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The 2010 Ig Nobel Prize

Friday, October 1, 2010

Have your ever seen a Nobel laureate putting a bra on his face? Well… you can see three.

It is the time of the year for Ig Nobel Prize again….. 😉

Charles Krupa / AP

Nobel laureates Roy Glauber (Physics, 2005), Sheldon Glashow (Physics, 1979) and James Muller (Peace, 1985) demonstrate how bra cups that can be converted to emergency gas masks during the 2010 Ig Nobel Prize ceremony at Harvard. The bra-mask invention won one of the not-completely-serious scientific prizes in 2009. Charles Krupa / AP

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2010-9-29

Wednesday, September 29, 2010

John F. Rawlsa, Eve M. Mellgrena and Stephen L. Johnson1, a. How the Zebrafish Gets Its Stripes. Developmental Biology
Volume 240, Issue 2, 15 December 2001, Pages 301-314.

Kelsh RN, Schmid B, Eisen JS.  Genetic Analysis of Melanophore Development in Zebrafish Embryos. Developmental Biology
Volume 225, Issue 2, 15 September 2000, Pages 277-293.

Lee Y, Nachtrab G, Klinsawat PW, Hami D, Poss KD.   Ras controls menalocyte expansion during zebrafish fin stripe regeneration. Dis Model Mech. 2010 Jul-Aug;3(7-8):496-503. Epub 2010 May 18.

Johnson SL, Rawls JF.  Zebrafish kit mutation reveals primary and secondary regulation of melanocyte development during fin stripe regeneration. Development 127, 3715-3724 (2000).

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2010-09-25 New articles we read this week

Saturday, September 25, 2010

Genetics and Genomics

  1. Heard E, Tishkoff S, Todd JA, Vidal M, Wagner GP, Wang J, Weigel D, Young R. Ten years of genetics and genomics: what have we achieved and where are we heading? Nat Rev Genet. 2010 Oct;11(10):723-733. Epub 2010 Sep 7. PubMed PMID: 20820184.

Gene therapy

  1. Persons DA. Gene therapy: Targeting β-thalassaemia. Nature. 2010 Sep 16;467(7313):277-8. PubMed PMID: 20844523.
  2. Cavazzana-Calvo M, Payen E, Negre O, Wang G, Hehir K, Fusil F, Down J, Denaro M, Brady T, Westerman K, Cavallesco R, Gillet-Legrand B, Caccavelli L, Sgarra R, Maouche-Chrétien L, Bernaudin F, Girot R, Dorazio R, Mulder GJ, Polack A, Bank A, Soulier J, Larghero J, Kabbara N, Dalle B, Gourmel B, Socie G, Chrétien S, Cartier N, Aubourg P, Fischer A, Cornetta K, Galacteros F, Beuzard Y, Gluckman E, Bushman F, Hacein-Bey-Abina S, Leboulch P. Transfusion independence and HMGA2 activation after gene therapy of human β-thalassaemia. Nature. 2010 Sep 16;467(7313):318-22. PubMed PMID: 20844535.

Imaging

  1. Watanabe K, Nishimura Y, Oka T, Nomoto T, Kon T, Shintou T, Hirano M, Shimada Y, Umemoto N, Kuroyanagi J, Wang Z, Zhang Z, Nishimura N, Miyazaki T, Imamura T, Tanaka T. In vivo imaging of zebrafish retinal cells using fluorescent coumarin derivatives. BMC Neurosci. 2010 Sep 15;11:116. PubMed PMID: 20843315.

Neuroscience

  1. Williams PR, Suzuki SC, Yoshimatsu T, Lawrence OT, Waldron SJ, Parsons MJ, Nonet ML, Wong RO.
    In vivo development of outer retinal synapses in the absence of glial contact. J Neurosci. 2010 Sep 8;30(36):11951-61. PMID: 20826659

