Biology posts
- May 7, 2013
- 10:41 AM
- 30 views
Detecting picograms of protein in the secretome
by Kasra Hassani in The Parasite Diary
Posted by Kasra When designing experiments in the lab, we usually say we cannot check for everything. Well, what if we could?! Meissner et al. used only 150,000 macrophages per sample to analyze their secretome. They have been able to detect and quantify protein abundances at the picogram level in a label-free system. Picogram detection [...]... Read more »
Meissner F, Scheltema RA, Mollenkopf HJ, & Mann M. (2013) Direct proteomic quantification of the secretome of activated immune cells. Science (New York, N.Y.), 340(6131), 475-8. PMID: 23620052
- May 7, 2013
- 08:15 AM
- 28 views
No Bacterium Is An Island
by Moselio Schaechter in Small Things Considered
To paraphrase an old adage, no bacterium is an island. Indeed, bacteria in nature exist as polymicrobial communities where interactions between individuals influence activities of the entire population. This is especially true of pathogenic bacteria, although it has been mostly ignored because we frequently isolate a single species from an infection site and prescribe antibiotic therapy based upon this information. A recent paper by Korgaonkar and coworkers highlights that this practice is somew........ Read more »
Korgaonkar A, Trivedi U, Rumbaugh KP, & Whiteley M. (2013) Community surveillance enhances Pseudomonas aeruginosa virulence during polymicrobial infection. Proceedings of the National Academy of Sciences of the United States of America, 110(3), 1059-64. PMID: 23277552
- May 7, 2013
- 03:38 AM
- 30 views
Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)
by Martha Serrano in genome ecology evolution etc
1. How genomes evolve in natural populations? is a question that, despite to be a long-standing search for geneticists, recent molecular genomic approaches may help to understand. Their evolution among natural populations may be shaped by forces derived from … Continuer la lecture →... Read more »
Staubach F, Lorenc A, Messer PW, Tang K, Petrov DA, & Tautz D. (2012) Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS genetics, 8(8). PMID: 22956910
- May 7, 2013
- 03:38 AM
- 51 views
Music and Cannabis; What’s the Connection?
by Mark Fonseca Rendeiro in United Academics
When you bring up the subject of listening to music while stoned, you get a range of responses, almost all of them positive. While you might enjoy a song in a non-altered state, under the influence of Cannabis, it has been established that listening to and creating music is somehow a deeper and more intense experience. The disputed issue that arises is why this happens and if the feeling is real.... Read more »
Webster, P. (2001) Marijuana and Music. Journal of Cannabis Therapeutics, 1(2), 93-105. DOI: 10.1300/J175v01n02_05
- May 6, 2013
- 01:04 PM
- 55 views
The Aspens that were left behind
by Jes in Biogeography Bits
When climates change, species move. It’s a fact of life on Earth and probably has been for the past 542 million years, even when species don’t have legs or wings or fins to get them from place to place.
Quaking aspen is one example of a seemingly stationary species that has managed in just the past 20,000 years to expand into the largest range of any native North American tree.... Read more »
Callahan, C., Rowe, C., Ryel, R., Shaw, J., Madritch, M., & Mock, K. (2013) Continental-scale assessment of genetic diversity and population structure in quaking aspen (Populus tremuloides) . Journal of Biogeography. DOI: 10.1111/jbi.12115
- May 6, 2013
- 08:21 AM
- 14 views
The Art of Microbial Alchemy
by Moselio Schaechter in Small Things Considered
In 2001, Kashefi and collaborators published an article in Applied and Environmental Microbiology reporting the surprising finding that several iron-reducing microbes can use gold as an electron acceptor for their respiration. These microbial alchemists included both mesophilic and thermophilic bacteria as well as hyperthermophilic archaea. The beauty of this process is that the oxidized form of gold provided to the microbes, Au(III), is soluble, whereas its reduced form, Au(0), is insoluble. He........ Read more »
Kashefi K, Tor JM, Nevin KP, & Lovley DR. (2001) Reductive precipitation of gold by dissimilatory Fe(III)-reducing bacteria and archaea. Applied and environmental microbiology, 67(7), 3275-9. PMID: 11425752
- May 6, 2013
- 08:20 AM
- 20 views
A Good Defense Is Worth Stealing
by Moselio Schaechter in Small Things Considered
One widely-used tactic for defense against phage and other mobile genetic elements is to deploy a CRISPR-Cas system (click here and here) to recognize and chop them into pieces. Based on sequenced genomes, 60% of Bacteria and 90% of Archaea have the wherewithal to dispatch invaders this way. But phages also have to protect themselves against enemies, including other mobile elements. Knowing a good thing when they see it—and they have seen it from the receiving end often—some phages have stol........ Read more »
Seed KD, Lazinski DW, Calderwood SB, & Camilli A. (2013) A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature, 494(7438), 489-91. PMID: 23446421
- May 6, 2013
- 07:00 AM
- 41 views
May 6, 2013
by Erin Campbell in HighMag Blog
Our bodies have multiple fronts for battling viruses, and it’s impressive that any of those suckers manage to invade our bodies at all. When virus particles do make their way into a cell, it’s important for biologists to understand their pathway through a cell in order to create drug therapies and vaccines. Today’s image is from a paper describing the use of high resolution imaging to understand this process.The polarized cells that line our digestive and respiratory tracts for........ Read more »
Boulant, S., Stanifer, M., Kural, C., Cureton, D., Massol, R., Nibert, M., & Kirchhausen, T. (2013) Similar uptake but different trafficking and escape routes of reovirus virions and infectious subvirion particles imaged in polarized Madin-Darby canine kidney cells. Molecular Biology of the Cell, 24(8), 1196-1207. DOI: 10.1091/mbc.E12-12-0852
- May 6, 2013
- 04:36 AM
- 59 views
The ESSENCE of autism comorbidity?
