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  • May 19, 2011
  • 12:00 PM

Full Text And Details For Nature Letter “Data Archiving Is A Good Investment”

by Heather Piwowar in Research Remix

We hope publishing the argument in this high-visibility venue will inspire hallway conversations amongst scientists and influence how they view long-term data archive funding. Particularly those scientists who also wear hats in funding agencies!... Read more »

Piwowar, HA, Vision, TJ, & Whitlock, MC. (2011) Data archiving is a good investment. Nature, 473(7347), 285-285. DOI: 10.1038/473285a  

Piwowar HA, Vision TJ, & Whitlock MC. (2011) Data from: Data archiving is a good investment. Dryad Digital Repository. info:/10.5061/dryad.j1fd7

  • May 19, 2011
  • 11:25 AM

Birds-of-paradise: encountered in passing, on the street

by Darren Naish in Tetrapod Zoology

I love seeing tetrapod-themed art, especially in unexpected places. While in London recently I noticed this 'tropical bird' painting on a piece of wooden boarding, erected to conceal building work. As you can see (larger version below), the work is mostly a brilliant montage of birds-of-paradise (properly Paradisaeidae), the remarkable resplendent "rainforest crows in fancy dress"* of New Guinea and its surrounds.

* Sherman Suter, 1998. Read the rest of this post... | Read the comments on this post...... Read more »

Barker FK, Cibois A, Schikler P, Feinstein J, & Cracraft J. (2004) Phylogeny and diversification of the largest avian radiation. Proceedings of the National Academy of Sciences of the United States of America, 101(30), 11040-5. PMID: 15263073  

  • May 19, 2011
  • 10:43 AM

ASM New Orleans: Here we come!

by microbialmodus in Microbial Modus

The American Society for Microbiology  Some of you may already be aware of the rapidly approaching 111th General Meeting of the American Society of Microbiology (ASM) in New Orleans, May 21st through the 24th.  I’m pretty excited to say this will be my very first opportunity to attend the ASM meeting.  This may be a [...]... Read more »

Miller JF, McFall-Ngai M, & Casadevall A. (2010) A New Design for the ASM General Meeting. mBio, 1(5). PMID: 21151775  

  • May 19, 2011
  • 10:30 AM

Belligerent Bipedal Beaus

by Kristina Killgrove in Powered By Osteons

What's tall, angry, and walks on two legs? Only hominin males, apparently.... Read more »

  • May 19, 2011
  • 08:00 AM

Anti-clotting factors in vampire bat saliva may save your life.

by EcoPhysioMichelle in C6-H12-O6

Yesterday I happened to see a tweet from the Ohio State University Medical Center's twitter account that linked to a press release discussing a new plasminogen activator that is currently undergoing clinical trials. The drug, desmoteplase, is modeled after a protein found in vampire bat saliva that prevents clots and platelet aggregation, which keeps the blood flowing while the bat is feeding. Plasminogen activators like desmoteplase are used to break down blood clots that are blocking blood flow to vital organs such as the heart, lungs, or brain.... Read more »

  • May 19, 2011
  • 07:00 AM

May 19, 2011

by Erin Campbell in HighMag Blog

If you read this blog, then you were probably the type of kid who used your toy microscope to look at the wound on your knee caused by your brother pushing you onto the ground (for example). You could see the skin around the scab stretching, and you knew there was some cool stuff going on there. I’m not sure if the authors from today’s image did this, but in a very sophisticated way they do now. Our cells and tissues are equipped with the ability to repair wounds caused by normal wear-and-tear and injury. When the plasma membrane of a single cell is torn, the membrane and underlying cytoskeleton must be repaired. A recent paper describes the use of early fruit fly embryos to understand what occurs during single-cell wound repair. The early fly embryo is a fantastic model for understanding this event because of its ease of genetic manipulation and the large size of what is technically one cell. Abreu-Blanco and colleagues found that there are three phases in single-cell wound repair—brief expansion of the wound, contraction of the membrane, and closure of the wound. Images above show the accumulation of actin around a healing wound. Left column shows the surface of wound, while the right column shows a cross section.BONUS!! Check out a movie of the image above here. Still want more movies from this paper? Click here.Abreu-Blanco, M., Verboon, J., & Parkhurst, S. (2011). Cell wound repair in Drosophila occurs through three distinct phases of membrane and cytoskeletal remodeling originally published in The Journal of Cell Biology, 193 (3), 455-464 DOI: 10.1083/jcb.201011018... Read more »

  • May 19, 2011
  • 05:00 AM

Lazarus Rising

by Nsikan Akpan in That's Basic Science

How a man survived for 90 minutes without a pulse.... Read more »

