Biology posts
- September 21, 2009
- 03:00 AM
- 780 views
Study finds biodiversity can conflict with wetland function
by Rob Goldstein in Conservation Maven
A new study challenges the commonly held view that biodiversity enhances wetland function...read more... Read more »
Weisner, Stefan, & Thiere, Geraldine. (2009) Effects of vegetation state on biodiversity and nitrogen retention in created wetlands: a test of the biodiversity-ecosystem functioning hypothesis. Freshwater Biology. DOI: 10.1111/j.1365-2427.2009.02288.x
- September 20, 2009
- 08:16 PM
- 1,102 views
A punk-size T-rex and an Eagle that ate children?!
by Student @ Fresno State in Darwin's Bulldogs
One trait that shows interesting evolutionary trends is the size of animals. Body size plays a significant role in the most important interactions between animals: competition (for resources or mates) and predation (for both predator and prey). Body size is also, of course, significant for a variety of physiological reasons. It's no surprise, therefore, that biologists spend a lot of time thinking about body size, and have discovered some intriguing patterns. For instance the so-called island ru........ Read more »
G. Grey. (1873) Description of the extinct gigantic bird of prey, Hokioi, by a Maori. Transactions of the New Zealand Institute, 435. info:/
Scofield, R., & Ashwell, K. (2009) Rapid Somatic Expansion Causes the Brain to Lag Behind: The Case of the Brain and Behavior of New Zealand's Haast's Eagle ( ) . Journal of Vertebrate Paleontology, 29(3), 637-649. DOI: 10.1671/039.029.0325
Sereno, P., Tan, L., Brusatte, S., Kriegstein, H., Zhao, X., & Cloward, K. (2009) Tyrannosaurid Skeletal Design First Evolved at Small Body Size. Science. DOI: 10.1126/science.1177428
- September 20, 2009
- 07:25 PM
- 664 views
How do we name Influenza A?
by Atila Iamarino in Influenza A (H1N1) Blog – English
Where do the name H1N1 and all the other names come from? What determines the number of H and N?
Established by WHO in1980 [1], the nomenclature of Influenza A consists of: type of host, in case the virus has not been isolated from humans; geographical region of origin; number of lineage; year of isolation and; [...]... Read more »
no authors. (1980) A revision of the system of nomenclature for influenza viruses: a WHO memorandum. Bulletin of the World Health Organization, 58(4), 585-91. PMID: 6969132
Subbarao, K. (1998) Characterization of an Avian Influenza A (H5N1) Virus Isolated from a Child with a Fatal Respiratory Illness. Science, 279(5349), 393-396. DOI: 10.1126/science.279.5349.393
Fouchier, R., Munster, V., Wallensten, A., Bestebroer, T., Herfst, S., Smith, D., Rimmelzwaan, G., Olsen, B., & Osterhaus, A. (2005) Characterization of a Novel Influenza A Virus Hemagglutinin Subtype (H16) Obtained from Black-Headed Gulls. Journal of Virology, 79(5), 2814-2822. DOI: 10.1128/JVI.79.5.2814-2822.2005
Liu, S., Ji, K., Chen, J., Tai, D., Jiang, W., Hou, G., Chen, J., Li, J., & Huang, B. (2009) Panorama Phylogenetic Diversity and Distribution of Type A Influenza Virus. PLoS ONE, 4(3). DOI: 10.1371/journal.pone.0005022
- September 20, 2009
- 01:58 PM
- 547 views
Thinking Outside the Niche
by Johnny in Ecographica
Ecologist and evolutionary biologist Dr. Mark McPeek (Professor at Dartmouth College, and Editor-in-Chief of The American Naturalist) spoke at Florida State Thursday and Friday of last week. Unfortunately, fieldwork prevented my attendance at the first lecture, but luckily I did manage to make Friday’s session. ... Read more »
Leibold, M., & McPeek, M. (2006) COEXISTENCE OF THE NICHE AND NEUTRAL PERSPECTIVES IN COMMUNITY ECOLOGY. Ecology, 87(6), 1399-1410. DOI: 10.1890/0012-9658(2006)87[1399:COTNAN]2.0.CO;2
- September 19, 2009
- 05:43 PM
- 664 views
Why Do We Sleep?
