1、基因组学Genomics,授课教师：牛登科http:/ 010-58802064,使用说明及版权声明,本课程的ppt是本人讲课过程中用作提示的符号，不代表讲课内容。部分内容可能作为反面教材来讲，但可能未在ppt中注明是反面的。使用此课程的ppt时，请慎重，切勿被误导。本课程的PPT文件来自Genomes 3教材辅助资料和国内外相关专家发表的论文，本人亦贡献部分文字和讨论。限于篇幅，对原著作者及部分文献作者未作专门致谢,敬请原谅。本课程的PPT文件的版权属于原教材作者、所参考文献的作者和本人。其中，本人贡献的部分读者可随意使用和传播，无任何限制。,教材和参考书,T. A. BROWN，2006.
2、 Genomes 3. Garland Science.A.M. Lesk, 2012. Introduction to Genomics 2nd edition. Oxford University Press.A. Fontdevila, 2011. the Dynamic Genome: A darwinian approach. Oxford University Press.Gene IXT. A. BROWN，2002. Genomes 2nd edition. NCBI-books: http:/www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=gen
3、omes袁建刚等译, 2002基因组, 科学出版社，译自1999版。最近有翻译的第二版.杨金水著, 2002基因组学，高等教育出版社。此书也有新版。S. Scherer. 2008. A Short Guide to the Human Genome. Cold Spring Harbor Laboratory Press.牛登科的博客: http:/ Science, Cell, PLoS BiologyNature Reviews .Annual Review in Trends in Current Opinion in Genome Research, Genome Biology,G
4、enomics vs molecular biology,Genomes attempts to bring a fresh approach to the teaching of molecular biology.The book is centered on genomes, not genes, in recognition of the fact that todays molecular biology is driven less by research into the activities of individual genes and more by genome sequ
5、encing and functional analysis.Reduce the overlapping with other courses, like molecular biology.,Genomics is divided into four parts,Part 1 Studying GenomesPart 2 Genome AnatomiesPart 3 How Genomes FunctionPart 4 How Genomes Replicate and EvolveAdd something like reference search and management, in
6、troduction to milestone articles, and discussion on how to do researches.,On the examination,Most of you will have a high score.A high score in this course is not very important for you.What is important? All that you learned in this course, in most cases, are not reflected accurately in the score.O
7、ur aim is a preparation for your research.Research is the first of all in next three years for you.,On the examination,Construct a hypothesis on the questions we discussed.Write a review.Or translate two reviews.A thought experiment in detail.付出的精力+认真的程度决定分数。,期末作业提交注意事项,期末论文文件名要求用学号姓名命名，如牛登科19931103
8、3005a.doc、 牛登科199311033005b.doc等。提交到：，抄送：邮件主题（subject）一栏注明“某某的基因组学作业”邮件正文中要求出现：课程名称、作业个数、作者姓名、学号、作业类型等信息。如果是翻译，要在作业文件中注明原文。作业自己至少保留到网上查到成绩时。,科研诚信从现在开始,以下行为类似于小孩的小偷小摸。如不制止，将来会犯大错：用高年级同学的作业来充数；抄袭网上或其他来源的文章。因应办法，必须提交Word文档，不要pdf等其他格式的文件，以便搜索比对。,一同学作业与高年级同学作业的比较共19处修订：插入7处；删除7处；格式5处,What are the functio
9、ns of intracellular membrane in eukaryotes?Provide a residence for some enzymesCompartmentation to sequester small molecules, either because they are valuable or because they might cause harm if allowed to diffuse,Something new,Something new,How to compartment the intercellular space of prokaryotes
10、once required?First consider the cristae in mitochondria.A three to four orders of magnitude smaller volume.Lane N. The vital question: energy, evolution, and the origins of complex life. London: W.W.Norton 2015.Bacteria sequester key metabolic steps into polyhedral protein compartments.,Something n
11、ew,Whats left for us,Consider evolution and phyolgenetic tree.Prokaryotes including eubacteria and archaebacteriaOrganelle genomes are similar with eubacterial genomes. From this point, what can we do to get a PhD?,French, S.L., Santangelo, T.J., Beyer, A.L., and Reeve, J.N. 2007. Transcription and
12、translation are coupled in Archaea. Mol. Biol. Evol. 24: 893-895.,Are transcription and translation are coupled in endosymbiotic organelles?,Shutt TE, Gray MW. Bacteriophage origins of mitochondrial replication and transcription proteins. Trends Genet. 2006;22:90-5.,Something New,Why are transcripti
13、onand translation coupled in prokaryotes?The coupling of transcription and translation is important in that it allows a special type of control, called attenuation.,Gowrishankar, J. and Harinarayanan, R. 2004. Why is transcription coupled to translation in bacteria? Mol. Microbiol. 54: 598-603.Do yo
14、u have some ideas on eukaryotes?,Niu DK (2007). Protecting exons from deleterious R-loops: a potential advantage of having introns. Biology Direct 2: 11.,J W Roberts Science 2010;328:436-437,Published by AAAS,Coupled syntheses inhibit backtracking-associated pauses,Are backtracking and pause dangero
15、us?,Coupling of transcription and translation,The story is nearly finished.Just nearly, something else are need to do and to think.Implications that we can draw from these results, i.e. related questions we may study based on these articles.参考我的博客http:/ readings,Heinhorst S, Cannon GC: A new, leaner
16、 and meaner bacterial organelle. Nat Struct Mol Biol 2008, 15:897-898.Sutter M, Boehringer D, Gutmann S, Gunther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, Ban N: Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nat Struct Mol Biol 2008, 15:939-947.Yeates TO,
17、Kerfeld CA, Heinhorst S, Cannon GC, Shively JM: Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat Rev Microbiol 2008, 6:681-691.Milo R, Jorgensen P, Moran U, Weber G, Springer M: BioNumbers-the database of key numbers in molecular and cell biology. Nucleic Acids R
18、es 2009, doi:10.1093/nar/gkp1889.,Further readings,Tanaka S, Sawaya MR, Yeates TO: Structure and Mechanisms of a Protein-Based Organelle in Escherichia coli. Science 2010, 327:81-84.Kang S, Douglas T: Some Enzymes Just Need a Space of Their Own. Science 2010, 327:42-43.Murat D et al: Cell Biology of Prokaryotic Organelles. Cold Spring Harb Perspect Biol 2:a000422, 2010,
