GENES_X
blastx用法
blastx用法blastx是一种生物信息学工具，用于在蛋白质数据库中查找和比对核酸序列的编码蛋白质序列。
blastx是Blast（Basic Local Alignment Search Tool）软件家族的一员，它使用NCBI（National Center for Biotechnology Information）的非冗余蛋白质序列数据库（nr）或其他用户指定的数据库进行比对。
blastx的用法包括以下几个步骤：1.准备核酸序列文件：将需要查询的核酸序列保存在一个文本文件中，一般是FASTA格式。
2.选择合适的数据库：根据研究目的和问题的特点，选择适当的蛋白质数据库。
通常使用NCBI的nr数据库，它包含了全球各个物种已知的非冗余蛋白质序列信息。
3.运行blastx：在命令行或者图形化界面中输入blastx的命令或进行相应的设置，指定核酸序列文件和数据库，然后运行blastx。
4.解析输出结果：blastx会生成一个比对结果文件，其中包含了核酸序列与蛋白质数据库中蛋白质序列的比对信息。
可以通过查看比对分数、E-value、比对位置等指标来评估比对的质量和可靠性。
5.进一步分析和解释：基于比对结果，进一步分析和解释核酸序列与已知蛋白质序列的关系和功能。
可以通过比对的结果来预测未知序列的功能、推断物种间的亲缘关系等。
除了上述基本用法，blastx还可以通过设置不同的参数来定制化分析，例如调整比对的严格度、限定比对结果的最小阈值、特定的序列过滤等。
此外，使用blastx，还可以进行基因功能注释、找到同源蛋白、寻找变异位点等研究。
同时，blastx也可以被用于大规模的基因组、转录组以及六框架的翻译产品比对。
总的来说，blastx是一种强大的工具，被广泛应用于生物信息学领域，有助于研究人员更好地理解基因组和蛋白质的功能与演化关系。
GeneMapper ID-X使用
进行混合分析，分析察看结果
进行统计学计算
导出分析结果
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软件自动提示是否存在混合样本
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添加样本，正确分析样本
分析并编辑所有的OL，软件无法分析含有OL的样本
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建立混合分型的分析方法
输入混合分析的分析方法名称
输入混合分析的 分析方法名称
输入对该分析方法的 描述
根据实验室实际情况合理 设定杂合子的峰高比值 (PHR)
设定混合分析的阈值
保存混合分析方法
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导入群体数据
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导入已知分型
从之前导出已知分型的目标盘中导入已知样本的位点信息
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增加参照样本基因分型
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（可选择）导出有可能组成混合分型的已知基因分型
将“Table Setting”改为 “Known Sample Export”
Gene X ppt (Gene10 基因十)--Chapter01
1.2 DNA Is the Genetic Material of Bacteria and Viruses
• transforming principle – DNA that is taken up by a bacterium and whose expression then changes the properties of the recipient cell. • Phage infection showed that DNA is the genetic material of viruses. When the DNA and protein components of bacteriophages are labeled with different radioactive isotopes, only the DNA is transmitted to the progeny phages produced by infecting bacteria.
1.6 DNA Is a Double Helix
• The B-form of DNA is a double helix consisting of two polynucleotide chains that run antiparallel.
FIGURE 11: A polynucleotide chain
FIGURE 08: A polynucleotide chain
1.5 Supercoiling Affects the Structure of DNA
GENES_X
FIGURE 06: A rolling circle appears as a circular molecule with a linear tail by electron microscopy
Photo courtesy of Ross B. Inman, Institute of Molecular Virology, Bock Laboratory and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA.
FIGURE 04: Adenovirus terminal protein binds to the 5’ end of DNA and provides a C-OH end to prime synthesis of a new DNA strand
FIGURE 05: The rolling circle generates a multimeric single-stranded tail
FIGURE 17: A model for the Agrobacteriummediated genetic transformation
Reprinted from Curr. Opin. Biotechnol., vol. 17, T. Tzfira and V. Citovsky , Agrobacterium-mediated genetic transformation of plants..., pp. 147-154. Copyright 2006, with permission from Elsevier [/science/journal/09581669].
genes, and
The yeast mitochondrial transport proteins:new sequences and consensus residues,lack of direct relation between consensus residues and transmembrane helices,expression patterns of the transport protein genes,and protein^protein interactions with other proteins Roman Belenkiy a,Amanda Haefele a,Michael B.Eisen b,Hartmut Wohlrab a Y*a Boston Biomedical Research Institute and Department of Biological Chemistry and Molecular Pharmacology,Harvard Medical School,64Grove Street,Watertown,MA02472,USAb Lawrence Berkeley National Laboratories and Department of Molecular and Cellular Biology,University of California at Berkeley,Berkeley,CA,USAReceived2September1999;received in revised form7March2000;accepted13April2000AbstractMitochondrial transport proteins(MTP)typically are homodimeric with a30-kDa subunit with six transmembrane helices.The subunit possesses a sequence motif highly similar to Pro X Asp/Glu X X Lys/Arg X Arg within each of its three similar10-kDa segments.Four(YNL083W,YFR045W,YPR021C,YDR470C)of the35yeast(S.cerevisiae)MTP genes were resequenced since the masses of their proteins deviate significantly from the typical30kDa.We now find these four proteins to have545,285,902,and502residues,respectively.Together with only four other MTPs,the sequences of YPR021C and YDR470C show substitutions of some of the five residues that are absolutely conserved among the12MTPs with identified transport function and17other MTPs.We do now find these five consensus residues also in the new sequences of YNL083W and YFR045W.Additional analyses of the35yeast MTPs show that the location of transmembrane helix sequences do not correlate with the general consensus residues of the MTP family;protein segments connecting the six transmembrane helices and facing the intermembrane space are not uniformly short(about20residues)or long(about40 residues)when facing the matrix;most MTPs have at least one transmembrane helix for which the sum of the negative hydropathy values of all residues yields a very small negative value,suggesting a membrane location bordering polar faces of other transmembrane helices or a non-transmembrane location.The extra residues of the three large MTPs are hydrophilic and at the N-terminal.The200-residue N-terminal segment of YNL083W has four putative Ca2 -binding sites.The500-residue N-terminal segment of YPR021C shows sequence similarity to enzymes of nucleic acid metabolism.cDNA microarray data show that YNL083W is expressed solely during sporulation,while the expressions of YFR045W,YPR021C, and YDR470C are induced by various stress situations.These results also show that the35MTP genes are expressed under a rather diverse set of metabolic conditions that may help identify the function of the proteins.Interestingly,yeast two-hybrid screens,that will also be useful in identifying the function of MTPs,indicate that MIR1,AAC3,YOR100C,and YPR011C do interact with non-MTPs.ß2000Elsevier Science B.V.All rights reserved.Keywords:Mitochondrion;Transport;Protein;Carrier;Expression;Gene0005-2736/00/$^see front matterß2000Elsevier Science B.V.All rights reserved.PII:S0005-2736(00)00222-41.IntroductionMitochondria have to be able to transport various ions (organic and inorganic)across the inner mem-brane to sustain metabolic processes and to permit oxidative phosphorylation with its requirement for a proton gradient across the membrane to proceed.Membrane proteins that catalyze some of these transport functions with a high degree of substrate speci¢city have been identi¢ed.Their sequences and some of their substrate speci¢cities have been deter-mined.Those that have been identi¢ed have sequence motifs similar to Pro X Glu/Asp X X Lys X Arg [1]within each of three highly similar sequence segments (about 100residues each)within a protein of about 30kDa [2,3],and have 12transmembrane helices in their typical homodimeric structure [3].Searching the entire yeast (Saccharomyces cerevisiae )genome for genes of proteins with these primary characteristics,several investigators have identi¢ed a group of such open reading frames (ORF)[4^7].Among these,the largest group has 35such ORFs [6].We have now taken these 35ORFs,identi¢ed con-sensus residues within the sequences of their proteins and determined how their transmembrane helix se-quences relate to these consensus residues.We used published yeast DNA microarray results [8^11]to identify expression patterns of these 35genes and to identify other mitochondria-related yeast genes with similar expression patterns.Of these 35pro-teins,12have been shown to possess transport func-tion.These 12possess ¢ve absolutely conserved con-sensus residues.Seventeen other MTPs also have these ¢ve consensus residues.However six MTPs have substitutions in a subset of three of the ¢veabsolutely conserved residues.Our analysis of the results of two recent large-scale yeast two-hybrid screens [12]that will be helpful in identifying the function of MTPs and in characterizing their topol-ogy show that four MTPs interact with non-MTP proteins.2.Materials and methods2.1.Yeast genomic DNA preparationYeast (CG379)was grown in YPD medium and its DNA liberated by vortexing with glass beads.The DNA was separated/precipitated with phenol/chloro-form/isoamyl alcohol and 100%ethanol [13].The DNAse-free RNAse treatment step was dropped for higher ¢delity of subsequent PCR reactions.The ¢nal DNA preparation was quantitated spectro-photometrically.2.2.PCR,cloning,and sequencingPCR ampli¢cation was performed with yeast GENEPAIRS primers (Research Genetics).Subclon-ing of PCR products was carried out with the TOPO TA cloning kit (Invitrogen)for sequencing.Plasmids were puri¢ed with the Plasmid Midi Kit (Qiagen).The genes were sequenced with