Category Archives: Science News

World’s Hottest Chile Pepper Discovered:

Researchers at New Mexico State University recently discovered the world’s hottest chile pepper. Bhut Jolokia, a variety of chile pepper originating in Assam, India, has earned Guiness World Records’ recognition as the world’s hottest chile pepper by blasting past the previous champion Red Savina.

Decoding Effects Of Toxins On Embryo Development Apparent:

Changes in gene expression patterns in zebrafish embryos resulting from exposure to environmental toxins can identify the individual toxins at work, according to research published in the online open access journal Genome Biology. The genetic response of zebrafish to each toxin can be read like a barcode, offering researchers a potential method for identifying the effects of the toxin on developing vertebrate embryos.

‘Nervous’ Birds Take More Risks:

Scientists have shown that birds with higher stress levels adopt bolder behaviour than their normally more relaxed peers in stressful situations. A University of Exeter research team studied zebra finches, which had been selectively bred to produce three distinct types — ‘laid-back’, ‘normal’ and ‘stressed’ — based on their levels of stress hormone. The group was surprised to find that the ‘stressed’ birds were bolder and took more risks in a new environment than the group that was usually more laid-back.

Same-sex Attraction Is Genetically Wired In Nematode’s Brain:

University of Utah biologists genetically manipulated nematode worms so the animals were attracted to worms of the same sex — part of a study that shows sexual orientation is wired in the creatures’ brains.

Secrets Behind Butterfly Wing Patterns Uncovered:

The genes that make a fruit fly’s eyes red also produce red wing patterns in the Heliconius butterfly found in South and Central America, finds a new study by a UC Irvine entomologist.

Ancient DNA Reveals That Some Neanderthals Were Redheads:

Ancient DNA retrieved from the bones of two Neanderthals suggests that at least some of them had red hair and pale skin, scientists report in the journal Science. The international team says that Neanderthals’ pigmentation may even have been as varied as that of modern humans, and that at least 1 percent of Neanderthals were likely redheads.

Colorful View For First Land Animals:

When prehistoric fish made their first forays onto land, what did they see? According to a study published in the online open access journal, BMC Evolutionary Biology, it’s likely that creatures venturing out of the depths viewed their new environment in full colour.

Endangered Wandering Albatross Catches Prey Differently Than Previously Thought:

An international team of scientists has overturned an ecological study on how some animals search for food. Previously it was believed that wandering albatrosses and other species forage using a Lévy flight strategy – a cluster of short moves connected by infrequent longer ones. Published this week in the journal Nature, the team discovered that further analyses and new data tell a different story for the albatrosses and possibly for other species too.

Age Increases Chance Of Success As Two-timer For Coal Tit Males:

Older coal tit males conceive significantly more offspring with a ‘bit’ on the side than younger ones. The coal tit appears to live a strictly monogamous life. Couples often stay together for their whole lives. But researchers found out that’s only a façade. This indigenous songbird is among the top ten two-timers worldwide.

Not ‘Junk DNA’ After All: Tiny RNAs Play Big Role Controlling Genes:

A study by researchers at the Yale Stem Cell Center for the first time demonstrates that piRNAs, a recently discovered class of tiny RNAs, play an important role in controlling gene function.

As always on Fridays, there are new papers published in PLoS Genetics, PLoS Pathogens and PLoS Computational Biology. A few picks – but you go and check them all out:
Surveillance of Arthropod Vector-Borne Infectious Diseases Using Remote Sensing Techniques: A Review:

Kalluri et al. review the status of remote sensing studies of arthropod vectorborne diseases, including simple image classification techniques associating land use and land cover types with vector habitats, and more complex statistical models linking satellite-derived multi-temporal meteorological observations with vector biology and abundance.

Contrasting Infection Strategies in Generalist and Specialist Wasp Parasitoids of Drosophila melanogaster:

The authors use two kinds of wasp venom to compare the benefits and drawbacks of relatively immune suppressive versus relatively immune evasive parasite infection strategies in a natural system.

Copy Number Variants and Common Disorders: Filling the Gaps and Exploring Complexity in Genome-Wide Association Studies:

Xavier Estivill and Lluís Armengol explore the contribution of copy number variants to common human disorders and evaluate the caveats of SNP-based genome-wide association scans in covering regions of the genome that could play an important role in disease susceptibility.

Ten Simple Rules for Doing Your Best Research, According to Hamming:

The thoughts of mathematician Richard Hamming on ‘How to do great science’, presented at the Bell Communications Research Colloquium Seminar in 1986, serve as a preface to the Ten Simple Rules series.

Getting Started in Tiling Microarray Analysis:

In the first article of the new “Getting Started In…” series from the ISCB and PLoS Computational Biology, Dr. Xiaole Shirley Liu introduces tiling microarray analysis. The series provides an essential introductory aid for students and researchers aiming to start out in different areas of bioinformatics, computational biology, and genomics.

Via Russlings (here, here and here so far), information about the effects of San Diego wildfires on the San Diego Zoo:
San Diego zoo ordered closed, Wild Animal park in immediate danger
Fire Update from the Panda Station from a blog by a zoo researcher, and Fire Update from the Wild Animal Park from the Zoo public relations person.
Finally, the oft-updated fire page of the San Diego Zoo blog: October 2007 Fire Updates
Apparently, the zoo was quite threatened, but survived OK and will re-open soon after a big clean-up. Some of the employees were affected by the wildfire, though, and some animals are sheltered indoors during the fire.

Travelling delayed me a little bit, but as you already learned to expect by now, new articles get published on PLoS ONE on Tuesday afternoons. Before I showcase the papers I personally find interesting, first let me remind you to join in the discussion on our ongoing Journal Club on the article Parts, Wholes, and Context in Reading: A Triple Dissociation: read, rate, annotate, comment, blog about and send trackbacks if your software supports them. Now, to this week’s wealth of papers – 24 appeared this week and here are those I like the best:
Analysis of the Trajectory of Drosophila melanogaster in a Circular Open Field Arena:

Studying the neural mechanisms of behavior often requires researchers to accurately follow the movement of a free-living organism over extended periods of time. In this study, Valente and colleagues use a video tracking system to record and describe the behavior and interaction of a single fly walking in an open arena. The methods used in this study may prove valuable for other similar behavioral studies.

Mast Fruiting Is a Frequent Strategy in Woody Species of Eastern South America:

The synchronized production of large seed crops in the tropics is thought to be extremely rare. These authors developed a model for the variability of seed production of 20 climbing vine species and 28 tree species in a Central French Guianan tropical rainforest over a five-year period. Their results reveal that almost a quarter of the species studied showed patterns of synchronized mass seed production, suggesting that the process may encourage species coexistence.

Growth Environment and Sex Differences in Lipids, Body Shape and Diabetes Risk:

This paper reports a cross-sectional study that aims to investigate whether the place of birth and early life environment is associated with ischaemic heart disease (IHD), diabetes and obesity risks in men and women. The results show that differences in early life environment affect IHD risk in men and women differently. Such dichotomies may explain the trends and sex differences in IHD that are seen with economic development.

Different Transcript Patterns in Response to Specialist and Generalist Herbivores in the Wild Arabidopsis Relative Boechera divaricarpa:

Plants defend themselves against herbivorous insects, utilizing both constitutive and inducible defenses. Induced defenses are controlled by several phytohormone-mediated signaling pathways. Here, we analyze transcriptional changes in the North American Arabidopsis relative Boechera divaricarpa in response to larval herbivory by the crucifer specialist lepidopteran Plutella xylostella (diamondback moth) and by the generalist lepidopteran Trichoplusia ni (cabbage semilooper), and compare them to wounding and exogenous phytohormone application.
We use a custom macroarray constructed from B. divaricarpa herbivory-regulated cDNAs identified by suppression subtractive hybridization and from known stress-responsive A. thaliana genes for transcript profiling after insect herbivory, wounding and in response to jasmonate, salicylate and ethylene. In addition, we introduce path analysis as a novel approach to analyze transcript profiles. Path analyses reveal that transcriptional responses to the crucifer specialist P. xylostella are primarily determined by direct effects of the ethylene and salicylate pathways, whereas responses to the generalist T. ni are influenced by the ethylene and jasmonate pathways. Wound-induced transcriptional changes are influenced by all three pathways, with jasmonate having the strongest effect.
Our results show that insect herbivory is distinct from simple mechanical plant damage, and that different lepidopteran herbivores elicit different transcriptional responses.

Horizontal Gene Transfer Regulation in Bacteria as a “Spandrel” of DNA Repair Mechanisms:

Horizontal gene transfer (HGT) is recognized as the major force for bacterial genome evolution. Yet, numerous questions remain about the transferred genes, their function, quantity and frequency. The extent to which genetic transformation by exogenous DNA has occurred over evolutionary time was initially addressed by an in silico approach using the complete genome sequence of the Ralstonia solanacearum GMI1000 strain. Methods based on phylogenetic reconstruction of prokaryote homologous genes families detected 151 genes (13.3%) of foreign origin in the R. solanacearum genome and tentatively identified their bacterial origin. These putative transfers were analyzed in comparison to experimental transformation tests involving 18 different genomic DNA positions in the genome as sites for homologous or homeologous recombination. Significant transformation frequency differences were observed among these positions tested regardless of the overall genomic divergence of the R. solanacearum strains tested as recipients. The genomic positions containing the putative exogenous DNA were not systematically transformed at the highest frequencies. The two genomic “hot spots”, which contain recA and mutS genes, exhibited transformation frequencies from 2 to more than 4 orders of magnitude higher than positions associated with other genes depending on the recipient strain. These results support the notion that the bacterial cell is equipped with active mechanisms to modulate acquisition of new DNA in different genomic positions. Bio-informatics study correlated recombination “hot-spots” to the presence of Chi-like signature sequences with which recombination might be preferentially initiated. The fundamental role of HGT is certainly not limited to the critical impact that the very rare foreign genes acquired mainly by chance can have on the bacterial adaptation potential. The frequency to which HGT with homologous and homeologous DNA happens in the environment might have led the bacteria to hijack DNA repair mechanisms in order to generate genetic diversity without losing too much genomic stability.

Illusory Stimuli Can Be Used to Identify Retinal Blind Spots:

Identification of visual field loss in people with retinal disease is not straightforward as people with eye disease are frequently unaware of substantial deficits in their visual field, as a consequence of perceptual completion (“filling-in”) of affected areas. We attempted to induce a compelling visual illusion known as the induced twinkle after-effect (TwAE) in eight patients with retinal scotomas. Half of these patients experience filling-in of their scotomas such that they are unaware of the presence of their scotoma, and conventional campimetric techniques can not be used to identify their vision loss. The region of the TwAE was compared to microperimetry maps of the retinal lesion. Six of our eight participants experienced the TwAE. This effect occurred in three of the four people who filled-in their scotoma. The boundary of the TwAE showed good agreement with the boundary of lesion, as determined by microperimetry. For the first time, we have determined vision loss by asking patients to report the presence of an illusory percept in blind areas, rather than the absence of a real stimulus. This illusory technique is quick, accurate and not subject to the effects of filling-in.

Ancestral Inference and the Study of Codon Bias Evolution: Implications for Molecular Evolutionary Analyses of the Drosophila melanogaster Subgroup:

Reliable inference of ancestral sequences can be critical to identifying both patterns and causes of molecular evolution. Robustness of ancestral inference is often assumed among closely related species, but tests of this assumption have been limited. Here, we examine the performance of inference methods for data simulated under scenarios of codon bias evolution within the Drosophila melanogaster subgroup. Genome sequence data for multiple, closely related species within this subgroup make it an important system for studying molecular evolutionary genetics. The effects of asymmetric and lineage-specific substitution rates (i.e., varying levels of codon usage bias and departures from equilibrium) on the reliability of ancestral codon usage was investigated. Maximum parsimony inference, which has been widely employed in analyses of Drosophila codon bias evolution, was compared to an approach that attempts to account for uncertainty in ancestral inference by weighting ancestral reconstructions by their posterior probabilities. The latter approach employs maximum likelihood estimation of rate and base composition parameters. For equilibrium and most non-equilibrium scenarios that were investigated, the probabilistic method appears to generate reliable ancestral codon bias inferences for molecular evolutionary studies within the D. melanogaster subgroup. These reconstructions are more reliable than parsimony inference, especially when codon usage is strongly skewed. However, inference biases are considerable for both methods under particular departures from stationarity (i.e., when adaptive evolution is prevalent). Reliability of inference can be sensitive to branch lengths, asymmetry in substitution rates, and the locations and nature of lineage-specific processes within a gene tree. Inference reliability, even among closely related species, can be strongly affected by (potentially unknown) patterns of molecular evolution in lineages ancestral to those of interest.

A New Method to Extract Dental Pulp DNA: Application to Universal Detection of Bacteria:

Dental pulp is used for PCR-based detection of DNA derived from host and bacteremic microorganims. Current protocols require odontology expertise for proper recovery of the dental pulp. Dental pulp specimen exposed to laboratory environment yields contaminants detected using universal 16S rDNA-based detection of bacteria.
We developed a new protocol by encasing decontaminated tooth into sterile resin, extracting DNA into the dental pulp chamber itself and decontaminating PCR reagents by filtration and double restriction enzyme digestion. Application to 16S rDNA-based detection of bacteria in 144 teeth collected in 86 healthy people yielded a unique sequence in only 14 teeth (9.7%) from 12 individuals (14%). Each individual yielded a unique 16S rDNA sequence in 1-2 teeth per individual. Negative controls remained negative. Bacterial identifications were all confirmed by amplification and sequencing of specific rpoB sequence.
The new protocol prevented laboratory contamination of the dental pulp. It allowed the detection of bacteria responsible for dental pulp colonization from blood and periodontal tissue. Only 10% such samples contained 16S rDNA. It provides a new tool for the retrospective diagnostic of bacteremia by allowing the universal detection of bacterial DNA in animal and human, contemporary or ancient tooth. It could be further applied to identification of host DNA in forensic medicine and anthropology.

St. Bernard Study Shows Human-directed Evolution At Work:

The St Bernard dog – named after the 11th century priest Bernard of Menthon – is living proof that evolution does occur, say scientists. Biologists at The University of Manchester say that changes to the shape of the breed’s head over the years can only be explained through human-directed evolution through selective breeding, an artificial version of natural selection.

Humans And Monkeys Share Machiavellian Intelligence:

When it comes to their social behavior, people sometimes act like monkeys, or more specifically, like rhesus macaques, a type of monkey that shares with humans strong tendencies for nepotism and political maneuvering, according to research by Dario Maestripieri, an expert on primate behavior and an Associate Professor in Comparative Human Development and Evolutionary Biology at the University of Chicago.

Critically Endangered Amur Leopard Captured:

A rare Amur leopard (Panthera pardus orientalis), one of only an estimated 30 left in the wild has been captured and health-checked by experts from a consortium of conservation organizations, before being released.