by Paul Whiteley in Questioning Answers
Like Charlie Bucket looking through the sweet shop window at the delicious chocolates produced by the workforce of a certain Mr Willy Wonka (the candyman no less), I am always quite interested in the goings-on at the IMFAR autism research conference. The candyman can... @ Wikipedia This year (2013) proved to be a bit of a vintage, as once again the great and the good presented their Wonka bars of autism research; thus hinting at the direction of future autism research and what y........ Read more »
Höglund Carlsson, L., Norrelgen, F., Kjellmer, L., Westerlund, J., Gillberg, C., & Fernell, E. (2013) Coexisting Disorders and Problems in Preschool Children with Autism Spectrum Disorders. The Scientific World Journal, 1-6. DOI: 10.1155/2013/213979
- May 5, 2013
- 11:44 AM
- 52 views
Pumping fuel from bacteria
In my last post I discussed a bioengineered E. coli strain capable of producing an engine compatible biofuel. I hailed the finding as more efficient than ordinary biofuels because this technique has less environmental impact than biofuels from crops, for example, or cellulose, which instead use great amounts of water and forest land. I did some more reading on the topic and found out that, surprise surprise, there are some costs in harvesting biofuels from bacteria as well, so my discussion was ........ Read more »
Dunlop, M., Dossani, Z., Szmidt, H., Chu, H., Lee, T., Keasling, J., Hadi, M., & Mukhopadhyay, A. (2011) Engineering microbial biofuel tolerance and export using efflux pumps. Molecular Systems Biology. DOI: 10.1038/msb.2011.21
Doshi, R., Nguyen, T., & Chang, G. (2013) Transporter-mediated biofuel secretion. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1301358110
- May 5, 2013
- 05:57 AM
- 56 views
More on 'Bugs as Drugs'
by Christen Rune Stensvold in Blastocystis Parasite Blog
A follow-up on Carl Zimmer's post in "Phenomena" (National Geographic) on 'Bugs as Drugs'.... Read more »
Hyman P, Atterbury R, & Barrow P. (2013) Fleas and smaller fleas: virotherapy for parasite infections. Trends in microbiology. PMID: 23540830
van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG.... (2013) Duodenal infusion of donor feces for recurrent Clostridium difficile. The New England journal of medicine, 368(5), 407-15. PMID: 23323867
Weinstock JV. (2012) Autoimmunity: The worm returns. Nature, 491(7423), 183-5. PMID: 23135449
- May 5, 2013
- 05:22 AM
- 77 views
The (Lack of) Changes in Ecological Research
by gunnardw in The Beast, the Bard and the Bot
Ecology is a rapidly changing, dynamic field of research. In recent decades, there’s been a major shift from considering ecosystems as stable and poised to seeing them as systems that are in constant flux. At least, that’s what ecologists want (us) to believe. But how much of this claimed change has been able to seep [...]... Read more »
Carmel, Y., Kent, R., Bar-Massada, A., Blank, L., Liberzon, J., Nezer, O., Sapir, G., & Federman, R. (2013) Trends in Ecological Research during the Last Three Decades – A Systematic Review. PLoS ONE, 8(4). DOI: 10.1371/journal.pone.0059813
- May 4, 2013
- 12:40 AM
- 61 views
Help: My freaky protein doesn’t have structure. And it aggregates!
