Post List

  • September 17, 2010
  • 02:30 PM
  • 639 views

Oxygen-Deprived Microbial Growth on Formate: A Renewable Energy Source?

by Michael Long in Phased

Jung-Hyun Lee, Sung Gyun Kang (Korean Ocean Research and Development Institute, and University of Science and Technology, Korea) and coworkers have found a microorganism which grows at 80 degrees Celsius, and uses formate to synthesize both hydrogen and adenosine triphosphate (energy) molecules, in oxygen-deprived conditions. This news feature was written on September 17, 2010.... Read more »

Kim, Y. J., Lee, H. S., Kim, E. S., Bae, S. S., Lim, J. K., Matsumi, R., Lebedinsky, A. V., Sokolova, T. G., Kozhevnikova, D. A., Cha, S.-S.... (2010) Formate-driven growth coupled with H2 production. Nature, 467(7313), 352-355. DOI: 10.1038/nature09375  

  • September 17, 2010
  • 01:37 PM
  • 1,744 views

'SAR by C13 NMR'

by The Curious Wavefunction in The Curious Wavefunction

The biggest utility of NMR spectroscopy in drug discovery is in assessing three things; whether a particular ligand binds to a protein, what site on the protein it binds, and what parts of the ligand interact with the protein. Over the last few years a powerful technique named ‘SAR by NMR’ has emerged which is now widely used in ligand screening. In this technique, changes in the resonances of ligand and protein protons are observed to pinpoint the ligand binding site and corresponding residues. Generally when a ligand binds to a protein, both its and the protein’s rotational correlation time decreases; the result is a broadening of signals in the spectrum which can be used to detect ligand binding. One of the most effective methods in this general area is Saturation Transfer Difference (STD) spectroscopy. As the name indicates, it hinges on the transfer of magnetization between protein and ligand; the resulting decrease in intensity of ligand signals can provide valuable information about proximity of ligand protons with specific protein residues.But these kinds of techniques suffer from some drawbacks. One straightforward drawback is that signals from protein and ligand may simply overlap. Secondly, the broadening may be so much as to virtually make the signals disappear. Thirdly from a practical perspective, it is hard to get sufficient amounts of N15-labeled protein (usually obtained by growing bacteria on a N15-rich source and then purifying the proteins of interest).To circumvent some of these problems, a team at Abbott Laboratories has come up with a neat and relatively simple method which they call ‘labeled ligand displacement’. The method involves synthesizing a protein-binding probe that has been selectively labeled with C13. Protein binding broadens and diminishes the signals of this probe. However, when a high-affinity ligand is then added, it displaces the probe and we get recovery of the C13 signals. The authors illustrate this paradigm with several proteins of pharmaceutical interest, including heat-shock protein and carbonic anhydrase.The method is relatively simple. For one thing, using a commercially available C13-labeled building block for synthesizing a ligand is easier than obtaining a N15-labeled protein. The biggest merit of the method though is the fact that it hinges on C13 signals very specific to the probe; thus there is no complicating overlap of signals. And finally, the ligand seems to be general enough to be applied to any protein. Only time will tell how much it is utilized, but for now it seems like a neat addition to the arsenal of NMR methods for studying protein-ligand interactions.Swann, S., Song, D., Sun, C., Hajduk, P., & Petros, A. (2010). Labeled Ligand Displacement: Extending NMR-Based Screening of Protein Targets ACS Medicinal Chemistry Letters, 1 (6), 295-299 DOI: 10.1021/ml1000849... Read more »

Swann, S., Song, D., Sun, C., Hajduk, P., & Petros, A. (2010) Labeled Ligand Displacement: Extending NMR-Based Screening of Protein Targets. ACS Medicinal Chemistry Letters, 1(6), 295-299. DOI: 10.1021/ml1000849  

  • September 17, 2010
  • 01:28 PM
  • 1,274 views

More cool polariton stuff

by Joerg Heber in All That Matters

Earlier this week I wrote about some of the exciting polaritons in semiconductors. And just a few days later, there is another intriguing paper on this topic out. Something that I speculate(!) might lead to new types of quantum computers. But to recapitulate, polaritons are object that form when light interacts with electronic excitations. What I [...]... Read more »

