Genomics-ope or Hype-
10xgenomics 3’转录组建库流程 -回复
10xgenomics 3’转录组建库流程-回复10x Genomics 3’转录组建库流程是一种先进的技术，用于分析和研究细胞的转录组。
这项技术可以高通量地分析单个细胞的转录组，并提供高质量的数据，以研究细胞的功能和特异性。
本文将逐步介绍10x Genomics 3’转录组建库流程的各个步骤，并解释每个步骤的原理和操作。
第一步：细胞分离和裂解在10x Genomics 3’转录组建库流程中，首先要将目标细胞从组织样本中分离出来。
这可以通过传统的细胞培养、机械分离或离心等方法实现。
分离后的细胞需要裂解以释放细胞内的RNA。
常用的裂解方法包括化学法、机械法和热裂解法。
裂解后的细胞溶液将用于后续的转录组测序。
第二步：细胞浆中的RNA逆转录在10x Genomics 3’转录组建库流程中，细胞溶液中的RNA将通过逆转录反应转化为cDNA。
逆转录反应可使用10x Genomics提供的Reverse Transcription Master Mix进行。
此反应中将使用随机引物和特定引物，使RNA模板与引物结合并逆转录为cDNA。
随机引物能产生全长cDNA，而特定引物仅能逆转录cDNA的3’端。
第三步：cDNA的修饰和扩增在10x Genomics 3’转录组建库流程的这一步骤中，将对cDNA进行修饰和扩增。
首先，在修饰步骤中，使用10x Genomics提供的LibraryAmplification Primer进行扩增，引物序列包含了一个barcode和一个用于放大cDNA的序列。
随后，在扩增步骤中，使用Polymerase Chain Reaction（PCR）方法进行cDNA的扩增。
此步骤可以增加cDNA的数量，并为后续的测序步骤提供足够的cDNA。
第四步：文库构建和样品准备在10x Genomics 3’转录组建库流程的这一步骤中，将进行文库构建和样品准备。
首先，将扩增的cDNA进行剪切，并连接引物，形成单链文库。
10x genomics3’ 转录组建库流程 -回复
10x genomics3’ 转录组建库流程-回复10x genomics 3'转录组建库流程转录组测序是一种非常重要的技术，用于研究生物体内的全体基因表达情况。
10x genomics 3'转录组建库是一种常用的高通量测序技术，它可以将低成本、高质量的转录组测序帮助我们研究基因的功能和调控机制。
本文将一步一步详细介绍10x genomics 3'转录组建库的流程。
第一步：样品准备准备好的RNA样品是进行10x genomics 3'转录组建库流程的基础。
样品质量对于后续的实验结果至关重要，所以我们要注意样品的纯度和完整性。
最好使用组织样品或者培养细胞样品，以确保获取到高质量的RNA。
对于动物组织样品，我们可以通过快速的组织破碎和RNA提取方法获得高质量的RNA。
对于细胞样品，我们可以直接使用RNA提取试剂盒进行RNA提取。
第二步：RNA破碎和合成cDNA在该步骤中，我们需要将RNA破碎成较短的片段，并合成一链cDNA。
首先，我们将RNA破碎成约200-500碱基的片段，这可以通过加入破碎缓冲液和钙离子来实现。
破碎后的RNA片段将用于合成一链cDNA。
在这一步中，我们使用10x genomics的GEM（Gel Bead和Emulsion）技术创建反应小瓶，其中含有GEM Bead和酶。
将破碎的RNA片段与GEM Bead一起加入到反应小瓶中，并进行逆转录反应。
在逆转录反应中，RNA片段的poly(A)尾部（如果存在的话）将被逆转录酶延伸，从而合成一链cDNA。
在反应完成后，我们获得了单个的GEM 小颗粒，每个小颗粒都包含有附着的RNA片段和cDNA。
第三步：建库和放大在该步骤中，我们需要将cDNA进行二次扩增并建立测序文库。
首先，我们需要加入引物P5和P7，这些引物将在下一步的PCR扩增过程中使用。
然后，在进行PCR扩增前，我们需要对GEM小颗粒进行裂解，释放出cDNA。
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从轮叶党参中分离到的一种新的脱水素基因(英文文献)
BMBreports338BMB reports*Corresponding author. T el: 82-31-201-2688; Fax: 82-31-202-2687;E-mail: dcyang@khu.ac.krReceived 17 October 2007, Accepted 26 December 2007K eywords: Abiotic stress, Codonopsis lanceolata , Dehydrin (DHN), Semi-quantitative RT-PCRIsolation of a novel dehydrin gene from Codonopsis lanceolata and analysis of its response to abiotic stressesRama Krishna Pulla 1,2, Yu-Jin Kim 1, Myung Kyum Kim 1, Kalai Selvi Senthil 3, Jun-Gyo In 4 & Deok-Chun Yang 1,*1Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung Hee University, Seocheon-dong, Kiheung-gu Yongin, Kyunggi-do, South Korea, 2Kongunadu Arts and Science College, Coimbatore, Tamil Nadu, 641029, India. 3Avinashilingam University for Women, Coimbatore, 641043, India. 4Biopia Co., Ltd., Yongin, KoreaDehydrins (DHNs) compose a family of intrinsically unstructured proteins that have high water solubility and accumulate during late seed development at low temperature or in water-deficit conditions. They are believed to play a protective role in freez-ing and drought-tolerance in plants. A full-length cDNA encod-ing DHN (designated as ClDhn ) was isolated from an oriental medicinal plant Codonopsis lanceolata , which has been used widely in Asia for its anticancer and anti-inflammatory properties. The full-length cDNA of ClDhn was 813 bp and contained a 477 bp open reading frame (ORF) encoding a polypeptide of 159 amino acids. Deduced ClDhn protein had high similarities with other plant DHNs. RT-PCR analysis showed that different abiotic stresses such as salt, wounding, chilling and light, trig-gered a significant induction of ClDhn at different time points within 4-48 hrs post-treatment. This study revealed that ClDhn assisted C. lanceolata in becoming resistant to dehydration. [BMB reports 2008; 41(4): 338-343]INTRODUCTIONPlants have developed defensive strategies against various stresses that arise from frequent environmental fluctuations to which they are exposed. Drought and low temperatures are the most severe factors limiting plant growth and yield. More than 100 genes have been shown to be responsive to such conditions and they are believed to function either during the physiological protection of cells from water-deficiencies or temperature-changes or in the regulation of gene expression (1-3).DHNs are proteins that are known to accumulate in vegetative plant tissues under stress conditions, such as low temperature, drought, or salt-stress (2, 4-6). These proteins have been catego-rized as late embryogenesis abundant (LEA) proteins (7, 8).DHNs have been subdivided into five classes according to thepresence of highly conservative segments: YnSK 2, Kn, KnS, SKn and Y 2Kn. The K-segment (EKKIGIMDKIKEKLPG) is a conserved 15-mer lysine-rich sequence characteristic of DHNs, which may be present in one or several copies (5). The K-segment can form an amphiphathic α-helix structure that may interact with lipid components of bio-membranes and partially denatured proteins like chaperones (6, 9). The S-segment consists of contiguous ser-ine residues in the centre of the protein, which may be phosphorylated. They are involved in nuclear transport through their binding to nuclear localization signal peptides (6). The Y-segment with the consensus sequence DEYGNP, shares some similarities to the nucleotide-binding site of chaperones in plants and bacteria (5, 10). Another conserved domain contained in many DHNs is ϕ-segment (repeated Gly and polar amino acids), which interacts with and stabilizes membranes and macro-molecules, preventing structural damage and maintaining the activity of essential enzymes (11).DHNs have been found in the cytoplasm (12), nucleus (12, 13), mitochondria (14), vacuole (15), and chloroplasts (16). They are known to associate with membranes (17, 18), pro-teins (19) and excess salt ions (15, 20). Several DHN genes have been isolated and characterized from different species, including cor47, erd10 and erd14 from Arabidopsis thaliana ; Hsp90, BN59, BN115 and Bnerd10 from Brassica napus ; cor39 and wcs19 from Triticum aestivum (bread wheat); and cor25 from Brassica rapa subsp. Pekinensis (21). Many studies have reported a positive correlation between the accumulation of DHN transcripts or proteins and tolerance to freezing, drought, and salinity (12, 17, 22-24). Moreover, mod-ulation of transcripts by light has been reported for many DHN-encoding genes in drought- or cold-stressed plants (25-28). Although the biochemical functions and physiological roles of DHNs are still unclear, their sequence character-izations and expression patterns suggest that they may play a positive role in plant-response and adaptation to abiotic stress that leads to cellular dehydration. Indeed, many studies have indicated that transgenic plants with DHNs have a better stress-tolerance, recovery or re-growth after drought and freez-ing stress than that of the control (8, 29, 30).Thus far, there are no reports on isolation of the DHN gene from the oriental medicinal plant Codonopsis lanceolata . ThisCodonopsis lanceolata dehydrin geneRama Krishna Pulla, et al.339BMBreportsFig. 1. Nucleotide sequence and de-duced amino acid sequence of a ClDhn cDNA isolated from C. lanceolata . Num-bers on the left represent nucleotide positions. The deduced amino acid se-quence is shown in a single-letter code below the nucleotide sequence. The as-terisk denotes the translation stop signal.Amino acids in two double boxes repre-sent the Y-segment and amino acids in a single box the S-segment, respectively.The two underlined sequences represent the K-segments.plant belongs to the family of Campanulaceae (bellflower fam-ily), which contains many famous oriental medicinal plants such as Platycodon grandiflorum (Chinese bellflower or balloon flow-er), Codonopsis pilosula and Adenophora triphylla (nan sha shen). The roots of these plants have been used as herbal drugs to treat bronchitis, cough, spasm, macrophage-mediated immune responses and inflammation, and has also been administered as a tonic (31). C. lanceolata grows in North-eastern china, Korea, and far eastern Siberia. Despite their medicinal importance, little genomic study of this plant has been carried out. In this study, we characterized an Y 2SK 2 type DHN gene from C. lanceolata and analyzed its expression in response to various abiotic stresses.RESULTS AND DISCUSSIONIsolation and characterization of the full length cDNA of the ClDhn geneAs part of a genomic project to identify genes in the medicinal plant C. lanceolata , a cDNA library consisting of about 1,000 cDNAs was previously constructed. A cDNA encoding a dehy-drin (DHN), designated ClDhn was isolated and sequenced. The sequence data of ClDhn has been deposited in GenBank under accession number AB126059. As