by Kim Lewis in Small Things Considered
The majority of bacteria will not grow on nutrient medium in the lab. The basic experiment is simple: take a sample from the environment, such as marine sediment or soil, mix with water, vortex, allow it to settle, dilute supernatant and take two droplets. Plate one on a Petri dish...... Read more »
D'Onofrio A, Crawford JM, Stewart EJ, Witt K, Gavrish E, Epstein S, Clardy J, & Lewis K. (2010) Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chemistry , 17(3), 254-64. PMID: 20338517
Last month, we discussed the garage doors of the body’s ion channels, the millions of microscopic machines that control the heart’s beat and the nervous system’s communication. Benoît Roux and his colleagues employed 25 million computational hours to model the potassium channel voltage sensor, a kind of garage door control box that determines when the [...]... Read more »
Cuello LG, Jogini V, Cortes DM, Pan AC, Gagnon DG, Dalmas O, Cordero-Morales JF, Chakrapani S, Roux B, & Perozo E. (2010) Structural basis for the coupling between activation and inactivation gates in K( ) channels. Nature, 466(7303), 272-5. PMID: 20613845
Cuello LG, Jogini V, Cortes DM, & Perozo E. (2010) Structural mechanism of C-type inactivation in K( ) channels. Nature, 466(7303), 203-8. PMID: 20613835
The short of it...
Creationists often put physicians on a pedestal as the scientists doing the real work in biology, useful work of improving human health and well-being as opposed to the pontificating, abstract work of the evolutionists. But, can we really understand human aliments outside of the light of evolution? Well worn examples of antibiotic resistance vividly illustrate the folly of ignoring evolutionary processes in medicine. Cancer however is another example of evolution in action. T........ Read more »
Domazet-Lošo, T., & Tautz, D. (2010) Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa. BMC Biology, 8(1), 66. DOI: 10.1186/1741-7007-8-66
Queller, D. (2003) Single-Gene Greenbeard Effects in the Social Amoeba Dictyostelium discoideum. Science, 299(5603), 105-106. DOI: 10.1126/science.1077742
Velicer, G., Kroos, L., & Lenski, R. (2000) Developmental cheating in the social bacterium Myxococcus xanthus. Nature, 404(6778), 598-601. DOI: 10.1038/35007066
Eating problems are not a diagnostic criteria for autism spectrum disorder (ASD). Anecdotally, many parents of autistic children report difficulty with mealtime and food selection. A recent study from the University of New Mexico describes the type and extent of eating problems in a group of preschool children with ASD.The research team surveyed 24 parents of children with ASD and compared them with a group of 24 parents with a typically developing child. The primary measure was an instrument........ Read more »
Provost B, Crowe TK, Osbourn PL, McClain C, & Skipper BJ. (2010) Mealtime behaviors of preschool children: comparison of children with autism spectrum disorder and children with typical development. Physical , 30(3), 220-33. PMID: 20608859
As iGEM season is now properly underway, I thought I'd have a look at a synthetic biology paper and found this fairly awesome one about programming bacteria to hunt out and destroy atrazine, a chemical herbicide pollutant. One of the most exciting things about this work was that it didn't just involve bacteria with the ability to remove atrazine from the environment but to actively migrate towards the chemical and then destroy it.The chemical structure of atrazineThe bacteria are controlled usin........ Read more »
Sinha J, Reyes SJ, & Gallivan JP. (2010) Reprogramming bacteria to seek and destroy an herbicide. Nature chemical biology, 6(6), 464-70. PMID: 20453864
GPCRs are extremely important proteins both for pure and applied science research, but they are also very difficult to crystallize and hence structural information on them has been sparse. Naturally in such a case, computational modeling can be expected to be of great value of providing insight into GPCR structure and function. However, even though progress has been impressive, such modeling still has to overcome many challenges. A recent review lists some of them.Firstly, in the absence of crys........ Read more »
Yarnitzky T, Levit A, & Niv MY. (2010) Homology modeling of G-protein-coupled receptors with X-ray structures on the rise. Current opinion in drug discovery , 13(3), 317-25. PMID: 20443165
Another significant piece in the mind-body puzzle comes from this new study where obsessive-compulsive behavior in mice was cured by a bone marrow transplant. A rare form of a genetic disorder in mice causes a “hair pulling” disorder, very similar to its human counterpart trichotillomania. In their new findings published in Cell, Mario Capecchi and [...]... Read more »
Chen SK, Tvrdik P, Peden E, Cho S, Wu S, Spangrude G, & Capecchi MR. (2010) Hematopoietic origin of pathological grooming in Hoxb8 mutant mice. Cell, 141(5), 775-85. PMID: 20510925
I recently read a very interesting point/counterpoint on the use of ‘sex’ and ‘gender’ in physiological research from last month’s AJP:RICP. In Point: a call for proper usage of “gender” and “sex” in biomedical publications, King points out that sex and gender are often used interchangeably when the variable involved is very clearly sex and [...]... Read more »
King, B. (2010) Point: a call for proper usage of "gender" and "sex" in biomedical publications. AJP: Regulatory, Integrative and Comparative Physiology, 298(6). DOI: 10.1152/ajpregu.00694.2009
Geary, N. (2010) Counterpoint: physiologists should not distinguish "sex" and "gender". AJP: Regulatory, Integrative and Comparative Physiology, 298(6). DOI: 10.1152/ajpregu.00113.2010
Victoria Braithwaite’s Do Fish Feel Pain? is not a technical book. The type is large and the prose is easy to understand.