Stem cells

  1. Zwaka TP. Stem cells: Troublesome memories. Nature. 2010 Sep 16;467(7313):280-1. PubMed PMID: 20844526.
  2. Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Aryee MJ, Ji H, Ehrlich LI, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, McKinney-Freeman S, Naveiras O,  Yoon TJ, Irizarry RA, Jung N, Seita J, Hanna J, Murakami P, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg AP, Daley GQ. Epigenetic memory in  induced pluripotent stem cells. Nature. 2010 Sep 16;467(7313):285-90. PubMed PMID: 20644535.
  3. Ji H, Ehrlich LI, Seita J, Murakami P, Doi A, Lindau P, Lee H, Aryee MJ, Irizarry RA, Kim K, Rossi DJ, Inlay MA, Serwold T, Karsunky H, Ho L, Daley GQ, Weissman IL, Feinberg AP. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010 Sep 16;467(7313):338-42. Epub 2010 Aug 15. PubMed PMID: 20720541.
  4. Aguirre A, Rubio ME, Gallo V. Notch and EGFR pathway interaction regulates neural stem cell number and self-renewal. Nature. 2010 Sep 16;467(7313):323-7. PubMed PMID: 20844536; PubMed Central PMCID: PMC2941915.

Zebrafish

  1. Van Otterloo E, Li W, Bonde G, Day KM, Hsu MY, Cornell RA. Differentiation of zebrafish melanophores depends on transcription factors AP2 alpha and AP2 epsilon. PLoS Genet. 2010 Sep 16;6(9). pii: e1001122. PubMed PMID: 20862309.
  2. Maurer CM, Schönthaler HB, Mueller KP, Neuhauss SC.  Distinct retinal deficits in a zebrafish pyruvate dehydrogenase-deficient mutant. J Neurosci. 2010 Sep 8;30(36):11962-72. PMID: 20826660
  3. Gavriouchkina D, Fischer S, Ivacevic T, Stolte J, Benes V, Dekens MP. Thyrotroph embryonic factor regulates light-induced transcription of repair genes in zebrafish embryonic cells. PLoS One. 2010 Sep 7;5(9):e12542. PubMed PMID: 20830285; PubMed Central PMCID: PMC2935359.
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The script of an interesting lecture

Thursday, September 23, 2010

There is an interesting article in this week nature’s careers’ section that talks about the risks that young scientists should take to make a difference.

“The right kind of risk – More young scientists should dedicate a portion of their attention to high-risk research despite the potential downside, argues Abraham Loeb.”

The article is adapted from a lecture that the script is available here.

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2010-09-19 new articles we read this week

Sunday, September 19, 2010

Development

  1. Hamra FK. Gene targeting: Enter the rat. Nature. 2010 Sep 9;467(7312):161-3. PubMed PMID: 20829783.

Genomics

  1. Bayley H. Nanotechnology: Holes with an edge. Nature. 2010 Sep 9;467(7312):164-5. PubMed PMID: 20829786.

Medicine

  1. Willyard C. The real war on drugs. Nat Med. 2010 Sep;16(9):948-52. PubMed PMID: 20823866.
  2. Dolgin E. Personalized investigation. Nat Med. 2010 Sep;16(9):953-5. PubMed PMID: 20823867.
  3. Kaynar AM, Shapiro SD. NET loss of air in cystic fibrosis. Nat Med. 2010 Sep;16(9):967-9. PubMed PMID: 20823877.
  4. Ellis LM, Fidler IJ. Finding the tumor copycat: Therapy fails, patients don’t. Nat Med. 2010 Sep;16(9):974-5. PubMed PMID: 20823880.
  5. Van Dyke T. Finding the tumor copycat: Approximating a human cancer. Nat Med. 2010 Sep;16(9):976-7. PubMed PMID: 20823881.
  6. Bonham VL, Dover GJ, Brody LC. Screening student athletes for sickle cell trait – a social and clinical experiment. N Engl J Med. 2010 Sep 9;363(11):997-9. PubMed PMID: 20825310.
  7. Rezaie R, Singer PA. Global health or global wealth? Nat Biotechnol. 2010 Sep;28(9):907-9. PubMed PMID: 20829824.

Retinal development

  1. Prasov L, Brown NL, Glaser T. A critical analysis of Atoh7 (Math5) mRNA splicing in the developing mouse retina. PLoS One. 2010 Aug 24;5(8). pii: e12315. PubMed PMID: 20808762; PubMed Central PMCID: PMC2927423.
  2. Erickson T, French CR, Waskiewicz AJ. Meis1 specifies positional information in the retina and tectum to organize the zebrafish visual system. Neural Dev. 2010 Sep 1;5(1):22. [Epub ahead of print] PubMed PMID: 20809932.
  3. Ben Fredj N, Hammond S, Otsuna H, Chien CB, Burrone J, Meyer MP. Synaptic activity and activity-dependent competition regulates axon arbor maturation, growth arrest, and territory in the retinotectal projection. J Neurosci. 2010 Aug 11;30(32):10939-51. PubMed PMID: 20702722.

