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Sense of fairness in animals

Wednesday, October 31, 2012

Just come across this interesting video the other day..

 

which is an except from this TED talk : Frans de Waal: Moral behavior in animals


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2012-10-28 new articles we read this week

Sunday, October 28, 2012

Science special section – Forces in Development

  1. Purnell BA. Forces in development. Forceful thinking. Introduction. Science. 2012 Oct 12;338(6104):209. doi: 10.1126/science.338.6104.209. PubMed PMID: 23066070.
  2. Kicheva A, Cohen M, Briscoe J. Developmental pattern formation: insights from physics and biology. Science. 2012 Oct 12;338(6104):210-2. doi: 10.1126/science.1225182. Review. PubMed PMID: 23066071.
  3. Furusawa C, Kaneko K. A dynamical-systems view of stem cell biology. Science.  2012 Oct 12;338(6104):215-7. doi: 10.1126/science.1224311. Review. PubMed PMID: 23066073.
  4. Newman SA. Physico-genetic determinants in the evolution of development. Science. 2012 Oct 12;338(6104):217-9. doi: 10.1126/science.1222003. PubMed PMID: 23066074.
  5. Behrndt M, Salbreux G, Campinho P, Hauschild R, Oswald F, Roensch J, Grill SW, Heisenberg CP. Forces driving epithelial spreading in zebrafish gastrulation. Science. 2012 Oct 12;338(6104):257-60. doi: 10.1126/science.1224143. PubMed PMID: 23066079.

Visual sciences

  1. Hardie RC, Franze K. Photomechanical responses in Drosophila photoreceptors. Science. 2012 Oct 12;338(6104):260-3. doi: 10.1126/science.1222376. PubMed PMID: 23066080.

Neural behaviour

  1. Fernandes AM, Fero K, Arrenberg AB, Bergeron SA, Driever W, Burgess HA. Deep Brain Photoreceptors Control Light-Seeking Behavior in Zebrafish Larvae. Curr Biol. 2012 Sep 18. pii: S0960-9822(12)00944-X. doi: 10.1016/j.cub.2012.08.016. [Epub ahead of print] PubMed PMID: 23000151.

Retinal development

  1. Xiang M. Intrinsic control of mammalian retinogenesis. Cell Mol Life Sci. 2012 Oct 12. [Epub ahead of print] PubMed PMID: 23064704.

Eye diseases

  1. Sahly I, Dufour E, Schietroma C, Michel V, Bahloul A, Perfettini I, Pepermans E, Estivalet A, Carette D, Aghaie A, Ebermann I, Lelli A, Iribarne M, Hardelin JP, Weil D, Sahel JA, El-Amraoui A, Petit C. Localization of Usher 1 proteins to the photoreceptor calyceal processes, which are absent from mice. J Cell Biol. 2012 Oct 15;199(2):381-99. doi: 10.1083/jcb.201202012. Epub 2012 Oct 8. PubMed PMID: 23045546; PubMed Central PMCID: PMC3471240.

Medicine

  1. Krogsbøll LT, Jørgensen KJ, Grønhøj Larsen C, Gøtzsche PC. General health checks in adults for reducing morbidity and mortality from disease. Cochrane Database Syst Rev. 2012 Oct 17;10:CD009009. doi: 10.1002/14651858.CD009009.pub2. PubMed PMID: 23076952.

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The Nobel Prize in Chemistry 2012

Sunday, October 14, 2012

was awarded jointly to Robert J. Lefkowitz and Brian K. Kobilka

“for studies of G-protein-coupled receptors“

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The Nobel Prize in Physiology or Medicine 2012

Monday, October 8, 2012

was awarded jointly to Sir John Gurdon and Shinya Yamnaka

“for the discovery that mature cells can be reprogrammed to become pluripotent”

They also won the Lasker Award in 2009.

 

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Why is it dark at night?

Saturday, October 6, 2012

This is not related to biology but is a question that is in my mind for a while….
 



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The Lasker Awards 2012

Sunday, September 23, 2012

Albert Lasker Basic Medical Research Award goes to

Michael Sheetz, James Spudich and Ronald Vale

For discoveries concerning the cell’s protein-folding machinery, exemplified by cage-like structures that convert newly made proteins into their biologically active forms.

Lasker~DeBakey Clinical Medical Research Award goes to

Roy Calne and Thomas E. Starzl

For the development of liver transplantation, which has restored normal life to thousands of patients with end-stage liver disease.

I highly recommend reading their essays published in Nature Medicine.

