Monthly Archives: May 2009

Clock Quotes

Sleep is that golden chain that ties health and our bodies together.
– Thomas Dekker

New and Exciting in PLoS ONE

There are 25 new articles in PLoS ONE today and there were 21 yesterday. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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Introducing Ida – the great-great-great-great-grandmother (or aunt)

Another super-cool day at PLoS (one of those days when I wish I was not telecommuting, but sharing in the excitement with the colleagues at the Mothership) – the publication of a very exciting article describing a rarely well-preserved fossil of a prehistoric primate in a lineage to which we all belong as well:
Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology by Jens L. Franzen, Philip D. Gingerich, Jörg Habersetzer, Jørn H. Hurum, Wighart von Koenigswald and B. Holly Smith
The fossil, named Ida (the scientific name is Darwinius masillae, a new genus), was discovered in Messel Pit, Germany and lived around 47 million years ago. The fossil is 95% complete – an incredibly complete fossil for an early primate – and along with the skeleton also contains the outline of the body and the contents of the gut. From such rich information, the scientists were able to deduce that Ida was a herbivorous female of about nine months of age.
Ida fig-s62.jpg
[The image is Fig. S6 of the PLoS ONE article, published under the Creative Commons Attribution License; any reuse should cite the authors and journal.]
Unlike lemurs, Darwinius masillae does not have a “toothcomb” and a “grooming claw,” but like primates in the lineage that also contains humans, Ida has opposable big toes, nail-bearing fingers and toes, and a foot bone called the talus bone.
Check out Bex’s blog post on everyONE for more details as well as the interactive Ida website and, of course, read the paper itself – 27 pages of details, Open Access, thus free for all to see!
As always, you should rate the article, post notes and comments and send trackbacks when you blog about this paper. You can also easily place this article on various social services (CiteULike, Connotea, Stumbleupon, Facebook, Digg and Mendeley) with just one click. Bex and I will collect all the media and blog coverage and post the links to the best on everyONE blog later this week, and that will be linked from the PLoS ONE homepage as well.
I would like to use this opportunity to thank the PLoS ONE production team who did a tremendous job in getting the paper out in record time. Despite the paper being available for only minutes, the mainstream media has already run with the story. I expect that science bloggers, with their expertise, will provide more detailed and in-depth coverage of the paper (and skip the silly “missing link” trope) once they digest the scientific information in the paper.

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Clock Quotes

Never try to tell everything you know. It may take too short a time.
– Norman Ford

My picks from ScienceDaily

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Welcome the newest SciBling!

It is a great pleasure to welcome an old friend, John Dupuis, to Scienceblogs.com. As you may recall, John and I interviewed each other last year – first I interviewed John, then shortly after, John interviewed me.
This morning, Confessions of a Science Librarian moved from blogspot to Scienceblogs.com – so go and say Hello!

Today’s carnivals

Scientia Pro Publica #4 – In Memory of Stephen Jay Gould – is up on The Primate Diaries
Carnival of the Green #180 is up on Ethical superstore

Sex Week on Deep Sea News

It is Sex Week on Deep Sea News.
It started with The Sand Dollar Love Shack: A Special Echinoblog to DSN and followed by ‘Sleezy’ sponge sexuality and more is yet to come for the rest of the week.

Call for articles: User-led Science, Citizen Science, Popular Science

A special issue of JCOM, Journal of Science Communication, has just issued a call for submissions, with the deadline moved to June 1st, 2009:

Science is increasingly being produced, discussed and deliberated with cooperative tools by web users and without the institutionalized presence of scientists. “Popular science” or “Citizen science” are two of the traditional ways of defining science grassroots produced outside the walls of laboratories. But the internet has changed the way of collecting and organising the knowledge produced by people – peers – who do not belong to the established scientific community. In this issue we want to discuss:
– How web tools are changing and widening this way of participating in the production of scientific knowledge. Do this increase in participation consist in a real shift towards democratizing science or on the contrary is merely a rhetoric which do not affect the asymmetrical relationships between citizens and institutions?
– The ways in which both academic and private scientific institutions are appropriating this knowledge and its value. Do we need a new model to understand these ways of production and appropriation? Are they part of a deeper change in productive paradigms?
We would like to collect both theoretical contributions and research articles which address for example case studies in social media and science, peer production, the role of private firms in exploiting web arenas to collect scientific/medical data from their costumers, online social movements challenging communication incumbents, web tools for development.
Interested authors should submit an extended abstract of no more than 500 words (in English) to the issue editor by May 15, 2009. We will select three to five papers for inclusion in this special issue. Abstracts should be sent to the JCOM’s editorial office (jcom-eo@jcom.sissa.it) by email and NOT via the regular submission form.

You may remember that I mentioned this journal before. Of course, if you look closely, you’ll find an article by me, and two articles that mention me in there – all written during or right after my visit to Trieste last year. So, start writing!

Clock Quotes

You know the great thing about TV? If something important happens anywhere at all in the world, no matter what time of the day or night, you can always change the channel.
– Jim Ignatowski

Turtle in front of my door

Rainy day, so yummy earthworms are out and about:
turtle 001.jpg
turtle 002.jpg
turtle 003.jpg

Clock Quotes

Don’t limit a child to your own learning, for he was born in another time.
– Jewish proverb

A Radical Transparency society is difficult to describe in a SF novel

Radical Transparency removes almost all potentials for conflict. Why?
Conflict requires secrecy by some people (bad guys), which is why neither utopian nor anti-utopian novels try to describe such a society in which everything done by everyone – individual, corporation, government – is completely transparent. When everything is out in the open, conflict is difficult to do.
It is hard to write a gripping novel without conflict. Who will read a lyrical ode to a perfect society? Readers need good guys beating up on bad guys in the Final Battle.
In many dystopias, transparency is one-way, i.e., a powerful entity (corporation or government) which is itself totally secretive can know everything about every citizen at every time.
But a two-way transparency makes conflict impossible.
Still, I’d like to see a SF novel giving it a try – even if it works around the problem by subverting the Radical Transparency society: exploring the way it works when it works, and what conflict happens when a group or an individual manages to opt out of it and keeps something secret.
And how do you achieve Radical Transparency? If it is mandatory, it is a dictatorship (or spying at a massive scale), or is there a benevolent way to do that? If it is voluntary, someone can always subvert it (pure Game Theory here).
Example: if what every government official says, does or types is immediately visible to everyone, it is impossible to plan a war as enemies will see the plans. Does it mean there are no wars, or that people subvert the transparency by planning wars in non-obvious ways – coded language, etc.
Discuss.

