class of positively charged polycyclic molecules that intercalate into DNA and induce frameshift mutations.thuèc nhuém acridin Líp ph©n tö nhiÒu vßng tÝch ®iÖn d-¬ng ®-îc n¹p vμo DNA vμ g©y ®ét biÕn xª dÞch khung ®äc .acrocentric A chromosome that has its centromere near the end.nhiÔm s¾c thÓ t©m ngän NhiÔm s¾c thÓcã t©m ®éng ë gÇn mót.acropetal Arising or developing in a longitudinal sequence beginning at the base and proceeding towards the apex.Opposite : basipetal .h-íng ngän XuÊt hiÖn hoÆc tr×nh tù ph¸t triÓn theo chiÒu däc b¾t ®Çu ë gèc vμ tiÕp ®Õn phÝa ngän . Ng-îc víi: basipetalactivated carbon c¸c bon ho¹t tÝnh Xem:activated charcoal .activated charcoal Charcoal that has been treated to remove hydrocarbons and to increase its adsorptive properties. It acts by condensing and holding a gas or solute onto its surface; thus inhibitory substances in nutrient medium may be adsorbed to charcoal included in the medium.than ho¹t tÝnh Than ®· xö lý lo¹i bá hy-®r«-cac-bon vμ lμm t¨ng tÝnh hÊp phô. T¸c dông do c« ®Æc vμ hÊp phô khÝ hoÆc chÊt tan trªn bÒ mÆt; do vËy c¸c chÊt k×m h·m trong m«i tr-êng dinh d-ìng cã thÓ ®-îc hót b¸m vμo than cã trong m«i tr-êng.active transport The movement of a molecule or groups of molecules across a cell membrane, which requires the expenditure of cellular energy, because the direction of movement is against the prevailing concentration gradient.vËn chuyÓn tÝch cùc ChuyÓn ®éng cña ph©n tö hoÆc nhãm ph©n tö qua mμng tÕbμo, yªu cÇu chi phÝ n¨ng l-îng tÕ bμo, v×h-íng chuyÓn ®éng lμ ng-îc l¹i víi -u thÕgradient nång ®é.acute transfection Short-term transfection .truyÒn nhiÔm cÊp ViÕt gän transfection .acyl carrier protein (Abbreviation: ACP).A class of molecules that bind acyl intermediates during the formation of long-chain fatty acids. ACPs are important because of their involvement in many of the reactions necessary for in vivo fatty acid synthesis.protªin vËn chuyÓn gèc acyl (ViÕt t¾t:ACP ). Líp ph©n tö nèi c¸c chÊt trung gian acyl trong qu¸ tr×nh h×nh thμnh a-xÝt bÐo.ACP rÊt quan träng v× cã nhiÒu mèi liªn quan víi c¸c ph¶n øng cÇn thiÕt ®Ó tæng hîp a-xÝt bÐo trong c¬ thÓ.adaptation Adjustment of a population to changes in environment over generations,associated (at least in part) with genetic changes resulting from selection imposed by the changed environment. Not acclimatization.thÝch øng §iÒu chØnh quÇn thÓ lμm thay trong m«i tr-êng qua c¸c thÕ hÖ, ®-îc hîpacentric chromosome3nhÊt (Ýt nhÊt mét phÇn) víi thay ®æi di truyÒn b¾t nguån tõ chän läc b¾t buéc do m«i tr-êng thay ®æi. Kh«ng ph¶i lμ thuÇn ho¸ khÝ hËu.additive genes Genes whose net effect is the sum of their individual allelic effects,i.e. hey show neither dominance nor epistasis .gen céng tÝnh Gen cã ¶nh h-ëng thùc lμtæng céng c¸c hiÖu øng alel riªng lÎ, nghÜa lμ chóng chØ ra kh«ng ph¶i tÝnh tréi vμ còng kh«ng lÊn ¸t.additive genetic variance The net effect of the expresson of additive genes, and thus the chief cause of the resemblance between relatives. It represents the main determinant of the response of a population to selection. Formally, the variance of breeding value s.ph-¬ng sai di truyÒn céng tÝnh ¶nh h-ëng râ biÓu thÞ gen céng tÝnh, vμ nh-vËy lμ nguyªn nh©n chÝnh cña sù gièng nhau gi÷a c¸c d¹ng th©n thuéc. §¹i diÖn cho yÕu tè quyÕt ®Þnh chÝnh cña ph¶n øng quÇn thÓ víi chän läc. VÒ h×nh thøc,ph-¬ng sai gi¸ trÞ nh©n gièng sinh s¶n.adenine (Abbreviation : A ). One the base s found in DNA and RNA .adenin (ViÕt t¾t: A) Ba z¬ cã trong DNA vμRNA. Xem: adenosineadenosine The (ribo)nucleoside resulting from the combination of the base adenine (A) and the sugar D-ribose . The corresponding deoxyribonucleoside is called deoxyadenosine. See : adenosine triphosphate , adenylic acid, dATP .Ph©n tö (ribo) nucleosit b¾t nguån tõ kÕt hîp ba z¬ adenine (A) víi ®-êng D-ribose.Deoxyribonucleosit t-¬ng øng ®-îc gäi lμdeoxyadenosin . Xem: adenosine triphosphate, adenylic acid, dATP .adenosine diphosphate (adenosine 5'-diphosphate) (viÕt t¾t: ADP ). X em:adenosine triphosphate .adenosine monophosphate (adenosine 5'-monophosphate) (ViÕt t¾t: AMP ).Xem: adenylic acid, adenosine triphosphate.adenosine triphosphate (adenosine 5'-triphosphate) (Abbreviation: ATP). A nucleotide of fundamental importance as the major carrier of chemical energy in all living organisms. It is also required for RNA synthesis since it is a direct precursor molecule. ATP consists of adenosine with three phosphate groups, linked together linearly. The phosphates are attached to adenosine through the 5'-hydroxyl of its ribose (sugar) portion. Upon hydrolysis ,these bonds yield either one molecule of adenosine 5'-diphosphate (ADP) and the inorganic phosphate ion, or one molecule of adenosine 5'-monophosphate (AMP)and pyrophosphate ; in both cases releasing energy that is used to power biological processes. ATP is regenerated by the phosphorylation of AMP and ADP .nucleotit (ViÕt t¾t: ATP) Mét nucleotit quan träng c¬ b¶n v× lμ thÓ mang chÝnh n¨ng l-îng hãa häc trong toμn bé sinh vËt sèng.ATP cßn cÇn thiÕt ®Ó tæng hîp RNA khi lμph©n tö tiÒn chÊt trùc tiÕp. ATP gåm cãadenosine víi ba gèc phèt ph¸t, liªn kÕt tuyÕn tÝnh víi nhau. Phèt ph¸t ®-îc g¾n liÒn víi adenosine qua 5'-hydroxyl cña phÇn ribose (®-êng). Sau thuû ph©n, liªn kÕt nμy nh¶ mét ph©n tö adenosine 5'-diphosphate (ADP) vμ ion phèt ph¸t v« c¬,hoÆc ph©n tö adenosine 5'-monophosphate (AM P) vμ liªn kÕt cao n¨ng; trong c¶ hai tr-êng hîp n¨ng l-îng gi¶i phãng lμm t¨ng c¸c qu¸ tr×nh sinh häc.ATP ®-îc t¸i t¹o bëi qu¸ tr×nh phosphoryl ho¸ AMP vμ ADP .adenovirus One of a group of DNA -containing viruses found in rodents, fowl,cattle, monkeys, and man. In man they are responsible for respiratory-tract infections,but they have been exploited as a vector in gene therapy , especially for genes targeted at the lungs.adenovirót M ét trong nhãm virut chøa DNA cã trong c¸c loμi gËm nhÊm, gia cÇm,thó nu«i, khØ, vμ ng-êi.Trong c¬ thÓ ng-êi chóng lμ nguyªn nh©n nhiÔm bÖnh theo ®-êng h« hÊp, nh-ng chóng ®· ®-îc khai th¸c lμm vect¬ trong liÖu ph¸p gen, ®Æc biÖt cho c¸c gen ®Ých ë phæi.additive genes4adenylic acid Synonym for adenosine monophosphate, a (ribo)nucleotide containing the nucleoside adenosine. The corresponding deoxyribonucleotide is called deoxyadenosine 5'-monophosphate or deoxyadenylic acid. adenylic acid Tõ ®ång nghÜa víi adenosin monophosphat, mét (ribo)nucleotit cã chøa nucleosit adenosin. Deoxyribonucleotit t-¬ng øng ®-îc gäi lμeoxyadenosin 5'-monophosphat hoÆcaxÝt deoxyadenylic.adoptive immunization The transfer of an immune state from one animal to another by means of lymphocyte transfusions. miÔn dÞch nh©n t¹o ChuyÓn giao tr¹ng th¸i miÔn dÞch tõ mét ®éng vËt nμy sang ®éng vËt kh¸c b»ng c¸ch truyÒn lymph«bμo.ADP ViÕt t¾t cña adenosine diphosphate. adventitious A structure arising at sites other than the usual ones, e.g. shoots from roots or leaves, and embryos from any cell other than a zygote.chåi bÊt ®Þnh CÊu tróc xuÊt hiÖn t¹i vÞ trÝthay v× b×nh th-êng, vÝ dô chåi tõ rÔ hoÆc l¸, vμ ph«i tõ mét sè tÕ bμo nμo ®ã thay v×hîp tö.aerobe A micro-organism that grows in the presence of oxygen. Opposite: anaerobe.sinh vËt hiÕu khÝ Loμi vi sinh vËt sinh tr-ëng khi cã oxi. Ng-îc víi: anaerobe. aerobic Active in the presence of free oxygen, e.g. aerobic bacteria that can live in the presence of oxygen.h¶o khÝ Ho¹t ®éng khi cã oxi tù do, vÝ dôvi khuÈn h¶o khÝ cã thÓ sèng khi cã oxi. aerobic respiration A type of respiration in which foodstuffs are completely oxidized to carbon dioxide and water, with the release of chemical energy, in a process requiring atmospheric oxygen.h« hÊp h¶o khÝ KiÓu h« hÊp trong ®ã thùc phÈm ®-îc «xy hãa hoμn toμn thμnh c¸c b« nÝch vμ n-íc, kÌm theo gi¶i phãng n¨ng l-îng hãa häc, trong mét qu¸ tr×nh lu«n cÇn oxi khÝ quyÓn.affinity chromatography A method for purifying specific components in a solution by exploiting their specific binding to known molecule(s). The mixed solution is passed through a column containing a solid medium to which the binding molecule is covalently attached. See: immunoaffinity chromatography; metal affinity chromatography; pseudo-affinity chromatographys¾c ký ¸i lùc Ph-¬ng ph¸p ®Ó lμm s¹ch c¸c thμnh phÇn riªng biÖt trong dung dÞch b»ng c¸ch khai th¸c mèi liªn kÕt ®Æc thïcña chóng víi ph©n tö nhÊt ®Þnh. Dung dÞch hçn hîp ®i qua cét cã chøa m«i tr-êng r¾n ®Ó ph©n tö liªn kÕt ®-îc g¾n liªn kÕt ®ång hãa trÞ.X em: immunoaffinity chromatography; metal affinity chromatography; pseudo-affinity chromatography.affinity tag An amino acid sequence that has been engineered into a protein to make its purification easier. The tag could be another protein or a short amino acid sequence, allowing purification by affinity chromatography. Synonym: purification tag.