I'm really behind on the answers. I'll do the easier one first, so MM08 will be next.Remember this myserious organism from a while ago? Johan got it: it's Hoplonympha, a parabasalian gut endosymbiont! (Opisthokont was also on the right track)Hoplonympha. top: SEM of whole organism (F indicates flagella), the long strips are actually ectosymbiotic bacteria, as evident in the TEM cross section on the bottom. CM - cytoplasmic [inner] membrane, OM - outer membrane, SL - S-layer. Note that unlike in........ Read more »
Noda, S., Inoue, T., Hongoh, Y., Kawai, M., Nalepa, C., Vongkaluang, C., Kudo, T., & Ohkuma, M. (2006) Identification and characterization of ectosymbionts of distinct lineages in Bacteroidales attached to flagellated protists in the gut of termites and a wood-feeding cockroach. Environmental Microbiology, 8(1), 11-20. DOI: 10.1111/j.1462-2920.2005.00860.x
CARPENTER, K., CHOW, L., & KEELING, P. (2009) Morphology, Phylogeny, and Diversity of (Parabasalia: Hypermastigida) of the Wood-Feeding Cockroach . Journal of Eukaryotic Microbiology, 56(4), 305-313. DOI: 10.1111/j.1550-7408.2009.00406.x
OHKUMA, M. (2008) Symbioses of flagellates and prokaryotes in the gut of lower termites. Trends in Microbiology, 16(7), 345-352. DOI: 10.1016/j.tim.2008.04.004
Stingl, U. (2004) Symbionts of the gut flagellate Staurojoenina sp. from Neotermes cubanus represent a novel, termite-associated lineage of Bacteroidales: description of 'Candidatus Vestibaculum illigatum'. Microbiology, 150(7), 2229-2235. DOI: 10.1099/mic.0.27135-0
een to a library lately? Those of you who, like me, get their current literature via the internet, probably thoroughly repressed the memory of literature research without a search mask, but there are things that stay with you. Such as the smell of old books.
Turns out that there is more to this smell that meets the… uh… nose.... Read more »
One of the common misconceptions about biological evolution is that the process pushes organisms towards a pinnacle of perfection in which the ‘most evolved species’ maintain dominance over ‘less evolved’ or ‘lower organisms.’ Often closely associated with this mistaken belief is the erroneous idea that, by virtue of braininess, our own species – Homo sapiens - currently holds sovereignty over evolution’s hypothetical pinnacle. These egocentric a........ Read more »
D'Angelo, K. (1997) Faxon institute colloquium on scholarly communications issues. Serials Review, 23(2), 91-96. DOI: 10.1016/S0098-7913(97)90058-7
Some nagging uncertainties remain on progress in stem cell medicine - and especially progress in reprogramming easily obtained somatic cells into patient-specific pluripotent stem cells. These uncertainties will be answered and addressed in the years ahead, but this one springs to mind today: it is possible that cells from older people may be altered or damaged in ways that prevent their effective use as-is in the sort of autologous stem cell therapies presently envisaged. That would be a setbac........ Read more »
Suhr, S., Chang, E., Rodriguez, R., Wang, K., Ross, P., Beyhan, Z., Murthy, S., & Cibelli, J. (2009) Telomere Dynamics in Human Cells Reprogrammed to Pluripotency. PLoS ONE, 4(12). DOI: 10.1371/journal.pone.0008124
Historical places of worship may harbor biodiversity
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Metcalfe, K., Ffrench-Constant, R., & Gordon, I. (2009) Sacred sites as hotspots for biodiversity: the Three Sisters Cave complex in coastal Kenya. Oryx, 44(01), 118. DOI: 10.1017/S0030605309990731
Cold and flu season has hit the Rochester area recently, as evidenced by the recent uptick in the number of students missing class on account of colds and flu. Fortunately there are ways to minimize your chances of getting a...... Read more »
Sloane, H., & Birch, T. (1755) An Account of Inoculation by Sir Hans Sloane, Bart. Given to Mr. Ranby, to be Published, Anno 1736. Communicated by Thomas Birch, D. D. Secret. R. S. Philosophical Transactions (1683-1775), 49(1), 516-520. DOI: 10.1098/rstl.1755.0073