Systems biology  & Gene regulatory network

  1. Shoval O, Goentoro L, Hart Y, Mayo A, Sontag E, Alon U. Fold-change detection and scalar symmetry of sensory input fields. Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15995-6000. Epub 2010 Aug 20. PubMed PMID: 20729472.
  2. Serb JM, Orr MC, West Greenlee MH. Using evolutionary conserved modules in gene networks as a strategy to leverage high throughput gene expression queries. PLoS One. 2010 Sep 2;5(9). pii: e12525. PubMed PMID: 20824082; PubMed Central PMCID: PMC2932711.
  3. de Bivort BL. Derivation of large-scale cellular regulatory networks from biological time series data. Methods Mol Biol. 2010;662:149-65. PubMed PMID: 20824470.
  4. Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH, Sinha S. Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol. 2010 Aug 17;8(8). pii: e1000456. PubMed PMID: 20808951; PubMed Central PMCID: PMC2923081.
  5. Kuttykrishnan S, Sabina J, Langton LL, Johnston M, Brent MR. A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription. Proc Natl Acad Sci U S A. 2010 Sep 1. [Epub ahead of print] PubMed PMID: 20810924.
  6. Sun L, Becskei A. Systems biology: The cost of feedback control. Nature. 2010 Sep 9;467(7312):163-4. PubMed PMID: 20829785.
  7. Eldar A, Elowitz MB. Functional roles for noise in genetic circuits. Nature. 2010 Sep 9;467(7312):167-73. PubMed PMID: 20829787.
  8. Lestas I, Vinnicombe G, Paulsson J. Fundamental limits on the suppression of molecular fluctuations. Nature. 2010 Sep 9;467(7312):174-8. PubMed PMID: 20829788.

Toxicology

  1. Larsen MG, Baatrup E. Functional behavior and reproduction in androgenic sex reversed zebrafish (Danio rerio). Environ Toxicol Chem. 2010 Aug;29(8):1828-33. PubMed PMID: 20821638.
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2010-09-11 New articles we read this week

Saturday, September 11, 2010

Systems biology and Genomics

  1. Chen WW, Niepel M, Sorger PK. Classic and contemporary approaches to modeling biochemical reactions. Genes Dev. 2010 Sep 1;24(17):1861-75. PubMed PMID: 20810646.
  2. Schatz MC, Delcher AL, Salzberg SL. Assembly of large genomes using second-generation sequencing. Genome Res. 2010 Sep;20(9):1165-73. Epub 2010 May 27. PubMed PMID: 20508146.
  3. Zhuravel D, Fraser D, St-Pierre S, Tepliakova L, Pang WL, Hasty J, Kærn M. Phenotypic impact of regulatory noise in cellular stress-response pathways. Syst Synth Biol. 2010 Jun;4(2):105-116.
  4. Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods. 2010 Sep;7(9):709-15. Epub 2010 Aug 15. PubMed PMID: 20711195.

Imaging

  1. Peng H, Ruan Z, Long F, Simpson JH, Myers EW. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat Biotechnol. 2010 Apr;28(4):348-53. Epub 2010 Mar 14. PubMed PMID: 20231818; PubMed Central PMCID: PMC2857929.
  2. Peng H, Ruan Z, Atasoy D, Sternson S. Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model. Bioinformatics. 2010 Jun 15;26(12):i38-46. PubMed PMID: 20529931; PubMed Central PMCID: PMC2881396.
  3. Liu X, Long F, Peng H, Aerni SJ, Jiang M, Sánchez-Blanco A, Murray JI, Preston E, Mericle B, Batzoglou S, Myers EW, Kim SK. Analysis of cell fate from single-cell gene expression profiles in C. elegans. Cell. 2009 Oct 30;139(3):623-33. PubMed PMID: 19879847.
  4. Long F, Peng H, Liu X, Kim SK, Myers E. A 3D digital atlas of C. elegans and its application to single-cell analyses. Nat Methods. 2009 Sep;6(9):667-72. Epub 2009 Aug 16. PubMed PMID: 19684595; PubMed Central PMCID: PMC2882208.
  5. Peng H, Long F, Liu X, Kim SK, Myers EW. Straightening Caenorhabditis elegans images. Bioinformatics. 2008 Jan 15;24(2):234-42. Epub 2007 Nov 19. PubMed PMID: 18025002.