Today’s carnivals

The Giant’s Shoulders #11 is up on Curving Normality
Friday Ark #243 is up on Modulator
And the next Praxis will be on a new date – May 21st – on The Lay Scientist

Clock Quotes

As every cat owner knows, nobody owns a cat.
– Ellen Perry Berkeley

My picks from ScienceDaily

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Clock Quotes

I discovered I always have choices and sometimes it’s only a choice of attitude.
– Judith M. Knowlton

New and Exciting in PLoS this week

I’d like to start today with Big Congratulations to the amazing PLoS IT/Web team for finishing the complex and long task of migrating all seven PLoS Journals onto the TOPAZ/Ambra platform. This week, the last of the seven journals, PLoS Biology, was successfully moved. This means that you can now rate the articles, post notes and comments and send trackbacks to articles in PLoS Biology just like you could do it on the other six titles that were migrated over the last couple of years. While I don’t know exactly what is in the planning, I am sure that the team will continue to make regular upgrades and improvements of the platform and the site and to work on integrating the seven journals with each other.
So, while the PLoS Biology crew took an understandable week off during the migration, let’s see what’s new in the other six journals this week: PLoS Medicine, PLoS Genetics, PLoS Computational Biology, PLoS Pathogens, PLoS Neglected Tropical Diseases and PLoS ONE. Here are my own picks for the week – you go and look for your own favourites:
No More Free Drug Samples?:

Everybody likes something free, and free prescription drug samples are no exception. Patients love to receive them, and doctors feel good about handing them out. The practice of providing free drug samples is based on the tacit assumption that “sampling” does much more good than harm. In two separate news releases within the past year by the Pharmaceutical Research and Manufacturers of America (PhRMA), the trade organization that represents the country’s largest and leading drug companies, a senior vice president claimed that free samples improve patient care, foster appropriate medication use, and help millions of financially struggling patients. He averred further that samples benefit physicians by exposing them to new treatment options [1],[2]. In this essay, we question the assumption that good trumps harm when prescription drugs are provided free to practicing doctors. We argue that “sampling” is not effective in improving drug access for the indigent, does not promote rational drug use, and raises the cost of care.

Bumble Bees (Bombus spp) along a Gradient of Increasing Urbanization:

Bumble bees and other wild bees are important pollinators of wild flowers and several cultivated crop plants, and have declined in diversity and abundance during the last decades. The main cause of the decline is believed to be habitat destruction and fragmentation associated with urbanization and agricultural intensification. Urbanization is a process that involves dramatic and persistent changes of the landscape, increasing the amount of built-up areas while decreasing the amount of green areas. However, urban green areas can also provide suitable alternative habitats for wild bees. We studied bumble bees in allotment gardens, i.e. intensively managed flower rich green areas, along a gradient of urbanization from the inner city of Stockholm towards more rural (periurban) areas. Keeping habitat quality similar along the urbanization gradient allowed us to separate the effect of landscape change (e.g. proportion impervious surface) from variation in habitat quality. Bumble bee diversity (after rarefaction to 25 individuals) decreased with increasing urbanization, from around eight species on sites in more rural areas to between five and six species in urban allotment gardens. Bumble bee abundance and species composition were most affected by qualities related to the management of the allotment areas, such as local flower abundance. The variability in bumble bee visits between allotment gardens was higher in an urban than in a periurban context, particularly among small and long-tongued bumble bee species. Our results suggest that allotment gardens and other urban green areas can serve as important alternatives to natural habitats for many bumble bee species, but that the surrounding urban landscape influences how many species that will be present. The higher variability in abundance of certain species in the most urban areas may indicate a weaker reliability of the ecosystem service pollination in areas strongly influenced by human activity.

Avian Influenza Virus Glycoproteins Restrict Virus Replication and Spread through Human Airway Epithelium at Temperatures of the Proximal Airways:

Influenza type A viruses are endemic in aquatic birds but can cross the species barrier to infect the human respiratory tract. While transmission from birds to humans is rare, the introduction of novel avian influenza viruses into immunologically naïve human populations has significant pandemic potential. Avian influenza viruses are adapted for growth at 40°C, the temperature of the avian enteric tract. However, the human proximal airways, the likely site of initial inoculation by influenza viruses, are maintained at a cooler temperature (32°C), suggesting that zoonotic transmission may be limited by temperature differences between the two hosts. Using an in vitro model of human ciliated airway epithelium, we show that avian influenza viruses grow well at 37°C, a temperature reflective of distal airways, but are restricted for infection at 32°C. A panel of genetically manipulated human influenza viruses possessing avian or avian-like surface glycoproteins were also restricted at 32°C, but not 37°C, suggesting that avian virus glycoproteins are not adapted for efficient infection at the temperature of the proximal airways. Thus, avian influenza virus infection is restricted in the human proximal airways due to the cooler temperature of this region, thus limiting the likelihood of zoonotic and subsequent human-to-human transmission of these viruses.

Do Electronic Health Records Help or Hinder Medical Education?:

Background to the debate: Many countries worldwide are digitizing patients’ medical records. In the United States, the recent economic stimulus package (“the American Recovery and Reinvestment Act of 2009”), signed into law by President Obama, includes $US17 billion in incentives for health providers to switch to electronic health records (EHRs). The package also includes $US2 billion for the development of EHR standards and best-practice guidelines. What impact will the rise of EHRs have upon medical education? This debate examines both the threats and opportunities.

A “Shallow Phylogeny” of Shallow Barnacles (Chthamalus):

We present a multi-locus phylogenetic analysis of the shallow water (high intertidal) barnacle genus Chthamalus, focusing on member species in the western hemisphere. Understanding the phylogeny of this group improves interpretation of classical ecological work on competition, distributional changes associated with climate change, and the morphological evolution of complex cirripede phenotypes. We use traditional and Bayesian phylogenetic and ‘deep coalescent’ approaches to identify a phylogeny that supports the monophyly of the mostly American ‘fissus group’ of Chthamalus, but that also supports a need for taxonomic revision of Chthamalus and Microeuraphia. Two deep phylogeographic breaks were also found within the range of two tropical American taxa (C. angustitergum and C. southwardorum) as well. Our data, which include two novel gene regions for phylogenetic analysis of cirripedes, suggest that much more evaluation of the morphological evolutionary history and taxonomy of Chthamalid barnacles is necessary. These data and associated analyses also indicate that the radiation of species in the late Pliocene and Pleistocene was very rapid, and may provide new insights toward speciation via transient allopatry or ecological barriers.

Reconstructing the History of Yeast Genomes:

Some 12 years ago, Wolfe and colleagues demonstrated that Saccharomyces cerevisiae is the descendant of an ancient whole-genome duplication event [1],[2], much to the consternation of many of those who had recently completed the sequencing of this yeast [3], the first eukaryotic nuclear genome to be sequenced. Despite persistent rejectionist argument [4], this breakthrough discovery has been amply confirmed [5],[6] and has been the starting point for scores of papers on yeast evolution and phylogeny, culminating in the Yeast Gene Order Browser [7] and the paper by Gordon et al. in this issue of PLoS Genetics [8].