I had to read this book, because many of the issues around fish pain are the same as those raised for invertebrate pain (Puri and Faulkes 2010; this post). Fish researchers are about five years ahead of the invertebrate researchers.
Braithwaite’s answer to the question posed in her title is...
Spoiler alert! Click the heading of the post to read more.
H........ Read more »
Bshary, R., Hohner, A., Ait-el-Djoudi, K., & Fricke, H. (2006) Interspecific communicative and coordinated hunting between groupers and giant moray eels in the Red Sea. PLoS Biology, 4(12). DOI: 10.1371/journal.pbio.0040431
Brathwaite V. (2010) Do fish feel pain?. Oxford University Press, 1-194. info:/978-0-19-955120-0
Tracey Jr., W., Wilson, R., Laurent, G., & Benzer, S. (2003) painless, a Drosophila gene essential for nociception. Cell, 113(2), 261-273. DOI: 10.1016/S0092-8674(03)00272-1
Short comments about what I’ve been reading (besides several hundred influenza articles): Hedskog, C., Mild, M., Jernberg, J., Sherwood, E., Bratt, G., Leitner, T., Lundeberg, J., Andersson, B., & Albert, J. (2010). Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing PLoS ONE, 5 (7) DOI: 10.1371/journal.pone.0011345 The whole deep sequencing thing is [...]... Read more »
Hedskog, C., Mild, M., Jernberg, J., Sherwood, E., Bratt, G., Leitner, T., Lundeberg, J., Andersson, B., & Albert, J. (2010) Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing. PLoS ONE, 5(7). DOI: 10.1371/journal.pone.0011345
Evaluations of clinical faculty typically incorporate comments from rotating medical students and residents regarding their teaching ability. In the Emergency Department (ED), how do you balance your pressing clinical responsibilities with teaching?There were 28 Canadian medical students and residents in their focus group interviews in this qualitative study. Learners were asked what qualities made a good EM teacher. Answers were transcribed and coded. There were 14 positive qualities identified........ Read more »
Thurgur, L., Bandiera, G., Lee, S., & Tiberius, R. (2005) What Do Emergency Medicine Learners Want from Their Teachers? A Multicenter Focus Group Analysis. Academic Emergency Medicine, 12(9), 856-861. DOI: 10.1197/j.aem.2005.04.022
You can tell a person's personality from the words they use. Neurotics have a penchant for negative words; agreeable types for words pertaining to socialising; and so on. We know this from recordings of people's speech and from brief writing tasks. Now Tal Yarkoni has extended this line of research to the blogosphere by analysing the content of 694 blogs - containing an average of 115,000 words written over an average period of about two years - and matching this with the bloggers' (predominantl........ Read more »
Yarkoni, T. (2010) Personality in 100,000 Words: A large-scale analysis of personality and word use among bloggers. Journal of Research in Personality, 44(3), 363-373. DOI: 10.1016/j.jrp.2010.04.001
I am excited to announce the publication of another mushroom genome this week. The mushroom Schizophyllum commune is an important model system for mushroom biology, development of genome was sequenced as part of efforts at the Joint Genome Institute and a collection of international researchers. The data and analyses from these efforts are presented in a publication [...]... Read more »
Ohm, R., de Jong, J., Lugones, L., Aerts, A., Kothe, E., Stajich, J., de Vries, R., Record, E., Levasseur, A., Baker, S.... (2010) Genome sequence of the model mushroom Schizophyllum commune. Nature Biotechnology. DOI: 10.1038/nbt.1643
Depression is common in patients with Parkinson’s disease (mean prevalence 17% in patients with Parkinson’s). It can be the first sign of the disease. It can be treated with antidepressants. There is little evidence that patients with Parkinson’s disease might benefi t more from any
one particular class of antidepressants than any others. The problem with [...]
