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Wisdom of the week 2011-10-23 – What you are worring about this morning is irrelevant

Sunday, October 23, 2011

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Steve Jobs Stanford Commencement Speech 2005

Saturday, October 22, 2011

I have never got a chance to listen to this famous speech by Steve Jobs and have finally listened to it because of all the recently coverages after he has passed away. It is actually quite insightful and I would like to share with all of you.


 

I am actually quite interested in his upcoming biography, which has already triggered some interesting discussions. For example, read Steve Jobs Bio: Its 6 Most Surprising Reveals from Wired.com.

 

 

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Beware of Penguin thieves!

Thursday, October 20, 2011

It is fair to say that there is still so much to learn about animal behaviour. 🙂

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2011-10-08 New articles we read this week

Saturday, October 8, 2011

Funding

  1. Roebber PJ, Schultz DM. Peer review, program officers and science funding. PLoS One. 2011 Apr 12;6(4):e18680. PubMed PMID: 21533268; PubMed Central PMCID: PMC3075261.
    • The most interesting conclusion is – the best strategy is to submit more applications when funding rate drops below 15%.

Neuroscience

  1. Peelen MV, Kastner S. Is that a bathtub in your kitchen? Nat Neurosci. 2011 Sep 27;14(10):1224-6. doi: 10.1038/nn.2936. PubMed PMID: 21952264.

Genomics

  1. Adli M, Bernstein BE. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc. 2011 Sep 29;6(10):1656-68. doi: 10.1038/nprot.2011.402. PubMed PMID: 21959244.
  2. Keller A, Leidinger P, Bauer A, Elsharawy A, Haas J, Backes C, Wendschlag A, Giese N, Tjaden C, Ott K, Werner J, Hackert T, Ruprecht K, Huwer H, Huebers J, Jacobs G, Rosenstiel P, Dommisch H, Schaefer A, Müller-Quernheim J, Wullich B, Keck B, Graf N, Reichrath J, Vogel B, Nebel A, Jager SU, Staehler P, Amarantos I, Boisguerin V, Staehler C, Beier M, Scheffler M, Büchler MW, Wischhusen J, Haeusler SF, Dietl J, Hofmann S, Lenhof HP, Schreiber S, Katus HA, Rottbauer W, Meder B, Hoheisel JD, Franke A, Meese E. Toward the blood-borne miRNome of human diseases. Nat Methods. 2011 Sep 4;8(10):841-3. doi: 10.1038/nmeth.1682. PubMed PMID: 21892151.

Development/ Stem cells

  1. Friedrich Ben-Nun I, Montague SC, Houck ML, Tran HT, Garitaonandia I, Leonardo TR, Wang YC, Charter SJ, Laurent LC, Ryder OA, Loring JF. Induced pluripotent stem cells from highly endangered species. Nat Methods. 2011 Sep 4;8(10):829-31.  doi: 10.1038/nmeth.1706. PubMed PMID: 21892153.
    • Commentary: Selvaraj V, Wildt DE, Pukazhenthi BS. Induced pluripotent stem cells for conserving endangered species? Nat Methods. 2011 Sep 29;8(10):805-7. doi: 10.1038/nmeth.1715. PubMed PMID: 21959133.
  2. Pera MF. The proteomes of native and induced pluripotent stem cells. Nat Methods. 2011 Sep 29;8(10):807-8. doi: 10.1038/nmeth.1707. PubMed PMID: 21959134.

Genetics/ Optogenetics

  1. Toettcher JE, Gong D, Lim WA, Weiner OD. Light-based feedback for controlling intracellular signaling dynamics. Nat Methods. 2011 Sep 11;8(10):837-9. doi: 10.1038/nmeth.1700. PubMed PMID: 21909100.
    • Commentary: Haugh JM. Cells see the light to bring signaling under control. Nat Methods. 2011 Sep 29;8(10):808-9. doi: 10.1038/nmeth.1708. PubMed PMID: 21959135.

Imaging

  1. Ghosh KK, Burns LD, Cocker ED, Nimmerjahn A, Ziv Y, Gamal AE, Schnitzer MJ. Miniaturized integration of a fluorescence microscope. Nat Methods. 2011 Sep 11;8(10):871-8. doi: 10.1038/nmeth.1694. PubMed PMID: 21909102.

