The -omics. Y'know all those new-fangled disciplines which have sprung up to describe how sciences looks at genes, bacteria, etc. We used to call it plain old scientific analysis, but now depending on what your sample medium or technology or your target species is, its been rebranded and repackaged as an -omic.Shepherdess @ Wikipedia I've talked about a few of the -omics quite a bit on this blog and their relationship to systems biology; ranging from microbiomics (studying bacteria) to epi........ Read more »
Emond P, Mavel S, Aïdoud N, Nadal-Desbarats L, Montigny F, Bonnet-Brilhault F, Barthélémy C, Merten M, Sarda P, Laumonnier F.... (2013) GC-MS-based urine metabolic profiling of autism spectrum disorders. Analytical and bioanalytical chemistry. PMID: 23571465
Mavel, S., Nadal-Desbarats, L., Blasco, H., Bonnet-Brilhault, F., Barthélémy, C., Montigny, F., Sarda, P., Laumonnier, F., Vourc′h, P., Andres, C.... (2013) 1H–13C NMR-based urine metabolic profiling in autism spectrum disorders. Talanta, 95-102. DOI: 10.1016/j.talanta.2013.03.064
This Month in Blastocystis Research is a bit meagre, but here's a chance to listen to a 1h related Blastocystis case story podcast...
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Sakalar C, Uyar Y, Yürürdurmaz MA, Tokar S, Yeşilkaya H, Gürbüz E, Kuk S, & Yazar S. (2013) [Cloning of Blastocystis sp Subtype 3 Small-subunit Ribosomal DNA]. Turkiye parazitolojii dergisi / Turkiye Parazitoloji Dernegi , 37(1), 13-8. PMID: 23619039
Ozyurt M, Kurt O, Mølbak K, Nielsen HV, Haznedaroglu T, & Stensvold CR. (2008) Molecular epidemiology of Blastocystis infections in Turkey. Parasitology international, 57(3), 300-6. PMID: 18337161
Hey Julie,I hope you've had a fun week. I saw a new in-press publication with your name on it - "Smelling more or less: Investigating the olfactory experience of the domestic dog" - looks like a really great study, and so timely after my last post about dogs and olfactory enrichment! Looking forward to reading it (and all those other cool Learning and Motivation articles) over the weekend. So did you do your homework? Did you watch this clip from the Sydney Opera H........ Read more »
Kogan Lori R., Schoenfeld-Tacher Regina, & Simon Allen A. (2012) Behavioral effects of auditory stimulation on kenneled dogs. Journal of Veterinary Behavior: Clinical Applications and Research, 7(5), 268-275. DOI: 10.1016/j.jveb.2011.11.002
Wells D, Graham L, & Hepper P. (2002) The influence of auditory stimulation on the behaviour of dogs housed in a rescue shelter. Animal Welfare, 11(4), 385-393. http://www.ufaw.org.uk/v11main.php
A point mutation in a gene leads to a phenomenal effect on the phenotype. It is a classic Biochemistry textbook case study, Sickle Cell Anemia. The mutant hemoglobin has a Valine instead of the Glutamic acid. The change is highly observable in the form of a debilitating condition. But, not all point mutations in the protein sequence are debilitating, and sometimes they give rise to something spectacular. One such example is the White Tiger, frequently mistaken as an albino. The recent publicatio........ Read more »
It's hard to keep your footing in a steep tunnel made of loose dirt while others are scrambling around and over your body. Harder still in pitch blackness. That's why fire ants build tunnels that will catch them when they fall—a strategy human engineers might want to steal.
