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  • September 28, 2010
  • 09:41 AM

Deriving Inhibitory Peptides from Globular Protein–Protein Interactions

by Nir London in Macromolecular Modeling Blog

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 »

  • September 28, 2010
  • 06:33 AM

The Cretaceous birds and pterosaurs of Cornet: part II, the pterosaurs

by Darren Naish in Tetrapod Zoology

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 »

  • September 28, 2010
  • 12:15 AM

Transfer of transgenic crop toxins to aquatic ecosystems potentially widespread in the industrial Corn Belt of the U.S.

by Phil Camill in Global Change: Intersection of Nature and Culture

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

  • September 27, 2010
  • 11:30 PM

Because publishing your paper is only half of the job

by Rogue in Into Oblivion

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 »

  • September 27, 2010
  • 08:08 PM

Choosing an algorithm – benchmarking bioinformatics

by Grant Jacobs in Code for life

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 »

  • September 27, 2010
  • 02:33 PM

Autumnal parasites

by Lucas in thoughtomics

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.
Poor acorn.
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  

  • September 27, 2010
  • 01:00 PM

Commuting to Work

by Moselio Schaechter in Small Things Considered

by Elio

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 »

Høgslund S, Revsbech NP, Kuenen JG, Jørgensen BB, Gallardo VA, van de Vossenberg J, Nielsen JL, Holmkvist L, Arning ET, & Nielsen LP. (2009) Physiology and behaviour of marine Thioploca. The ISME journal, 3(6), 647-57. PMID: 19262616  

  • September 27, 2010
  • 12:19 PM

Pleiades Promoter Project

by Eva Amsen in the Node

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  

  • September 27, 2010
  • 11:41 AM

Sub-angstrom modeling of complexes between flexible peptides and globular proteins

by Nir London in Macromolecular Modeling Blog

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 »

  • September 27, 2010
  • 09:59 AM

Innate Immune Memory in Mosquitoes: The Latest Buzz in the Fight against Malaria

by Kelly Grooms in Promega Connections

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  

  • September 27, 2010
  • 08:42 AM

News about the Integrated Microbial Genomes (IMG) resource

by Jennifer in OpenHelix

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  

  • September 27, 2010
  • 07:11 AM

How do miRNAs affect protein production?

by Becky in It Takes 30

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 »

  • September 27, 2010
  • 05:08 AM

You've discovered a whacky wood-eating catfish? So what's new? | GrrlScientist

by GrrlScientist in GrrlScientist

The press has recently been abuzz with news of a newly discovered species of catfish that eats wood, of all things... Read more »

  • September 27, 2010
  • 03:35 AM

Story of X

by Razib Khan in Gene Expression

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 »

  • September 26, 2010
  • 10:59 PM

Humans 1, Environment 0

by CJA Bradshaw in ConservationBytes

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  

  • September 26, 2010
  • 08:14 PM

Cold start of Life: Ice as a protocellular medium for RNA replication

by Olexandr Isayev in

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 »

Attwater, J., Wochner, A., Pinheiro, V., Coulson, A., & Holliger, P. (2010) Ice as a protocellular medium for RNA replication. Nature Communications, 1(6), 1-8. DOI: 10.1038/ncomms1076  

  • September 26, 2010
  • 02:55 PM

Guest Post - Survival of the fittest?

by Lab Rat in Lab Rat

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  

  • September 26, 2010
  • 01:07 PM

FDA: there to protect us

by Science Exploiter in Science Exploits

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:/

  • September 26, 2010
  • 11:00 AM

Evo-devo of digital reduction in amphibians

by Kele in Kele's Science Blog

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 »

  • September 26, 2010
  • 10:06 AM

Shadows on the wall: « Truth never triumphs, but its opponents eventually die »

by Rogue in Into Oblivion

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 »

Petsko GA. (2010) Shadows on the wall. Genome biology, 11(9), 136. PMID: 20863416  

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