Systems Biology/ Gene Regulatory Network

  1. Foss EJ, Radulovic D, Shaffer SA, Goodlett DR, Kruglyak L, Bedalov A. Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms. PLoS Biol. 2011 Sep;9(9):e1001144. Epub 2011 Sep 6. PubMed PMID: 21909241; PubMed Central PMCID: PMC3167781.
  2. Splinter E, de Laat W. The complex transcription regulatory landscape of our genome: control in three dimensions. EMBO J. 2011 Sep 27. doi: 10.1038/emboj.2011.344. [Epub ahead of print] PubMed PMID: 21952046.
  3. Lynch VJ, Leclerc RD, May G, Wagner GP. Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet. 2011 Sep 25. doi: 10.1038/ng.917. [Epub ahead of print] PubMed PMID:
    21946353.
  4. Garg A, Mohanram K, De Micheli G, Xenarios I. Implicit methods for qualitative modeling of gene regulatory networks. Methods Mol Biol. 2012;786:397-443. PubMed PMID: 21938638.

Brg1

  1. Hu G, Schones DE, Cui K, Ybarra R, Northrup D, Tang Q, Gattinoni L, Restifo NP, Huang S, Zhao K. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Res. 2011 Aug 31. [Epub ahead of print] PubMed PMID: 21795385.

Retina

  1. Qin Z, Kidd AR 3rd, Thomas JL, Poss KD, Hyde DR, Raymond PA, Thummel R. FGF signaling regulates rod photoreceptor cell maintenance and regeneration in zebrafish. Exp Eye Res. 2011 Sep 17. [Epub ahead of print] PubMed PMID: 21945172.
  2. Dal Molin M, Hong SM, Hebbar S, Sharma R, Scrimieri F, de Wilde R, Mayo SC, Goggins M, Wolfgang CL, Schulick RD, Lin MT, Eshleman JR, Hruban RH, Maitra A, Matthaei H. Loss of expression of the SWI/SNF chromatin remodeling subunit
    BRG1/SMARCA4 is frequently observed in intraductal papillary mucinous neoplasms of the pancreas. Hum Pathol. 2011 Sep 20. [Epub ahead of print] PubMed PMID: 21940037.

Virology

  1. Cohen J, Enserink M. Virology. False positive. Science. 2011 Sep 23;333(6050):1694-701. PubMed PMID: 21940874.

Material Science

  1. Nosonovsky M. Materials science: slippery when wetted. Nature. 2011 Sep 21;477(7365):412-3. doi: 10.1038/477412a. PubMed PMID: 21938059.

Synthetic Biology

  1. Enyeart PJ, Ellington AD. Synthetic biology: a yeast for all reasons. Nature. 2011 Sep 21;477(7365):413-4. doi: 10.1038/477413a. PubMed PMID: 21938060.

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The Nobel Prize in Physiology or Medicine 2011

Monday, October 3, 2011

The Nobel Prize in Physiology or Medicine 2011 was awarded to Bruce A. Beutler and Jules A. Hoffmann for their discoveries concerning the activation of innate immunity, and Ralph M. Steinman for his discovery of the dendritic cell and its role in adaptive immunity. A press release about the basic findings can be found here.

Bruce A. Beutler

Jules A. Hoffmann

Ralph M. Steinman

 

 

 

 

 

 

 

 

 

 

Update 1:  On 10/13/2011, our lab had a journal club on one of the original key publications – Steinman RM, Witmer MD. Lymphoid dendritic cells are potent stimulators of the primary mixed leukocyte reaction in mice. Proc Natl Acad Sci U S A. 1978 Oct;75(10):5132-6. PubMed PMID: 154105; PubMed Central PMCID: PMC336278.

Update 2: Ralph Steinman passed away the Friday before the prize announcement. There are a few interesting news articles on his hard work until the final days and effort on designing new therapies based on his discovery.

From Reuters: Insight: Nobel winner’s last big experiment: Himself

From BBC: Nobel winner Ralph Steinman’s quest to cure cancer – including his own

Update 3: 10/29/2011. A news article from Nature.

Gravitz L. A fight for life that united a field. Nature. 2011 Oct 11;478(7368):163-4. doi: 10.1038/478163a. PubMed PMID: 21993732.

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2011-10-01 new articles we read this week

Saturday, October 1, 2011

Neuroscience

  1. Nishimoto S, Vu AT, Naselaris T, Benjamini Y, Yu B, Gallant JL. Reconstructing Visual Experiences from Brain Activity Evoked by Natural Movies. Curr Biol. 2011 Sep 22. [Epub ahead of print] PubMed PMID: 21945275.
    • A group of Berkeley scientists have used fMRI to probe into our brains and “see” how we see the world.
    • Press release; and more technical information from the authors’ website.