Michael Sheetz, James Spudich, Ronald Vale, Roy Calne, Thomas E. Starzl

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2012 Ig Nobel prize!

Sunday, September 23, 2012

From the Ig Nobel prize website:

PSYCHOLOGY PRIZE: Anita Eerland and Rolf Zwaan [THE NETHERLANDS] and Tulio Guadalupe [PERU, RUSSIA, and THE NETHERLANDS] for their study “Leaning to the Left Makes the Eiffel Tower Seem Smaller”

REFERENCE: “Leaning to the Left Makes the Eiffel Tower Seem Smaller: Posture-Modulated Estimation,” Anita Eerland, Tulio M. Guadalupe and Rolf A. Zwaan, Psychological Science, vol. 22 no. 12, December 2011, pp. 1511-14.

ATTENDING THE CEREMONY: Tulio Guadalupe. [NOTE: Two days after the ceremony, Anita Eerland and Rolf Zwaan will marry each other, in the Netherlands.]

 

PEACE PRIZE: The SKN Company [RUSSIA], for converting old Russian ammunition into new diamonds.

ATTENDING THE CEREMONY: Igor Petrov

 

ACOUSTICS PRIZE: Kazutaka Kurihara and Koji Tsukada [JAPAN] for creating the SpeechJammer — a machine that disrupts a person’s speech, by making them hear their own spoken words at a very slight delay.

REFERENCE: “SpeechJammer: A System Utilizing Artificial Speech Disturbance with Delayed Auditory Feedback“, Kazutaka Kurihara, Koji Tsukada, arxiv.org/abs/1202.6106. February 28, 2012.

ATTENDING THE CEREMONY: Kazutaka Kurihara and Koji Tsukada

 

NEUROSCIENCE PRIZE: Craig Bennett, Abigail Baird, Michael Miller, and George Wolford [USA], for demonstrating that brain researchers, by using complicated instruments and simple statistics, can see meaningful brain activity anywhere — even in a dead salmon.

REFERENCE: “Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon: An argument for multiple comparisons correction,” Craig M. Bennett, Abigail A. Baird, Michael B. Miller, and George L. Wolford, 2009.
REFERENCE: “Neural Correlates of Interspecies Perspective Taking in the Post-Mortem Atlantic Salmon: An Argument For Multiple Comparisons Correction,” Craig M. Bennett, Abigail A. Baird, Michael B. Miller, and George L. Wolford, Journal of Serendipitous and Unexpected Results, vol. 1, no. 1, 2010, pp. 1-5.

ATTENDING THE CEREMONY: Craig Bennett, Abigail Baird, Michael Miller, and George Wolford

 

CHEMISTRY PRIZE: Johan Pettersson [SWEDEN and RWANDA]. for solving the puzzle of why, in certain houses in the town of Anderslöv, Sweden, people’s hair turned green.

ATTENDING THE THE CEREMONY: Johan Pettersson

 

LITERATURE PRIZE: The US Government General Accountability Office, for issuing a report about reports about reports that recommends the preparation of a report about the report about reports about reports.

REFERENCE: “Actions Needed to Evaluate the Impact of Efforts to Estimate Costs of Reports and Studies,” US Government General Accountability Office report GAO-12-480R, May 10, 2012.

 

PHYSICS PRIZE: Joseph Keller [USA], and Raymond Goldstein [USA and UK], Patrick Warren, and Robin Ball [UK], for calculating the balance of forces that shape and move the hair in a human ponytail.

REFERENCE: “Shape of a Ponytail and the Statistical Physics of Hair Fiber Bundles.” Raymond E. Goldstein, Patrick B. Warren, and Robin C. Ball, Physical Review Letters, vol. 198, no. 7, 2012.
REFERENCE: “Ponytail Motion,” Joseph B. Keller, SIAM [Society for Industrial and Applied Mathematics] Journal of Applied Mathematics, vol. 70, no. 7, 2010, pp. 2667–72.

ATTENDING THE CEREMONY: Joseph Keller, Raymond Goldstein, Patrick Warren, Robin Ball

 

FLUID DYNAMICS PRIZE: Rouslan Krechetnikov [USA, RUSSIA, CANADA] and Hans Mayer [USA] for studying the dynamics of liquid-sloshing, to learn what happens when a person walks while carrying a cup of coffee.

REFERENCE: “Walking With Coffee: Why Does It Spill?” Hans C. Mayer and Rouslan Krechetnikov, Physical Review E, vol. 85, 2012.

