There are several forms of peptide-protein interactions, one of which are globular PPIs mediated by a dominant linear peptide at the interface. To what extent could peptides extracted from a globular protein monomer be used to inhibit the interaction to its partner? In this work, we have investigated the possibility of deriving peptides from the interface of globular proteins to design inhibitors that would compete with their native interaction.
... Read more »
London N, Raveh B, Movshovitz-Attias D, & Schueler-Furman O. (2010) Can Self-Inhibitory Peptides be Derived from the Interfaces of Globular Protein-Protein Interactions?. Proteins. PMID: 20607702
It's always been clear that pterosaurs were present in the Cornet assemblage (for the background on Cornet and its archosaur fossils, you need to have read part I).
However, exactly what sort of pterosaurs are present at Cornet has been somewhat uncertain: the Late Jurassic ctenochasmatoid Cycnorhamphus, ornithocheirids and the Early Cretaceous Asian dsungaripterid Dsungaripterus were all reported from the assemblage during the 1980s (e.g., Jurcsák & Popa 1984) but, as with the birds, the........ Read more »
DYKE, G., BENTON, M., POSMOSANU, E., & NAISH, D. (2010) Early Cretaceous (Berriasian) birds and pterosaurs from the Cornet bauxite mine, Romania. Palaeontology. DOI: 10.1111/j.1475-4983.2010.00997.x
Genetically modified organisms (GMOs) are back in the news. A few days ago, NPR featured a couple of blog posts (here and here) considering whether the new GMO “supersized” salmon will be harmful to aquatic ecosystems.
A concern with GMOs is that—like the early adoption of pesticides—potential risks are being borne by the environment and consumers [...]... Read more »
Jennifer L. Tank, Emma J. Rosi-Marshall, Todd V. Royer, Matt R. Whiles, Natalie A. Griffiths, Therese C. Frauendorf, and David J. Treering. (2010) Occurrence of maize detritus and a transgenic insecticidal protein (Cry1Ab) within the stream network of an agricultural landscape. Proceedings of the National Academy of Sciences. info:/10.1073/pnas.1006925107
The title of this posting refers to the excellent article from David Dobbs I bookmarked very recently. I’d like to present you a very interesting initiative from French bioscience research program for high-school students called « Tous chercheurs ». The Community Page of the very last PLoS Biology is dedicated to this project and I find it really great. Because, indeed, publishing your science paper is only half of the job.... Read more »
Hammond, C., Karlin, D., & Thimonier, J. (2010) Creative Research Science Experiences for High School Students. PLoS Biology, 8(9). DOI: 10.1371/journal.pbio.1000447
You’ve been asked to to run a bioinformatics analysis. How do you choose what algorithm to use?
My first suggestion would be to talk to experienced bioinformatics scientists or computational biologists. It’s a lot quicker, and it’ll save you making mistakes that the research literature assumes you know better not to. You’ll also avoid the trap [...]... Read more »
Aniba, M., Poch, O., & Thompson, J. (2010) Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Research. DOI: 10.1093/nar/gkq625
Sometimes I come across crazy parasite stories when I’m browsing scientific archives online. But this time was different, when a story came to me straight from the Dutch woodlands.
A week ago, someone asked me to find out what was happening to some poor acorns that were found in a broadleaf forest. The acorns [...]... Read more »
Stone, G., van der Ham, R., & Brewer, J. (2008) Fossil oak galls preserve ancient multitrophic interactions. Proceedings of the Royal Society B: Biological Sciences, 275(1648), 2213-2219. DOI: 10.1098/rspb.2008.0494
by Moselio Schaechter in Small Things Considered
An underwater microbial mat has been found in fairly shallow waters off the coast of Chile and, according to headlines (click here and here), it’s the size of Greece, or about 132,000 km2 (or for us norte-americanos, about the size of Alabama). These communities of sulfide-oxidizing bacteria have been known for some time, but their attention has been highlighted by the recent version of the Census of Marine Life. In fact, they were discovered in 1963 by the oceanographer and microbiol........ Read more »
Teske A, Jørgensen BB, & Gallardo VA. (2009) Filamentous bacteria inhabiting the sheaths of marine Thioploca spp. on the Chilean continental shelf. FEMS microbiology ecology, 68(2), 164-72. PMID: 19573198
A recent paper in PNAS describes the development of MiniPromoters: human DNA promoters of less than 4 kb, designed to drive gene expression in specific areas of the brain. The initiative is called the Pleiades Promoter Project, and so far they have confirmed brain-region specific activity in knockin mice for 27 of their MiniPromoters. The [...]... Read more »
Portales-Casamar, E., Swanson, D., Liu, L., Leeuw, C., Banks, K., Ho Sui, S., Fulton, D., Ali, J., Amirabbasi, M., Arenillas, D.... (2010) A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proceedings of the National Academy of Sciences, 107(38), 16589-16594. DOI: 10.1073/pnas.1009158107
We present Rosetta FlexPepDock, a novel tool for refining coarse peptide–protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub-angstrom backbone quality, over an extensive and general benchmark of 89 peptide–protein interactions.
