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Fetal stem cells can repair mom’s heart after heart attack

From Discover magazine: “Helpful Mouse Fetuses Naturally Send Stem Cells to Mom to Fix Her Damaged Heart”

The punchline is

When a pregnant mouse has a heart attack, her fetus donates some of its stem cells to help rebuild the damaged heart tissue.

The original article is available here.

Kara RJ, Bolli P, Karakikes I, Matsunaga I, Tripodi J, Tanweer O, Altman P, Shachter NS, Nakano A, Najfeld V, Chaudhry HW. Fetal Cells Traffic to Injured Maternal Myocardium and Undergo Cardiac Differentiation. Circ Res. 2011 Nov 14. [Epub ahead of print] PubMed PMID: 22082491.

Can Lytro camera be an economical replacement of confocal microscopy?

These days with tight budget and poor economy, I am always intrigued in finding ways to conserve my research funding, which I think is a responsible approach to research rather than the big spending and throwing-away-old-but-good-equipment mentality. For example, all monitors in my office are old, unwanted CRT monitors. The oldest one is a Sony Trinitron that I picked up as a postdoc at Harvard in 2004, when they were throwing away many CRTs and replacing them with the sexy LCD monitors. It is still running great and I wish I could pick up more at that time.

Anyway, there is an interesting new consumer camera called Lytro that has just been launched recently. It is based on a revolutionized light field concept that can capture not just the color and intensity, but also the vector direction of the light. Thus, information with regards to the location of the object be extracted after image acquisition; in other words, one can “focus” after image acquisition in the computer. This concept is originated from the Ph.D. research of Ren Ng, Lytro’s CEO, at Stanford.

I think the concept can potentially be applicable to research imaging in life-science. For example, in fluorescent imaging, we always want to acquire information from a very specific focal plane of the specimen. One fancy way to exclude the out-of-focus information is by confocal microscopy,  a fancier way of imaging which is not a cheap at all. From my limited understanding, Lytro’s principle can potentially be applicable to generate an effect that is similar to confocal on a regular fluorescent microscope, perhaps with some essential modifications of the algorithms. If that is possible, then Lytro can be a very economical replacement (a few hundreds) of confocal (hundreds of thousands). I immediately emailed them about that and asked for the possibility of getting a unit to play with. Of course they said thank you for the great idea, but no, we won’t be able to send you one.

I do hope someone, including Lytro, who has time and interest, can figure this application out… then we can have a $400 confocal! Think about capturing all the confocal market in the field!

All students should realize what is going on in the country and your sister institutions

and the reasons behind the OWS movement.

From boingboing:

Police officer pepper-sprays seated, non-violent students at UC Davis

Interview with a pepper-sprayed UC Davis student

Photo:Brian Nguyen/The Aggie. From: boingboing.net

2011-11-20 new articles we read this week

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.

The Mouse Trap – the issues with using animal model for medical research

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?

Douglas Prasher and the Green Fluorescent Protein

Douglas Prasher by Miller Mobley

The other day I shared the story of Douglas Prasher‘s with the medical students in my class.  Dr. Prasher’s contribution to the study of Green Fluorescent Protein had ultimately led to the Nobel Prize in Chemistry in 2008; however he was not one of the laureates because of life circumstances. During my preparation, I read some of the stories again and came across this recent article “How Bad Luck & Bad Networking Cost Douglas Prasher a Nobel Prize” published in the Discover Magazine. The article provides an in-depth coverage of the struggles that Dr. Prasher has  gone through over the years. I have been deeply impressed with his determination and noble attitudes over the years despite the difficult situations. I also really like the amazing portraits that Miller Mobley took for this article in the Discover Magazine.  The lighting and composition of his work is outstanding that each picture is like an intense and charming moment that is frozen in time, including the ones for Dr. Prasher.

The genome of the naked mole rat!

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.


				

2011-10-29 new articles we read this week

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.

How data interpretation can be distorted by its presentation

Gary Schwitzer, Publisher of HealthNewsReview.org

 

The other day my reading of Three common mistakes in medical journalism brought me to the original blog article How the News Media May Hurt – Not Help – Health Literacy Efforts. The author Gary Schwitzer discusses nicely three issues of data presentation in public media that may lead to distortion of interpretation of the findings from medical research.

  1. Absolute versus relative risk/benefit data
  2. Association does not equal causation
  3. How we discuss screening tests

This is a good reminder of how to present our data and draw conclusions from the analysis fairly in scientific publications.

A simple mountant that makes embryo transparent

The other day my colleague Don Ready in the department forwarded an interesting news article from The New York Times that describes a very simple mountant to makes tissue samples very transparent without affecting the fluorescence signal. That substantially helps imaging thick samples. The technique, which is called Scale, is published in Nature Neuroscience.

A 3d reconstruction of neurons labeled by fluorescent protein in mouse brain treated with Scale; Provided by Atsushi Miyawaki to the New York Times

The most interesting aspect about Scale is that it is made up with cheap chemicals that one can find in the lab (urea, glycerol and triton-X 100). It was actually discovered by a random but careful observation in the lab. That makes me wonder how much we have missed every time when we follow a protocol “religiously”.