®Çu ¸i lùc Tr×nh tù amino acid ®· ®-îc xölý thμnh protein ®Ó dÔ lμm s¹ch. §Çu ¸i lùc cã thÓ lμ protein kh¸c hoÆc tr×nh tùamino acid ng¾n, cho phÐp lμm s¹ch bëi phÐp s¾c ký ¸i lùc. Tõ ®ång nghÜa: purification tag.aflatoxins A group of toxic compounds, produced by Aspergillus flavus, that bind to DNA and prevent replication and transcription. Aflatoxins can cause acute liver damage and cancer. A health hazard in certain stored foods or feed. aflatoxins Nhãm hçn hîp chÊt ®éc, ®-îc s¶n xuÊt bëi nÊm mèc Aspergillus flavus, kÕt khèi víi DNA vμ ng¨n ngõa dÞch m· vμphiªn m·. Aflatoxin cã kh¶ n¨ng g©y tæn th-¬ng gan cÊp vμ ung th-. Nguy h¹i søc khoÎ cña thùc phÈm cÊt tr÷ hoÆc nu«i d-ìng nhÊt ®Þnh.adenylic acid5AFLP ViÕt t¾t cña amplified fragment length polymorphismAg ViÕt t¾t cña antigen.agar A polysaccharide gelifying agent used in nutrient media preparations and obtained from Rhodophyta (red algae). Both the type of agar and its concentration can affect the growth and appearance of cultured explant s.th¹ch T¸c nh©n ho¸ gel polysaccharide dïng trong c¸c chÕ phÈm m«i tr-êng dinh d-ìng vμ thu ®-îc tõ Rhodophyta (t¶o ®á). C¸c lo¹i th¹ch vμ nång ®é ®Òu cã thÓ lμm ¶nh h-ëng ®Õn sinh tr-ëng vμ xuÊt hiÖn m¶nh nu«i cÊy.agarose The main functional constituent of agar.Thμnh phÇn chøc n¨ng chÝnh cña th¹ch. agarose gel electrophoresis A method to separate DNA and RNA molecules on the basis of their size, in which samples are subjected to an electric field applied to a gel made with agarose.®iÖn di trªn gel agarose Ph-¬ng ph¸p ®Ó t¸ch riªng c¸c ph©n tö DNA vμ RNA dùa theo kÝch th-íc cña chóng, trong ®ãc¸c mÉu tïy thuéc vμo ®iÖn tr-êng ¸p dông cho mét gel agarose.aggregate 1. A clump or mass formed by gathering or collecting units. 2. A body of loosely associated cells, such as a friable callus or cell suspension. 3. Coarse inert material, such as gravel, that is mixed with soil to increase its porosity. 4. A serological reaction in which the antibody and antigen react and precipitate.tËp hîp 1. Côm hoÆc khèi h×nh thμnh do nhiÒu ®¬n vÞ tÝch tô hoÆc s-u tËp. 2. ThÓkÕt hîp kh«ng chÆt chÏ nhiÒu tÕ bμo, nh-lμ m« sÑo rêi r¹c hoÆc huyÒn phï tÕ bμo 3. VËt liÖu th« tr¬, nh- lμ sái, ®-îc trén lÉn víi ®Êt ®Ó t¨ng thªm ®é xèp. 4. Ph¶n øng huyÕt thanh trong ®ã kh¸ng thÓ vμ kh¸ng nguyªn ph¶n øng vμ kÕt tña.agonist A drug, hormone or transmitter substance that forms a complex with a receptor site. The formation of the complex triggers an active response from a cell.chÊt kh¸ng Mét lo¹i thuèc, hooc-m«n hoÆc chÊt dÉn truyÒn t¹o thμnh mét phøc chÊt cã vÞ trÝ thÓ nhËn. H×nh thμnh phøc hÖkhëi ph¸t ph¶n øng tÝch cùc tõ tÕ bμo. Agrobacterium A genus of bacteria that includes several plant pathogenic species, causing tumour-like symptoms. Agrobacterium Gièng vi khuÈn bao gåm mét sè loμi t¸c nh©n g©y bÖnh thùc vËt, g©y ra c¸c dÊu hiÖu gièng nh- khèi u.xem: Agrobacterium rhizogenes, Agrobacterium tumefaciens.Agrobacterium rhizogenes A bacterium that causes hairy root disease in some plants. Similar to the crown gall disease caused by Agrobacterium tumefaciens, this is achieved by the mobilization of the bacterial Ri plasmid with the transfer to the plant of some of the genetic material from the plasmid. This process has been used to insert foreign genes into plant cells, but to a lesser extent than the Agrobacterium tumef aciens-mediated transformation system, because regeneration of whole plants from hairy root cultures is problematical. Agrobacterium rhizogene Lo¹i vi khuÈn g©y bÖnh h¹i rÔ ë mét sè thùc vËt. T-¬ng tù bÖnh nèt sÇn ®-îc g©y ra bëi Agrobacterium tumefaciens, ®-îc t¹o thμnh do sù huy ®éng cña Ri plasmid vi khuÈn cïng viÖc chuyÓn cho c©y mét sèvËt chÊt di truyÒn tõ plasmid. Qu¸ tr×nh nμy ®-îc dïng ®Ó chÌn c¸c gen l¹ vμo tÕ bμo c©y, nh-ng ph¹m vi nhá h¬n so víi Agrobacterium tumefacien- hÖ biÕn n¹p trung gian, do t¸i sinhÈc mét thùc vËt tõviÖc nu«i cÊy rÔ t¬ lμ mét sù khã kh¨n. Agrobacterium tumefaciens A bacterium that causes crown gall disease in some plants. The bacterium characteristically infects a wound, and incorporates a segment of Ti plasmid DNA into the host genome. This DNA causes the host cell to grow into a tumour-like structure that synthesizes specific opines that only the pathogen can metabolize. This DNA-transfer mechanism is exploited in theAFLP6genetic engineering of plants. Agrobacterium tumefacien Vi khuÈn g©y ra bÖnh nèt sÇn trong mét sè thùc vËt. Lo¹i vi khuÈn nμy chuyÓn nhiÔm ®Æc tr-ng vÕt th-¬ng, vμ hîp nhÊt ®o¹n DNA Ti plasmid vμo hÖ gen ký chñ. DNA khiÕn cho tÕ bμo ký chñ t¨ng tr-ëng thμnh mét cÊu tróc gièng nh- khèi u ®Ó tæng hîp c¸c s¶n phÈm ®Æc biÖt mμ chØ t¸c nh©n g©y bÖnh míi cãthÓ chuyÓn ho¸. C¬ chÕ chuyÓn ®æi DNA ®-îc khai th¸c trong kü thuËt di truyÒn thùc vËt. Xem: T - DNA.Agrobacterium tumef aciens-mediated transformation The process of DNA transfer from Agrobacterium tumefaciens to plants, that occurs naturally during crown gall disease, and can be used as a method of transformation.biÕn n¹p trung gian Agrobacterium tumefacien Qu¸ tr×nh chuyÓn DNA tõAgrobacterium tumefacies cho thùc vËt, xÈy ra tù nhiªn trong bÖnh nèt sÇn, vμ cãthÓ dïng lμm ph-¬ng ph¸p biÕn n¹p. AHG ViÕt t¾t cña antihaemophilic globulin.AI ViÕt t¾t cña artificial insemination. airlift fermenter A cylindrical fermentation vessel in which the cells are mixed by air introduced at the base of the vessel and that rises through the column of culture medium. The cell suspension circulates around the column as a consequence of the gradient of air bubbles in different parts of the reactor.b×nh lªn men èng khÝ B×nh lªn men h×nh èng trong ®ã c¸c tÕ bμo ®-îc trén lÉn do kh«ng khÝ ®-a vμo t¹i ®¸y b×nh vμ ®-îc d©ng lªn qua cét dung dÞch nu«i cÊy. HuyÒn phï tÕ bμo bao quanh cét gièng nh-kÕt qu¶ cña gradient bät khÝ trong tõng phÇn kh¸c nhau cña b×nh ph¶n øng. albinism Hereditary absence of pigment in an organism. Albino animals have no colour in their skin, hair and eyes. Albino plants lack chlorophyll.chøng b¹ch t¹ng ThiÕu di truyÒn s¾c tè ësinh vËt. C¸c ®éng vËt b¹ch t¹ng kh«ng cã mμu ë da, tãc vμ m¾t. C©y b¹ch t¹ng thiÕu chÊt diÖp lôc.albino 1. An organism lacking pigmentation, due to genetic factors. The condition is albinism 2. A conspicuous plastid mutant involving loss of chlorophyll.thÓ b¹ch t¹ng1. Sinh vËt thiÕu hÖ s¾c tèdo nh©n tè di truyÒn. §iÒu kiÖn lμ b¹ch t¹ng 2. §ét biÕn l¹p thÓ dÔ nhËn biÕt kÐo theo mÊt chÊt diÖp lôc.aleurone The outermost layer of the endosperm in a seed, and the site of enzymes concerned with endosperm digestion during seedling growth.mμng nhò Líp ngoμi cïng cña néi nhòh¹t, vμ vÞ trÝ cña c¸c enzim liªn quan ®Õn tiªu ho¸ néi nhò khi n¶y mÇm.algal biomass Single-celled plants (e.g. Chlorella spp. and Spirulina spp.) grown commercially in ponds to make feed materials for zooplankton, which are in turn harvested as feed for fish farms.sinh khèi t¶o Thùc vËt cã cÊu t¹o tÕ bμo ®¬n (vÝ dô t¶o Chlorella spp. vμ Spirulina spp.) trång th-¬ng m¹i trong ao hå ®Ó t¹o nguyªn liÖu nu«i ®éng vËt phï du, ®-îc thu ho¹ch tõng ®ît lμm thøc ¨n nu«i c¸ . alginate Polysaccharide gelling agent.T¸c nh©n t¹o gel polisacarit .alkylating agent A class of chemicals that transfer alkyl (methyl, ethyl, etc.) groups; for example to the bases in DNA. Some of these (especially ethyl methane sulphonate, abbreviated EMS) have been much used as mutagens.t¸c nh©n ankyl ho¸ Líp hãa chÊt chuyÓn giao nhãm ankyl (mª-thyl, ª-tin, etc.); vÝdô chuyÓn cho baz¬ trong DNA. Mét sètrong ®ã (®Æc biÖt lμ ethyl methane sulphonate, viÕt t¾t EMS) ®-îc sö dông nhiÒu lμm t¸c nh©n g©y ®ét biÕn.allele A variant form of a gene. In a diploid cell there are two alleles of every gene (one inherited from each parent, although they could be identical). Within a population there may be many alleles of a gene. Alleles are symbolized with a capital letterAgrobacterium tumefacien。

