Posts tagged ‘medical research’

Retinal Development

  1. Kwan KM, Otsuna H, Kidokoro H, Carney KR, Saijoh Y, Chien CB. A complex choreography of cell movements shapes the vertebrate eye. Development. 2012 Jan;139(2):359-72. PubMed PMID: 22186726.
  2. Morgan JL, Soto F, Wong RO, Kerschensteiner D. Development of cell type-specific connectivity patterns of converging excitatory axons in the retina. Neuron. 2011 Sep 22;71(6):1014-21. Epub 2011 Sep 21. PubMed PMID: 21943599; PubMed Central PMCID: PMC3184549.

Stem cells

  1. Salero E, Blenkinsop TA, Corneo B, Harris A, Rabin D, Stern JH, Temple S. Adult Human RPE Can Be Activated into a Multipotent Stem Cell that Produces Mesenchymal Derivatives. Cell Stem Cell. 2012 Jan 6;10(1):88-95. PubMed PMID: 22226358.
    • Commentary: Trounson A, Grieshammer U. Chimeric Primates: Embryonic Stem Cells Need Not Apply. Cell. 2012 Jan 4. [Epub ahead of print] PubMed PMID: 22225613.
  2. Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods. 2011 Sep 11;8(10):821-7. doi: 10.1038/nmeth.1699. PubMed PMID: 21983960.

Genetics

  1. Zhang F, Vierock J, Yizhar O, Fenno LE, Tsunoda S, Kianianmomeni A, Prigge M, Berndt A, Cushman J, Polle J, Magnuson J, Hegemann P, Deisseroth K. The microbial opsin family of optogenetic tools. Cell. 2011 Dec 23;147(7):1446-57. PubMed PMID: 22196724.
  2. McMahon MA, Rahdar M, Porteus M. Gene editing: not just for translation anymore. Nat Methods. 2011 Dec 28;9(1):28-31. doi: 10.1038/nmeth.1811. PubMed PMID: 22205513.
  3. Zhao S, Ting JT, Atallah HE, Qiu L, Tan J, Gloss B, Augustine GJ, Deisseroth K, Luo M, Graybiel AM, Feng G. Cell  type–specific channelrhodopsin-2 transgenic mice for optogenetic dissection of neural circuitry function. Nat Methods. 2011 Sep;8(9):745-52. PubMed PMID: 21985008; PubMed Central PMCID: PMC3191888.

Genomics

  1. Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol. 2011 Dec 25;30(1):90-8. doi: 10.1038/nbt.2057. PubMed PMID: 22198700.
    • Commentary: Misteli T. Parallel genome universes. Nat Biotechnol. 2012 Jan 9;30(1):55-6. doi: 10.1038/nbt.2085. PubMed PMID: 22231096.
  2. Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O’Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2011 Dec  18;30(1):78-82. doi: 10.1038/nbt.2065. PubMed PMID: 22178993.
  3. Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol. 2011 Nov 13;30(1):99-104. doi: 10.1038/nbt.2024. PubMed PMID: 22081020.

Systems Biology

  1. Young JW, Locke JC, Altinok A, Rosenfeld N, Bacarian T, Swain PS, Mjolsness E, Elowitz MB. Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nat Protoc. 2011 Dec 15;7(1):80-8. doi: 10.1038/nprot.2011.432. PubMed PMID: 22179594.
  2. Dutkowski J, Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 2011 Sep;7(9):e1002180. Epub 2011 Sep 29. PubMed PMID: 21980275; PubMed Central PMCID: PMC3182870.

Neuroscience

  1. Kralj JM, Douglass AD, Hochbaum DR, Maclaurin D, Cohen AE. Optical recording of action potentials in mammalian neurons using a microbial rhodopsin. Nat Methods. 2011 Nov 27;9(1):90-5. doi: 10.1038/nmeth.1782. PubMed PMID: 22120467; PubMed Central PMCID: PMC3248630.
    • Commentary: Looger LL. Running in reverse: rhodopsins sense voltage. Nat Methods. 2011 Dec 28;9(1):43-4. doi: 10.1038/nmeth.1817. PubMed PMID: 22205516.
  2. Pan YA, Choy M, Prober DA, Schier AF. Robo2 determines subtype-specific axonal projections of trigeminal sensory neurons. Development. 2012 Feb;139(3):591-600. Epub 2011 Dec 21. PubMed PMID: 22190641; PubMed Central PMCID: PMC3252355.
  3. 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 Oct 11;21(19):1641-6. Epub 2011 Sep 22. PubMed PMID: 21945275.
  4. Cavallari N, Frigato E, Vallone D, Fröhlich N, Lopez-Olmeda JF, Foà A, Berti R, Sánchez-Vázquez FJ, Bertolucci C, Foulkes NS. A blind circadian clock in cavefish reveals that opsins mediate peripheral clock photoreception. PLoS Biol. 2011 Sep;9(9):e1001142. Epub 2011 Sep 6. PubMed PMID: 21909239; PubMed Central PMCID: PMC3167789.