  • May 19, 2011
  • 01:11 AM

Over-estimating extinction rates

by CJA Bradshaw in ConservationBytes

I meant to get this out yesterday, but was too hamstrung with other commitments. Now the media circus has beat me to the punch. Despite the lateness (in news-time) of my post, my familiarity with the analysis and the people involved gives me a unique insight, I believe. So a couple of months ago, Fangliang He and [...]... Read more »

  • May 18, 2011
  • 03:55 PM

Phytoplankton Resiliency to the Chicxulub Mass Extinction

by Michael Long in Phased

Phytoplankton can rebound after nearly a century of dormancy in the dark, explaining why these microbes were resilient after the most recent global photosynthesis disruption and the accompanying mass extinction.... Read more »

  • May 18, 2011
  • 01:00 PM

The end of Universals?

by Sean Roberts in The Adventures of Auck

Dunn et al. (2011) has come in for a lot of flack, but are the differences in dependencies between language families really all that different?... Read more »

Michael Dunn,, Simon J. Greenhill,, Stephen C. Levinson, & . (2011) Evolved structure of language shows lineage-specific trends in word-order universals. Nature, 79-82. info:/

  • May 18, 2011
  • 11:53 AM

The end of universals?

by Sean Roberts in A Replicated Typo 2.0


Woah, I just read some of the responses to Dunn et al. (2011) “Evolved structure of language shows lineage-specific trends in word-order universals” (language log here, Replicated Typo coverage here).  It’s come in for a lot of flack.  One concern raised at the LEC was that, considering an extreme interpretation, there may be no affect of . . . → Read More: The end of universals?... Read more »

Michael Dunn,, Simon J. Greenhill,, Stephen C. Levinson, & . (2011) Evolved structure of language shows lineage-specific trends in word-order universals. Nature, 79-82. info:/

  • May 18, 2011
  • 09:08 AM

Pigs with Ebola Zaire: a whole new can o' worms

by Tara Smith in Aetiology

Ebola has long been associated with wildlife. From the early days, bats were viewed as a potential reservoir (though it wasn't confirmed that they actually harbored the virus until 2005). Contact with wild animals--particularly primates which were butchered for food--was also long thought to be a risk factor, and now we know that primates can become ill with Ebola and pass the virus to humans.

What hadn't been examined until 2008 were pigs. I mean, it's not exactly the animal you associate with central Africa, where many of the Ebola cases have been concentrated. However, pigs are much more plentiful in the Philippines, where another Ebola subtype--Ebola Reston--is thought to lurk. The Reston strain actually was first documented in the United States, where twice it was associated with outbreaks in primates originating from the Philippines. When the facility in the Philippines was closed down in 1997, Reston disappeared for 11 years--until it surfaced in pigs in 2008.

The ecology of Ebola Reston in the Philippines isn't known--unlike African Ebola strains (and their cousin, Marburg), no bats have been caught in that country and tested positive for the virus, though they probably serve as a reservoir of the virus in the Philippines just as they do in Africa. So it was a huge surprise when pigs from that country tested positive for Ebola Reston--and so did 6 of their human caretakers, suggesting cross-species transmission. (I should note here that the Reston strain has yet to be linked to any symptomatic infections in humans--the pig farmers who tested positive probably had no idea they'd been infected and did not show any clinical signs of illness). Pigs hadn't previously been linked to any Ebola infection, so this brought in a whole other wrinkle when it came to Ebola transmission--the possibility of being exposed to Ebola via contaminated food, and the potential for pig populations to harbor the filovirus (and transmit it to their caretakers, as we have seen with outbreaks of Nipah and Hendra viruses).

A new study delves further into Ebola in pigs. Instead of using the Reston strain, they use the much-more-deadly Zaire strain. This is the one that movies are made about; the one which can cause outbreaks so nasty that they kill up to 90% of those who are infected. Why use Zaire instead of the Reston strain--the one which has actually infected pigs in nature? Well, the researchers wanted to find an animal that's easier to work with than primates (there are all kinds of very strict regulations when it comes to working with non-human primates), so if pigs could work as a good model for human Ebola disease, that would make studying the virus just a bit easier. (In any case, for any live Ebola work, it still needs to be done in a biosafety level 4 environment, meaning complete spacesuits and the whole works).