Medicine

  1. Physician, know thyself. Lancet. 2010 Sep 4;376(9743):743. PubMed PMID: 20816524.

Eye disease

  1. Li L, Nakaya N, Chavali VR, Ma Z, Jiao X, Sieving PA, Riazuddin S, Tomarev SI, Ayyagari R, Riazuddin SA, Hejtmancik JF.  A Mutation in ZNF513, a Putative Regulator of Photoreceptor Development, Causes Autosomal-Recessive Retinitis Pigmentosa. Am J Hum Genet. 2010 Aug 25;. [Epub ahead of print] PMID: 20797688

Neuroscience and behaviour

  1. Feitl KE, Ngo V, McHenry MJ.  Are fish less responsive to a flow stimulus when swimming? J Exp Biol. 2010 Sep 15;213(Pt 18):3131-7. PubMed PMID: 20802114.
  2. Youk H, van Oudenaarden A. Microbiology: Altruistic defence. Nature. 2010 Sep 2;467(7311):34-5. PubMed PMID: 20811443.

Education

  1. Ditty JL, Kvaal CA, Goodner B, Freyermuth SK, Bailey C, Britton RA, Gordon SG, Heinhorst S, Reed K, Xu Z, Sanders-Lorenz ER, Axen S, Kim E, Johns M, Scott K, Kerfeld CA. Incorporating genomics and bioinformatics across the life sciences curriculum. PLoS Biol. 2010 Aug 10;8(8):e1000448. PubMed PMID: 20711478; PubMed Central PMCID: PMC2919421.

Stem cell

  1. Buxboim A, Discher DE. Stem cells feel the difference. Nat Methods. 2010 Sep;7(9):695-7. PubMed PMID: 20805798.
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Neil Tyson talks about UFOs and the argument from ignorance.

Saturday, September 11, 2010

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2010-09-05 New articles we read this week

Sunday, September 5, 2010

Development

    1. Wright MA, Mo W, Nicolson T, Ribera AB. In vivo evidence for transdifferentiation of peripheral neurons. Development. 2010 Sep;137(18):3047-56. Epub 2010 Aug 4. PubMed PMID: 20685733.
    2. Egger B, Gold KS, Brand AH. Notch regulates the switch from symmetric to asymmetric neural stem cell division in the Drosophila optic lobe. Development. 2010 Sep;137(18):2981-7. Epub 2010 Aug 4. PubMed PMID: 20685734.
    3. Chaabouni M, Etchevers H, De Blois MC, Calvas P, Waill-Perrier MC, Vekemans M, Romana SP. Identification of the IRX B genes cluster as candidate genes in severe dysgenesis of the ocular anterior segment. Invest Ophthalmol Vis Sci. 2010 Feb 17. [Epub ahead of print] PubMed PMID: 20164457.
    4. McCurley AT, Callard GV. Time Course Analysis of Gene Expression Patterns in Zebrafish Eye During Optic Nerve Regeneration. J Exp Neurosci. 2010 Jul 13;2010(4):17-33. PubMed PMID: 20740047.

      Neuroscience

        1. Nakane Y, Ikegami K, Ono H, Yamamoto N, Yoshida S, Hirunagi K, Ebihara S, Kubo Y, Yoshimura T. A mammalian neural tissue opsin (Opsin 5) is a deep brain photoreceptor in birds. Proc Natl Acad Sci U S A. 2010 Aug 24;107(34):15264-8. Epub 2010 Aug 2. PubMed PMID: 20679218.
        2. Altimus CM, Güler AD, Alam NM, Arman AC, Prusky GT, Sampath AP, Hattar S. Rod photoreceptors drive circadian photoentrainment across a wide range of light intensities. Nat Neurosci. 2010 Sep;13(9):1107-12. Epub 2010 Aug 15. PubMed PMID: 20711184.
        3. Zheng YL, Amin ND, Hu YF, Rudrabhatla P, Shukla V, Kanungo J, Keshavpany S, Grant P, Albers W, Pant HC. A 24 residue peptide (P5), derived from P35, the CDK5 neuronal activator, specifically inhibits CDK5/P25 hyperactivity and tau hyperphosphorylation. J Biol Chem. 2010 Aug 18;. [Epub ahead of print]
          PMID: 20720012