New Light Trap Captures Larval Stage Of New Species; DNA Barcode Technology Used:

When David Jones, a fisheries oceanographer at the Cooperative Institute for Marine and Atmospheric Studies (CIMAS) located at the University of Miami’s Rosenstiel School, set out to design a better light trap to collect young reef fishes, he never imagined his invention would contribute to the discovery of a new species. But, after finding a goby that didn’t quite fit any known description, his catch turned out to be the answer to another scientist’s twenty-five-year-old research conundrum. The larval stage captured in Jones’s new trap was matched to the adult form of a previously unknown species of reef fish by new DNA barcoding technology — which confirmed both were members of a new species.

New articles in PLoS Pathogens, PLoS Computational Biology and PLoS Genetics were published on Friday. My picks for this week are:
Influenza Virus Transmission Is Dependent on Relative Humidity and Temperature:

In temperate regions influenza epidemics recur with marked seasonality: in the northern hemisphere the influenza season spans November to March, while in the southern hemisphere epidemics last from May until September. Although seasonality is one of the most familiar features of influenza, it is also one of the least understood. Indoor crowding during cold weather, seasonal fluctuations in host immune responses, and environmental factors, including relative humidity, temperature, and UV radiation have all been suggested to account for this phenomenon, but none of these hypotheses has been tested directly. Using the guinea pig model, we have evaluated the effects of temperature and relative humidity on influenza virus spread. By housing infected and naïve guinea pigs together in an environmental chamber, we carried out transmission experiments under conditions of controlled temperature and humidity. We found that low relative humidities of 20%-35% were most favorable, while transmission was completely blocked at a high relative humidity of 80%. Furthermore, when guinea pigs were kept at 5 °C, transmission occurred with greater frequency than at 20 °C, while at 30 °C, no transmission was detected. Our data implicate low relative humidities produced by indoor heating and cold temperatures as features of winter that favor influenza virus spread.

Brightness and Darkness as Perceptual Dimensions:

Vision scientists have long adhered to the classic opponent-coding theory of vision, which states that bright-dark, red-green, and blue-yellow form mutually exclusive color pairs. According to this theory, it is not possible to see both brightness and darkness at a single spatial location, or an extended set of locations, such as a uniform surface. One corollary of this statement is that all perceivable grey shades vary along a continuum from bright to dark. At first glance, the notion that brightness and darkness cannot coexist on a single surface accords with our common-sense notion that a given grey shade cannot be simultaneously both brighter and darker than any other grey shade. The results presented here suggest that this common-sense notion is not supported by experimental data. Our results imply that a given grey shade can indeed be simultaneously brighter and darker than another grey shade. This seemingly paradoxical conclusion arises naturally if one assumes that brightness and darkness constitute the dimensions of a two-dimensional perceptual space in which points represent grey shades. Our results may encourage scientists working in related fields to question the assumption that perceptual variables, rather than sensory variables, are encoded in opponent pairs.

Copy Number Variants and Common Disorders: Filling the Gaps and Exploring Complexity in Genome-Wide Association Studies:

Genome-wide association scans (GWASs) using single nucleotide polymorphisms (SNPs) have been completed successfully for several common disorders and have detected over 30 new associations. Considering the large sample sizes and genome-wide SNP coverage of the scans, one might have expected many of the common variants underpinning the genetic component of various disorders to have been identified by now. However, these studies have not evaluated the contribution of other forms of genetic variation, such as structural variation, mainly in the form of copy number variants (CNVs). Known CNVs account for over 15% of the assembled human genome sequence. Since CNVs are not easily tagged by SNPs, might have a wide range of copy number variability, and often fall in genomic regions not well covered by whole-genome arrays or not genotyped by the HapMap project, current GWASs have largely missed the contribution of CNVs to complex disorders. In fact, some CNVs have already been reported to show association with several complex disorders using candidate gene/region approaches, underpinning the importance of regions not investigated in current GWASs. This reveals the need for new generation arrays (some already in the market) and the use of tailored approaches to explore the full dimension of genome variability beyond the single nucleotide scale.

Power Of Altruism Confirmed In Wikipedia Contributions:

The beauty of open-source applications is that they are continually improved and updated by those who use them and care about them. Dartmouth researchers looked at the online encyclopedia Wikipedia to determine if the anonymous, infrequent contributors, the Good Samaritans, are as reliable as the people who update constantly and have a reputation to maintain.

X-effect: Female Chromosome Confirmed A Prime Driver Of Speciation:

Researchers at the University of Rochester believe they have just confirmed a controversial theory of evolution. The X chromosome is a strikingly powerful force in the origin of new species.

Accessory Protein Determines Whether Pheromones Are Detected:

Pheromones are like the molecules you taste as you chomp on a greasy french fry: big and fatty. In research to be published in Nature*, Rockefeller University researchers reveal an unanticipated role for a new CD36-like protein to help cells detect these invisible communication signals that drive a wide range of behaviors, from recognizing a sibling to courting a mate, a finding that may explain what pheromone communication, pathogen recognition and fat taste perception all have in common.

Women More Likely Than Men To Be Affected By Acne As Adults:

While acne is oftentimes as much a part of being a teenager as dating and Friday night football games, a new study examining the prevalence of acne in adults age 20 and older confirms that a significant proportion of adults continue to be plagued by acne well beyond the teenage years. In particular, women experience acne at higher rates than their male counterparts across all age groups 20 years and older.

Sex Hormone Signature Indicates Gender Rather Than Just Chromosomes:

Help with assigning gender could one day be at hand for intersex individuals whose genital phenotypes and sex chromosomes don’t match, thanks to the discovery of a stable sex hormone signature in our cells.

How Singing Bats Communicate:

Bats are the most vocal mammals other than humans, and understanding how they communicate during their nocturnal outings could lead to better treatments for human speech disorders, say researchers at Texas A&M University.

Anne-Marie has more on this story.

Feeling Sleepy Is All In Your Genes:

Genes responsible for our 24 hour body clock influence not only the timing of sleep, but also appear to be central to the actual restorative process of sleep, according to research published in BMC Neuroscience. The study identified changes in the brain that lead to the increased desire and need for sleep during time spent awake.

Cringe at the title. Someone please send me the paper itself…
Level Of Oxytocin In Pregnant Women Predicts Mother-child Bond:

Humans are hard-wired to form enduring bonds with others. One of the primary bonds across the mammalian species is the mother-infant bond. Evolutionarily speaking, it is in a mother’s best interest to foster the well-being of her child; however, some mothers just seem a bit more maternal than others do. Now, new research points to a hormone that predicts the level of bonding between mother and child.

Kate already covered this study expertly.
Modafinil Is Effective In Treating Excessive Sleepiness, Study Suggests:

A study published in the October 15 issue of the Journal of Clinical Sleep Medicine finds that modafinil is well-tolerated in the treatment of excessive sleepiness associated with disorders of sleep and wakefulness such as shift work sleep disorder, obstructive sleep apnea (OSA) and narcolepsy, and does not affect cardiovascular or sleep parameters.

Feminism And Romance Go Hand In Hand:

Contrary to popular opinion, feminism and romance are not incompatible and feminism may actually improve the quality of heterosexual relationships, according to Laurie Rudman and Julie Phelan, from Rutgers University in the US. Their study* also shows that unflattering feminist stereotypes, that tend to stigmatize feminists as unattractive and sexually unappealing, are unsupported.

Pathway Required For Normal Reproductive Development Identified:

Massachusetts General Hospital (MGH) clinical researchers, in collaboration with basic scientists from the University of California, Irvine (UC Irvine) have identified a new molecular pathway required for normal development of the reproductive, olfactory and circadian systems in both humans and mice. In their report to appear in the Proceedings of the National Academy of Sciences, the team describes defects in a gene called PROK2 (prokineticin 2) in human siblings with two different forms of infertility. The UC Irvine team had previously reported that mice lacking PROK2 had abnormal olfactory structures and disrupted circadian rhythm.

I’d like to read this paper as well, please….

Dawn Of Animal Vision Discovered:

By peering deep into evolutionary history, scientists at the University of California, Santa Barbara have discovered the origins of photosensitivity in animals. The scientists studied the aquatic animal Hydra, a member of Cnidaria, which are animals that have existed for hundreds of millions of years. The authors are the first scientists to look at light-receptive genes in cnidarians, an ancient class of animals that includes corals, jellyfish, and sea anemones.

Ecologists Discover City Is ‘Uber-forest’ For Big Owls:

Charlotte has a spooky secret: the North Carolina city is home to a robust population of very large barred owls — a species long-believed by ornithologists to require old growth forest for survival. According to ecologists doing the most extensive field study ever done on the species, the owls see urban life as an upgrade on the old woods, and Charlotteans are not at all creeped out by the big birds that share their yards.

Endangered Wild Ox Given Lifeline:

Twenty years after its discovery in the forested mountains of Vietnam, local authorities here have agreed to establish new nature reserves to protect a critically endangered wild ox.

Some Tropical Birds Depend Completely On Army Ants To Flush Out Prey:

In the jungles of Central and South America, a group of birds has evolved a unique way of finding food — by following hordes of army ants and letting them do all the work.

Bone Structure ‘Vastly Different’ Than Previously Believed:

Researchers have discovered that the structure of human bones is vastly different than previously believed — findings which will have implications for how some debilitating bone disorders are treated.

Ear Infection Superbug Discovered To Be Resistant To All Pediatric Antibiotics:

Researchers have discovered a strain of bacteria resistant to all approved drugs used to fight ear infections in children, according to an article in the Journal of the American Medical Association. A pair of pediatricians discovered the strain because it is their standard practice to perform an uncommon procedure called tympanocentesis (ear tap) on children when several antibiotics fail to clear up their ear infections. The procedure involves puncturing the child’s eardrum and draining fluid to relieve pressure and pain. Analyzing the drained fluid is the only way to describe the bacterial strain causing the infection.

Upper Midwest Forests Are Losing Diversity, Complexity:

Forests in the nation’s Upper Midwest have changed greatly since the time of the early settlers. And more changes may be coming.

Tuna Fishing Fleets In The Pacific Pose Danger To Wildlife At Sea:

Thousands of seabirds and significant numbers of sharks and marine turtles are being caught and killed each year in long-line fishing nets targeting southern bluefin tuna, reveals a new WWF report.

After Drought, Diversity Dries Up And Ponds All Look The Same:

An ecologist at Washington University in St. Louis has discovered that after ponds dry up through drought in a region, when they revive, the community of species in each pond tends to be very similar to one another, like so many suburban houses made of ticky tacky.

Unique Spoon-billed Bird Facing Extinction:

Populations of one of the world’s strangest birds have crashed over the last decade, and surveys this summer of its breeding grounds in the remote Russian province of Chukotka suggest that the situation is now critical. The charismatic, and rather aptly named, Spoon-billed Sandpiper Eurynorhynchus pygmeus, is now worryingly close to becoming extinct. With only 200-300 pairs left, conservationists are calling for urgent help to tackle the decline.

Thirtieth Anniversary Of Discovery Of Third Domain Of Life:

Thirty years ago this month, researchers at the University of Illinois published a discovery that challenged basic assumptions about the broadest classifications of life. Their discovery – which was based on an analysis of ribosomal RNA, an ancient molecule essential to the replication of all cells – opened up a new field of study, and established a first draft of the evolutionary “tree of life.”

There are 21 new articles published tonight on PLoS ONE. As always, read, rate, comment, annotate, volunteer to do a Journal Club, and, if you blog about it, send trackbacks….Here are my picks:
A Televised, Web-Based Randomised Trial of an Herbal Remedy (Valerian) for Insomnia:

To combat the symptoms of insomnia, many people resort to non-prescribed herbal remedies such as valerian. In this randomised trial, the authors recruited 405 participants through a televised Norwegian health program and found only moderately beneficial effects of valerian on people with insomnia. However, the methods used to execute this trial suggest new ways of conducting research to evaluate the effects of health care interventions, and of improving public understanding and use of randomised trials.

Small-Scale Fisheries Bycatch Jeopardizes Endangered Pacific Loggerhead Turtles:

Industrial-scale fisheries are known to cause a decline in the number of large migratory animals through unintended catches. However the impact of smaller fisheries on these animals is poorly known. In this paper, Peckham and colleagues use satellite tracking data to monitor 30 North Pacific loggerhead turtles over a period of 10 years. Their results reveal that small-scale fisheries may be as detrimental to large migratory species as the larger industrial-scale fisheries.

Preventing Establishment: An Inventory of Introduced Plants in Puerto Villamil, Isabela Island, Galapagos:

As part of an island-wide project to identify and eradicate potentially invasive plant species before they become established, a program of inventories is being carried out in the urban and agricultural zones of the four inhabited islands in Galapagos. This study reports the results of the inventory from Puerto Villamil, a coastal village representing the urban zone of Isabela Island. We visited all 1193 village properties to record the presence of the introduced plants. In addition, information was collected from half of the properties to determine evidence for potential invasiveness of the plant species. We recorded 261 vascular taxa, 13 of which were new records for Galapagos. Most of the species were intentionally grown (cultivated) (73.3%) and used principally as ornamentals. The most frequent taxa we encountered were Cocos nucifera (coconut tree) (22.1%) as a cultivated plant and Paspalum vaginatum (salt water couch) (13.2%) as a non cultivated plant. In addition 39 taxa were naturalized. On the basis of the invasiveness study, we recommend five species for eradication (Abutilon dianthum, Datura inoxia, Datura metel, Senna alata and Solanum capsicoides), one species for hybridization studies (Opuntia ficus-indica) and three species for control (Furcraea hexapetala, Leucaena leucocephala and Paspalum vaginatum).

Identification and Classification of Hubs in Brain Networks:

Brain regions in the mammalian cerebral cortex are linked by a complex network of fiber bundles. These inter-regional networks have previously been analyzed in terms of their node degree, structural motif, path length and clustering coefficient distributions. In this paper we focus on the identification and classification of hub regions, which are thought to play pivotal roles in the coordination of information flow. We identify hubs and characterize their network contributions by examining motif fingerprints and centrality indices for all regions within the cerebral cortices of both the cat and the macaque. Motif fingerprints capture the statistics of local connection patterns, while measures of centrality identify regions that lie on many of the shortest paths between parts of the network. Within both cat and macaque networks, we find that a combination of degree, motif participation, betweenness centrality and closeness centrality allows for reliable identification of hub regions, many of which have previously been functionally classified as polysensory or multimodal. We then classify hubs as either provincial (intra-cluster) hubs or connector (inter-cluster) hubs, and proceed to show that lesioning hubs of each type from the network produces opposite effects on the small-world index. Our study presents an approach to the identification and classification of putative hub regions in brain networks on the basis of multiple network attributes and charts potential links between the structural embedding of such regions and their functional roles.

The Origins of Novel Protein Interactions during Animal Opsin Evolution:

Biologists are gaining an increased understanding of the genetic bases of phenotypic change during evolution. Nevertheless, the origins of phenotypes mediated by novel protein-protein interactions remain largely undocumented.
Here we analyze the evolution of opsin visual pigment proteins from the genomes of early branching animals, including a new class of opsins from Cnidaria. We combine these data with existing knowledge of the molecular basis of opsin function in a rigorous phylogenetic framework. We identify adaptive amino acid substitutions in duplicated opsin genes that correlate with a diversification of physiological pathways mediated by different protein-protein interactions.
This study documents how gene duplication events early in the history of animals followed by adaptive structural mutations increased organismal complexity by adding novel protein-protein interactions that underlie different physiological pathways. These pathways are central to vision and other photo-reactive phenotypes in most extant animals. Similar evolutionary processes may have been at work in generating other metazoan sensory systems and other physiological processes mediated by signal transduction.