Vision

  1. Kingdom FA. Binocular vision: the eyes add and subtract. Curr Biol. 2012 Jan 10;22(1):R22-4. PubMed PMID: 22240475.

Education

  1. Vanderford NL. Broadening PhD curricula. Nat Biotechnol. 2012 Jan 9;30(1):113-4. doi: 10.1038/nbt.2091. PubMed PMID: 22231111.

Medical Research

  1. Reed JC, White EL, Aubé J, Lindsley C, Li M, Sklar L, Schreiber S. The NIH’s role in accelerating translational sciences. Nat Biotechnol. 2012 Jan 9;30(1):16-9. doi: 10.1038/nbt.2087. PubMed PMID: 22231085.
  2. Hudson KL. Genomics, health care, and society. N Engl J Med. 2011 Sep 15;365(11):1033-41. Review. PubMed PMID: 21916641.
  3. Devi S. Lasker Foundation honours malaria researcher. Lancet. 2011 Sep 24;378(9797):1129. PubMed PMID: 21969956.

Zebrafish

  1. Thummel R, Bailey TJ, Hyde DR. <em>In vivo</em> Electroporation of Morpholinos into the Adult Zebrafish Retina. J Vis Exp. 2011 Dec 27;(58). pii: 3603. doi: 10.3791/3603. PubMed PMID: 22231802.
  2. Lawrence C. Advances in zebrafish husbandry and management. Methods Cell Biol. 2011;104:429-51. Review. PubMed PMID: 21924176.

Evolution

  1. Pearlman SM, Serber Z, Ferrell JE Jr. A mechanism for the evolution of phosphorylation sites. Cell. 2011 Nov 11;147(4):934-46. PubMed PMID: 22078888; PubMed Central PMCID: PMC3220604.

 

A warm Chinese-style welcoming at the entrance!

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

I recently visited the Eye Hospital at Wenzhou Medical College, where they have very good research infrastructure that has integrated various aspects of basic and clinical ophthalmology research together. I gave two talks over there and had a great interaction with everyone. I did not get a chance to take many pictures but here are a few snapshots of some interesting things that I have seen. One particularly impressive setup in their group is a large meeting and relaxing area that is right next to the research laboratories. Conducting a successful research is about communication and conversation; merely having good equipment is not enough, it is crucial to have effective interaction between research members at all levels. With a wonderful atmosphere as such, I can totally imagine the colleagues from Wenzhou will have very fruitful and exciting interactions. Indeed, the teachers there are very sincere and down-to-earth, and the students are very enthusiastic in learning new ideas. Many of them were in fact courageous enough to ask questions and discussed their ideas during and after my lectures. This is really contradictory to the stereotype of many quiet and obedient Asian students. No wonder their group has a very rigorous research and education program.

A nicely decorated balcony for students to take a break or spend time thinking about research!

A well lit meeting area for research group members to interact. I had an enjoyable lunch and conversation with several students here.

It is really gratifying to see that there are many Chinese Institutes conducting good research. When the West is undermining their good research infrastructure in the midst of a poor economy, it is not surprising that the East is going to catch up and will lead the scientific research in the near term future.

A glimpse of the prosperous Wenzhou city from my hotel room.

Medicine

There seems to be a new effective drug for Cystic Fibrosis!

  1. Ramsey BW, Davies J, McElvaney NG, Tullis E, Bell SC, Dřevínek P, Griese M, McKone EF, Wainwright CE, Konstan MW, Moss R, Ratjen F, Sermet-Gaudelus I, Rowe SM, Dong Q, Rodriguez S, Yen K, Ordoñez C, Elborn JS; VX08-770-102 Study Group. A CFTR potentiator in patients with cystic fibrosis and the G551D mutation. N Engl J Med. 2011 Nov 3;365(18):1663-72. PubMed PMID: 22047557.
    • Commentary: Davis PB. Therapy for cystic fibrosis–the end of the beginning? N Engl J Med. 2011 Nov 3;365(18):1734-5. PubMed PMID: 22047565.
    • News coverage: “Cystic Fibrosis Drug a Game Changer?” from WebMD.com

Medical Research

*These two articles point out the problems of using animal models for research if the goal is to extract translational values and how mouse model, the gold standard for disease research, can actually be a poor reference standard because of the ways we want to standardize the biological tool for testing.