The authors did 2 studies. In the first, they inoculated 6 pigs with Ebola Zaire, via a combination of intranasal, intraocular, and oral routes of infection. (Interestingly, no injection, which can be a key way Ebola is spread). They had an additional 2 pigs that they inoculated the same way with a saline solution, and housed them separately from the Ebola-inoculated animals. The goal of this experiment was to look at the pathogenesis of a virulent Ebola strains in the pig model. The infected animals all developed fevers and respiratory disease, with some internal hemorrhaging and evidence of airway replication by Ebola. Infectious virus was found at low levels in nasal washes and oral and rectal swabs; one animal also had a low level of virus in the blood. Higher levels of virus were found in various organs, including the heart and bladder, while the highest levels were found in lung tissue.

In the second experiment, they inoculated 3 new pigs in the same fashion, but then added in 4 additional (uninoculated) animals to stay with them, and kept 2 additional control animals in a separate area so that they could investigate pig-to-pig transmission of the virus. They did find viral RNA from the mucosa of all contact animals, and infectious virus was detected from 2 of 4, demonstrating that the virus can be passed among pigs.

Notably, pigs didn't seem to develop severe systemic disease from Ebola, as primates do--the main symptoms exhibited were respiratory, which the pathology supports (finding little virus in the blood, but a lot in the lungs). This suggests that even for Ebola Zaire, infection in a pig could be mistaken for other respiratory diseases, such as influenza or PRRS virus (porcine respiratory and reproductive syndrome virus, which the initial pigs in the Phillipenes were co-infected with). So, Ebola may be circulating even more than we realize in the pig population, disguised by its commonplace symptoms.

A commentary published in tandem with the research article ponders the issue of foodborne Ebola, suggesting that this is a remote possibility and noting that butchering infected animals in the wild in Africa has certainly spread the virus. However, solely eating meat as a means of infection hasn't been reported, and cooking likely destroys any risk (similar to influenza viruses). Like influenza virus, Ebola doesn't seem to survive long in most environments, but it's also noted that differences in African food storage (with little refrigeration) versus more typical cold storage may affect that as a risk factor, possibly prolonging the life of the virus when held in the cold. I think foodborne transmission is unlikely, but it can't be completely ruled out right now.

Because of the respiratory symptoms, does this mean Ebola could enter the population via meat from animals that farmers don't consider very ill, or put butchers at a heightened risk of infection during slaughter? This to me is more concerning than simple foodborne transmission. With Reston, at least no human symptoms have been observed, but if pigs (and potentially other animals?) can present with Ebola Zaire as a rather generic respiratory infection...well, that could spell trouble in a lot of different ways. It means that telling individuals to simply avoid sick-looking primates (and bats) is going to be even more woefully inadequate than it already is. Plus, it raises the remote-but-not-completely-outside-the-realm-of-possibility of someone intentionally spreading the virus via animals that are infected in this manner.

Science fiction? Maybe. Probably. Hopefully. But this research opens the door on many new lines of investigation and once again, raises even more questions.

Kobinger GP, Leung A, Neufeld J, Richardson JS, Falzarano D, Smith G, Tierney K, Patel A, & Weingartl HM (2011). Replication, Pathogenicity, Shedding, and Transmission of Zaire ebolavirus in Pigs. The Journal of infectious diseases PMID: 21571728 Read the comments on this post...... Read more »

Kobinger GP, Leung A, Neufeld J, Richardson JS, Falzarano D, Smith G, Tierney K, Patel A, & Weingartl HM. (2011) Replication, Pathogenicity, Shedding, and Transmission of Zaire ebolavirus in Pigs. The Journal of infectious diseases. PMID: 21571728  

  • May 18, 2011
  • 08:47 AM

Tip of the Week: Allen Institute’s Brain Explorer

by Jennifer in OpenHelix

Not that long ago Mary posted on updates that occurred recently at the Allen Institute for Brain Science & hinted that there might be a tip coming about their cool 3D Brain Explorer tool – well, today’s the day! As Mary mentions in her post, the Allen Institute has created some phenomenal tools and detailed datasets for brain

From the Brain Explorer documentation, the Explorer allows users to:

# View a fully interactive version of the Allen Human Brain Atlas in 3D for two donors.
*View gene expression data in 3D: partially-inflated white matter surfaces are colored by gene expression values of nearby samples.... Read more »

  • May 18, 2011
  • 06:18 AM

Necks for sex? No thank you, we're sauropod dinosaurs

by Darren Naish in Tetrapod Zoology

If asked "Why do giraffes have such long necks?", the majority of people - professional biologists among them - will answer that it's something to do with increasing vertical reach and hence feeding range. But while the 'increased vertical reach' or 'increased feeding envelope' hypothesis has always been the most popular explanation invoked to explain the giraffe's neck, it isn't the only one.