Things need to get transported around inside of our cells. For example, proteins meant to detect extracellular signals like hormones must move to the cell surface; otherwise they won't work. Much of this cargo gets moved through small balloon-like structures called vesicles. Rather than drifting randomly, these "balloons" move along tracks in the cell called microtubules; long, filamentous proteins that form a skeleton within the cell. ike a train, these "balloons" require a motor to pull the........ Read more »
Cai D, McEwen DP, Martens JR, Meyhofer E, & Verhey KJ. (2009) Single molecule imaging reveals differences in microtubule track selection between Kinesin motors. PLoS biology, 7(10). PMID: 19823565
A recent paper in Bioinformatics investigates the effect of read-mapping biases on detecting allele-specific expression (ASE) from RNA-Seq data. The authors generated 16 million 36-bp cDNA reads in each of two HapMap individuals on the Illumina/Solexa platform. When evaluating known SNPs for evidence of ASE, they observed that heterozygous SNPs exhibited a mapping bias favoring [...]... Read more »
Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, & Pritchard JK. (2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics (Oxford, England), 25(24), 3207-12. PMID: 19808877
One of the things I forgot to mention in yesterday's post about why I like AMO physics is that AMO systems have proven to be outstanding tools for solving problems from other fields of physics. In particular, ultra-cold atoms have proven to be a fantastic venue for studying problems from condensed matter physics. There's a comprehensive review of the subject in this Reviews of Modern Physics paper, which is also freely available on the arxiv. I say "comprehensive review," but, of course, it's al........ Read more »
Phagehunter.org is proud to have J. Kandler, a microbiology graduate student at Emory University, present to us this interesting post on a defense feature common in our immune system, but being utilized by bacteria as well.After Halloween, I came across this spooky article in Science describing yet another way bacteria are dodging antibiotics. Don’t worry, there’s a silver lining! Gusarov and his colleagues may have found a new target for the antibiotic industry, bacterial nitric oxide synth........ Read more »
Gusarov I, Shatalin K, Starodubtseva M, & Nudler E. (2009) Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics. Science (New York, N.Y.), 325(5946), 1380-4. PMID: 19745150
Very recently, an interesting study was published looking at the risk of early mortality among metabolically-healthy obese individuals – a topic we’ve covered on a number of occasions on Obesity Panacea. The authors of this landmark study published in the journal Diabetes Care are actually close friends of ours (Dr. Jennifer Kuk and Dr. Christopher Ardern), and both are alumni of Queen’s university. Now that the media frenzy surrounding their recent study has subsided, Dr. Kuk ........ Read more »
Kuk, J., & Ardern, C. (2009) Are Metabolically Normal but Obese Individuals at Lower Risk for All-Cause Mortality?. Diabetes Care, 32(12), 2297-2299. DOI: 10.2337/dc09-0574
In recent evolution news, a research article published this month in the Proceedings of the National Academy of Sciences has demonstrated that the brains of elephants and humans have followed similar adaptive paths.... Read more »
Goodman, M., Sterner, K., Islam, M., Uddin, M., Sherwood, C., Hof, P., Hou, Z., Lipovich, L., Jia, H., Grossman, L.... (2009) Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries. Proceedings of the National Academy of Sciences, 106(49), 20824-20829. DOI: 10.1073/pnas.0911239106
At the American Society of Hematology meeting last weekend, I had the pleasure of listening to an enlightening education session on CML from Drs Brian Druker, John Goldman, Moshe Talpaz and Tim Hughes, all leading lights in the field. Prof...... Read more »
Buchdunger E, Zimmermann J, Mett H, Meyer T, Müller M, Druker BJ, & Lydon NB. (1996) Inhibition of the Abl protein-tyrosine kinase in vitro and in vivo by a 2-phenylaminopyrimidine derivative. Cancer research, 56(1), 100-4. PMID: 8548747