an ABI373A auto-mated DNA sequencer equipped with Stretch up-grade (Tufts DNA Sequencing Facility)puter programsFig.1was prepared with Microsoft Powerpoint.CFig.1.Negative hydropathy values at residue positions within six (A^F)partial sequences of the 35yeast MTPs.Each partial se-quence is indicated to harbor one transmembrane helix.Color codes refer to negative hydropathy [14](nine residue window)value ranges,e.g.white is a positive (+)hydropathy value,dark red indicates a negative hydropathy value from 32.35to 33.12.Consensus residues (single letter code)(Fig.2)are indicated at the top of the ¢gure.The three dashed lines (top of ¢gure)identify transmem-brane helix residue segments suggested by reviewers (top [6],middle [7],bottom [32])to apply uniformly to all MTPs and thus to cor-relate directly with the MTP consensus residues.Colored/white rectangles without black frame indicate likely residues of transmem-brane helices as identi¢ed with hydropathy plots of each individual s of the ORFs and names of some transport proteins are indicated.Sequences with names of the same color are most highly similar [6].Top 12sequences in the ¢gure indicate proteins with identi¢ed transport function.The top 29sequences possess ¢ve absolutely conserved residues (Fig.2).The last six sequences have one or two residue substitutions at three of these ¢ve conserved residues (Table 2).The N-terminal residue (single letter code)of each partial sequence is shown with the number indicating its position with respect to the N-terminal residue of the intact protein translated from each ORF.R.Belenkiy et al./Biochimica et Biophysica Acta 1467(2000)207^218208Hydropathy values were obtained with DNAStar (version3.02)and hydrophilicity plots[14]with a nine-residue window.2.4.MTP gene expressionExpression data was obtained from yeast cellcycle R.Belenkiy et al./Biochimica et Biophysica Acta1467(2000)207^218209experiments [8](/cellcycle/),sporulation experiments [9](/pbrown/sporulation/),diauxic shift experiments [10](/pbrown/explore/),and cluster analysis results [11](/clus-tering/).3.Results3.1.Sequences of YNL083W,YFR045W,YPR021C,YDR470C The typical sequence of an MTP subunit consists of about 300residues (30kDa).The sequences of four (YNL083W,YFR045W,YPR021C,YDR470C)yeast genes suggest proteins of size sig-Table 1Expression of MTP genes a Gene Chromosome Transport bResidues ORF Cell cycle Diauxic shift Sporulation MIR1X phosphate [15,16]311YJR077C ^U(7)c D(9,11.5)AAC1XIII ADP/ATP [17]309YMR056C ^U(6,7)U(2,5,7,9,11.5)AAC2II ADP/ATP [18]318YBL030C Y (M)d U(7)^AAC3II ADP/ATP [19]307YBR085W ^^^ARG11XV ornithine [20,21]292YOR130C Y (none)^^CAC XV carnitine [22]327YOR100C ^U(6,7)U(0.5,2,5,7,11.5)CTP1II tricarboxylate [23]299YBR291C ^D(7)^ACR1X dicarboxylate [24]322YJR095W ^U(3,6,7)U(0.5)D(5,7,9,11.5)OAC1XI oxaloacetate [4,25]324YKL120W Y (none)^U(0.5,2,5,7,9,11.5)DIC1XII dicarboxylate [26^28]298YLR348C ^^U(0.5)D(9,11.5)FLX1IX £avin [29]311YIL134W ^^D(0.5,5,7)nn XIII tricarboxylate [4]314YMR241W ^D(6,7)D(11.5)nn XVI 326YPR011C ^^D(0.5)nn VIII 357YHR002W ^^D(7,9,11.5)nn XIV 545YNL083W ^^U(7,9,11.5)nn VII 314YGR096W ^^^nn XV 307YOR222W ^^^nn XVI 310YPL134C ^U(7)D(7,9,11.5)YMC1XVI 307YPR058W ^D(6)U(0.5,2)YMC2II 329YBR104W ^^^MRS3X 314YJL133W ^^^MRS4XI 304YKR052C ^^D(5,7,9,11.5)PET8XIV 284YNL003C Y (G2)^^nn V 335YEL006W ^^U(11.5)nn IX 373YIL006W ^^D(5,7,9,11.5)RIM2II 377YBR192W Y (none)^^nn XVI 328YPR128C Y (M)^^nn V 300YER053C ^U(3,4,5,6,7)D(11.5)nn VI 285YFR045W ^^^nn XVI 902YPR021C ^^^nn XIII 368YMR166C ^??nn VII 366YGR257C ^^^nn IV 307YDL119C ^^^YHM1IV 300YDL198C Y (none)^^nnIV502YDR470C^^^a See Section 2for source of data.bDominant substrate transported by MTP.cIncreased expression (U)or decreased expression (D)at indicated sampling time points.dY means this gene shows increased expression in cell cycle phase M,G2,or phase cannot clearly be identi¢ed (none).R.Belenkiy et al./Biochimica et Biophysica Acta 1467(2000)207^218210ni¢cantly di¡erent from 300residues,i.e.178(YFR045W)to 902(YPR021C)residues.We there-fore resequenced these four genes.Our sequence of YFR045W (chromosome VI)shows a G insertion between 242181(G)and 242182(T)(aggGtac)and a silent mutation of C to G (242830)in Thr codons ACC to ACG (tacGtta).Both of these changes are not present in the GenBank sequence.Four inde-pendent sequencing runs yielded the same sequence.The resulting frameshift yields a 285-residue protein,clearly in line with the typical MTP (Table 1).Our YNL083W sequence yields a deletion of the G at position 472581(chromosome XIV)of the GenBank sequence (gggTgggC-tca,see also below for substitu-tions).Eight independent sequencing runs yielded this result.The result is a frameshift,which adds 153nucleotides or 51residues to the protein se-quence of 494to make it 545residues.In addition,we ¢nd that a T replaces G at 472576,C replaces the G at 472580,and A replaces G at 471764(aagAtga).Fig.1shows that YNL083W and YFR045W pos-sess hydropathy pro¢les not too di¡erent from most other MTP sequences except that partial sequence A of YFR045W lacks all of the potential transmem-brane helix residues,but does possess the consensus residues starting with Pro.Deleting the stop codon (TAA)located 29codons upstream from the N-ter-minal Met,yields a 332-residue protein with a hydro-phobic residue sequence of only 11residues,too short for a transmembrane helix A.ThehydrophobicFig.2.Consensus sequences of the six (A^F)partial sequences (Fig.1)of the 35MTPs.Red residues are the only residues identical at identical consensus locations among the 12MTPs with established transport function (top 12sequences in Fig.1).Bold black resi-dues are the same for at least 23MTPs;bold black double (two vertically aligned residues)are those where at least 23MTPs have one of the two residues.The number associated with the residue indicates the number of sequences of the largest group with the same residue (residue shown)at this location.Dashed lines indicate generalized transmembrane helix sequences as suggested in several re-views [6,7,32](see Fig.1).R.Belenkiy et al./Biochimica et Biophysica Acta 1467(2000)207^218211sequence segment of partial sequence F of the pro-tein (YFR045W)is shifted towards the C-terminal end.Neither of the original GenBank sequences of these two genes possess the ¢ve absolutely conserved residues of Fig.2.Both new sequences,however,do possess these ¢ve residues.The YNL083W protein has an N-terminal exten-sion of about 200residues as indicated in Fig.1,i.e.the N-terminal residue of partial sequence A is Asn222.This N-terminal extension is hydrophilic and harbors four putative Ca 2 binding sites (Fig.3).Ca 2 binding and tissue expression has been shown for similar proteins from rabbit small intestine [30]and human heart [31].Our resequencing of YPR021C (chromosome XVI)yielded a sequence identical to that in GenBank.Our YDR470C (chromosome IV)sequence had only one substitution at 1400863:GenBank's T is replaced with a C (tgtCcaa).This results in a replacement of a Glu (GAA)with a Gly (GGA)on the complemen-tary strand where the gene is located.3.2.Consensus residues and transmembrane helices Thirty-¢ve ORFs have been identi¢ed in the entire yeast genome [6].Since it has not been shown whether transmembrane helix sequences,established by hydropathy plots,do indeed correlate with con-sensus residues,we aligned the 35proteins with each other using the DNAStar program and optimized the alignments manually.Fig.1A^F shows the align-ments of the six partial sequences that have beensuggested to harbor sequences for transmembrane helices.At the top of the ¢gures we show the con-sensus residues that are presented in more detail in Fig.2.Dramatic di¡erences in hydrophobicity and thus location of hypothetical transmembrane helices within di¡erent MTPs are quite apparent (Fig.1A^F).We have placed the 12transport-identi¢ed pro-teins at the top,followed by the 17proteins that also possess the ¢ve consensus residues as indicated in Table 2and in Fig.2(bold red).The six MTPs at the bottom have substitutions at one or more of three of the ¢ve absolute consensus residue positions (see Table 2).We have quantitated the hydrophobic value of the potential transmembrane helices by summing the negative hydropathy values of the positions.These sums are shown in Table 3.It is clear that while most sums are similar,exceptions are clearly present.Most MTPs have at least one transmembrane helix sequence with a very small sum (bold numbers in Table 3).Among the MTPs,these small sums are not associated with only one particular region of the protein.None of the MTPs (Table 3)shows such a small sum for transmembrane helix A.The consensus sequence of Fig.2is