Kate reviews the latest paper by Ellen Ketterson et al. and since she did it so well, I decided not to do it myself, as it comes too close to my own stuff…
Mountain Top Removal? See why this is not a good idea.
Two conservatives, two views on environmentalism (and no, I will not go into details why I disagree with both of them):
The Embrace of Environmentalism Will Be the Doom of Traditional Religion
Interview with Seymour Garte, Author of Where We Stand
The Mystery of the Sleepy Teenager – pay attention!
Raleigh News & Observer covers the local angle on the story about queen honeybee pheromones.
In the same issue in which it showcased feminist bloggers (including Feministe, Feministing, Pandagon and Echidne of the Snakes), Newsweek also had an article on the 10 hottest nerds, who are supposedly the “10 of the most esteemed biologists” in the world. But, as Jonathan noted, all of them are old, white, rich, politically powerful bosses of big genomics labs. Those are not the revolutionaries for the 21st century as Newsweek says. I can, in a matter of a few seconds, come up with 10 names of brilliant biologists who are young, female or non-white and truly poised to change biology in the 21st century, none of whom work in genomics, and that is just those I have met in person! You add your own names….
The first World Toilet Summit, organized by World Toilet Organization (via Thomas Goetz).

Fish Get Insomnia, Eyes Wide Open, Say Sleep Researchers:

Scientists at the Stanford University School of Medicine have hooked a fish that suffers from insomnia in their quest to understand the genetics behind sleep disorders.

Ugly Duckling Mole Rats Might Hold Key To Longevity:

Who would have thought that the secrets to long life might exist in the naked, wrinkled body of one of the world’s ugliest animals? Probably not many, but current research may be leading seekers of the Fountain of Youth to a strange little beast — the naked mole rat.

Note: I think blind mole rats are beautiful. Stop callin them ‘ugly’!
Deep Sea Discoveries Off Canada’s East Coast:

Researchers from Fisheries and Oceans Canada and Memorial University of Newfoundland took part in an exciting survey of unexplored depths of the Atlantic Ocean during a three-week mission in July 2007. Deep water corals were a primary focus of the research.

Why Do Leaves Change Color In The Fall?:

Many of the colors we see in fall are always present, but normally they’re hidden from view, says UW-Madison Arboretum native plant gardener Susan Carpenter.

Brain Imaging Shows Similarities & Differences In Thoughts Of Chimps And Humans:

In the first study of its kind, researchers at the Yerkes National Primate Research Center, Emory University, used functional brain imaging to assess resting-state brain activity in chimpanzees as a potential window into their mental world and to compare chimpanzee brain activity to that of humans.

Testosterone Turns Male Junco Birds Into Blustery Hunks — And Bad Dads:

The ability to ramp up testosterone production appears to drive male dark-eyed juncos to find and win mates, but it comes with an evolutionary cost. Big fluctuations in testosterone may also cause males to lose interest in parenting their own young, scientists have learned.

Blind To Beauty: How And Where Do We Process Attractiveness?:

Beauty may be in the eye of the beholder, but according to research conducted by a UBC medical student, eye candy fails to find a sweet tooth in patients with a rare disorder.

After Drought, Diversity Dries Up And Ponds All Look The Same:

An ecologist at Washington University in St. Louis has discovered that after ponds dry up through drought in a region, when they revive, the community of species in each pond tends to be very similar to one another, like so many suburban houses made of ticky tacky.

A Gene Divided Reveals The Details Of Natural Selection:

In a molecular tour de force, researchers at the University of Wisconsin-Madison have provided an exquisitely detailed picture of natural selection as it occurs at the genetic level.

Monday – the day for checking in PLoS Biology and PLoS Medicine for the newest published articles. And there is some good stuff:
Characterization of Sleep in Zebrafish and Insomnia in Hypocretin Receptor Mutants

Sleep disorders are common and poorly understood. Further, how and why the brain generates sleep is the object of intense speculations. In this study, we demonstrate that a bony fish used for genetic studies sleeps and that a molecule, hypocretin, involved in causing narcolepsy, is conserved. In humans, narcolepsy is a sleep disorder associated with sleepiness, abnormal dreaming, and paralysis and insomnia. We generated a mutant fish in which the hypocretin system was disrupted. Intriguingly, this fish sleep mutant does not display sleepiness or paralysis but has a 30% reduction of its sleep time at night and a 60% decrease in sleep bout length compared with non-mutant fish. We also studied the relationships between the hypocretin system and other sleep regulatory brain systems in zebrafish and found differences in expression patterns in the brain that may explain the differences in behavior. Our study illustrates how a sleep regulatory system may have evolved across vertebrate phylogeny. Zebrafish, a powerful genetic model that has the advantage of transparency to study neuronal networks in vivo, can be used to study sleep.

Also check the accompanying synopsis: Let Sleeping Zebrafish Lie: A New Model for Sleep Studies:

Although the function of sleep is hotly debated, one thing is clear–we, and most other animals, cannot do without it. In a new study, Yokogawa et al. describe how zebrafish sleep, finding both striking similarities to mammalian sleep and its regulation and intriguing differences.

Also, on the 4th birthday of PLoS Biology, a good editorial: When Is Open Access Not Open Access?

Since 2003, when PLoS Biology was launched, there has been a spectacular growth in “open-access” journals. The Directory of Open Access Journals (http://www.doaj.org/), hosted by Lund University Libraries, lists 2,816 open-access journals as this article goes to press (and probably more by the time you read this). Authors also have various “open-access” options within existing subscription journals offered by traditional publishers (e.g., Blackwell, Springer, Oxford University Press, and many others). In return for a fee to the publisher, an author’s individual article is made freely available and (sometimes) deposited in PubMed Central (PMC). But, as open access grows in prominence, so too has confusion about what open access means, particularly with regard to unrestricted use of content–which true open access allows. This confusion is being promulgated by journal publishers at the expense of authors and funding agencies wanting to support open access.

And check these two important articles on observatinal studies in epidemiology:
The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement: Guidelines for Reporting Observational Studies
Strengthening the Reporting of Observational Studies in Epidemiology (STROBE): Explanation and Elaboration

Humans Perceive Others’ Fear Faster Than Other Emotions:

You may not be fully dressed without a smile, but a look of horror will make a faster first impression. Vanderbilt University researchers have discovered that the brain becomes aware of fearful faces more quickly than those showing other emotions.

Pasturing Cows Convert Soil To A Source Of Methane, Potent Greenhouse Gas:

The cow as a killer of the climate: This inglorious role of our four-legged friends, peaceful in itself, is well-enough recognised, because, with their digestion, the animals produce methane, which is expelled continuously. Now, however, a team of German scientists from the Institute of Soil Ecology of the GSF – National Research Center for Environment and Health (Helmholtz Association of German Research Centres) and Czech colleagues at the Budweis Academy of Science have been able to show that bovine animals can also boost the production of this climate gas in soil.

Portable Diagnostic System For Foot-and-mouth Disease And Avian Flu Designed:

Smiths Detection is to launch a portable detection system that will enable veterinarians to carry out on-site diagnosis of animal diseases such as foot-and-mouth and avian flu. This new technology means vets will be able to diagnose diseases in livestock and birds in the field in less than 90 minutes rather than having to send samples for laboratory analysis.

Red Wine And Grape Juice Help Defend Against Food-borne Diseases, Study Suggests:

Red wine is known to have multiple health benefits. Researchers at the University of Missouri-Columbia have found that red wine may also protect humans from common food-borne diseases.

Want Antioxidants? Have You Eaten Micro-algae Lately?:

Some consumers want more than just their traditional nourishment requirements met. Micro-algae (eaten by humans in pre-Columbian America) are more than just nutritive. Spirulina microalgae could be a good source of antioxidants due to the presence of carotenoids deriving from chlorophyll, and provide bacterial growth inhibiting action because of certain fatty acids. Microalgae have turned out to be a potential alternative to the use of synthetic sources for these ingredients.

Buying And Selling Habitats To Help Wildlife:

Tradable permits are all the rage in environmental policy. They are already used internationally to reduce carbon emissions and improve air quality. A group of economists and ecologists from the UK, the Netherlands and Germany, are working together to find out whether such schemes could work for wildlife too. So far, it looks promising, but probably only for cultural landscapes like farmland.

As always on Fridays, there are new articles published in PLoS Computational Biology, PLoS Genetics and PLoS Pathogens. Look around to see what’s new. My pick for this week:
Inconsistencies in Neanderthal Genomic DNA Sequences:

One of the enduring questions in human evolution is the relationship of fossil groups, such as Neanderthals, with people alive today. Were Neanderthals direct ancestors of contemporary humans or an evolutionary side branch that eventually died out? Two recent papers describing the sequencing of Neanderthal nuclear DNA from fossil bone held promise for finally answering this question. However, the two studies came to very different conclusions regarding the ancestral role of Neanderthals. In this paper, we reanalyzed the data from the two original studies. We found that the two studies are inconsistent with each other, which implies that the data from at least one of the studies is probably incorrect. The likely culprit is contamination with modern human DNA, which we believe compromised the findings of one of the original Neanderthal DNA studies.

New Hearing Mechanism Discovered:

MIT researchers have discovered a hearing mechanism that fundamentally changes the current understanding of inner ear function. This new mechanism could help explain the ear’s remarkable ability to sense and discriminate sounds. Its discovery could eventually lead to improved systems for restoring hearing.

People Are Programmed To Love Chocolate, Study Finds:

For the first time, scientists have linked the all-too-human preference for a food — chocolate — to a specific, chemical signature that may be programmed into the metabolic system and is detectable by laboratory tests. The signature reads ‘chocolate lover’ in some people and indifference to the popular sweet in others, the researchers say.

Green Algae: The Nexus Of Plant-Animal Ancestry:

Genes of a tiny, single-celled green alga called Chlamydomonas reinhardtii may contain scores more data about the common ancestry of plants and animals than the richest paleontological dig. This work is described in an article in Science.

Frozen Sperm Worked For White Rhino:

Scientists from the Leibniz Institute for Zoo and Wildlife Research in Berlin successfully inseminated a rhino with formerly frozen sperm. This world-first artificial insemination of a white rhino with frozen rhino sperm took place in Budapest Zoo.

Spread Of Endogenous Retrovirus K Is Similar In The DNA Of Humans And Rhesus Monkeys:

According to paleontologic and molecular studies, the chimpanzee (Pan troglodytes) is the closer relative to the humans (Homo sapiens) and that both lineages had a common ancestor at 5 to 7 million years ago.

Benefits Of 80 Million Years Without Sex:

Scientists have discovered how a microscopic organism has benefited from nearly 80 million years without sex. Bdelloid rotifers are asexual organisms, meaning that they reproduce without males. Without sex, these animals lack many of the ways in which sexual animals adapt over generations to survive in their natural environment.

Herding Aphids: How ‘Farmer’ Ants Keep Control Of Their Food:

Chemicals on ants’ feet tranquilise and subdue colonies of aphids, keeping them close-by as a ready source of food, says new research. The study throws new light on the complex relationship between ants and the colonies of aphids whose sugary secretions the ants eat.

Discovery Of Retinal Cell Type Ends 40-year Search:

A research team combining high-energy physicists from the University of California, Santa Cruz, and neuroscientists from the Salk Institute in La Jolla, Calif., has discovered a type of retinal cell that may help monkeys, apes, and humans see motion.

Ticks Don’t Come Out In The Wash:

Before venturing into tick-infested territory, you used a topical repellent on exposed skin and outer clothing. When you returned, you did a body check and threw your clothes in the wash. But clean clothes may not be tick-free clothes. When he found a live lone star tick (Amblyomma americanum) on the agitator of his washing machine, Agricultural Research Service (ARS) entomologist John Carroll decided to find out how tough ticks are. So he bagged up nymphs from two species–the lone star tick and the deer tick, (Ixodes scapularis), the creature that transmits Lyme disease–and put them in the washing machine.

In Biology, Polarization Is A Good Thing:

Using a molecular cellular compass, individual cells in complex organisms know which way is up or down, in epithelial cells known as apical-basal polarity. Determining the orientation is essential for an individual cell to perform it’s designated tasks. Now it appears that the same compass also defines the direction of cells when migrating by establishing a morphological back and a front.

Tiny Crow Camera Spies On Clever Birds:

A new technique developed by Oxford University zoologists enables researchers to ‘hitch a ride’ with wild birds and witness their natural and undisturbed behaviour. The scientists developed miniaturised video cameras with integrated radio-tags that can be carried by wild, free-flying birds. Using this new ‘video-tracking’ technology, they spied on the behaviour of New Caledonian crows, a species renowned for its sophisticated use of tools, recording behaviours never seen before.

Diet With A Little Meat Uses Less Land Than Many Vegetarian Diets:

A low-fat vegetarian diet is very efficient in terms of how much land is needed to support it. But adding some dairy products and a limited amount of meat may actually increase this efficiency, Cornell researchers suggest.

Early Apes Walked Upright 15 Million Years Earlier Than Previously Thought, Evolutionary Biologist Argues:

An extraordinary advance in human origins research reveals evidence of the emergence of the upright human body plan over 15 million years earlier than most experts have believed. More dramatically, the study confirms preliminary evidence that many early hominoid apes were most likely upright bipedal walkers sharing the basic body form of modern humans.

Difference Between Fish And Humans: Century-old Developmental Question Answered:

Embryologists at UCL (University College London) have helped solve an evolutionary riddle that has been puzzling scientists for over a century. They have identified a key mechanism in the initial stages of an embryo’s development that helps differentiate more highly evolved species, including humans, from less evolved species, such as fish. The findings of the research, funded by the Biotechnology and Biological Sciences Research Council (BBSRC), were published online by the journal Nature.

As usual on Tuesday nights, lots of cool stuff got published on PLoS ONE today. Here are some of my picks, but you should check all 30 of them (so, this week I am correct – there are now 1000+ articles on PLoS ONE):
Large-Scale Mitochondrial DNA Analysis of the Domestic Goat Reveals Six Haplogroups with High Diversity:

Studying the genetic diversity of domesticated animals can provide insights into their domestication, and even the history of human migration. In this paper Pompanon and colleagues study mitochondrial DNA diversity of the domestic goat from 2430 animals from widespread Old World geographic origins. The researchers find a very high degree of mitochondrial diversity amongst goats, but suggest that even with such a large dataset, little can be concluded about the origin of goat domestication.

The Environmental Dependence of Inbreeding Depression in a Wild Bird Population:

Evolutionary genetic theory suggests that if related individuals breed, their offspring are likely to be less “fit” (or evolutionarily successful) than outbred offspring, because of the increased chance of inheriting two copies of a harmful recessive gene. The authors of this paper analysed the interaction between environment and inbreeding on individual fitness in a population of great tits. Their results suggest that in wild populations, the interaction between inbreeding and environment on fitness may be considerable.

