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  • March 30, 2011
  • 01:07 AM

Tip of the Week: MetaPhoOrs, orthology and paralogy predictions

by Trey in OpenHelix

The researchers and developers at PhylomeDB haven’t rested on their laurels. I did a tip of the week on PhylomeDB 3 months ago and not too long ago I was checking over there and found the team had created another useful database and analysis tool, MetaPhoOrs. What is MetaPhoOrs? To quote from the homepage:
MetaPhOrs is a public repository of phylogeny-based orthology and paralogy predictions that were computed using resources available in seven popular homology prediction services (Phylome........ Read more »

  • March 29, 2011
  • 11:48 AM

Ratting out landmines and tuberculosis

by Iddo Friedberg in Byte Size Biology

Thanks to John Stevenson for drawing my attention to this one: Giant African Pouched Rats are trained as detectors; a good solution for low-income countries and communities. HeroRATS, as they are called, come in two "models": landmine detectors and tuberculosis detectors. Rats born in captivity (captured rats are impossible to train) are trained to sniff out landmines in historically war-ravaged zones where many landmines are laying unmapped, and using other detection or disposal tech........ Read more »

Poling, A., Weetjens, B., Cox, C., Mgode, G., Jubitana, M., Kazwala, R., Mfinanga, G., & Huis in 't Veld, D. (2010) Using Giant African Pouched Rats to Detect Tuberculosis in Human Sputum Samples: 2009 Findings. American Journal of Tropical Medicine and Hygiene, 83(6), 1308-1310. DOI: 10.4269/ajtmh.2010.10-0180  

Alan Poling, Bart J. Weetjens, Christophe Cox, Negussie W. Beyene, & Andrew Sully. (2010) USING GIANT AFRICAN POUCHED RATS (CRICETOMYS GAMBIANUS) TO DETECT LANDMINES. The Psychological Record, 60(4), 715-728. info:other/

  • March 29, 2011
  • 11:36 AM

The Ghosts of Yellowstone

by Rob Mitchum in ScienceLife

Paleontologists often deal with time scales in the hundreds of millions of years, reading the messages of fossils to learn about life on Earth long before humans arrived on the scene. But bones aren’t limited to providing insight on prehistoric ecosystems. The skeletal fragments left behind by animals at their final resting place can be [...]... Read more »

  • March 29, 2011
  • 11:15 AM

Virus-Killers: Are virophages alive?

by Brooke N in Smaller Questions

Highlights new virophage (OLV) found in Organic Lake, Antarctica and includes a brief background of Sputnik, original virophage found in Paris.... Read more »

La Scola, B., Desnues, C., Pagnier, I., Robert, C., Barrassi, L., Fournous, G., Merchat, M., Suzan-Monti, M., Forterre, P., Koonin, E.... (2008) The virophage as a unique parasite of the giant mimivirus. Nature, 455(7209), 100-104. DOI: 10.1038/nature07218  

  • March 29, 2011
  • 10:15 AM

Big Crayfish Could Be Key to Population Stability

by Nature Education in Student Voices

Any respectable Cajun restaurant in the United States serves crayfish (although ...... Read more »

  • March 29, 2011
  • 09:28 AM

Video: Physical Attraction

by Jack Serle in Elements Science

Beauty is in the eye of the beholder. With so many images of an idealised beauty thrown at us every day, how does this affect our judgement? Richard Masters investigates

Related posts:Video: the unhealthy option – transfats and fastfood
... Read more »

Swami, V., Furnham, A., Chamorro-Premuzic, T., Akbar, K., Gordon, N., Harris, T., Finch, J., & Tovee, M. (2010) More Than Just Skin Deep? Personality Information Influences Men's Ratings of the Attractiveness of Women's Body Sizes. The Journal of Social Psychology, 150(6), 628-647. DOI: 10.1080/00224540903365497  

  • March 29, 2011
  • 09:05 AM

Moths that pass in the night: Reproductive isolation due to pickiness, or just bad timing?

by Jeremy Yoder in Denim and Tweed

On a summer night in a Florida corn field, a female armyworm moth emerges from her underground cocoon and spreads her wings to dry in the humid air. Over the next few weeks, she will fly miles away in search of a mate, and a likely-looking patch of host plants on which to lay her eggs.