"Slips and missteps are likely a constant, recurring feature of life underground," says Nick Gravish, a graduate student in Daniel Goldman's rheology and biomechanics lab at Georgia Tech. Yet ants have to traverse their........ Read more »
Gravish, N., Monaenkova, D., Goodisman, M., & Goldman, D. (2013) Climbing, falling, and jamming during ant locomotion in confined environments. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1302428110
A new study shows that the U.S. land and water resources could likely support the growth of enough algae to produce up to 25 billion gallons (94.6 million m3) of algae-based renewable biodiesel a year.... Read more »
Venteris, E., Skaggs, R., Coleman, A., & Wigmosta, M. (2013) A GIS Cost Model to Assess the Availability of Freshwater, Seawater, and Saline Groundwater for Algal Biofuel Production in the United States. Environmental Science , 47(9), 4840-4849. DOI: 10.1021/es304135b
The Irish Famine (or “Great Potato Famine” if you live outside the Emerald Isle) killed one million people and forced another million to leave the country between 1845 and 1852. It was caused by a blight on the country’s main food stock—the Irish “Lumper” potato. Now, researchers have identified the genome of the blight behind the famine.... Read more »
Kentaro Yoshida, Verena J. Schuenemann, Liliana M. Cano, Marina Pais, Bagdevi Mishra, Rahul Sharma, Christa Lanz, Frank N. Martin, Sophien Kamoun, Johannes Krause.... (2013) The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. eLife. arXiv: 1305.4206v1
--> The mycobiome is starting to get a little traction!When will we know the weight of the fungi on and in our bodies? The human microbiota has been recognized as hugely important in the last few years, but that has almost entirely focused on bacteria. I’ve been interested in the mycobiome of the human built environment for a while, and I certainly haven’t been alone. People tend to think of fungi as a problem in buildings, on or in plants, and in the outside air. However, there is ........ Read more »
Iliev, I., Funari, V., Taylor, K., Nguyen, Q., Reyes, C., Strom, S., Brown, J., Becker, C., Fleshner, P., Dubinsky, M.... (2012) Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis. Science, 336(6086), 1314-1317. DOI: 10.1126/science.1221789
Findley, K., Oh, J., Yang, J., Conlan, S., Deming, C., Meyer, J., Schoenfeld, D., Nomicos, E., Park, M., Becker, J.... (2013) Topographic diversity of fungal and bacterial communities in human skin. Nature. DOI: 10.1038/nature12171
There isn’t a cell biologist out there who doesn’t fantasize about reaching her hands into a cell and physically manipulating whatever protein or structure that she obsesses over. While we can’t do that with our own hands, optical tweezers can…and the information we learn is invaluable. Today’s image is from a paper that uses optical tweezers to measure the forces within a mitotic spindle.The mechanics within a mitotic spindle are complicated, and cannot be fully understood........ Read more »
Ferraro-Gideon, J., Sheykhani, R., Zhu, Q., Duquette, M., Berns, M., & Forer, A. (2013) Measurements of forces produced by the mitotic spindle using optical tweezers. Molecular Biology of the Cell, 24(9), 1375-1386. DOI: 10.1091/mbc.E12-12-0901
Sheykhani, R., Baker, N., Gomez-Godinez, V., Liaw, L., Shah, J., Berns, M., & Forer, A. (2013) The role of actin and myosin in PtK2 spindle length changes induced by laser microbeam irradiations across the spindle. Cytoskeleton, 70(5), 241-259. DOI: 10.1002/cm.21104
Bats need to eat a lot to keep flying. So, the more efficiently they can take in food, the better. for the nectar-eating bat Glossophaga soricina, this has meant the evolution of a sophisticated tongue. ... Read more »
Harper CJ, Swartz SM, & Brainerd EL. (2013) Specialized bat tongue is a hemodynamic nectar mop. Proceedings of the National Academy of Sciences of the United States of America. PMID: 23650382
This week we would like to introduce you to the work of Professor Vera Krymskaya, Associate Professor of Medicine at the University of Pennsylvania Perelman School of Medicine. Professor Krymskaya’s primary research interest is how signalling pathways cause disease when … Continue reading →... Read more »
Goncharova EA, Goncharov DA, Eszterhas A, Hunter DS, Glassberg MK, Yeung RS, Walker CL, Noonan D, Kwiatkowski DJ, Chou MM.... (2002) Tuberin regulates p70 S6 kinase activation and ribosomal protein S6 phosphorylation. A role for the TSC2 tumor suppressor gene in pulmonary lymphangioleiomyomatosis (LAM). The Journal of biological chemistry, 277(34), 30958-67. PMID: 12045200
Goncharova EA, Goncharov DA, Fehrenbach M, Khavin I, Ducka B, Hino O, Colby TV, Merrilees MJ, Haczku A, Albelda SM.... (2012) Prevention of alveolar destruction and airspace enlargement in a mouse model of pulmonary lymphangioleiomyomatosis (LAM). Science translational medicine, 4(154). PMID: 23035046
Picking up on my infatuation with all things Hsp, today more on the effects of two of the large Hsps on Candida albicans biofilm formation and virulence in mice and worms.Ssa1, a member of the Hsp70 family, is traditionally implicated in protein folding and entwining. Following heat shock, Ssa1 expression increases, which is a hallmark of heat shock proteins. Recently, Ssa1’s role in Candida albicans’ virulence has been extensively characterized. A series of experiments involving C. al........ Read more »
Fiori, A., Kucharikova, S., Govaert, G., Cammue, B., Thevissen, K., & Van Dijck, P. (2012) The Heat-Induced Molecular Disaggregase Hsp104 of Candida albicans Plays a Role in Biofilm Formation and Pathogenicity in a Worm Infection Model. Eukaryotic Cell, 11(8), 1012-1020. DOI: 10.1128/EC.00147-12
Sun JN, Solis NV, Phan QT, Bajwa JS, Kashleva H, Thompson A, Liu Y, Dongari-Bagtzoglou A, Edgerton M, & Filler SG. (2010) Host cell invasion and virulence mediated by Candida albicans Ssa1. PLoS pathogens, 6(11). PMID: 21085601
What would be like to teach a class or describe someone about a protein, without visualizing its structure? Boring is one word that pops in my mind. I vividly remember the professor drawing two blobs touching each other, to describe protein-protein interaction, while explaining it either on the blackboard or on the transparencies of a over-head projector. Those were the days! Tracing back nearly 60 years back, when John Kendrew showed everyone a coiled mess, it has fueled every scientist's ........ Read more »
Craig, P., Michel, L., & Bateman, R. (2013) A survey of educational uses of molecular visualization freeware. Biochemistry and Molecular Biology Education, 41(3), 193-205. DOI: 10.1002/bmb.20693
This appeared earlier today on the Facebook feed I Fucking Love Science:
I remember seeing a shark documentary as a kid, hosted by Burgess Meredith, if I remember correctly. It made the same basic claim about great white sharks: too big to have predators, nobody had ever seen them die except by accident or by human hands, blah blah blah, therefore “some have suggested” they are immortal.