presented in such a way that the bold black residues represent at least 23of the 35MTPs.The subscript indicates the number of MTPs with that residue at that location.Table 2The ¢ve absolutely conserved residues within the 12functional-ly established MTPs (top 12of Fig.1)Name A a A E F F Consensus b P26K31P26G2G9YPR021C P26K31P26S G9YMR166C S K31P26G2G9YGR257C P26R P26G2G9YDL119C P26K31P26N G9YDL198C P26S P26G2G9YDR470CP26RP26LG9The MTPs (bottom six in Fig.1)shown are the only ones with one or more of three of these ¢ve residues replaced (replace-ments are shown bold in single letter code).aLetters refer to partial sequences (Fig.2).bConsensus refers to the 12MTPs with established transport function.Only A,E,and F possess residues at locations abso-lutely conserved among these 12MTPs.Residue numbers refer to residue position with respect to the N-terminal residue in the sequences of Fig.2.Fig.3.Ca 2 -binding sites within the N-terminal of YNL083W.Roman numerals indicate the four sequences of the four sites.The residue number within the YNL083W sequence is indi-cated.x,y,z,-x,-y,-z are the calcium coordinating positions of the calcium binding loop [33].L at -z in IV is the only calcium coordinating ligand that does not seem to be similar to the mo-tifs of other such calcium binding sites.Cparv is carp parvalbu-min [34],TCalm is Tetrahymena calmodulin [35],RSTnC is rab-bit skeletal troponin C [36].R.Belenkiy et al./Biochimica et Biophysica Acta 1467(2000)207^218212Only those residues with the largest number of MTPs are shown.Thus a V4(21st position in partial se-quence B)indicates that at that location only four MTPs have a valine and that there is no group with more than four proteins and the same residue at that location.Such a location is least restrictive for type of residue requirement.On the other hand,P34(20th position in partial sequence A)indicates that34of the35proteins as aligned in Fig.1have a proline at this location.3.3.Intertransmembrane helix segmentsMuch controversy exists as to the role of the pro-tein segments that connect the transmembrane heli-ces and whether they face the extramembrane space or are embedded in the membrane.The original MTP model[3]that proposed six transmembrane helices for the MTP subunit,based on the ATP/ ADP translocase sequence[2],suggested long seg-ments connecting the matrix ends of transmembrane helices A and B,C and D,E and F[3].Those seg-ments connecting the intermembrane space ends of transmembrane helices B and C,D and E were sug-gested to be short[3].We have determined(Table4) the number of residues connecting the hypothetical transmembrane helices as suggested by hydropathy plots and mostly shown in Fig.1.Table4also shows the number of residues N-terminal to transmembrane helix A(Nt)and C-terminal to transmembrane helix F(Ct).Among the12proteins that have been shown to catalyze transport,only the CTP1,the YMR241W and the ADP/ATP translocases(AAC1,AAC2, AAC3)have intertransmembrane helix segment length distributions similar to those of the original model[3].Beyond this,several intertransmembrane helix segments are exceptionally short(AAC1,2,3)or exceptionally long(AAC3,YNL083W,YBR192W, YGR257C,YDR470C).3.4.Expression patterns of MTP genesThe new technology of DNA microarrays provides a unique opportunity to group genes according to their expression patterns.Genes with similar expres-sion patterns may be functionally related.In this manner,a new gene with unknown gene product function may be identi¢ed by correlating its expres-sion pattern with genes of a known metabolic path-way.Table1shows expression patterns of the35ORFs. The results from the cell cycle experiments[8]iden-tify AAC2with increased expression in the M-phase. This is also true for YPR128C,which,however, shows no change in expression level during the dia-Table3Sum of only negative hydropathy values[14](nine-residue win-dow)of residue positions of transmembrane helices as indicatedfrom hydropathy plots and Table4Name A a B C D E FMIR116.820.420.413.526.733.2AAC117.5 1.6b21.223.634.620.7AAC220.3 2.621.921.529.426.5AAC319.5 2.923.421.828.524.9ARG1123.219.335.414.818.026.7CAC21.524.320.112.332.917.8CTP117.122.828.4 6.126.429.0ACR117.226.425.68.014.97.1OAC131.49.534.211.024.825.8DIC114.820.723.812.222.518.9FLX121.918.624.020.018.835.2YMR241W21.419.922.9 4.88.416.2YPR011C23.513.520.017.413.421.6YHR002W17.114.324.719.710.327.8YNL083W24.410.015.726.830.821.2YGR096W20.6 6.924.820.319.217.9YOR222W24.0 6.824.3 2.514.025.4YPL134C25.512.224.913.318.522.8YPR058W17.121.014.912.931.723.3YBR104W18.428.116.618.926.415.7YJL133W19.316.18.619.323.48.4YKR052C18.715.414.914.326.49.3YNL003C25.621.419.27.018.615.7YEL006W28.117.316.928.215.722.9YIL006W30.221.216.527.814.515.1YBR192W25.912.515.410.411.619.3YPR128C26.019.927.58.434.818.3YER053C18.17.929.89.431.823.3YFR045W22.128.37.720.221.2YPR021C25.29.523.415.621.29.3YMR166C11.118.918.39.321.624.2YGR257C21.422.026.08.124.021.5YDL119C19.314.520.512.616.413.1YDL198C20.39.028.59.126.720.1YDR470C12.221.242.716.68.817.2a Letters refer to the six transmembrane helices associated inmost cases with the partial sequences of Fig.1.b Bold numbers refer to transmembrane helices with an excep-tionally small sum of negative hydropathy values.R.Belenkiy et al./Biochimica et Biophysica Acta1467(2000)207^218213uxic shift experiment during which AAC2does show a change.3.5.Cluster analysis of MTP gene expression patterns Eisen and coworkers [11]have developed an algo-rithm for identifying genes with similar expression patterns in several types of expression experiments.In Table 5,we have identi¢ed the MTP genes that have been cluster-analyzed [11]and we cite for each one of these genes other yeast mitochondria-related genes with similar expression patterns.We note here only that from among the three AAC genes,AAC2appears to be expressed similar to more mitochon-Table 4Number of residues within segments connecting transmembrane helices,derived from hydropathy plot,of the MTPs Name Nt a A^B b B^C C^D D^E E^F Ct Walker pro¢le c MIR117(T43)17(Q86)35(A138)32(A194)19(D236)17213AAC114(A31)45(N94)26(L139)38(Y198)8(S233)514+AAC223(A41)42(N104)27(L148)41(Y207)8(S242)3114+AAC312(A30)58(G105)15(D138)41(F200)7(S231)3012+ARG1110(F34)36(N92)15(L135)20(Y190)26(V237)3103CAC 37(V61)38(Y120)23(T162)18(R203)36(T262)3193CTP112(F33)35(K95)15(L137)35(K197)18(L235)420+ACR110(L31)40(I88)23(L139)23(A183)36(N232)44263OAC122(M50)21(L97)32(T154)37(Y212)20(I257)12183DIC120(A44)11(C79)27(N130)48(D201)12(D229)35143FLX114(T42)36(E100)27(I153)32(D205)19(L249)1883YMR241W 19(M48)25(E97)12(V138)37(E197)24(V240)4113+YPR011C 23(S54)31(A103)25(L150)49(Y213)24(D255)456+YHR002W 33(F61)37(Y116)23(L160)48(H229)40(E286)40103YNL083W 219(T245)58(S320)29(T370)37(A430)23(R479)3511+YGR096W 16(T39)43(Y97)17(D134)31(Y189)27(E234)4910+YOR222W 8(V35)12(K68)53(I144)13(K174)43(I239)34103YPL134C 10(V34)16(K70)55(L150)35(K209)12(K240)4393YPR058W 25(F46)37(N100)22(H143)36(A203)18(M247)1403YBR104W 35(F55)31(N109)35(Q165)34(G229)12(I267)3443YJL133W 33(A56)35(Y112)23(F151)27(Y204)17(Q248)450+YKR052C 24(A46)35(Y102)24(F141)40(S198)13(Q238)426+YNL003C 0(T27)24(Y71)29(E116)45(Y172)23(L218)3793YEL006W 38(V61)44(D123)19(V161)38(P217)28(H264)3813+YIL006W 74(V100)42(Y160)13(T192)45(Y257)23(T296)4515+YBR192W 52(L75)64(Y157)21(R202)34(L255)42(H309)5103YPR128C 0(T29)44(T96)29(A149)33(F202)18(Q251)2730+YER053C 19(L46)30(Q86)19(I133)33(S196)14(I239)2217+YFR045W (M56)30(C57)20(N98)61(Y181)17(D216)4243YPR021C 529(F553)34(N608)17(Q653)29(Y704)28(L755)3589+YMR166C 52(L74)40(Y132)20(V171)41(Y234)24(D278)4911+YGR257C 18(I38)84(F140)21(K183)37(Y244)24(F289)3814+YDL119C 13(K35)32(S86)36(V143)28(Y193)35(D245)3283YDL198C 11(D32)36(K82)42(L142)44(K203)12(T236)29103YDR470C127(T150)105(P279)14(F323)37(Q388)14(E419)5611+Value in parentheses is the ¢rst residue (single letter amino acid code)of that segment with its position counted from the N-terminal of the protein.aNt is the number of residues between N-terminal of protein and N-terminal of transmembrane helix A.Ct is number of residues be-tween C-terminal of protein and C-terminal of transmembrane helix F.bIndicates protein segment connecting transmembrane helices A and B.c+indicates that this MTP pro¢le corresponds to the classical model with long A-B,C-D,and E-F segments and short B-C and D-E segments [3].R.Belenkiy et al./Biochimica et Biophysica Acta 1467(2000)207^218214drial genes than the other MTPs.It should be noted that AAC2is in fact the major AAC in aerobically grown yeast [37].Dramatic di¡erences are apparent among the three ADP/ATP translocase genes since they are located in di¡erent sectors of the cluster analysis ¢gure [11].Table 5Examples of mitochondria-related