In 1996, Robert Simmons and Lue Scheepers argued that the giraffe neck functions as a sexual signal: they said that the necks of males are bigger and thicker than those of females, that the necks of males continue growing throughout life, that females prefer males with bigger necks, and that giraffe necks don't provide any obvious benefit in vertical reach or foraging range, contra the 'traditional', 'increased feeding envelope' hypothesis (Simmons & Scheepers 1996). This has become known as the 'necks for sex' hypothesis [obvious sexual dimorphism in giraffes (Giraffa camelopardalis angolensis/G. angolensis) shown above; image by Hans Hillewaert, from wikipedia]. Read the rest of this post... | Read the comments on this post...... Read more »

Taylor, M. P., Hone, D. W. E., Wedel, M. J., & Naish, D. (2011) The long necks of sauropods did not evolve primarily through sexual selection. Journal of Zoology. info:/10.1111/j.1469-7998.2011.00824.x

  • May 17, 2011
  • 11:45 PM

Force-Enhanced, Non-Covalent Cell-Cell Binding

by Michael Long in Phased

A bacterial appendage has evolved to bind to epithelial cells much more strongly with increasing mechanical force.... Read more »

Aprikian, P., Interlandi, G., Kidd, B. A., Le Trong, I., Tchesnokova, V., Yakovenko, O., Whitfield, M. J., Bullitt, E., Stenkamp, R. E., Thomas, W. E.... (2011) The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor. PLoS Biology, 9(5). DOI: 10.1371/journal.pbio.1000617  

  • May 17, 2011
  • 02:55 PM

Antivirals and Suicide

by Neuroskeptic in Neuroskeptic

A case report from India describes a man who became suicidally depressed while being given drugs to treat a viral infection:A 43-year-old man diagnosed with chronic hepatitis C viral infection ... was started on therapy with interferon -α-2a and ribavirin ... Screening tests for hepatitis B virus, hepatitis A virus, and HIV were negative.In initial 3 months of start of therapy with IFN-α-2a and ribavirin, the patient experienced adverse effects in the form of high-grade fever, malaise, myalgia, and fatigue which were relieved by paracetamol. After 16 weeks of therapy, the patient reported to experience feeling of guilt, anxiety, fear, and sadness.He wanted to keep himself isolated from family and friends. He started blaming himself for financial crises he was facing that time. He was unable to perform his job as school teacher. Hamilton Depression Rating Scale (HDRS-17) revealed the patient to be suffering from moderate to severe depression with score of 15.He was given psychotherapy for the same. Paroxetine and zolpidem were started [but] he did not respond significantly to antidepressants over 3 weeks. After 25 days of starting antidepressants, the patient attempted suicide but was rescued in time.IFN-α-2a and ribavirin were withheld for 1 month and antidepressants were continued. Patient's condition normalized and he started taking interest in self and surroundings. He started following his normal routine.He was then put back on the drugs for 3 weeks, but he got depressed again. So treatment was aborted and he was back to feeling fine within a week.Interferons are powerful antivirals but they have the dubious honor of being one of the few medical drugs clearly implicated in causing depression. Others include reserpine, an anti-hypertensive and rimonabant, a weight-loss drug (it got banned for this reason).The anti-malarial mefloquine can cause a range of neuropsychiatric symptoms including depression but also hallucinations and nightmares, as can the HIV drug efavirenz which I covered recently.Most people who take each of these drugs don't experience problems but in a non-trivial minority it happens. It obviously poses a serious problem for doctors, but it's also very interesting for people researching mood and depression. Work out why these drugs cause depression, and it might help work out why people get "normal" clinical depression.For example, just recently it was shown that mefloquine has a unique and unusual effect on cells in the dopamine system of the brain, responsible for motivation and pleasure. Whether this explains the side-effects is an open question but without mefloquine we wouldn't even be able to ask it.As for interferons, which are actually not drugs as such but rather molecules produced by the immune system during infections, it's given rise to the inflammation theory of depression. There's always a risk, though, that by focussing too much on just one class of depressing drug, you'll end up with a narrow theory that can't account for the others.Inder D, Rehan HS, Yadav M, Manak S, & Kumar P (2011). IFN-α-2a (Interferon) and ribavirin induced suicidal attempt in a patient of chronic HCV: A rare case report. Indian journal of pharmacology, 43 (2), 210-1 PMID: 21572662... Read more »

  • May 17, 2011
  • 02:32 PM

Social Behavior in Palaeocene Metatherians

by Jim Ryan in Wild Mammals

Textbooks often describe late Cretaceous or early Palaeocene mammals as small, nocturnal, and solitary (Figure 1). That description has recently been amended thanks to a remarkable suite of fossil metatherians from Bolivia.