shown in Fig. 1, ClDhn is 813 bp in length and it has an open reading frame (ORF) of 477 bp nucleotide with an 87-nucleotide upstream sequence and a 248-nucleotide downstream sequence. The ORF of ClDhn starts at nucleotide position 88 and ends at position 565. ClDhn encodes a precursor protein of 159 amino acids resi-dues with no predicted signal peptide at the N-terminal. The calculated molecular mass of the protein is approximately 16.7kDa with a predicated isoelectric point of 6.87. In the deduced amino acid sequence of ClDhn protein, the total number of neg-atively charged residues (Asp +Glu) amounted to 21 while the total number of positively charged residues (Arg +Lys) was 20. In addition, transmembrane helix prediction (TMHMMv2.0) did not identify any transmembrane helices in the deduced protein, implying that the protein did not function in the membrane but might function within the cytosolic or nuclear compartment.Homology analysisA GenBank Blastp search revealed that ClDhn had the highest sequence homology to the carrot (Daucus carota ) DHN (BAD86644) with 51% identity and 61% similarity. ClDhn also shared homology with ginseng (Panax ginseng ) DHN5 (ABF48478, 50% identity and 60% similarity), wild potato (Solanum commersonii ) DHN (CAA75798, 50% identity and 58% similarity), robusta coffee (Coffea canephora ) DHN1α (ABC55670, 47% identity and 55% similarity), grape (Vitis vin-ifera ) DHN (ABN79618, 47% identity and 57% similarity), American beech (Fagus sylvatica ) DHN (CAE54590, 46% iden-tity and 56% similarity), tobacco (Nicotiana tabacum ) DHN (BAD13498, 45% identity and 56% similarity), sunflower (Helianthus annuus ) DHN (CAC80719, 45% identity and 52% similarity), and soybean (Glycine max ) DHN (AAB71225, 44% identity and 52% similarity). The DHNs showing the highest similarities were Y 2SK 2 type DHNs except grape (Vitis vinifera ) DHN (YSK 2 type) (32). Thus ClDhn might belong to Y 2SK 2 type DHNs based on the two Y-segments, one S-segment, and two K-segments present in its amino acid sequence. Phylogenetic analysis of ten of the plant DHNs were carried out using theCodonopsis lanceolata dehydrin gene Rama Krishna Pulla, et al.340BMB reportsFig. 2. A phylogenetic tree based on DHN amino acid sequence, showing the phylogenetic relationship between ClDhn and other plant DHNs . The tree was constructed using the Clustal X method (Neighbor-joining method) and a bar represents 0.1 substitutions peramino acid position.Fig. 3. Alignment of ClDhn with the most closely related DHNs from carrot (Daucus carota , BAD86644), ginseng (Panax ginseng DHN5, ABF48478), com-merson’s wild potato (Solanum commer-sonii , CAA75798), robusta coffee (Coffea canephora , ABC55670), grape (Vitis vin-ifera , ABN79618), American beech (Fagus sylvatica , CAE54590), tobacco (Nicotiana tabacum , BAD13498), sunflower (Helian-thus annuus , CAC80719) and soybean (Glycine max , AAB71225). Gaps are marked with dashes. The conserved ami-no acid residues are shaded and Y-, S-, and K-segments are shown.Clustal X program (Fig. 2). Fig. 3 is a sequence alignment result of ClDhn and other closely related DHNs .The differential expression of ClDhn in different organs of C . lanceolataThe expression patterns of ClDhn in different C . lanceolata or-gans were examined using RT-PCR analysis. Almost similar levels of ClDhn -mRNA expression were observed in leaves and roots, whereas ClDhn was expressed in slightly higher lev-els in the stems. (Data was not shown).Expression of ClDhn in response to various stressesExpression patterns of ClDhn under various conditions were ex-amined using RT-PCR analysis. Fig. 4A showed the accumu-lation of ClDhn -mRNA in response to 100 mM ABA in MS agar. ABA is a hormone secreted when environmental conditions be-come dry. Expression of ClDhn was induced and reached a maximum level after 12 hrs, and then gradually decreased. When plants are submitted to dehydration the endogenous con-tent of ABA increases, with ABA mediating the closure of the stomata. Several studies have identified ABA as a key hormone in the induction pathway of many inducible genes including DHN , in response to drought (33-36). 100 μM of ABA in sprayCodonopsis lanceolata dehydrin geneRama Krishna Pulla, et al.341BMBreportsFig. 4. RT-PCR analyses of the expressions of ClDhn gene in the leaves of C. lanceolata at various time points (h) post-treatment with various stresses: A, 100 mM ABA; B, 100 mM NaCl; C, wounding; D, chilling and E, light treatment. Actin was used as an internal control.induced DHN-levels in Brassica napus and increased its ex-pression up to 48 hrs after treatment with ABA (37). 100 μM of ABA in MS agar induced DHN -levels in rice and cause a max-imum expression level at 1 hr post-treatment (10).Fig. 4B shows the accumulation of ClDhn mRNA in re-sponse to salt stress (100 mM NaCl). ClDhn expression was in-duced at 4 hrs post-treatment and gradually increased until 48 hrs. In Brassica napus , 250 mM NaCl added in the nutrient medium induced DHN-expression and reached a maximum at 48 hrs post-treatment (37). The application of NaCl to soil brought on a progressive decrease of the pre-dawn leaf water potential, a decrease of stomatal-conductance and a growth- reduction. Osmotic potential increase during salt treatmentcould result from Na ＋ or Cl −absorption and from the synthesis of compatible compounds (38).Under wounding stress, ClDhn gene transcription was in-duced at 4 hrs post-treatment and gradually increased until 48 hrs (Fig. 4C). Richard et al . (39) discussed that the cumulative effect of wounding on transcript accumulation could also be associated with greater water-loss through more open surfaces arising from the wounding treatment.Under cold treatment, increase of ClDhn transcripts was ob-served at 4 hrs post-treatment and gradually increased until 48 hrs (Fig. 4D). Induction of DHN by low temperatures has been observed in numerous plants (17, 38). Overexpression of citrus DHN improved the cold tolerance in tobacco (18). Overexpre-ssion of multiple DHN genes in Arabidopsis resulted in accu-mulation of the corresponding DHNs to levels similar or higher than in cold-acclimated wild-type plants (24). Another example showed that overexpression of the acidic DHN WCOR410 could improve freezing tolerance in transgenic strawberry leaves (29). Fig. 4E shows that ClDhn gene expression was induced bylight stress and increased continuously until 48 hrs post-treat-ment. Natali et al . (40) showed that the G-box (CACGTGGC), a motif found in the promoter region of many light regulated genes, was found in the DHN gene promoter of helianthus and that DHN was responsive to light stress (41).In conclusion, we isolated a new dehydrin gene (ClDhn ) from C. lanceolata and characterized its expression in response to various stresses. ClDhn was induced by various stresses related to wa-ter-deficiency (ABA, salt, wounding and cold) and was induced by light, similar to other DHN genes isolated from other plants.MATERIALS AND METHODSPlant materialsCodonopsis lanceolata were grown in vitro on MS medium supplemented with 3% sucrose and 0.8% agar under the 16 hrs light and 8 hrs dark period. Its growth was maintained by regular subculture every 4 weeks. Abiotic stress studies were carried out on plants that were subcultured for one month. To analyze gene expression in different organs, samples were col-lected from leaves, roots and stem of C. lanceolata plants.Sequence analysesThe full-length ClDhn gene was analyzed using the softwares BioEdit, Clustal X, Mega 3 and other databases listed below; NCBI (http://www.ncbi.nlm.nih), SOPMA (http://npsa-pbil.ibcp /npsaautomat.pl?page=npsopma.html).Stress assaysTo investigate the response of the ClDhn gene to various stress-es, the third leaves with petioles from C. lanceolata were used. For treatment with ABA (100 mM) and NaCl (100 mM), leaf samples were incubated in media containing each compound at 25o C for 48 hrs. For mechanical wounding stress, excised leaves were wounded with a needle puncher (42). Chilling stress was applied by exposing the leaves to a temperature of 4o C (43). To investigate the ClDhn gene-expressions in light, leaves were incubated under an electrical lamp with a light in-tensity of 24 mol m-2 s-1 for 48 hrs. All treatments were carried out on MS media with or without the treatment solution (ABA, NaCl). All treated plant materials were immediately frozen in liquid nitrogen and stored at -70o C until further analysis.Semi-quantitative RT-PCR analysisTotal RNA was extracted from various whole plant tissues (leaves, stem, roots) of C. lancolata using the Rneasy mini kit (Qiagen, Valencia, CA, USA). For RT-PCR (reverse tran-scriptase-PCR), 800 ng of total RNA was used as a template for reverse transcription using oligo (dT) primer (0.2 mM)(INTRON Biotechnology, Inc., South Korea) for 5 mins at 75oC. The reaction mixture was then incubated with AMV Reverse Transcriptase (10 U/μl) (INTRON Biotechology, Inc., SouthKorea) for 60 mins at 42oC. The reaction was inactivated byheating the mixture at 94oC for 5 mins. PCR was then per-Codonopsis lanceolata dehydrin gene Rama Krishna Pulla, et al.342BMB reportsformed using a 1 μl aliquot of the first stand cDNA in a final volume of 25 μl containing 5 pmol of specific primers for cod-ing of ClDhn gene (forward, 5'-AAA GAG AGA GAA AAT GGC AGG TTA C-3'; reverse, 5'-GGA GTA GTT GTT GAA GTT CTC TGC T-3') were used. As a control, the primers spe-cific to the C. lanceolata actin gene were used (forward, 5'-CAA GAA GAG CTA CGA GCT ACC CGA TGG-3'; reverse, 5'-CTC GGT GCT AGG GCA GTG ATC TCT TTG CT-3'). PCR was carried out using 1 μl of taq DNA polymerase (Solgent Co., South Korea) in a thermal cycler programmed as follows:an initial denaturation for 5 mins at 95oC, 30 amplification cy-cles [30 s at 95o C (denaturation), 30 s at 53o C (annealing), and90 s at 72oC (polymerization)], followed by a final elongation for 10 mins at 72o C. Actin was used as an internal control to normalize each sample for variations in the amount of RNA used.AcknowledgementsThis work was supported by the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korea government (MOST) (No. R01-2006-000-11178-0).REFERENCES1.Bray, E. A. (2002) Classification of the genes differentially expressed during water-deficit stress in Arabidopsis thali-ana : An analysis using micro array and differential ex-pression data. Ann. Bot. 89, 803-811.2.Ingram, J. and Bartels, D. (1996) The molecular basis of dehydration tolerance in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47, 377-403.3.Kim, S. J., Jeong, D. H., An, G. and Kim, S. R. (2005) Characterization of a drought-responsive gene, OsTPS1, identified by the T-DNA gene-trap system in rice. J. Plant Biol. 48, 371-379.4.Allagulova, Ch. R., Gimalor, F. R., Shakirova, F. M. and Vakhitov, V. A. (2003) The plant dehydrins: Structure and putative functions. Biochemistry (Mosc .) 68, 945-951.5.Close, T. J. (1996) Dehydrins: emergence of a biochemical role of a family of plant dehydration proteins. Physiol. Plant. 97, 795-803.6.Close, T. J. (1997) Dehydrins: a commonalty in the re-sponse of plants to dehydration and low temperature. Physiol. Plant. 100, 291-296.7.Dure, L., Crouch, M., Harada, J., Ho, T-HD., Mundy, J. and Quatrano, R. (1989) Common amino acid sequence domains among the LEA proteins of higher plants. Plant. Mol. Biol. 12, 475-486.8.Hara, M., Terashima, S., Fukaya, T. and Kuboi, T. (2003) Enhancement of cold tolerance and inhibition of lipid per-oxidation by citrus dehydrin in transgenic tobacco. Planta. 217, 290-298.9.Ismail, A. M., Hall, A. E. and Close, T. J. (1999) Allelic variation of a dehydrin gene cosegregates with chilling tolerance during seedling emergence. Proc. Natl. Aca. Sci. U.S.A. 96, 13566-13570.10.Lee, S. C., Lee, M. Y., Kim, S. J., Jun, S. H., An, G. andKim, S. R. (2005) Characterization of an abiotic stress-in-ducible dehydrin gene OsDhn1 in rice (Oryza sativa L .). Mol. Cells. 19, 212-218.11.Svensson J, Ismail, A. M., Palva, E. T. and Close, T. J. (2002) Dehydrins. In: Storey KB, Storey JM (eds) Sensing, signaling and cell adaptation. Elsevier Science B. V., Amsterdam, 99, pp. 155-171.12.Houde, M., Daniel, C., Lachapelle, M., Allard, F., Laliberte, S. and Sarhan, F. (1995) Immunolocalization of freezing- tolerance-associated proteins in the cytoplasm and nucleo-plasm of wheat crown tissues. Plant J. 8, 583-593.13.Godoy, J. A., Lunar, R., Torres-Schumann, S., Moreno, J., Rodrigo, R. M. and Pintor-Toro, J. A. (1994) Expression tis-sue distribution and subcellular localization of dehydrin TAS14 in salt stressed tomato plants. Plant Mol. Biol. 26, 1921-1934.14.Borovskii, G. B., Stupnikova, I. V., Antipina, A. I., Vladimirova, S. V. and Voinikov, V. K. (2002) Accumulation of dehydrin-like proteins in the mitochondria of cereals in re-sponse to cold, freezing, drought and ABA treatment. BMC Plant Biol. [electronic resource] 2, 5.15.Heyen, B. J., Alsheikh, M. K., Smith, E. A., Torvik, C. F., Seals, D. F. and Randall, S. K. (2002) The calcium-binding activity of a vacuole-associated, dehydrin-like protein is regulated by phosphorylation. Plant Physiol. 130, 675-687. 16.Mueller, J. K., Heckathorn, S. A. and Fernando, D. (2003) Identification of a chloroplast dehydrin in leaves of ma-ture plants. Int. J. Plant Sci. 164, 535-542.17.Danyluk, J., Perron, A., Houde, M., Limin, A., Fowler, B., Benhamoun, N. and Sarhan, F. (1998) Accumulation of an acidic dehydrin in the vicinity of plasma membrane dur-ing cold acclimation of wheat. Plant Cell. 10, 623-638.18.Koag, M. C., Fenton, R. D., Wilkens, S. and Close, T. J. (2003) The binding of maize DHN1 to lipid vesicles. Gain of structure and lipid specificity. Plant Physiol. 131, 309-316. 19.Rinne, P. L. H., Kaikuranta, P. L. M., van der Plas, L. H. W. and van der Schoot, C. (1999) Dehydrins in cold-accli-mated apices of birch (Betula pubescens Ehrh.): production, localization and potential role in rescuing enzyme function during dehydration. Planta. 209, 377-388.20.Alsheikh, M. K., Heyen, B. J. and Randall, S. K. (2003) Ion binding properties of the dehydrin ERD14 are dependent upon phosphorylation. J. Biol. Chem. 278, 40882-40889. 21.Fan, Z. and Wang, X. (2006) Isolation and Characterization of a Novel Dehydrin Gene from Capsella bursa-pastoris. J. Molecular Biology 40, 52-60.22.Cheng, Z., Targolli, J., Huang, X. and Wu, R. (2002) Wheat LEA genes, PMA80 and PMA1959, enhance dehydration tolerance of transgenic rice (Oryza sativa L.). Mol. Breed. 10, 71-82.23.Ismail, A. M., Hall, A. E. and Close, T. J. (1999) Purification and partial characterization of a dehydrin involved in chill-ing tolerance during seedling emergence of cowpea. Plant Physiol. 120, 237-244.24.Puhakainen, T., Hess, M. W., Mäkelä, P., Svensson, J., Heino, P. and Palva, E. T. (2004) Over expression of mul-tiple dehydrin genes enhances tolerance to freezing stress in Arabidopsis. Plant Mol. Biol. 54, 743-753.25.Chauvin, L. P., Oude, M. and Sarhan, F. (1993) A leaf-spe-cific gene stimulated by light during wheat acclimation to low temperature. Plant Mol. Biol. 23, 255-265.Codonopsis lanceolata dehydrin geneRama Krishna Pulla, et al.343 BMB reports 26.Crosatti, C., Polverino, D. L. P., Bassi, R. and Cattivelli, L.(1999) The interaction between cold and light controls the expression of the cold-regulated barley gene cor14b and the accumulation of the corresponding protein. Plant Physiol. 119, 671-680.27.Ohno, R., Takumi, S. and Nakamura, C. (2003) Kinetics oftranscript and protein accumulation of a low-molecular weight wheat LEA D-11 dehydrin in response to low temperature. J. Plant Physiol. 160, 193-200.28.Panta, G. R., Rieger, M. W. and Rowland, L. J. (2001)Effect of cold and drought stress on blue berry dehydrin accumulation. J. Hort. Sci. Biotech. 76, 549-556.29.Houde, M., Dallaire, S., N’Dong, D. and Sarhan, F. (2004)Over expression of the acidic dehydrin WCOR410 im-proves freezing tolerance in transgenic strawberry leaves. Plant Biotech. J. 2, 381-388.30.Yin, Z., Pawlowicz, I., Bartoszewski, G., Malinowski, R.,Malepszy, S. and Rorat, T. (2004) Transcritional expression of a Solanum sogarandinum pGT Dhn10 gene fusion in cucumber, and its correlation with chilling tolerance in transgenic seedling. Cell Mol. Biol. Lett. 9, 891-902.31.Lee, K. T., Choi, J., Jung, W. T., Nam, J. H., Jung, H. J. andPark, H. J. (2002) Structure of a New Echinocystic Acid Bisdesmoside Isolated from Codonopsis lanceolata Roots and the Cytotoxic Activity of Prosapogenins. J. Agric. Food Chem. 50, 4190-4193.32.Xiao, H. and Nassuth, A. (2006) Stress- and development-induced expression of spliced and unspliced transcripts from two highly similar dehydrin1 genes in V. riparia and V . vinifera. Plant Cell Rep. 25, 968-977.33.Bray, E. A. (1997) Plant responses to water deficit. TrendsPlant Sci. 2, 48-54.34.Chandler, P. M. and Robertson, M. (1994) Gene expressionregulated by abscisic acid and its relation to stress tolerance. Annu. Rev. Plant Physiol. Plant Mol. Biol. 45, 113-141.35.Rabbani, M. A., Maruyama, K., Abe, H., Kyan, M. A.,Katsura, K., Yoshiwara, K., Shinozaki, K. and Yamaguchi- Shinozaki, K. (2003) Monitoring expression profiles of ricegenes under cold drought and high salinity and abscisic acid application using cDNA micro array and RNA gel-blot analyses. Plant Physio. 