Related posts:Understanding Depression in Kidney Disease
Psychiatrists don’t Use Scales to Measure Outcome in Dep........ Read more »
Bxarone P, Poewe W, Albrecht S, Debieuvre C, Massey D, Rascol O, Tolosa E, & Weintraub D. (2010) Pramipexole for the treatment of depressive symptoms in patients with Parkinson's disease: a randomised, double-blind, placebo-controlled trial. Lancet neurology, 9(6), 573-80. PMID: 20452823
I really wanted to talk about this article before. A few weeks ago, it was published in Science a work by an extensive work by a high number of researchers, focused in the review and discussion of indicators of global indicators of biodiversity. Citing the article, in 2002 world leaders committed, through the Convention on [...]... Read more »
Butchart, S., Walpole, M., Collen, B., van Strien, A., Scharlemann, J., Almond, R., Baillie, J., Bomhard, B., Brown, C., Bruno, J.... (2010) Global Biodiversity: Indicators of Recent Declines. Science, 328(5982), 1164-1168. DOI: 10.1126/science.1187512
Secretariat of the Convention on Biological Diversity (2010) Global Biodiversity Outlook 3., & Montréal, 94 pages. (2010) Global Biodiversity Outlook 3. Convention on Biological Diversity. info:other/
I think I’ll keep this one light today. I had a few ideas I was working on, but this seems easy. I’ve recently started a second blog – ilikeclouds. I’ll give some back story before I get to the related science. About a year ago I started to think – what about clouds? Not a [...]... Read more »
Ikegaya, H., & Suganami, H. (2008) Correlation between Climate and Crime in Eastern Tokyo. Canadian Journal of Criminology and Criminal Justice/La Revue canadienne de criminologie et de justice pénale, 50(2), 225-238. DOI: 10.3138/cjccj.50.2.225
Li Y, & Fernie G. (2010) Pedestrian behavior and safety on a two-stage crossing with a center refuge island and the effect of winter weather on pedestrian compliance rate. Accident; analysis and prevention, 42(4), 1156-63. PMID: 20441826
Denissen, J., Butalid, L., Penke, L., & van Aken, M. (2008) The effects of weather on daily mood: A multilevel approach. Emotion, 8(5), 662-667. DOI: 10.1037/a0013497
Randler, C. (2008) Morningness‐Eveningness Comparison in Adolescents from Different Countries around the World. Chronobiology International, 25(6), 1017-1028. DOI: 10.1080/07420520802551519
Sci’s not gonna lie, the past several days have been, to say the least, incredibly stressful. I have no idea when blogging went from something that was fun and interesting to something that took up my entire life, but WHOA DUDES. The end result is stress, and Sci has been eating junkfood, not sleeping, and [...]... Read more »
Vialou V, Robison AJ, Laplant QC, Covington HE 3rd, Dietz DM, Ohnishi YN, Mouzon E, Rush AJ 3rd, Watts EL, Wallace DL.... (2010) DeltaFosB in brain reward circuits mediates resilience to stress and antidepressant responses. Nature neuroscience, 13(6), 745-52. PMID: 20473292
BMC Neurology has just published the findings of a group of Dutch researchers in their quest to develop multidisciplinary guidelines for treatment of CRPS. They looked at literature from 1980 – 2005. It is a major piece of work and I reckon it deserves publication. It is also a shocker when one produces such a [...]... Read more »
 Perez, R., Zollinger, P., Dijkstra, P., Thomassen-Hilgersom, I., Zuurmond, W., Rosenbrand, K., Geertzen, J., & Task force, T. (2010) Evidence based guidelines for complex regional pain syndrome type 1. BMC Neurology, 10(1), 20. DOI: 10.1186/1471-2377-10-20
Below is a draft of a chapter I’m writing for Subjective Time, an upcoming book from MIT Press edited by Valtteri Arstila and Dan Lloyd. In a bowling alley, a professional player launches his ball down the lane. As the ball rolls toward the pins, our visual experience of it is smooth and seamless. The [...]... Read more »
Holcombe, A. (2009) Seeing slow and seeing fast: two limits on perception. Trends in Cognitive Sciences, 13(5), 216-221. DOI: 10.1016/j.tics.2009.02.005
Kline, K., & Eagleman, D. (2008) Evidence against the temporal subsampling account of illusory motion reversal. Journal of Vision, 8(4), 13-13. DOI: 10.1167/8.4.13
VanRullen R, Reddy L, & Koch C. (2005) Attention-driven discrete sampling of motion perception. Proceedings of the National Academy of Sciences of the United States of America, 102(14), 5291-6. PMID: 15793010
From Schlupp, I., Riesch, R., Tobler, M., Plath, M., Parzefall, J., & Schartl, M. (2010) Behavioral Ecology and Sociobiology
Straight men let’s face it. We will do anything if we think females will find it attractive. No matter how ludicrous, expensive, or time-consuming it may be, we will do it. The rise of mullets and Camaros . . . → Read More: 70’s Porn Staches and the Female Fish Who Love Them... Read more »
Schlupp, I., Riesch, R., Tobler, M., Plath, M., Parzefall, J., & Schartl, M. (2010) A novel, sexually selected trait in poeciliid fishes: female preference for mustache-like, rostral filaments in male Poecilia sphenops. Behavioral Ecology and Sociobiology. DOI: 10.1007/s00265-010-0996-y
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