ATTENDING THE CEREMONY: Rouslan Krechetnikov

 

ANATOMY PRIZE: Frans de Waal [The Netherlands and USA] and Jennifer Pokorny [USA] for discovering that chimpanzees can identify other chimpanzees individually from seeing photographs of their rear ends.

REFERENCE: “Faces and Behinds: Chimpanzee Sex Perception” Frans B.M. de Waal and Jennifer J. Pokorny, Advanced Science Letters, vol. 1, 99–103, 2008.

ATTENDING THE CEREMONY: Frans de Waal and Jennifer Pokorny

 

MEDICINE PRIZE: Emmanuel Ben-Soussan and Michel Antonietti [FRANCE] for advising doctors who perform colonoscopies how to minimize the chance that their patients will explode.

REFERENCE: “Colonic Gas Explosion During Therapeutic Colonoscopy with Electrocautery,” Spiros D Ladas, George Karamanolis, Emmanuel Ben-Soussan, World Journal of Gastroenterology, vol. 13, no. 40, October 2007, pp. 5295–8.
REFERENCE: “Argon Plasma Coagulation in the Treatment of Hemorrhagic Radiation Proctitis is Efficient But Requires a Perfect Colonic Cleansing to Be Safe,” E. Ben-Soussan, M. Antonietti, G. Savoye, S. Herve, P. Ducrotté, and E. Lerebours, European Journal of Gastroenterology & Hepatology, vol. 16, no. 12, December 2004, pp 1315-8.

ATTENDING THE THE CEREMONY: Emmanuel Ben-Soussan

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2012-09-10 New articles we read this week

Tuesday, September 11, 2012

Retinal Development

  1. Salbreux G, Barthel LK, Raymond PA, Lubensky DK. Coupling mechanical deformations and planar cell polarity to create regular patterns in the zebrafish retina. PLoS Comput Biol. 2012 Aug;8(8):e1002618. Epub 2012 Aug 23. PubMed PMID: 22936893; PubMed Central PMCID: PMC3426565.
  2. Chen M, Wang K, Lin B. Development and degeneration of cone bipolar cells are  independent of cone photoreceptors in a mouse model of retinitis pigmentosa. PLoS One. 2012;7(8):e44036. Epub 2012 Aug 31. PubMed PMID: 22952865.
  3. He J, Zhang G, Almeida AD, Cayouette M, Simons BD, Harris WA. How variable clones build an invariant retina. Neuron. 2012 Sep 6;75(5):786-98. PubMed PMID: 22958820.
    • Commentary: Chen Z, Li X, Desplan C. Deterministic or stochastic choices in retinal neuron specification. Neuron. 2012 Sep 6;75(5):739-42. PubMed PMID: 22958814.

Eye disease

  1. Murakami Y, Matsumoto H, Roh M, Suzuki J, Hisatomi T, Ikeda Y, Miller JW, Vavvas DG. Receptor interacting protein kinase mediates necrotic cone but not rod cell death in a mouse model of inherited degeneration. Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14598-603. Epub 2012 Aug 20. PubMed PMID: 22908283.
  2. Kohl S, Coppieters F, Meire F, Schaich S, Roosing S, Brennenstuhl C, Bolz S, van Genderen MM, Riemslag FC; the European Retinal Disease Consortium, Lukowski R, den Hollander AI, Cremers FP, De Baere E, Hoyng CB, Wissinger B. A Nonsense Mutation in PDE6H Causes Autosomal-Recessive Incomplete Achromatopsia. Am J Hum Genet. 2012 Sep 7;91(3):527-532. Epub 2012 Aug 16. PubMed PMID: 22901948.
  3. Manzini MC, Tambunan DE, Hill RS, Yu TW, Maynard TM, Heinzen EL, Shianna KV, Stevens CR, Partlow JN, Barry BJ, Rodriguez J, Gupta VA, Al-Qudah AK, Eyaid WM, Friedman JM, Salih MA, Clark R, Moroni I, Mora M, Beggs AH, Gabriel SB, Walsh CA. Exome Sequencing and Functional Validation in Zebrafish Identify GTDC2 Mutations as a Cause of Walker-Warburg Syndrome. Am J Hum Genet. 2012 Sep 7;91(3):541-7. PubMed PMID: 22958903.