Wnt and TGF-β Expression in the Sponge Amphimedon queenslandica and the Origin of Metazoan Embryonic Patterning:

The origin of metazoan development and differentiation was contingent upon the evolution of cell adhesion, communication and cooperation mechanisms. While components of many of the major cell signalling pathways have been identified in a range of sponges (phylum Porifera), their roles in development have not been investigated and remain largely unknown. Here, we take the first steps toward reconstructing the developmental signalling systems used in the last common ancestor to living sponges and eumetazoans by studying the expression of genes encoding Wnt and TGF-β signalling ligands during the embryonic development of a sponge.
Using resources generated in the recent sponge Amphimedon queenslandica (Demospongiae) genome project, we have recovered genes encoding Wnt and TGF-β signalling ligands that are critical in patterning metazoan embryos. Both genes are expressed from the earliest stages of Amphimedon embryonic development in highly dynamic patterns. At the time when the Amphimedon embryos begin to display anterior-posterior polarity, Wnt expression becomes localised to the posterior pole and this expression continues until the swimming larva stage. In contrast, TGF-β expression is highest at the anterior pole. As in complex animals, sponge Wnt and TGF-β expression patterns intersect later in development during the patterning of a sub-community of cells that form a simple tissue-like structure, the pigment ring. Throughout development, Wnt and TGF-β are expressed radially along the anterior-posterior axis.
We infer from the expression of Wnt and TGF-β in Amphimedon that the ancestor that gave rise to sponges, cnidarians and bilaterians had already evolved the capacity to direct the formation of relatively sophisticated body plans, with axes and tissues. The radially symmetrical expression patterns of Wnt and TGF-β along the anterior-posterior axis of sponge embryos and larvae suggest that these signalling pathways contributed to establishing axial polarity in the very first metazoans.

Maladaptation and the Paradox of Robustness in Evolution:

Organisms use a variety of mechanisms to protect themselves against perturbations. For example, repair mechanisms fix damage, feedback loops keep homeostatic systems at their setpoints, and biochemical filters distinguish signal from noise. Such buffering mechanisms are often discussed in terms of robustness, which may be measured by reduced sensitivity of performance to perturbations.
I use a mathematical model to analyze the evolutionary dynamics of robustness in order to understand aspects of organismal design by natural selection. I focus on two characters: one character performs an adaptive task; the other character buffers the performance of the first character against perturbations. Increased perturbations favor enhanced buffering and robustness, which in turn decreases sensitivity and reduces the intensity of natural selection on the adaptive character. Reduced selective pressure on the adaptive character often leads to a less costly, lower performance trait.
The paradox of robustness arises from evolutionary dynamics: enhanced robustness causes an evolutionary reduction in the adaptive performance of the target character, leading to a degree of maladaptation compared to what could be achieved by natural selection in the absence of robustness mechanisms. Over evolutionary time, buffering traits may become layered on top of each other, while the underlying adaptive traits become replaced by cheaper, lower performance components. The paradox of robustness has widespread implications for understanding organismal design.

Homeotic Evolution in the Mammalia: Diversification of Therian Axial Seriation and the Morphogenetic Basis of Human Origins:

Despite the rising interest in homeotic genes, little has been known about the course and pattern of evolution of homeotic traits across the mammalian radiation. An array of emerging and diversifying homeotic gradients revealed by this study appear to generate new body plans and drive evolution at a large scale.
This study identifies and evaluates a set of homeotic gradients across 250 extant and fossil mammalian species and their antecedents over a period of 220 million years. These traits are generally expressed as co-linear gradients along the body axis rather than as distinct segmental identities. Relative position or occurrence sequence vary independently and are subject to polarity reversal and mirroring. Five major gradient modification sets are identified: (1)-quantitative changes of primary segmental identity pattern that appeared at the origin of the tetrapods ; (2)-frame shift relation of costal and vertebral identity which diversifies from the time of amniote origins; (3)-duplication, mirroring, splitting and diversification of the neomorphic laminar process first commencing at the dawn of mammals; (4)-emergence of homologically variable lumbar lateral processes upon commencement of the radiation of therian mammals and ; (5)-inflexions and transpositions of the relative position of the horizontal septum of the body and the neuraxis at the emergence of various orders of therian mammals. Convergent functional changes under homeotic control include laminar articular engagement with septo-neural transposition and ventrally arrayed lumbar transverse process support systems.
Clusters of homeotic transformations mark the emergence point of mammals in the Triassic and the radiation of therians in the Cretaceous. A cluster of homeotic changes in the Miocene hominoid Morotopithecus that are still seen in humans supports establishment of a new “hominiform” clade and suggests a homeotic origin for the human upright body plan.

Nullomers: Really a Matter of Natural Selection?:

Nullomers are short DNA sequences that are absent from the genomes of humans and other species. Assuming that nullomers are the signatures of natural selection against deleterious sequences in humans, the use of nullomers in drug target identification, pesticide development, environmental monitoring, and forensic applications has been envisioned.
Here, we show that the hypermutability of CpG dinucleotides, rather than the natural selection against the nullomer sequences, is likely the reason for the phenomenal event of short sequence motifs becoming nullomers. Furthermore, many reported human nullomers differ by only one nucleotide, which reinforces the role of mutation in the evolution of the constellation of nullomers in populations and species. The known nullomers in chimpanzee, cow, dog, and mouse genomes show patterns that are consistent with those seen in humans.
The role of mutations, instead of selection, in generating nullomers cast doubt on the utility of nullomers in many envisioned applications, because of their dependence on the role of lethal selection on the origin of nullomers.

Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys:

We detected 19 complete endogenous retroviruses of the K family in the genome of rhesus monkey (Macaca mulatta; RhERV-K) and 12 full length elements in the genome of the common chimpanzee (Pan troglodytes; CERV-K). These sequences were compared with 55 human HERV-K and 20 CERV-K reported previously, producing a total data set of 106 full-length ERV-K genomes. Overall, 61% of the human elements compared to 21% of the chimpanzee and 47% of rhesus elements had estimated integration times less than 4.5 million years before present (MYBP), with an average integration times of 7.8 MYBP, 13.4 MYBP and 10.3 MYBP for HERV-K, CERV-K and RhERV-K, respectively. By excluding those ERV-K sequences generated by chromosomal duplication, we used 63 of the 106 elements to compare the population dynamics of ERV-K among species. This analysis indicated that both HERV-K and RhERV-K had similar demographic histories, including markedly smaller effective population sizes, compared to CERV-K. We propose that these differing ERV-K dynamics reflect underlying differences in the evolutionary ecology of the host species, such that host ecology and demography represent important determinants of ERV-K dynamics.

SIRNA-Directed In Vivo Silencing of Androgen Receptor Inhibits the Growth of Castration-Resistant Prostate Carcinomas:

Prostate carcinomas are initially dependent on androgens, and castration or androgen antagonists inhibit their growth. After some time though, tumors become resistant and recur with a poor prognosis. The majority of resistant tumors still expresses a functional androgen receptor (AR), frequently amplified or mutated.
To test the hypothesis that AR is not only expressed, but is still a key therapeutic target in advanced carcinomas, we injected siRNA targeting AR into mice bearing exponentially growing castration-resistant tumors. Quantification of siRNA into tumors and mouse tissues demonstrated their efficient uptake. This uptake silenced AR in the prostate, testes and tumors. AR silencing in tumors strongly inhibited their growth, and importantly, also markedly repressed the VEGF production and angiogenesis.
Our results demonstrate that carcinomas resistant to hormonal manipulations still depend on the expression of the androgen receptor for their development in vivo. The siRNA-directed silencing of AR, which allows targeting overexpressed as well as mutated isoforms, triggers a strong antitumoral and antiangiogenic effect. siRNA-directed silencing of this key gene in advanced and resistant prostate tumors opens promising new therapeutic perspectives and tools.

Implementing Routine HIV Testing: The Role of State Law:

In September 2006, the Centers for Disease Control and Prevention (CDC) recommended routine HIV testing for all Americans aged 13-64, which would eliminate requirements for written consent and pretest counseling as previously required. However, this approach may conflict with state requirements concerning pretest counseling and informed consent for HIV testing. Our survey of state HIV testing laws demonstrates that the majority of states have HIV testing requirements that are inconsistent with the CDC’s recommendations. Moreover, states that have recently amended their laws have not eased the requirements for pretest counseling and informed consent. The reasons for the persistence of these legal requirements must be understood to effect policy changes to increase HIV testing.

Moderate Neonatal Stress Decreases Within-Group Variation in Behavioral, Immune and HPA Responses in Adult Mice:

The significance of behavioral neuroscience and the validity of its animal models of human pathology largely depend on the possibility to replicate a given finding across different laboratories. Under the present test and housing conditions, this axiom fails to resist the challenge of experimental validation. When several mouse strains are tested on highly standardized behavioral test batteries in different laboratories, significant strain×lab interactions are often detected. This limitation, predominantly due to elevated within-group variability observed in control subjects, increases the number of animals needed to address fine experimental questions. Laboratory rodents display abnormal stress and fear reactions to experimental testing, which might depend on the discrepancy between the stability of the neonatal environment and the challenging nature of the adult test and housing conditions.
Stimulating neonatal environments (e.g. brief maternal separations, increased foraging demands or maternal corticosterone supplementation) reduce stress and fear responses in adulthood. Here we tested whether reduced fearfulness associated with experimental testing would also reduce inter-individual variation. In line with our predictions, we show that a moderate elevation in neonatal corticosterone through maternal milk significantly reduces fear responses and inter-individual variability (average 44%) in adult mouse offspring.
We observed reduced variation in pain perception, novelty preference, hormonal stress response and resistance to pathogen infection. This suggests that the results of this study may apply to a relatively broad spectrum of neuro-behavioral domains. Present findings encourage a reconsideration of the basic principles of neonatal housing systems to improve the validity of experimental models and reduce the number of animals used.

Adaptive Evolution of a Stress Response Protein:

Some cancers are mediated by an interplay between tissue damage, pathogens and localised innate immune responses, but the mechanisms that underlie these linkages are only beginning to be unravelled.
Here we identify a strong signature of adaptive evolution on the DNA sequence of the mammalian stress response gene SEP53, a member of the epidermal differentiation complex fused-gene family known for its role in suppressing cancers. The SEP53 gene appears to have been subject to adaptive evolution of a type that is commonly (though not exclusively) associated with coevolutionary arms races. A similar pattern of molecular evolution was not evident in the p53 cancer-suppressing gene.
Our data thus raises the possibility that SEP53 is a component of the mucosal/epithelial innate immune response engaged in an ongoing interaction with a pathogen. Although the pathogenic stress mediating adaptive evolution of SEP53 is not known, there are a number of well-known candidates, in particular viruses with established links to carcinoma.

Habitat Fragmentation, Variable Edge Effects, and the Landscape-Divergence Hypothesis:

Edge effects are major drivers of change in many fragmented landscapes, but are often highly variable in space and time. Here we assess variability in edge effects altering Amazon forest dynamics, plant community composition, invading species, and carbon storage, in the world’s largest and longest-running experimental study of habitat fragmentation. Despite detailed knowledge of local landscape conditions, spatial variability in edge effects was only partially foreseeable: relatively predictable effects were caused by the differing proximity of plots to forest edge and varying matrix vegetation, but windstorms generated much random variability. Temporal variability in edge phenomena was also only partially predictable: forest dynamics varied somewhat with fragment age, but also fluctuated markedly over time, evidently because of sporadic droughts and windstorms. Given the acute sensitivity of habitat fragments to local landscape and weather dynamics, we predict that fragments within the same landscape will tend to converge in species composition, whereas those in different landscapes will diverge in composition. This ‘landscape-divergence hypothesis’, if generally valid, will have key implications for biodiversity-conservation strategies and for understanding the dynamics of fragmented ecosystems.

As always, look around, read the articles, rate them, post comments and annotations, send trackbacks if you blog about them, and if you want to do a Journal Club on one of them, let me know.

A newspaper should hire me to be that guy whose only job is to write titles and headlines. I can make them as misleading and sensationalist as the best of ’em!
But really, this year’s Nobel Prize for Physics is going to Albert Fert and Peter Grunberg for the invention of Giant Magnetoresistance. And yes, one of the many thingamajigs that uses this technology is iPod. But it makes for such a cool headline….

Why Are Huge Numbers Of Camels Dying In Africa And Saudi Arabia?:

More than 2000 dromedaries — Arabian camels — have died since August 10 in Saudi Arabia. Various theories have been put forward to explain the numerous deaths. For several years, the Sahel and the Horn of Africa have also seen similar numbers of deaths. In 1995-1996, CIRAD worked on a fatal epizootic disease affecting dromedaries in Ethiopia.

Humans Unknowing Midwives For Pregnant Moose:

When it’s time for moose to give birth in the Greater Yellowstone Ecosystem, they head to where it is safest from predators — namely closer to people, according to a new study by the Wildlife Conservation Society. Published in the Royal Society’s journal Biology Letters, the study says that moose avoid predation of their calves by grizzly bears by moving closer to roads and other infrastructure prior to giving birth.

Ancient African Megadroughts May Have Driven Human Evolution — Out Of Africa:

From 135,000 to 90,000 years ago tropical Africa had megadroughts more extreme and widespread than any previously known for that region, according to new research.

Chronic Arguing With Your Spouse May Raise Your Heart Disease Risk:

Individuals whose close relationships have negative aspects, such as conflict and adverse exchanges, appear to have an increased risk of heart disease than those with more positive close relationships, according to a new report.

Genetic Dissection of Behavioural and Autonomic Effects of Δ9-Tetrahydrocannabinol in Mice and the accompanying editorial Understanding Cannabinoid Psychoactivity with Mouse Genetic Models:

The fact that cannabis is the most widely used illicit drug has motivated a great deal of research aimed at understanding how it produces its psychoactive effects. Here I use the term psychoactive to describe the mild euphoria, altered perceptions, sense of relaxation, and sociability that often, but not always, accompany recreational cannabis use. Despite the difficulties inherent in working with lipophilic cannabinoids such as Δ9-tetrahydrocannabinol (THC), which is the primary psychoactive component of cannabis, our understanding of the mechanism of action of these compounds at the cellular level has increased dramatically over the past 20 years. However, a complete understanding of how cannabis elicits its psychoactive effects would include an appreciation of its actions at the cellular and network level as well as an identification of the neural circuits perturbed. The cannabinoid field has now matured to the point where investigators can begin to relate the cellular mechanisms of THC action to the behavioral effects of cannabis.

