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  • July 28, 2010
  • 06:02 PM

New crops: perennial grains?

by Thomas Kluyver in Thomas' Plant-Related Blog

Most of our staple crops are annuals—plants that grow from seed, produce the next generation of seeds and then die, all in one year. In particular, the ‘big three’ crops, rice, wheat and maize, are all annuals. What would life be like if we instead grew perennials—plants that last more than one year? No more [...]... Read more »

Glover, J., Reganold, J., Bell, L., Borevitz, J., Brummer, E., Buckler, E., Cox, C., Cox, T., Crews, T., Culman, S.... (2010) Increased Food and Ecosystem Security via Perennial Grains. Science, 328(5986), 1638-1639. DOI: 10.1126/science.1188761  

  • July 28, 2010
  • 04:13 PM

If I had my way, we’d just sequence everything

by Holly Bik in Deep Sea News

Transcriptomics of any variety is the study of RNA molecules (messenger RNAs, ribosomal RNAs, transcript RNAs and non-coding RNAs) present in a cell at any given time. By sequencing RNA molecules, we can get a snapshot of the genes being expressed in a cell, tissue, organism, or even whole community of organisms at a given place and time. These type of studies used to be carried out in a limited fashion using quantitative PCR (qPCR) or microarrays, but new sequencing technologies (454, Illumin........ Read more »

Hewson, I., Poretsky, R., Beinart, R., White, A., Shi, T., Bench, S., Moisander, P., Paerl, R., Tripp, H., Montoya, J.... (2009) In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii. The ISME Journal, 3(5), 618-631. DOI: 10.1038/ismej.2009.8  

Moran, M.A. (2009) Metatranscriptomics: Eavesdropping on complex microbial communities. Microbe, 4(7), 329-335. info:/

  • July 28, 2010
  • 03:33 PM

Fisheries Collapse: When Predator Becomes Prey

by Daniel Bassett in Chew the Fat

In marine ecosystems overfishing of top predators has led to major changes in ecosystem properties at the most basic level. This is likely to be because a change in the food web directly changes the feedback mechanisms that are inherent within any ecosystem. In marine ecosystems a typical pattern occurs after overfishing, which includes a low abundance of predatory fish and a high abundance of small, pelagic, forage fish. These small fish are themselves predators of the eggs and larvae of marine........ Read more »

  • July 28, 2010
  • 03:21 PM

Climate and the Lion's Magnificent Mane

by Laura Klappenbach in About Animals / Wildlife

A lion's mane is more than just a bushy bunch of fur framing its face. It's a declaration of a lion's vitality, fighting prowess and dominance as well as an acknowledgement of the climate in which the lion lives. This is the conclusion made by scientists who studied nearly 300 lions in Tanzania's Ngorongoro Crater and Serengeti National Park.

Only male lions (Panthera leo) grow manes—females lack the long fur around their face and neck. This difference in appearance between the sexes mean........ Read more »

  • July 28, 2010
  • 02:46 PM

Models for the evolution of bacterial resistance

by Lab Rat in Lab Rat

I wrote about Quorum Sensing recently, the ability of bacteria to communicate with each other via small molecules which they can both excrete and sense. A lot of the research done on quorum sensing aims to find ways to block the system, as it is one of the main communication methods used to switch on virulence genes, and other genes which make the bacteria more infectious, and more likely to cause harm.Blocking quorum sensing would not in theory kill the bacteria, but it would give more time for........ Read more »

  • July 28, 2010
  • 01:03 PM

Plankton Doom?

by Journal Watch Online in Journal Watch Online

Climate change may be taking the bloom off the plankton. Researchers say they’ve found “unequivocal” evidence of long-term declines in the ocean’s teeming populations of microscropic algae, which form the base of the marine food web. Warming surface waters appear to be a main culprit, the researchers report in today’s Nature.