Folic Acid Supplementation and Spontaneous Preterm Birth: Adding Grist to the Mill?:

Preterm birth is increasing, and complicates 12% of deliveries in the United States. It is the dominant cause of neonatal mortality. Preterm birth also accounts for one in three children with vision impairment, one in five with mental retardation, and almost half with cerebral palsy [1]. Babies born weighing under 2,500 g are at heightened risk in adulthood of diabetes and cardiovascular disease [1]. These short- and long-term sequelae make the prevention of preterm birth a public health priority.

Discovery of Mating in the Major African Livestock Pathogen Trypanosoma congolense:

The protozoan parasite, Trypanosoma congolense, is one of the most economically important pathogens of livestock in Africa and, through its impact on cattle health and productivity, has a significant effect on human health and well being. Despite the importance of this parasite our knowledge of some of the fundamental biological processes is limited. For example, it is unknown whether mating takes place. In this paper we have taken a population genetics based approach to address this question. The availability of genome sequence of the parasite allowed us to identify polymorphic microsatellite markers, which were used to genotype T. congolense isolates from livestock in a discrete geographical area of The Gambia. The data showed a high level of diversity with a large number of distinct genotypes, but a deficit in heterozygotes. Further analysis identified cryptic genetic subdivision into four sub-populations. In one of these, parasite genotypic diversity could only be explained by the occurrence of frequent mating in T. congolense. These data are completely inconsistent with previous suggestions that the parasite expands asexually in the absence of mating. The discovery of mating in this species of trypanosome has significant consequences for the spread of critical traits, such as drug resistance, as well as for fundamental aspects of the biology and epidemiology of this neglected but economically important pathogen.

Now, this is Open Science!

One by one, brave people are opening up science, serving as examples of how things can and should be done openly with no ill consequences.
Today – examples of two such pioneers.
First, Bryan Perkins published his research on his blog. Go and read it and post comments, ask questions, help him improve the work. If the feedback is good, who knows, he may submit it to a peer-reviewed journal. In any case, it is much better for data to be out in the open, available to anyone who knows how to use Google search, than gathering dust in some manila folder.
Second, Darren Begley, a graduate student at University of Washington will livestream his PhD defense on Tuesday May 19th at 4 p.m. PT (1pm EST). You can watch his defense live on UStream. I am not sure if anyone in the room will be checking UStream during the defense to see if there are questions from the online audience, but that would be so incredibly cool if they did and if Darren actually answers them at the end of his defense.

Today’s carnivals

I and the Bird #100 is up on Nature Blog Network
Change of Shift: Volume 3, Number 23 is up on Emergiblog

Clock Quotes

Sometimes the best gain is to lose.
– George Herbert

Last call for submissions for ‘Praxis’ and ‘The Giants’ Shoulders’

Only two ways left to submit!
Next edition of The Giant’s Shoulders will be on May 15th on Curving Normality. History of science, ‘classical’ papers? If you have blogged about those over the past 30 days, please send in your entry.
I understand that the next edition of Praxis will also be on May 15th on The Lay Scientist. Next month, it will be on Quiche Morraine and in July here on A Blog Around The Clock – we need hosts for after that! Let Martin or me know if you are interested.

Laziness in reporting – what’s new?

You may have heard about a recent Wikipedia hoax:

A WIKIPEDIA hoax by a 22-year-old Dublin student resulted in a fake quote being published in newspaper obituaries around the world.
The quote was attributed to French composer Maurice Jarre who died at the end of March.
It was posted on the online encyclopedia shortly after his death and later appeared in obituaries published in the Guardian, the London Independent, on the BBC Music Magazine website and in Indian and Australian newspapers

Yup. Journalists check their sources carefully. Especially the despised untrustworthy Wikipedia, only a notch above the unruly mobs of bloggers.
But that’s not new.
Back in 1899, there was no Wikipedia, but there were Dictionaries. Trustworthy. Except when they are not. Pwnd.

New and Exciting in PLoS ONE

There are 18 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
The Abdominal Circulatory Pump:

Blood in the splanchnic vasculature can be transferred to the extremities. We quantified such blood shifts in normal subjects by measuring trunk volume by optoelectronic plethysmography, simultaneously with changes in body volume by whole body plethysmography during contractions of the diaphragm and abdominal muscles. Trunk volume changes with blood shifts, but body volume does not so that the blood volume shifted between trunk and extremities (Vbs) is the difference between changes in trunk and body volume. This is so because both trunk and body volume change identically with breathing and gas expansion or compression. During tidal breathing Vbs was 50-75 ml with an ejection fraction of 4-6% and an output of 750-1500 ml/min. Step increases in abdominal pressure resulted in rapid emptying presumably from the liver with a time constant of 0.61±0.1SE sec. followed by slower flow from non-hepatic viscera. The filling time constant was 0.57±0.09SE sec. Splanchnic emptying shifted up to 650 ml blood. With emptying, the increased hepatic vein flow increases the blood pressure at its entry into the inferior vena cava (IVC) and abolishes the pressure gradient producing flow between the femoral vein and the IVC inducing blood pooling in the legs. The findings are important for exercise because the larger the Vbs the greater the perfusion of locomotor muscles. During asystolic cardiac arrest we calculate that appropriate timing of abdominal compression could produce an output of 6 L/min. so that the abdominal circulatory pump might act as an auxiliary heart.

Using Classical Population Genetics Tools with Heterochroneous Data: Time Matters!:

New polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations. We first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony (~10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism θ, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck). Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus), for which large mtDNA haplotypes have been reported over a substantial time period (22-130 thousand years ago (KYA)). Considering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of populations and inappropriate conservation decisions. We therefore argue for systematically considering heterochroneous models when analyzing heterochroneous samples covering a large time scale.

