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  • April 26, 2010
  • 11:05 PM

A plant virus that switched to vertebrates

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 »

  • April 26, 2010
  • 08:01 PM

An Impressive Demonstration of Targeted Cancer Destruction

by Reason in Fight Aging!

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 the end result that reaches the clinic is based on the immensely more beneficial approach. Here is one example of a targeted technology demonstration that uses dendrimers to tie together various components of the therapy. Firstly a popular press piece followed by the published research results: Scientists make cancer cells vanish Scottish scientists have made cancer tumours vanish within 10 days by sending DNA to seek and destroy the cells. The system, developed at Strathclyde and Glasgow universities, is being hailed as a breakthrough because it appears to eradicate tumours without causing harmful side-effects. ... In laboratory experiments the Strathclyde research team used a plasma protein called transferrin, which carries iron through the blood, to...... 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  

  • April 26, 2010
  • 05:04 PM

ResearchBlogCast #4: Fewer big fish in the sea

by Dave Munger in News

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  

  • April 26, 2010
  • 03:26 PM

Choosing a genome browser for your organism…

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 »

  • April 26, 2010
  • 01:00 PM

True or False: All Metazoans Need O2

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  

  • April 26, 2010
  • 11:00 AM

While we're talking genomes...

by Alistair Dove in Deep Type Flow'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 »

  • April 26, 2010
  • 10:00 AM

Marine protected areas benefit some fish... but not others

by Rob Goldstein in Conservation Maven

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  

  • April 26, 2010
  • 09:49 AM

Forensic Phenotyping: What DNA Can (and Cannot) Tell Us About a Criminal’s Appearance.

by Terri Sundquist in Promega Connections

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  

  • April 26, 2010
  • 09:09 AM

Can you say epistasis?

by Kent in Uncommon Ground

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 »

Dowell, R., Ryan, O., Jansen, A., Cheung, D., Agarwala, S., Danford, T., Bernstein, D., Rolfe, P., Heisler, L., Chin, B.... (2010) Genotype to Phenotype: A Complex Problem. Science, 328(5977), 469-469. DOI: 10.1126/science.1189015  

  • April 26, 2010
  • 08:00 AM

Don’t mention abiogensis

by Zen Faulkes in NeuroDojo

“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.

They’re scared.

The first reason they give to separate evolution from the question of the origin of life (a.k.a. abiogenesis) is:

(S)tudents often hold more tightly to a supernatural account for the origin of life than they do to a supernatural account for how the diversity of life arose(.)
This sounds dangerously like self-censorship.

I can almost hear Basil Fawlty’s voice in my head: “Whatever you do, don’t mention the origin of life!”

We talk about the branching pattern of classification as evidence for evolution. We talk about commonalities of living things as evidence for evolution. When you examine those pieces of evidence for evolution, it is a logical inference that life originated on this planet once. To completely separate natural selection and abiogenesis does a disservice to both.

Darwin, as usual, was ahead of the game and saw the two were logically connected. The last chapter of Origin (first edition), he wrote:

(A)ll living things have much in common, in their chemical composition, their germinal vesicles, their cellular structure, and their laws of growth and reproduction. ... Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.
Rice and colleagues also argue that abiogenesis is more the domain of physics and chemistry than biology. This sounds like an easy excuse for timid teachers: “Not my department, have a nice day.”

Scientists working on the origin of life problem are going to be testing hypotheses that life originated following the regular laws of chemistry and physics. That is, they will be testing materialistic hypotheses. Yes, some people are going to have problems with that for religious reasons, and won’t like that science does not allow for the immaterial. Yes, scientists currently have fewer responses to religious objections to abiogenesis.

But there is no point in trying to hide the science around the origin of life under the rug in an effort to get people to buy into evolution. It’s cowardly way to teach science.