... Read more »
Raveh B, London N, & Schueler-Furman O. (2010) Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins, 78(9), 2029-40. PMID: 20455260
For many of us mosquitoes are an itchy aggravation. They come in the evenings in the warmer months. They disrupt hikes, camping trips and picnics, leaving behind itching reminders that have us reaching for antihistamines and no-itch creams. For people in some areas of the world however, mosquitoes are more than just a pest with [...]... Read more »
Rodrigues J, Brayner FA, Alves LC, Dixit R, & Barillas-Mury C. (2010) Hemocyte differentiation mediates innate immune memory in Anopheles gambiae mosquitoes. Science (New York, N.Y.), 329(5997), 1353-5. PMID: 20829487
I’ve got a few news items regarding IMG, or Integrated Microbial Genomes, from the DOE Joint Genome Institute. The first item is that their Sept 2010 release occurred this week. IMG is now on version 3.2, has updated features and a bunch of new/revised genomes. I’ve begun updating our tutorial & will let you know when that is released. It’s not the craziest level of tool changes that I’ve seen from this group, but dang, they SURE don’t rest on their laurels! The........ Read more »
Ditty, J., Kvaal, C., Goodner, B., Freyermuth, S., Bailey, C., Britton, R., Gordon, S., Heinhorst, S., Reed, K., Xu, Z.... (2010) Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. PLoS Biology, 8(8). DOI: 10.1371/journal.pbio.1000448
A recent paper from the Bartel and Weissman groups (Guo et al. Mammalian microRNAs predominantly act to decrease target mRNA levels, Nature 466 835-40, PMID: 20703300) provides an interesting snapshot of the journey of a field from consensus to controversy to (one day?) consensus again. At issue is the question of how microRNAs — small [...]... Read more »
Guo H, Ingolia NT, Weissman JS, & Bartel DP. (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466(7308), 835-40. PMID: 20703300
Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, & Brown PO. (2009) Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS biology, 7(11). PMID: 19901979
The press has recently been abuzz with news of a newly discovered species of catfish that eats wood, of all things... Read more »
Nelson, J., Wubah, D., Whitmer, M., Johnson, E., & Stewart, D. (1999) Wood-eating catfishes of the genus Panaque: gut microflora and cellulolytic enzyme activities. Journal of Fish Biology, 54(5), 1069-1082. DOI: 10.1111/j.1095-8649.1999.tb00858.x
German, D. (2009) Inside the guts of wood-eating catfishes: can they digest wood?. Journal of Comparative Physiology B, 179(8), 1011-1023. DOI: 10.1007/s00360-009-0381-1
A month ago I pointed to a short communication in Nature Genetics which highlighted differences in the patterns of variation between the X chromosome and the autosome. I thought it would be of interest to revisit this, because it’s a relatively short piece with precise and crisp results which we can ruminate upon.
Sometimes there is [...]... Read more »
Hammer MF, Woerner AE, Mendez FL, Watkins JC, Cox MP, & Wall JD. (2010) The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. Nature genetics. PMID: 20802480
While travelling to our Supercharge Your Science workshop in Cairns and Townsville last week (which, by the way, went off really well and the punters gave us the thumbs up – stay tuned for more Supercharge activities at a university near you…), I stumbled across an article in the Sydney Morning Herald about the state [...]... Read more »
Australian Bureau of Statistics. (2010) Measures of Australia's Progress. Report. info:other/
Raudsepp-Hearne, C., Peterson, G., Tengö, M., Bennett, E., Holland, T., Benessaiah, K., MacDonald, G., & Pfeifer, L. (2010) Untangling the Environmentalist's Paradox: Why Is Human Well-being Increasing as Ecosystem Services Degrade?. BioScience, 60(8), 576-589. DOI: 10.1525/bio.2010.60.8.4
The hot spot for life on early Earth may have been a very cold place. Tiny pockets and channels that form inside ice can contain and protect replicating molecules, researchers report September 21 in Nature Communications. The paper suggests that life could have sprung from icy slush covering a freshwater lake, rather than a broiling [...]... Read more »
I'm very excited about this post, which is a guest post from my sister! She's an undergrad doing biochemistry at Bristol University, and she's currently taking a year working in a research laboratory as part of her degree. She's working with Plasmodium at the moment (which is the little protist that causes malaria) but has sent me a bacteria-related post because she knows me, and she knows my blog and who doesn't love bacteria?Post - survival of the fittest?Bacteria have always been very adapta........ Read more »
Lee HH, Molla MN, Cantor CR, & Collins JJ. (2010) Bacterial charity work leads to population-wide resistance. Nature, 467(7311), 82-5. PMID: 20811456
Yesterday while walking home from the store, I bumped into a neighbor who seemed out of sorts. Pulling me aside, he told me of numerous health problems which have developed recently, most of which he blames on a new medicine. I don't doubt his sincerity, but it did raise some questions. For instance: has he imagined the symptoms? It sounds terrible to suggest such a thing, but when starting a new treatment how many of us have suddenly noticed something which perhaps we never took notice of........ Read more »
P.J. Landrigan. (2000) Bad Policy, Worse Medicine. Pediatrics, 106(6), 1482-1483. info:/
Synopsis: Alberch and Gale: “A Developmental Analysis of an Evolutionary Trend: Digital Reduction in Amphibians” (1985). In this paper, the authors looked at different foot morphologies in extant amphibians and performed some experimental embryology with a few of the species. The induced developmental change followed the natural variation found by the authors! Details below! This [...]... Read more »
Alberch, P., & Gale, E. (1985) A Developmental Analysis of an Evolutionary Trend: Digital Reduction in Amphibians. Evolution, 39(1), 8. DOI: 10.2307/2408513
Gregory Petsko wrote a small comment in the very last Genome Biology titled Shadows on the wall. A very angry but still contained one, nicely written and important to think about. Here is some of my thoughts about. Gregory Petsko discusses a question related to what people call « paradigms » and innovation. Paradigm is a word [...]... Read more »
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