My picks from ScienceDaily

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Clock Quotes

I’m an early bird, and I’m a night owl. So I’m wise and have worms.
– Michael Scott

Today’s carnivals

Encephalon #70 is up on SharpBrains
Carnival of Space #102 is up on TheSpacewriter’s Ramblings
Grand Rounds Vol. 5 No. 34 is up at Health Blogs Observatory
The Carnival of the Green #179 is up on OrganicMania
Friday Ark #242 is up on Modulator

Brown Anole Portrait (video)

Carel P. Brest van Kempen (yes, the artist who did the banner of this blog) submitted this video for a contest. I am not sure how the voting goes, but perhaps lots of visits to this YouTube video are the thing they are looking for:

New and Exciting in PLoS ONE

There are 22 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Ants Sow the Seeds of Global Diversification in Flowering Plants:

The extraordinary diversification of angiosperm plants in the Cretaceous and Tertiary periods has produced an estimated 250,000-300,000 living angiosperm species and has fundamentally altered terrestrial ecosystems. Interactions with animals as pollinators or seed dispersers have long been suspected as drivers of angiosperm diversification, yet empirical examples remain sparse or inconclusive. Seed dispersal by ants (myrmecochory) may drive diversification as it can reduce extinction by providing selective advantages to plants and can increase speciation by enhancing geographical isolation by extremely limited dispersal distances. Using the most comprehensive sister-group comparison to date, we tested the hypothesis that myrmecochory leads to higher diversification rates in angiosperm plants. As predicted, diversification rates were substantially higher in ant-dispersed plants than in their non-myrmecochorous relatives. Data from 101 angiosperm lineages in 241 genera from all continents except Antarctica revealed that ant-dispersed lineages contained on average more than twice as many species as did their non-myrmecochorous sister groups. Contrasts in species diversity between sister groups demonstrated that diversification rates did not depend on seed dispersal mode in the sister group and were higher in myrmecochorous lineages in most biogeographic regions. Myrmecochory, which has evolved independently at least 100 times in angiosperms and is estimated to be present in at least 77 families and 11 000 species, is a key evolutionary innovation and a globally important driver of plant diversity. Myrmecochory provides the best example to date for a consistent effect of any mutualism on large-scale diversification.

Nest Making and Oxytocin Comparably Promote Wound Healing in Isolation Reared Rats:

Environmental enrichment (EE) fosters attachment behavior through its effect on brain oxytocin levels in the hippocampus and other brain regions, which in turn modulate the hypothalamic-pituitary axis (HPA). Social isolation and other stressors negatively impact physical healing through their effect on the HPA. Therefore, we reasoned that: 1) provision of a rat EE (nest building with Nestlets®) would improve wound healing in rats undergoing stress due to isolation rearing and 2) that oxytocin would have a similar beneficial effect on wound healing. In the first two experiments, we provided isolation reared rats with either EE or oxytocin and compared their wound healing to group reared rats and isolation reared rats that did not receive Nestlets or oxytocin. In the third experiment, we examined the effect of Nestlets on open field locomotion and immediate early gene (IEG) expression. We found that isolation reared rats treated with Nestlets a) healed significantly better than without Nestlets, 2) healed at a similar rate to rats treated with oxytocin, 3) had decreased hyperactivity in the open field test, and 4) had normalized IEG expression in brain hippocampus. This study shows that when an EE strategy or oxytocin is given to isolation reared rats, the peripheral stress response, as measured by burn injury healing, is decreased. The findings indicate an association between the effect of nest making on wound healing and administration of the pro-bonding hormone oxytocin. Further elucidation of this animal model should lead to improved understanding of how EE strategies can ameliorate poor wound healing and other symptoms that result from isolation stress.

The Effect of Adult Aggression on Habitat Selection by Settlers of Two Coral-Dwelling Damselfishes:

Coral-reef fishes experience a major challenge when facing settlement in a multi-threat environment, within which, using settlement cues, they need to select a suitable site. Studies in laboratories and artificial setups have shown that the presence of conspecific adults often serves as a positive settlement cue, whose value is explained by the increased survival of juveniles in an already proven fit environment. However, settlement in already inhabited corals may expose the recruits to adult aggression. Daily observations and manipulation experiments were used in the present study, which was conducted in the natural reef. We revealed differential strategies of settlers, which do not necessarily join conspecific adults. Dascyllus aruanus prefer to settle near (not with) their aggressive adults, and to join them only after gaining in size; whereas Dascyllus marginatus settlers in densely populated reefs settle independently of their adult distribution. Our results present different solutions to the challenges faced by fish recruits while selecting their microhabitat, and emphasize the complexity of habitat selection by the naïve settlers. Although laboratory experiments are important to the understanding of fish habitat selection, further studies in natural habitats are essential in order to elucidate the actual patterns of settlement and habitat selection, which are crucial for the survival of coral-reef fish populations.

On the Origin of Indonesian Cattle:

Two bovine species contribute to the Indonesian livestock, zebu (Bos indicus) and banteng (Bos javanicus), respectively. Although male hybrid offspring of these species is not fertile, Indonesian cattle breeds are supposed to be of mixed species origin. However, this has not been documented and is so far only supported by preliminary molecular analysis. Analysis of mitochondrial, Y-chromosomal and microsatellite DNA showed a banteng introgression of 10-16% in Indonesian zebu breeds. East-Javanese Madura and Galekan cattle have higher levels of autosomal banteng introgression (20-30%) and combine a zebu paternal lineage with a predominant (Madura) or even complete (Galekan) maternal banteng origin. Two Madura bulls carried taurine Y-chromosomal haplotypes, presumably of French Limousin origin. In contrast, we did not find evidence for zebu introgression in five populations of the Bali cattle, a domestic form of the banteng. Because of their unique species composition Indonesian cattle represent a valuable genetic resource, which potentially may also be exploited in other tropical regions.

Kinetic Works (video)


Art by Deb Todd Wheeler

Clock Quotes

Sometimes I wonder if we live life by reliving life, rather than by living life.
– Michael Landon

Hardware or Software: Searching for the Genetic Basis for Biological Diversity

Are you up to date on the hot debate in biology regarding how genes influence evolution? Some scientists contend genes are in the driver’s seat. Others assign more pull to regulatory factors controlling genetic expression. At noon, Wednesday, May 27, come hear Duke biologist Greg Wray explore the importance of it all in a talk entitled “Hardware or Software: Searching for the Genetic Basis for Biological Diversity.”
You may not want to miss this one. After Wray’s talk, Pizza Talk embarks on its traditional three-month summer vacation. The next nine-month series debuts in September.
Sigma Xi Pizza Lunch is free and open to science journalists and science communicators of all stripes. Feel free to forward this message to anyone who might be interested in attending. RSVPs are required (for a reliable slice count) to cclabby AT amsci DOT org.
Directions to Sigma XI:http://www.sigmaxi.org/about/center/directions.shtml

Undergraduate science summer camp at Petnica Science Center

Petnicacrowd.jpgPetnica Science Center has been doing science summer camps for high school graduates and undergrads for 25 years and many of its alumni went on to have good careers in science both in Serbia and abroad:

Petnica Science Center is the biggest and, probably, the oldest independent nonprofit organization for extracurricular science education in SE Europe. Since 1982, Petnica has organized more than 2,500 programs (seminars, workshops, research camps…) for nearly 50,000 students and science teachers in 15 disciplines of science, technology and humanities. Majority of programs are designed for secondary-school students although there are a lot of programs for primary-school pupils, university students and science teachers. Attendants of regular Petnica programs are coming from all countries of former Yugoslavia and all these courses are being realized in Serbian language. However, Petnica occasionally organizes programs (like PI) in English for international participants.