HCV-HIV Coinfection: Simple Messages from a Complex Disease:

Hepatitis C virus (HCV) and HIV infection are both major global health problems, each with their own specific unsolved and difficult issues of prevention, pathogenesis, and therapy. For HIV, many of the clinical problems experienced are related to loss of immunological control over relatively commonly encountered pathogens. In most of these cases (e.g., cytomegalovirus [CMV], Pneumocystis jiroveci. human herpesvirus-8), normal immunological control is quite efficient, and these organisms behave as “opportunists.” HCV is slightly different, in that immunological control in normal HIV-uninfected individuals is often poor, and HCV infection alone can lead to the gradual evolution of end-stage liver disease in normal hosts. However, although a consensus is forming about the basic details of the immune responses associated with acute control of HCV monoinfection, the long-term relationships between immune responses, viral load, and most importantly, disease progression in those who are persistently infected are still poorly understood.

Genes From The Father Facilitate The Formation Of New Species:

The two closely related bird species, the collared flycatcher and the pied flycatcher, can reproduce with each other, but the females are more strongly attracted to a male of their own species. This has been shown by an international research team directed by Anna Qvarnström at Uppsala University and published in Science. They demonstrate that the gene for this sexual preference is found on the sex chromosome that is inherited from the father and that only females have a copy of. The discovery sheds new light on how new species are formed.

Primitive Plants Use Heat And Odor To Woo Pollinating Insects:

University of Utah scientists discovered a strange method of reproduction in primitive plants named cycads: The plants heat up and emit a toxic odor to drive pollen-covered insects out of male cycad cones, and then use a milder odor to draw the bugs into female cones so the plants are pollinated.

When Taking A Long Time Is Seen As A Good Thing:

Consumers often use the length of time a service takes as a measure of its quality. The longer a session lasts, the better the value. Indeed, a new study shows that this holds true even when judging something primarily by its duration can backfire — for example when a longer exercise program is actually less effective than a shorter regimen or for a lock-picking service.

Brain Images Make Cognitive Research More Believable:

People are more likely to believe findings from a neuroscience study when the report is paired with a colored image of a brain as opposed to other representational images of data such as bar graphs, according to a new Colorado State University study.

New Insights Into The Evolution Of The Human Genome:

Which came first, the chicken genome or the egg genome? Researchers have answered a similarly vexing (and far more relevant) genomic question: Which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates?

Elephants’ Fear Of Angry Bees Could Help To Protect Them:

At a time when encroaching human development in former wildlife areas has compressed African elephants into ever smaller home ranges and increased levels of human-elephant conflict, a study in Current Biology, suggests that strategically placed beehives might offer a low-tech elephant deterrent and conservation measure.

Malaria Research Booming, But Scientific And Technical Gaps Apparent, Report Shows:

Malaria drug and vaccine research is booming. According to a new report launched in the UK by Australian researchers at The George Institute for International Health, 16 new malaria vaccine candidates are now in clinical trials; six new malaria drugs are about to reach the market; and by 2011 we will have up to 12 new anti-malarial drug product registered. However, this unprecedented level of malaria R&D activity is not necessarily all good news. The report’s authors found that the high number of malaria vaccine candidates was the result of scientific and technical gaps and lacking policy coordination rather than a reflection of cohesive global activity. Lack of coordination and planning mean that invested funding and efforts are not delivering as much as they should, and may be costing donors tens of millions of dollars.

How Do Cells Sense And Respond To Messages? Major Signal Transduction Discovery Made:

The chemical process known as acetylation plays a central role in cytokine receptor signal transduction – a fundamental biochemical cascade inside cells that controls the activity of antiviral and tumor-suppressing genes.

In Birds, Expecting To Mate Leads To Higher Fertilization Rates:

From an evolutionary perspective, the primary task of an organism is to pass along its genes to future generations. Such genetic transmission is usually assumed to be instinctive. However, a new study shows that species also learn to adapt to their surroundings in order to increase their “reproductive fitness”– the likelihood that they will successfully reproduce.

For Honey Bee Queens, Multiple Mating Makes Her Attractive To Workers:

The success of the “reign” of a honey bee queen appears to be determined to a large degree by the number of times she mates with drone bees.That is what research by scientists in the Department of Entomology and W.M. Keck Center for Behavioral Biology at North Carolina State University suggests. Dr. Freddie-Jeanne Richard, a post-doctoral research associate; Dr. David Tarpy, assistant professor and North Carolina Cooperative Extension apiculturist; and Dr. Christina Grozinger, assistant professor of insect genomics, found that the number of times a honey bee queen mates is a key factor in determining how attractive the queen is to the worker bees of a hive.

Chimpanzees, Unlike Humans, Apply Economic Principles To Ultimatum Game:

New research from the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany shows that unlike humans, chimpanzees conform to traditional economic models. The research used a modification of one of the most widely used and accepted economic tools, the ultimatum game.

New Telomere Discovery Could Help Explain Why Cancer Cells Never Stop Dividing:

A group working at the Swiss Institute for Experimental Cancer Research (ISREC) in collaboration with the University of Pavia has discovered that telomeres, the repeated DNA-protein complexes at the end of chromosomes that progressively shorten every time a cell divides, also contain RNA.

Key Step Bird Flu Virus Takes To Spread Readily In Humans Identified:

Since it first appeared in Hong Kong in 1997, the H5N1 avian flu virus has been slowly evolving into a pathogen better equipped to infect humans. The final form of the virus, biomedical researchers fear, will be a highly pathogenic strain of influenza that spreads easily among humans.

Why Emotionally Charged Events Are So Memorable:

Both extensive psychological research and personal experiences confirm that events that happen during heightened states of emotion such as fear, anger and joy are far more memorable than less dramatic occurrences.

Negativity Is Contagious, Study Finds:

Though we may not care to admit it, what other people think about something can affect what we think about it. This is how critics become influential and why our parents’ opinions about our life choices continue to matter, long after we’ve moved out. But what kind of opinions have the most effect” An important new study in the Journal of Consumer Research reveals that negative opinions cause the greatest attitude shifts, not just from good to bad, but also from bad to worse.

Simplest Circadian Clocks Operate Via Orderly Phosphate Transfers:

Researchers at Harvard University and the Howard Hughes Medical Institute have found that a simple circadian clock found in some bacteria operates by the rhythmic addition and subtraction of phosphate groups at two key locations on a single protein. This phosphate pattern is influenced by two other proteins, driving phosphorylation to oscillate according to a remarkably accurate 24-hour cycle.

Related: A Circadian Clock that works in a test-tube explained and Bacteria do it differently…

As always on Friday, there are new article published in the community journals – PLoS Pathogens, PLoS Computational Biology and PLoS Genetics. Here are few of my picks:
Growth of H5N1 Influenza A Viruses in the Upper Respiratory Tracts of Mice
A Single Mutation in the PB1-F2 of H5N1 (HK/97) and 1918 Influenza A Viruses Contributes to Increased Virulence
Universally Sloppy Parameter Sensitivities in Systems Biology Models
Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene

Fossil Data Plugs Gaps In Current Knowledge, Study Shows:

Researchers have shown for the first time that fossils can be used as effectively as living species in understanding the complex branching in the evolutionary tree of life.

Cilia: Small Organelles, Big Decisions:

Johns Hopkins researchers say they have figured out how human and all animal cells tune in to a key signal, one that literally transmits the instructions that shape their final bodies. It turns out the cells assemble their own little radio antenna on their surfaces to help them relay the proper signal to the developmental proteins “listening” on the inside of the cell.

Avoiding Sweets May Spell A Longer Life, Study In Worms Suggests:

A new study in Cell Metabolism reveals that worms live to an older age when they are unable to process the simple sugar glucose. Glucose is a primary source of energy for the body and can be found in all major dietary carbohydrates as a component of starches and other forms of sugar, including sucrose (table sugar) and lactose.

Engineers Study Brain Folding In Higher Mammals:

Engineers at Washington University in St. Louis are finding common ground between the shaping of the brain and the heart during embryonic development.

Fungus Genome Yielding Answers To Protect Grains, People And Animals:

Why a pathogen is a pathogen may be answered as scientists study the recently mapped genetic makeup of a fungus that spawns the worst cereal grains disease known and also can produce toxins potentially fatal to people and livestock.

Large-scale Head Lice Finding Kits Effective:

Working with parents and schools to provide a bug busting approach to head lice is helping to reduce infestation levels, tackle health inequalities and reduce healthcare costs, according to a review in the Journal of Clinical Nursing.

Hydrothermal Vents: Hot Spots Of Microbial Diversity:

Thousands of new kinds of marine microbes have been discovered at two deep-sea hydrothermal vents off the Oregon coast by scientists at the MBL (Marine Biological Laboratory) and University of Washington’s Joint Institute for the Study of Atmosphere and Ocean.

Census Of Protein Architectures Offers New View Of History Of Life:

The present can tell you a lot about the past, but you need to know where to look. A new study appearing this month in Genome Research reveals that protein architectures – the three-dimensional structures of specific regions within proteins – provide an extraordinary window on the history of life.

Genes Determine Mate Choice, At Least For Fat Tailed Dwarf Lemurs:

How do we choose our mates? For quite some time now, scientists suspect that it is not for looks or fashion, neither for love or sympathy. It may be the genes that determine our preference for certain males or females. A new study provides support for this idea by looking at lemurs in Madagascar.

Beyond A ‘Speed Limit’ On Mutations, Species Risk Extinction:

Harvard University scientists have identified a virtual “speed limit” on the rate of molecular evolution in organisms, and the magic number appears to be 6 mutations per genome per generation — a level beyond which species run the strong risk of extinction as their genomes lose stability.

Genetic Differences In Clover Make One Type Toxic:

That clover necklace you make for your child could well be a ring of poison. That’s because some clovers have evolved genes that help the plant produce cyanide — to protect itself against little herbivores, such as snails, slugs and voles, that eat clover. Other clover plants that do not make cyanide are found in climates with colder temperatures. So, in picking your poison, er, clover, ecology and geography play important roles.

Spouses Often Mirror Each Other’s Health Habits:

If one spouse exercises, quits smoking, stops drinking alcohol, receives a flu shot, or undergoes a cholesterol screening, the other spouse is more likely to do the same, according to a new study in Health Services Research.

Galapagos Hawk’s Evolutionary History Illuminated:

Scientists at the University of Missouri-St. Louis used DNA sequences from feather lice to study how island populations of their host, the Galápagos Hawk might have colonized the Galápagos islands, home to the endangered and declining raptor.

Huge New Dinosaur Had A Serious Bite:

The newest dinosaur species to emerge from Grand Staircase-Escalante National Monument had some serious bite, according to researchers from the Utah Museum of Natural History at the University of Utah.

New Species Of Frog Discovered: Smallest Indian Land Vertebrate:

The India’s smallest land vertebrate, a 10-millimeter frog, has been discovered from the Western Ghats of Kerala by Delhi University Systematics Biologist, S D Biju and his colleagues.

No Faking It, Crocodile Tears Are Real:

When someone feigns sadness they “cry crocodile tears,” a phrase that comes from an old myth that the animals cry while eating. Now, a University of Florida researcher has concluded that crocodiles really do bawl while banqueting – but for physiological reasons rather than rascally reptilian remorse.

Sea Otter, Peregrine Falcon Back From The Brink Of Extinction But Other Species At Risk In Canada:

There’s good news and bad news in the report the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) just dropped on the Minister of the Environment’s desk.

New Suspect Identified In West Nile Deaths Of Pelicans:

Stable flies are the latest suspect that may be involved in the West Nile virus deaths of hundreds of pelican chicks at the Medicine Lake National Wildlife Refuge in northeast Montana. West Nile virus killed 800 to 1,000 pelican chicks in 2003, averaged 400 in each of the next three summers and more than 600 this year.

Individual Differences Caused By Shuffled Chunks Of DNA In The Human Genome:

A study by Yale researchers offers a new view of what causes the greatest genetic variability among individuals — suggesting that it is due less to single point mutations than to the presence of structural changes that cause extended segments of the human genome to be missing, rearranged, or present in extra copies.

How ‘Mother Of Thousands’ Makes Baby Plants:

New research shows how the houseplant “mother of thousands” (Kalanchoe diagremontiana) makes the tiny plantlets that drop from the edges of its leaves. Having lost the ability to make viable seeds, the plant has shifted some of the processes that make seeds to the leaves, said Neelima Sinha, professor of plant biology at UC Davis.

Red Wine Ingredient — Resveratrol — Fights Diabetes In Mice:

Even relatively low doses of resveratrol–a chemical found in the skins of red grapes and in red wine–can improve the sensitivity of mice to the hormone insulin, according to a new report. As insulin resistance is often characterized as the most critical factor contributing to the development of type 2 diabetes, the findings “provide a potential new therapeutic approach for preventing or treating” both conditions, the researchers said.

In Dogs, A Shortcut To Mapping Disease Genes:

Nearly two years ago, Broad Institute researchers and their colleagues announced they had successfully decoded the genome of the domestic dog, a species coaxed into hundreds of distinct types through selective breeding by humans over the past two centuries.

Dogs That Bite Children Have Often Not Bitten Kids Before:

Dogs that bite children have often not bitten kids before, but they tend to have underlying behavioural or medical problems, indicates research in the journal Injury Prevention.

Biologists Close In On Mystery Of Sea Turtles’ ‘Lost Years’:

Biologists have found a major clue in a 50-year-old mystery about what happens to green sea turtles after they crawl out of their sandy nests and vanish into the surf, only to reappear several years later relatively close to shore.

Of Mice And Men: New Male Contraceptives Successful In Rodents And Humans:

Pills, sponges, IUDs, diaphragms — women have many options for planning their fertility, none of them quite perfect. But what if men want to help out? They have only two options — vasectomy, which is usually permanent, and condoms, which are crucial for dating but get old in long-term relationships. Will men ever have a way to reliably make sure that nobody is every calling them “Daddy” before they are ready?

There are 37 new articles on PLoS ONE today, breaking the 1000 barrier! Yes, there are now more than a thousand papers on ONE. And this week is again an embarassment of riches – so many bloggable papers! And here are some of my quick picks for this week – read them, rate them, annotate them, blog about them:
Composition and Hierarchical Organisation of a Spider Silk:

Albeit silks are fairly well understood on a molecular level, their hierarchical organisation and the full complexity of constituents in the spun fibre remain poorly defined. Here we link morphological defined structural elements in dragline silk of Nephila clavipes to their biochemical composition and physicochemical properties. Five layers of different make-ups could be distinguished. Of these only the two core layers contained the known silk proteins, but all can vitally contribute to the mechanical performance or properties of the silk fibre. Understanding the composite nature of silk and its supra-molecular organisation will open avenues in the production of high performance fibres based on artificially spun silk material.