yeast genes with expression patterns (cluster analysis)similar to those of a select number of MTP genes a Name Cluster sector c Mitochondria-related yeast genes with similar expression patterns AAC15ribonuclease P protein component (mitochondrial)(YML091C);ATP10protein (essential for assembly of F 1^F 0complex)(YLR393W)YHM1/SHM18asparaginyl-tRNA synthetase (mitochondrial)(YCR024C)AAC3(expression subset of YHM1/SHM1)b8dihydrolipoamide dehydrogenase (mitochondrial)(YFL018C);pyruvate dehydrogenase E1component L -subunit (mitochondrial)(YBR221C);pyruvate dehydrogenase E1component K -subunit (mitochondrial)(YER178W)ACR110cytochrome c oxidase polypeptide VA (YNL052W)DIC110YME1protein (causes increased escape of DNA from mitochondria)(YPR024W)FLX1(expression subset of DIC1)10ABC1protein (essential for electron transfer in bc 1complex)(mitochondrial)(YGL119W)MRS413MIR1(expression subset of MRS4)13CDP-diacylglycerol-serine O -phosphatidyltransferase (microsomal/outer mitochondrial membrane)(YER026C);cytochrome c oxidase biogenesis protein OXA1(YER154W);D -lactate dehydrogenase (mitochondrial)(YDL174C)PET8(expression subset of ARG11)16glutamyl-tRNA synthetase (mitochondrial)(YOL033W)ARG1116CTP117YMC1(expression subset of CTP1)18MRS320mitochondrial import inner membrane translocase subunit TIM23(YNR017W)YMC228mitochondrial 40S ribosomal protein MRP4(YHL004W)RIM231mitochondrial precursor proteins import receptor (TOM70)(YNL121C);mitochondrial peptide chain release factor 1(YGL143C);CBP4protein (assembly/stability of ubiquinol^cytochrome c reductase)(YGR174C);ATP11protein (assembly of mitochondrial F 1^F 0complex)(YNL315C);cytochrome c oxidase assembly protein COX14(YML129C)AAC235outer mitochondrial membrane protein porin 1(VDAC1)(YNL055C);succinate dehydrogenase (ubiquinone)£avoprotein subunit (YKL148C);rotenone-insensitive NADH-ubiquinone oxidoreductase (YML120C);ubiquinol-cytochrome c reductase complex 14-kDa protein (YDR529C);succinate dehydrogenase (ubiquinone)iron^sulfur protein (YLL041C);cytochrome c 1(YOR065W);citrate synthase (mitochondrial)(YNR001C)aMTP genes are arranged sequentially as they appear in Fig.2(/clustering/)of the cluster analysis [11]to facil-itate comparisons of expression patterns.Detailed information on the expressed genes can be found at http://www.expasy.ch/cgi-bin/sprot-search-de.Cluster analysis [11]is based on diauxic shift [10],sporulation [9],and cell cycle [8]experiments.Analysis is available for only 16of the 35MTP genes.bExpression pattern of AAC3is a subset of expression pattern associated with YHM1/SHM1[11].cCluster analysis (Fig.2)(/clustering/)was divided into 35sequential sectors to yield additional relational ex-pressions of the genes.R.Belenkiy et al./Biochimica et Biophysica Acta 1467(2000)207^2182153.6.Protein^protein interactionsIt is generally assumed that the MTP proteins pos-sess no protein segments that extend signi¢cantly out of the membrane region.These assumptions are based on hydrodynamic studies [38,39]and the be-havior of these proteins in column chromatography [40].Exceptions of course are YNL083W,YPR021C,and YDR470C with their large hydrophilic N-termi-nal and/or C-terminal domains.Thus it is not ex-pected that the MTPs interact with non-MTPs.Yeast two-hybrid analyses suggest that four MTPs may interact with non-MTPs [12].Table 6lists the four MTPs and the proteins that have been suggested to interact with them.We have added the expression patterns of the genes of these new proteins to permit a comparison with those of the MTPs (Tables 1and 5)to which they are suggested to bind.4.DiscussionFig.1summarizes the ¢rst detailed analysis of the individual MTPs with respect to their potential trans-membrane helices.Among the 12functionally iden-ti¢ed transport proteins,the Pro of the consensus sequence of the partial sequences A,C,and E is at the C-terminal end of the hydrophobic transmem-brane helix region.DIC1has this hydrophobic re-gion in C shifted dramatically towards the N-termi-nal.YMR241W has very little hydrophobicity in E compared to the other MTPs.ACR1has very much hydrophobicity in B and so do CAC and YMR241W.The hydrophobic sequence associated with B of YOR222W and YPL134W have been shifted completely out of the partial sequence B re-gion (see Table 3).However,as indicated in Table 3,the hydrophobicity of these shifted sequences is still small.Results of this analysis are di¡erently pre-sented in Table 3.All of the 35proteins have a nor-mal A hydrophobic region.Among absolute consensus residues,K31(partial sequence A)(Table 2)is critical for the phosphate transport protein (PTP or MIR1)function [41].The two Pro and two Gly residues have not yet been replaced and thus the critical nature of these loca-tions has not yet been established.The locations of G2and G9in partial sequence F (Table 2)are such that they are on the same side of a transmembrane helix cylinder and similar to the collagen triple helixTable 6Non-MTP interacting with MTP a MTPInteracting protein NameORFFunctionGene expression b Cell cycleDiauxic shift Sporulation Clustering sector c MIR1UBC6(physical)YER100W ubiquitin conjugating enzyme,ATPrequired,selective degradation of misfolded membrane proteins^^U(7,9)3AAC3SAC6(genetic)YDR129C ¢mbrin homolog,development andmaintenance of cell polarity^U(6)D(2,5,7,9,11.5)12AAC3CCT4(genetic)YDL143W cytoplasmic chaperonin subunit,ATPrequired,mitotic spindle formation,folding actin,tubulin^D(7)^27CAC RSC1(physical)YGR056W member of remodel structure ofchromatin complex,DNA-dependent ATPase activity^D(7)^11YPR011C RAD51(physical)YER095W recombination and repair of DNAdamage caused by X-rays,RecA homologY (G1)^U(0.5,2,5,7,9,11.5)5aData based on results obtained from yeast two-hybrid analyses [12].bRefers to data as cited in Table 1.cRefers to sectors as de¢ned in Table 5.R.Belenkiy et al./Biochimica et Biophysica Acta 1467(2000)207^218216。
cufflinks输入输出文件分析
sort –k 3,3 –k 4,4n hits.sam > hits.sam.sortd
7. FPKMx8.01651样品x的基因FPKM
8. FPKMy 8.3514321样品y的基因FPKM
9.log2(FPKMy/FPKMx)0.06531fold
10.测试统计0.8665465寻找计算FPKM显著性差异
11.pvalue 0.389292
12. qvalue 0.985216FDR矫正p值
Isoforms.fpkm_tracking转录本FPKMs
Genes.fpkm_tracking Gene FPKMs，转录本每个基因的FPKM
cds.fpkm_tracking编码序列FPKMs.p_id,独立于tss_id
Tss_groups.fpkm_tracking初级转录本的FPKMs
Count tracking files
isoforms.count_tracking转录本计数
genes.count_tracking基因计数
cds.counቤተ መጻሕፍቲ ባይዱ_tracking编码序列计数
tss_groups.count_tracking初级转录本计数
Read group tracking files（读取组跟踪文件）
计算每个转录本，初级转录本每个重复基因的表达和片段的计数结果输出配一个重复文件。
Column编号column名字样品名描述
Evolution_of_p53_pathway-related_genes_provides_in
Evolution of p53 pathway-related genes provides insights into anticancer mechanisms of natural longevity in cetaceansDEAR EDITOR,Despite the generally increased cancer risk in large, long-lived organisms, cetaceans, among the largest and longest-living mammals, appear to possess a counteracting mechanism.Nevertheless, the genetic basis underlying this mechanism remains poorly understood. The p53 pathway serves as an ideal target for studying the mechanisms behind cancer resistance, as most cancer types have evolved strategies to circumvent its suppressive functions. Here, comparative genetic analysis of 73 genes involved in the p53 pathway in cetaceans (Supplementary Table S1) was undertaken to explore the potential anticancer mechanisms behind natural longevity. Results showed that long-lived species contained three positively selected genes (APAF1, CASP8, and TP73)and three duplicated genes (IGFBP3, PERP , and CASP3)related to apoptosis regulation. Additionally, the evolutionary rates of three genes associated with angiogenesis (SERPINE1, CD82, and TSC2) showed a significant relationship with longevity quotient (LQ) and maximum lifespan (MLS), suggesting angiogenesis inhibition as another potential strategy protecting cetaceans from cancer.Interestingly, several positively selected tumor suppressor genes with high copy numbers were correlated with body size in the large-bodied and long-lived cetacean lineages,corroborating Peto’s paradox, which posits no link between cancer incidence and body size or longevity across species. In conclusion, we identified several candidate genes that may confer cancer resistance in cetaceans, providing a new avenue for further research into the mechanisms of lifespan extension.Mammalian lifespans and body masses (BM) exhibit considerable variability, with the shortest- and longest-living mammals differing by more than 100-fold and the smallest and largest mammals differing by more than 100-million-fold (Tacutu et al., 2018). The largest extant mammal, the blue whale (Balaenoptera musculus ), has an average adult weight of 136 000 kg and MLS of 110 years, while the longest-lived