Petnicasmrdi.jpgAfter a decade of wars and sanctions, Serbia has a moderate elected government, nice economic growth and is safe (you can browse my blog for posts related to the area). It is also a huge European center for birding/birdwatching and wildlife. It also needs to recover from a decade of brain-drain and no other scientific institution there is as worthy of support as Petnica. Adventure, science, visiting a beautiful and interesting place – think about it and sign up for their Petnica International summer science on August 2nd to 15th, 2009:

The aim of this program is to enable young scientists to practice scientific research by working on their own research and presenting their results and ideas. Students will also have a chance to attend various theoretical lectures and laboratory exercises, to learn how to use some important software packages and experience work in the field.
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Interested students should fill in the student application form, write a personal statement, and provide two letters of recommendation. The personal statement should list your interests and explain why you would like to attend PI 2009, as well as anything else you think is important for us to know. All registration materials should be submitted by e-mail to pi AT petnica DOT rs no later than May 31, 2009. The program fee – including tuition, learning materials, accommodation, meals, admittance to the recreation center and field trips, is €500. There are no application fees. Also 30 percent of the total number of pupils will be funded by the organizers, and if you need financial support, do not hesitate and contact us.

Petnicasunce.jpgIf you are still hesitant, you should read this ‘Science in School’ article: Learning through research: a Serbian tradition:

Twenty-five years ago, in a village called Petnica, 100 kilometres south-east of Belgrade, an unusual science education centre was founded and soon became a hideaway for many rebellious secondary-school and university students from all over Yugoslavia. The attractive landscape and rich natural resources, such as a canyon, caves and archaeological sites, caught these students’ attention. Even though they were deeply unsatisfied with the formal education system, they were truly enthusiastic about nature and scientific work, and realised there was much more to education than school. Long before Petnica was formally established, some camps were organised for students of Belgrade University and members of a movement called Young Researchers of Serbia. Eventually, they managed to find government support to start an organisation with a few employees, a pile of books and a couple of Spectrum computers. Thanks to their efforts, an extracurricular educational centre was established for future generations of curious minds.
Petnicabiblioteka.jpgSince its beginning in 1982, Petnica Science Center has organised nearly 2300 programmes (seminars, workshops, camps and small conferences) for more than 40 000 secondary-school pupils, university students and teachers interested in science and technology. Today, Petnica is the largest independent, non-profit organisation for out-of-school science education in south-eastern Europe. Programmes at Petnica help students to focus on the scientific method and to write science reports and papers.

Read the whole thing. Then sign up for the summer program.

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Clock Quotes

My Birthday! what a different sound
That word had in my youthful ears;
And how each time the day comes round,
Less and less white its mark appears.

– Thomas Moore

Miss Baker’s students – how to excite teens about science (video)

Miss Baker went to the Two Cultures conference in NYC, and there she showed this video of her students:

43

For a whole year, I knew the answer to the Ultimate Question of Life, the Universe, and Everything. Starting today, I am ignorant again.

Why social insects do not suffer from ill effects of rotating and night shift work?

