Cancer has emerged as a fundamentally genetic disease, where mutations in genes cause cells to go haywire. Yet, finding out exactly which mutations are responsible for a certain type of cancer is a daunting task. A recent report in Nature which details the cataloging of tens of thousands of mutations in tens of thousands of tumors illustrates the merits and dangerous pitfalls of such an approach.The article talks about the International Cancer Genome Consortium (ICGC), formed in 2008, whose task........ Read more »
A few weeks ago I reviewed a paper on the the genetics of the Cape Coloured population. Within it there was a refrence to another paper, Deconstructing Jaco: genetic heritage of an Afrikaner. The title refers to the author himself. It was an analysis of his own pedigree going back to the 17th century, along [...]... Read more »
Greeff, J. (2007) Deconstructing Jaco: Genetic Heritage of an Afrikaner. Annals of Human Genetics, 71(5), 674-688. DOI: 10.1111/j.1469-1809.2007.00363.x
Indeed, the amount of HIV diversity within a single infected individual can exceed the variability generated over the course of a global influenza epidemic, the latter of which results in the need for a new vaccine each year. 1
That was said as part of a discussion on HIV vaccines, but let’s think about it from [...]... Read more »
Ramakrishnan, M., Tu, Z., Singh, S., Chockalingam, A., Gramer, M., Wang, P., Goyal, S., Yang, M., Halvorson, D., & Sreevatsan, S. (2009) The Feasibility of Using High Resolution Genome Sequencing of Influenza A Viruses to Detect Mixed Infections and Quasispecies. PLoS ONE, 4(9). DOI: 10.1371/journal.pone.0007105
Kuroda, M., Katano, H., Nakajima, N., Tobiume, M., Ainai, A., Sekizuka, T., Hasegawa, H., Tashiro, M., Sasaki, Y., Arakawa, Y.... (2010) Characterization of Quasispecies of Pandemic 2009 Influenza A Virus (A/H1N1/2009) by De Novo Sequencing Using a Next-Generation DNA Sequencer. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010256
Conservationists often place the greatest value on protecting large contiguous habitat areas. However, as two new studies in the journal Biological Conservation show, single, isolated trees on agricultural lands can a give big boost to wildlife species...... Read more »
by Vincent Racaniello in virology blog
Viruses can be transmitted to completely new host species that they have not previously infected. Usually host defenses stop the infection before any replication and adaptation can take place. On rare occasions, a novel population of viruses arises in the new host. These interspecies infections can sometimes be deduced by sequence analyses, providing a glimpse [...]... Read more »
Gibbs, M. (1999) Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus. Proceedings of the National Academy of Sciences, 96(14), 8022-8027. DOI: 10.1073/pnas.96.14.8022
As targeted therapies for cancer have progressed in the labs over the past few years, there have been a handful that stood out from the pack: animal studies in which advanced cancers evaporated rapidly and with few or no side effects. This is what a promising field of medical research looks like once it's underway: a wide range of results that are as good as or somewhat better than existing treatments, and a few that are immensely more beneficial. Researchers gravitate towards what works, and th........ Read more »
Koppu S, Oh YJ, Edrada-Ebel R, Blatchford DR, Tetley L, Tate RJ, & Dufès C. (2010) Tumor regression after systemic administration of a novel tumor-targeted gene delivery system carrying a therapeutic plasmid DNA. Journal of controlled release : official journal of the Controlled Release Society, 143(2), 215-21. PMID: 19944722
As more and more commercial fishers compete for fewer and fewer fish, ecologists are beginning to explore the impact. What happens when all or most of the big fish are caught? Does the rest of the ecosystem somehow compensate?
As we do each week, Kevin Zelnio, Razib Khan, and I have chosen a journal article to [...]... Read more »
Shackell, N., Frank, K., Fisher, J., Petrie, B., & Leggett, W. (2009) Decline in top predator body size and changing climate alter trophic structure in an oceanic ecosystem. Proceedings of the Royal Society B: Biological Sciences, 277(1686), 1353-1360. DOI: 10.1098/rspb.2009.1020
by Mary in OpenHelix
There are a number of genome browsers out there–we’ve covered that a number of times. And there are always new ones coming along. With the onslaught of sequence data we’re about to get from high-throughput sequencing, more and more research groups, communities, and individuals are going to need to choose a genome browser to use [...]... Read more »
Sen, T., Harper, L., Schaeffer, M., Andorf, C., Seigfried, T., Campbell, D., & Lawrence, C. (2010) Choosing a genome browser for a Model Organism Database: surveying the Maize community. Database. DOI: 10.1093/database/baq007
Andorf, C., Lawrence, C., Harper, L., Schaeffer, M., Campbell, D., & Sen, T. (2010) The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps. Bioinformatics, 26(3), 434-436. DOI: 10.1093/bioinformatics/btp556
by Moselio Schaechter in Small Things Considered
by Elio Life without air—a term coined by Louis Pasteur, the discoverer of anaerobiosis—has been thought to be exclusively a property of microbes, be they prokaryotic...... Read more »
Danovaro R, Dell'anno A, Pusceddu A, Gambi C, Heiner I, & Møbjerg Kristensen R. (2010) The first metazoa living in permanently anoxic conditions. BMC biology, 30. PMID: 20370908
...here's something distinctly more marine.
A little while ago I drew attention to Andrea Marshall's paper showing that there's not one but possibly three species of manta ray (see Whats A Manta Do?). In the preamble for that post, I drew analogy between mantas and killer whales as monotypic species; that is, the only members of their genus, a taxonomic one-of-a-kind. Well blow me down if ... Read more »
Morin, P., Archer, F., Foote, A., Vilstrup, J., Allen, E., Wade, P., Durban, J., Parsons, K., Pitman, R., Li, L.... (2010) Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Research. DOI: 10.1101/gr.102954.109
A new study demonstrates that the outcomes of fully protected, no-take areas in the ocean differ among fish species.