A few weeks ago, I wrote that the goal of a structural biology research program ought to be to "characterize the conformation and energy of key, functionally-relevant members of the protein's structural ensemble and identify the pathways between them." The Nature paper last week, among other examples I mentioned in the preceding post, described functionally significant minor members of the native-state ensemble, and this is certainly an area where structural studies are making a l........ Read more »
Gardino, A., Villali, J., Kivenson, A., Lei, M., Liu, C., Steindel, P., Eisenmesser, E., Labeikovsky, W., Wolf-Watz, M., Clarkson, M.W.... (2009) Transient Non-native Hydrogen Bonds Promote Activation of a Signaling Protein. Cell, 139(6), 1109-1118. DOI: 10.1016/j.cell.2009.11.022
Researchers in Spain measure the impacts of salvage logging on bird communities (it's not good)... Read more »
CASTRO, J., MORENO-RUEDA, G., & HÃDAR, J. (2009) Experimental Test of Postfire Management in Pine Forests: Impact of Salvage Logging versus Partial Cutting and Nonintervention on BirdâSpecies Assemblages. Conservation Biology. DOI: 10.1111/j.1523-1739.2009.01382.x
A new study uses a creative experimental design to test whether changing the author gender effects the outcome of the peer review process...... Read more »
Borsuk, R., Aarssen, L., Budden, A., Koricheva, J., Leimu, R., Tregenza, T., & Lortie, C. (2009) To Name or Not to Name: The Effect of Changing Author Gender on Peer Review. BioScience, 59(11), 985-989. DOI: 10.1525/bio.2009.59.11.10
Songbirds have evolved special areas in the brain that are used for song learning and song production. Two types of output connections from a cortical area known as HVC (proper name) each go to two ‘separate’ pathways. Some HVC neurons connect directly with neurons in a brain area called RA (robust nucleus of the archopallium), [...]... Read more »
Leblois, A., Bodor, A., Person, A., & Perkel, D. (2009) Millisecond Timescale Disinhibition Mediates Fast Information Transmission through an Avian Basal Ganglia Loop. Journal of Neuroscience, 29(49), 15420-15433. DOI: 10.1523/JNEUROSCI.3060-09.2009
For Sci, the weird science tends to come in spurts (heh heh...heh). There will be times when I am literally digging through Pubmed trying to find ANYTHING ODD AT ALL, and then there are times, like now, when people are tweeting and emailing and g-chatting and all but screaming in my ear with the weird. Got enough crazy sexual crap around here to last for WEEKS.
And a good thing, too, cause it's all about premature ejaculation, and don't we all wish we could last for weeks...
So we........ Read more »
Waldinger, M., Quinn, P., Dilleen, M., Mundayat, R., Schweitzer, D., & Boolell, M. (2005) A Multinational Population Survey of Intravaginal Ejaculation Latency Time. The Journal of Sexual Medicine, 2(4), 492-497. DOI: 10.1111/j.1743-6109.2005.00070.x
Coastal vegetation may not offer much protection against tsunamis
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Feagin, R., Mukherjee, N., Shanker, K., Baird, A., Cinner, J., Kerr, A., Koedam, N., Sridhar, A., Arthur, R., Jayatissa, L.... (2009) Shelter from the storm? Use and misuse of coastal vegetation bioshields for managing natural disasters. Conservation Letters. DOI: 10.1111/j.1755-263X.2009.00087.x
There is an interesting review  (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and [...]... Read more »
Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2009) Calling International Rescue: knowledge lost in literature and data landslide!. Biochemical Journal, 424(3), 317-333. DOI: 10.1042/BJ20091474
Fink, J., Kushch, S., Williams, P., & Bourne, P. (2008) BioLit: integrating biological literature with databases. Nucleic Acids Research, 36(Web Server). DOI: 10.1093/nar/gkn317
Shotton, D., Portwin, K., Klyne, G., & Miles, A. (2009) Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article. PLoS Computational Biology, 5(4). DOI: 10.1371/journal.pcbi.1000361
Pafilis, E., O'Donoghue, S., Jensen, L., Horn, H., Kuhn, M., Brown, N., & Schneider, R. (2009) Reflect: augmented browsing for the life scientist. Nature Biotechnology, 27(6), 508-510. DOI: 10.1038/nbt0609-508
Pettifer, S., Thorne, D., McDermott, P., Marsh, J., Villéger, A., Kell, D., & Attwood, T. (2009) Visualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics, 10(Suppl 6). DOI: 10.1186/1471-2105-10-S6-S19
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