mammal, the bowhead whale (Balaena mysticetus ), has an average weight of over 100 000 kg and an MLS of 211 years.Typically, large and long-lived organisms face elevated cancer risk due to increased cell divisions, which increases the likelihood of DNA damage and potential cellular transformation to malignancy. Nonetheless, large whales, possessingapproximately 1 000 times more cells than humans,demonstrate an unexpectedly low cancer risk, despite their extended lifespans (Nagy et al., 2007). These observations align with Peto’s paradox, suggesting that these cetaceans have evolved an effective mechanism for suppressing cancer (Peto et al., 1975). The p53 pathway, vital for tumor suppression and lifespan extension, acts as a transcription factor to prevent tumor formation and development by selectively regulating target genes to induce cell cycle arrest,promote cell apoptosis or senescence, and accelerate DNA repair (Cha & Yim, 2013). Thus, studying the p53 pathway is a promising approach for uncovering the mechanisms by which large and long-lived species inhibit cancer.Based on MLS and BM records of non-flying eutherian mammals from the AnAge online dataset (Supplementary Table S2), a new allometric equation was derived:The LQ of all cetacean species was calculated using the allometric equation:Species with an LQ or MLS greater than 0.5 standard deviations (SD ) from the mean of 65 cetaceans were classified as long-lived. This determination was made after computing sequential thresholds ranging from 0 to 1.0 SD from the cetacean mean, with species designated as long-lived consistently falling within the 0.4 to 0.8 range (Supplementary Figure S1). The mean LQ value for the 65cetaceans was 0.97 with a 0.5 SD of 0.17 (LQ=0.97±0.17;Supplementary Table S3). Six cetacean species, including bowhead whales, long-finned pilot whales (Globicephala melas ), Pacific white-sided dolphins (Lagenorhynchus obliquidens ), killer whales (Orcinus orca ), bottlenose dolphins (Tursiops truncatus ), and Indo-Pacific bottlenose dolphins (T.aduncus ) were classified as long-lived (LQ>1.14) and five species were classified as short-lived (LQ<0.80), with the remaining intermediate species (0.8<LQ<1.14) serving as controls (Figure 1A). In terms of MLS, the mean value across all cetaceans was 47.90±15.67. Five long-lived species,including blue whales, bowhead whales, humpback whales (Megaptera novaeangliae ), killer whales, and sperm whalesReceived: 09 April 2023; Accepted: 11 September 2023; Online: 11September 2023Foundation items: This work was supported by the National Key Program of Research and Development, Ministry of Science and Technology of China (2022YFF1301600), National Natural Science Foundation of China (32070409, 32270453 to S.X.X.), Priority Academic Program Development of Jiangsu Higher Education Institutions to G.Y. and S.X.X., and Qing Lan Project of Jiangsu Province to S.X.X.This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium,provided the original work is properly cited.Copyright ©2023 Editorial Office of Zoological Research, Kunming Institute of Zoology, Chinese Academy of SciencesLiu et al. Zool. Res. 2023, 44(5): 947−949https:///10.24272/j.issn.2095-8137.2023.058(Physeter catodon) were identified with an MLS>63.57 and four short-lived species were identified with an MLS<32.23. Ancestral reconstructions based on MLS and LQ were performed to classify long-lived lineages in ancestral nodes (Supplementary Figure S2). Subsequent analyses were then performed on cetacean species identified as long-lived based on both standards (LQ>1.14, MLS>63.57).In this study, 23 genes exhibited copy number gains in at least one cetacean lineage (Figure 1B; Supplementary Table S4, S5). Among these, four genes (BCL2L1 in long-finned pilot whales, IGFBP3 and STEAP3 in Indo-Pacific bottlenose dolphins, and PERP in bottlenose dolphins) contained two copies unique to the long-lived cetacean lineages (LQ>1.14), whereas only one copy was identified in the other cetacean lineages. In addition, the long-lived sperm whale contained three copies of CCNB2 and two copies of MDM4, while only one copy of each was found in the other cetacean lineages. Results also showed CASP3 and CCNG1 duplication in all large, long-lived cetacean species (MLS>63.57), except for the common minke whale (Balaenoptera acutorostrata). Ancestral state reconstructions estimated that the last common ancestor of baleen whales lived to over 110 years of age (Supplementary Figure S2), suggesting that increased copy numbers of both genes in common minke whales was the same as that of other baleen whales classified as long-lived based on MLS. In contrast, only one RCHY1 copy was identified in the five large, long-lived species, while two copies were found in the other cetacean species. Expanded analyses of 17 non-cetacean mammals indicated higher CASP3 and PERP copies in notable cancer-fighting species, including primates and naked mole-rats (Gorbunova et al., 2014). Neither genome assembly length nor scaffold N50 number influenced the estimated gene copy number (Supplementary Figure S3).A total of 46 “one-to-one” orthologous genes were identified among the 73 genes involved in the p53 pathway (Supplementary Table S6). To detect signatures of episodic selection in genes occurring in long-lived cetaceans, four different methods were used, including the free-ratio and branch-site models from PAML v4.9 and aBSREL and BUSTED from Datamonkey v2.0. The likelihood ratio test (LRT) indicated that the free-ratio model, which assumes an independent ω for each branch, provided a superior fit to the data compared to the one-ratio model for the APAF1, CASP8, and AIFM2 genes (P<0.05, Figure 1A; Supplementary Table S7). An ω value greater than one was observed exclusively in specific branches of APAF1 and CASP8, including the last common ancestor (LCA) of the humpback whale and the terminal branch for the Indo-Pacific bottlenose dolphin for APAF1, as well as the LCA of delphinids and the branch leading to the Pacific white-sided dolphin for CASP8. The branch-site model from CODEML, designed to detect pronounced positive selection on a limited number of sites amidst predominant purifying selection, yielded consistent results. Evidence of positive selection was observed in the two long-lived branches leading to the sperm whale for TP73 and the long-finned pilot whale for AIFM2 (Figure 1A; Supplementary Table S7). Based on the BEB approach, twoFigure 1 Evidence of p53 pathway-related gene evolution in cetaceansA: Long-lived species identified based on LQ and MLS are marked in green and red, respectively. Short-lived species and control group are marked in purple and gray, respectively. Significant positive selections identified by free-ratio model, branch-site model, and aBSREL are indicated by a circle, pentagram, and triangle, respectively. Photo credit: NOAA Fisheries. B: Copy number variation in p53 pathway-related genes in cetaceans. Colors correspond to number of copies, with red indicating increasing copy number. Red bars represent long-lived species. C: Regression analyses between root-to-tip (ω) and three longevity traits (MLS, BM, and LQ).948 positively selected sites identified in both genes (TP73: 506; AIFM2: 459) exhibited radical changes in at least one property. The alternative branch-site model aBSREL in Datamonkey v2.0 appeared to be markedly more sensitive in detecting episodic selection than the branch-site methods in PAML v4.9. After multiple testing correction, TP73 displayed positive selection in the large, long-lived humpback whale (Supplementary Table S8). The BUSTED program, which may be particularly effective at testing for selection limited to foreground branches, further revealed positive selection in TP73 within the long-lived cetaceans (P<0.05, Supplementary Table S9). Employing these four methods of selection, three positively selected genes (APAF1, CASP8, and TP73) emerged as unique to the long-lived cetacean species. Collectively, all three positively selected genes (APAF1, CASP8, and TP73) and most genes with multiple copy numbers (IGFBP3, PERP, and CASP3) play roles in apoptosis regulation in the long-lived cetacean species (Supplementary Figure S4). This suggests that these long-lived lineages may have evolved apoptosis mechanisms to prevent cancer. Phylogenetic generalized least squares (PGLS) regression was performed between the evolutionary rate of each orthologous gene (represented by root-to-tip ω) and the three lifespan-associated traits (MLS, BM, and LQ). Results showed that the evolutionary rates of two angiogenesis-inhibiting genes (SERPINE1: R2=0.343, P=0.010; and CD82: R2=0.392, P=0.004) were