133, 1755-1767.36.Shinozaki, K. and Yamaguchi-Shinozaki, K. (1996) Mole-cular responses to drought and cold stress. Curr. Opin. Biotechnol. 7, 161-167.37.Deng, Z. X., Pang, Y. Z., Kong, W. W., Chen, Z. H., Wang, X. L., Liu, X. J., Pi, Y., Sun, X. F. and Tang, K. X. ( 2005) A novel ABA dependent dehydrin ERD10 gene from Brassica napus. DNA seq. 16, 28-35.38.Caruso, A., Morabito, D., Delmotte, F., Kahlem, G. and Carpin, S. (2002) Dehydrin induction during drought and osmotic stress in Populus. Plant Physiol. Biochem. 40, 1033-1042.39.Richard, S., Morency, M. J., Drevet, C., Jouanin, L. and S´eguin, A. (2000) Isolation and characterization of a de-hydrin gene from white spruce induced upon wounding, drought and cold stresses. Plant Mol. Biol. 43, 1-10.40.Natali., Giordani, T., Lercari, B., Maestrini, P., Cozza, R., Pangaro, T., Vernieri, P., Martinelli, F. and Cavallini. (2007) A. Light induces expression of a dehydrin-encoding gene during seedling de-etiolation in sunflower (Helianthus an-nuus L .). J. Plant Physiol. 164, 263-273.41.Menkens, A. E., Schindler, U. and Cashmore, A, R. (1995) The G-box: a ubiquitous regulatory DNA element in plants bound by the GBF family of bZIP proteins. Trends Biochem Sci. 20, 506-510.42.Huh, G. H., Lee, S. J., Bae, Y. S., Liu, J. R. and Kwak, S. S. (1997) Molecular cloning and characterization of cDNAs for anionic and neutral peroxidases from suspension cul-tured cells of sweet potato and their differential expression in response to stress. Mol. Gen. Genet. 255, 382-391.43.Wu, W., Pang, Y., Shen, G., Lu, J., Lin, J., Wang, J., Sun, X. and Tang, K. (2006) Molecular Cloning, Characterization and Expression of a Novel Trehalose-6-phosphate Synthase Homologue from Ginkgo biloba. J. Biochem. Mol. Biol. 39, 158-166.。
JMP深度文章_基因技术帮助美国农业部确保作物安全2015-05-06
基因技术帮助美国农业部确保作物安全JMP® Genomics帮助研究人员清除玉米的病原体关键词：生命科学、基因序列、食品安全、JMP® Genomics、数据分析、数据可视化挑战：美国农业部的研究人员需要分子生物学家和统计学家共同进行研究项目，领域涉及解决作物产量，人体营养以及环境问题的有效途径。
解决方案：来自SAS公司的全新生命科学软件 JMP Genomics不仅提供强大的海量数据分析能力，而且仅通过点击鼠标点击就可实现的数据可视化，使得非统计专业的人员容易使用和理解。
效果：美国农业部的研究中心广泛地运用JMP Genomics，范围遍及25个州。
戴比博伊工作在数字的世界中。
作为地区统计员为美国农业部的农业研究服务（USDA），她帮助美国农业部的研究人员设计实验，分析结果并将这些结果转换为统计学相关的格式。
博伊所在研究所位于密西西比州的斯德维尔，杰克逊西北方向两小时车程，她与美国南部五个州的超过250名科学家合作，研究领域包括作物的产量、蜜蜂的行为、流体沉淀以及特定食物的营养价值等等。
曾经有三位统计学家一起服务与她所负责的地区，包括肯塔基州、田纳西州、阿拉巴马州、密西西比州和路易斯安那州。
现在，她是团队中唯一的统计师。
她解释说：“在她所在组的分子生物学家必须能够亲自做许多工作。
”JMP Genomics的产品经理香农.康纳斯说：“来自SAS公司的JMP Genomics软件是为了便于研究人员和统计人员一起高效地工作而设计的。
通过提供菜单驱动的JMP界面与SAS连接，JMP Genomics提供的先进分析方法，交互式图形，实验设计工具吸引着它们所支持的生物统计学家和分子生物学家。
”美国农业部一直依靠SAS®软件，因其强大的数据分析能力。
2006年初SAS推出了应用于基因研究的桌面可视化软件JMP Genomics。
九月，美国农业部就购买了30套软件，广泛的被缅因州、明尼苏达州、密西西比州等25个州的研究人员所使用。
范文《转基因大豆对幼鼠出生时体重和存活率的影响》（对照试验性研究..
Influence of Genetically modified Soya大豆on the Birth-Weight and Survival of RatPups仔Abstract1 Investigation of the influence of GM soya on the birthrate and survival of the offspring 后代of Wistar rats2 were performed. A group of female rats were fed GM soya flour before mating 交配and pregnancy. The control group of females were fed traditional soya and the third group of females, the positive control group, received feed without any soya. The weight and the mortality死亡rate of the newborn pups were analyzed. The study showed that there was a very high rate of pup mortality (55.6%) in the GM soya group in comparison with the control group and the positive control group (9% and 6.8% respectively. Moreover, death in the first group continued during lactation哺乳, and the weights of the survivors are lower those from the other two groups. It was revealed in these experiments, that GM soya could have a negative influence on the offspring of Wistar rats.Introduction2 The term genetically modified organism (GMO3s) refers to plants, microbes and animals with genes transferred from other species in order to produce certain novel characteristics (for example resistance to pests, or herbicides) and are produced by recombinant DNA technology. Four main sources of the hazards危险of GMO are discussed by scientists worldwide: 1) those due to the new genes, and gene products introduced; 2) unintended effects inherent内在的to the technology; 3) interactions between foreign genes and host genes; and 4) those arising from the spread of the introduced genes by ordinary cross-pollination异花授粉as well as by horizontal gene transfer (World Scientists’Statement 2000).3 GM crops contain material, which is not present in them under natural conditions,and they form a part of our daily diet. To understand what effect they can have on us and on our animals it is vitally important to study the influence of these GM plants in different organisms for several generations. At the present, these studies are lacking from the scientific literature. Also, several detrimental effects of GM crops had been showed on the metabolism of animals. The hazard of genetically modified organisms (GMO) was shown for animals and the environment in many investigations (Traavik 1995; Ho and Tappeser 1997; Pusztai 1999 and 2001; Kuznetcov et al. 2004 and others).Earlier it was shown that consumption of GM food by animals led to the negative changes in their organisms. Experiments, conducted by A. Pusztai showed that potatoes modified by the insertion of the gene of the snowdrop lectin4 (an insecticidal proteins), stunted the growth of rats, significantly affected some of their vital organs, including the kidneys, thymus, gastrocnemius muscle and others (1998) and damaged their intestines and their immune system (Ewen and Pusztai 1999). Similar effect of GM potatoes on rats was obtained at Institute of Nutrition in Russia (Ermakova 2005).4 It is put forward in the risk assessment documents that the GM components of transformed plants are completely destroyed in the digestive tract of humans and animals, together with the other genetic material found in them. However, foreign DNA plasmids5 are steadier against the digestion than it was originally believed. Plasmid DNA and GM DNA were found in microorganisms of the intestine and in saliva (Mercer et al. 1998; Coghlan 2002). Experimental researches in mice showed that ingested foreign DNA can persist in fragmented form in the gastrointestinal tract, penetrate the intestinal wall, and reach the nuclei of leukocytes, spleen and liver cells (Schubbert et al. 1994). In another research of Schubbert et al. (1998) the plasmid containing the gene for the green fluorescent protein6 (pEGFP-C1) or bacteriophage M13 DNA were fed to pregnant mice. Foreign DNA, orally ingested by pregnant mice, was discovered in blood (leukocytes), spleen, liver, heart, brain, testes and other organs of foetuses and newborn animals. The authors considered that maternally ingested foreign DNA could be potential mutagens for the developing fetus. At the same time Brake and Evenson (2004) analyzing the testis in mice as a sensitive biomonitor of potential toxic, didn’t find negative effects of transgenic soybean diet on fetal, postnatal, puber talor adult testicular development.5 There is a lack of investigations on the influence of GM crops on mammals,especially on their reproductive function. Therefore, it was decided that we undertake a study to see the effect of the most commonly used GM crop on the birth rate, mortality and weight gain of rat pups, whose mother were fed diets supplemented with the Roundup- Ready soya, a kind of GM food.MethodsAnimals6 Wistar rats were used in the experiment. The animals were brought up to sexual maturity on laboratory rat feed. When their weight reached about 180-200g, the female rats were divided into 3 groups, and housed in groups (3 rat/cage), and kept under normal laboratory conditions.7 The feeding scheme was as follows. Females in every cage daily received dry pellets from a special container placed on the top of their cage. Those rats receiving soya flour supplement, were given the soya flour in a small container placed inside their cage (20g x 40 ml water) for three rats and, so 5-7g flour for each rat every day.Experiment8 One group of female rats of 180-200g weight was allocated to the experimental group, and received 5-7 soy a flour/rat/day prepared from Roundup-Ready soya, added to the rat feed for two weeks. Another group females (3) were allocated to the control group, but their diet was supplemented with the same amount of soya flour, prepared from the traditional soya in which only traces (0.08+ 0.04%) of the GM construct was present, most likely