Genetics

  1. Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14508-13. Epub 2012 Aug 1. PubMed PMID: 22853953.
  2. Papers related to ENCODE
      1. Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res. 2012 Sep;22(9):1748-59. PubMed PMID: 22955986.
      2. Stamatoyannopoulos JA. What does our genome encode? Genome Res. 2012 Sep;22(9):1602-11. PubMed PMID: 22955972.
      3. Frazer KA. Decoding the human genome. Genome Res. 2012 Sep;22(9):1599-601. PubMed PMID: 22955971.
    1. Nature (with links to Genome Research papers)
      1. Skipper M, Dhand R, Campbell P. Presenting ENCODE. Nature. 2012 Sep6;489(7414):45. doi: 10.1038/489045a. PubMed PMID: 22955612.
      2. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. Genomics: ENCODE explained. Nature. 2012 Sep 6;489(7414):52-5. doi: 10.1038/489052a. PubMed PMID: 22955614.
      3. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome.Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. PubMed PMID: 22955616.
      4. Thurman RE, et al., The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232. PubMed PMID: 22955617.
      5. Neph S, et al., An expansive human regulatory lexicon encoded in transcription factor footprints. Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212. PubMed PMID:22955618.
      6. Gerstein MB, et al., Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245. PubMed PMID: 22955619.
      7. Djebali S, et al., Landscape of transcription in human cells. Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233. PubMed PMID: 22955620.

Oxidative Stress

  1. Mukaigasa K, Nguyen LT, Li L, Nakajima H, Yamamoto M, Kobayashi M. Genetic Evidence of an Evolutionarily Conserved Role for Nrf2 in the Protection against Oxidative Stress. Mol Cell Biol. 2012 Sep 4. [Epub ahead of print] PubMed PMID: 22949501.

Stem cells

  1. Sancho-Martinez I, Baek SH, Izpisua Belmonte JC. Lineage conversion methodologies meet the reprogramming toolbox. Nat Cell Biol. 2012 Sep 3;14(9):892-9. doi: 10.1038/ncb2567. PubMed PMID: 22945254.
  2. Loh KM, Lim B. Epigenetics: Actors in the cell reprogramming drama. Nature. 2012 Aug 30;488(7413):599-600. doi: 10.1038/488599a. PubMed PMID: 22932382.

Medicine

  1. Asch DA, Volpp KG. What business are we in? The emergence of health as the business of health care. N Engl J Med. 2012 Sep 6;367(10):888-9. Epub 2012 Aug 30. PubMed PMID: 22931228.
  2. Fani Marvasti F, Stafford RS. From sick care to health care–reengineering prevention into the U.S. system. N Engl J Med. 2012 Sep 6;367(10):889-91. PubMed PMID: 22931257.
  3. Barnes KA, Kroening-Roche JC, Comfort BW. The developing vision of primary care. N Engl J Med. 2012 Sep 6;367(10):891-3. PubMed PMID: 22931258.
  4. Baker M. Doctors back circumcision. Nature. 2012 Aug 30;488(7413):568. doi: 10.1038/488568a. PubMed PMID: 22932355.
  5. Nature Outlook HPV
    1. Crow JM. HPV: The global burden. Nature. 2012 Aug 30;488(7413):S2-3. doi: 10.1038/488S2a. PubMed PMID: 22932437.

Nutrition

  1. Maxmen A. Calorie restriction falters in the long run. Nature. 2012 Aug 30;488(7413):569. doi: 10.1038/488569a. PubMed PMID: 22932356.

Ethics, Social and Legal Issues

  1. Greenland P, Fontanarosa PB. Ending honorary authorship. Science. 2012 Aug 31;337(6098):1019. PubMed PMID: 22936744.

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2012-09-03 new articles we read this week

Sunday, September 2, 2012

Stem cells

  1. Nakano T, Ando S, Takata N, Kawada M, Muguruma K, Sekiguchi K, Saito K, Yonemura S, Eiraku M, Sasai Y. Self-formation of optic cups and storable stratified neural retina from human ESCs. Cell Stem Cell. 2012 Jun 14;10(6):771-85. PubMed PMID: 22704518.
  2. Cyranoski D. Tissue engineering: The brainmaker. Nature. 2012 Aug 23;488(7412):444-6. doi: 10.1038/488444a. PubMed PMID: 22914148.
    • An interesting article about Dr. Sasai who leads the team to make the eye cup from human ESCs as described above and from mouse ESCs, among many other interesting discoveries!