That I can remember the end of the show all these years later shows you what a terrific close........ Read more »
Klapper Wolfram, Kühne Karen, Singh Kumud K, Heidorn Klaus, Parwaresch Reza, & Krupp Guido. (1998) Longevity of lobsters is linked to ubiquitous telomerase expression. FEBS Letters, 439(1-2), 143-146. DOI: 10.1016/S0014-5793(98)01357-X
University of Illinois at Urbana-Champaign researchers have developed a cradle and app for the iPhone that uses the phone’s built-in camera and processing power as a biosensor to detect toxins, proteins, bacteria, viruses and other molecules. Having such sensitive biosensing capabilities in the field could enable on-the-spot tracking of groundwater contamination, combine the phone’s GPS … Read More →... Read more »
Drinking pruno is a risky endeavor, both in terms of its offense to culinary sensibilities and to one's health. However, turned stomachs are not the only hazard here; you may add a desire to avoid botulism to your list of reasons to shy away from you'r mates latest batch of prison hooch. The soil-dwelling bacterium Clostridium botulinum can contaminate fruits and veggies, and, in warm, oxygen-deprived conditions, produces the neuroparalytic toxin botulinum. Even more wholesome DIY ende........ Read more »
Centers for Disease Control and Prevention (CDC). (2013) Notes from the field: botulism from drinking prison-made illicit alcohol - Arizona, 2012. MMWR. Morbidity and mortality weekly report, 62(5), 88. PMID: 23388552
Gene expression is very complex. My paper, which was published in Cell today, just shows that it is more complicated than previously realized. Traditionally, eukaryotic gene expression is divided into five steps: Transcription (mRNA synthesis): this step is subdivided into … Continue reading →... Read more »
Haimovich, G., Medina, D., Causse, S., Garber, M., Millán-Zambrano, G., Barkai, O., Chávez, S., Pérez-Ortín, J., Darzacq, X., & Choder, M. (2013) Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis. Cell, 153(5), 1000-1011. DOI: 10.1016/j.cell.2013.05.012
Haimovich G, Choder M, Singer RH, & Trcek T. (2013) The fate of the messenger is pre-determined: A new model for regulation of gene expression. Biochimica et biophysica acta, 1829(6-7), 643-53. PMID: 23337853
Since my last blog post, where I shared my thoughts on BRCA1, BRCA2, and preventive mastectomies, I've been asked what else can a woman do to reduce her risk of breast cancer. I've heard a big deal about vitamin D, so I did a bit of research on the matter. As a disclaimer, I should tell you up front that, though many correlations between vitamin D deficiency and cancer risk have been found, just as many have been refuted or found inconclusive. You can read more about it on the wikipedia page.Wha........ Read more »
Crew, K. (2013) Vitamin D: Are We Ready to Supplement for Breast Cancer Prevention and Treatment?. ISRN Oncology, 1-22. DOI: 10.1155/2013/483687
I recently volunteered to help organise an event run by the Canadian Science Policy Centre that looked at the status of women in science and technology. To be frank, I was mightily fearful about participating in such an event. I … Continue reading →... Read more »
An episode of the BBC program Horizon on 'Big Data' recently caught my attention. The content was a fascinating insight into how we are living in a data-rich age and how trawling/mining/dredging such data has the ability to advance medicine, predict crime and even make someone a few quid/dollars/euros on the stock market.Gone (data) fishing @ Wikipedia I'm a big believer in big data. In particular how, with the right sources, technology, techniques and people, big data might be able t........ Read more »
Mizejewski GJ, Lindau-Shepard B, & Pass KA. (2013) Newborn screening for autism: in search of candidate biomarkers. Biomarkers in medicine, 7(2), 247-60. PMID: 23547820
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