Posts tagged ‘evolution’

Genomics

  1. Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013 Oct 21;14(10):R115. [Epub ahead of print] PubMed PMID: 24138928.
  2. News: FDA Tells Google-Backed 23andMe to Halt DNA Test Service

Evolution

  1. Kolb AW, Ané C, Brandt CR. Using HSV-1 Genome Phylogenetics to Track Past Human Migrations. PLoS One. 2013 Oct 16;8(10):e76267. doi: 10.1371/journal.pone.0076267. PubMed PMID: 24146849; PubMed Central PMCID:PMC3797750.
Neuroscience
  1. Clark C, Austen O, Poparic I, Guthrie S. a2-Chimaerin Regulates a Key Axon Guidance Transition during Development of the Oculomotor Projection. J Neurosci.  2013 Oct 16;33(42):16540-51. doi: 10.1523/JNEUROSCI.1869-13.2013. PubMed PMID:24133258.
  2. Lange M, Neuzeret F, Fabreges B, Froc C, Bedu S, Bally-Cuif L, Norton WH. Inter-individual and inter-strain variations in zebrafish locomotor ontogeny. PLoS One. 2013;8(8):e70172. doi: 10.1371/journal.pone.0070172. eCollection 2013.  PubMed PMID: 23950910; PubMed Central PMCID: PMC3739779.

 HIV/AIDS

  1. News: Two famously ‘cured’ Boston HIV sufferers are found to STILL have the virus ‘hiding’ in their blood 

 

Evolution

  1. Feuda R, Hamilton SC, McInerney JO, Pisani D. Metazoan opsin evolution reveals a simple route to animal vision. Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18868-72. doi: 10.1073/pnas.1204609109. Epub 2012 Oct 29. PubMed PMID: 23112152; PubMed Central PMCID: PMC3503164.

Genetics

  1. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science. 2013 Jan 3. [Epub ahead of print] PubMed PMID: 23287718.
  2. Mali P, Yang L, Esvelt KM, Aach J, Guell M, Dicarlo JE, Norville JE, Church GM. RNA-Guided Human Genome Engineering via Cas9. Science. 2013 Jan 3. [Epub ahead of print] PubMed PMID: 23287722.

Evolution

  1. Ramani AK, Chuluunbaatar T, Verster AJ, Na H, Vu V, Pelte N, Wannissorn N, Jiao A, Fraser AG. The majority of animal genes are required for wild-type fitness. Cell. 2012 Feb 17;148(4):792-802. PubMed PMID: 22341449.
  2. Loehlin DW, Werren JH. Evolution of shape by multiple regulatory changes to a growth gene. Science. 2012 Feb 24;335(6071):943-7. PubMed PMID: 22363002.

Psychology and human behaviour

  1. Pazda AD, Elliot AJ, Greitemeyer T. Sexy red: Perceived sexual receptivity mediates the red-attraction relation in men viewing woman. J Exp Soc Psychol. 2012; 48: 787-790
  2. Cohen S, Schulz MS, Weiss E, Waldinger RJ. Eye of the Beholder: The Individual and Dyadic Contributions of Empathic Accuracy and Perceived Empathic Effort to Relationship Satisfaction. J Fam Psychol. 2012 Feb 27. [Epub ahead of print] PubMed PMID: 22369462.

Men like it when women let them know when they’re happy. Women like it when men share their anger and frustration.

Evidently we women see a man’s willingness to share negative feelings as a sign that he’s invested in the relationship. Cohen says: “That’s telling her something about his availability to engage in the conflict.”

Men feel exactly the opposite about those moments of conflict: They see it as a threat to the relationship. Instead, Cohen says, “They do derive satisfaction when their girlfriends or wives are happy.”

Stem cells/ development

  1. White YA, Woods DC, Takai Y, Ishihara O, Seki H, Tilly JL. Oocyte formation by mitotically active germ cells purified from ovaries of reproductive-age women. Nat Med. 2012 Feb 26;18(3):413-21. doi: 10.1038/nm.2669. PubMed PMID: 22366948; PubMed Central PMCID: PMC3296965.

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.