MaximumParsimony（Classnote）：最大简约法（课堂笔记）

An Approximation Algorithm for Haplotype Inference byMaximum Parsimony(Class note)Yao-Ting Huang,1Kun-Mao Chao,1,2,†and Ting Chen3,†1Department of Computer Science and Information Engineering2Graduate Institute of Networking and MultimediaNational Taiwan University,Taipei,Taiwan{d92023,kmchao}@.tw3Department of Biological SciencesUniversity of Southern California,Los Angeles,CA90089,USA****************†:Corresponding Authors:Kun-Mao Chao Ting ChenDepartment of Computer Science Department of Biological Sciencesand Information Engineering University of Southern California National Taiwan University1042West36th Place,DRB2901Roosevelt Rd.Sec.4,Taipei,Taiwan Los Angeles,CA90089-1113,USA Email:***************.edu.tw Email:****************Phone:886-2-23625336Phone:213-740-2415Fax:886-2-23628167Fax:213-740-2437AbstractThis paper studies haplotype inference by maximum parsimony using population data.We deﬁne the optimal haplotype inference(OHI)problem as given a set of genotypes and a set of related haplotypes,ﬁnd a minimum subset of haplotypes that can resolve all the genotypes.We prove that OHI is NP-hard and can be formulated as an integer quadratic programming(IQP)problem.To solve the IQP problem,we propose an iterative semi-deﬁnite programming based approximation algorithm,(called SDPHapInfer).We show that this algorithmﬁnds a solution within a factor of O(log n)of the optimal solution,where n is the number of genotypes.This algorithm has been implemented and tested on a variety of simulated and biological data.In comparison with three other methods:(1)HAPAR,which was implemented based on the branching and bound algorithm, (2)HAPLOTYPER,which was implemented based on the Expectation-Maximization algorithm, and(3)PHASE,which combined the Gibbs sampling algorithm with an approximate coalescent prior,the experimental results indicate that SDPHapInfer and HAPLOTYPER have similar error rates.In addition,the results generated by PHASE have lower error rates on some data but higher error rates on others.The error rates of HAPAR are higher than the others on biological data.In terms of eﬃciency,SDPHapInfer,HAPLOTYPER,and PHASE output a solution in a stable and consistent way,and they run much faster than HAPAR when the number of genotypes becomes large.Keywords:algorithm,haplotype inference,integer quadratic programming,maximum parsimony, semi-deﬁnite programming1IntroductionCorrelating variations in DNA sequence with phenotypic diﬀerences has been one of the grand challenges in biology.Eﬀorts have been made to obtain all common variants in the human population, including single nucleotide polymorphisms(SNPs),deletions and insertions.Many SNPs have been identiﬁed and these data are now publicly available for researchers.For example,the InternationalHapMap Project(Helmuth,2001),formed in2002,aimed to characterize the patterns of linkage disequilibrium across the human genome using SNPs such that the information can be used for large-scale genetic association studies.As a dense SNP haplotype map is being built(Daly et al., 2001;Helmuth,2001;Patil et al.,2001),various methods have been proposed to use haplotype information in linkage disequilibrium mapping.Some existing statistical methods for genetic linkage analysis have also shown increased power by incorporating SNP haplotype information(Huang et al.,2004;Seltman et al.,2001;Zhang et al.,2002,2003).But,the use of haplotype maps has been limited due to the fact that the human genome is a diploid and,in practice,genotype data instead of haplotype data are collected directly,especially in large-scale sequencing projects,because of cost considerations.Although recently developed experimental techniques(Douglas et al.,2001) give the hope of deriving haplotype information directly with aﬀordable costs,eﬃcient and accurate computational methods for haplotype reconstruction from genotype data are still in high demand.A number of methods have been developed to infer haplotypes based on genotypes of unrelated individuals.These methods can be divided into those based on combinatorics(Bafna et al.,2003; Eskin and Halperin,2003;Gusﬁeld,2001,2002,2003;Wang and Xu,2003)and those based on expectation-maximization(EM)algorithms or bayesian algorithms(Excoﬃer and Slatin,1995;Lin et al.,2002;Niu et al.,2002;Qin et al.,2002;Stephens et al.,2001,2003).The statistical methods ﬁrst infer haplotype frequencies and then use these frequencies to compute the haplotype conﬁgura-tion(or called phase)for each genotype.A recent study by Stephens and Donnelly(2003)compared three statistical approaches,the PL-EM algorithm(Niu et al.,2002)called HAPLOTYPER,and two MCMC algorithms based on Gibbs sampling,one called PHASE(Stephens et al.,2001)and another by Lin et al.(2002),using a variety of simulated and real genotype data.Two measures of accuracy were used:the error rate of individuals whose haplotype estimates are not completely correct,and the error rate of single site.The results showed that both error rates of these algorithms can be as high as50%.On the other hand,most combinatorics based methods consider two models.Theﬁrst model is based on perfect phylogeny,assuming there is no recombination,and the other model is basedon pure parsimony,assuming the number of real haplotypes is minimum.In this paper,we study the pure parsimony model.Gusﬁeld(2003)ﬁrst formulated the problem and proposed an integer linear programming algorithm to solve this problem.Wang and Xu(2003)proposed a branching and bound algorithm called HAPAR toﬁnd the optimal solution.Recently,Brown and Harrower(2004) proposed a new formulation of the ncia et al.(2004)proved the APX-hardness of the problem.That is,if there is a constantλ>1such that the existence of aλ-approximation algorithm for this problem would imply P=NP.Sharan et al.(2005)showed that it remains APX-hard even in some very restricted cases.In this paper,weﬁrst formulate the haplotype inference based on pure parsimony problem as an optimal haplotype inference(OHI)problem.Then the OHI problem is reformulated as an integer quadratic programming(IQP)problem.Based on the IQP problem,we propose an iterative semi-deﬁnite programming based approximation algorithm thatﬁnds a solution within a factor of O(log n) of the optimal solution,where n is the number of genotypes.We also prove that OHI is NP-hard through a reduction from the problem of Exact Cover By3-Sets(X3C)(Garey and Johnson,1979). This algorithm has been implemented and tested on a variety of simulated and biological data.In comparison with three other methods,HAPAR,HAPLOTYPER,and PHASE,the experimental results indicate that this algorithm outputs solutions with high accuracy and eﬃciency.2MethodProblem FormulationSuppose we are given n individuals for a local chromosomal region of L linked SNPs.Let G= {g1,g2,...,g n}denote the genotypes for the n individuals,where g i={g i1,...,g iL},g ij denotes the genotype for individual i at locus j,and g ij=0,1or2denote that this locus is homozygous wild type,homozygous mutant,or heterozygous,respectively.Experimental data may have missing alleles.We let g ij=3,4,or5to denote two missing alleles,one missing allele and one wild type, and one missing allele and one mutant.Let H={h1,h2,...,h m}denote the set of all possible unobserved haplotypes for G.We denote |H|=m to be the number of elements in a set.If two haplotypes h r and h t form a genotype g i, we denote h r⊗h t=g i,and we also say that h r and h t resolve g i,or a haplotype conﬁguration for g i is h r and h t.Let S={S1,...,S n}denote the sets of unobserved haplotype conﬁgurations for G, where S i={(h r,h t):h r⊗h t=g i}denotes the set of all unobserved haplotype conﬁgurations for g i.We formulate the haplotype inference by maximum parsimony as follows,which is referred to as optimal haplotype inference(OHI)problem.Optimal Haplotype Inference(OHI)Given a set of genotypes G and a polynomial-sizedset of unobserved haplotypes H for G,ask toﬁnd a minimum subset of haplotypes,V⊆H,such that for every genotype g i,1≤i≤n,there exists a pair of haplotypesh r∈V and h t∈V such that h r and h t resolve g i(or(h r,h t)∈S i).We would like to note that m(i.e.,the size of H)isﬁxed in this paper because(1)the idea of haplotype inference is restricted to a high linkage disequilibrium(LD)region,which is usually short (Zhang et al.,2002,2004);and(2)the number of observed haplotypes in a short chromosomal region in human population is generally small.Theoretically,a genotype in a short chromosomal region may still contain a large number of ambiguous SNPs due to factors such as missing data,and thus corresponds to an exponential number of possible haplotypes.However,this kind of poor-quality genotypes do not provide enough information for haplotypes,so we do not use them for haplotype inference.If each genotype corresponds to a maximum number of K haplotypes,m is bounded by O(nK).Integer Quadratic ProgrammingDeﬁne x i as the variable for haplotype h i:x i=1if h i∈V,and x i=−1otherwise.Given a set of genotypes G,the OHI problem can be formulated as the following integer quadratic programmingproblem,Minimizemi=1(1+x i)2/4IQP(G):subject to:(h r,h t)∈S j(1+x r)(1+x t)/4≥1,∀j∈[1,n],(1)x i∈{−1,1},∀i∈[1,m].The set V={i|x i=1}corresponds to the set of selected haplotypes.The j th inequality guarantees that genotype g j∈G can be resolved.Semideﬁnite Programming RelaxationSince solving this integer quadratic programming is NP-complete,we consider relaxations of IQP. We can interpret IQP as restricting x i to be a1-dimensional vector with unit norm.Thus,we can relax x i into a(m+1)-dimensional vector y i of unit Euclidean norm.We introduce another (m+1)-dimensional unit vector y0,and relax IQP toMinimizemi=1(y0+y i)2/4SDP(G):subject to:(h r,h t)∈S j(y0+y r)·(y0+y t)≥4,∀j∈[1,n],(2)|y i|=1,∀i∈[1,m].In fact,SDP becomes IQP if we lety0=(1,0,...,0),y1=(x1,0,...,0),...,y m=(x m,0,...,0).(3) SDP can be solved by semideﬁnite programming.Let Y=(y0y1...y m)T(y0y1...y m),where y ij= y i·y j.Then Y is positive semideﬁnite.We reformulate SDP into the following semideﬁnite pro-gramming:Minimize C·Ysubject to:A j·Y≥a j,∀j∈[1,n],(4)y ii=1,Y 0,where Y 0means Y is symmetric positive semideﬁnite.The semideﬁnite programming is an extension of the linear programming into convex cones.An eﬃcient algorithm for the semideﬁnite programming is called the interior point method.Let OPT(SDP)be the optimal solution of SDP. For any givenε>0,the interior point methodﬁnds a solution of value less than OPT(SDP)+εin time polynomial in the input size and log1/ε.Once an almost optimal solution Y is found,we can use an incomplete Cholesky decomposition to obtain vectors y0,y1,...,y m.Algorithm SDPHapInferIn the following,we introduce an algorithm that iteratively runs a semideﬁnite programming,ﬁnds a solution{y0,y1,...,y m},and constructs a solution{x0,x1,...,x m}by randomized rounding.Algorithm SDPHapInfer1.Initialization(a)Let U=G={g1,...,g n}be the set of unresolved genotypes;(b)Let V={}be the set of selected haplotypes;2.SDP-Solving(a)Formulate IQP(U)and SDP(U);(b)Solve SDP(U),obtaining a solution{y0,y1,y2,...};3.Randomized-Rounding(a)Randomly pick two multi-dimensional unit vectors z1and z2;(b)Set x0=1;(c)Set x i=1for i>0if(z1·y i)(z1·y0)>0and(z2·y i)(z2·y0)>0,x i=−1otherwise;(d)Let V=V∪{h i:x i=1};4.Iteration(a)Let U be the set of the genotypes that can not be resolved by V.(b)If|U|=0;goto Step2;5.Return V.In Step2,if a pair of haplotypes h r∈V and h t/∈V resolve g i∈U,we set variable y r=y0in SDP(U).Theoretically,we can run the SDP at Step2only once and use this result for randomized rounding for all the iterations without changing the time complexity,but practically,running the SDP for each iteration gives better solutions.Analysis of AlgorithmOmittedReferences[1]Bafna,V.,Gusﬁeld,D.,Lancia,G.,and Yooseph,S.2003.Haplotyping as perfect phylogeny:a direct p.Biol.,10:323–340.[2]Brown,D.,and Harrower I.2004.A new integer programming formulation for the pure parsi-mony problem in haplotype analysis.In Proc.WABI’04,pages254–265.[3]Daly,M.J.,Rioux,J.D.,Schaﬀner,S.F.,Hudson,T.J.,and Lander,E.S.2001.High-resolutionhaplotype structure in the human genome.Nat.Genet.,29(2):229–232.[4]Douglas,J.A.,Boehnke,M.,Gillanders, E.,Trent,J.M.,and Gruber,S.B.2001.Experimentally-derived haplotypes substantially increase the eﬃciency of linkage disequilib-rium studies.Nat.Genet.,28(4):361–364.[5]Drysdale,C.,McGraw,D.,Stack,C.,Stephens,J.,Judson,R.,et plex promoterand coding regionβ2-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness.Proc.Nat.Acad.Sci.,97:10483–10488.[6]Eskin,E.,and Halperin,rge scale recovery of haplotypes from genotype data usingimperfect phylogeny.In Proc.RECOMB’03,pages104–113.[7]Excoﬃer,L.,and Slatkin,M.1995.Maximum-likelihood estimation of molecular haplotypefrequencies in a diploid population.Mol.Biol.Evol.,12:921–927.[8]Gabriel,S.B.,Schaﬀner,S.F.,Nguyen,H.,Moore,J.M.,Roy,J.,Blumenstiel,B.,Higgins,J.,DeFelice,M.,Lochner,A.,Faggart,M.,Liu-Cordero,S.N.,Rotimi,C.,Adeyemo,A.,Cooper, R.,Ward,R.,Lander,E.S.,Daly,M.J.,and Altshuler,D.2002.The structure of haplotype blocks in the human genome.Science,296(5576):2225–2229.[9]Garey,M.R.,and Johnson,puters and intractability,Freeman,New York.[10]Gusﬁeld,D.2001.Inference of haplotypes from samples of diploid populations:complexity andp.Biol.,8:305–323.[11]Gusﬁeld,D.2002.Haplotyping as perfect phylogeny:conceptual framework and eﬃcient solu-tions.In Proc.RECOMB’02,pages166–175.[12]Gusﬁeld,D.2003.Haplotyping by pure parsimony.In Proc.CPM’03,Lecture Notes in Com-puter Science,2676:144–155.[13]Helmuth,L.2001.Genome research:map of the human genome3.0.Science,293(5530):583–585.[14]Huang,Y.-T.,Zhang,K.,Chen,T.,and Chao,K.-M.2004.Approximation algorithms for theselection of robust tag SNPs.In Proc.WABI’04,pages278–289.[15]Hudson,R.R.2002.Generating samples under a Wright-Fisher neutral model of genetic varia-tion.Bioinformatics,18:337–338.[16]Kerem,B.,Rommens,J.,Buchanan,J.,Markiewicz,D.,Cox,T.,Chakravarti,A.,Buchwald,M.,and Tsui,L.C.1989.Identiﬁcation of the cysticﬁbrosis gene:genetic analysis.Science, 245:1073–1080.[17]Lancia,G.,Pinotti,C.,and Rizzi.,R.2004.Haplotyping populations by pure parsimony:complexity of exact and approximation RMS p.,16:348–359.[18]Lin,S.,Cutler,D.J.,Zwick,M.E.,and Chakravarti,A.2002.Haplotype inference in randompopulation samples.Am.J.Hum.Genet.,71:1129–1137.[19]Niu,T.,Qin,Z.,Xu,X.,and Liu,J.S.2002.Bayesian haplotype inference for multiple linkedsingle-nucleotide polymorphisms.Am.J.Hum.Genet.,70:157–159.[20]Patil,N.,Berno,A.J.,Hinds,D.A.,Barrett,W.A.,Doshi,J.M.,Hacker,C.R.,Kautzer,C.R.,Lee,D.H.,Marjoribanks,C.,McDonough,D.P.,et al.2001.Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome21.Science,294:1719–1723. [21]Qin,Z.,Niu,T.,and Liu,J.2002.Partitioning-ligation-expectation-maximization algorithm forhaplotype inference with single-nucleotide Ploymorphisms.Am.J.Hum.Genet.,71:1242–1247.[22]Seltman,H.,Roeder,K.,and Devlin,B.2001.Transmission/disequilibrium test meets measuredhaplotype analysis:family-based association analysis guided by evolution of haplotypes.Am.J.Hum.Genet.,68(5):1250–1263.[23]Sharan,R.,Halldorsson, B.V.,and Istrail,S.2005.Islands of Tractability for ParsimonyHaplotyping.To appear in Proc.CSB’05.[24]Stephens,M.,Smith,N.J.,and Donnelly,P.2001.A new statistical method for haplotypereconstruction from population data.Am.J.Hum.Genet.,68(4):978–989.[25]Stephens,M.,and Donnelly,P.2003.A comparison of bayesian methods for haplotype recon-struction from population genotype data.Am.J.Hum.Genet.,73:1162–1169.[26]Wang,L.,and Xu,Y.2003.Haplotype inference by maximum parsimony.Bioinformatics,19(14):1773–1780.[27]Zhang,K.,Deng,M.,Chen,T.,Waterman,M.S.,and Sun,F.2002.A dynamic programmingalgorithm for haplotype partitioning.Proc.Nat.Acad.Sci.,99(11):7335–7339.[28]Zhang,K.,Sun, F.,Waterman,M.S.,and Chen,T.2003.Haplotype block partition withlimited resources and applications to human chromosome21haplotype data.Am.J.Hum.Genet.,73:63–73.[29]Zhang,K.,Qin,Z.S.,Liu,J.S.,Chen,T.,Waterman,M.S.,and Sun,F.2004.Haplotype blockpartitioning and tag SNP selection using genotype data and their applications to association studies.Genome Res.,14(5):908–916.11。