          Medicine

            1. Dietz HC. New Therapeutic Approaches to Mendelian Disorders. N Engl J Med 2010; 363:852-863. http://www.nejm.org/doi/full/10.1056/NEJMra0907180
            2. Khor CC, Fan Q, Goh L, Tan D, Young TL, Li YJ, Seielstad M, Goh DL, Saw SM.  Support for TGFB1 as a susceptibility gene for high myopia in individuals of Chinese descent. Arch Ophthalmol. 2010 Aug;128(8):1081-4. PMID: 20697017
            3. Holahan CJ, Schutte KK, Brennan PL, Holahan CK, Moos BS, Moos RH. Late-Life Alcohol Consumption and 20-Year Mortality. Alcohol Clin Exp Res. 2010 Aug 24. [Epub ahead of print] PubMed PMID: 20735372.

              Genomics

                1. Vogel C, de Sousa Abreu R, Ko D, Le SY, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol. 2010 Aug 24;6:400. PubMed PMID: 20739923.
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                  Journal club on Sep-17-2010

                  Thursday, September 2, 2010

                  I suggest we read a paper recently published in Science. The title is “Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa”. Retinal pigmentosa is so far found to be caused by diverse mutations in 44 genes. Patients with this diease will irreversibly lose their vision, as rod photoreceptors will die early and cone photoreceptor will be light-insensitive owing to the morphological change. But normally cone photoreceptors could persist longer. In this study, the authers genetically targeted a light activated chloride pump, which is one of the candidates for reactivating vertebrate photoreceptors, into the photorecepors of mouse models of retinitis pigmentosa by means of adneo-associated viruses, and successfully restored their light sensitivity. They also found the protein could reactivate the light-insensitive human photoreceptors in ex vivo retinas. Is this a good news for people who suffer from retinitis pigmentosa and blindness? Let’s find out together.

                  Link to the paper:

                  http://www.sciencemag.org/cgi/content/full/329/5990/413

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                  2010-08-29 New articles we read this week

                  Monday, August 30, 2010

                  Ethics

                  1. Coors ME, Glover JJ, Juengst ET, Sikela JM. The ethics of using transgenic non-human primates to study what makes us human. Nat Rev Genet. 2010 Sep;11(9):658-62. PubMed PMID: 20717156.

                  Systems biology

                  1. Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP. Computational solutions to large-scale data management and analysis. Nat Rev Genet. 2010 Sep;11(9):647-57. PubMed PMID: 20717155.
                  2. Morelli LG, Ares S, Herrgen L, Schröter C, Jülicher F, Oates AC. Delayed coupling theory of vertebrate segmentation. HFSP J. 2009;3(1):55-66. Epub 2008 Dec 10.

                  Evolution

                  1. Klingenberg CP. Evolution and development of shape: integrating quantitative approaches. Nat Rev Genet. 2010 Sep;11(9):623-35. Epub 2010 Aug 10. PubMed PMID: 20697423.
                  2. Cockburn A. Evolutionary biology: Oh sibling, who art thou? Nature. 2010 Aug 19;466(7309):930-1. PubMed PMID: 20725030.
                  3. Cornwallis CK, West SA, Davis KE, Griffin AS. Promiscuity and the evolutionary transition to complex societies. Nature. 2010 Aug 19;466(7309):969-72. PubMed PMID: 20725039.

                  Aging and neuroscience

                  1. Valdez G, Tapia JC, Kang H, Clemenson GD Jr, Gage FH, Lichtman JW, Sanes JR. Attenuation of age-related changes in mouse neuromuscular synapses by caloric restriction and exercise. Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14863-8. Epub 2010 Aug 2. PubMed PMID: 20679195.

                  Genomics, Genetics

                  1. Hutt D, Balch WE. Cell Biology. The proteome in balance. Science. 2010 Aug 13;329(5993):766-7. PubMed PMID: 20705837.
                  2. Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, Haig D, Dulac C. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science. 2010 Aug 6;329(5992):643-8. Epub 2010 Jul 8. PubMed PMID:20616232.
                  3. Gregg C, Zhang J, Butler JE, Haig D, Dulac C. Sex-specific parent-of-origin allelic expression in the mouse brain. Science. 2010 Aug 6;329(5992):682-5. Epub 2010 Jul 8. PubMed PMID: 20616234.
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