resulting from cross-contamination. We also introduced a positive control group (in two cages: 3x3), which had not been exposed to soya flour. Therefore females have only got the standard laboratory feed without any supplementation, although it is acknowledged that the energy and protein content of this diet was less than in the other two groups.9 After two weeks on the diets all groups of 3 females were mated with two healthy males of the same age, who have never been exposed to soya flour supplements. First the one, then the other male was put into the cage for 3 days. In order to avoid infection of females, the sperm count and quality has not been determined. We carried on with3feeding the respective diets to all females during mating and pregnancy. Upon delivery, all females were transferred to individual cages, and the amount of soya supplement was increased by an additional g for every pup born. Lab feed and water was available for all animals during the experimental period. When rat pups opened their eyes and could feed themselves (from 13-14 days of age), the daily dose of soya supplement was increased till 2-3g for every pup, although all rats had free approach to the soya. All rats ate their soya portions well. Organs of some pups were taken out and weighed.Statistical analysis10 The level of mortality was analyzed by the one-way ANOVA7, using of Newman-Keuls test8 for share distribution. The pup’s weight and its distribution were checked by Mann-Whitney test9 and Chi-square10 in StatSoft Statistica v6.0 Multilingua (Russia).Results11 By the end of the experiment, from the 15 females included in the experiment, 11 gave birth and produced a total of 132 rat pups. The 4 rats who became pregnant from 6 females on the positive control diet gave birth to 44 pups (an average of 11 pups/female), while the four females, from the six on GM soya flour supplemented groups gave birth to 45 (11.3 pups/female), and 3 from traditional soya group—33 pups (11 pups/mother).12 Supplementation of the diet of the females with GM soya led to the death of 25 pups, out of the 45 born by the end of the third week of lactation, while during the same period on the traditional soya supplemented diets only 3 pups died from 33. The mortality in the positive control group was also 3, but from the larger number of pups born, as it seen in Table 1. High pup mortality was generally characteristic for females fed the GM soya flour (Table2).13 Among the pups from the females fed the positive control diet, 2 pups died during the first week, and 1 during the second week after delivery. All pups from females fed traditional soya flour died during the first week after birth. However, pups from females fed the GM soya flour supplemented diet kept dying during lactation period as it is evidentfrom Table3.14 In two weeks after their birth the weight of pups (with SE) from the GM soya supplemented group was less (23.95g ±1.5g) than that of the pups of the positive control group (30.03g±1.1g; p<0.005), or from the traditional soya flour supplemented group (27.1g±0.9g; p< 0.1). Since the number of surviving pups were so different, the weigh distribution of the pups were compared in Table 4. From the data it is evident, that 36% of the pups from the GM soya group weighed less than 20 g, in comparison with the 6% in the positive control group, and with the 6.7% found in the traditional soya supplemented diet group (Table 4). Study of pup’s organs mass showed that the organs of small pups from GM group were tiny in comparison with the same of other groups except the brain mass (Table 5). This fact indicated that the pups from the GM group were the same age as others, but changes were occurred with the development of internal organs. Slight negative effect was found in the group which received the traditional soya, but this effect was not significant. No mortality of females and survived young pups eating the GM soya flour supplemented diet was observed.Discussion15 The reproductive behaviour of female rats fed on standard laboratory feed supplemented with soya flour prepared from either genetically modified soya or traditional soya was studied to see the effect of the diet on pregnancy, lactation and the growth of the rat pups. Since it is well established that raw soybean contains a number of anti-nutrients, such as the lectins, trypsin inhibitors, etc. (Pusztai et al. 1998), and also female hormone-like substances, it was thought to be necessary to compare these data also with those from a positive control group when animals were not exposed to any soya flour supplementation.16 In order to understand the mechanism how this widely consumed GM crop exerts its influence on the reproductive performance of mammals and their offspring, it would be necessary to perform complex researches, including histological, genetic and embryo-toxicological investigations. However, we had to restrict our experiments only for a short time-span, and starting to feed the female rats two weeks before mating. However,5unlike the experiments of Brake and Evenson (2004), who started to feed pregnant mice, in our experiments the diets supplemented with GM or traditional soya flours were already given to the female rats 2 weeks before mating already, and we continued to treat them with their respective diet until the pups were weaned.17 Upon delivery, very unexpectedly a very high rate of pup mortality (55.6%) was observed in the the group of females whose diet was supplemented with the GM soya flour in comparison with the pups of both the positive control (6.8%) and the traditional soya flour supplemented (9%) groups. Also, in this group the pups continued to die over the period of lactation, which occurred only in the GM soya fed group. At the same time, the weights of the surviving rat pups were also lower. It is the more surprising, since the pups were smaller, about half, therefore more milk should have been available for the individual pups. They should have a better chance to grow optimally, unless the amount, and/or the quality of the milk were not affected by consuming the GM soya flour.18 Our data allow us to speculate and presume that the negative effect of GM soya on the newborn pups could be mediated by two possible factors. Firstly, it can be the result of transformation, and insertion of the foreign genes, which could enter into the sexual/stem cells, or/and into cells of the fetus, as it was observed by Schubbert et al. (1998). Secondly, negative effect of GM soya could be mediated by the accumulation of Roundup residues in GM soya residues. However, no mortality was observed with female rats, nor with the young pups survived, although they also began to eat the GM soya, it is supposed that the effect could be mediated by the two first factors. (2,086 words)ReferencesBrake DG and Evenson DP (2004). 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Ingested foreign (phage M13) DNA survives transiently in the gastrointestinal tract and enters the blood stream of mice. Molecules. Genes and Genetics 242: 495-504.Schubbert R, Hohiweg U, Renz D and Doerfier W (1998). On the fate of orally ingested foreign DNA in mice: chromosomal association and placental transmission in the fetus. Molecules. Genes and Genetics 259: 569-576.7Traavik T (1999). Too Early May Be Too Late. Ecological Risks Associated with the Use of Naked DNA as a Biological Tool for Research, Production and Therapy (Norwegian).Report for the Directorate for Nature Research Tungasletta 2, 7005 Trondheim. English Translation, 1999.World Scientists Statement. Supplementary Information of the Hazards of Genetic Engineering Biotechnology. Third World Network. 2000.911。
基因英语词汇翻译