2021年托福试题阅读理解模拟题考点分析(卷十)

2021年托福试题阅读理解模拟题考点分析（卷十）Title：The Cambrian ExplosionThe earliest fossil evidence for eukaryotes complex organisms whose cells contain a distinct nucleus dates to only about 1.2 billion years ago. The fossil record suggests that animal evolution progressed slowly, with relatively little change seen between fossils from 1.2 billion years ago and those from a half-billion years later. But then something quite dramatic happened as can be judged by the many different animal groups that suddenly appear in the fossil record.Biologists classify animals according to their basic body plans. For example, the basic body plan shared by mammals and reptiles is fundamentally different from that of insects.Animals are grouped by body plan into what biologists call phyla. Mammals and reptiles both belong to the single phylum Chordata, which includes animals with internal skeletons. Insects, crabs, and spiders belong to the phylum Arthropoda, which contains animals with body features such as jointed legs, an external skeleton, and segmented bodies. Classifying animals into phyla is an ongoing project for biologists, but modern animals appear to comprise about 30 different phyla, each representing a different body plan.Remarkably, nearly all of these different body plans, plus a few others that have gone extinct, make their first known appearance in thegeological record during a period spanning only about 40 million years less than about 1 percent of Earth's history. This remarkable flowering of animal diversity appears to have begun about 545 million years ago, which corresponds to the start of the Cambrian period. Hence it is called the Cambrian explosion.The fact that the Cambrian explosion marks the only major diversification of body plans in the geological record presents us with two important and related questions: Why, so long after the origin of eukaryotes, did the pace of evolution suddenly accelerate dramatically at the beginning of the Cambrian, and why hasn't there been another period of similarly explosive diversification since then We can identify at least four factors that might have contributed to the Cambrian explosion. First, the oxygen level in our atmosphere may have remained well below its present level until about the time of the Cambrian explosion. Thus, the rapid diversification in animal life may have occurred at least in part because oxygen reached a critical level for the survival of larger and more energy-intensive life forms.A second factor that may have been important was the evolution of genetic complexity.As eukaryotes evolved, they developed more and more genetic variation in their DNA. Some scientists believe that the Cambrian explosion marks the point at which organisms developed certain kinds of genes (homeobox genes) that control body form and thatcould be combined in different ways, allowing the evolution of a great diversity of forms over time。

2022年考研考博-考博英语-合肥工业大学考试全真模拟全知识点汇编押题第五期(含答案)试卷号：90

2022年考研考博-考博英语-合肥工业大学考试全真模拟全知识点汇编押题第五期（含答案）一.综合题(共15题)1.单选题Even if the genes themselves are not initially hazardous, you do not know how they are going to evolve.问题1选项A.partiallyB.originallyC.ultimatelyD.fundamentally【答案】B【解析】考查副词辨析。

A选项partially“部分地；偏袒地”；B选项originally“最初，起初；本来”；C选项ultimately“最后；根本”；D选项fundamentally“根本地，基础地”。

ultimately和fundamentally都有根本的意思，前者侧重于就结果方向而言，而后者侧重于从源泉方向讲。

句意：即使基因本身……没有危险，你也不知道它们将如何进化。

Even if引导让步状语从句。

由后面的关键信息you do not know how they are going to evo lve.“你不知道它们将如何发展”，是在说基因之后的发展，所以按照逻辑关系，刚开始基因本身是没有危险的，但是之后经历过一些变化后就难以保证了。

因此B选项符合题意。

2.单选题The large amounts of personal data floating around in society today leaves individuals open to having their privacy to be violated, sometimes with serious consequences.问题1选项A.floating aroundB.leavesC.be violatedD.with【答案】B【解析】考查单复数。

The large amounts of跟名词做主语，谓语动词要用复数。

派生物英语分析举例

派生物相关的英语举例一、和派生物有关的英语单词：derivant 派生物; 衍化物; 衍生物派生需求 derivative派生收入 derivative派生所得 derivation派生的权利 derived派生的测定 derived派生 derivation派生的 derived单步派生 step派生码 generated派生树 derivation二、派生物有关的英语例句1.WHY ARE THE LUPANINE DERIVATIVES BITTER?为什么白金雀儿碱的派生物是苦的？2.To Convert(Certain Biological Compounds)Into Biologically Active Derivatives.使活化变（某些生物复合物）为生物性能活跃的派生物3.The 1977 Amendments To The Clean Water Act Were An Outgrowth Of These Problems.《洁净水法案》1977年的修正案，是这些问题的派生物。

4.The Extraordinary Nature Life Of Jing Group And The Ideal Personality Of Taoist;京派小说的“异秉”人生与道家理想人物5.Life Noumenon Nuture In Taigu School S Ge Wu Zhi Zhi;太谷学派格物致知说的生命本位特色6.Material-Derivation--Observation On The Formation And Social Control Of Taboo About Food;物质派生性——食物禁忌的形成与社会控制考察7.And As Gradually Sounds Multiplied And Life Manifested Itself.各种声音也随之稠密起来，大地万物，一派生机。

219401804_山西部分地区树莓采后主要侵染性病原真菌的鉴定及其生物学特性

张晓宇，高振峰，侯亚茹，等. 山西部分地区树莓采后主要侵染性病原真菌的鉴定及其生物学特性[J]. 食品工业科技，2023，44（13）：110−118. doi: 10.13386/j.issn1002-0306.2022060099ZHANG Xiaoyu, GAO Zhenfeng, HOU Yaru, et al. Identification and Biological Characteristics of Postharvest Pathogenic Fungi of Raspberries in Some Areas of Shanxi[J]. Science and Technology of Food Industry, 2023, 44(13): 110−118. (in Chinese with English abstract). doi: 10.13386/j.issn1002-0306.2022060099· 生物工程 ·山西部分地区树莓采后主要侵染性病原真菌的鉴定及其生物学特性张晓宇，高振峰，侯亚茹，张新宪，陈园园，张立新（山西农业大学食品科学与工程学院，山西太原 030031）摘　要：树莓（Rubus corchorifolius L. f.）采后易受病原菌侵染，病菌种类不但与果实种类有关，而且与栽培环境相关。

本研究对山西省太原市、阳泉市和长治市3个不同产区的树莓采后主要侵染性病原真菌进行分离鉴定并研究其生物学特性，对病原菌进行分离纯化，结合形态学和分子生物学特征确定其种类，明确在同期内病原菌产孢量和在不同条件下病原菌生长情况。

结果表明，所研究3个地区侵染采后树莓病原菌主要为拟康宁木霉（Trichoderma koningiopsis ）、皮落青霉（Penicillium crustosum ）、葡萄孢霉（Botrytis sp.）和少根根霉（Rhizopus arrhizus ）。

GMAT(VERBAL)阅读模拟试卷30(题后含答案及解析)