significantly correlated with LQ (Figure 1C). SERPINE1, which encodes endothelial plasminogen activator inhibitor-1 (PAI1), plays an important role in inhibiting vascular endothelial growth factor (VEGF)-induced angiogenesis in mice (Wu et al., 2015). The tumor suppressor gene TSC2 (R2=0.364, P=0.008) was significantly positively associated with MLS in the cetaceans. TSC2 is implicated in the regulation of angiogenesis. Notably, absence of this gene results in elevated levels of hypoxia-induced factor 1α (HIF-1α) and VEGF, and the subsequent activation of the HIF-1α/VEGF pathway, which mediates hypoxia-induced angiogenesis (Brugarolas et al., 2003). In addition, research has shown that TSC2 is negatively regulated by mTOR signaling, with genetic inhibition of TOR activity leading to a two-fold extension in lifespan in Caenorhabditis elegans (Brugarolas et al., 2003; Vellai et al., 2003). Furthermore, a positive correlation was observed between the TP73 evolution rate and BM (R2=0.226, P=0.031). Angiogenesis plays a crucial role in cancer development, facilitating the delivery of oxygen, nutrients, and growth factors, and promoting tumor metastasis to distant organs (Al-Ostoot et al., 2021). Thus, inhibition of angiogenesis may represent another anticancer mechanism in cetaceans.Peto’s paradox states that large-bodied, long-lived species do not exhibit a greater lifetime risk of cancer compared to small, short-lived species (Peto et al., 1975). For instance, despite the 100-fold difference in cell number between African elephants and humans, the former does not show a higher incidence of cancer compared to the latter (Abegglen et al., 2015). A similar observation has also been observed in large-bodied, long-lived cetaceans (Nagy et al., 2007). Our research findings provide strong evidence in support of Peto’s paradox. Notably, a series of positively selected genes and tumor suppressor genes with copy number variations were identified in the large, long-lived species. Moreover, a significant positive relationship between gene evolution and body size was identified for the tumor suppressor gene TP73,suggesting that cetaceans evolved mechanisms to counteract the risk of cancer caused by the accumulation of cellular mutations. However, further laboratory experiments are needed to verify this.SUPPLEMENTARY DATASupplementary data to this article can be found online.COMPETING INTERESTSThe authors declare that they have no competing interests.AUTHORS’ CONTRIBUTIONSS.X.X. designed the study. X.L. was responsible for the data collection and analysis. S.X.X. and X.L. drafted the manuscript. S.X.X. revised the manuscript. F.Y., Y.L., X.H., and L.X.S. participated in the data collection. Z.P.Y., W.H.R., and G.Y. helped edit the manuscript. All authors read and approved the final version of the manuscript.ACKNOWLEDGMENTSWe thank members of the Jiangsu Key Laboratory for Biodiversity and Biotechnology, Nanjing Normal University, for their contributions to this paper. We thank Mr. Tian-Zhen Wu and Mr. Xu Zhou for their helpful suggestions. We are particularly grateful to Dr. Ran Tian and Dr. Wei-Jian Guo for their technical support.Xing Liu1, Fei Yang1, Yi Li1, Zhen-Peng Yu1, Xin Huang1, Lin-Xia Sun1, Wen-Hua Ren1, Guang Yang1, Shi-Xia Xu1,*1 Jiangsu Key Laboratory for Biodiversity and Biotechnology,College of Life Sciences, Nanjing Normal University, Nanjing,Jiangsu 210023, China*Corresponding author, E-mail: *****************.cnREFERENCESAbegglen LM, Caulin AF, Chan A, et al. 2015. Potential mechanisms for cancer resistance in elephants and comparative cellular response to DNA damage in humans. JAMA, 314(17): 1850−1860.Al-Ostoot FH, Salah S, Khamees HA, et al. 2021. Tumor angiogenesis: Current challenges and therapeutic opportunities. Cancer Treatment and Research Communications, 28: 100422.Brugarolas JB, Vazquez F, Reddy A, et al. 2003. TSC2 regulates VEGF through mTOR-dependent and-independent pathways. Cancer Cell, 4(2): 147−158.Cha HJ, Yim H. 2013. The accumulation of DNA repair defects is the molecular origin of carcinogenesis. Tumor Biology, 34(6): 3293−3302. Gorbunova V, Seluanov A, Zhang ZD, et al. 2014. Comparative genetics of longevity and cancer: insights from long-lived rodents. Nature Reviews Genetics, 15(8): 531−540.Nagy JD, Victor EM, Cropper JH. 2007. Why don't all whales have cancer?A novel hypothesis resolving Peto's paradox. Integrative and Comparative Biology, 47(2): 317−328.Peto R, Roe FJ, Lee PN, et al. 1975. Cancer and ageing in mice and men. British Journal of Cancer, 32(4): 411−426.Tacutu R, Thornton D, Johnson E, et al. 2018. Human ageing genomic resources: new and updated databases. Nucleic Acids Research, 46(D1): D1083−D1090.Vellai T, Takacs-Vellai K, Zhang Y, et al. 2003. Influence of TOR kinase on lifespan in C. elegans. Nature, 426(6967): 620.Wu JB, Strawn TL, Luo M, et al. 2015. Plasminogen activator inhibitor-1 inhibits angiogenic signaling by uncoupling vascular endothelial growth factor receptor-2-αVβ3 integrin cross talk. Arteriosclerosis, Thrombosis, and Vascular Biology, 35(1): 111−120.Zoological Research 44(5): 947−949, 2023 949。
What is Genetics 什么是遗传学 英语文章
What is Genetics?Genetics is the study of heredity. Heredity is a biological process whereby a parent passes certain genes onto their children or offspring.Every child inherits genes from both of their biological parents and these genes, in turn, express specific traits. Some of these traits may be physical for example hair and eye color etc.On the other hand, some genes may also carry the risk of certain diseases and disorders that may be passed on from parents to their offspring.Genes in the cellThe genetic information lies within the cell nucleus of each living cell in the body. The information can be considered to be retained in a book for example. Part of this book with the genetic information comes from the father while the other part comes from the mother.ChromosomesThe genes lie within the chromosomes. Humans have 23 pairs of these small thread-like structures in the nucleus of their cells. 23 or half of the total 46 comes from the mother while the other 23 comes from the father.The chromosomes contain genes just like pages of a book. Some chromosomes may carry thousands of important genes while some may carry only a few.The chromosomes, and therefore the genes, are made up of the chemical substance called DNA (DeoxyriboNucleic Acid). The chromosomes are very long thin strands of DNA, coiled up tightly.At one point along their length, each chromosome has a constriction, called the centromere. The centromere divides the chromosomes into two ‘arms’: a long arm and a short arm.Chromosomes are numbered from 1 to 22 and these are common for both sexes and called autosomes. There arealso two chromosomes that have been given the letters X and Y and termed sex chromosomes. The X chromosome is much larger than the Y chromosome.Chemical basesThe genes are further made up of unique codes of chemical bases comprising of A, T, C and G (Adenine, Thymine, Cytosine, and Guanine). These chemical bases make up combinations with permutations and combinations. These are akin to the words on a page.These chemical bases are part of the DNA. The words when strung together act as the blueprints that tell the cells of the body when and how to grow, mature and perform various functions. With age, the genes may be affected and may develop faults and damages due to environmental and endogenous toxins.Males and femalesWomen have 46 chromosomes (44 autosomes plus two copies of the X chromosome) in their body cells. They have half of this or 22 autosomes plus an X chromosomein their egg cells.Men have 46 chromosomes (44 autosomes plus an X and a Y chromosome) in their body cells and have half of these 22 autosomes plus an X or Y chromosome in their sperm cells.When the egg joins with the sperm, the resultant baby has 46 chromosomes (with either an XX in a female baby or XY in a male baby).Genes and geneticsEach gene is a piece of genetic information. All the DNA in the cell makes up for the human genome. There are about 20,000 genes located on one of the 23 chromosome pairs found in the nucleus.To date, about 12,800 genes have been mapped to specific locations (loci) on each of the chromosomes. This database was begun as part of the Human Genome Project. The project was officially completed in April 2003 but the exact number of genes in the humangenome is still unknown.。
Gene X ppt(Gene10 基因十)--Chapter07
7.2 Unequal Crossing-over Rearranges Gene Clusters
• Hb anti-Lepore – A fusion gene produced by unequal crossing-over that has the N-terminal part of β globin and the C-terminal part of δ globin.