Many previous studies have shown that not all species increase in abundance in no-take areas, and this study indicates that the conservation benefits depend partly on the fish’s life history and ecological traits.... Read more »
Claudet, J., Osenberg, C., Domenici, P., Badalamenti, F., Milazzo, M., Falcón, J., Bertocci, I., Benedetti-Cecchi, L., García-Charton, J., Goñi, R.... (2010) Marine reserves: Fish life history and ecological traits matter. Ecological Applications, 20(3), 830-839. DOI: 10.1890/08-2131.1
All Points Bulletin: Wanted for Murder: A Redheaded, Blue-Eyed, Left-Handed Smoker Who Likes to Ski, Has an Elevated Risk of Cancer, Is Allergic to Cashews, and Has a Birthmark the Shape of Wisconsin OK, the thought of issuing such a specific physical description of a suspect seems ridiculous to us now, but can we expect [...]... Read more »
Valenzuela, R., Henderson, M., Walsh, M., Garrison, N., Kelch, J., Cohen-Barak, O., Erickson, D., John Meaney, F., Bruce Walsh, J., Cheng, K.... (2010) Predicting Phenotype from Genotype: Normal Pigmentation. Journal of Forensic Sciences, 55(2), 315-322. DOI: 10.1111/j.1556-4029.2009.01317.x
From last week's Science:We generated a high-resolution whole-genome sequence and individually deleted 5100 genes in Σ1278b, a Saccharomyces cerevisiae strain closely related to reference strain S288c. Similar to the variation between human individuals, Σ1278b and S288c average 3.2 single-nucleotide polymorphisms...... Read more »
“Origin” means beginning. So it’s unfortunate that the best known book on the subject of evolution is On the Origin of Species. Because the theory of evolution is not about the origin of life.
A recent article by Paz-y-Miño and Espinoza made that rookie mistake. And they got called on it. And quite right, too. The letter writers, Rice and colleagues, however, are upset not just because Paz-y-Miño and Espinoza use the theory too loosely.
The first reason they give t........ Read more »
Paz-y-Miño C., G., & Espinosa, A. (2009) Acceptance of Evolution Increases with Student Academic Level: A Comparison Between a Secular and a Religious College. Evolution: Education and Outreach, 2(4), 655-675. DOI: 10.1007/s12052-009-0175-7
Rice, J., Warner, D., Kelly, C., Clough, M., & Colbert, J. (2010) The Theory of Evolution is Not an Explanation for the Origin of Life. Evolution: Education and Outreach. DOI: 10.1007/s12052-010-0225-1
Advocates of open access publishing have argued that making scientific studies freely available will expand the dissemination of the research - particularly in developing countries where people and institutions are less likely to afford subscriptions. A new study, however, calls this assumption into question...... Read more »
CALVER, M., & STUART BRADLEY, J. (2010) Patterns of Citations of Open Access and Non-Open Access Conservation Biology Journal Papers and Book Chapters. Conservation Biology. DOI: 10.1111/j.1523-1739.2010.01509.x
A somewhat cryptic comment a few days ago on a year-old post on domestication eventually led us to an intriguing 2007 article in The Times which we unaccountably seem to have missed the first time around. The article quotes liberally from a Journal of Archaeological Science paper which puts forward something of an unorthodox take [...]... Read more »
KEREM, Z., LEVYADUN, S., GOPHER, A., WEINBERG, P., & ABBO, S. (2007) Chickpea domestication in the Neolithic Levant through the nutritional perspective. Journal of Archaeological Science, 34(8), 1289-1293. DOI: 10.1016/j.jas.2006.10.025
Since I just spent hours staring at onychophorans (instead of studying), gonna skimp out on the Sunday Protist this week. So here's a wonderful alien-looking freak with a proboscis, Rostronympha; I totally demand an SEM of this, by the way:Parabasalid Rostronympha. Image by Guy Brugerolle via Micro*scope.I can't find the original description at the moment, but vaguely recall having searched for it ambitiously once and failed miserably. It's supposed to be (Duboscq, Grassé & Rose, 1937), wit........ Read more »
Cepicka, I., Hampl, V., & Kulda, J. (2010) Critical Taxonomic Revision of Parabasalids with Description of one new Genus and three new Species. Protist. DOI: 10.1016/j.protis.2009.11.005
Ron Milo (Weizmann Institute of Science, Israel) and coworkers have developed theoretical carbon fixation cycles that are improvements over the Calvin-Benson cycle by up to a factor of 3. This news feature was written on April 25, 2010.... Read more »
Bar-Even, A., Noor, E., Lewis, N. E., & Milo, R. (2010) Design and analysis of synthetic carbon fixation pathways. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0907176107
An article about the Fungal Genetics Stock Center written by the curators provides some insight into the 50 year history of this resource. It is a great summary of how the stock center has grown over the years and demonstrates how it is an essential aspect of how research on filamentous fungi is possible. The [...]... Read more »
McCluskey K, Wiest A, & Plamann M. (2010) The Fungal Genetics Stock Center: a repository for 50 years of fungal genetics research. Journal of Biosciences, 35(1), 119-26. PMID: 20413916
Scientists identify multiple species of killer whale
... Read more »
Morin, P.A. et al. (2010) Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Research. DOI: 10.1101/gr.102954.109
Do you write about peer-reviewed research in your blog? Use ResearchBlogging.org to make it easy for your readers — and others from around the world — to find your serious posts about academic research.
If you don't have a blog, you can still use our site to learn about fascinating developments in cutting-edge research from around the world.
Research Blogging is powered by SMG Technology.
To learn more, visit seedmediagroup.com.