ResearchBlogging.orgMost people are aware that social insects, like honeybees, have three “sexes”: queens, drones and workers.
Drones are males. Their only job is to fly out and mate with the queen after which they drop dead.
Female larvae fed ‘royal jelly’ emerge as queens. After mating, the young queen takes a bunch of workers with her and sets up a new colony. She lives much longer than other bees and spends her life laying gazillions of eggs continuously around the clock, while being fed by workers.
Female larvae not fed the ‘royal jelly’ emerge as workers.
Workers perform a variety of jobs in the hive. Some are hive-cleaners, some are ‘nurses’ (they feed the larvae), some are queen’s chaperones (they feed the queen), some are guards (they defend the hive and attack potential enemies) and some are foragers (they collect nectar and pollen from flowers and bring it back to the hive).
What most people are not aware of, though, is that there is a regular progression of ‘jobs’ that each worker bee goes through. The workers rotate through the jobs in an orderly fashion. They all start out doing generalized jobs, e.g., cleaning the hive. Then they move up to doing a more specialized job, for instance being a nurse or taking care of the queen. Later, they become guards, and in the end, when they are older, they become foragers – the terminal phase.
This pattern of behavioral development is called “age polyethism” (poly = many, ethism = expression of behavior), or sometimes “temporal polyethism” (image from BeeSpotter):
Age polyethism.jpg
This developmental progression in behavior is accompanied by changes in brain structure, patterns of neurotransmitter and hormone synthesis and secretion, and patterns of gene expression in the central nervous system.
Some years ago (as in “more than ten years ago”) Gene Robinson and his students started looking at daily patterns of activity in honeybees. The workers in their early stages are doing jobs inside the hive, where it is always dark. They clean the hive, take care of the eggs and pupae, and feed the larvae and the queen around the clock. Each individual bee sometimes works and sometimes sleeps, without any semblance of a 24-hour pattern. Different individuals work and sleep at different, apparently random times. The hive as a whole is thus constantly busy – there is always a large subset of workers performing their duties, day and night.
As they get older, they start doing the jobs, like being guards, that expose them to the outside of the hive, thus to the light-dark and temperature cycles of the outside world.
Finally, the foragers only go out during the daytime and have clear and distinct daily rhythms. Furthermore, the foragers have to consult an internal clock in order to orient towards the Sun in their travels, as well as to be able to communicate the distance and location of flowers to their mates in the hive using the ‘waggle dance’. As bees are social insects, it is difficult to keep individuals in isolation for longer periods of time, but it has been done successfully and, in such studies, foragers exhibit both freerunning (in constant darkness) and entrained (in light-dark cycles) circadian rhythms, while younger workers do not.
In the Robinson lab, then PhD student Dan Toma and postdoc Guy Bloch did much of the early and exciting work on figuring out how the rhythmicity develops in individual worker bees as they pass through the procession of ‘jobs’.
In an early study, they measured levels of expression of mRNA of the core clock gene Period (Per). The gene was expressed at low levels and no visible daily rhythm in early-stage workers, but at much higher levels and in a circadian fashion in foragers.
As the levels of expression were measured crudely – in entire bee brains – it was impossible at the time to be sure which of the two potential mechanisms were operating: 1) the celluular clock did not work until the bee became a forager, or 2) the cellular clocks were working, but different cells were not synchronized with each other, producing a collectively arrhythmic output: both as measured by gene expression of the entire brain and as measured by behavior of the live bee.
Either way, the study showed correlation: the appearance of the functional circadian clock coincided with other changes in the brain structure, brain chemistry and bee behavior. They could not say at the time what causes what, or even if the syncronicity of changes was purely coincidental. They needed to go beyond correlation and for that they needed to experimentally change the timing to see if various processes can be dissociated or if they are tightly bound to each other.
And there is a clever way to do this! First, they took some hives and removed all the foragers from it. This disrupted the harmony of the division of labor in the hive – too many cleaners and nurses, but nobody is bring the food home. When that happens, the behavioral development of other workers speeds up dramatically – in no time, some nurses and guards develop into foragers. And, lo and behold, the moment they became foragers, they developed rhythms in behavior and rhythms of the Per gene expression in the brain. So, as the development is accelerated, everything about it is accelerated at the same rate: gene expression, brain structure, neurochemistry, and behavioral rhythmicity.
Nice, but then they did something even better. They removed most of the cleaners and nurses from some hives. Again, the balance of the division of labor was disrupted – plenty of food is arriving into the hive but there is not enough bees inside to take care of that food, process it, feed the larvae, etc. What happened then? Well, some of the foragers went back into the hive and started performing the house-keeping duties instead of flying out and about. And, interestingly, their brain structure and chemistry reverted its development to resemble that of cleaners and nurses. They lost behavioral rhythmicity and started working randomly around the clock. And the rhythm of clock-gene expression disappeared as well.
So, genetic, neural, endocrine, circadian and behavioral changes all go together at all times. Social structure of the colony, through the patterns of pheromones present in the hive, affects the gene expression, brain development and function, and behavior of individual bees. Just like the gene expression and behavioral patterns, the patterns of melatonin synthesis and secretion in honeybee brains is low and arrhythmic in young workers and becomes greater and rhythmic in foragers. With the recent sequencing of the honeybee genome, the potential for future research in honeybee chronobiology looks promising and exciting.
But are these findings generalizable or are they specific to honeybees? How about other species of bees or other social insects, like wasps, ants and termites? Are they the same?
Other species of socials insects have been studied in terms of age polyethism as well. The earliest study I am aware of (let me know if there is an older one) studying behavioral rhytmicity in relation to behavioral development was a 2004 Naturwissenschaften paper by Sharma et al. on harvester ants. In that study, different castes of worker ants exhibited different patterns – some were strongly diurnal, some nocturnal, some had strange shifts in period, and some were arrhythmic. Those with rhythms could entrain to light-dark cycles as well as display freerunning rhythms in constant darkness.
Just last month, a new paper on harvester ants came out in BMC Ecology (Open Access). In it, Ingram et al. show that foragers have circadian rhythms (both in constant darkness and entrained to LD cycles) in expression of Period gene (as well as behavioral rhythms), while ants working on tasks inside the hive do not exhibit any rhythms either in clock-gene expression or in behavior, suggesting that the connection between age polyethism and the development of the circadian clock may be a universal property of all social insects.
We know that in humans, night-shift and rotating-shift schedules are bad for health as the body is in the perpetual state of jet-lag: the numerous clocks in our bodies are not synchronized with each other. We have evolved to be diurnal animals, entrained to environmental light cycles and not traveling over many time zones within hours, or working around the clock. Social insects have evolved a different strategy to deal with the potentially ill effects of shift-work: switch off the clock entirely until one develops far enough that time-keeping becomes a requirement.
Yang, L., Qin, Y., Li, X., Song, D., & Qi, M. (2007). Brain melatonin content and polyethism in adult workers of Apis mellifera and Apis cerana (Hym., Apidae) Journal of Applied Entomology, 131 (9-10), 734-739 DOI: 10.1111/j.1439-0418.2007.01229.x
Sharma, V., Lone, S., Goel, A., & Chandrashekaran, M. (2004). Circadian consequences of social organization in the ant species Camponotus compressus Naturwissenschaften, 91 (8) DOI: 10.1007/s00114-004-0544-6
Ingram, K., Krummey, S., & LeRoux, M. (2009). Expression patterns of a circadian clock gene are associated with age-related polyethism in harvester ants, Pogonomyrmex occidentalis BMC Ecology, 9 (1) DOI: 10.1186/1472-6785-9-7

Clock Quotes

The time is near at hand which must determine whether Americans are to be free or to be slaves.
– George Washington

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Clock Quotes

Cats seem to go on the principle that it never does any harm to ask for what you want.
– Joseph Wood Krutch

Open Access. What Open Access? (video)

New and Exciting in PLoS ONE

There are 11 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
To Be or Not to Be a Flatworm: The Acoel Controversy:

Since first described, acoels were considered members of the flatworms (Platyhelminthes). However, no clear synapomorphies among the three large flatworm taxa – the Catenulida, the Acoelomorpha and the Rhabditophora – have been characterized to date. Molecular phylogenies, on the other hand, commonly positioned acoels separate from other flatworms. Accordingly, our own multi-locus phylogenetic analysis using 43 genes and 23 animal species places the acoel flatworm Isodiametra pulchra at the base of all Bilateria, distant from other flatworms. By contrast, novel data on the distribution and proliferation of stem cells and the specific mode of epidermal replacement constitute a strong synapomorphy for the Acoela plus the major group of flatworms, the Rhabditophora. The expression of a piwi-like gene not only in gonadal, but also in adult somatic stem cells is another unique feature among bilaterians. These two independent stem-cell-related characters put the Acoela into the Platyhelminthes-Lophotrochozoa clade and account for the most parsimonious evolutionary explanation of epidermal cell renewal in the Bilateria. Most available multigene analyses produce conflicting results regarding the position of the acoels in the tree of life. Given these phylogenomic conflicts and the contradiction of developmental and morphological data with phylogenomic results, the monophyly of the phylum Platyhelminthes and the position of the Acoela remain unresolved. By these data, both the inclusion of Acoela within Platyhelminthes, and their separation from flatworms as basal bilaterians are well-supported alternatives.

Evolutionary Repercussions of Avian Culling on Host Resistance and Influenza Virulence:

Keeping pandemic influenza at bay is a global health priority. Of particular concern is the continued spread of the influenza subtype H5N1 in avian populations and the increasing frequency of transmission to humans. To decrease this threat, mass culling is the principal strategy for eradicating influenza in avian populations. Although culling has a crucial short-term epidemiological benefit, evolutionary repercussions on reservoir hosts and on the viral population have not been considered. To explore the epidemiological and evolutionary repercussions of mass avian culling, we combine population genetics and epidemiological influenza dynamics in a mathematical model parameterized by clinical, epidemiological, and poultry data. We model the virulence level of influenza and the selection on a dominant allele that confers resistance against influenza [1], [2] in a poultry population. Our findings indicate that culling impedes the evolution of avian host resistance against influenza. On the pathogen side of the coevolutionary race between pathogen and host, culling selects for heightened virulence and transmissibility of influenza. Mass culling achieves a short-term benefit at the expense of long-term detriments: a more genetically susceptible host population, ultimately greater mortality, and elevated influenza virulence.