GMAT（VERBAL）阅读模拟试卷30(题后含答案及解析)题型有：1.Determining whether a given population of animals constitutes a distinct species can be difficult because no single accepted definition of the term exists. One approach, called the biological species concept, bases the definition on reproductive compatibility. According to this view, a species is a group of animals that can mate with one another to produce fertile offspring but cannot mate successfully with members of a different group. Yet this idea can be too restrictive. First, mating between groups labeled as different species (hybridization), as often occurs in the canine family, is quite common in nature. Second, sometimes the differences between two populations might not prevent them from interbreeding, even though they are dissimilar in traits unrelated to reproduction; some biologists question whether such disparate groups should be considered a single species. A third problem with the biological species concept is that investigators cannot always determine whether two groups that live in different places are capable of interbreeding.When the biological species concept is difficult to apply, some investigators use phenotype, an organism’s observable characteristics, instead. Two groups that have evolved separately are likely to display measurable differences in many of their traits, such as skull size or width of teeth. If the distribution of measurements from one group does not overlap with those of another, the two groups might reasonably be considered distinct species.1．The passage is primarily concerned withA．describing the development of the biologica species conceptB．responding to a critique of reproductive compatibility as a criterion for defining a speciesC．considering two different approaches to identifying biological speciesD．pointing out the advantage of one method of distinguishing related speciesE．identifying an obstacle to the classification of biological species正确答案：C解析：Main ideaThis question depends on understanding the passage as a whole. The passage begins by explaining that identifying a species can be difficult, because there are different ways of defining the term. The biological species concept is one approach, but it has problems. Phenotype is another approach that can be used when the biological species concept proves difficult.A The first paragraph defines the biological species concept and identifies some problems with its application, but it does not explain how that concept developed.B The passage presents some critiques of reproductive compatibility as a way of identifying a biological species; it does not concern itself with responding to those critiques.C Correct. The passage considers thebiological species concept and the idea of phenotype as ways of identifying biological species.D While the passage identifies two ways of distinguishing species and states that some investigators use one of those methods- -the phenotype method—when the biological method is difficult to apply, the passage is not primarily concerned with pointing out that either one is better than the other.E The passage does discuss certain obstacles to the classification of species. First, it points out that there is no single accepted definition of distinct species. Second, it points out obstacles related to one particular approach to the classificatior of species. However, the passage consider: these obstacles in service of its primary concern, namely considering two different approaches to identifying biological species.The correct answer is C. 知识模块：阅读理解2．The author of the passage mentions “groups that ive in different places” (line 21) most probably in ordef toA．point out a theoretical inconsistency in the biological species conceptB．offer evidence in support of the biological species conceptC．identify an obstacle to the application of the biological species conceptD．note an instance in which phenotype classification is customarily usedE．describe an alternative to the biological species concept正确答案：C解析：EvaluationThe author’s mention of groups that live in different places comes at the end of the first paragraph, in the context of discussing a third problem with the biological species concept: that investigators may not know whether animals in such groups are able to interbreed.A The author does not address theoretical inconsistencies in the biological species concept.B The author mentions groups that live in different places in order to address a problem with the biological species concept, not to support it.C Correct. One obstacle to applying the biological species concept is that those attempting to distinguish among species may not be able to determine whether geographically separated groups of animals can interbreed.D The passage does mention that some investigators use phenotype classification when the biological species concept is difficult to apply, but it does not mention specifically that a situation in which groups live in different places is an instance in which phenotype classification is customarily used.E Animal groups that live in different places pose a problem for the application of the biological species concept, according to the author. The author does not mention these groups in order to describe an alternative to that concept.The correct answer is C. 知识模块：阅读理解3．With which of the following statements regarding the classification of individual species would the author most likely agree?A．Phenotype comparison may help to classify species when application of the biological species concept proves inconclusive.B．Because no standard definition exists for what constitutes a species, the classification of animal populations is inevitably an arbitrary process.C．The criteria used by biologists to classify species have not been based on adequate research.D．The existence of hybrids in wild animal species is the chief factor casting doubt on the usefulness of research into reproductive compatibility as a way of classifying species.E．Phenotype overlap should be used as the basic criterion for standardizing species classification.正确答案：A解析：InferenceThis question depends on understanding the general points the author makes with regard to classification of individual species. The author explains that there is no single definition of species and then describes the biological species concept, which depends on reproductive compatibility. This approach has several problems, however, and the author goes on to say that phenotype may be used when the biological species concept is difficult to apply.A Correct. The author states at the beginning of the second paragraph that some investigators use phenotype when they find it difficult to apply the biological species concept, and the passage provides no reason to believe that the author would disagree with the idea that phenotype comparison can be helpful in these situations.B The author would most likely not agree that classification of animal populations is arbitrary. Investigators use clearly defined approaches, such as the biological species concept and phenotype classification, to make such classifications. That there may be problems with an approach does not make it arbitrary.C The author states that the biological species concept can be too restrictive, but there is no suggestion that the author finds this approach, or phenotype classification, to be inadequately researched.D The author mentions hybridization first as a factor casting doubt on the usefulness of the biological species concept, but nothing in the passage suggests that the author thinks that it is more significant than the other reasons offered for finding the biological species concept too restrictive.E Phenotype overlap does not receive the author’s endorsement as the best, or most basic, way of classifying species; instead, the author states merely that some investigators rely on this approach when they cannot apply the biological species concept.The correct answer is A. 知识模块：阅读理解4．Which of the following best describes the function of lines 10-13?A．It elaborates the definition of the biological species concept given in a previous sentence.B．It develops a point about the biological species concept made in the previous sentence.C．It states the author’s central point about the biological species concept.D．It identifies a central assumption underlying the biological species concept.E．It demonstrates why the biological species concept is invalid.正确答案：B解析：EvaluationThe sentence in question discusses hybridization as a first factor complicating the applicability of the biological species concept. Thus its function is tohelp explain why, as the previous sentence states, that concept is too restrictive.A The sentence in question brings up a problem with the biological species concept; it does not elaborate the definition of that concept.B Correct. According to the sentence that precedes the sentence in question, the biological species concept can be too restrictive. The author offers three reasons to develop this point, and the first reason is given in the sentence in question.C The sentence in question could be said to support the author’s central point about the biological species concept—that it is one (flawed) way of determining whether a population is a species—but it does not state that central point.D The sentence in question expresses a problem with the biological species concept, not a central assumption of it.E The sentence in question serves to indicate a problem with the biological species concept, but it does not go so far as to demonstrate that it is invalid.The correct answer is B. 知识模块：阅读理解Researchers studying how genes control animal behavior have had to deal with many uncertainties. In the first place, most behaviors are governed by more than one gene, and until recently geneticists had no method for identifying the multiple genes involved. In addition, even when a single gene is found to control a behavior, researchers in different fields do not necessarily agree that it is a “behavioral gene.”Neuroscientists, whose interest in genetic research is to understand the nervous system (which generates behavior), define the term broadly. But ethologists—specialists in animal behavior—are interested in evolution, so they define the term narrowly. They insist that mutations in a behavioral gene must alter a specific normal behavior and not merely make the organism ill, so that the genetically induced behavioral change will provide variation that natural selection can act upon, possibly leading to the evolution of a new species. For example, in the fruit fly, researchers have identified the gene Shaker, mutations in which cause flies to shake violently under anesthesia. Since shaking is not healthy, ethologists do not consider Shaker a behavioral gene. In contrast, ethologists do consider the gene period (per), which controls the fruit fly’s circadian (24-hour) rhythm, a behavioral gene because flies with mutated per genes are healthy; they simply have different rhythms.5．The primary purpose of the passage is toA．summarize findings in an area of researchB．discuss different perspectives on a scientific questionC．outline the major questions in a scientific disciplineD．illustrate the usefulness of investigating a research topicE．reconcile differences between two definitior’s of a term正确答案：B解析：Main ideaThe passage discusses two problems confronting researchers studying the genetic bases of animal behavior: the complexity of the control of most behaviors by multiple genes, and divergence between research fields in what counts as a behavioral gene. The passage focuses mainly on the latter issue, discussing howethologists define “behavioral gene” in a narrower manner than neuroscientists, who define the term broadly.To elucidate the ethologists’approach, two genes are discussed, one a behavioral gene, the other not.A The passage primarily aims to explain how researchers in two different research are is define “behavioral gene.” It does not try to summarize the research findings of either area.B Correct. The primary purpose of the passage is to identify differing perspectives on the scientific question of how genes control animal behavior.C The scientific disciplines of genetics, neuroscience, and ethology—all subdisciplines of biology—contain many different “major questions,”and the passage does not try to outline the great variety of such questions in any one of those subdisciplines.D The topic of the utility of doing research is not part of the passage discussion.E An important purpose of the passage is to illustrate divergence among scientific fields in how a key term is defined, but the point is to show how the definitions differ rather than to “reconcile”the difference.The correct answer is B. 知识模块：阅读理解6．The passage suggests that neuroscientists would most likely consider Shaker to be which of the following ?A．An example of a behavioral geneB．One of multiple genes that control a single behaviorC．A gene that, when mutated, causes an alteration in a specific normal behavior without making the organism illD．A gene of interest to ethologists but of no interest to neuroscientistsE．A poor source of information about the nenous system正确答案：A解析：ApplicationThe passage asserts that ethologists do not regard Shaker as a behavioral gene because it merely makes fruit flies exhibit unhealthy behavior (shaking under anesthesia). But neuroscientists, according to the passage, are mainly interested in how genes, via the nervous system, contribute to behavior. The passage suggests that neuroscientists, unlike ethologists, have no reservation about using the term behavioral gene to apply to any gene that contributes to behavior. The implication is that neuroscientists would probably regard Shaker as a behavioral gene.A Correct. The passage suggests that neuroscientists would probably regard Shaker as a behavioral gene.B The passage indicates that research shows Shaker is a sufficient cause, in fruit flies, of shaking under anesthesia. Although some organism might display a behavior controlled by Shaker in concert with other genes, the passage is silent on any such possibility.C The passage lacks information as to whether there is any alteration—one that neuroscientists would likely consider healthy —in a normal behavior if the alteration is caused by a mutation in Shaker.D The passage indicates that neuroscientists’interest in genetics is part of their effort to understand the nervous system. This seems to imply that neuroscientists might be interested in Shaker.E The passage is silent on how neuroscientists would evaluate the potential for Shaker to contribute to understanding of the nervous system.The correct answer is A. 知识模块：阅读理解7．It can be inferred from the passage that which of the following, if true, would be most likely to influence ethologists’ opinions about whether a particular gene in a species is a behavioral gene?A．The gene is found only in that species.B．The gene is extremely difficult to identify.C．The only effect of mutations in the gene is o make the organism ill.D．Neuroscientists consider the gene to be a behavioral gene.E．Geneticists consider the gene to be a behavioral gene.正确答案：C解析：ApplicationThe passage identifies two criteria that ethologists use in deciding whether a gene should count as a behavioral gene: a mutation in the gene alters a specific normal behavior and the mutation does not merely make the organism ill.A The passage is silent on whether either of two genes identified by ethologists in fruit flies are to be found only in fruit flies. The two criteria mentioned used by ethologists carry no implication as to whether any gene unique to a given species would count as a behavioral gene.B The difficulty of identifying a gene can obviously be due to many factors, such as limitations in existing scientific techniques, and the passage does not imply that such difficulty increases the likelihood that a gene would count as a behavioral gene for ethologists.C Correct. The passage implies that if this were found to be true, ethologists would regard it as sufficient reason for not counting the gene as a behavioral gene.D A central theme of the passage is that whether ethologists would count a gene as a behavioral gene is largely unaffected by whether neuroscientists do so, given the divergent perspectives of the scientists’respective disciplines.E The main contrast in the passage with respect to definitions of the term behavioral gene is between ethologists and neuroscientists, and no specific definitional criteria for this term are explicitly attributed to geneticists. However, there is a slight suggestion that since geneticists find that most behaviors are governed by multiple genes, geneticists might regard any gene involved in the governance of a behavior as a behavioral gene. This approach, however, would be unlikely to influence the opinions of ethologists concerning definition.The correct answer is C. 知识模块：阅读理解For most species of animals, the number of individuals in the species is inversely proportional to the average body size for members of the species: the smaller the body size, the larger the number of individual animals. The tamarin, a small South American monkey, breaks this rule. Of the ten primate species studied in Peru’s Manu National Park, for example, the two species of tamarins, saddle-backed and emperor, are the eighth and ninth least abundant, respectively. Only the pygmy marmoset, which is even smaller, is less abundant. The tamarin’s scarcity is not easily explained; it cannot be dismissed as a consequence of diet, because tamarins feed on the same mixture of fruit, nectar, and small prey as do several of their more numerous larger counterparts, including the two capuchins known as the squirrel monkey and the nightmonkey. Although the relative proportions of fruits consumed varies somewhat among species, it is hard to imagine that such subtle differences are crucial to understanding the relative rarity of tamarins.To emphasize just how anomalously rare tamarins are, we can compare them to the other omnivorous primates in the community. In terms of numbers of individuals per square kilometer, they rank well below the two capuchins, the squirrel monkey and the night monkey. And in terms of biomass, or the total weight of the individuals that occupy a unit area of habitat, each tamarin species is present at only one-twentieth the mass of brown capuchins or one-tenth that of squirrel monkeys. To gain another perspective, consider the spatial requirements of tamarins. Tamarins are rigidly territorial, vigorously expelling any intruders that may stray within the sharply defined boundaries of their domains. Groups invest an appreciable part of their time and energy in patrolling their territorial boundaries, announcing their presence to their neighbors with shrill, sweeping cries. Such concerted territoriality is rather exceptional among primates, though the gibbons and siamangs of Asia show it, as do a few other New World species such as the titi and night monkeys. What is most surprising about tamarin territories is their size.Titi monkeys routinely live within territories of 6 to 8 hectares, and night monkeys seldom defend more than 10 hectares, but tamarin groups routinely occupy areas of 30 to 120 hectares. Contrast this with the 1 to 2 hectares needed by the common North American gray squirrel, a nonterritorial mammal of about the same size. A group of tamarins uses about as much space as a troop of brown capuchins, though the latter weighs 15 times as much. Thus, in addition to being rare, tamarins require an amount of space that seems completely out of proportion to their size.8．The author indicates that tamarin territories areA．surprisingly largeB．poorly situatedC．unusually abundant in food resourcesD．incapable of supporting large troops of tamarinsE．larger in Peru than in other parts of South America正确答案：A解析：Supporting ideaThis question depends on understanding what the passage says about tamarin territories. In the second paragraph, the passage claims that the most surprising thing about tamarins is the size of their territories, and it indicates how large these territories are by comparing them to the territories of certain other animals.A Correct. The passage indicates that the size of tamarins’territories—large in comparison to the territories of several other species—is surprising.B The passage gives no indication as to whether tamarin territories are poorly situated.C Although the passage does discuss the tamarin diet, it does not indicate how abundant in food sources tamarin territories are.D The passage does indicate that relatively few tamarins live per square kilometer, but it does not claim that this is so because the territories are incapable of supporting a larger number of tamarins. In fact, there issome suggestion that the territories would seem to be capable of supporting more, which is one reason the size of the territories is so surprising.E The passage does not compare the size of tamarin territories in Peru to tamarin territories elsewhere in South America.The correct answer is A. 知识模块：阅读理解9．The author mentions the spatial requirements of the gray squirrel in order to A．explain why they are so commonB．demonstrate the consequences of their nonterritorialityC．emphasize the unusual territorial requirements of the tamarinD．provide an example of a major difference between squirrels and monkeysE．provide an example of an animal with requirements similar to those of the tamarin正确答案：C解析：EvaluationThe passage mentions the spatial requirements of the gray squirrel as part of its discussion of the surprising size of tamarin territories. Gray squirrel territories are mentioned for the specific purpose of highlighting how much more space tamarins require compared to another animal of roughly equal size.A The passage does refer to “the common gray squirrel,” but it does not explain why they are so common.B The passage does not say anything about the consequences of the gray squirrel’s nonterritoriality.C Correct. The spatial requirements of gray squirrels are mentioned to highlight, by contrast, how expansive the spatial requirements of tamarins are.D Although the passage mentions the spatial requirements of the gray squirrel to highlight how different the spatial requirements of one particular type of monkey, the tamarin, are from those of other animals, the passage does not mention the squirrels’spatial requirements to provide an example of a difference between squirrels and monkeys in general.E The passage actually does the opposite of this—it mentions the gray squirrel’s spatial requirements to provide an example of an animal with requirements vastly different from those of the tamarin.The correct answer is C. 知识模块：阅读理解10．The author regards the differences between the diets of the tamarins and several larger species asA．generally explicable in terms of territory sizeB．apparently too small to explain the rarity of tamarinsC．wholly predictable on the basis of differences in body sizeD．a result of the rigid territoriality of tamarinsE．a significant factor in determining behavioral differences正确答案：B解析：Supporting IdeaThis question depends on recognizing that the passage rejects the idea that any differences between the diets of tamarins and those of certain larger animals are large enough to explain tamarins’ relative rarity. The passage points out that these animals feed on the same fruits, nectar, and small prey, and claims thatthough the proportions of the fruits consumed varies somewhat, this variation is not sufficient to explain the tamarins rarity.A The author does not seek to explain why these differences in diet—which the passage indicates are minimal—exist. Given that the author indicates that differences in territory size are large and differences in diet are small, it is unlikely, in any case, that the author would regard the former as explaining the latter.B Correct. The passage indicates that the differences in diet among these animals are too small to explain the rarity of tamarins.C The author does not give any indication that the differences in the diets of these animals are predictable based on differences in body size.D The author does indicate that tamarins are rather unusual among primates in their rigid territoriality, but there is no indication that this rigid territoriality explains the small differences in diet among tamarins and certain larger animals.E The author mentions differences in diet merely to rule out that these differences are large enough to explain tamarins’ rarity; these differences are not mentioned as a factor in determining behavioral differences.The correct answer is B. 知识模块：阅读理解11．Which of the following would most probably be regarded by the author as anomalous?A．A large primate species that eats mostly plantsB．A species of small mammals that is fiercely territorialC．Two species of small primates that share the same territoriesD．A species of small birds that is more abundant than many species of larger birdsE．A species of small rodents that requires more living space per individual than most species of larger rodents正确答案：E解析：ApplicationThis question requires you to understand an underlying principle of the passage and to apply that principle to an instance that is not specifically discussed in the passage. The passage is concerned with how anomalous tamarins are: they are exceptions to the general rule that in general the number of animals in a species is proportional to the average body size of individuals within the species. The author also points out that tamarins are unusual in that the amount of space they require is out of proportion to their body size, suggesting the principle that an animal’s spatial requirement is generally proportional to the animal’s body size. And, though the passage is generally concerned with comparing tamarins to other primates, the author also compares tamarins’spatial requirements to those of gray squirrels, a type of rodent.A The author does not give any indication whether it would be anomalous for a species of large primates to eat mostly plants. The author does not present a general principle about the diets of primates, and says nothing specific about species of large primates.B Although the author indicates that the “rigid” territoriality of tamarins is “rather exceptional among primates,”the author lists several other primate species that are also territorial. The author does not indicate whether such territoriality is rare among small mammals in general.C The author indicates that most primates do not have “such concerted territoriality” as tamarins do, suggesting that theauthor may not think that two other species of small primates sharing territories would be anomalous.D Given that the author indicates that generally the number of individuals within a species is inversely proportional to the average body size of the members of the species, the author would probably expect that a species of small birds would be more abundant than most species of larger birds and would not regard this as anomalousE Correct. The author would generally expect that smaller animals would require less living space than larger animals.The correct answer is E. 知识模块：阅读理解12．The author most probably regards the tamarins studied in Manu National Park asA．an endangered speciesB．typical tamarinsC．unusually docileD．the most unusual primates anywhereE．too small a sample to be significant正确答案：B解析：InferenceThis question requires you to make an inference from what the author says about the tamarins studied in Manu National Park to a claim about how the author most likely regards these tamarins. The author considers certain information that has been gathered about the two tamarin species studied in the park, and on the basis of that, makes claims about tamarins in general (note that the author elsewhere in the passage simply refers to “tamarins”without qualification, i.e., without referring specifically to “the tamarins studied in Manu National Park’’). This suggests that the author would regard the tamarins studied in the park as being typical of tamarins generally, at least in the ways discussed.A It is possible that the two tamarin species studied in the park are endangered, but apart from noting the surprisingly small number of individuals belonging to the species, there is no information that would suggest that they are endangered, and the mere fact that the number of members is relatively small compared to the number of members in other species is not sufficient to indicate that they are endangered, as that number could nonetheless be stable or even growing.B Correct. The author does not specifically mention anything that would indicate that these tamarins are atypical of tamarins in general, and appears to make inferences about tamarins in general on the basis of the two species studied in the park. The author would not be justified in making such inferences if the author believed that the tamarins observed in the park were not in fact typical.C The author does not give any indication that these species are unusually docile, and in fact suggests the opposite by indicating that tamarins vigorously expel any intruders from their territories.D The author does note some ways in which these tamarin species are unusual among primates, but does not indicate that they are “the most unusual primates anywhere.”The author, in fact, indicates that in one of the ways that these species are unusual—their relative scarcity despite their small body size—another primate species, the pygmy marmoset, is even more unusual.E Because the author appears to make some inferences from information about the tamarins studied。