 

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 read several classic papers when I am planning projects with some of you. This is a very good review paper on the fundamental architecture of retina. There are a lot useful histological facts and observations. It has great discussions on how the retinal architecture has evolved and in turn provides the necessary visual functions to the animal. I believe you will also find this review paper useful.

Reference

Masland RH. The fundamental plan of the retina. Nat Neurosci. 2001 Sep;4(9):877-86.[PubMed][Nat Neurosci]

This is a series of papers from a recent Sackler colloquium of the National Academy of Sciences entitled “In the Light of Evolution III: Two Centuries of Darwin“. You can watch most of the presentations online here. The conference papers are published in a supplemental issue of the PNAS.

I read Daniel Dennett‘s paper because of my personal interest. He is a philosopher in science. In his paper, he provides a simple overview on why it is not necessary to have an intelligent designer to make complicated biological machines.

Reference

Dennett D. Darwin’s “strange inversion of reasoning”. Proc Natl Acad Sci U S A. 2009 Jun 15. [PubMed][pdf]

Why do we laugh? Is there any evolutionary significance? Well, instead of pondering about these questions… why not tickle a primate to find it out?

Humans aren’t the only ones who like it in the armpit. Our fellow great apes — orangutans, chimps, bonobos and gorillas — also squeal in response to tickling, and new research shows this behavior may be the evolutionary root of human laughter.

….

Laughter is a key component of social interaction in humans. Humans are 30 times more likely to laugh when in the company of other humans than not, and tickling is inherently social — no animal is capable of tickling itself. Understanding the origins of laughter can also lend insight to the evolution of language, as both behaviors involve breath control and vocal cord vibrations.

References

Human Laughter Echoes Chimp Chuckles [Wired]

Ross MD, Owren MJ, Zimmermann E. Reconstructing the Evolution of Laughter in Great Apes and Humans. 2009 June [Current Biology]

A fundamental but elusive step in the early evolution of life on Earth has been replicated in a laboratory.

Researchers synthesized the basic ingredients of RNA, a molecule from which the simplest self-replicating structures are made. Until now, they couldn’t explain how these ingredients might have formed.

….

No matter how they combined the ingredients — a sugar, a phosphate, and one of four different nitrogenous molecules, or nucleobases — ribonucleotides just wouldn’t form. Sutherland’s team took a different approach “and successfully synthesized RNA” in a laboratory conditions resembled those of the life-originating “warm little pond”.

References:

Life’s First Spark Re-Created in the Laboratory [Wired]

Powner MW, Gerland B, Sutherland JD. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature. 2009 May 14;459(7244):239-42. [PubMed][Nature]

We briefly mentioned the idea of silent mutation in the lab meeting the other day when we discussed how DNA mutations can cause diseases. In general, a polymorphism in the wobble (3rd) position of the DNA codon often would not change the amino acid sequence. However, that doesn’t mean everything would be the same or the polymorphism would have no effect on the resulting system. It has long been known that there is codon bias, the preference of using particular codons, among different organisms. This may have implications on the fitness of the animals and evolution.

Josh Plotkin’s group at the University of Pennsylvania has recently done a very interesting study on this topic in Science magazine. They synthesized a synthetic library of 154 green fluorescent protein (GFP) with an average of 114 silent mutations between each pair. They found the expressing of these GFPs in E. Coli, as measured by fluorescence of the GFP, can vary as much as 250 fold! Further analyses revealed that this expression difference did not correlate with the codon bias but more to the secondary structures of the RNA.

As it turned out, RNA with more stable secondary structure was harder to be translated into protein and hence a lower expression level. Also, the stability near 5′ start codon explained most of the expression variation, which indicates the rate limiting step of gene expression was primarily translation initiation. They further predicted and experimentally validated GFP variants with rare codon usage, which presumably were more difficult to produce, would be highly expressed if attached with a 5′ sequence with weaker RNA secondary structure. Therefore silent mutations are not that silent after all, it depends on whether you have the right ear to hear.

Reference

Kudla G, Murray AW, Tollervey D, Plotkin JB. Coding-sequence determinants of gene expression in Escherichia coli. Science. 2009 Apr 10;324(5924):255-8.Click here to read [PubMed][Science]