by Neuroskeptic in Neuroskeptic
Why do we sleep? Because otherwise, we'd always be doing stuff.This is the theory advanced by UCLA sleep researcher Jerome Siegel (website) in a new paper, Sleep viewed as a state of adaptive inactivity (free pdf). It's part of a Nature Reviews Neuroscience special issue on the evolution of the nervous system. Siegel proposes that the evolutionary function of sleep is simply to ensure that animals are only active when the benefits of movement (mostly access to food, and mates) outweigh the costs........ Read more »
Siegel, J. (2009) Sleep viewed as a state of adaptive inactivity. Nature Reviews Neuroscience, 10(10), 747-753. DOI: 10.1038/nrn2697
- September 19, 2009
- 04:04 PM
- 884 views
Fish vs. Fuel
by Journal Watch Online in Journal Watch Online
Biofuel targets conflict with plans to protect Gulf of Mexico
... Read more »
Costello, C., Griffin, W., Landis, A., & Matthews, H. (2009) Impact of Biofuel Crop Production on the Formation of Hypoxia in the Gulf of Mexico. Environmental Science , 2147483647. DOI: 10.1021/es9011433
- September 19, 2009
- 05:06 AM
- 1,749 views
'Crhaptophytes' and the Chromalveolate Hypothesis
by Psi Wavefunction in Skeptic Wonder
Procrastination with about a million things (including overdue blog posts) is the perfect time to blog a freshly published paper. Although I can't quite figure out how to make the preceding sentence make any sense syntactically...Warning: This post contains copious amounts of obscure phylogeny and taxonomy. Discussed by a cell biologist. Proceed with caution.I've probably carelessly alluded before to the Chromalveolate Hypothesis by Cavalier-Smith (eg. 2002 Curr Biol). In any case, I tend to go ........ Read more »
Moore, R., Oborník, M., Janouškovec, J., Chrudimský, T., Vancová, M., Green, D., Wright, S., Davies, N., Bolch, C., Heimann, K.... (2008) A photosynthetic alveolate closely related to apicomplexan parasites. Nature, 451(7181), 959-963. DOI: 10.1038/nature06635
Cavalier-Smith, T. (2002) Chloroplast Evolution: Secondary Symbiogenesis and Multiple Losses. Current Biology, 12(2). DOI: 10.1016/S0960-9822(01)00675-3
KEELING, P., BURGER, G., DURNFORD, D., LANG, B., LEE, R., PEARLMAN, R., ROGER, A., & GRAY, M. (2005) The tree of eukaryotes. Trends in Ecology , 20(12), 670-676. DOI: 10.1016/j.tree.2005.09.005
KEELING, P. (2009) Chromalveolates and the Evolution of Plastids by Secondary Endosymbiosis. Journal of Eukaryotic Microbiology, 56(1), 1-8. DOI: 10.1111/j.1550-7408.2008.00371.x
Okamoto, N., Chantangsi, C., Horák, A., Leander, B., & Keeling, P. (2009) Molecular Phylogeny and Description of the Novel Katablepharid Roombia truncata gen. et sp. nov., and Establishment of the Hacrobia Taxon nov. PLoS ONE, 4(9). DOI: 10.1371/journal.pone.0007080
REYESPRIETO, A., MOUSTAFA, A., & BHATTACHARYA, D. (2008) Multiple Genes of Apparent Algal Origin Suggest Ciliates May Once Have Been Photosynthetic. Current Biology, 18(13), 956-962. DOI: 10.1016/j.cub.2008.05.042
- September 18, 2009
- 02:49 PM
- 837 views
Returning the Rainbow
by Kristopher Hite in Tom Paine's Ghost
Red-Green color blindness is caused by a deficiency in opsin genes. These genes codes for photoreceptor proteins of the same name positioned in the cone cells of the eye's retina to receive photons (light). When light hits these photoreceptor proteins a tiny molecule buried inside changes its shape by swinging its bond angles and begins a signal transduction cascade. The signal of "red" or "green" is passed from this tiny "g-coupled" protein receptor along the optic nerve and eventually to the b........ Read more »
Mancuso, K., Hauswirth, W., Li, Q., Connor, T., Kuchenbecker, J., Mauck, M., Neitz, J., & Neitz, M. (2009) Gene therapy for red–green colour blindness in adult primates. Nature. DOI: 10.1038/nature08401
- September 18, 2009
- 11:51 AM
- 782 views
Beautiful tumors
by iayork in Mystery Rays from Outer Space
A new technique called optical frequency domain imaging (OFDI) provides amazing images of tumors (especially their blood vessels) in situ.