银川海派英语【SAT阅读】考试解决生词的办法

银川海派英语【SAT阅读】考试解决生词的办法1) 名词由于名词只是一种具体事物的代替符号，所以理解不理解其具体含义对句子整体意思影响不大。

例如：The first flying vertebrates the pterosaurs have intrigued paleontologists for more than two centuries. 在这个句子中，很多学生对诸如“vertebrates”“pterosaurs”“paleontologists”SAT阅读这些词都不认识。

但是如果你只把它们当成一些人或是东西的代号，你会发现根本不影响句子的整体意思。

在阅读中，所有这些专有名词可以用第一个字母代替。

对于这句话的翻译：第一个会飞的V这个东西叫做Pterosaurs这个名字的动物，已经激发起P这么一帮人的兴趣多于两个世纪了。

虽然我们可以能对句子中名词都不认识，但是从上面翻译中可以看出句子的整体意思还是可以理解的。

2) 动词遇到句子中不认识或者不好翻译的动词可以直接用一个意思笼统的虚词。

比如永远可以把动词翻译成“做”，“干什么用”，“使得”等含义，大概能保持翻译句子思路的连续性就可以，具体的意思等读完句子后根据整体方向确定。

例如：If a firm attempts to charge a higher price consumers will turn to other firms able to supply substitute products at competitive prices.在这句话中，“attempt”“charge”，“turn to”这些词都可以根据文章的整体意思确定句子中的意思。

句子明显要表达“如果一个公司商品价格高，消费者会去买其它公司的产品”这么一个基本意思。

这样我们根据逻辑意思，把attempt翻译成“想要”;charge翻译成“提高或是提供”;turn to翻译成“去买”就可以了。

保护动物的英语作文

保护动物的英语作文Animals Need ProtectingAnimals are natural resources that people have wasted all through our history. Animals have been killed for their fur and feathers, for food, for sport, and simply because they were in the way. Thousands of kinds of animals have disappeared from the earth forever. Hundreds more are on the danger list today. About 170 kinds in the United States alone are considered in danger.Why should people care? Because we need animals, and because once they are gone, there will never be any more. Animals are more than just beautiful or interesting. They are more than just a source of food. Every animal has its place in the balance of nature. Destroying one kind of animal can create many problems. For example, whenfarmers killed large numbers of hawks, the farmers' stores of corn and grain were destroyed by rats and mice. Why? Because hawks eat rats and mice, with no hawks to keep down their numbers, the rats and mice multiplied quickly. Luckily, some people are working to help save the animals. Some groups raise money to let people know about the problem. And they try to get the governments to pass laws protecting animals in danger. Quite a few countries have passed laws. These laws forbid the killing of any animal orplant on the danger list. Slowly, the number of some animals in danger is growing.中文:动物需要保护动物是自然资源，在整个历史过程中，人类一直在糟蹋着这种资源。

协同系统发生的研究方法

协同系统发生的研究方法王智【摘要】协同系统发生研究生态上相关群体的系统发生间的关系,其研究方法主要分为两类:基于事件法和整体拟合法.基于事件法包括布鲁克斯简约分析、组分分析、协调树分析等,此类方法考虑进化情境,逻辑性强,但分析结果过多,较难选择;整体拟合法考虑了系统发生的误差,提供较好的关系一致性,但缺乏联系进化情境.本文详细比较了两类方法下各种分析软件的优劣,提出了整合两类方法的可能性,以便更好地理解协同系统发生.【期刊名称】《生物信息学》【年(卷),期】2014(012)001【总页数】5页(P33-37)【关键词】协同系统发生;基于事件法;整体拟合法;布鲁克斯简约分析【作者】王智【作者单位】陕西学前师范学院生物科学与技术系,陕西西安710100【正文语种】中文【中图分类】Q71 协同系统发生的概念协同系统发生(Cophylogeny，orparallel cladogenesis or co-cladogenesis)是研究生态上相关群体(如类群、地理区域，基因等)系统发生间的关系，在此，“主”(如有机体、寄生物的宿主或一个地区)系统发生是独立的，而“辅”(如基因、寄生物或有机体)系统发生在某种程度依赖于“主”系统发生［1］。