by Vicky Doronina in Protein Solubility Blog
A biochemist about to attempt membrane protein purification knows that she is in the beginning of a difficult time in her career. However, there is another wide class of proteins, which are also difficult to purify, because they readily form protein aggregates or are plain insoluble. These are so called intrinsically disordered proteins (IDPs); but just a disordered domain within an otherwise nicely folded globular protein can be enough for the overexpressed protein to aggregate.... Read more »
Dunker, A., Silman, I., Uversky, V., & Sussman, J. (2008) Function and structure of inherently disordered proteins. Current Opinion in Structural Biology, 18(6), 756-764. DOI: 10.1016/j.sbi.2008.10.002
Uversky, V. (2013) Unusual biophysics of intrinsically disordered proteins. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1834(5), 932-951. DOI: 10.1016/j.bbapap.2012.12.008
- May 3, 2013
- 11:00 PM
- 63 views
Evolutionary economics and game theory
by Artem Kaznatcheev in Evolutionary Games Group
Like the agents they study, evolutionary economics is highly heterogeneous. Models are ad-hoc and serve as heuristic guides to specific problems. This is similar to theoretical biology, where evolutionary models are independent of each other. Even the general theory of inclusive fitness does not provide a non-controversial unifying framework. Although there is no single framework, evolutionary economists are united by four main assumptions about the world:... Read more »
Hodgson, G., & Huang, K. (2010) Evolutionary game theory and evolutionary economics: are they different species?. Journal of Evolutionary Economics, 22(2), 345-366. DOI: 10.1007/s00191-010-0203-3
- May 3, 2013
- 05:48 PM
- 11 views
Scatological Scents
by Mini Watsa in SurroundScience
Ever since tamarins were first captured from the wild to serve as research models in laboratories, we have been curious about their use of odour for communication. These miniature monkeys … Continue reading →... Read more »
Threlfall C., Law B., & Banks P. B. (2013) Odour cues influence predation risk at artificial bat roosts in urban bushland. Biology Letters, 9(3), 20121144-20121144. DOI: 10.1098/rsbl.2012.1144
- May 3, 2013
- 05:41 PM
- 25 views
Brain Voodoo Goes Electric
by Neuroskeptic in Neuroskeptic_Discover
Four years ago, neuroscientists became aware of an ominous-sounding manuscript entitled “Voodoo Correlations In Social Neuroscience”. This piece was eventually published under a more prosaic name but it still hit home, with nearly 500 citations so far. To me, this paper marked the start of a new era of ‘critical’ (in the proper sense of [...]... Read more »
Kilner, J. (2013) Bias in a common EEG and MEG statistical analysis and how to avoid it. Clinical Neurophysiology. DOI: 10.1016/j.clinph.2013.03.024
- May 3, 2013
- 05:33 PM
- 46 views
Chop It While It’s Hot! An Enzyme-Free Alternative to Hydroxymethylated DNA Detection
by Xueguang S. in EpiBeat
5-hydroxymethylcytosine (5-hmC) has been widely studied in many biological contexts, but the precise mechanistic functions of this epigenetic modification remain largely unknown. Some evidence suggests that 5-hmC may be an intermediate in the process of DNA demethylation because it can be further oxidized to form 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC), which are recognized and eliminated ...... Read more »
Mao W, Hu J, Hong T, Xing X, Wang S, Chen X, & Zhou X. (2013) A convenient method for selective detection of 5-hydroxymethylcytosine and 5-formylcytosine sites in DNA sequences. Organic . PMID: 23629475
- May 3, 2013
- 03:40 PM
- 72 views
Why blogging science is rewarding!
by Ragothamanyennamalli in Getting to know Structural Bioinformatics
... Read more »
Bik HM, & Goldstein MC. (2013) An introduction to social media for scientists. PLoS biology, 11(4). PMID: 23630451
- May 3, 2013
- 02:03 PM
- 56 views
Tone-Deaf Birds Disrupt Society, Are Easier to Get into Bed
by Elizabeth Preston in Inkfish
While male birds are singing elaborate arias and flashing their feathers, it's easy to imagine their female counterparts are unimportant actors. Duller and quieter, all a lady bird has to do is hold still and let one of these frantic performers mate with her. Yet in brown-headed cowbirds, at least, the quiet female keeps the whole society in order. Scientists discovered this by targeting a tiny portion of the female brain and frying it.
Males of the species Molothrus ater use the........ Read more »
Maguire, S., Schmidt, M., & White, D. (2013) Social Brains in Context: Lesions Targeted to the Song Control System in Female Cowbirds Affect Their Social Network. PLoS ONE, 8(5). DOI: 10.1371/journal.pone.0063239
- May 3, 2013
- 11:32 AM
- 72 views
Taking Two Antibiotics for Quick Recovery?
by Geetanjali Yadav in United Academics
Did you ever take two or more antibiotics in order to get rid of a disease? New research in PLOS Biology suggests that this is not a wise thing to do. Drug resistant bacteria grow faster than their weaker counter parts when resources are limiting and many antibiotics are consumed.... Read more »
Pena-Miller R, Laehnemann D, Jansen G, Fuentes-Hernandez A, Rosenstiel P, Schulenburg H, & Beardmore R. (2013) When the most potent combination of antibiotics selects for the greatest bacterial load: the smile-frown transition. PLoS biology, 11(4). PMID: 23630452
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