“(a) OFDI images of representative control and treated tumors 5 d after initiation of antiangiogenic VEGFR-2. The lymphatic
vascular networks are also presented (blue) for both tumors. (b) Quantification of tumor volume and vascular geometry and
morphology in [...]... Read more »
Vakoc, B., Lanning, R., Tyrrell, J., Padera, T., Bartlett, L., Stylianopoulos, T., Munn, L., Tearney, G., Fukumura, D., Jain, R.... (2009) Three-dimensional microscopy of the tumor microenvironment in vivo using optical frequency domain imaging. Nature Medicine. DOI: 10.1038/nm.1971
- September 18, 2009
- 11:36 AM
- 667 views
That’s So Random
by Journal Watch Online in Journal Watch Online
Spread of biological invasions is highly unpredictable
... Read more »
Melbourne, B., & Hastings, A. (2009) Highly Variable Spread Rates in Replicated Biological Invasions: Fundamental Limits to Predictability. Science, 325(5947), 1536-1539. DOI: 10.1126/science.1176138
- September 18, 2009
- 10:22 AM
- 684 views
Energy and the Brain
by AK in AK's Rambling Thoughts
The questions of how much energy is used by the brain, especially its various parts, and how it's used are important. For one thing, our understanding of the brain depends strongly on functional magnetic resonance imaging (fMRI), which in turn has a number of built-in assumptions and open questions regarding how blood flow and nutrient concentrations relate to energy usage within the tiny regions (voxels) that it can resolve.[7] [8] When dividing the brain into "parts" I'm talking not so mu........ Read more »
Alle, H., Roth, A., & Geiger, J. (2009) Energy-Efficient Action Potentials in Hippocampal Mossy Fibers. Science, 325(5946), 1405-1408. DOI: 10.1126/science.1174331
- September 18, 2009
- 08:00 AM
- 1,520 views
Interfering with interferon
by Vincent Racaniello in virology blog
During a discussion about blogging on the Coast to Coast Bio Podcast, it was suggested that science professors should spend more time writing about their research – by explaining what problems they are trying to solve, how they approach them, and why they are interesting. My goal here at virology blog is mainly to teach virology. But explaining what we do in my virology laboratory can be an effective instructional tool.... Read more »
Drahos J, & Racaniello VR. (2009) Cleavage of IPS-1 in cells infected with human rhinovirus. Journal of virology. PMID: 19740998
Barral, P., Sarkar, D., Fisher, P., & Racaniello, V. (2009) RIG-I is cleaved during picornavirus infection. Virology, 391(2), 171-176. DOI: 10.1016/j.virol.2009.06.045
Barral, P., Morrison, J., Drahos, J., Gupta, P., Sarkar, D., Fisher, P., & Racaniello, V. (2007) MDA-5 Is Cleaved in Poliovirus-Infected Cells. Journal of Virology, 81(8), 3677-3684. DOI: 10.1128/JVI.01360-06
Papon L, Oteiza A, Imaizumi T, Kato H, Brocchi E, Lawson TG, Akira S, & Mechti N. (2009) The viral RNA recognition sensor RIG-I is degraded during encephalomyocarditis virus (EMCV) infection. Virology. PMID: 19733381
- September 18, 2009
- 06:50 AM
- 1,569 views
Popular, personal and public data at PLoS
by Duncan Hull in O'Really?