Scientists have long studied […] Read More »... Read more »

Boyce, D., Lewis, M., & Worm, B. (2010) Global phytoplankton decline over the past century. Nature, 466(7306), 591-596. DOI: 10.1038/nature09268  

  • July 28, 2010
  • 09:36 AM

Past lives caught in the dust of trees

by Alun in AlunSalt

I’m currently working at the Annals of Botany to help out with their social media side. There’s a bit more to it than subtly dropping links to their site, like this one. At the moment I’m struggling with the Facebook integration, but there’s a fun side too. I wouldn’t have browsed AoB if I’d not... Read more »

Mercader, J., Bennett, T., Esselmont, C., Simpson, S., & Walde, D. (2009) Phytoliths in woody plants from the Miombo woodlands of Mozambique. Annals of Botany, 104(1), 91-113. DOI: 10.1093/aob/mcp097  

  • July 28, 2010
  • 09:12 AM

Forest canopy height: why do we care?

by Hannah Waters in Culturing Science – biology as relevant to us earthly beings

If you’ve been on the internet at all in the past week, you’ve probably seen these lovely images from NASA, visualizing the height of tree canopies around the world.  They’ve been on science sites along with art ones.  In a sense, that alone is useful: using beautiful visuals to make people think about the world [...]... Read more »

  • July 28, 2010
  • 12:12 AM

Stem Cells and Diabetes

by Scicurious in Neurotic Physiology

*I would like to start with a disclaimer. My laptop is broken (AGAIN), and until I invest in a new harddrive, I am going to have to write all the posts on this little netbook, Ruby, who, while intrepid, can’t do JACK when it comes to images. Which means I’ll have to add the images [...]... Read more »

  • July 27, 2010
  • 07:45 PM

The Wednesday Post (28/07/2010)

by thomastu in Disease Prone

Micro-needle patches. Some recent papers from both Journal of Virology and Nature shows the feasibility for using centimetre-wide patches with hundreds of thousands half millimetre long micro-needles to deliver vaccines painlessly. I heard about these at a conference a couple of years ago, but it’s only now that they’ve resurfaced with some really promising potential [...]... Read more »

Sullivan, S., Koutsonanos, D., del Pilar Martin, M., Lee, J., Zarnitsyn, V., Choi, S., Murthy, N., Compans, R., Skountzou, I., & Prausnitz, M. (2010) Dissolving polymer microneedle patches for influenza vaccination. Nature Medicine. DOI: 10.1038/nm.2182  

  • July 27, 2010
  • 04:19 PM

Snap, phenotype, genotype and fitness

by Razib Khan in Gene Expression

One of the main criticisms of the population genetic pillar of the modern evolutionary synthesis was that too often it was a game of “beanbag genetics”. In other words population geneticists treated genes as discrete independent individual elements within a static sea. R.A. Fisher and his acolytes believed that the average effect of fluctuations of [...]... Read more »

Rosas U, Barton NH, Copsey L, Barbier de Reuille P, & Coen E. (2010) Cryptic Variation between Species and the Basis of Hybrid Performance. PLoS biology, 8(7). PMID: 20652019  

  • July 27, 2010
  • 01:48 PM

Breathing Fire

by Journal Watch Online in Journal Watch Online

Call it a hot topic. A study suggesting that intentional forest blazes could significantly cut carbon dioxide (CO2) emissions from wildfires in the Western United States has prompted a piquant scholarly quarrel. The exchange highlights the challenge forest managers may face in balancing plans to use fire to restore forest ecosystems with efforts to curb […] Read More »... Read more »

  • July 27, 2010
  • 12:03 PM

Pass the clams, please: A strategy for object retrieval in the octopus.

by Mike Mike in Cephalove

          I recently blogged about a line of research on octopus reaching movements, but I left out an important study for time's sake.  I promised to cover it promptly, and so I'm making good on that promise here.  To recap:          It has been shown that reaching movements by octopuses are controlled by the nervous system of the arms relatively autonomously from the central nervous system; that........ Read more »

  • July 27, 2010
  • 11:17 AM

Twenty Million Papers in PubMed: A Triumph or a Tragedy?

by Duncan Hull in O'Really?