Her brief adult life will be shaped in many ways by the life she led as a larva, feeding on domestic corn. She could easily find other grasses to feed her offspring, but she'll probably seek out another cornfield........ Read more »

  • March 29, 2011
  • 06:30 AM

Miniaturizing medicine

by Becky in It Takes 30

You’ve probably seen NMR machines at some point during your career.  They usually have their own room, often with an extra-high ceiling to allow the operator to insert the sample without bumping his or her head.  So it may surprise you to know that a miniaturized NMR machine that you can literally hold in the [...]... Read more »

Haun JB, Castro CM, Wang R, Peterson VM, Marinelli BS, Lee H, & Weissleder R. (2011) Micro-NMR for Rapid Molecular Analysis of Human Tumor Samples. Science translational medicine, 3(71). PMID: 21346169  

  • March 29, 2011
  • 05:10 AM

The flat and the fit

by Razib Khan in Gene Expression

The Pith: In evolution if you want to win in the long run you don’t want all your eggs in one basket, even if that’s the choicest basket. Sh*t happens, and you better have some back up strategies.
Diversity is a major question in evolutionary biology. In particular, why is there so much diversity, so that the tree of life manifests a multitude of morphs? Might there not be some supreme replicator which emerges from the maelstrom to conquer all before it? This is actually the scenari........ Read more »

  • March 28, 2011
  • 04:44 PM

A Word of Caution on Mesenchymal Stem Cells

by Sanford- Burnham in Beaker

We still don’t quite know enough about many of the existing stem cell types to predict exactly how they will behave when transplanted into a patient. Each of the many different types of stem cells has its unique repertoire of behaviors, and its own benefits and drawbacks (not to mention ethical implications). A recent paper and editorial in Experimental Neurology hammers home the possible dangers of one particular very popular and oft-used type of stem cell. Here, researchers found that brain ........ Read more »

Grigoriadis N, Lourbopoulos A, Lagoudaki R, Frischer JM, Polyzoidou E, Touloumi O, Simeonidou C, Deretzi G, Kountouras J, Spandou E.... (2011) Variable behavior of autologous bone marrow mesenchymal stem cells transplanted in experimental autoimmune encephalomyelitis. Experimental Neurology. info:/doi:10.1016/j.expneurol.2011.02.021

  • March 28, 2011
  • 04:14 PM

You can take a horse out of the wild, but you cannot take the wild out of a horse…

by Dr. Carin Bondar in Dr. Carin Bondar - Biologist With a Twist

Feral horse populations are alive and well on several continents including North America, Europe, Australia and India.  Feral horses – referring to specimens that are free roaming but with a domesticated ancestry – live in herds (harems) that are comprised of a dominant stallion, sub-dominant males, and several females.  The majority of the foals in [...]... Read more »

Bartoš, L., Bartošová, J., Pluháček, J., & Šindelářová, J. (2011) Promiscuous behaviour disrupts pregnancy block in domestic horse mares. Behavioral Ecology and Sociobiology. DOI: 10.1007/s00265-011-1166-6  

  • March 28, 2011
  • 02:35 PM

Digitizing Jane Goodall's Legacy at Duke

by Jason Goldman in The Thoughtful Animal

A new piece by me today at the Scientific American Guest Blog, on some exciting news from the Jane Goodall Institute and Duke University:

Fifty years ago, in the summer of 1960 - the same year that a US satellite snapped the first photo of the Earth from space, the same year that the CERN particle accelerator became operational, the same year that the Beatles got their name - a 26-year-old Jane Goodall got on a plane in London and went for the first time to Gombe Stream Game Reserve, in Tanzani........ Read more »

Goodall, J., & Pintea, L. (2010) Securing a future for chimpanzees. Nature, 466(7303), 180-181. DOI: 10.1038/466180a  

Pusey AE, Pintea L, Wilson ML, Kamenya S, & Goodall J. (2007) The contribution of long-term research at Gombe National Park to chimpanzee conservation. Conservation biology : the journal of the Society for Conservation Biology, 21(3), 623-34. PMID: 17531041  

  • March 28, 2011
  • 12:40 PM

In which I try to explain why "heritability" is not quite the same thing as "heritable"

by Jeremy Yoder in Denim and Tweed

Robert Kurzban responds in the ongoing "adaptive" homophobia kerfuffle (henceforth, the O.A.H.K.) with continued confusion about how biologists identify possible adaptations and test to see whether natural selection is responsible for them. He notes that one effect of natural selection is to remove heritable variation in traits under selection, so that many traits which are probably adaptations—arguably, sometimes the best-adapted traits—actually have zero heritability.