Imaging

  1. Small A. Faster and more versatile tools for super-resolution fluorescence microscopy. Nat Methods. 2012 Jun 28;9(7):655-6. doi: 10.1038/nmeth.2079. PubMed PMID: 22743767.
  2. Weber M, Huisken J. Omnidirectional microscopy. Nat Methods. 2012 Jun 28;9(7):656-7. doi: 10.1038/nmeth.2022. PubMed PMID: 22743768.
  3. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012 Jun 28;9(7):676-82. doi: 10.1038/nmeth.2019. PubMed PMID: 22743772.
  4. Kankaanpää P, Paavolainen L, Tiitta S, Karjalainen M, Päivärinne J, Nieminen J, Marjomäki V, Heino J, White DJ. BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nat Methods. 2012 Jun 28;9(7):683-9.doi: 10.1038/nmeth.2047. PubMed PMID: 22743773.
  5. de Chaumont F, Dallongeville S, Chenouard N, Hervé N, Pop S, Provoost T, Meas-Yedid V, Pankajakshan P, Lecomte T, Le Montagner Y, Lagache T, Dufour A, Olivo-Marin JC. Icy: an open bioimage informatics platform for extended reproducible research. Nat Methods. 2012 Jun 28;9(7):690-6. doi: 10.1038/nmeth.2075. PubMed PMID: 22743774.
  6. Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE. Biological imaging software tools. Nat Methods. 2012 Jun 28;9(7):697-710. doi: 10.1038/nmeth.2084. PubMed PMID: 22743775.
  7. Ronneberger O, Liu K, Rath M, Rueß D, Mueller T, Skibbe H, Drayer B, Schmidt T, Filippi A, Nitschke R, Brox T, Burkhardt H, Driever W. ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains. Nat Methods. 2012  Jun 17;9(7):735-42. doi: 10.1038/nmeth.2076. PubMed PMID: 22706672.
  8. Lubeck E, Cai L. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat Methods. 2012 Jun 3;9(7):743-8. doi: 10.1038/nmeth.2069. PubMed PMID: 22660740; PubMed Central PMCID: PMC3418883.
  9. Tomer R, Khairy K, Amat F, Keller PJ. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat Methods. 2012 Jun 3;9(7):755-63. doi: 10.1038/nmeth.2062. PubMed PMID: 22660741.
  10. The quest for quantitative microscopy. Nat Methods. 2012 Jul;9(7):627. PubMed PMID: 22930824.
  11. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012 Jul;9(7):671-5. PubMed PMID: 22930834.

Systems Biology

  1. Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell. 2012 Jul 20;150(2):389-401. PubMed PMID: 22817898; PubMed Central PMCID: PMC3413483.
    • Commentary: Freddolino PL, Tavazoie S. The dawn of virtual cell biology. Cell. 2012 Jul 20;150(2):248-50. PubMed PMID: 22817888.

Genomics/Genetics

  1. Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A, Wong WS, Sigurdsson G, Walters GB, Steinberg S, Helgason H, Thorleifsson G, Gudbjartsson DF, Helgason A, Magnusson OT, Thorsteinsdottir U, Stefansson K. Rate of de novo mutations and the importance of father’s age to disease risk. Nature. 2012 Aug 23;488(7412):471-5. doi: 10.1038/nature11396. PubMed PMID: 22914163.
    • A new study that shows the older the father is, the more the mutations that he will pass to the next generation!
    • News: Callaway E. Fathers bequeath more mutations as they age. Nature. 2012 Aug 23;488(7412):439. doi: 10.1038/488439a. PubMed PMID: 22914142.
    • Commentary: Kondrashov A. Genetics: The rate of human mutation. Nature. 2012 Aug 23;488(7412):467-8. doi: 10.1038/488467a. PubMed PMID: 22914161.
  2. Schuster-Böckler B, Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature. 2012 Aug 23;488(7412):504-7. PubMed PMID: 22820252.

Development

  1. Lefebvre JL, Kostadinov D, Chen WV, Maniatis T, Sanes JR. Protocadherins mediate dendritic self-avoidance in the mammalian nervous system. Nature. 2012 Aug 23;488(7412):517-21. PubMed PMID: 22842903; PubMed Central PMCID: PMC3427422.
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Robotic researcher

Sunday, July 8, 2012

It is interesting that I come across this article about a robot that can conduct research and the article about the lack of jobs for scientists at the same time. A group of Japanese scientists have built a robot for conducting research experiments that may be too dangerous for human. From the cnet.com by Tim Hornyak: “Two-armed robot takes on risky lab work”

Unlike most assembly robots, its arms have seven joints, allowing it to use human tools and to perform humanlike motions easily. It automates lab work and can do tasks such as culturing more quickly and accurately than human lab techs.

From Cnet.com; Video screenshot by Tim Hornyak/CNET

As I am running a lab myself and always hope to get more data, the second I saw the setup with the pipettes, PCR and dry baths, I could not stop thinking “wouldn’t it be nice to have one of these robots to work in the lab for 24 hours…. “.

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