基因英语词汇翻译Aactivation domain 活化结构域adapters 连接物adenine 腺嘌呤adenosine 腺ADP (adenosine diphosphate) 腺二磷酸affinity column 亲和柱AFLP (amplified fragment length polymorphisms) 增值性断片长度多态现象agrobacterium 农杆菌属alanine 丙氨酸allele 等位基因amber mutation 琥珀型突变AMP (adenosine monophosphate) 腺一磷酸ampicillin 氨?青霉素anchor primer 锚状引物annealing 退火annealing temperature 退火温度anticodon 反密码子AP-PCR (arbitrarily primed PCR) 任意引物聚合?链反应arbitrary primer 任意引物ATP (adenosine triphosphate) 腺三磷酸autosome 常染色体腺苷脱氨酶缺乏症 adenosine deaminasedeficiency (ADA) 腺病毒 adenovirusAlagille综合征 Alagille syndrome等位基因 allele氨基酸 amino acids动物模型 animal model抗体 antibody凋亡 apoptosis路-巴综合征ataxia-telangiectasia常染色体显性autosomal dominant常染色体 autosomeBbaculovirus 杆状病毒base pair ..基对base sequence ..基顺序beta-galactosidase ..-半乳糖? beta-glucuronidase ..-葡糖醛酸糖? bioluminescence 生物发光bioremediation 生物降解biotechnology 生物技术blotting 印迹法blue-white selection 蓝白斑筛选细菌人工染色体 bacterial artificial chromosome (BAC)碱基对 base pair先天缺陷birth defect骨髓移植bone marrow transplantation blunt end 平(整末)端Ccatalyst 催化剂cDNA library 反向转录DNA库centromere 着丝体centrosome 中心体chemiluminescence 化学发光chiasma 交叉chromomere 染色粒chromoplast 有色体chromosomal aberration 染色体畸变chromosomal duplication 染色体复制chromosomal fibre 染色体牵丝chromosome 染色体chromosome complement 染色体组chromosome map 染色体图chromosome mutation 染色体突变clone 克隆cloning 无性繁殖系化codon 密码子codon degeneracy 密码简并codon usage 密码子选择cohesive end 黏性末端complementary DNA (cDNA) 反向转录DNA complementary gene 互补基因consensus sequence 共有序列construct 组成cosmids 黏性质粒crossing over 互换cyclic AMP (cAMP) 环腺酸cytosine 胞嘧啶癌 cancer后选基因 candidate gene癌 carcinomacDNA文库 cDNA library 细胞cell染色体 chromosome克隆 cloning密码 codon天生的 congenital重叠群 contig囊性纤维化 cystic fibrosis 细胞遗传图 cytogenetic mapDdark band 暗带deamination 脱氨基作用decarboxylation 脱羧基作用degenerate code 简并密码degenerate PCR 退化性聚合?链反应dehydrogenase 脱氢?denaturation 变性deoxyribonucleoside diphospahte 脱氧核糖核一磷酸deoxyribonucleoside monophospahte 脱氧核糖核二磷酸deoxyribonucleoside triphospahte 脱氧核糖核三磷酸deoxyribose 去(脱)氧核糖dicarboxylic acid 二羧酸digoxigenin 洋地黄毒diploid 二倍体DNA (deoxyribonucleic acid) 去(脱)氧核糖核酸DNA binding domain DNA结合性结构域DNA fingerprinting DNA指纹图谱DNA helicase DNA解螺旋?DNA kinase DNA激?DNA ligase DNA连接?DNA polymer DNA聚合物DNA polymerase DNA聚合?double helix 双螺旋double-strand 双链缺失 deletion脱氧核糖核酸 deoxyribonucleic acid (DNA) 糖尿病 diabetes mellitus二倍体 diploidDNA复制 DNA replicationDNA测序 DNA sequencing显性的 dominant双螺旋 double helix复制 duplicationEelectroporation 电穿孔endonuclease 内切核酸? enhancer 增强子enterokinase 肠激? episome 游离基因ethidium bromide 溴乙锭eukaryotic 真核生物的euploid 整倍体exonuclease 外切核酸?expressed-sequence tags 表达的序列标记片段extron 外含子电泳electrophoresis 酶enzyme外显子exonFF factor F因子FAD (flavine adenine dinucleotide) 黄素腺嘌呤二(双)核酸feedback control 反馈控制feedback inhibition 反馈抑制feedback mechanism 反馈机制first filial (F1) generation 第一子代FISH (fluoresence in situ hybridization) 荧光原位杂交forward mutation 正向突变F-pilus F纤毛functional complementation 功能性互补作用fusion protein 融合蛋白家族性地中海热familial Mediterraneanfever 荧光原位杂交fluorescence in situhybridization (FISH) 脆性X染色体综合征Fragile X syndromeGgel electrophoresis 凝胶电泳gene 基因gene cloning 基因克隆gene conversion 基因转变gene duplication 基因复制gene flow 基因流动gene gun 基因枪gene interaction 基因相互作用gene locus 基因位点gene mutation 基因突变gene regulation 基因调节gene segregation 基因分离gene therapy 基因治疗geneome 基因组/ 染色体组genetic map 基因图genetic modified foods (GM foods) 基因食物genetics 遗传学genetypic ratio 基因型比/ 基因型比值genome 基因组/ 染色体组genomic library 基因组文库genotype 基因型giant chromosome 巨染色体globulin 球蛋白glucose-6-phosphate dehydrogenase 6-磷酸葡萄糖脱氢?GP (glycerate phosphate) 磷酸甘油酸脂GTP (guanine triphosphate) 鸟三磷酸guanine 鸟嘌呤基因扩增gene amplification基因表达gene expression基因图谱gene mapping基因库gene pool基因治疗gene therapy基因转移gene transfer遗传密码genetic code (A TGC)遗传咨询genetic counseling遗传图genetic map遗传标记genetic marker遗传病筛查genetic screening基因组genome基因型genotype种系germ lineHhaploid 单倍体haploid generation 单倍世代heredity 遗传heterochromatin 异染色质Hfr strain 高频重组菌株holoenzyme 全?homologous 同源的housekeeping gene 家务基因hybridization 杂交单倍体haploid造血干细胞hematopoietic stem cell 血友病hemophilia 杂合子heterozygous高度保守序列highly conserved sequence Hirschsprung病Hirschsprung's disease纯合子homozygous人工染色体human artificial chromosome (HAC)人类基因组计划Human Genome Project human immunodeficiency virus (HIV)/ 人类免疫缺陷病毒acquired immunodeficiency syndrome (AIDS) 获得性免疫缺陷综合征huntington舞蹈病Huntington's diseaseIimmunoglobulin 免疫球蛋白in vitro 在体外/ 在试管内in vivio 在体内independent assortment 独立分配induced mutation 诱发性突变induction 诱导initiation codon 起始密码子inosine 次黄insert 插入片段insertional inactivation 插入失活interference 干扰intergenic 基因间的interphase 间期intragenic 基因内的intron 内含子inversion 倒位isocaudarner 同尾酸isoschizomer 同切点?Kkanamycin 卡那毒素klenow fragment 克列诺夫片段Llac operon 乳糖操纵子ligase 连接? ligation 连接作用light band 明带linker 连接体liposome 脂质体locus 位点Mmap distance 图距离map unit 图距单位mature transcript 成熟转录物metaphase 中期methylase 甲基化? methylation 甲基化作用microarray 微列microinjection 微注射missense mutation 错差突变molecular genetics 分子遗传学monoploid 单倍体monosome 单染色体messenger RNA (mRNA) 信使RNA multiple alleles 复(多)等位基因mutagen 诱变剂mutagenesis 诱变mutant 突变体mutant gene 突变基因mutant strain 突变株mutation 突变mutation rate 突变率muton 突变子畸形malformation描图mapping标记marker黑色素瘤melanoma孟德尔Mendel, Johann (Gregor)孟德尔遗传Mendelian inheritance信使RNA messenger RNA (mRNA)[分裂]中期metaphase微阵技术microarray technology线立体DNA mitochondrial DNA单体性monosomy小鼠模型mouse model多发性内分泌瘤病multiple endocrine neoplasia, type 1 (MEN1)NNAD (nicotinamide adenine dinucleotide) 烟醯胺腺嘌呤二核酸NADP (nicotinamide adenine dinucleotide phosphate) 烟醯胺腺嘌呤二核酸磷酸nicking activity 切割活性nonsense codon 无意义密码子nonsense mutation 无意义突变Northern blot Northern印迹法nuclear DNA 核DNAnuclear gene 核基因nuclease 核酸?nucleic acid 核酸nucleoside 核nucleoside triphosphate 核三磷酸nucleotidase 核酸?nucleotide 核酸nucleotide sequence 核酸序列神经纤维瘤病neurofibromatosis尼曼-皮克病Niemann-Pick disease, type C (NPC)RNA印记Northern blot核苷酸nucleotide神经核nucleusOoligonucleotide 寡核酸one gene one polypeptide hypothesis 一个基因学说operon 操纵子oxidative decarboxylation 氧化脱羧作用oxidative phosphorylation 氧化磷酸化作用寡核苷酸oligo癌基因oncogenePpeptide ? peptide bond ?键phagemids 噬菌粒phosphorylation 磷酸化作用physical map 物理图谱plasmid 质粒point mutation 点突变poly(A) tail poly(A)尾polymerase 聚合?polyploid 多倍体positional cloning 位置性无性繁殖系化primary transcript 初级转录物primer 引物probe 探针prokaryotic 原核的promoter 启动子protease 蛋白?purine 嘌呤pyrimidine 嘧啶Parkinson病Parkinson's disease血系/谱系pedigree表型phenotype物理图谱physical map多指畸形/多趾畸形polydactyly聚合酶链反应polymerase chain reaction (PCR)多态性polymorphism定位克隆positional cloning原发性免疫缺陷primary immunodeficiency 原核pronucleus前列腺癌prostate cancerRrandom segregation 随机分离RAPD (rapid amplified polymorphic DNA) 快速扩增多态DNAreading frame 阅读码框recessive gene 隐性基因recombinant 重组体recombinant DNA technology 重组DNA技术recombination 重组regulator (gene) 调控基因replica 复制物/ 印模replica plating 复制平皿(板)培养法replication 复制replication origin 复制起点reporter gene 报道基因repression 阻遏repressor 阻遏物repressor gene 阻遏基因resistance strain 抗药性菌株restriction 限制作用restriction enzyme 限制性内切? restriction mapping 限制性内切?图谱retrovirus 反转录病毒reverse transcription 反转录作用RFLP (restricted fragment length polymorphisms) 限制性断片长度多态现象ribonucleotide 核糖核酸ribose 核糖ribosomal RNA (rRNA) 核糖体RNA ribosome 核糖体RNA (ribonucleic acid) 核糖核酸RNA polymerase I RNA聚合?IRNA polymerase II RNA聚合?IIRNA polymerase III RNA聚合?IIIR-plasmid R质粒/ 抗药性质粒隐性recessive逆转录病毒retrovirus核糖核酸ribonucleic acid (RNA)核糖体ribosomeSsecond filial (F2) generation 第二子代self-ligation 自我连接作用shuttle vectors 穿梭载体sigma factor ..因子single nucleotide polymorphism 单核酸多态性single-stranded DNA 单链DNAsister chromatid 姊妹染色单体sister chromosome 姊妹染色体site-directed mutagenesis 定点诱变somatic cell 体细胞Southern blot Southern印迹法splice 拼接star activity 星号活性stationary phase 静止生长期sticky end 黏性末端stop codon 终止密码子structural gene 结构基因supernatant 上层清液supressor 抑制基因序列标记位点sequence-tagged site (STS) 联合免疫缺陷severe combined immunodeficiency (SCID)性染色体sex chromosome伴性的sex-linked体细胞somatic cellsDNA印记Southern blot光谱核型spectral karyotype (SKY)替代substitution自杀基因suicide gene综合征syndromeTtelophase 末期template 模板terminator 终止子tetracycline 四环素thymine 胸腺嘧啶tissue culture 组织培养transcription 转录作用transfer RNA (tRNA) 转移RNA transformation 转化作用transgene 转基因translation 翻译/ 平移transmembrane 跨膜triplet 三联体triplet code 三联体密码triploid 三倍体技术转让technology transfer转基因的transgenic易位translocation三体型trisomy肿瘤抑制基因tumor suppressor geneVvector 载体WWestern blot Western印迹法Wolfram综合征Wolfram syndromeY 酵母人工染色体yeast artificial chromosome (YAC)。
Plant_genomics2
真核生物利用端粒来解决线形DNA复制问题
端粒是一段由很短的重复单位组成的串联重复序列，并存在一个 单链的 3′ 末端。端粒的总体长度受遗传控制。 DNA 复制时，端粒序列会缩短，但通过端粒酶，可以使端粒伸长， 从而达到一种动态平衡。 端粒酶是一种核酸蛋白复合体，含有 RNA，可以作为合成端粒一 条链的模板。因此，端粒酶是一种反转录酶。
DnaA 蛋白浓度的调控作用
细菌基因组复制结束后，细胞中 DNA 含量增加了一 倍；而细胞中部分 DnaA 蛋白可能黏附在细胞膜上。因 此，从复制结束到细胞分裂结束一段时间内，没有足够 的 DnaA 蛋白来启动新的一轮复制。
DNA 甲基化的调控作用
dam 甲基化酶能够使 腺嘌呤甲基化。 在 DNA 复制之 前，复制原点中 的 GATC 位点是 完全甲基化的。 复制结束时则呈 半甲基化状态。 必须等待一段时 间，由甲基化酶 使之变成完全甲 基化后，才能重 新开始启动复制。
人 类 端 粒 的 合 成
真核生物核小体的复制
复制中双链解开时，核小体即解体。但双链一旦合成，即组装 新的核小体。新核小体中的组蛋白是随机组装的，既包含旧的，也 包含新合成的。
基因组复制的调控
基因组复制完成后，不能立即再进行复制，而必须等到细胞分裂之后， 这样才能保证细胞中染色体倍数不变。因此，基因组复制必须与细胞周 期相协调。 真核生物基因组存在许多复制子，但在细胞分裂间期，不是整个基因组 同时进行复制的，而是每一时刻都只有一小部分的复制子被激活，且激 活的复制子都集中在某些区域。但对复制原点的激活顺序是怎样选择的？ 复制原点的序列是否包含了这方面的遗传信息？这些问题尚不清楚。 另外，真核生物中复制机器如何鉴别已复制过的和未复制过的复制原点， 从而保证每个复制原点只被启动一次？这方面的遗传信息是存在于 DNA 序列中，还是存在于与复制有关的蛋白质中？这些问题也有待回答。 目前已知原核生物基因组复制存在两种调控机制，即DnaA蛋白浓度和 DNA甲基化。
genomicsproteomics
Goals of Human Genome Project
What does the draft human genome sequence tell us?
address the ethical, legal, and social issues (ELSI) that may arise from the project.
各国政府在HGP研究中所占的份额
各国在HGP研究中所占的份额
美国 54% 英国 33% 日本 7% 法国 2.8% 德国 2.2% 中国 1%
❖Because they lack the -OH (which allows nucleotides to join a growing DNA strand), replication stops.