Sexual Risk Factors for HIV Infection in Early and Advanced HIV Epidemics in Sub-Saharan Africa: Systematic Overview of 68 Epidemiological Studies:

It is commonly assumed that sexual risk factors for heterosexual HIV transmission in sub-Saharan Africa, such as multi-partner sex, paid sex and co-infections, become less important as HIV epidemics mature and prevalence increases.
We conducted a systematic review of 68 African epidemiological studies from 1986 to 2006 involving 17,000 HIV positive adults and 73,000 controls. We used random-effects methods and stratified results by gender, time, background HIV prevalence rates and other variables. The number of sex partners, history of paid sex, and infection with herpes simplex virus (HSV-2) or other sexually-transmitted infections (STIs) each showed significant associations with HIV infection. Among the general population, the odds ratio (OR) of HIV infection for women reporting 3+ sex partners versus 0-2 was 3.64 (95%CI [2.87-4.62]), with similar risks for men. About 9% of infected women reported ever having been paid for sex, versus 4% of control women (OR = 2.29, [1.45-3.62]). About 31% of infected men reported ever paying for sex versus 18% of uninfected men (OR = 1.75, [1.30-2.36]). HSV-2 infection carried the largest risk of HIV infection: OR = 4.62, [2.85-7.47] in women, and OR = 6.97, [4.68-10.38] in men. These risks changed little over time and stratification by lower and higher HIV background prevalence showed that risk ratios for most variables were larger in high prevalence settings. Among uninfected controls, the male-female differences in the number of sex partners and in paid sex were more extreme in the higher HIV prevalence settings than in the lower prevalence settings.
Multi-partner sex, paid sex, STIs and HSV-2 infection are as important to HIV transmission in advanced as in early HIV epidemics. Even in high prevalence settings, prevention among people with high rates of partner change, such as female sex workers and their male clients, is likely to reduce transmission overall.

Inflated Impact Factors? The True Impact of Evolutionary Papers in Non-Evolutionary Journals:

Amongst the numerous problems associated with the use of impact factors as a measure of quality are the systematic differences in impact factors that exist among scientific fields. While in theory this can be circumvented by limiting comparisons to journals within the same field, for a diverse and multidisciplinary field like evolutionary biology, in which the majority of papers are published in journals that publish both evolutionary and non-evolutionary papers, this is impossible. However, a journal’s overall impact factor may well be a poor predictor for the impact of its evolutionary papers. The extremely high impact factors of some multidisciplinary journals, for example, are by many believed to be driven mostly by publications from other fields. Despite plenty of speculation, however, we know as yet very little about the true impact of evolutionary papers in journals not specifically classified as evolutionary. Here I present, for a wide range of journals, an analysis of the number of evolutionary papers they publish and their average impact. I show that there are large differences in impact among evolutionary and non-evolutionary papers within journals; while the impact of evolutionary papers published in multidisciplinary journals is substantially overestimated by their overall impact factor, the impact of evolutionary papers in many of the more specialized, non-evolutionary journals is significantly underestimated. This suggests that, for evolutionary biologists, publishing in high-impact multidisciplinary journals should not receive as much weight as it does now, while evolutionary papers in more narrowly defined journals are currently undervalued. Importantly, however, their ranking remains largely unaffected. While journal impact factors may thus indeed provide a meaningful qualitative measure of impact, a fair quantitative comparison requires a more sophisticated journal classification system, together with multiple field-specific impact statistics per journal.

Ant Species Differences Determined by Epistasis between Brood and Worker Genomes:

Epistasis arising from physiological interactions between gene products often contributes to species differences, particularly those involved in reproductive isolation. In social organisms, phenotypes are influenced by the genotypes of multiple interacting individuals. In theory, social interactions can give rise to an additional type of epistasis between the genomes of social partners that can contribute to species differences. Using a full-factorial cross-fostering design with three species of closely related Temnothorax ants, I found that adult worker size was determined by an interaction between the genotypes of developing brood and care-giving workers, i.e. intergenomic epistasis. Such intergenomic social epistasis provides a strong signature of coevolution between social partners. These results demonstrate that just as physiologically interacting genes coevolve, diverge, and contribute to species differences, so do socially interacting genes. Coevolution and conflict between social partners, especially relatives such as parents and offspring, has long been recognized as having widespread evolutionary effects. This coevolutionary process may often result in coevolved socially-interacting gene complexes that contribute to species differences.

Phylogeny, Diet, and Cranial Integration in Australodelphian Marsupials:

Studies of morphological integration provide valuable information on the correlated evolution of traits and its relationship to long-term patterns of morphological evolution. Thus far, studies of morphological integration in mammals have focused on placentals and have demonstrated that similarity in integration is broadly correlated with phylogenetic distance and dietary similarity. Detailed studies have also demonstrated a significant correlation between developmental relationships among structures and adult morphological integration. However, these studies have not yet been applied to marsupial taxa, which differ greatly from placentals in reproductive strategy and cranial development and could provide the diversity necessary to assess the relationships among phylogeny, ecology, development, and cranial integration. This study presents analyses of morphological integration in 20 species of australodelphian marsupials, and shows that phylogeny is significantly correlated with similarity of morphological integration in most clades. Size-related correlations have a significant affect on results, particularly in Peramelia, which shows a striking decrease in similarity of integration among species when size is removed. Diet is not significantly correlated with similarity of integration in any marsupial clade. These results show that marsupials differ markedly from placental mammals in the relationships of cranial integration, phylogeny, and diet, which may be related to the accelerated development of the masticatory apparatus in marsupials.

Effects of Insemination Quantity on Honey Bee Queen Physiology:

Mating has profound effects on the physiology and behavior of female insects, and in honey bee (Apis mellifera) queens, these changes are permanent. Queens mate with multiple males during a brief period in their early adult lives, and shortly thereafter they initiate egg-laying. Furthermore, the pheromone profiles of mated queens differ from those of virgins, and these pheromones regulate many different aspects of worker behavior and colony organization. While it is clear that mating causes dramatic changes in queens, it is unclear if mating number has more subtle effects on queen physiology or queen-worker interactions; indeed, the effect of multiple matings on female insect physiology has not been broadly addressed. Because it is not possible to control the natural mating behavior of queens, we used instrumental insemination and compared queens inseminated with semen from either a single drone (single-drone inseminated, or SDI) or 10 drones (multi-drone inseminated, or MDI). We used observation hives to monitor attraction of workers to SDI or MDI queens in colonies, and cage studies to monitor the attraction of workers to virgin, SDI, and MDI queen mandibular gland extracts (the main source of queen pheromone). The chemical profiles of the mandibular glands of virgin, SDI, and MDI queens were characterized using GC-MS. Finally, we measured brain expression levels in SDI and MDI queens of a gene associated with phototaxis in worker honey bees (Amfor). Here, we demonstrate for the first time that insemination quantity significantly affects mandibular gland chemical profiles, queen-worker interactions, and brain gene expression. Further research will be necessary to elucidate the mechanistic bases for these effects: insemination volume, sperm and seminal protein quantity, and genetic diversity of the sperm may all be important factors contributing to this profound change in honey bee queen physiology, queen behavior, and social interactions in the colony.

The Genetic Signature of Sex-Biased Migration in Patrilocal Chimpanzees and Humans:

A large body of theoretical work suggests that analyses of variation at the maternally inherited mitochondrial (mt)DNA and the paternally inherited non-recombining portion of the Y chromosome (NRY) are a potentially powerful way to reveal the differing migratory histories of men and women across human societies. However, the few empirical studies comparing mtDNA and NRY variation and known patterns of sex-biased migration have produced conflicting results. Here we review some methodological reasons for these inconsistencies, and take them into account to provide an unbiased characterization of mtDNA and NRY variation in chimpanzees, one of the few mammalian taxa where males routinely remain in and females typically disperse from their natal groups. We show that patterns of mtDNA and NRY variation are more strongly contrasting in patrilocal chimpanzees compared with patrilocal human societies. The chimpanzee data we present here thus provide a valuable comparative benchmark of the patterns of mtDNA and NRY variation to be expected in a society with extremely female-biased dispersal.

Non-Invasive In Vivo Imaging of Calcium Signaling in Mice:

Rapid and transient elevations of Ca2+ within cellular microdomains play a critical role in the regulation of many signal transduction pathways. Described here is a genetic approach for non-invasive detection of localized Ca2+ concentration ([Ca2+]) rises in live animals using bioluminescence imaging (BLI). Transgenic mice conditionally expressing the Ca2+-sensitive bioluminescent reporter GFP-aequorin targeted to the mitochondrial matrix were studied in several experimental paradigms. Rapid [Ca2+] rises inside the mitochondrial matrix could be readily detected during single-twitch muscle contractions. Whole body patterns of [Ca2+] were monitored in freely moving mice and during epileptic seizures. Furthermore, variations in mitochondrial [Ca2+] correlated to behavioral components of the sleep/wake cycle were observed during prolonged whole body recordings of newborn mice. This non-invasive imaging technique opens new avenues for the analysis of Ca2+ signaling whenever whole body information in freely moving animals is desired, in particular during behavioral and developmental studies.

Design and Pre-Clinical Evaluation of a Universal HIV-1 Vaccine:

One of the big roadblocks in development of HIV-1/AIDS vaccines is the enormous diversity of HIV-1, which could limit the value of any HIV-1 vaccine candidate currently under test.
To address the HIV-1 variation, we designed a novel T cell immunogen, designated HIVCONSV, by assembling the 14 most conserved regions of the HIV-1 proteome into one chimaeric protein. Each segment is a consensus sequence from one of the four major HIV-1 clades A, B, C and D, which alternate to ensure equal clade coverage. The gene coding for the HIVCONSV protein was inserted into the three most studied vaccine vectors, plasmid DNA, human adenovirus serotype 5 and modified vaccine virus Ankara (MVA), and induced HIV-1-specific T cell responses in mice. We also demonstrated that these conserved regions prime CD8+ and CD4+ T cell to highly conserved epitopes in humans and that these epitopes, although usually subdominant, generate memory T cells in patients during natural HIV-1 infection.
Therefore, this vaccine approach provides an attractive and testable alternative for overcoming the HIV-1 variability, while focusing T cell responses on regions of the virus that are less likely to mutate and escape. Furthermore, this approach has merit in the simplicity of design and delivery, requiring only a single immunogen to provide extensive coverage of global HIV-1 population diversity.

My picks for today:
Segregation of Odor Identity and Intensity during Odor Discrimination in Drosophila Mushroom Body:

Considerable progress has been made in understanding how olfaction works as the receptor proteins, sensory neurons, and brain circuitry responsible have become increasingly well-characterized. However, olfactory processing in higher brain centers, where neuronal activity is assembled into the perception of odor quality, is poorly understood. Here, we have addressed how the mushroom body (MB)–a secondary olfactory center–is involved in olfactory discrimination. We manipulated the MB by ablation, disruption of synaptic transmission, and interruption of key cellular signaling molecules in naïve flies and in flies trained to discriminate odors. We first show that although both odor identity and intensity are encoded in the MB, only the former requires Gαq-dependent signaling and is necessary for naïve flies to spontaneously discriminate different odors. We then show that training flies to alter their olfactory response requires Gαs-mediated signaling in MB for both odor intensity and odor identity. We have thus identified (i) segregation of odor identity and odor intensity at the MB level in naïve flies and (ii) different G-protein-dependent signaling pathways for spontaneous versus experience-dependent olfactory discrimination.

Viral Evolution in the Genomic Age:

Genome sequence data will undoubtedly deliver much to the study of viral pathogens and their diseases. A prominent example of this new genomic perspective is influenza A virus, for which a large-scale genome sequencing project begun in the year 2005 has, to date, generated around 2,500 complete viral genomes [1]. While this alone is newsworthy, the rise of rapid, high-throughput genome “pyrosequencing” promises to take the production of viral genomes to a level once unimaginable [2].

Saber-toothed Cat Was More Like A Pussycat Than A Tiger:

In public imagination, the sabre-toothed cat Smilodon ranks alongside Tyrannosaurus rex as the ultimate killing machine. Powerfully built, with upper canines like knives, Smilodon was a fearsome predator of Ice-Age America’s lost giants. For more than 150 years, scientists have debated how this iconic predator used its ferocious fangs to kill its prey. Now a new Australian study, published recently in the US Proceedings of the National Academy of Science, hopes to lay the arguments to rest. And the results will put in dent in Smilodon’s reputation.

Thriving Hybrid Salamanders Contradict Common Wisdom:

A new UC Davis study not only has important findings for the future of California tiger salamanders, but also contradicts prevailing scientific thought about what happens when animal species interbreed.

Three-way Mating Game Of North American Lizard Found In Distant European Relative:

An intricate three-way mating struggle first observed in a species of North American lizard has been discovered in a distant relative, the European common lizard. The two species are separated by 5,000 miles and 175 million years of evolution, yet they share behavioral and reproductive details right down to the gaudy colors of the males, according to new research published in the November issue of American Naturalist.

Saving Microscopic Threatened Species:

The Smithsonian’s National Zoo recently acquired 12,000 new animals–microscopic Elkhorn coral larvae harvested by National Zoo scientists in Puerto Rico–as part of an international collaborative program to raise the threatened species. National Zoo scientists hope to one day return the animals, once they are grown, to their wild ocean habitat.

Saltwater Crocodiles Can Find Their Way Home:

Three crocodiles relocated from their homes in Far North Queensland have been tracked swimming between 10 and 30 kilometres per day according to a collaborative research project by The University of Queensland, Australia Zoo and Queensland Parks and Wildlife Service.
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The results highlighted the success of satellite tracking for crocodiles allowing continuous tracking without human interference.
Professor Franklin said “Satellite technology is a great way of tracking these really cryptic animals which are difficult to follow.
“The success of the study was also recognition of the skills and knowledge that Steve Irwin brought to the project.”
He said Steve Irwin was a major driving force behind the study, and his intellectual and logistical support complimented the knowledge, experience and contributions made by the other team members.
“He also gave us the assistance of the croc team from Australia Zoo, who are highly skilled in the capture and care of crocodiles.”
All three monitored crocodiles were moved by helicopter between 52 and 130 kilometres away but still found their way back to their capture sites. One crocodile was flown across Cape York Peninsula from the west to east coast, and then circumnavigated the peninsula to return home.
He said crocodiles probably used many factors such as its position to the sun, magnetic fields, sight, and smell to navigate.

Sea Otter, Peregrine Falcon Back From The Brink Of Extinction But Other Species At Risk In Canada:

There’s good news and bad news in the report the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) just dropped on the Minister of the Environment’s desk.

Chesapeake Bay’s Habitats Threatened By Global Warming:

A new report on the impact of global warming on the Chesapeake Bay calls for a major shift in how land is managed in the bay to protect the nation’s most prized hunting and fishing grounds.

Surprise In The Organic Orchard — A Healthier Worm In The Apple:

Insects can catch more than a cold from certain viruses. Some viruses can be lethal to pest species – turning their insides to soup – without harming beneficial insects or other organisms. Hence they are used as an environmentally friendly means of biological crop protection worldwide. The proverbial worm in the apple, the codling moth caterpillar, has been controlled in European orchards for years with a baculovirus called codling moth granulovirus (CpGV). But in southwest Germany, some organic apple growers noticed that the virus was losing its effectiveness. Pest resistance to chemical insecticides is common in agriculture, but resistance to viruses had never been a problem in the past.

Going Fishing? Catch-and-release In Less Than Four Minutes, Please:

Recreational fishing that involves catch-and-release may seem like just good fun, and that released fish go on to live happily ever after, but a recent study at the University of Illinois shows that improper handling techniques by anglers can increase the likelihood of released fish being caught by predators.