The Public Library of Science (PLoS) is a non-profit organisation committed to making the world’s scientific and medical literature freely accessible to everyone via open access publishing. As recently announced they have just published the first article-level metrics (e.g. web server logs and related information) for all articles in their library. This is novel, interesting [...]... Read more »
Ioannidis, J. (2005) Why Most Published Research Findings Are False. PLoS Medicine, 2(8). DOI: 10.1371/journal.pmed.0020124
Kirsch, I., Deacon, B., Huedo-Medina, T., Scoboria, A., Moore, T., & Johnson, B. (2008) Initial Severity and Antidepressant Benefits: A Meta-Analysis of Data Submitted to the Food and Drug Administration. PLoS Medicine, 5(2). DOI: 10.1371/journal.pmed.0050045
Lacasse, J., & Leo, J. (2005) Serotonin and Depression: A Disconnect between the Advertisements and the Scientific Literature. PLoS Medicine, 2(12). DOI: 10.1371/journal.pmed.0020392
Levy, S., Sutton, G., Ng, P., Feuk, L., Halpern, A., Walenz, B., Axelrod, N., Huang, J., Kirkness, E., Denisov, G.... (2007) The Diploid Genome Sequence of an Individual Human. PLoS Biology, 5(10). DOI: 10.1371/journal.pbio.0050254
Holy, T., & Guo, Z. (2005) Ultrasonic Songs of Male Mice. PLoS Biology, 3(12). DOI: 10.1371/journal.pbio.0030386
Franzen, J., Gingerich, P., Habersetzer, J., Hurum, J., von Koenigswald, W., & Smith, B. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE, 4(5). DOI: 10.1371/journal.pone.0005723
The PLoS Medicine Editors. (2006) The Impact Factor Game. PLoS Medicine, 3(6). DOI: 10.1371/journal.pmed.0030291
Voight, B., Kudaravalli, S., Wen, X., & Pritchard, J. (2006) A Map of Recent Positive Selection in the Human Genome. PLoS Biology, 4(3). DOI: 10.1371/journal.pbio.0040072
Hagmann, P., Cammoun, L., Gigandet, X., Meuli, R., Honey, C., Wedeen, V., & Sporns, O. (2008) Mapping the Structural Core of Human Cerebral Cortex. PLoS Biology, 6(7). DOI: 10.1371/journal.pbio.0060159
Bourne, P. (2005) Ten Simple Rules for Getting Published. PLoS Computational Biology, 1(5). DOI: 10.1371/journal.pcbi.0010057
Lawrence, P. (2006) Men, Women, and Ghosts in Science. PLoS Biology, 4(1). DOI: 10.1371/journal.pbio.0040019
Hull, D., Pettifer, S., & Kell, D. (2008) Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web. PLoS Computational Biology, 4(10). DOI: 10.1371/journal.pcbi.1000204
Beltrao, P., & Serrano, L. (2007) Specificity and Evolvability in Eukaryotic Protein Interaction Networks. PLoS Computational Biology, 3(2). DOI: 10.1371/journal.pcbi.0030025
Beltrao, P., & Serrano, L. (2005) Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions. PLoS Computational Biology, 1(3). DOI: 10.1371/journal.pcbi.0010026
Ho, B., & Dill, K. (2006) Folding Very Short Peptides Using Molecular Dynamics. PLoS Computational Biology, 2(4). DOI: 10.1371/journal.pcbi.0020027
Saunders, N., Beltrão, P., Jensen, L., Jurczak, D., Krause, R., Kuhn, M., & Wu, S. (2009) Microblogging the ISMB: A New Approach to Conference Reporting. PLoS Computational Biology, 5(1). DOI: 10.1371/journal.pcbi.1000263
Ho, B., & Agard, D. (2009) Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations. PLoS Computational Biology, 5(4). DOI: 10.1371/journal.pcbi.1000343
Wolschin, F., & Gadau, J. (2009) Deciphering Proteomic Signatures of Early Diapause in Nasonia. PLoS ONE, 4(7). DOI: 10.1371/journal.pone.0006394
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- September 18, 2009
- 06:42 AM
- 952 views
HMMoC and HMMConverter
by Thomas Mailund in Mailund on the Internet
I just want to say a few words about a short paper I read last week, and a paper that is a few years old now but related to it.