Odorant-Dependent Generation of Nitric Oxide in Mammalian Olfactory Sensory Neurons:

The gaseous signalling molecule nitric oxide (NO) is involved in various physiological processes including regulation of blood pressure, immunocytotoxicity and neurotransmission. In the mammalian olfactory bulb (OB), NO plays a role in the formation of olfactory memory evoked by pheromones as well as conventional odorants. While NO generated by the neuronal isoform of NO synthase (nNOS) regulates neurogenesis in the olfactory epithelium, NO has not been implicated in olfactory signal transduction. We now show the expression and function of the endothelial isoform of NO synthase (eNOS) in mature olfactory sensory neurons (OSNs) of adult mice. Using NO-sensitive micro electrodes, we show that stimulation liberates NO from isolated wild-type OSNs, but not from OSNs of eNOS deficient mice. Integrated electrophysiological recordings (electro-olfactograms or EOGs) from the olfactory epithelium of these mice show that NO plays a significant role in modulating adaptation. Evidence for the presence of eNOS in mature mammalian OSNs and its involvement in odorant adaptation implicates NO as an important new element involved in olfactory signal transduction. As a diffusible messenger, NO could also have additional functions related to cross adaptation, regeneration, and maintenance of MOE homeostasis.

Cell Lineage of the Ilyanassa Embryo: Evolutionary Acceleration of Regional Differentiation during Early Development:

Cell lineage studies in mollusk embryos have documented numerous variations on the lophotrochozoan theme of spiral cleavage. In the experimentally tractable embryo of the mud snail Ilyanassa, cell lineage has previously been described only up to the 29-cell stage. Here I provide a chronology of cell divisions in Ilyanassa to the stage of 84 cells (about 16 hours after first cleavage at 23°C), and show spatial arrangements of identified nuclei at stages ranging from 27 to 84 cells. During this period the spiral cleavage pattern gives way to a bilaterally symmetric, dorsoventrally polarized pattern of mitotic timing and geometry. At the same time, the mesentoblast cell 4d rapidly proliferates to form twelve cells lying deep to the dorsal ectoderm. The onset of epiboly coincides with a period of mitotic quiescence throughout the ectoderm. As in other gastropod embryos, cell cycle lengths vary widely and predictably according to cell identity, and many of the longest cell cycles occur in small daughters of highly asymmetric divisions. While Ilyanassa shares many features of embryonic cell lineage with two other caenogastropod genera, Crepidula and Bithynia, it is distinguished by a general tendency toward earlier and more pronounced diversification of cell division pattern along axes of later differential growth.

Clock Quotes

One may walk over the highest mountain one step at a time.
– John Wanamaker

My picks from ScienceDaily

Unprecedented Data On Circadian Rhythms Revealed:

Fluctuations in light intensity allow restoring the regularity of circadian rhythms. This is the main conclusion of the work carried out by Javier Buceta, group leader of The.Si.M.Bio.Sys. Group(Theoretical and In Silico Modelling of Biological Systems) from the Co.S.Mo Lab -based at the Barcelona Science Park- and Antoni Díez-Noguera, dean at the Faculty of Pharmacy of the University of Barcelona and group leader of Chronobiology at the Department of Physiology of the said faculty.

Scientists Surprised By Unexpected Emergence Of Periodical Cicadas — Four Years Early:

Periodical cicadas, insects best known for their 17-year long life cycle, are emerging four years early in several Atlantic states. The emergence was first noticed in Greensboro, NC, on Monday and has since been reported in Maryland.
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The cause of these early emergences is unknown, but Kritsky, in a paper to be published in the Proceedings of the Indiana Academy of Science, has found evidence suggesting that mild winters can affect the trees that young cicadas feed upon which in turn interferes with the cicadas’ timekeeping resulting in their emerging early. “This phenomenon might be another biological response to increasing temperatures,” Kritsky said.

‘Gecko Vision’: Key To Future Multifocal Contact Lens?:

Nocturnal geckos are among the very few living creatures able to see colors at night, and scientists’ discovery of series of distinct concentric zones may lead to insight into better cameras and contact lenses. The key to the exceptional night vision of the nocturnal helmet gecko is a series of distinct concentric zones of different refractive powers, according to a new study.

The Open Laboratory 2009 – the submissions so far

OpenLab logo.jpg
Here are the submissions for OpenLab 2009 to date and, as someone who has been through this three times already, I have to say I am impressed both by the number and the quality of submissions to date. And it’s only early May!
As we have surpassed 130 entries, all of them, as well as the “submit” buttons and codes, are under the fold. You can buy the 2006, 2007 and 2008 editions at Lulu.com. Please use the submission form to add more of your and other people’s posts (remember that we are looking for original poems, art, cartoons and comics, as well as essays):

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New and Exciting in PLoS ONE

There are 23 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Does Sleep Really Influence Face Recognition Memory?:

Mounting evidence implicates sleep in the consolidation of various kinds of memories. We investigated the effect of sleep on memory for face identity, a declarative form of memory that is indispensable for nearly all social interaction. In the acquisition phase, observers viewed faces that they were required to remember over a variable retention period (0-36 hours). In the test phase, observers viewed intermixed old and new faces and judged seeing each before. Participants were classified according to acquisition and test times into seven groups. Memory strength (d′) and response bias (c) were evaluated. Substantial time spent awake (12 hours or more) during the retention period impaired face recognition memory evaluated at test, whereas sleep per se during the retention period did little to enhance the memory. Wakefulness during retention also led to a tightening of the decision criterion. Our findings suggest that sleep passively and transiently shelters face recognition memory from waking interference (exposure) but does not actively aid in its long-term consolidation.

Diurnally Entrained Anticipatory Behavior in Archaea:

By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms). The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle. Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature) on O2 diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime.

Hippocampal Lesions Impair Rapid Learning of a Continuous Spatial Alternation Task:

The hippocampus is essential for the formation of memories for events, but the specific features of hippocampal neural activity that support memory formation are not yet understood. The ideal experiment to explore this issue would be to monitor changes in hippocampal neural coding throughout the entire learning process, as subjects acquire and use new episodic memories to guide behavior. Unfortunately, it is not clear whether established hippocampally-dependent learning paradigms are suitable for this kind of experiment. The goal of this study was to determine whether learning of the W-track continuous alternation task depends on the hippocampal formation. We tested six rats with NMDA lesions of the hippocampal formation and four sham-operated controls. Compared to controls, rats with hippocampal lesions made a significantly higher proportion of errors and took significantly longer to reach learning criterion. The effect of hippocampal lesion was not due to a deficit in locomotion or motivation, because rats with hippocampal lesions ran well on a linear track for food reward. Rats with hippocampal lesions also exhibited a pattern of perseverative errors during early task experience suggestive of an inability to suppress behaviors learned during pretraining on a linear track. Our findings establish the W-track continuous alternation task as a hippocampally-dependent learning paradigm which may be useful for identifying changes in the neural representation of spatial sequences and reward contingencies as rats learn and apply new task rules.