Regeneration

  1. Ramachandran R, Zhao XF, Goldman D. Ascl1a/Dkk/{beta}-catenin signaling pathway is necessary and glycogen synthase kinase-3{beta} inhibition is sufficient for zebrafish retina regeneration. Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15858-63. Epub 2011 Sep 12. PubMed PMID: 21911394.
  2. Zupanc GK, Sîrbulescu RF. Adult neurogenesis and neuronal regeneration in the central nervous system of teleost fish. Eur J Neurosci. 2011 Sep;34(6):917-29. doi: 10.1111/j.1460-9568.2011.07854.x. PubMed PMID: 21929625.

Zebrafish

  1. Zhu C, Smith T, McNulty J, Rayla AL, Lakshmanan A, Siekmann AF, Buffardi M, Meng X, Shin J, Padmanabhan A, Cifuentes D, Giraldez AJ, Look AT, Epstein JA, Lawson ND, Wolfe SA. Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish. Development. 2011 Oct;138(20):4555-64. PubMed PMID: 21937602.

Ageing

* A series of articles on the validity of sir2’s role in longevity.

  1. Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott  M, Sutphin GL, Leko V, McElwee JJ, Vazquez-Manrique RP, Orfila AM, Ackerman D, Au C, Vinti G, Riesen M, Howard K, Neri C, Bedalov A, Kaeberlein M, Soti C, Partridge L, Gems D. Absence of effects of Sir2 overexpression on lifespan in C.  elegans and Drosophila. Nature. 2011 Sep 21;477(7365):482-5. doi: 10.1038/nature10296. PubMed PMID: 21938067.
  2. Viswanathan M, Guarente L. Regulation of Caenorhabditis elegans lifespan by sir-2.1 transgenes. Nature. 2011 Sep 21;477(7365):E1-2. doi: 10.1038/nature10440. PubMed PMID: 21938026.
    • Commentary: Lombard DB, Pletcher SD, Cantó C, Auwerx J. Ageing: longevity hits a roadblock. Nature. 2011 Sep 21;477(7365):410-1. doi: 10.1038/477410a. PubMed PMID: 21938058.
    • News article in Boston.com  “New research challenges work on a longevity gene“

Plant

  1. Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X, Yin Y, Wang C, Zhang T, Zhu D, Zhang D, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen J, Wang J, Wang M, Zhang Q, Zhang J, Zen K, Zhang CY. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res. 2011 Sep 20. doi: 10.1038/cr.2011.158. [Epub ahead of print] PubMed PMID: 21931358.
    • Plant miRNA can get into human by food consumption and affect physiological response!
    • News artcile in the Scientist. “Plant RNAs Found in Mammals“

Zebrafish/ Evolution

  1. Whiteley AR, Bhat A, Martins EP, Mayden RL, Arunachalam M, Uusi-Heikkilä S, Ahmed AT, Shrestha J, Clark M, Stemple D, Bernatchez L. Population genomics of wild and laboratory zebrafish (Danio rerio). Mol Ecol. 2011 Sep 16. doi: 10.1111/j.1365-294X.2011.05272.x. [Epub ahead of print] PubMed PMID: 21923777.
  2. Catchen JM, Braasch I, Postlethwait JH. Conserved synteny and the zebrafish genome. Methods Cell Biol. 2011;104:259-85. PubMed PMID: 21924168.

 

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Dr. Fox Effect

Saturday, October 1, 2011

To find out how useful the student evaluation on a lecture is, an interesting experiment was done many years ago that the researcher found an actor to deliver a lecture that he had no idea about. He only tried to make it sound impressive and confusing.  Interestingly, most students, despite being trained scientists from different fields, found that the lecture was great and they had learned from Dr. Fox. The results were so profound that they call it Dr. Fox effect now. A great coverage on this experiment can be found from weirdexperiments.com.

 


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2011 Ig Nobel prize

Friday, September 30, 2011

The 2011 Ig Nobel prize ceremony just took place last night! Here is a list of the winners, a news coverage article and a youtube video of the ceremony.

 

Update: On 10/6/2011, our lab had a journal club mainly on the psychology prize, but we also talked about various interesting things related to different awards in this year.

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2011 Lasker Award

Monday, September 26, 2011

This is mainly for female scientists in the lab and particularly for Chinese female scientists. This year’s Lasker Award is given to Tu Youyou, a Senior Chinese female researcher, for her discovery of artemisinin which is used to treat malaria. Artemisinin is extracted from our precious traditional chinese medicine. The Lasker Award for Basic Medical Research goes to two scientists who study chaperonins.