The first is out in advanced access in Nucleic Acids Research:
HMMConverter 1.0: a toolbox for hidden Markov models
Lam and Meyer
Hidden Markov models (HMMs) and their variants [...]... Read more »
Lam, T., & Meyer, I. (2009) HMMCONVERTER 1.0: a toolbox for hidden Markov models. Nucleic Acids Research. DOI: 10.1093/nar/gkp662
Lunter, G. (2007) HMMoC a compiler for hidden Markov models. Bioinformatics, 23(18), 2485-2487. DOI: 10.1093/bioinformatics/btm350
- September 18, 2009
- 05:00 AM
- 988 views
Making offshore renewable energy good for marine habitat
by Rob Goldstein in Conservation Maven
Despite past conflicts between wind power and habitat, scientists make the case that offshore renewable energy might be good for marine biodiverisity...read more... Read more »
Inger, R., Attrill, M., Bearhop, S., Broderick, A., James Grecian, W., Hodgson, D., Mills, C., Sheehan, E., Votier, S., Witt, M.... (2009) Marine renewable energy: potential benefits to biodiversity? An urgent call for research. Journal of Applied Ecology. DOI: 10.1111/j.1365-2664.2009.01697.x
- September 17, 2009
- 09:54 PM
- 821 views
Ninja viruses, a (free) radical take on aging and more in my picks of the week from RB
by Alejandro Montenegro-Montero in MolBio Research Highlights
Another week has gone by and some very interesting molbio blog posts have been aggregated into Researchblogging.org. Every week [see my inaugural post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that... Read more »
Moltedo, B., Lopez, C., Pazos, M., Becker, M., Hermesh, T., & Moran, T. (2009) Cutting Edge: Stealth Influenza Virus Replication Precedes the Initiation of Adaptive Immunity. The Journal of Immunology, 183(6), 3569-3573. DOI: 10.4049/jimmunol.0900091
Lapointe, J., & Hekimi, S. (2009) When a theory of aging ages badly. Cellular and Molecular Life Sciences. DOI: 10.1007/s00018-009-0138-8
Gupta, P., Onder, T., Jiang, G., Tao, K., Kuperwasser, C., Weinberg, R., & Lander, E. (2009) Identification of Selective Inhibitors of Cancer Stem Cells by High-Throughput Screening. Cell, 138(4), 645-659. DOI: 10.1016/j.cell.2009.06.034
- September 17, 2009
- 07:48 PM
- 710 views
Sarcopenia is an Inflammation-Related Issue?
by Reason in Fight Aging!
Sarcopenia is the name (fairly recently) given to age-related muscle loss, a situation that most people find themselves in with advancing age. In past years, researchers have investigated whether this might related to tendencies for diet to change with age, such as reduced protein intake for example. Interestingly, however, there is also solid evidence for the practice of calorie restriction to slow the process of sarcopenia. Back in 2005, one group of scientists painted a fairly convincing argu........ Read more »
Rieu I, Magne H, Savary-Auzeloux I, Averous J, Bos C, Peyron MA, Combaret L, & Dardevet D. (2009) Reduction of low grade inflammation restores blunting of postprandial muscle anabolism and limits sarcopenia in old rats. The Journal of physiology. PMID: 19752122
- September 17, 2009
- 05:10 PM
- 754 views
Evolutionary enamel loss linked to molecular decay of enamel-specific gene
by Greg Laden in Greg Laden's Blog
The evolutionary history of mammals can be reviewed as the evolutionary history of tooth loss. The early mammals had many teeth, and every now and then in evolutionary time, a tooth is lost wiht subsequent species arriving from that n-1 toothed form having that smaller number of teeth. With ver few exceptions, no mammals have added a tooth during the history of mammals. (Excepting maybe the very very earliest period, but probably not.)
Well, the loss of enamel itself is also an evolutionary ........ Read more »
Meredith, R., Gatesy, J., Murphy, W., Ryder, O., & Springer, M. (2009) Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals. PLoS Genetics, 5(9). DOI: 10.1371/journal.pgen.1000634
- September 17, 2009
- 04:44 PM
- 1,501 views
White-Eyes Killing Off Native Birds In Hawaii
by Christie Wilcox in Observations of a Nerd
Introduced and invasive species are a hot topic in ecology. Even when brought in for good reason, introduced species can have unforeseen negative impacts on the environment and the species around them. Take Cane Toads, for example. They were introduced to Australia to control a particular bug, but ended up eating everything they could fit in their mouths, especially native, endangered species. Or look at the mongoose, brought to Hawaii to control rat populations. While it does enjoy the invasive........ Read more »
Leonard A. Freed, & Rebecca L. Cann. (2009) Negative Effects of an Introduced Bird Species on Growth and Survival in a Native Bird Community. Current Biology. info:/
- September 17, 2009
- 01:22 PM
- 1,048 views
RIP for MFRTA?
by ouroboros in Ouroboros: Research in the biology of aging
A prominent scholar of the CLK-1 story has called the coroner on the mitochondrial free radical theory of aging (MFRTA). From Lapointe & Hekimi:
When a theory of aging ages badly
According to the widely acknowledged mitochondrial free radical theory of aging (MFRTA), the macromolecular damage that results from the production of toxic reactive oxygen species [...]... Read more »
Lapointe, J., & Hekimi, S. (2009) When a theory of aging ages badly. Cellular and Molecular Life Sciences. DOI: 10.1007/s00018-009-0138-8
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