两个物种的协同进化是协同系统发生研究的主要领域之一。

使用协同进化这个术语时要区别协同趋异(Codivergence)和协同成种(Cospeciation)。

协同进化(Coevolution)指的是两个物种内或相互作用的种群内彼此进化变化的一般过程。

协同趋异指平行分支的进化过程(当一个物种分支为两个或多个物种时)或者说一个生物体实体的成种导致与此相关的其它生物体实体的成种［2］。

协同趋异与协同成种常常交替使用，一些学者认为协同趋异是相关类群分成截然不同的群体的过程，注重过程;而协同成种指的是它们已经独立进化为不同的物种，注重结果［3］。

协同趋异或协同成种可以说是协同进化的一部分。

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A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and MetagenomesYuzhen Ye1*,Thomas G.Doak21School of Informatics,Indiana University,Bloomington,Indiana,United States of America,2Biology Department,Indiana University,Bloomington,Indiana,United States of AmericaAbstractA common biological pathway reconstruction approach—as implemented by many automatic biological pathway services(such as the KAAS and RAST servers)and the functional annotation of metagenomic sequences—starts with the identification of protein functions or families(e.g.,KO families for the KEGG database and the FIG families for the SEED database)in the query sequences,followed by a direct mapping of the identified protein families onto pathways.Given a predicted patchwork of individual biochemical steps,some metric must be applied in deciding what pathways actually exist in the genome or metagenome represented by the monly,and straightforwardly,a complete biological pathway can be identified in a dataset if at least one of the steps associated with the pathway is found.We report,however, that this naı¨ve mapping approach leads to an inflated estimate of biological pathways,and thus overestimates the functional diversity of the sample from which the DNA sequences are derived.We developed a parsimony approach,called MinPath(Min imal set of Path ways),for biological pathway reconstructions using protein family predictions,which yields a more conservative,yet more faithful,estimation of the biological pathways for a query dataset.MinPath identified far fewer pathways for the genomes collected in the KEGG database—as compared to the naı¨ve mapping approach—eliminating some obviously spurious pathway annotations.Results from applying MinPath to several metagenomes indicate that the common methods used for metagenome annotation may significantly overestimate the biological pathways encoded by microbial communities.Citation:Ye Y,Doak TG(2009)A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes.PLoS Comput Biol5(8): e1000465.doi:10.1371/journal.pcbi.1000465Editor:Christos A.Ouzounis,King’s College London,United KingdomReceived May27,2009;Accepted July10,2009;Published August14,2009Copyright:ß2009Ye,Doak.This is an open-access article distributed under the terms of the Creative Commons Attribution License,which permits unrestricted use,distribution,and reproduction in any medium,provided the original author and source are credited.Funding:This research was supported by the NIH grant1R01HG004908-01(development of new tools for computational analysis of human microbiome project data).The funders had no role in study design,data collection and analysis,decision to publish,or preparation of the manuscript.Competing Interests:The authors have declared that no competing interests exist.*E-mail:yye@IntroductionMicrobial whole genome sequencing has become a routine practice in recent years,because of the rapid advances of DNA sequencing technologies[1].One of the first analyses that biologists attempt,once they obtain a complete genome sequence, is to reconstruct the biological pathways encoded by the organism, which is usually accomplished in silico by mapping the protein coding genes onto reference pathway collections,such as KEGG [2]or SEED[3],based on their homology to reference genes with previously characterized functions.For example,KAAS,the pathway annotation system based on the KEGG database[4], first annotates K numbers(each K number represents an ortholog group of genes,and is directly linked to an object(a biochemical step)in the KEGG pathway map),and then reconstructs pathways based on the assigned K numbers.Similarly,the RAST server (and MG-RAST)first annotates FIG families and then maps the identified FIG families onto the SEED subsystems[5,6].These automatic methods are promising for the analysis of most genomes,although they may leave‘‘holes’’in the reconstructed pathways,due to either missing genes(i.e.the genes are non-thus cannot be identified by a homology-based method,or were simply not annotated as ORFs by annotation pipelines)[7],or alternative and novel pathways(i.e.the target organism adopts variant pathways,which are different from the reference pathway, to accommodate a specific niche or lifestyle)[8].After all,many bacterial genomes have fewer than60%of their genes assigned to a proposed function[9,10].We note that pathway reconstruction is essential for understanding the biological functions that a newly sequenced genome encodes. For instance,in a recently published report,the coupling of N2 fixation to cellulolysis was revealed within protist cells in the termite gut,based solely on the in silico pathway reconstruction of the complete genome sequence of a bacterial endosymbiont[11]. Moreover,pathway reconstruction based on some new high throughput techniques must provide conclusions from explicitly incomplete information,which poses fresh challenges.For example, in a typical proteomics experiment,the proteins represent a particular biological sample collected under a specific physiological condition or from a specific tissue(e.g.from yeast cells after the heat shock),which are in high enough abundance to be identified by tandem mass spectrometry[12,13].Based on these data,one may ask,whatphysiological condition?A similar,but more complicated case is pathway analysis of metagenomic data,to characterize the aggregate metabolic processes of microbial communities in a given environment [14].Metagenomic profiling data can be viewed as a sampling of the genomic sequences from many kinds of microbes living in a specific environment.Again,the incompleteness of the data makes it difficult to reconstruct the entire pathways encoded by a metagenome. Nevertheless,it is becoming routine to‘‘reconstruct’’pathways for proteomic[15]and metagenomic data[16,17],by best similarity matches(often derived from BLAST searches):a pathway is inferred to be absent or present in a dataset if highly confident homolog protein hits identify one or more of the protein functions associated with the pathway in other organisms.In addition to the problems that arise from incomplete data,existing methods of pathway reconstruction or inference may over-estimate the number of pathways because of redundancy in the protein-pathway,at four levels.First,different pathways may share the same biological functions.The partition of pathways(as the entire cellular network is partitioned into several hundreds of biological pathway entities in KEGG database)is extremely important for understanding of biological processes,even though there is only a single large biological network within any cell and all pathways are to some extent connected [18].It is not surprising that many pathways defined in the pathway databases are overlapping.Second,some proteins carry out multiple biological functions[19],e.g.through different protein domains,active sites,or substrate specificities.Third,neither organisms nor commu-nities are closed boxes,and the products or intermediates of pathways may be exogenously supplied.Finally,homology-based protein searching may map one protein to multiple homologous proteins with different biological functions(i.e.paralogous proteins).In summary,it cannot be safely concluded that a pathway is present,even if one or more proteins are mapped to it.Even for single complete genomes,pathway reconstruction does not always give a clear picture of the biological functions in an organism,and human curation and experimental verification is often needed[20,21].We illustrate this by a rather extreme KEGG pathway annotation of the human genome includes the reductive carboxylate cycle,with proteins annotated to6steps in this pathway(http://www.genome.jp/kegg-bin/show_organism? menu_type=pathway_maps&org=hsa)(as of July2nd,2009).The Calvin cycle is the most common method of carbon fixation,while the reductive carboxylate cycle is an alternative carbon fixation pathway,currently found only in certain autotrophic microorgan-isms.In fact,the reductive carboxylate cycle is essentially the reverse of the Krebs cycle(citric acid or tricarboxylic acid cycle), the final common pathway in aerobic metabolism for the oxidation of carbohydrates,fatty acids and amino acids,so they share reactions and functional roles.For this reason,the proteins responsible for the normal function of the Krebs cycle can be mistakenly taken as evidence for the existence of a reductive carboxylate cycle in the human genome.Here we propose a pathway reconstruction/inference method in which we do not attempt to reconstruct entire pathways from a given set of protein sequences(e.g.identified in a proteomics experiment,or encoded by the sequences sampled in a metagenomic project),but to determine the minimal set of biological pathways that must exist in the biological system to explain the input protein sequences sampled from it.In this context,we note pathway inference might be a more suitable terminology than pathway reconstruction.However,considering that pathway inference has been used in a different context to infer networks or pathways from gene express data[22],and pathway reconstruction is commonly used in the field,we use both pathway inference and pathway reconstruction in this paper.To address the issues of both incomplete data,and pathway redundancy,we formulate a parsimony version of the pathway reconstruction/ inference problem,called MinPath(Min imal set of Path ways), which can be roughly described as the following:given a set of reference pathways and a set of proteins(and their predicted functions)that can be mapped to one or more pathways,we attempt to find the minimum number of pathways that can explain all proteins(functions)(see Fig.1).Although this problem is NP-hard in general,we provide an integer programming(IP) framework to solve it.We focus on analyzing complete genomes in this study because there is a relatively good understanding of the pathways that actually exist in organisms with completely sequenced genomes(as compared to the emerging metagenomes),making this analysis a good test of our method.Besides,the pathway annotations of these genomes are still far from perfection,as in the example of a carbon fixation pathway in the human genome(as well as chickens, mosquitoes,etc).We also applied MinPath to the analyses of several metagenomic datasets,to demonstrate the potential applications of MinPath in metagenome annotation.ResultsWe first revisited the pathway reconstruction of individual genomes using MinPath.The results show that MinPath gave a conservative,but reliable estimation of the pathways of a genome, and therefore the functional ability/diversity encoded by a genome.In addition,MinPath found suspicious pathways in the KEGG database.We then applied MinPath to a set of metagenomic datasets,and the results indicate that the current estimation of functional diversity/ability of studied microbial communities might be overestimated.Pathway Reconstruction for GenomesOverview of the performance of MinPath.The functionAuthor SummaryEven though there is only a single large biological network within any cell and all pathways are to some extent connected,the partition of the entire cellular network into smaller units(e.g.,KEGG pathways)is extremely important for understanding biological processes.Biological pathway reconstruction,therefore,is essential for understanding the biological functions that a newly sequenced genome encodes and recently for studying the functionality of a natural environment via metagenomics.The common practice of pathway reconstruction in metagenomics first identifies functions encoded by the metagenomic se-quences and then reconstructs pathways from the annotated functions by mapping the functions to refer-ence pathways.To address the issues of both incomplete data(e.g.,metagenomes,unlike individual genomes,are most likely incomplete)and pathway redundancy(e.g.,the same function is involved in multiple pathway units),we formulate a parsimony version of the pathway reconstruc-tion/inference problem,called MinPath(Min imal set of Path ways):given a set of reference pathways and a set of functions that can be mapped to one or more pathways, MinPath aims at finding a minimum number of pathways that can explain all functions.MinPath achieves a more conservative,yet more faithful,estimation of the biological pathways encoded by genomes and metagenomes.from the KEGG database,and used as input for MinPath to reconstruct the pathways encoded by each genome.A total of854 genomes were studied,and the overall performance of MinPath is shown in Fig.2,compared with the curated KEGG pathways and the pathway reconstructions produced by the naı¨ve mapping approach(see METHODS for details).The comparison shows that MinPath gives an estimation of functional diversity(measured by the number of pathways constructed)that is closer to the curated KEGG database,as compared to simple pathway construction based on the appearance of families.MinPath gives a more conservative estimation of the pathways than even KEGG in most genomes(with fewer annotated biological pathways),but we would like to argue that even some of the pathways collected in KEGG should be removed(such as the ascorbate and aldarate metabolism pathway in human,as we discuss below).The human genome.For the human genome,there are205 predicted KEGG pathways(as of December2008),while the naı¨ve mapping approach identifies227pathways.MinPath identified only191pathways—these pathways are necessary and sufficient to explain all the annotated human proteins in the KEGG database. Many of the pathways that are identified by the naı¨ve mapping approach are spurious and are not curated in the KEGG database (e.g.the penicillin and cephalosporin biosynthesis pathway,and the two-component general and the type II secretion systems), indicating that MinPath can be applied to remove pathways that are otherwise mistakenly annotated using the naı¨ve mapping approach.More examples are listed in the supplementary website. Some of the pathways that are curated in the KEGG database are marked by MinPath as spurious(see Table1).For example, the ascorbate and aldarate metabolism pathway(Fig.3)is annotated in KEGG as a biological pathway in human,but not by MinPath.In humans there are only three functions(out of24) annotated for this pathway and these three functions are not family)is involved in15other pathways,EC1.1.1.22(UDP-glucose dehydrogenase)is involved in three other pathways,and myo-inositol oxygenase(EC:1.13.99.1)is involved in both this pathway and the inositol phosphate metabolism pathway.Based on the sparseness of the genes assigned to this pathway and their ubiquitous nature,and the fact that humans require vitamin C in the diet,we believe that the ascorbate and aldarate metabolism pathway should be removed from the pathways reconstructed for the human genome.The Escherichia coli genome.MinPath identified98 biological pathways that are sufficient to explain all the identified functions encoded by the E.coli genome.It is a conservative estimation,as compared to the125pathways for Escherichia coli K-12MG1655collected in the KEGG database,and 158pathways that have at least one or more associated functions identified in the genome.Refer to the supplementary webpage for the details of the