Does The Victim Affect Snake Venom Composition?:

A snake’s intended prey might affect the type and evolution of toxins in their venom, research published in BMC Evolutionary Biology shows. In snakes, venom composition varies both between species and within a particular species. Land snakes feed on a range of animals and birds, so scientists think that these snakes need a diverse array of toxins in their venom. Sea snakes, on the other hand, tend to have a more restricted diet, feeding only on fish. The toxins in these snakes have now been shown to be less diverse than those in terrestrial snakes.

Tiny Animals Exposed To Outer Space:

“For the first time ever, animals are now being exposed to an unmitigated space environment, with both vacuum conditions and cosmic radiation,” says the ecologist Ingemar Jönsson, a researcher at Kristianstad University in Sweden. One of the aims of sending the tiny tardigrades into space is to find out whether they can cope with the rugged conditions in space, which has previously been predicted but never tested.

Antarctic Plants And Animal Life Survived Ice Ages:

Springtails, mites, worms and plant life could help solve the mystery of Antarctica’s glacial history according to new research published in the journal Science.

Fish Diet Linked To Evolution, Ten Million Year Old Chipped Teeth Show:

Chips from 10 million years ago have revealed new insights into fish diets and their influence on fish evolution, according to new research featured in this week’s issue of the journal Science. The chips were found, along with scratches, on the teeth of fossil stickleback fish and reveal for the first time how changes in the way an animal feeds control its evolution over thousands of years.

Does Your Mood Take A Nosedive Each November?:

If you notice that your mood, energy level and motivation take a nosedive each November only to return to normal in April, you may have Seasonal Affective Disorder (SAD), according to Loyola University Health System doctors.

Hormone-driven Effects On Eating, Stress Mediated By Same Brain Region:

A hormone system linked to reducing food consumption appears to do so by increasing stress-related behaviors, according to a new study. Mediated by a hormone receptor protein known as the corticotropin-releasing factor type 2 (CRF2) receptor, the system has attracted recent interest for its role in regulating food intake, say Vaishali Bakshi and Ned Kalin, professors in the Department of Psychiatry at the University of Wisconsin-Madison School of Medicine and Public Health.

Program Provides Blueprint For Recruiting Minorities To Science And Engineering:

The Model Institutions for Excellence Program (MIE) funded by the National Science Foundation (NSF) and the National Aeronautics and Space Administration (NASA) has developed a body of work over the past 11 years demonstrating successful strategies for recruiting underrepresented minority students to science and engineering fields and supporting their successful completion of science degrees.

Babies Raised In Bilingual Homes Learn New Words Differently Than Infants Learning One Language:

Research on the learning process for acquiring two languages from birth found differences in how bilingual babies learned words compared to monolingual babies. The research suggests that bilingual babies follow a slightly different pattern when using detailed sound information to learn differences between words.

Altruism Evolved From Maternal Behavior, Wasp Genetics Study Suggests:

Researchers at the University of Illinois have used an innovative approach to reveal the molecular basis of altruistic behavior in wasps. The research team focused on the expression of behavior-related genes in Polistes metricus paper wasps, a species for which little genetic data was available when the study was begun. Like honey bee workers, wasp workers give up their reproductive capabilities and focus entirely on nurturing their larval siblings, a practice that seems to defy the Darwinian prediction that a successful organism strives, above all else, to reproduce itself. Such behaviors are indicative of a eusocial society, in which some individuals lose, or sacrifice, their reproductive functions and instead work to benefit the larger group.

City Birds Better Than Rural Species In Coping With Human Disruption:

Birds that hang out in large urban areas seem to have a marked advantage over their rural cousins — they are adaptable enough to survive in a much larger range of conditions.

Crabs Prefer A Take-out Meal:

Shore crabs (Carcinus maenas) catch their food at food-rich spots and subsequently eat it elsewhere. With this take-out strategy the crabs maximise their food uptake and keep competing crabs at a distance, says Dutch researcher Isabel Smallegange.

Is There Any Validity To The So-called 5-second Rule?:

If a piece of toast fell on the floor, would you pick it up and eat it? You probably would if you believe in the 5-second rule, which suggests that your spilled breakfast stays germ-free as long as you snatch it up in five seconds.

Cockroaches Are Morons In The Morning, Geniuses In The Evening:

In its ability to learn, the cockroach is a moron in the morning and a genius in the evening. Dramatic daily variations in the cockroach’s learning ability were discovered by a new study performed by Vanderbilt University biologists and published online recently in the Proceedings of the National Academy of Sciences.

DNA Extracted From Woolly Mammoth Hair:

Stephan C. Schuster and Webb Miller of Penn State, working with Thomas Gilbert from Copenhagen and a large international consortium, discovered that hair shafts provide an ideal source of ancient DNA — a better source than bones and muscle for studying the genome sequences of extinct animals. Their research achievement, described in a paper to be published in the journal Science on Sept. 28, includes the sequencing of entire mitochondrial genomes from 10 individual woolly mammoths.

What Protects Us From Sunburn Also Protects Crayfish Against Bacteria:

The production of melanin in our skin helps protect us from the sun’s rays, but it also helps protect invertebrate animals — in their case, by encapsulating attacking fungi and parasites.

Second Extremely Resistant Bacteria Sequenced Is Surprisingly Different From First:

Researchers have completed the whole-genome sequence of Deinococcus geothermalis, which is only the second extremely radiation- and desiccation-resistant bacterium to be sequenced.

How The Zebrafish Gets His Stripe:

Scientists have discovered how the zebrafish (Danio rerio) develops one of its four stripes of pigment cells. Their findings add to the growing list of tasks carried out by an important molecule that is involved in the arrangement of everything from nerve cells to reproductive cells in the developing embryo.

Solving A Dragonfly Flight Mystery:

Dragonflies adjust their wing motion while hovering to conserve energy, according to a Cornell University study of the insect’s flight mechanics. The revelation contradicts previous speculation that the change in wing motion served to enhance vertical lift.

Mice Teeth Explain The Troubles With Human Wisdom Teeth:

During evolution, many of a species’ properties are shaped by ecological interactions. This is readily evident in mammalian teeth, whose many features closely reflect what each species eats. However, for a long time scientists have suspected that genetic and developmental interactions may also influence species-specific properties. Now, researchers at the University of Helsinki’s Institute of Biotechnology show how development affects the evolution of teeth, and have devised a simple developmental model to predict aspects of teeth across many species. The results were published in Nature.

Vitamin C Is Essential For Plant Growth:

Scientists from the University of Exeter and Shimane University in Japan have proved for the first time that vitamin C is essential for plant growth. This discovery could have implications for agriculture and for the production of vitamin C dietary supplements.

New Animal And Plant Species Found In Vietnam:

World Wildlife Fund scientists have just announced the discovery of 11 new animal and plant species in a remote area in central Vietnam. They say this underscores the importance of conservation efforts in the ancient tropical forests of the region.

Primate Sperm Competition: Speed Matters:

Researchers at UC San Diego and UC Irvine have found evidence that supports the theory that reproductive competition during the evolution of primate species has occurred at the level of sperm cell motility.

Clever Plants ‘Chat’ Over Their Own Network:

Recent research from Vidi researcher Josef Stuefer at the Radboud University Nijmegen reveals that plants have their own chat systems that they can use to warn each other.

You Can Teach An Old Dog New Tricks — With The Right Diet:

These supplements, acetyl-l-carnitine and alpha lipoic acid, are continuing to be studied in work with humans, and scientists believe they may provide a new approach to the neurodegeneration and cognitive decline common with aging.

Amazon Forest Shows Unexpected Resiliency During Drought:

Drought-stricken regions of the Amazon forest grew particularly vigorously during the 2005 drought, according to new research.

New Species Of Bacteria Feeds On Natural Gas:

A German-American research team of biologists and geochemists has discovered hitherto unknown anaerobic bacteria in marine sediments which need only propane or butane for growth, as recently reported by the scientific journal “Nature.”

Rare Albino Ratfish Has Eerie, Silvery Sheen:

A ghostly, mutant ratfish caught off Whidbey Island in Washington state is the only completely albino fish ever seen by both the curator of the University of Washington’s 7.2 million-specimen fish collection and a fish and wildlife biologist with more than 20 years of sampling fish in Puget Sound.

Could Iron Fertilization Of Oceans Combat Global Warming?:

Several times over the past century, scientists and environmental engineers have proposed spreading slurries of dissolved iron into the oceans in order to “fertilize” the waters and promote vast blooms of marine plants (phytoplankton). Phytoplankton consume carbon dioxide as they grow, and this growth can be stimulated in certain ocean basins by the addition of iron, a necessary micronutrient.

Steve Irwin’s last paper is not the only exciting article to appear on PLoS ONE today – there are 40 more, and here are a few I am excited about – a veritable embarassment of riches! When am I ever going to find time to read them all!
Oxytocin in the Circadian Timing of Birth (hey, it’s by Erik Herzog, so you know I’ll blog about this paper in a separate post later):

Very little is known about the molecular components that determine the timing for birth in mammals. This study compares the timing of births between mice with and without the chemical oxytocin (OT) when exposed to shifts in the light cycle. The results show that OT-deficient mice give birth at random times throughout the light cycle, while mice with OT maintain a normal clustered birth profile, thus suggesting that oxytocin is necessary in the timing of birth.

A Visual Pathway Links Brain Structures Active during Magnetic Compass Orientation in Migratory Birds:

The magnetic compass of migratory birds has been suggested to be light-dependent. Retinal cryptochrome-expressing neurons and a forebrain region, “Cluster N”, show high neuronal activity when night-migratory songbirds perform magnetic compass orientation. By combining neuronal tracing with behavioral experiments leading to sensory-driven gene expression of the neuronal activity marker ZENK during magnetic compass orientation, we demonstrate a functional neuronal connection between the retinal neurons and Cluster N via the visual thalamus. Thus, the two areas of the central nervous system being most active during magnetic compass orientation are part of an ascending visual processing stream, the thalamofugal pathway. Furthermore, Cluster N seems to be a specialized part of the visual wulst. These findings strongly support the hypothesis that migratory birds use their visual system to perceive the reference compass direction of the geomagnetic field and that migratory birds “see” the reference compass direction provided by the geomagnetic field.

Do Individual Females Differ Intrinsically in Their Propensity to Engage in Extra-Pair Copulations?:

While many studies have investigated the occurrence of extra-pair paternity in wild populations of birds, we still know surprisingly little about whether individual females differ intrinsically in their principal readiness to copulate, and to what extent this readiness is affected by male attractiveness.
To address this question I used captive zebra finches (Taeniopygia guttata) as a model system. I first measured female readiness to copulate when courted by a male for the first time in life. Second, I conducted choice-chamber experiments to assess the mating preferences of individual females prior to pair formation. I then paired females socially with a non-desired mate and once they had formed a stable pair bond, I observed the inclination of these females to engage in extra-pair copulations with various males. Females showing a high readiness to copulate when courted by a male for the first time in life were much more likely to engage in extra-pair copulations later in life than others. Male attractiveness, as measured in choice tests, was a useful predictor of whether females engaged in extra-pair copulations with these males, but, surprisingly, the attractiveness of a female’s social partner had no effect on her fidelity. However, it remained unclear what made some males more attractive than others. Contrary to a widespread but rarely tested hypothesis, females did not preferentially copulate with males having a redder beak or singing at a higher rate. Rather it seemed that song rate was a confounding factor in choice-chamber experiments: song attracted the female’s attention but did not increase the male’s attractiveness as a copulation partner.
Intrinsic variation in female readiness to copulate as well as variation in the attractiveness of the extra-pair male but not the social partner decided the outcome of extra-pair encounters.

Evolution of Female Preference for Younger Males:

Previous theoretical work has suggested that females should prefer to mate with older males, as older males should have higher fitness than the average fitness of the cohort into which they were born. However, studies in humans and model organisms have shown that as males age, they accumulate deleterious mutations in their germ-line at an ever-increasing rate, thereby reducing the quality of genes passed on to the next generation. Thus, older males may produce relatively poor-quality offspring. To better understand how male age influences female mate preference and offspring quality, we used a genetic algorithm model to study the effect of age-related increases in male genetic load on female mate preference. When we incorporate age-related increases in mutation load in males into our model, we find that females evolve a preference for younger males. Females in this model could determine a male’s age, but not his inherited genotype nor his mutation load. Nevertheless, females evolved age-preferences that led them to mate with males that had low mutation loads, but showed no preference for males with respect to their somatic quality. These results suggest that germ-line quality, rather than somatic quality, should be the focus of female preference in good genes models.

Causal Inference in Multisensory Perception:

Perceptual events derive their significance to an animal from their meaning about the world, that is from the information they carry about their causes. The brain should thus be able to efficiently infer the causes underlying our sensory events. Here we use multisensory cue combination to study causal inference in perception. We formulate an ideal-observer model that infers whether two sensory cues originate from the same location and that also estimates their location(s). This model accurately predicts the nonlinear integration of cues by human subjects in two auditory-visual localization tasks. The results show that indeed humans can efficiently infer the causal structure as well as the location of causes. By combining insights from the study of causal inference with the ideal-observer approach to sensory cue combination, we show that the capacity to infer causal structure is not limited to conscious, high-level cognition; it is also performed continually and effortlessly in perception.

Antagonistic Bacterial Interactions Help Shape Host-Symbiont Dynamics within the Fungus-Growing Ant-Microbe Mutualism:

Conflict within mutually beneficial associations is predicted to destabilize relationships, and theoretical and empirical work exploring this has provided significant insight into the dynamics of cooperative interactions. Within mutualistic associations, the expression and regulation of conflict is likely more complex than in intraspecific cooperative relationship, because of the potential presence of: i) multiple genotypes of microbial species associated with individual hosts, ii) multiple species of symbiotic lineages forming cooperative partner pairings, and iii) additional symbiont lineages. Here we explore complexity of conflict expression within the ancient and coevolved mutualistic association between attine ants, their fungal cultivar, and actinomycetous bacteria (Pseudonocardia). Specifically, we examine conflict between the ants and their Pseudonocardia symbionts maintained to derive antibiotics against parasitic microfungi (Escovopsis) infecting the ants’ fungus garden. Symbiont assays pairing isolates of Pseudonocardia spp. associated with fungus-growing ants spanning the phylogenetic diversity of the mutualism revealed that antagonism between strains is common. In contrast, antagonism was substantially less common between more closely related bacteria associated with Acromyrmex leaf-cutting ants. In both experiments, the observed variation in antagonism across pairings was primarily due to the inhibitory capabilities and susceptibility of individual strains, but also the phylogenetic relationships between the ant host of the symbionts, as well as the pair-wise genetic distances between strains. The presence of antagonism throughout the phylogenetic diversity of Pseudonocardia symbionts indicates that these reactions likely have shaped the symbiosis from its origin. Antagonism is expected to prevent novel strains from invading colonies, enforcing single-strain rearing within individual ant colonies. While this may align ant-actinomycete interests in the bipartite association, the presence of single strains of Pseudonocardia within colonies may not be in the best interest of the ants, because increasing the diversity of bacteria, and thereby antibiotic diversity, would help the ant-fungus mutualism deal with the specialized parasites.