A quick search on today reveals that the freely available American database of biomedical literature has just passed the 20 million citations mark*. Should we celebrate or commiserate passing this landmark figure? Is it a triumph or a tragedy that PubMed® is the size it i... Read more »

Halevy, A., Norvig, P., & Pereira, F. (2009) The Unreasonable Effectiveness of Data. IEEE Intelligent Systems, 24(2), 8-12. DOI: 10.1109/MIS.2009.36  

Torvik VI, & Smalheiser NR. (2009) Author Name Disambiguation in MEDLINE. ACM transactions on knowledge discovery from data, 3(3). PMID: 20072710  

Islamaj Dogan R, Murray GC, Névéol A, & Lu Z. (2009) Understanding PubMed user search behavior through log analysis. Database : the journal of biological databases and curation. PMID: 20157491  

  • July 27, 2010
  • 10:34 AM

Can Computers Help Scientists With Their Reading?

by Rob Mitchum in ScienceLife

The public perception of science in action typically involves a person in a white coat pouring brightly-colored fluids in and out of test tubes. Sure, a little bit of that does go on in a laboratory. But before the glassware is broken out, a lot of less glamorous stuff has to happen. Every experiment is [...]... Read more »

Evans, J., & Rzhetsky, A. (2010) Machine Science. Science, 329(5990), 399-400. DOI: 10.1126/science.1189416  

  • July 27, 2010
  • 10:11 AM

Enhanced biodiversity-ecosystem function relationships in polluted systems

by Marc Cadotte in The EEB and flow

*note: this text was adapted from an Editor's Choice I wrote for the Journal of Applied Ecology.In this era of species loss and habitat degradation, understanding the link between biodiversity and functioning of species assemblages is a critically important area of research. Two decades of research has shown that communities with more species or functional types results in higher levels of ecosystem functioning, such as nutrient processing rates, carbon sequestration and productivity, among........ Read more »

  • July 27, 2010
  • 10:10 AM

Those who cannot remember the past are condemned to repeat it.

by Sam W in From C to Carnivore

  Source: BBC Remember the baiji dolphin? It was declared functionally extinct only 4 years ago and was the first cetacean to be wiped out due to humans. It was at a time when I was just turning my awareness towards nature and human impact and I remember being struck by the loss of a [...]... Read more »

Stone, R. (2010) Last Stand on the Yangtze. Science, 329(5990), 378-378. DOI: 10.1126/science.329.5990.378  

Turvey ST, Barrett LA, Yujiang H, Lei Z, Xinqiao Z, Xianyan W, Yadong H, Kaiya Z, Hart T, & Ding W. (2010) Rapidly shifting baselines in Yangtze fishing communities and local memory of extinct species. Conservation biology : the journal of the Society for Conservation Biology, 24(3), 778-87. PMID: 20067488  

  • July 27, 2010
  • 10:01 AM

Abnormal Circulating Cells in Lung Cancer Patients: Possible New Technique for Identification

by Sally Church in Pharma Strategy Blog

A while back I wrote about how circulating tumour cells (CTC's) see here and here, can be used as a potential new surrogate measure for prostate cancer, so it was with great interest that I read an excellent article (free...... Read more »

  • July 27, 2010
  • 09:05 AM

Before they were yucca moths

by Jeremy Yoder in Denim and Tweed

Yuccas and yucca moths have one of the most peculiar pollination relationships known to science. The moths are the only pollinators of yuccas, carrying pollen from flower to flower in specialized mouthparts and actively tamping it into the tip of the pistil. Before she pollinates, though, each moth lays eggs in the flower—the developing yucca seeds will be the only thing her offspring eat. How does such a specialized, co-adapted interaction evolve in the first place? My coauthors and I attemp........ Read more »

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