7/28/2019 Assigned Journal Papers for PY571 Spring 2013 (1-2-3)

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Assigned Journal Papers for PY571: Introduction to Biological Physics

Spring 2013

WEEK #1 (for Research Diary due 1/20/2013)

Smallest form of life thus far discoveredLineages of Acidophilic Archaea Revealed by Community Genomic Analysis Bakeret al. Science 22 December 2006:

Vol. 314. no. 5807, pp. 1933 - 1935

http://www.sciencemag.org/cgi/content/abstract/314/5807/1933

also news report appeared on this at :

http://www.spaceref.com/news/viewpr.rss.html?pid=21532

Focus: Questions for reading:

a.

What is shotgun genomic sequencingb. What is FISH (fluorescencein situ hybridization)(see Figure 3 of paper)

Week#2 (for Research Diary due 1/27/2013)

Gibson, D. G. et al. Science 219 1214-1219 (2008)

First Complete chemical synthesis of genes for an complete organism (Craig Venter)http://www.sciencemag.org/cgi/content/abstract/1151721

Focus: Questions for reading:1. What is current technical capability to synthesize chemically DNA.2. What tricks did the Venter group use.3. What are watermarks.4. Did they create new life?5. How might this approach be used in the future.

Also you can look at link below from NYTimes on the new field of Synthetic Biology

See also related Science paper -Lartigue, C. Science 325,5948 (2009)

http://www.sciencemag.org/content/325/5948/1693.abstract

http://www.the-scientist.com/blog/display/55913/

WEEK #3 (For Resarch J ournal due 2/3/2013)

http://www.sciencemag.org/cgi/content/abstract/314/5807/1933http://www.sciencemag.org/cgi/content/abstract/314/5807/1933http://www.spaceref.com/news/viewpr.rss.html?pid=21532http://www.spaceref.com/news/viewpr.rss.html?pid=21532http://www.sciencemag.org/cgi/content/abstract/1151721http://www.sciencemag.org/cgi/content/abstract/1151721http://www.sciencemag.org/content/325/5948/1693.abstracthttp://www.sciencemag.org/content/325/5948/1693.abstracthttp://www.the-scientist.com/blog/display/55913/http://www.the-scientist.com/blog/display/55913/http://www.the-scientist.com/blog/display/55913/http://www.sciencemag.org/content/325/5948/1693.abstracthttp://www.sciencemag.org/cgi/content/abstract/1151721http://www.spaceref.com/news/viewpr.rss.html?pid=21532http://www.sciencemag.org/cgi/content/abstract/314/5807/1933

7/28/2019 Assigned Journal Papers for PY571 Spring 2013 (1-2-3)

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You have a choice of two papers to review this week:

1) Chow, B. Y., X. Han, A. S. Dobry, X. Qian, A. S. Chuong, M. Li, M. A.Henninger, G. M. Belfort, Y. Lin, P. E. Monahan, and E. S. Boyden. High-performance genetically targetable optical neural silencing by light-driven

proton pumps. Nature (2010) 463:98-102.

Focus Questions for Reading:

1) How does Arch3 act to silence neurons?2) What protein is used to activate nerves by light.3) How does this compare with earlier attempts?4) How is Arch3 incorporated into neurons?5) How can light mediated silencing of nerves be used in brain research?6) Why would it be an advantage to red-shift the absorption of Arch3?

or

M.F. Hagan and D. Chandler Dyanic Pathways for Viral Capsid Assembly BiophysicalJournal, Volume 91, Issue 1, 42-54, 1 July 2006

http://www.cell.com/biophysj/abstract/S0006-3495(06)71706-4

Focus Questions for reading:

1) What is a capsid protein?2) How did they simulate dyanics capsid assembly?3) What are main barriers to capsid assembly?4) What other self-assembling systems could this approach be applied to?

http://www.cell.com/biophysj/issue?pii=S0006-3495(06)X7046-7http://www.cell.com/biophysj/abstract/S0006-3495(06)71706-4http://www.cell.com/biophysj/abstract/S0006-3495(06)71706-4http://www.cell.com/biophysj/abstract/S0006-3495(06)71706-4http://www.cell.com/biophysj/issue?pii=S0006-3495(06)X7046-7