Transcript Document

基因组学Genomics
授课教师：牛登科
http://cmb.bnu.edu.cn/teachers/niudk.htm
[email protected]
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. 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 IX
• T. A. BROWN，2002. Genomes 2nd edition. NCBI-books:
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=genomes
• 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://blog.sciencenet.cn/u/DNAgene
Journals
•
•
•
•
•
•
Nature, Science, Cell, PLoS Biology
Nature Reviews ….
Annual Review in …
Trends in …
Current Opinion in …
Genome Research, Genome Biology
Genomics 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 today's molecular
biology is driven less by research into the
activities of individual genes and more by
genome sequencing and functional analysis.
• Reduce the overlapping with other courses, like
molecular biology.
Genomics is divided into four parts
•
•
•
•
Part 1 Studying Genomes
Part 2 Genome Anatomies
Part 3 How Genomes Function
Part 4 How Genomes Replicate and Evolve
• Add something like reference search and
management, introduction 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.
• Our 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
199311033005a.doc、 牛登科199311033005b.doc等。
• 提交到：[email protected]，抄送：[email protected]
• 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
Something new
• What are the functions of intracellular
membrane in eukaryotes?
• Provide a residence for some enzymes
• Compartmentation to sequester small
molecules, either because they are
valuable or because they might cause
harm if allowed to diffuse
• ……
Something new
• How to compartment the
intercellular space of
prokaryotes 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 & Company; 2015.
• Bacteria sequester key
metabolic steps into
polyhedral protein
compartments.
Something new
What’s left for us
• Consider evolution and phyolgenetic tree.
• Prokaryotes including eubacteria and
archaebacteria
• Organelle 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
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 transcription
• and 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 you have some ideas on eukaryotes?
Niu DK (2007). Protecting exons from deleterious R-loops:
a potential advantage of having introns. Biology Direct 2: 11.
Coupled syntheses
inhibit backtracking-associated pauses
J W Roberts Science 2010;328:436-437
Published by AAAS
Are backtracking and pause dangerous?
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://blog.sciencenet.cn/home.php?mod=
space&uid=61772&do=blog&id=479446
Further readings
• Heinhorst S, Cannon GC: A new, leaner 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, 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 Res 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, 327:4243.
• Murat D et al: Cell Biology of Prokaryotic
Organelles. Cold Spring Harb Perspect Biol
2:a000422, 2010