This is true. But it........ Read more »

  • March 28, 2011
  • 12:18 PM

Is Bigger Really Better?

by Christie Wilcox in Observations of a Nerd

I have to confess, when I saw a global map of average penis size flying around twitter, I was like a eighth grade boy finding his first nudie magazine - I couldn't help but take a peek. After a brief heart attack (it's in cm, not inches), my inner scientist started asking silly questions. You know, the kind of things that would only occur to a scientist when looking at a map of penis size like, "is this just a stochastic distribution?" "is there any reason why this pattern would occur?" and of c........ Read more »

Ponchietti R, Mondaini N, Bonafè M, Di Loro F, Biscioni S, & Masieri L. (2001) Penile length and circumference: a study on 3,300 young Italian males. European urology, 39(2), 183-6. PMID: 11223678  

  • March 28, 2011
  • 12:00 PM

Tiarajudens: Over 265 Million Years of Sabertooths

by Laelaps in Laelaps

The way people have been talking about Tiarajudens eccentricus, you would think that this 265 million year old cousin of ours was unique among herbivores for having saber-fangs. It was not, but it does raise the question of what makes a saber-tooth in the first place.
Tiarajudens was not quite like any creature alive today. Described [...]... Read more »

  • March 28, 2011
  • 11:26 AM

A call for increased use of pharamacogenomic data in the clinic

by avi_wener in American Biotechnologist

In a recent review article published in the New England Journal of Medicine, authors Liewei Wang and a team from the Mayo Clinic discuss recent advances in the field of pharmacogenomics and the potential value that it holds for patient care with proper uptake by the medical community. Pharmacogenomics is the study of a patient’s [...]... Read more »

Wang L, McLeod HL, & Weinshilboum RM. (2011) Genomics and drug response. The New England journal of medicine, 364(12), 1144-53. PMID: 21428770  

  • March 28, 2011
  • 09:26 AM

Dermamoeba – Having your coat and eating it too

by Psi Wavefunction in Skeptic Wonder

We've been neglecting the micro-squishies lately (filose amoebae ain't proper squishies – too many fine protrusions in the way). Amoebozoa is a eukaryotic supergroup comprised of predominantly lobose amoebae, meaning their pseudopods are rounded and not fine and pointy (like those in the preceding post's organism – Filoreta). Aside from the test-bearing Arcellinids, amoebozoans tend to be naked amoebae ('gymnamoebae'), like the well-known Amoeba proteus, often erroneously referred to as a '........ Read more »

Smirnov AV, Bedjagina OM, & Goodkov AV. (2011) Dermamoeba algensis n. sp. (Amoebozoa, Dermamoebidae) – An algivorous lobose amoeba with complex cell coat and unusual feeding mode. European Journal of Protistology. info:/10.1016/j.ejop.2010.12.002

  • March 28, 2011
  • 09:15 AM

Protein Structure Analysis – How Far We’ve Come!

by Jennifer in OpenHelix

The team here at OpenHelix has recently updated our sponsored tutorials on two excellent structural biology resources, the RCSB Protein Data Bank (PBD) and the PSI-Nature Structural Biology Knowledgebase (PSI SBKB). Because the tutorials are sponsored by these resources they are free for anyone to view and download in full. You can access our training materials for the resources at our RCSB PDB landing page, or our PSI SBKB landing page. I’m very happy with both tutorial suites, so please........ Read more »

Berman, H. (2000) The Protein Data Bank. Nucleic Acids Research, 28(1), 235-242. DOI: 10.1093/nar/28.1.235  

Berman, H., Westbrook, J., Gabanyi, M., Tao, W., Shah, R., Kouranov, A., Schwede, T., Arnold, K., Kiefer, F., Bordoli, L.... (2009) The protein structure initiative structural genomics knowledgebase. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn790  

  • March 28, 2011
  • 08:49 AM

Income and IQ

by Jason Collins in Evolving Economics

As I noted in my recent post on Malcolm Gladwell’s Outliers, Gladwell ignored the possibility that traits with a genetic component other than IQ might play a role in determining success. His approach reminded me of a useful paper by Samuel Bowles and Herbert Gintis from 2002 on the inheritance of inequality. Bowles and Gintis [...]... Read more »

Bowles, S., & Gintis, H. (2002) The Inheritance of Inequality. Journal of Economic Perspectives, 16(3), 3-30. DOI: 10.1257/089533002760278686  

  • March 28, 2011
  • 07:00 AM

March 28, 2011

by Erin Campbell in HighMag Blog

We all need balance in our lives to be happy and healthy, and the little embryo versions of ourselves were no different. When our brain and nervous system developed, our neural precursor cells made sure there was a balance between proliferation and differentiation. A recent paper adds to our understanding of how this happens.The development of our nervous system is a process that relies on a delicate balance of growth and differentiation. Our neural precursor cells are progenitor cells that c........ Read more »

Kaltezioti, V., Kouroupi, G., Oikonomaki, M., Mantouvalou, E., Stergiopoulos, A., Charonis, A., Rohrer, H., Matsas, R., & Politis, P. (2010) Prox1 Regulates the Notch1-Mediated Inhibition of Neurogenesis. PLoS Biology, 8(12). DOI: 10.1371/journal.pbio.1000565  

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