Genetic Structure of Europeans: A View from the North-East:

Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (λ) (ranging from 1.00 to 4.21), fixation index (Fst) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).

Quantifying the Risk of Localised Animal Movement Bans for Foot-and-Mouth Disease:

The maintenance of disease-free status from Foot-and-Mouth Disease is of significant socio-economic importance to countries such as the UK. The imposition of bans on the movement of susceptible livestock following the discovery of an outbreak is deemed necessary to prevent the spread of what is a highly contagious disease, but has a significant economic impact on the agricultural community in itself. Here we consider the risk of applying movement restrictions only in localised zones around outbreaks in order to help evaluate how quickly nation-wide restrictions could be lifted after notification. We show, with reference to the 2001 and 2007 UK outbreaks, that it would be practical to implement such a policy provided the basic reproduction ratio of known infected premises can be estimated. It is ultimately up to policy makers and stakeholders to determine the acceptable level of risk, involving a cost benefit analysis of the potential outcomes, but quantifying the risk of spread from different sized zones is a prerequisite for this. The approach outlined is relevant to the determination of control zones and vaccination policies and has the potential to be applied to future outbreaks of other diseases.

Reduced Population Control of an Insect Pest in Managed Willow Monocultures:

There is a general belief that insect outbreak risk is higher in plant monocultures than in natural and more diverse habitats, although empirical studies investigating this relationship are lacking. In this study, using density data collected over seven years at 40 study sites, we compare the temporal population variability of the leaf beetle Phratora vulgatissima between willow plantations and natural willow habitats. The study was conducted in 1999-2005. The density of adult P. vulgatissima was estimated in the spring every year by a knock-down sampling technique. We used two measures of population variability, CV and PV, to compare temporal variations in leaf beetle density between plantation and natural habitat. Relationships between density and variability were also analyzed to discern potential underlying processes behind stability in the two systems. The results showed that the leaf beetle P. vulgatissima had a greater temporal population variability and outbreak risk in willow plantations than in natural willow habitats. We hypothesize that the greater population stability observed in the natural habitat was due to two separate processes operating at different levels of beetle density. First, stable low population equilibrium can be achieved by the relatively high density of generalist predators observed in natural stands. Second, stable equilibrium can also be imposed at higher beetle density due to competition, which occurs through depletion of resources (plant foliage) in the natural habitat. In willow plantations, competition is reduced mainly because plants grow close enough for beetle larvae to move to another plant when foliage is consumed. To our knowledge, this is the first empirical study confirming that insect pest outbreak risk is higher in monocultures. The study suggests that comparative studies of insect population dynamics in different habitats may improve our ability to predict insect pest outbreaks and could facilitate the development of sustainable pest control in managed systems.

Endocrine Activity of Extraembryonic Membranes Extends beyond Placental Amniotes:

During development, all amniotes (mammals, reptiles, and birds) form extraembryonic membranes, which regulate gas and water exchange, remove metabolic wastes, provide shock absorption, and transfer maternally derived nutrients. In viviparous (live-bearing) amniotes, both extraembryonic membranes and maternal uterine tissues contribute to the placenta, an endocrine organ that synthesizes, transports, and metabolizes hormones essential for development. Historically, endocrine properties of the placenta have been viewed as an innovation of placental amniotes. However, an endocrine role of extraembryonic membranes has not been investigated in oviparous (egg-laying) amniotes despite similarities in their basic structure, function, and shared evolutionary ancestry. In this study, we ask whether the oviparous chorioallantoic membrane (CAM) of chicken (Gallus gallus) has the capability to synthesize and receive signaling of progesterone, a major placental steroid hormone. We quantified mRNA expression of key steroidogenic enzymes involved in progesterone synthesis and found that 3β-hydroxysteroid dehydrogenase, which converts pregnenolone to progesterone exhibited a 464 fold increase in the CAM from day 8 to day 18 of embryonic development (F5, 68 = 89.282, p<0.0001). To further investigate progesterone synthesis, we performed explant culture and found that the CAM synthesizes progesterone in vitro in the presence of a steroid precursor. Finally, we quantified mRNA expression and performed protein immunolocalization of the progesterone receptor in the CAM. Collectively, our data indicate that the chick CAM is steroidogenic and has the capability to both synthesize progesterone and receive progesterone signaling. These findings represent a paradigm shift in evolutionary reproductive biology by suggesting that endocrine activity of extraembryonic membranes is not a novel characteristic of placental amniotes. Rather, we hypothesize that these membranes may share an additional unifying characteristic, steroidogenesis, across amniotes at large.

Cyanogenesis of Wild Lima Bean (Phaseolus lunatus L.) Is an Efficient Direct Defence in Nature:

In natural systems plants face a plethora of antagonists and thus have evolved multiple defence strategies. Lima bean (Phaseolus lunatus L.) is a model plant for studies of inducible indirect anti-herbivore defences including the production of volatile organic compounds (VOCs) and extrafloral nectar (EFN). In contrast, studies on direct chemical defence mechanisms as crucial components of lima beans’ defence syndrome under natural conditions are nonexistent. In this study, we focus on the cyanogenic potential (HCNp; concentration of cyanogenic glycosides) as a crucial parameter determining lima beans’ cyanogenesis, i.e. the release of toxic hydrogen cyanide from preformed precursors. Quantitative variability of cyanogenesis in a natural population of wild lima bean in Mexico was significantly correlated with missing leaf area. Since existing correlations do not by necessity mean causal associations, the function of cyanogenesis as efficient plant defence was subsequently analysed in feeding trials. We used natural chrysomelid herbivores and clonal lima beans with known cyanogenic features produced from field-grown mother plants. We show that in addition to extensively investigated indirect defences, cyanogenesis has to be considered as an important direct defensive trait affecting lima beans’ overall defence in nature. Our results indicate the general importance of analysing ‘multiple defence syndromes’ rather than single defence mechanisms in future functional analyses of plant defences.

Today’s carnivals

The latest Skeptic’s Circle is up on Ferret’s Cage
Carnival of the Liberals, Number 90 is up on Quiche Moraine

My picks from ScienceDaily

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Clock Quotes

There are times when fear is good. It must keep its watchful place at the heart’s controls. There is advantage in the wisdom won from pain.
– John Hoyer Updike