Lagoudakis, K., Pietka, B., Wouters, M., André, R., & Deveaud-Plédran, B. (2010) Coherent Oscillations in an Exciton-Polariton Josephson Junction. Physical Review Letters, 105(12). DOI: 10.1103/PhysRevLett.105.120403  

  • September 17, 2010
  • 12:49 PM
  • 1,709 views

Cosmology Can Possibly Solve the Neutrino Hierarchy Problem.

by Joseph Smidt in The Eternal Universe

There are three neutrino species in the standard model, hereafter refereed to as 1, 2, and 3, that we know have mass from atmospheric and solar neutrino oscillation experiments. Furthermore, data from these experiments put constraints on the mass-splittings between these three neutrinos.  From atmospheric experiments we know the mass differences between 2 and 3 is |M223| ~ 1.4x10-3 eV2 and from

... Read more »

Jimenez, R., Kitching, T., Peña-Garay, C., & Verde, L. (2010) Can we measure the neutrino mass hierarchy in the sky?. Journal of Cosmology and Astroparticle Physics, 2010(05), 35-35. DOI: 10.1088/1475-7516/2010/05/035  

  • September 17, 2010
  • 11:54 AM
  • 919 views

MET and KRAS amplification mediate resistance to MET inhibitors

by Sally Church in Pharma Strategy Blog

Here's an interesting paper that was just published in Cancer Research that describes some factors driving acquired resistance to MET inhibition with small molecules. MET inhibitors have gained a lot of attention recently (see Comoglio et al's review in the...... Read more »

  • September 17, 2010
  • 11:49 AM
  • 1,636 views

What’s Killing California’s Sea Otters?

by Southern Fried Scientist in Southern Fried Science



Sea Otters are turning up dead in central California. In 2007, 11 sea otters were recovered from Monterrey Bay. Over the last three years, dead otters washing up on beaches has reached a record high?
What could be causing all these otter deaths? Are there new predators in the area? Is there some kind of disease? [...]... Read more »

Miller, M., Kudela, R., Mekebri, A., Crane, D., Oates, S., Tinker, M., Staedler, M., Miller, W., Toy-Choutka, S., Dominik, C.... (2010) Evidence for a Novel Marine Harmful Algal Bloom: Cyanotoxin (Microcystin) Transfer from Land to Sea Otters. PLoS ONE, 5(9). DOI: 10.1371/journal.pone.0012576  

  • September 17, 2010
  • 11:30 AM
  • 600 views

Denouncing priests accused of child sexual abuse as rotten apples in an otherwise clean barrel

by SAGE Insight in SAGE Insight

Child sexual abuse in the Catholic Church: Revisiting the rotten apples explanation From Criminal Justice and Behavior The Pope’s first state visit to Britain this week has fuelled controversy, not least due to his recent comments expressing his “great sadness” over revelations of widespread abuse of children by Catholic priests, saying  ”authorities in the church have [...]... Read more »

  • September 17, 2010
  • 11:30 AM
  • 921 views

Darwinius Strikes Back

by Laelaps in Laelaps

If all that you knew about paleontology came from headlines alone, you could be excused for thinking that the science consists of little more than naming one obscure creature after another. There are a few petrified celebrities which can draw sustained attention – Tyrannosaurus and Triceratops foremost among them – but, in general, it seems [...]... Read more »

Gingerich, P., Franzen, J., Habersetzer, J., Hurum, J., & Smith, B. (2010) Darwinius masillae is a Haplorhine — Reply to Williams et al. (2010). Journal of Human Evolution. DOI: 10.1016/j.jhevol.2010.07.013  

Williams BA, Kay RF, Christopher Kirk E, & Ross CF. (2010) Darwinius masillae is a strepsirrhine-a reply to Franzen et al. (2009). Journal of human evolution. PMID: 20188396  