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

Graphic by Arenamontanus on Flickr. Used under a Creative Commons license.... Read more »

  • April 26, 2010
  • 07:00 AM

Does open-access publishing increase future citations of a study?

by Rob Goldstein in Conservation Maven

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 »

  • April 26, 2010
  • 06:58 AM

Early farmers got high on chickpeas?

by Jeremy in Agricultural Biodiversity Weblog

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  

  • April 26, 2010
  • 12:20 AM

Sunday Protist -- Rostronympha and latest parabasalian taxonomy

by Psi Wavefunction in Skeptic Wonder

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), with a later mention in PP Grasse, A Hollande (1963) Ann. Sci. Natur. Zool. Ser "Les flagelles des genres Holomastigotoides et. Rostronympha". Might as well order it sometime...And now onto a really nice taxonomic summary of parabsalians by Cepicka, Hampl and Kulda 2009 in Protist:Recently revised parabasalian taxonomy.There are now six classes: Trichomonadea, Hypotrichomonadea, Cristamonadea, Tritrichomonadea, Spirotrichonymphea and Trichonymphea. This will be on the final AND your next weekly spelling test. More importantly, this is how they relate:Phylogenetic relationships between the six new classes.Ok, I must run...will definitely get back to parabasalians in much more detail later. Some people in our department happen to be rather obsessed with them, and obsession can be contagious. But for now, feel free to join me in salivating over that really sweet diagram!Right, finals...Source: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... Read more »

  • April 25, 2010
  • 08:35 PM

Computational Improvement of Carbon Fixation

by Michael Long in Phased

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  

  • April 25, 2010
  • 08:03 PM

FGSC – a key partner in fungal biology research

by stajich in The Hyphal Tip

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 »

  • April 25, 2010
  • 04:34 PM

Then There Were Three

by Journal Watch Online in Journal Watch Online

Scientists identify multiple species of killer whale

... Read more »

  • April 25, 2010
  • 01:48 PM

On unfortunate juxtapositions

by Richard Grant in Confessions of a (former) Lab Rat

There's an Italian cafe/deli round the corner. It's a quiet place, which seems to suit the proprietors well in a Black Books-sort of way (although without the personality defects): they open when they feel like it and there are...... Read more »

  • April 25, 2010
  • 01:20 PM

Complete genome from a single cell - well, yes, *technically*

by Alistair Dove in Deep Type Flow

Its not quite marine science (hey, its my blog, so nerrr), but there's a paper in PLoS One this week where the authors describe the assembly of a genome sequence (all the DNA from beginning to end) from a single cell of a bacterium.  Normally it would take a whole bunch of cultured cells to do this, which limits genome sequencing to those bacteria that can be cultured and right now that isn't ... Read more »

Woyke, T., Tighe, D., Mavromatis, K., Clum, A., Copeland, A., Schackwitz, W., Lapidus, A., Wu, D., McCutcheon, J., McDonald, B.... (2010) One Bacterial Cell, One Complete Genome. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010314  

  • April 25, 2010
  • 12:34 PM

Obesity: the role of the immune system

by Iddo Friedberg in Byte Size Biology

Obesity is one symptom of several, which together constitute what is now termed metabolic syndrome. Morbid obesity is also associated with a host of other symptoms including high blood sugar, high blood lipids, insulin resistance and liver disorders. The root causes of which are traced back to excessive food consumption, reduced physical activity and in some cases, genetic predisposition.

I have written before on the connection found between gut microbe populations and metabolic syndrome.... Read more »

Vijay-Kumar, M., Aitken, J., Carvalho, F., Cullender, T., Mwangi, S., Srinivasan, S., Sitaraman, S., Knight, R., Ley, R., & Gewirtz, A. (2010) Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5. Science, 328(5975), 228-231. DOI: 10.1126/science.1179721  

  • April 25, 2010
  • 08:28 AM

Social onychophorans!