...An artist’s reconstruction of the stem metatherian Sinodelphys from the early Cretaceous. (From Prothero and Buell Evolution: What the Fossils Say and Why It Matters, 2007)

Tiupampa, a fossil rich site in the heart of Bolivia, has begun to yield a treasure-trove of early mammalian fossils. Among them are large numbers of well-preserved skulls and post cranial material from several stem metatherians (marsupials). A recent report by Ladevese and colleagues (2011) in the journal Nature describes an exceptionally large, and extraordinarily preserved group of skulls and skeletons from Pucadelphys andinus, a stem-metatherian. To date, 35 individuals have been recovered from these early Palaeocene deposits. What makes this find so unusual is that the skulls, mandibles, and post cranial skeletal material is so well preserved and that they were recovered from an area of just a few square meters. The skeletons remain articulated suggesting that the animals were buried rapidly during a catastrophic event (Figure 2).

...Skulls and partial skeletons of P. andinus from basal Palaeocene beds at Tiupampa (Bolivia). The lower plate depicts a fossil block and a reconstruction of the same two animals. (From Ladeveze et al.

...The catastrophic burial coupled with the fact that 35 individuals of P. andinus, including adults, sub-adults, and juveniles occur together within a few feet of one another suggests that these stem metatherians were social (or at least were very tolerant of other individuals). This population also exhibits fairly strong sexual dimorphism, with males 35% larger than females.

Sexual dimorphism in living metatherians appears connected with

semelparity, but P. andinus could not have been semelparous (because adult males, sub-adults and juveniles all co-occurred in the same population). Alternatively, sexual dimorphism may be related to male dominance over territorial females, but this is unlikely for the Palaeocene P. andinus populations since several adult males and females co-occurred in the population (suggesting that females were not territorial). Thus, it appears that the sexual size dimorphism in P. andinus was associated with male–male competition, and polygyny (where one male mates with multiple females during one breeding season).

Such gregariousness in stem metatherians contrasts sharply with the mostly solitary life styles of modern South American matatherians. Perhaps it is time to rethink the behavior of basal metatherians. Ladeveze et al. (2011) conclude that “social interactions occurred in metatherians as early as the basal Palaeocene and that solitary behavior may not be plesiomorphic for Metatheria as a whole.”

...Ladevèze, S., de Muizon, C., Beck, R., Germain, D., & Cespedes-Paz, R. ... Earliest evidence of mammalian social behaviour in the basal Tertiary of Bolivia Nature DOI: 10.1038/nature09987
... Read more »

  • May 17, 2011
  • 12:29 PM

The Life of a Countertop Croc

by Laelaps in Laelaps

Why a raven is like a writing desk – the infamous riddle put forward by Lewis Carroll’s Mad Hatter – was meant to be an incomprehensible mystery, but a fortuitous discovery made half a century ago answers the un-asked question of how a crocodile is like a countertop.
Nodular limestone is beautiful. The sedimentary looks like [...]... Read more »

GANDOLA, R., BUFFETAUT, E., MONAGHAN, N., & DYKE, G. (2006) SALT GLANDS IN THE FOSSIL CROCODILE METRIORHYNCHUS. Journal of Vertebrate Paleontology, 26(4), 1009-1010. DOI: 10.1671/0272-4634(2006)26[1009:SGITFC]2.0.CO;2  

  • May 17, 2011
  • 12:16 PM

Update on denosumab and SRE’s: data from the 147 trial

by Sally Church in Pharma Strategy Blog

A little over ten years ago, I lost my Father to metastatic prostate cancer, a brave fight that lasted only a few years since he was diagnosed with stage IV disease.   In many ways though, it was a bittersweet … Continue reading →
... Read more »

  • May 17, 2011
  • 10:12 AM

Not-so-similar fate of identical twins infected with HIV-1

by Vincent Racaniello in virology blog

For extra credit in my recently concluded virology course, I asked students to summarize a virology finding in the style of this blog. I received many excellent submissions which I plan to post here in the coming months. by Amanda Carpenter In 1983, identical twins boys simultaneously received a contaminated blood transfusion immediately after birth, [...]... Read more »

Tazi L, Imamichi H, Hirschfeld S, Metcalf JA, Orsega S, Pérez-Losada M, Posada D, Lane HC, & Crandall KA. (2011) HIV-1 infected monozygotic twins: a tale of two outcomes. BMC evolutionary biology, 62. PMID: 21385447  

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