Williams, B., Kay, R., & Kirk, E. (2010) New perspectives on anthropoid origins. Proceedings of the National Academy of Sciences, 107(11), 4797-4804. DOI: 10.1073/pnas.0908320107  

  • September 17, 2010
  • 10:33 AM
  • 1,108 views

Can seabirds overfish a resource? The case of cormorants in Estonia

by Hannah Waters in Culturing Science – biology as relevant to us earthly beings

“Overfishing” is a term associated with resource depletion, extinction, and human greed.  While the definition of overfishing is technically a subjective measure (How much fishing is too much?), it has been widely accepted to mean catching more of an aquatic … Continue reading →... Read more »

Dulvy, N., Sadovy, Y., & Reynolds, J. (2003) Extinction vulnerability in marine populations. Fish and Fisheries, 4(1), 25-64. DOI: 10.1046/j.1467-2979.2003.00105.x  

Vetemaa, M., Eschbaum, R., Albert, A., Saks, L., Verliin, A., Jurgens, K., Kesler, M., Hubel, K., Hannesson, R., & Saat, T. (2010) Changes in fish stocks in an Estonian estuary: overfishing by cormorants?. ICES Journal of Marine Science. DOI: 10.1093/icesjms/fsq113  

  • September 17, 2010
  • 10:30 AM
  • 1,791 views

the ongoing search for a simpler, neater universe

by Greg Fish in weird things

Astrophysics is not only a complicated discipline, but it’s becoming more and more esoteric, so much so that there seems to be an entire genre of deriving "groundbreaking papers" from obscure numerology, and the scientific community took a while to catch up with the Bogdanov brothers’ papers and show them to be just the sort [...]... Read more »

David F. Crawford. (2010) Observational evidence favours a static universe. n/a. arXiv: 1009.0953v1

  • September 17, 2010
  • 10:28 AM
  • 615 views

Stegosaurus Week: Playing the Stegosaur Name Game

by Brian Switek in Dinosaur Tracking

Measuring diversity in the fossil record can be a tricky task. Short of inventing time travel, there will be always be some uncertainty about how many species of dinosaur existed at any one place and time, and as we learn more about the fossil record it may turn out that what we once thought to [...]... Read more »

Carpenter, K. (2010) Species concept in North American stegosaurs. Swiss Journal of Geosciences, 103(2), 155-162. DOI: 10.1007/s00015-010-0020-6  

  • September 17, 2010
  • 10:12 AM
  • 1,327 views

Is Moral Psychology About Morals Or Their Function?

by Jason Goldman in The Thoughtful Animal

Quandaries such as those involving stealing a drug to save a spouse's life or whether or not to have an abortion have historically dominated the study of the development of moral thinking. The predominant research programs in psychology today use dilemmas in which one choice is deontologically correct (it is wrong to rotate a lever that will divert a train and kill one person instead of five), and the other is consequentially correct (kill one person if it will save five others).

Read the rest of this post... | Read the comments on this post...... Read more »

Haidt J. (2007) The new synthesis in moral psychology. Science (New York, N.Y.), 316(5827), 998-1002. PMID: 17510357  

  • September 17, 2010
  • 10:11 AM
  • 642 views

Brain Port: Seeing With Your Tongue

by A. Goldstein in WiSci

It sounds like a science fiction movie: a blind man wearing sunglasses licks a plastic lollipop and can suddenly see. This device, however, exists today. The Brain Port—a contraption comprised of a tiny video camera attached to a pair of sunglasses linked to a plastic “lollipop”—is enabling the blind to see . . . with [...]... Read more »

BACH-Y-RITA, P., COLLINS, C., SAUNDERS, F., WHITE, B., & SCADDEN, L. (1969) Vision Substitution by Tactile Image Projection. Nature, 221(5184), 963-964. DOI: 10.1038/221963a0  

  • September 17, 2010
  • 10:09 AM
  • 548 views

Brain Port: Seeing With Your Tongue

by agoldstein in WiSci

It sounds like a science fiction movie: a blind man wearing sunglasses licks a plastic lollipop and can suddenly see. This device, however, exists today. The Brain Port—a contraption comprised of a tiny video camera attached to a pair of sunglasses linked to a plastic “lollipop”—is enabling the blind to see . . . with their tongues.... Read more »