  1. Lynch VJ. Use with caution: developmental systems divergence and potential pitfalls of animal models. Yale J Biol Med. 2009 Jun;82(2):53-66. Review. PubMed PMID: 19562005; PubMed Central PMCID: PMC2701150.
  2. Martin B, Ji S, Maudsley S, Mattson MP. “Control” laboratory rodents are metabolically morbid: why it matters. Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6127-33. Epub 2010 Mar 1. PubMed PMID: 20194732; PubMed Central PMCID: PMC2852022.

Genomics

  1. Tariq MA, Kim HJ, Jejelowo O, Pourmand N. Whole-transcriptome RNAseq analysis from minute amount of total RNA. Nucleic Acids Res. 2011 Oct 1;39(18):e120. Epub 2011 Jul 6. PubMed PMID: 21737426; PubMed Central PMCID: PMC3185437.
  2. Compeau PE, Pevzner PA, Tesler G. How to apply de Bruijn graphs to genome assembly. Nat Biotechnol. 2011 Nov 8;29(11):987-91. doi: 10.1038/nbt.2023. PubMed PMID: 22068540.
  3. Ala-Korpela M, Kangas AJ, Inouye M. Genome-wide association studies and systems biology: together at last. Trends Genet. 2011 Oct 20. [Epub ahead of print] PubMed PMID: 22018481.

Regeneration

  1. Kroehne V, Freudenreich D, Hans S, Kaslin J, Brand M. Regeneration of the adult zebrafish brain from neurogenic radial glia-type progenitors. Development.  2011 Nov;138(22):4831-41. Epub 2011 Oct 17. PubMed PMID: 22007133.

Disease/Evolution

  1. Cusack BP, Arndt PF, Duret L, Roest Crollius H. Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes. PLoS Genet. 2011 Oct;7(10):e1002276. Epub 2011 Oct 13. PubMed PMID: 22022272; PubMed Central PMCID: PMC3192821.
    • Commentary: Wilke CO. Transcriptional robustness complements nonsense-mediated decay in humans. PLoS Genet. 2011 Oct;7(10):e1002296. Epub 2011 Oct 13. PubMed PMID:22022274; PubMed Central PMCID: PMC3192817.
  2. Shelly T, McInnis D. Road test for genetically modified mosquitoes. Nat Biotechnol. 2011 Nov 8;29(11):984-5. doi: 10.1038/nbt.2025. PubMed PMID: 22068534.

Eye Disease

  1. Johnson LV, Forest DL, Banna CD, Radeke CM, Maloney MA, Hu J, Spencer CN, Walker AM, Tsie MS, Bok D, Radeke MJ, Anderson DH. Cell culture model that mimics drusen formation and triggers complement activation associated with age-related macular degeneration. Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18277-82. Epub 2011 Oct 3. PubMed PMID: 21969589.
  2. Jiang L, Zhang H, Dizhoor AM, Boye SE, Hauswirth WW, Frederick JM, Baehr W. Long-term RNA interference gene therapy in a dominant retinitis pigmentosa mouse model. Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18476-81. Epub 2011 Oct 31. PubMed PMID: 22042849.

Evolution

  1. Liu R, Ochman H. Stepwise formation of the bacterial flagellar system. Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7116-21. Epub 2007 Apr 16. Erratum in: Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11507. PubMed PMID: 17438286; PubMed Central PMCID: PMC1852327.

Systems biology

  1. Navlakha S, Bar-Joseph Z. Algorithms in nature: the convergence of systems biology and computational thinking. Mol Syst Biol. 2011 Nov 8;7:546. doi: 10.1038/msb.2011.78. PubMed PMID: 22068329.
  2. Ala-Korpela M, Kangas AJ, Inouye M. Genome-wide association studies and systems biology: together at last. Trends Genet. 2011 Oct 20. [Epub ahead of print] PubMed PMID: 22018481.
  3. Cheong R, Rhee A, Wang CJ, Nemenman I, Levchenko A. Information transduction capacity of noisy biochemical signaling networks. Science. 2011 Oct 21;334(6054):354-8. Epub 2011 Sep 15. PubMed PMID: 21921160.

Biotech business

  1. Francisco M. Third-quarter biotech job picture. Nat Biotechnol. 2011 Nov 8;29(11):1052. doi: 10.1038/nbt.2037. PubMed PMID: 22068542.

I just come across with this article in Slate Magazine “The Mouse Trap – The dangers of using one lab animal to study every disease.” that talks in great details about the limitation of using animal model to look for new drugs to treat human diseases.  For example, the control healthy mouse can actually be metabolically abnormal because of the way we keep and grow them. A recent paper published in the PNAS has unveiled some of these issues.