Normally, this would be where another phosphate Is attached, but with no -OH group, a bond can not form and replication stops
Whole genome shotgun sequencing
Milestones of Human Genome Project
Milestones: ■ June 2000: Completion of a
working draft of the entire human genome ■ February 2019: Analyses of the working draft are published ■ April 2019: HGP sequencing is completed and Project is declared finished two years ahead of schedule
启动子和增强子区域中常见的顺式作用元件的英文
启动子和增强子区域中常见的顺式作用元件的英文【中英文实用版】Title: Common Cis-acting Elements in Promoter and Enhancer RegionsIn the intricate tapestry of gene regulation, cis-acting elements hold a position of paramount importance. These sequences, found within non-coding regions of the DNA, play a pivotal role in orchestrating the transcriptional machinery. Among them, the promoter and enhancer regions are hotspots for regulatory activity, harboring a myriad of cis-elements that are crucial for the precise control of gene expression.在基因调控的复杂网络中，顺式作用元件占据了至关重要的位置。
这些序列存在于DNA的非编码区域中，对调控转录机制起着关键作用。
其中，启动子和增强子区域是调控活动的热点，它们包含了诸多对精确控制基因表达至关重要的顺式元件。
Distinct from their trans-acting counterparts, cis-acting elements exert their influence locally, bound by the physical constraints of the genomic loci they inhabit. In the promoter region, for instance, the TATA box and the Initiator element are iconic cis-elements that facilitate the assembly of the transcriptional pre-initiation complex.与它们的反式作用对应物不同，顺式作用元件在其所处的基因座物理限制内局部发挥作用。
哈佛大学新研究揭示海绵基因组传达遗传复杂性的出现
哈佛大学新研究揭示海绵基因组传达遗传复杂性的出现哈佛大学最近研究了四个纲八个种海绵的转录组，专门寻找与动物复杂性相关的基因和途径，成果发表在Mol Biol Evol上。
哈佛大学最近研究了四个纲(Hexactinellida, Demospongiae, Homoscleromorpha and Calcarea)八个种海绵的转录组，专门寻找与动物复杂性相关的基因和途径，成果发表在Mol Biol Evol上。
海绵(多孔动物)是最早进化的动物，它滤食性身体计划是由复杂的含水系统组成的环细胞室组成的，在后生动物中非常独特。
它表示海绵与其他动物在肌肉和神经功能进化之前早有分歧，或表示海绵已失去这些特征。
Amphimedon和Oscarella基因组的分析支持这一观点——许多后生动物的关键基因在所研究的海绵中的是不存在的，但其他海绵中这些基因的存在是未知的。
哈佛大学最近研究了四个纲(Hexactinellida, Demospongiae, Homoscleromorpha and Calcarea)八个种海绵的转录组，专门寻找与动物复杂性相关的基因和途径，成果发表在Mol Biol Evol上。
他们在三种单细胞后鞭毛生物和两种两侧对称动物类群的转录组和基因组中寻找这些基因作为参考。
他们的分析表明，所有海绵纲与其他后生动物共享补充基因。
该团队发现Hexactinellid, Calcareous and Homoscleromorph三种海绵与非两侧对称动物相比共享给两侧对称动物更多的基因(由联川生物提供poly(A)RNA测序服务)。
他们还发现大多数分子代表参与细胞与细胞间的通信，发出信号，活跃在复杂的上皮细胞中，免疫识别和生殖系/性别，只有少数潜在的关键分子没有参与。
一个值得注意的发现是，所有寻常海绵纲(转录组和Amphimedon基因组)某些重要基因的缺失可能反映了主干谱系包括Hexactinellid, Calcareous and Homoscleromorph的分歧。
Unit4：Personalized Medicine 个人化药物
Personalized Medicine: Genomics and Stem Cell therapies.
Genomics: Example: Cancers – Tumor genotyping 2009 Science 326, 218-220ቤተ መጻሕፍቲ ባይዱ lung cancer non-small cell lung cancer most common EML4-ALK fusion others: mutations in EGFR, Iressa Genotype every lung cancer. Check for array of mutations. Target drug therapy based on specific genes mutated 15-20% of patient tumors can be matched to specific drug. Reality: better initially, then cancers develop resistance.
Personalized Medicine. Hope or Hype?
Diagnosing inherited forms of breast cancer: Up close and personal
Up to 10% of breast cancer can be shown to be inherited and most of these cancers are traceable to mutations in the BRCA1 or BRCA2 genes. /d/index.html
New Frontiers: Personalized Medicine. Hope or Hype?
分子生物学名词解释大全
分子生物学名词解释大全AAbundance (mRNA 丰度)：指每个细胞中mRNA 分子的数目。
Abundant mRNA(高丰度mRNA)：由少量不同种类mRNA组成，每一种在细胞中出现大量拷贝。
Acceptor splicing site (受体剪切位点)：内含子右末端和相邻外显子左末端的边界。
Acentric fragment(无着丝粒片段)：(由打断产生的)染色体无着丝粒片段缺少中心粒，从而在细胞分化中被丢失。
Active site(活性位点)：蛋白质上一个底物结合的有限区域。
Allele(等位基因)：在染色体上占据给定位点基因的不同形式。
Allelic exclusion(等位基因排斥)：形容在特殊淋巴细胞中只有一个等位基因来表达编码的免疫球蛋白质。
Allosteric control(别构调控)：指蛋白质一个位点上的反应能够影响另一个位点活性的能力。
Alu-equivalent family(Alu 相当序列基因)：哺乳动物基因组上一组序列，它们与人类Alu家族相关。
Alu family (Alu家族)：人类基因组中一系列分散的相关序列，每个约300bp长。
每个成员其两端有Alu 切割位点(名字的由来)。
α-Amanitin(鹅膏覃碱)：是来自毒蘑菇Amanita phalloides 二环八肽，能抑制真核RNA聚合酶，特别是聚合酶II 转录。
Amber codon (琥珀密码子)：核苷酸三联体UAG，引起蛋白质合成终止的三个密码子之一。
Amber mutation (琥珀突变)：指代表蛋白质中氨基酸密码子占据的位点上突变成琥珀密码子的任何DNA 改变。
Amber suppressors (琥珀抑制子)：编码tRNA的基因突变使其反密码子被改变，从而能识别UAG 密码子和之前的密码子。
Aminoacyl-tRNA (氨酰-tRNA)：是携带氨基酸的转运RNA，共价连接位在氨基酸的NH2基团和tRNA 终止碱基的3¢或者2¢－OH 基团上。
基因组学
1 Structural genomics and functiongenomics结构基因组学：经过基因作图、核苷酸分析来确定基因的组成和基因定位。
功能基因组学：在结果基因组学所获得的信息和产物的基础上，全面系统地分析基因的功能。
2 orthologous and paralogous genes直源基因：基因是那些不同种属生物间的同源基因，它们的共同祖先早于种属分化。
旁源基因：基因存在于同种生物中，常识多基因家族的成员，他们的祖先可能早于或晚于种属分化。
4 Enhancer trap and promoter trap增强子陷阱：将某报告基因与一个精巧的启动子相连，组成一增强子陷阱重组体，它不会自主起始转录，而需由被插入的细胞基因组中的增强子帮助才可转录。
若报告基因最终表达，则可推知插入位点附件有增强子或有基因，即实现了以增强子陷阱重组体发现增强子的目的。
启动子陷阱：通过将报告基因插入到细胞基因组的外显子上，一旦发现它与细胞基因组基因共同转录或表达，则可知该报告基因附件有启动子，从而起到了以之为诱饵发现启动子的目的。
5 Ac/Ds transposon and T-DNA insertionT-DNA插入：农杆菌中细胞中分别含有Ti质粒和Ri质粒，其上有一段T-DNA，农杆菌通过侵染植物伤口进入细胞后，可将T-DNA插入到植物基因组中。
Ac/Ds转座子：玉米中的一个转座子家族。
该家族的自主元件是Ac ,它包含和转座相关的酶,能使Ac 、Ds 元件发生转座。
而Ds是一种非自主元件,它单独不能发生转座,可以利用Ac 的转座酶发生转座。
Ac/Ds 系统的转座是通过剪切/粘贴的机制进行的。
请比较全基因组测序中克隆重叠群法（clone by clone）和鸟枪法（shotgunmethod）测序的优缺点。
鸟枪法：将分子打成片段，得到每个片段的序列，然后应用计算机搜索重叠区并构建主序列。
优点：测序速度快，并且不需要遗传或物理图谱。
现代分子生物学名词解释朱玉贤
现代分子生物学名词解释朱玉贤ABC模型：即控制花形态发生的模型。
该模型把四轮花器官同时发生作为基本前提，强调花形态突变体产生不同花器官的生理位置变化。
该模型中正常花的四轮结构的形成是由三组基因A、B、C共同作用完成的，每一轮花器官特征的决定分别依赖于A、B、C三组基因中的一组或两组基因的正常表达oA组基因控制萼片、花瓣的发育，B组基因控制花瓣、雄蕊的发育，C组基因控制雄蕊、心皮的发育oA、C 组基因互相拮抗，抑制对方在自身所控制的区域中表达，如其中任何一组或更多的基因发生突变而丧失功能，花的形态就出现异常。
AP位点(APsite)：所有细胞中都带有不同类型、能识别受损核酸位点的糖苷水解酶，它能特异性切除受损核苷酸上的N-β糖苷键，在DNA链上形成去嘌呤或去嘧啶位点，统称为AP位点。
cDNA(complementaryDNA)：在体外以mRNA为模板，利用反转录酶和DNA聚合酶合成的一段双链DNA。
C值(Cvalue)：通常是指一种生物单倍体基因组DNA的总量，以每细胞内的皮克(pg)数表示。
C值反常现象（Cvaluedox）：也称C值谬误。
指C值往往与种系的进化复杂性不一致的现象，即基因组大小与遗传复杂性之间没有必然的联系，某些较低等的生物C值却很大，如一些两柄动物的C值甚至比哺乳动物还大。
Dane颗粒：HBV完整颗粒的直径为42nm，称为Dane颗粒，由外膜和核壳组成，有很强的感染性。
DNA（deoxyribonucleicacid）：脱氧核糖核酸，是世界上所有已知高等真核生物和绝大部分低等生物的遗传物质。
DNA的半保留复制（semi-conservativereplication）：DNA在复制过程中，每条链分别作为模板合成新链，产生互补的两条链。
这样新形成的两个DNA分子与原来DNA分子的碱基顺序完全一样。
因此，每个子代分子的一条链来自亲代DNA，另一条链则是新合成的，这种复制方式被称为DNA的半保留复制。
Genomics第5章
一个典型的RNA茎环结构
② 可以像搜索蛋白质编码基因那样，搜索与功 能RNA基因相关的调控序列。这些调控序列与 蛋白质编码基因的调控序列是不同的，除了存 在于功能RNA基因上游之外，还可能存在于功 能RNA基因内部。
③ 在紧凑的较小基因组中，注意力直接朝向对 蛋白质编码基因广泛搜寻之后还剩下的区域中 。这些空位置通常并不空，仔细检查会发现多 个功能RNA基因的存在。
多数外显子-内含子边界具有的序列并不是所 示的序列，因此通过序列分析定位边界是一件 碰运气的事。