BACH-Y-RITA, P., COLLINS, C., SAUNDERS, F., WHITE, B., & SCADDEN, L. (1969) Vision Substitution by Tactile Image Projection. Nature, 221(5184), 963-964. DOI: 10.1038/221963a0  

  • September 17, 2010
  • 10:03 AM
  • 463 views

Mice, Men and Alzheimer’s

by Isobel in Promega Connections

I know that results in mice do not always translate to humans. I know that. I know that clinical trials can take years and that there are many hurdles between the first promising result in an animal model and the actual development of some form of treatment. Nevertheless I could not stifle a surge of [...]... Read more »

Boyd TD, Bennett SP, Mori T, Governatori N, Runfeldt M, Norden M, Padmanabhan J, Neame P, Wefes I, Sanchez-Ramos J.... (2010) GM-CSF upregulated in rheumatoid arthritis reverses cognitive impairment and amyloidosis in Alzheimer mice. Journal of Alzheimer's disease : JAD, 21(2), 507-18. PMID: 20555144  

  • September 17, 2010
  • 09:56 AM
  • 763 views

First step toward the holy grail of pain research? Molecular identity of a mechanically gated ion channel, Coste et al., 2010 Science

by JUNIORPROF in JUNIORPROF

For as long as I have been in pain research (and long before I ever even thought about pain research) the topic of mechanically-gated ion channels has been a huge deal. The reasons are simple: 1) We obtain information about … Continue reading →... Read more »

  • September 17, 2010
  • 09:55 AM
  • 1,364 views

Obese, but Metabolically Healthy: Is Weight Loss Beneficial? (Series Pt 5/5)

by Peter Janiszewski, Ph.D. in Obesity Panacea

So what have we learned thus far?
1. About a third of obese individuals fail to exhibit the metabolic complications commonly attributed to excess weight.
2. These same individuals also seem to be at the same relative risk of diabetes and cardiovascular disease as equally healthy, but lean individuals.
3. Nevertheless, despite being metabolically healthy, some evidence suggests that excess weight may put such obese individuals at risk for early mortality due to other, non-metabolic, factors.
4. This latter point would imply that all obese individuals should be encouraged to lose weight, despite their metabolic health. This, in fact, is in line with guidelines developed by leading health authorities which currently recommend weight reduction as the primary treatment strategy for all obese patients, regardless of metabolic health.  However, as we learned yesterday, weight loss via caloric restriction among metabolically healthy obese may actually result in a deterioration in insulin sensitivity, thereby increasing risk of developing type-2 diabetes.
Now, as most of you know, when a completely counter-intuitive finding like this comes along, where even the study authors fail to come up with a plausible mechanism, it is up to other researchers to follow up with additional research to either corroborate or refute this original finding.
Because I am personally drawn to paradoxical and counterintuitive findings in science, I was very intrigued by the findings of Karelis and colleagues and decided to follow up their study, but include a few variations:
a) Since the study of Karelis et al. only used female subjects, we wanted to ensure this wasn’t due to a gender effect and thus included both men and women.
b) Additionally, to test the possibility that their finding was driven only by modality of weight loss (caloric restriction, in their case) we employed a number of weight loss interventions (diet alone, exercise alone, and the combination of diet and exercise).
c) Finally, while the original study only looked at insulin sensitivity, we decided to assess changes in other variables of interest (body composition, blood lipids, glucose and insulin levels, etc.).
In our study, which has just been published in the prestigious journal, Diabetes Care, a total of 63 metabolically-healthy obese men and women and 43 metabolically-unhealthy obese men and women participated in 3-6 months of exercise and/or diet weight-loss intervention.
And what did we find?
First, body weight, waist circumference, and total and abdominal fat mass were significantly reduced in all subjects – regardless of gender, modality of weight loss, and metabolic status.
Second, in contrast to the findings of Karelis et al., insulin sensitivity IMPROVED after weight loss in both the metabolically-healthy (by about 20%) and metabolically-unhealthy obese individuals. However, the improvement was greater in the metabolically-unhealthy subjects. See figure below.