Martin B, Ji S, Maudsley S, Mattson MP. “Control” laboratory rodents are metabolically morbid: why it matters. Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6127-33. Epub 2010 Mar 1. PubMed PMID: 20194732; PubMed Central PMCID:  PMC2852022.

And I just notice that this slate article belongs to a series of article, including one that talks about my favorite – naked mole rats.

The Mouse Trap – The Trouble With Black-6A tiny alcoholic takes over the lab.

The Mouse Trap – The Anti-Mouse – Could a hairless African rodent be our secret weapon in the war on cancer?

Naked mole rat from Wikipedia

The genome sequence of the naked mole rat is published recently (Kim et al., 2011) ! This is an amazing creature that lives almost up to 30 years in captivity, 9 times longer than mice. At the same time they do not seem to suffer from cancer or a decline in fertility (Buffenstein 2008).

I have been fascinated by the research on the naked mole rats since I read an research article published by Vera Gorbunova’s group in 2009 (Seluanov et al., 2009). In this study, the authors elucidated the naturally occurred anti-cancer mechanism inside this creature. As it turns out, the cells from the naked mole rat will initiate a program to turn off cell growth as soon as the cells start touching each other in culture, a much earlier response than that in regular rats or mice. The most impressive finding is that this early program that can turn off cell growth actually uses the same cell division control mechanisms as in us, but it is just fine-tuned to respond to growth more sensitively. In the new study that sequenced the genome of the naked mole rat, a number of interesting findings have been found and may reveal other aspects of its longevity and physiology for this success and etc. I will save this for your own personal reading.

I find all these results beautiful and  powerfully remind us how studying our nature can lead to potentially important findings that can “translate” to human health; and how the “traditional” clinical research on human and classical animal models can miss the answer that is already out there.

Extended readings

  1. Buffenstein R. Negligible senescence in the longest living rodent, the naked mole-rat: insights from a successfully aging species. J Comp Physiol B. 2008 May;178(4):439-45. Epub 2008 Jan 8. Review. PubMed PMID: 18180931.
  2. Kim EB et al., Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature. 2011 Oct 12. doi: 10.1038/nature10533. [Epub ahead of print] PubMed PMID: 21993625.
  3. Seluanov A et al., Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat. Proc Natl Acad Sci U S A. 2009 Nov 17;106(46):19352-7. Epub 2009 Oct 26. PubMed PMID: 19858485; PubMed Central PMCID: PMC2780760.

				

Development

  1. Lander AD. Pattern, growth, and control. Cell. 2011 Mar 18;144(6):955-69. Review. PubMed PMID: 21414486; PubMed Central PMCID: PMC3128888.
  2. Braendle C, Felix MA. The other side of phenotypic plasticity: a developmental system that generates an invariant phenotype despite environmental variation. J Biosci. 2009 Oct;34(4):543-51. Review. PubMed PMID: 19920340.
  3. Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D. The dynamic architecture of Hox gene clusters. Science. 2011 Oct 14;334(6053):222-5. PubMed PMID: 21998387.

Genomics

  1. Sadeh R, Allis CD. Genome-wide “Re”-Modeling of Nucleosome Positions. Cell. 2011 Oct 14;147(2):263-6. PubMed PMID: 22000006.
  2. Lupski JR, Belmont JW, Boerwinkle E, Gibbs RA. Clan genomics and the complex architecture of human disease. Cell. 2011 Sep 30;147(1):32-43. PubMed PMID: 21962505.
  3. Raychaudhuri S. Mapping rare and common causal alleles for complex human diseases. Cell. 2011 Sep 30;147(1):57-69. PubMed PMID: 21962507; PubMed Central PMCID: PMC3198013.

Genetics

  1. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011 Oct 14;147(2):358-69. PubMed PMID: 22000014.

Funding

  1. Mervis J. Peer review. Beyond the data. Science. 2011 Oct 14;334(6053):169-71. PubMed PMID: 21998363.

Systems biology

  1. Liu C, Fu X, Liu L, Ren X, Chau CK, Li S, Xiang L, Zeng H, Chen G, Tang LH, Lenz P, Cui X, Huang W, Hwa T, Huang JD. Sequential establishment of stripe patterns in an expanding cell population. Science. 2011 Oct 14;334(6053):238-41.  PubMed PMID: 21998392.

Medical research

  1. Novarino G, Akizu N, Gleeson JG. Modeling human disease in humans: the ciliopathies. Cell. 2011 Sep 30;147(1):70-9. PubMed PMID: 21962508.