by Psi Wavefunction in Skeptic Wonder

As much as I'm obsessed with protists, I'm a rather promiscuous type when it comes to academic relationships, and thus can find the occasional non-protist cute and interesting. Forgive me if that is 'immoral', but I'm not Christian and thus am not obligated to be intellectually monogamous. So there.Onychophorans (velvet worms) are fucking adorable. Now, whether they are more or less adorable than, say, hypotrich ciliates or Apusomonas proboscidea, is open to debate (I remain loyal to my tribal academic affiliations in that regard), but there's no way you can look at this wonderful creature and not think it's damn cute:Something about onychophoran morphology resonates quite nicely with our innate aesthetic senses...or maybe it's just me. Some of them have really pretty patterns too, or come in absolutely bizarre colours. (Mayer & Herzsch 2007 BMC Evol Biol)A while back someone was waxing poetic about social spiders in class, which led me on quite an adventure. Since I had something very important to do that night, like an exam the following day or something, I got a lot of procrastination done: read about various social spiders (who also have an interesting story of evolutionary dead ends and conflicting levels of selection; oh, and a species with observed cooperative transport of large prey -- apparently fairly rare in arthropods), made my way to social pseudoscorpions (some of them apparently disperse by riding large insects like bugs or beetles), and then I hit upon this paper:Social behaviour in an Australian velvet worm, Euperipatoides rowelli (Onychophora: Peripatopsidae) (Reinhard & Rowell 2005 J Zool)Social behaviour in onychophorans? Seriously!? On a second thought, why the hell not? And then came a complete overload of cute that could've only been enhanced by better images...velvet worms who cuddle!Awww =D Reinhard & Rowell 2005 J ZoolAs cuddly as they may seem, these guys also have a strict social hierarchy involving an alpha female. Reinhard and Rowell (2005) describe a feeding process where a cricket was thrown into the petri dish and attacked by the adult onychophorans (who trap their prey with sticky salivary secretions). After subduing the cricket, the first female fed on the prey for nearly an hour, biting and chasing off any other individual that would approach. After that hour, other females were allowed to feed, and then eventually males and juveniles. Most of the males were feeding after the females left. A feminist's paradise.The interactions between individuals were observed and classified into dominant vs. subordinate: biting and chasing were done by the dominant individual (with the subordinate fleeing) whereas climbing was done by the subordinate and up to the decision of the dominant whether or not to be tolerated:Juveniles were generally left alone and tolerated. Meanwhile, the adults were involved in a constant display of aggression and submission. Females were dominant to the males. When groups of onychophorans from different logs (thus, different social groups) were pairs, individuals of both groups acted aggressively to each other, and despite the males insisting on climbing, no aggregations were formed as they were ruthlessly rejected. Thus, the social groups are stable and at least these onychophorans seem to be capable of kin recognition.The dominance hierarchy seemed largely size-dependent, with smaller females almost always being subservient to the larger individuals. It is believed that as in many other instances of sociality, social behaviour here aids in the cooperative capture of large prey. Curiously, the strict hierarchy when it comes to feeding, with the alpha female hoarding the entire prey, is not known in any other invertebrate.Onychophoran behaviour doesn't receive much attention, perhaps at least partly due to the onychophoran's idea of a perfect habitat not coinciding all too well with that of an ethologist: velvet worms love cold, damp places. So it wouldn't be too surprising if an entire group of social species were eventually discovered, perhaps even with separate origins. In fact, Reinhard and Rowell (2005) state that it is not even known whether sociality may be common for onychophorans in general. On the topic of behaviour, despite their cute and almost fluffy appearance, onychophorans can also be quite vicious. This one devoured a spider bigger than itself:Sticky spit vs. sticky silk. Quite surprisingly, the spit won this battle. (while checking whether this spider actually produces silk, found out that apprently tarantulas secrete adhesive silk from their feet...)It is thought that in order to partake in such complex social behaviours, the onychophoran must have a fairly well-developed region for higher level sensory processing. (considering the complexity of the visual and olfactory cues likely involved in this case, it seems quite plausible. That said, there may well be fairly intricate social interactions out there that do not rely on complex neurology, by executing much simpler rules...) Curiously, they seem to have structures similar to 'mushroom bodies' in arthropods responsible for visual and olfactory processing and regulating complex behaviours. Actually, that was just an excuse to show this stunning image:Onychophoran nervous system. Pseudocoloured to reflect the nerve depth in the confocal projection. Parts of the nervous system arise in a segmented fashion (eg. leg innervation), parts are repeated but not in a segmented way, and they also lack segmental ganglia as those in arthropods. Thus, onychophorans are slightly segmented in some respects, if you will, but still quite different fr... Read more »

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