Tu Youyou

Update: New review/commentary articles on this year’s Lasker Awards

  1. Rothman JE, Schekman R. Molecular mechanism of protein folding in the cell. Cell. 2011 Sep 16;146(6):851-4. Epub 2011 Sep 9. PubMed PMID: 21907398.
  2. Miller LH, Su X. Artemisinin: discovery from the chinese herbal garden. Cell. 2011 Sep 16;146(6):855-8. Epub 2011 Sep 9. PubMed PMID: 21907397.

 

 

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2011-09-24 new articles we read this week

Saturday, September 24, 2011

Imaging

  1. Paige JS, Wu KY, Jaffrey SR. RNA mimics of green fluorescent protein. Science. 2011 Jul 29;333(6042):642-6. PubMed PMID: 21798953.
    • A potential way to tag RNA by fluorescence similar to tag protein by GFP

Data analysis

  1. Spiegelhalter D, Pearson M, Short I. Visualizing uncertainty about the future. Science. 2011 Sep 9;333(6048):1393-400. PubMed PMID: 21903802.

Genetics

  1. Ott J, Kamatani Y, Lathrop M. Family-based designs for genome-wide association studies. Nat Rev Genet. 2011 Jun 1;12(7):465-74. doi: 10.1038/nrg2989. Review. PubMed PMID: 21629274.
  2. Browning SR, Browning BL. Haplotype phasing: existing methods and new developments. Nat Rev Genet. 2011 Sep 16;12(10):703-14. doi: 10.1038/nrg3054. PubMed PMID: 21921926.
  3. Sauna ZE, Kimchi-Sarfaty C. Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet. 2011 Aug 31;12(10):683-91. doi: 10.1038/nrg3051. PubMed PMID: 21878961.
  4. Kirkwood TB, Cordell HJ, Finch CE. Speed-bumps ahead for the genetics of later-life diseases. Trends Genet. 2011 Aug 6. [Epub ahead of print] PubMed PMID: 21824675.

Genomics

  1. Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet. 2011 Sep 7;12(10):671-82. doi: 10.1038/nrg3068. PubMed PMID: 21897427.

Development

  1. Kalsotra A, Cooper TA. Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet. 2011 Sep 16;12(10):715-29. doi: 10.1038/nrg3052. PubMed PMID: 21921927.

Evolution

  1. Tautz D, Domazet-Lošo T. The evolutionary origin of orphan genes. Nat Rev Genet. 2011 Aug 31;12(10):692-702. doi: 10.1038/nrg3053. PubMed PMID: 21878963.

Medicine

  1. The Lancet. Japan: universal health care at 50 years. Lancet. 2011 Aug 30. [Epub ahead of print] PubMed PMID: 21885103.
  2. Ikeda N, Saito E, Kondo N, Inoue M, Ikeda S, Satoh T, Wada K, Stickley A, Katanoda K, Mizoue T, Noda M, Iso H, Fujino Y, Sobue T, Tsugane S, Naghavi M, Ezzati M, Shibuya K. What has made the population of Japan healthy? Lancet. 2011 Aug 30. [Epub ahead of print] PubMed PMID: 21885105.
  3. Ikegami N, Yoo BK, Hashimoto H, Matsumoto M, Ogata H, Babazono A, Watanabe R, Shibuya K, Yang BM, Reich MR, Kobayashi Y. Japanese universal health coverage: evolution, achievements, and challenges. Lancet. 2011 Aug 30. [Epub ahead of print] PubMed PMID: 21885107.

Systems Biology

  1. Barnes CP, Silk D, Sheng X, Stumpf MP. Bayesian design of synthetic biological systems. Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15190-5. Epub 2011 Aug 29. PubMed PMID: 21876136.
  2. Wingler LM, Cornish VW. Reiterative Recombination for the in vivo assembly of libraries of multigene pathways. Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15135-40. Epub 2011 Aug 26. PubMed PMID: 21876185.
  3. Zeisel A, Köstler WJ, Molotski N, Tsai JM, Krauthgamer R, Jacob-Hirsch J,
    Rechavi G, Soen Y, Jung S, Yarden Y, Domany E. Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli. Mol Syst Biol. 2011 Sep 13;7:529. doi: 10.1038/msb.2011.62. PubMed PMID: 21915116.

Neuroscience

  1. Wolman MA, Jain RA, Liss L, Granato M. Chemical modulation of memory formation in larval zebrafish. Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15468-73. Epub 2011 Aug 29. PubMed PMID: 21876167.
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