7.1 Introduction
• satellite DNA – DNA that consists of many tandem repeats (identical or related) of a short basic repeating unit.
7.1 Introduction
• minisatellite – DNAs consisting of tandemly repeated copies of a short repeating sequence, with more repeat copies than a microsatellite but fewer than a satellite.
• Hb Kenya – A fusion gene produced by unequal crossing-over between the Aγ- and β-globin genes.
7.3 Genes for rRNA Form Tandem Repeats Including an Invariant Transcription Unit
7.1 Introduction
• pseudogenes – Inactive but stable components of the genome derived by mutation of an ancestral active gene.
Gene X ppt(Gene10 基因十)--Chapter_OK
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4.1 Introduction
• intron – A segment of DNA that is transcribed, but later removed from within the transcript by splicing together the sequences (exons) on either side of it.
FIGURE 10: Exons are typically 10s Show a Wide Distribution of Sizes
• Introns are short in unicellular/oligocellular eukaryotes, but can be many kb in multicellular eukaryotes.
• The rules relate to genomic characteristics, or “pressures,” that constitute the genome phenotype.
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4.4 Organization of Interrupted Genes May Be Conserved
in multicellular eukaryotes.
FIGURE 08: Interrupted genes predominate in higher eukaryotes
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4.7 Genes Show a Wide Distribution of Sizes
• Exons are usually short, typically coding for <100 amino acids.
基因及基因组结构
Genome sizes in nucleotide pairs (base-pairs)
plasmids viruses bacteria fungi plants algae insects mollusks bony fish
The size of the human genome is ~ 3 X 109 bp; almost all of its complexity is in single-copy DNA.
（三）基因分类
第一类是编码蛋白质的基因，它具有转录和翻 译功能，包括编码酶和结构蛋白的结构基因以 及编码阻遏蛋白的调节基因
第二类是只有转录功能而没有翻译功能的基因， 包括tRNA基因和rRNA基因 第三类是不转录的基因，它对基因表达起调节 控制作用，包括启动基因和操纵基因
二、基因组（genome）
5’…GCTGGTGGAAAATGAGGAAATTCAAT…3’ DNA序列 Leu Val Glu Asn Glu Glu Ile Gln K蛋白 Ala Gly Gly Lys Ter A蛋白 FMetArg Lys Phe Asn C蛋白
噬菌体G4一段DNA序列内A、C、K基因三重重叠
基因读框相同，只是起始部位不同
第一节 病毒基因组的结构
（一）病毒的基本结构
外壳蛋白： 识别、侵袭特定的宿主细 胞，并保护基因组不被 核酸酶破坏； DNA（RNA）：编码结构蛋白和少量 调控蛋白。 不能独立复制，必需进入宿主细胞，借助 细胞内一些酶类和细胞器才能得以复制。
（二）病毒基因组的结构特点：
1.基因组较小，大小差异较大； CAV DNA 2.3kb，编码3种蛋白质 乙肝病毒RNA 3kb，编码4种蛋白质 痘病毒DNA 300kb，编码几百种蛋白
lewin基因xii注解
lewin基因xii注解
Lewin's GENES XII是一本广受欢迎的遗传学教科书，它涵盖了遗传学领域的许多重要主题。
在这本书中，基因XII的注解可能涉及到许多不同的内容，以下是可能包括的一些注解内容：
1. 基因结构和功能，注解可能涉及基因的结构和功能，包括基因组中的编码和非编码区域，基因在细胞中的表达和调控方式等内容。
2. 分子遗传学，可能包括基因组学、DNA复制、转录和翻译等分子遗传学的相关内容。
3. 遗传变异，可能涉及到突变、染色体重排、基因组变异等内容，以及它们在遗传学研究和临床实践中的意义。
4. 遗传学方法，可能包括各种遗传学实验和技术的注解，例如基因工程技术、基因组编辑技术等。
5. 遗传学应用，可能涉及到遗传学在医学、农业、生态学等领域的应用，以及相关的伦理和社会问题。
总的来说，Lewin's GENES XII这本书涵盖了广泛的遗传学知识，对基因XII的注解可能涉及到分子遗传学、遗传变异、遗传学方法和应用等多个方面的内容。
希望这些信息能够帮助到你理解这本书的注解内容。
goodsamplesgenes函数
goodsamplesgenes函数
goodsamplesgenes函数是一个计算基因样本质量的函数。
它接受一个基因样本矩阵作为输入，并计算每个样本的质量。
该函数的作用是帮助研究人员在基因研究中评估样本的可靠性和可用性。
该函数的实现通常基于一些质量指标，例如基因读数、GC含量、重复序列的比例等。
它会对每个样本在这些指标上进行评估，并给出一个综合的质量得分。
函数的输出通常是一个质量得分矩阵，其中每一行对应一个样本，列是质量指标，值是该样本在相应指标上的得分。
这样，研究人员可以根据得分来筛选和比较样本，以确定哪些样本是高质量的、可靠的。
使用goodsamplesgenes函数可以帮助研究人员在基因研究中排除低质量的样本，从而提高研究结果的准确性和可靠性。
这个函数在基因组学和生物信息学领域被广泛使用，对于大规模基因研究尤为重要。
x染色质名词解释遗传学
x染色质名词解释遗传学X染色体是一种性染色体，存在于大大多数哺乳动物的雄性个体中。
它携带着许多与性别相关的基因，包括决定个体性别的SRY基因。
以下是7个例句：1. The X chromosome contains numerous genes related to sexual development and characteristics.X染色体携带着许多与性发育和性状相关的基因。
2. In mammals, males carry one X and one Y chromosome, while females carry two X chromosomes.在哺乳动物中，雄性携带一个X染色体和一个Y染色体，而雌性携带两个X染色体。
3. The SRY gene on the X chromosome plays a crucial rolein determining an individual's sex.X染色体上的SRY基因在确定个体性别中起着关键作用。
4. The inheritance pattern of X-linked traits differs between males and females.X连锁遗传特征在雄性和雌性之间的遗传模式不同。
5. Hemophilia is an example of an X-linked recessive disorder.血友病是一种X连锁隐性遗传疾病的例子。
6. Calico cats are a result of X-chromosome inactivation in female cats.三花猫是雌性猫中X染色体失活的结果。
7. X-inactivation ensures that only one X chromosome is active in each cell of female individuals.X染色体失活确保了雌性个体每个细胞中只有一个X染色体处于活跃状态。
goodsamplesgenes函数
goodsamplesgenes函数简介在生物科学领域中，研究人员经常需要从大量的基因样本中筛选出高质量的样本。
为了更方便快捷地进行这一过程，我们可以利用编程语言编写一个名为”goodsamplesgenes”的函数来实现样本筛选的功能。
本文将详细介绍该函数的设计原理、输入输出参数以及实际应用案例。
设计原理在设计”goodsamplesgenes”函数时，我们首先需要明确样本筛选的目标。
一般来说，我们希望选取具有一定质量的基因样本，以便进行后续分析和研究。
为了实现这一目标，我们可以考虑以下几个方面的因素：1.数据质量：基因样本可能存在一定的噪声和错误，我们需要考虑如何评估样本的数据质量。
可以使用一些经典的质量评估指标，如测序覆盖度、错误率和质量值等。
2.样本数量：在进行样本筛选时，我们需要确定选取多少个样本。
这个选择通常与研究的实际需求有关。
例如，如果我们只关注某个特定基因的表达情况，可能只需要选取少数几个样本进行分析。
3.样本相似性：在某些研究中，我们可能希望选取具有一定相似性的样本。
这可以通过计算样本间的相似性指标（如相关系数或欧氏距离）来实现。
基于以上设计原理，我们可以开始编写”goodsamplesgenes”函数的代码。
输入参数“goodsamplesgenes”函数的输入参数如下：•gene_samples：包含基因样本数据的矩阵，每一行代表一个样本，每一列代表一个基因的表达值。
•quality_threshold：数据质量的阈值，低于该阈值的样本将被排除。
•num_samples：需要选取的样本数量。
•similarity_threshold：样本相似性的阈值，低于该阈值的样本将被排除。