Importantly, this improvement was similar across all weight loss modalities. In other words, dietary caloric restriction did not have a unique negative effect on insulin sensitivity.
Finally, while the metabolically-unhealthy obese individuals also showed improvement in numerous other outcomes (triglycerides, fasting glucose and insulin, HDL-cholesterol, and total cholesterol), a reduction in fasting insulin was the only other metabolic improvement among the metabolically-healthy obese. This latter finding is not surprising given the normal baseline levels of most metabolic risk factors among metabolically-healthy obese individuals. That is, since they were healthy to begin with – they can only get so much healthier after weight loss (ceiling effect).
Thus, we found no evidence of deterioration in metabolic profile among metabolically-obese individuals who lost weight via a lifestyle intervention.
While limited health care resources dictate the need to prioritize high-risk obese individuals for aggressive treatment, to imply that obese individuals who are metabolically healthy should not lose weight may not be the most appropriate public health message.  Such a public health message may be particularly misguided at a time when the prevalence of obesity continues to increase, despite a greater public awareness of the benefits of weight loss. In this context, our findings reinforce current recommendations which suggest that all obese individuals should be encouraged to lose 5-10% body weight.
Bottom line?
Although a fair number of obese individuals may have a perfect metabolic profile, it appears they may still experience negative consequences of their excess weight. Furthermore, weight loss achieved via lifestyle intervention appears to still bring about some metabolic benefit among previously healthy obese individuals (it certainly doesn’t seem to harm health). Given the numerous non-metabolic benefits of weight loss (mobility, joint problems, psychological status, sexual function, etc.), all obese individuals have something to gain from a modest 5-10% weight loss.
Have a wonderful weekend,
Peter
References and Further Reading:
Janiszewski, P., & Ross, R. (2010). Effects of Weight Loss Among Metabolically Healthy Obese Men and Women Diabetes Care, 33 (9), 1957-1959 DOI: 10.2337/dc10-0547
... Read more »

  • September 17, 2010
  • 09:40 AM
  • 1,188 views

Survey of Scottish GPs and drug treatment

by Euan in Dr Euan Lawson| Doctor Writer

This was a follow up to a nationwide survey of GPs in Scotland completed in 2000. They used a similar questionnaire to the original study and sent it to a random sample of one in four Scottish GPs (n=1065). After a poor initial response they sent an abbreviated questionnaire on the key areas from the [...]... Read more »

Matheson C, Porteous T, van Teijlingen E, & Bond C. (2010) Management of drug misuse: an 8-year follow-up survey of Scottish GPs. The British journal of general practice : the journal of the Royal College of General Practitioners, 60(576), 517-20. PMID: 20594442  

  • September 17, 2010
  • 09:06 AM
  • 679 views

Glucosamine chondroitin = FAIL

by David Bradley in SciScoop Science Forum

Glucosamine and chondroitin do not work in alleviating the pain of osteoarthritis (of hip or knee), other than perhaps as an expensive placebo that sufferers who do gain some relief daren’t stop paying for. A new meta analysis of 10 trials amounting to 3803 patients has been carried out. On a 10 cm visual analogue [...]... Read more »

  • September 17, 2010
  • 09:00 AM
  • 697 views

Big Brained Humans: A Dangerous Idea?

by Daniel Bassett in Chew the Fat

Predation is a key driver of biological systems over both ecological and evolutionary timescales. Thus, to understand our role as Homo sapiens within this evolutionary framework we must look to the animal kingdom to find our place. This is important for anyone following an evolutionary eating plan as it gives our species an ecological context, which we can consider when making choices about our lifestyle and diet. In the latest edition of Behavioral Ecology, Shultz & Finlayson utilised a range of studies on vertebrate predators to establish the relationship between prey behavioral and ecological characteristics, and predator diet composition at the population level. Although this focuses on non-human species it is easy to extrapolate information from this data and find our place within the animal kingdom.... Read more »

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