(3)上游调控序列：可用来定位基因起始区。上 游调控序列是为了作为识别信号在参与基因表 达的DNA结合蛋白中发挥作用。
但是调控序列是变化的，因此，运用这些来定 位基因是有问题的。
这三种简单ORF扫描的衍生方法虽然有局限 性，但普遍适用们自己的特征，这些特 征可以用来帮助在基因组序列中发现它们。
（1）功能性RNA分子最重要的特征是能够折叠 成二级结构，如tRNA分子所具有的三叶草结构。
二级结构是通过分子内碱基配对形成的。为了 使分子内形成碱基配对，该分子中两部分的序列 必须是互补的。
这些特征提供了丰富的信息能够用来在基因组 序列中定位tRNA基因。
(4) 根据基因组的特征，另外的策略也可能适用 于单个生物体。
例如，脊椎动物基因组包含着许多基因上游都 有的CpG岛，这些序列大约有1kb，其中的GC 含量比整个基因组的平均含量要高。人类基因 中有40-50%的基因上游含有CpG岛。
3. 为功能性RNA定位基因
ORF扫描适用于蛋白质编码基因，但对于那 些功能性RNA基因，如rRNA和tRNA，它们不包 含ORF有一个能鉴别出所需 要的基因。
通过同源性搜索对未确定的外显子进行定位 ，以检测其功能。
genomics课件1
基因组学Genomics主要参考文献•基因组3 （Genomes 3): 〔英国〕布朗著（Brown T.A.），袁建刚等译，科学出版社，2009.•基因组学第2版：杨金水编著，高等教育出版社, 2007.•基因组研究手册：〔加拿大〕C.W. 森森主编，谢东等译,科学出版社，2009.•功能基因组学：徐子勤编著，科学出版社，2007.第一部分：基因组•基因组的结构（Genome Structure)•基因组的复制（Genome replication)•基因组的突变与修复（Genome mutation & repair）•基因组的表达（Genome expression）•基因组的克隆（Genome Cloning）•基因组的调控（Genome regulation)•基因组的重组（Genome recombination)遗传学与基因组学的里程碑•展望基因组学研究的未来，首先需要回顾我们经历过的不寻常的历程。
•从孟德尔遗传规律的发现（1866）和其在20世纪初被重新发现开始（1910）•DNA被确立是遗传的物质基础、DNA双螺旋结构的确定（1953）、遗传密码的阐明（1958）。
•DNA重组技术的发展（1973）。
•1977年sanger发明双脱氧dna测序方法及自动化程度日益提高的DNA化程度的建立。
•为1990年启动人类基因组计划（HGP）奠定了基因组学的基础（可见/nature/DNA50）。
•基因组序列这一指导生物发育和发挥功能的信息综合体，是当今生命科学革命的核心。
简单来讲，基因组学已经成为生物医学及植物学研究的核心和不可分割的学科。
基因组的来源•基因组（genome）来自德国汉堡大学H.威克勒教授（1920），用来表示真核生物染色体组或指生物的整套染色体所含有的全部DNA序列。
•基因组学（genomics) 系由T.罗德里克（T.Roderick) 1986 年首创，用来慨括涉及基因组作图、测序和整个基因组功能分析的遗传学学科分支。
基因组学11代谢组学课件
代谢组学的内容和特点
代谢组学的优点： 1）基因和蛋白表达的有效的微小变化会在代 谢物上得到放大，从而使检测更容易； 2）代谢组学的技术不需建立全基因组测序及 大量表达序列标签（EST）的数据库； 3）代谢物的种类要远小于基因和蛋白的数目， 每个生物体中代谢产物大约在103数量级，细 菌基因组中几千个基因； 4）因为代谢产物在各个生物体系中都是类似 的，所以代谢组学研究中采用的技术更通用；
基因组学11代谢组学课件
代谢组学的研究策略
代谢组学（Metabolomics）： 代谢组学分析揭示了研究的生物学系统中对限 定条件下的特定生物样品中所有代谢组分的全 面的定性和定量变化。外界环境的变化总是诱 导植物体产生交互式影响，有时这些影响会导 致一些与之不相关的代谢途径发生改变。为了 弄清所有的这些影响，代谢组学的分析是必不 可少的。在这个分析过程中，精密的分析方法 用来对一个样品种所有的化合物进行分析而不 需要对样品进行纯化。
基因组学11代谢组学课件
代谢组学的内容和特点
代谢组学的研究技术 核心技术是利用化学方法对不同状态下基
因表达的不同代谢产物进行比较
代谢物群矩阵clique-metabolite matrices 单一代谢物首先被鉴定出来，然后在不同的代谢物
组中寻找相关性； 这些既独立又相关的代谢物被用来鉴定代谢途径，
基因组学11代谢组学课件
代谢组学的技术平台
红外线光谱技术（IR）， 核磁共振技术（NMR）， 稀薄气液色谱技术（TLC）， 高效液相色谱技术（HPLC）， 高效毛细管电泳技术（HPCE）， 毛细管电泳与紫外线吸光率检测连用技术（CE/UV）， 毛细管电泳与激光诱导荧光检测连用技术（CE/LIF）， 毛细管电泳与质谱连用技术（CE/MS）， 气相色谱与质谱共用技术（GC/MS）， 液相色谱与质谱共用技术（LC/MS）， 液相色谱与质谱先后使用技术（LC/MS/MS）， 高效液相色谱与质谱和核磁共振技术功用（LC/NMR/MS）
宏基因组学2
Lecture 9: Genomics, proteomics and metagenomics in microbial ecologySources:Brock 10th edition, chapter 15Beja et al., bacterial rhodopsin: Evidence for a new type of pphototropy in the sea. Science 289:1902-1906.Beliaev, A.S. et al., 2002. Microarray transcription profiling of aShewanella oneidensis etrA mutant. Journal of Bacteriology184:4612-4616Rodriguz-Valera, F. 2004. Environmental genomics, the big picture?FEMS Microbiol. Lett. 231:153-158Schloss, P.D., and J. Handelsman. 2003 Biotechnological prospects frommetagenomics. Current Opinion in Biotechnology 14:303-310. Sequencing of a microbial genome:Genome annotation: Sequence ¥ “words” (i.e., coding regions, open reading frames [ORF])ORF is the sequence between astart codon and a stop codons if:100 codonscodon biasa Shine-Dalgarno sequenceis presentBlue L - tRNARed L - rRNAGreen ring – ORF’sOrange L - repeatSequencesRed bars - > 65% G+CYellow bars - < 65% G+CGenome analysis:Bioinformatics !!in silico analysesHomology searches – BlastX (proteins with > 50% sequence homology usually have thesame function)Relating putative genes to known functions of the organism e.g., Thermotoga maritimaA hyperthermophilic bacterium with a broad range of sugar utlilization capabilities. But .......approximately 40% of ORF’s in any genome have a function wedo not recognizeGenome expression studies – Functional genomicsExpression profiles and dynamics allude to functions Leading to experiments that address specific genes and systemsGene expression at the transcription levelPrinciple: Compare expression profile of all genes in the genome obtained under twodifferent conditions – DNA microarrays (DNA chips)under conditions 1 and 2 is labeleddifferentially with fluorescence dyesunder the RNA extract arehybridized to the same microarrayConditions:Growth conditions: Genes whose expression changes during growth on substrate X are most likely involved in a pathway that is essential for the utilization of this substrate. Effect of mutations: Expression of specific genes that is altered in a given mutant tells us that the function impaired in the mutant affects expression of these genesExample (Beliaev et al., 2002): Effect of a mutation in a gene that regulates growthunder anaerobic conditions in Shewanella oneidensis MR-1Gene expression at the translational level – proteomics (all the proteins present in the cell)Goal: Identify all the proteins in the cell and study when and under what environmental conditions they are expressedFirst step: Separation on a 2 dimension gel or by liquid chromatographySecond step: Identification and quantitation of the proteinsComparative studies: Label proteins differentially with isotopes of N and anaylze for relative levels of expressionAim: The ability to look at the expression patterns of whole genomes and proteoms will enable an understanding of how an organism integrates its various metabolic and regulatory systems to enable growth under a given set of conditions – System biologyEnvironmental metagenomics(Schloss and Handelsman, 2003)Definition: The culture-independent genomic analysis of microbial communities or the compound genome of the environmental microbiota.The challenge: Identify the clones that carry the genes for the functions we are interested in.Function-driven analysis:Advantages: Can find a “a needle in a haystack”Disadvantage: Depends on expression in a heterologoushostSequence-driven analysis:Advantage: Does not depend on gene expressionDisadvantage: What clones to sequence?What is it good for?Discovery – e.g., bacterial rhodopsin in marine bacteria (Baja et al., 2000) Discovery of new products – e.g., new antibioticsInformation on the biology of organisms in lineages for which very few representatives can be cultured。