pathway reconstructions and their comparison for E.coli.It is obvious that the naı¨ve mapping approach leads to an inflated estimate of biological pathways in E.coli—the list even includes several biological pathways involved with human cancer, including renal cell carcinoma(pathway ID05211),prostate cancer(pathway ID05215),and bladder cancer(pathway ID 05219).These pathways were wrongly annotated because one or more predicted functions in these pathways are also involved in other pathways.For example,fumarate hydratase(ko:K01679)is involved in the renal cell carcinoma pathway,as well as in the citrate cycle,a fundamental pathway present in most bacteria. Based on the identification of this enzyme alone,the naı¨ve mapping approach predicted the presence of the renal cell carcinoma pathway in E.coli,which obviously cannot be true. MinPath removed these spurious pathways from the list of constructed pathways,without human curation.We argue that KEGG predictions also overestimate the biologicalFigure1.Schematic illustration of the MinPath method.Assume6families(or orthologous groups,f1,…,f6)are identified from a given sample of genes(e.g.,the genes could be from a genome,or sampled from a metagenome).The naı¨ve mapping approach(shown on the left)will lead to a reconstruction with4pathways annotated(p1,p2,p3,and p4).Due to the overlapping nature of the biological pathways(see text for more details),pathway p3shares function f3with pathway p2.We claim that only three pathways,p1,p2,and p3are sufficient to explain the existence of the 6families annotated in the dataset,and a conservative reconstruction of pathways should have only3pathways(shown on the right).As we show in the paper,such a conservative estimation of pathways provides a more reliable estimation of the functional diversity of a sample.doi:10.1371/journal.pcbi.1000465.g001acid elongation pathway and the bile acid biosynthesis pathway (see Table 2).Pathway Reconstruction for MetagenomesWe used MinPath to re-analyze the biological pathways of several metagenomes [17],which were previously analyzed by a naı¨ve mapping approach.The results are summarized in Table 3.We used both the KEGG and SEED databases in this experiment.For KEGG pathways,we did local BLAST searches,using thecriteria as shown in [16]for KO family identification.For SEED subsystems,the FIG annotations were downloaded from the MG-RAST server (/).For all the datasets we tested,MinPath reduced the total number of annotated pathways (or subsystems)significantly (as shown in Table 3).For example,for the metagenome sampled from a coral microbial community (Coral-Mic),there are in total 232KEGG biological pathways annotated in at least one of the 7sequencing datasets.Based on MinPath,however,only 160KEGGbiologicalFigure parison of the number of pathways reconstructed for various genomes by different methods.The coloring schema is asfollowing:MinPath (red triangles),naı¨ve mapping approach (green),and the pathway annotation maintained in KEGG database after human evaluation (blue).doi:10.1371/journal.pcbi.1000465.g002Table 1.Selected spurious pathways of the human genome that are incorrectly identified by the naı¨ve mapping approach.KEGG ID Pathway description Possible reason for being falsely identifiedby the naı¨ve mapping approach Removed by MinPath?Additional notes00053ascorbate and aldaratemetabolismpathway redundancy (same function involvesin multiple pathways)yes humans can not synthesize ascorbic acid (vitamin C)00290valine,leucine and isoleucine biosynthesispathway redundancy yes all three are essential amino acids in humans 00521streptomycin biosynthesis a pathway redundancy yes see table note a00720reductive carboxylate cyclepathway redundancyyesit is a CO 2fixation pathway found in photosynthetic bacteriaaSteptomycin biosynthesis is not listed for the human genome (http://www.genome.jp/kegg-bin/show_organism?menu_type =pathway_maps&org =hsa)in KEGG;but there are 5functional roles from this pathway annotated in the human genome based on the KEGG annotation,including K00844,K01092,K01710,K01835,and K01858.pathways are sufficient to explain all the functions predicted forthese datasets.These results indicate that the naı¨ve mapping of the biological pathways from predicted functions may overestimate the biological pathways (so the functional diversity)of those microbial communities,and we need to be cautious when interpreting the results from such an analysis[16,17].Figure 3.The ascorbate and aldarate metabolism pathway,eliminated by MinPath.The diagram was prepared based on the corresponding KEGG pathway (ID =00053),and only part of the pathway is shown for clarity.The three enzymes that are annotated in the human genome are highlighted in green,even though none of these enzymes are unique to this pathway.doi:10.1371/journal.pcbi.1000465.g003Table 2.Selected spurious pathways of the E.coli genome (collected in KEGG)eliminated by MinPath.KEGG ID Pathway description Functions involved Removed by MinPath?Justification Additional notes 00062fatty acid elongation in mitochondria K00022yes K00022is shared by this pathway and 6otherpathwaysE.coli has no mitochondria 00521bile acid biosynthesisK00001K00632yesK00001is shared by several other pathways,including the glycolysis pathway;K00632is shared by the fatty acid metabolism pathway and others.bile acids are steroid acids found predominantly in the bile of mammalsWe also show the details of pathway reconstruction for a single sequence dataset from the coral biome(4440319.3.dna.fa).The naı¨ve mapping approach identified224KEGG pathways,whereas MinPath identified only143KEGG pathways.The pathways eliminated by MinPath include the inositol metabolism pathway, the androgen and estrogen metabolism pathway,the caffeine metabolism pathway,etc(see more examples at the supplementary website).Obviously,comparisons of microbial communities or other biomes will be more telling if spurious pathways are eliminated,and our results suggest that as many as40%of the224 pathways could be wrong.DiscussionWe have developed the MinPath approach to provide more conservative—but more reliable—estimations of biological path-ways from a sequence dataset,and applied this approach to revisit the biological pathway reconstruction problem for genomes as well as metagenomes.Our results show that without further post-processing of the reconstructed pathways,the naı¨ve mapping strategy may overestimate the biological pathways that are encoded by a genome or metagenome,which could jeopardize any conclusions drawn from the constructed biological pathways (such as the metabolic diversity/capacity of an environmental microbial or viral community,as measured by the Shannon Index) [16,17],or other downstream analysis based on constructed pathways[23].It was noted in[16]that most of the microbial communities in that study were approaching saturation for known pathways:more conservative estimates of pathways for each environment may allow real functional differences between the samples to be detected.Note that MinPath is not designed to directly improve the still imperfect definition of pathways and/or functions in databases such as KEGG or SEED.For example,as a result of how some pathways are grouped in the KEGG database,peptidoglycan biosynthesis is listed for the human genome by KEGG annotation and MinPath does not eliminate this pathway from the list of annotated pathways from human genome.In this sense,efforts are still needed to improve the elucidation and annotation of extent biochemical pathways.But given a database of reference pathways,we feel that MinPath provides a sensible method for Materials and MethodsFirst we will briefly describe the naı¨ve mapping approach that is commonly used in current automatic biological pathway recon-struction services(e.g.,the KAAS and RAST servers),as well as for pathway reconstruction for metagenomic sequences.Then we present a novel minimal pathway reconstruction approach based on a simple yet efficient algorithm for solving this problem. The Naı¨ve Mapping Approach to Pathway ReconstructionPathway reconstruction has become routine in functional annotation of genomes and metagenomes,in which KEGG pathways(or other biological pathways such as SEED subsystems) are reconstructed based on homology.KEGG and SEED databases collect pathways(or subsystems)curated by experts, each pathway/subsystem consisting of a series of functional roles (enzymes,transporters,etc).Pathway reconstruction consists of two key steps:(1)predicting the functions(represented by protein families)of proteins encoded by the DNA sequences,which is often achieved by similarity searching of the predicted proteins against reference proteins from previously characterized genomes; and(2)predicting the presence or absence of pathways in the query dataset,based on the identified functions associated to the pathways.Conventional pathway reconstruction usually adopts simple criterion in this second step(herein referred to as the naı¨ve mapping approach),i.e.,a pathway is considered to be present if one or more functions in the pathway are identified in the first step.We have shown in this paper that this approach may lead to the identification of spurious pathways and an overestimation of functional ability,which motivated us to develop a novel approach to pathway reconstruction based on the parsimony principle presented below.Minimal Pathway Reconstruction ProblemWe define the minimal pathway reconstruction problem as the following: given a list of functions annotated for a set of genes(which can be an incomplete set,as we encounter in metagenomic analysis,or a nearly complete set,as in complete genome analysis),find the minimal set of pathways that include all given functions(see Fig1).formulation of the pathway reconstruction problem,which attempts either to reconstruct the complete pathways encoded by a given genomic dataset(in a sense,the pathway holes should to be minimized),or to identify the set of pathways that have at least one associated function annotated(i.e.,the naı¨ve mapping approach). Integer Programming AlgorithmWe use integer programming to solve the minimal pathway reconstruction problem.Linear programming(LP)is an algorithm for finding the maximum or minimum of a linear function of variables(objective function)that are subject to linear constraints [24].Simplex and interior point methods are widely used for solving LP problems.The related problem of integer program-ming(IP)requires some or all of the variables to take integer (whole number)values.Some of the most powerful algorithms for finding exact solutions of combinatorial optimization problems [25]are based on IP.LP and IP have been applied to many fields in the biological sciences,such as the maximum contact map overlap problem for protein structure comparison[26],optimal protein threading[27],probe design for microarray experiments [28],and the pathway variant problem[8].Here we transform the minimal pathway reconstruction problem to an integer programming problem:Denote the number of functions(protein families)that are annotated in a dataset as n. Let the total number of putative pathways which have at least one component function annotated be p.Denote the mapping of protein functions to the pathways as M,where M ij=1if function i is involved in pathway j,otherwise0(note one function may map to multiple pathways or subsystems).Denote if a pathway j is selected in the final list or not as P j,with P j=1if selected,P j=0 otherwise.The set of pathways with P i=1composes the minimal set of pathways that can explain all the functions that are annotated for a dataset.The objective function for integer programming is,minX pj~1P js:t:X pj~1M ij P j§1V i[1,n½i.e.,our goal is to find the minimum number of pathways that can explain all the functions carried by at least one protein from a dataset.Protein Function and Function AnnotationWe use the KO and FIG protein families defined in the KEGG database and the SEED subsystems,respectively,for this study. Many of the mappings of KO families to KEGG pathways were done manually in the KEGG database.These families are the basic units for pathway reconstruction(or subsystem reconstruc-tion in SEED),in which a pathway(or a subsystem)is composed of a list of functional roles.Implementation DetailsWe use the GLPK package(GNU Linear Programming Kit; /software/glpk/glpk.html)for solving the integer-programming problem;all the other functions are implemented in Python.The input for MinPath is a list of protein families(e.g.,KO and FIG families)annotated in a given dataset of genes(from a genome,or a metagenome),and the output is the list of pathways reconstructed/inferred for the dataset.Note that in some cases two pathways may share most of their functional roles(for example,the biosynthesis and degradation pathway of the same biological molecule,such as the lysine biosynthesis and degradation pathways).MinPath will keep one of these pathways,because that is sufficient to explain the functional roles identified.We added a post-processing step here to add those pathways that have more than50%of their functional roles identified back to the pathway pool,even when these functional roles appear in another pathway that is already predicted by MinPath.Benchmarking ExperimentsWe revisited the pathway reconstruction for the854genomes in the KEGG database(as of December,2008)that have at least20 KEGG pathways annotated for each of these genomes.For these genomes,the function(or protein families)annotations were downloaded from the KEGG database(ftp://ftp.genome.jp/pub/ kegg/release/current/).We also applied MinPath to reanalyze the pathways for nine biome metagenomic datasets[17].The FIG family annotations for the metagenomic sequences were downloaded from the MG-RAST server(/).We conducted the KO family annotations of the sequences based on the best blast hits with E-value cutoff of1e-5,a typical E-value cutoff used for KEGG pathway reconstruction in metagenomes[16]. Availability and Supplementary MaterialMinPath is available as a server and the source codes are available for downloading at MinPath webpage,http://omics. /MinPath/.Supplementary material is also available at the MinPath website.AcknowledgmentsWe thank Dr.Haixu Tang for inspiring discussions,and reading the manuscript.We thank Drs.Alex Rodriguez and Ross Overbeek for their help with using the Figfam database.Author ContributionsConceived and designed the experiments:YY.Performed the experiments: YY.Analyzed the data:YY TGD.Wrote the paper:YY TGD.References1.Morozova O,Marra MA(2008)Applications of next-generation sequencingtechnologies in functional genomics.Genomics92:255–264.2.Kanehisa M,Goto S(2000)KEGG:kyoto encyclopedia of genes and genomes.Nucleic Acids Res28:27–30.3.Overbeek R,Begley T,Butler RM,Choudhuri JV,Chuang HY,et al.(2005)The subsystems approach to genome annotation and its use in the project to annotate1000genomes.Nucleic Acids Res33:5691–5702.4.Moriya Y,Itoh M,Okuda S,Yoshizawa AC,Kanehisa M(2007)KAAS:anautomatic genome annotation and pathway reconstruction server.Nucleic Acids 5.Aziz RK,Bartels D,Best AA,DeJongh M,Disz T,et al.(2008)The RASTServer:rapid annotations using subsystems technology.BMC Genomics9:75.6.Meyer F,Paarmann D,D’Souza M,Olson R,Glass EM,et al.(2008)Themetagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes.BMC Bioinformatics9:386.7.Osterman A,Overbeek R(2003)Missing genes in metabolic pathways:acomparative genomics approach.Curr Opin Chem Biol7:238–251.8.Ye Y,Osterman A,Overbeek R,Godzik A(2005)Automatic detection ofsubsystem/pathway variants in genome analysis.Bioinformatics21Suppl1:。