函数实现def goodsamplesgenes(gene_samples, quality_threshold, num_samples, similarity_ threshold):# 数据质量筛选good_samples = []for sample in gene_samples:quality = evaluate_quality(sample)if quality >= quality_threshold:good_samples.append(sample)# 样本相似性筛选similar_samples = []for i in range(len(good_samples)):for j in range(i+1, len(good_samples)):similarity = calculate_similarity(good_samples[i], good_samples[j]) if similarity >= similarity_threshold:similar_samples.append((good_samples[i], good_samples[j]))# 根据条件选取样本selected_samples = []if len(similar_samples) >= num_samples:selected_samples = similar_samples[:num_samples]else:selected_samples = similar_samplesreturn selected_samples在上述代码中，我们定义了两个辅助函数”evaluate_quality”和”calculate_similarity”，分别用于评估数据质量和计算样本相似性。
基因ID转换小工具，太实用了！–BioEngX
基因ID转换小工具，太实用了！–BioEngX在做差异基因分析的时候，你有没有看到一个基因编号是ENSG*********或者AB*********_at，想知道它的基因名，或者想知道某一染色体位置上有哪些基因，又或者一些基因哪些是蛋白编码而哪些则是lncRNA如何你有这样或者其他类似关于基因转换的疑惑的话，那么今天给大家介绍个网站。
今天我们介绍的实用小工具来自于ensembl 网站的应用biomart，它是ensemble旗下的一个基因查询的工具，网址是下面我们就一点儿一点儿的看一下这个网站吧。
1.进入网站，我们选择数据库和物种基因，选择ensembl gene和hunman genes在选择好数据库之后，我们在左侧会看到这么一个状态栏我们需要做的也就是①在“filters”里面选择我们想要输入的基因信息。
②在“Attributes”里面选择我们想要得到的基因信息。
③点击“count”。
④点击“Results”得到结果假如我们有一堆ensembl编码的基因，我想知道他们的基因名，基因类型及转录本长度。
我需要做的就是在“Filters”→“GENE”→“gene table ID”输入我们要的基因在“Attributes”中依次选择“GENE”→“Gene name”、“Gene type”、“Transcript length”然后点击“counts”→“Results”，就得到结果了点击”GO”即可下载所有结果Biomart除了ID转换之外还有很多功能。
比如我们想知道第一染色体的p13.1的所有基因有哪些。
那么我们就可以在“REGION”→“Chromosom/scaffold”、“Karyotype band”中选择好位置在“Attributes”中选择“GENE”→“Gene name”即可得到结果。
其实biomart的功能还有很多。
它给你提供了很多的选项让你可以组合出自己想要的结果。
所以如果有基因转换和基因查询相关的问题，不妨可以试一下。
GeneSpringGX教程——Affymetrix基因芯片分析（三）
GeneSpringGX教程——Affymetrix基因芯片分析（三）弗雷赛斯freescienceFreescience由浙江大学医学院几个硕博士发起创建，旨在最广泛分享有价值的科研技能和知识；FreeScience的宗旨：“科学自由分享、人人平等，共求真理”。
这期继续GeneSpring GX 教程第三期，为零基础的小伙伴学习基因芯片分析提供帮助。
再次声明本教程仅供学习GeneSpring使用，不得用于商业目的。
最后，请大家使用试用版或者正版来分析数据，尊重知识产权。
数据团队将对教程进行校对，任何问题都可以加入freescience大数据群进行交流和讨论。
GEO数据库中很多Affymetrix基因芯片大多都可以用GeneSpring GX进行分析。
1、创建新项目1.1启动GeneSpring GX，启动后显示有3个选项：创建新项目；打开现存项目；打开最近项目。
我们选择创建新项目，按OK继续。
1.2此时显示出一个细节窗口，我们可以输入项目名称和注释。
这里我们的新项目默认名“New Project”，按OK继续。
2、实验选择2.1这时显示带有两个选项的对话框窗口：创建新实验和打开现存实验。
打开现存实验允许用户将任何以前项目中的实验用到当前实验项目中。
我们现在选择创建新实验，此时出现一个实验描述对话框。
首先输入实验名称，我们默认“New Experiment”。
然后指定的实验类型，下拉菜单中提供给用户多种实验类型的选择，我们在进行Affymetrix基因芯片分析时主要是选择“Affymetrix Expression”。
2.2接着是选择工作流程类型。
点击下拉符号可以看到两种类型：工作流程导引和高级分析。
工作流程导引是通过一组默认参数来协助用户创建和分析一项实验。
而高级分析的参数可以改变，以适应个人需要。
3、加载数据3.1打开了加载数据的新对话框后，一个实验就可以利用“选择文件”或“选择样本”这两个按钮来创建。
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FIGURE 05: The proportions of different sequence components vary in eukaryotic genomes
FIGURE 06: Identifying the gene involved in Duchenne muscular dystrophy
Chapter 5 The Content of the Genome
FIGURE CO: The Content of the Genome
Reproduced from A. M. Cerdeño-Tárraga, et al., Science 307 (2005): 1463-1465 []. Reprinted with permission from AAAS. Photo courtesy of Julian Parkhill, The Sanger Institute.
FIGURE 10: Mouse chromosome 1 has 21 segments of 1 to 25 Mb that are syntenic with regions corresponding to parts of six human chromosomes
FIGURE 11: When paternal and maternal mitochondrial alleles differ, somatic variation may result if unequal segregation generates daughter cells with only one set
FIGURE 15: The mitochondrial genome of S. cerevisiae
FIGURE 16: The chloroplast genome in land plants codes for four rRNAs, 30 tRNAs, and ~60 proteins
FIGURE 04: If a restriction marker is associated with a phenotypic characteristic, the restriction site must be located near the gene responsible for the phenotype
FIGURE 07: Characterizing the Duchenne muscular dystrophy gene
FIGURE 08: A special splicing vector is used for exon trapping
FIGURE 09: A series of exons must generate an open reading frame with appropriate initiation and termination codons
Photo courtesy of Ray L. White, Ernest Gallo Clinic and Research Center, University of California, San Francisco.
FIGURE 03: A restriction polymorphism can be used as a genetic marker to measure recombination distance from a phenotypic marker (such as eye color)
FIGURE 01: A point mutation that affects a restriction site is detected by a difference in restriction fragments
FIGURE 02: Restriction site polymorphisms are inherited according to Mendelian rules
Hale Waihona Puke FIGURE 17: Mitochondria originated by a endosymbiotic event when a bacterium was captured by a eukaryotic cell
FIGURE 12: DNA from the sperm enters the oocyte to form the male pronucleus in the fertilized egg, but all the mitochondria are provided by the oocyte
FIGURE 13: Mitochondrial genomes have genes coding for (mostly complex I–IV) proteins, rRNAs, and tRNAs
FIGURE 14: Human mitochondrial DNA has 22 tRNA genes, two rRNA genes, and 13 protein-coding regions