Do Haematophagous Bugs Assess Skin Surface Temperature to Detect Blood Vessels?:

It is known that some blood-sucking insects have the ability to reach vessels under the host skin with their mouthparts to feed blood from inside them. However, the process by which they locate these vessels remains largely unknown. Less than 5% of the skin is occupied by blood vessels and thus, it is not likely that insects rely on a “random search strategy”, since it would increase the probability of being killed by their hosts. Indeed, heterogeneities along the skin surface might offer exploitable information for guiding insect’s bites.
We tested whether the bug Rhodnius prolixus can evaluate temperature discontinuities along the body surface in order to locate vessels before piercing the host skin. When placed over a rabbit ear, the bug’s first bites were mostly directed towards the main vessels. When insects were confronted to artificial linear heat sources presenting a temperature gradient against the background, most bites were directly addressed to the warmer linear source, notwithstanding the temperature of both, the source and the background. Finally, tests performed using uni- and bilaterally antennectomized insects revealed that the bilateral integration of thermal inputs from both antennae is necessary for precisely directing bites.
R. prolixus may be able to exploit the temperature differences observed over the skin surface to locate blood vessles. Bugs bite the warmest targets regardless of the target/background temperatures, suggesting that they do not bite choosing a preferred temperature, but select temperature discontinuities along the skin. This strategy seems to be an efficient one for finding blood vessels within a wide temperature range, allowing finding them on different hosts, as well as on different areas of the host body. Our study also adds new insight about the use of antennal thermal inputs by blood sucking bugs.

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks:

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.

Also:
Lactate, Fructose and Glucose Oxidation Profiles in Sports Drinks and the Effect on Exercise Performance
Cultural Diversity, Economic Development and Societal Instability
Stochastic Species Turnover and Stable Coexistence in a Species-Rich, Fire-Prone Plant Community
Global Patterns of City Size Distributions and Their Fundamental Drivers
Children’s Health Status: Examining the Associations among Income Poverty, Material Hardship, and Parental Factors
As always: read, rate, comment, annotate, use and reuse and, if you blog about the PLoS ONE papers, try to use the correct form of the URL in order to generate a trackback.

A bunch of new articles got published in PLoS Medicine and PLoS Biology yesterday. Here are my two picks, and you go and check the rest:
Brain Dynamics Underlying the Nonlinear Threshold for Access to Consciousness:

Understanding the neural mechanisms that distinguish between conscious and nonconscious processes is a crucial issue in cognitive neuroscience. In this study, we focused on the transition that causes a visual stimulus to cross the threshold to consciousness, i.e., visibility. We used a backward masking paradigm in which the visibility of a briefly presented stimulus (the “target”) is reduced by a second stimulus (the “mask”) presented shortly after this first stimulus. (Human participants report the visibility of the target.) When the delay between target and mask stimuli exceeds a threshold value, the masked stimulus becomes visible. Below this threshold, it remains nonvisible. During the task, we recorded electric brain activity from the scalp and reconstructed the cortical sources corresponding to this activity. Conscious perception of masked stimuli corresponded to activity in a broadly distributed fronto-parieto-temporal network, occurring from about 300 ms after stimulus presentation. We conclude that this late stage, which could be clearly separated from earlier neural events associated with subliminal processing and mask-target interactions, can be regarded as a marker of consciousness.

The Absolute Risk of Venous Thrombosis after Air Travel: A Cohort Study of 8,755 Employees of International Organisations:

Background.
Blood normally flows smoothly throughout the human body, supplying the brain and other vital organs with oxygen and nutrients. When an injury occurs, proteins called clotting factors make the blood gel or coagulate at the injury site. The resultant blood clot (thrombus) plugs the wound and prevents blood loss. Sometimes, however, a thrombus forms inside an uninjured blood vessel and partly or completely blocks the blood flow. A clot inside one of the veins (vessels that take blood to the heart) deep within the body is called a deep vein thrombosis (DVT). Symptoms of DVT (which usually occurs in the deep veins of the leg) include pain, swelling, and redness in one leg. DVT is usually treated with heparin and warfarin, two anticoagulant drugs that stop the blood clot growing. If left untreated, part of the clot (an embolus) can break off and travel to the lungs, where it can cause a life-threatening condition called pulmonary embolism (PE). Fortunately, DVT and PE are rare but having an inherited blood clotting disorder, taking an oral contraceptive, and some types of surgery are all risk factors for them. In addition, long-haul plane travel increases the risk of DVT and PE, known collectively as venous thrombosis (VT) 2- to 4-fold, in part because the enforced immobilization during flights slows down blood flow.
Why Was This Study Done?
Although the link between air travel and VT was first noticed in the 1950s, exactly how many people will develop DVT and PE (the absolute risk of developing VT) after a long flight remains unknown. This information is needed so that travelers can be given advice about their actual risk and can make informed decisions about trying to reduce that risk by, for example, taking small doses of anticoagulant medicine before a flight. In this study, the researchers have determined the absolute risk of VT during and after long-haul air travel in a large group of business travelers.
What Did the Researchers Do and Find?
The researchers enrolled almost 9,000 employees from several international companies and organizations and followed them for an average of 4.4 years. The details of flights taken by each employee were obtained from company records, and employees completed a Web-based questionnaire about whether they had developed VT and what risk factors they had for the condition. Out of 53 thrombi that occurred during the study, 22 occurred within eight weeks of a long-haul flight (a flight of more than four hours). From this and data on the total time employees spent on long-haul flights, the researchers calculated that these flights tripled the risk of developing VT, and that the absolute risk (the probability of something occurring in a certain time period) of a VT occurring shortly after such travel was one event per 4,656 flights. They also calculated that the risk of VT was increased by exposure to more flights during a short period and to longer flights and was greatest in the first two weeks after a flight. In addition, the risk of VT was particularly high in young employees, women taking oral contraceptives, and people who were short, tall or overweight.
What Do These Findings Mean?
The main finding of this study is that the absolute risk of VT after of a long-haul flight is low–only one passenger out of nearly 5,000 is likely to develop VT because of flying. However, the study included only healthy people without previous VT whose average age was 40 years, so the absolute risk of VT after long-haul flights might be higher in the general traveling population. Even so, this finding strongly suggests that prophylactic (preventative) use of anticoagulants by all long-haul travelers may not be justified because these drugs have potentially dangerous side effects (for example, they can cause uncontrolled bleeding). Subgroups of travelers with additional risk factors for VT might, however, benefit from the use of this and other prophylactic measures, but randomized trials are needed to find out who would benefit most from which prophylactic measure.

If You Want More Babies, Find A Man With A Deep Voice:

Men who have lower-pitched voices have more children than do men with high-pitched voices, researchers have found. And their study suggests that for reproductive-minded women, mate selection favours men with low-pitched voices.

Spaceflight Can Change Bacteria Into More Infectious Pathogens:

Space flight has been shown to have a profound impact on human physiology as the body adapts to zero gravity environments.

Making Bicycles That Balance Better:

For nearly 150 years, scientists have been puzzled by the bicycle. How on earth is it possible that a moving bicycle can, all by itself, be so stable? Researchers of the Delft University of Technology (TU Delft), working with colleagues from Cornell University and the University of Nottingham, UK, believe they have now found the ultimate model of the bicycle.

How Does The Brain Develop During Embryogenesis?:

One of the great questions of neurobiology, how the brain is built up during embryonic development, could be resolved by a young French scientist in an award winning project organised by the European Science Foundation (ESF) and the European Heads of Research Councils (EuroHORCS).

Controlling For Size May Also Prevent Cancer:

Scientists at Johns Hopkins recently discovered that a chemical chain reaction that controls organ size in animals ranging from insects to humans could mean the difference between normal growth and cancer.

New Dinosaur Species Found In Montana:

A dinosaur skeleton found 24 years ago near Choteau has finally been identified as a new species that links North American dinosaurs with Asian dinosaurs. The dinosaur would have weighed 30 to 40 pounds, walked on two feet and stood about three feet tall. The fossil came from sediment that’s about 80 million years old.

Hormone Therapy Boosts Sexual Interest But Not Memory, Study Suggests:

Hormone therapy in early post-menopause increases sexual interest, but does not improve memory, according to a new study. “Contrary to what we predicted, hormone therapy did not have a positive affect on memory performance in younger mid-life women,” said Pauline Maki, associate professor of psychiatry and psychology at the University of Illinois at Chicago, who led the study.

How The Brain Handles Surprise, Good And Bad:

Whether it’s a mugger or a friend who jumps out of the bushes, you’re still surprised. But your response–to flee or to hug–must be very different. Now, researchers have begun to distinguish the circuitry in the brain’s emotion center that processes surprise from the circuitry that processes the aversive or reward “valence” of a stimulus. C. Daniel Salzman and colleagues published their findings in the journal Neuron.

Official Kilogram Losing Mass: Scientists Propose Redefining It As A Precise Number Of Carbon Atoms:

How much is a kilogram? It turns out that nobody can say for sure, at least not in a way that won’t change ever so slightly over time. The official kilogram — a cylinder cast 118 years ago from platinum and iridium and known as the International Prototype Kilogram or “Le Gran K” — has been losing mass, about 50 micrograms at last check. The change is occurring despite careful storage at a facility near Paris.

The Science Of Collective Decision-making:

Why do some juries take weeks to reach a verdict, while others take just hours? How do judges pick the perfect beauty queen from a sea of very similar candidates? We have all wondered exactly why we did not win a certain award. Now, new psychological research explains how groups come to a collective decision.

Understanding The Neuron’s Green Architecture:

Being green is a lifestyle. Turns out, each of your neurons is deeply committed to that green lifestyle – and you didn’t even know it. In just a thousandth of a second, a neuron can dump up to 5,000 molecules of its chemical messenger – a neurotransmitter – into the synapse, where it will trigger an impulse in a neighboring nerve cell. The neuron is a recycler par excellence when it comes to these neurotransmitters. Neurons must not only ready neurotransmitter receptors to receive the signals coming fast and furious, but they must also recycle receptors that have been used. And you thought you had recycling problems?

Biologists Expose Hidden Costs Of Firefly Flashes: Risky Balance Between Sex And Death:

A new study by biologists at Tufts University has discovered a dark side lurking behind the magical light shows put on by fireflies each summer. Using both laboratory and field experiments to explore the potential costs of firefly courtship displays, the biologists have uncovered some surprising answers.

Bioluminescence Genes Found Through Metagenomic Study Of Deep Mediterranean:

Metagenomics is a revolutionary approach to study microbes. Rather than isolating pure cultures, the power of high-throughput sequencing is applied directly to environmental samples to obtain information about the genomes of the prokaryotic cells present in a specific habitat studied. The ocean is an ideal subject of this approach because of its enormous microbiota, whose biomass equals that of all other living organisms on earth is mostly microbial, and also because most of these microbes are extremely fastidious to cultivate.

New Strategy To Create Genetically-modified Animals Developed:

Researchers at the University of Pennsylvania School of Veterinary Medicine have demonstrated the potential of a new strategy for genetic modification of large animals. The method employs a harmless gene therapy virus that transfers a genetic modification to male reproductive cells, which is then passed naturally on to offspring.

The Petri Dish Is Taken To New Dimensions:

A team of Brown University biomedical engineers has invented a 3-D Petri dish that can grow cells in three dimensions, a method that promises to quickly and cheaply produce more realistic cells for drug development and tissue transplantation.

Scientific Nursing Top Gives Breastfeeding Babies A Brain Workout:

Breastfeeding babies could become smarter thanks to a scientifically designed ‘clever baby’ nursing top recently revealed by the University of Portsmouth.

New Understanding Of Basic Units Of Memory:

A molecular “recycling plant” permits nerve cells in the brain to carry out two seemingly contradictory functions — changeable enough to record new experiences, yet permanent enough to maintain these memories over time.

Velociraptor Had Feathers:

A new look at some old bones have shown that velociraptor, the dinosaur made famous in the movie Jurassic Park, had feathers. The discovery was made by paleontologists at the American Museum of Natural History and the Field Museum of Natural History.

Personal Genomes: Mainstream In Five Years, But Who Should Have Access?:

Imagine this: you visit your clinician, undergo genetic testing, and then you are handed a miniature hard drive containing your personal genome sequence, which is subsequently uploaded onto publicly accessible databases. This may sound like science fiction, but it is scientific fact, and it is already happening.

Key To Longer Life (in Flies) Lies In Just 14 Brain Cells:

Two years ago, Brown University researchers discovered something startling: Decrease the activity of the cancer-suppressing protein p53 and you can make fruit flies live significantly longer. Now the same team reports an intriguing follow-up finding. The p53 protein, they found, may work its lifespan-extending magic in only 14 insulin-producing cells in the fly brain.

Eat Less To Live Longer: Calorie Restriction Linked To Long Healthy Lives:

For nearly 70 years scientists have known that caloric restriction prolongs life. In everything from yeast to primates, a significant decrease in calories can extend lifespan by as much as one-third. But getting under the hood of the molecular machinery that drives this longevity has remained elusive.

The Best Both Of Worlds: How To Have Sex And Survive:

Researchers have discovered that even the gruesome and brutal lifestyle of the Evarcha culicivora, a blood gorging jumping spider indigenous to East Africa, can’t help but be tempted by that ‘big is beautiful’ mantra no matter what the costs.

Basic Research Robust In Face Of More University Patenting:

As universities continue transforming scientific discoveries into potentially lucrative patents, many wonder how this might be transforming academic science itself.

Why Are Some Groups Of Animals So Diverse?:

A new study of finger-sized Australian lizards sheds light on one of the most striking yet largely unexplained patterns in nature: why is it that some groups of animals have evolved into hundreds, even thousands of species, while other groups include only a few?

Why Conservation Efforts Often Fail:

Modern conservation techniques have brought us the resurgence of American bald eagles, sustainable forest harvests and the rescue of prized lobster fisheries. So how can modern conservation strategies also have wrought such failures, from the catastrophic loss of Guatemalan forests to the economy-crippling Klamath River salmon kill in 2006?

Brain Network Related To Intelligence Identified:

A primary mystery puzzling neuroscientists – where in the brain lies intelligence? – just may have a unified answer.

The title alone should provoke a storm in the blogosphere 😉
Prehistoric Aesthetics Explains Snail Biogeography Puzzle:

The answer to a mystery that long has puzzled biologists may lie in prehistoric Polynesians’ penchant for pretty white shells, a research team headed by University of Michigan mollusk expert Diarmaid Ó Foighil has found.

Who’s Afraid Of The Big, Bad Wolf? Coyotes:

While the wily coyote reigns as top dog in much of the country, it leads a nervous existence wherever it coexists with its larger relative, the wolf, according to a new study from the Wildlife Conservation Society. In fact, coyote densities are more than 30 percent lower in areas that they share with wolves.

Gene Involved in Human Language Development Also Involved In Bat Echolocation:

When it comes to the FOXP2 gene, humans have had most to shout about. Discoveries that mutations in this gene lead to speech defects and that the gene underwent changes around the time language evolved both implicate FOXP2 in the evolution of human language.

Mortality Of Plants Could Increase By 40 Percent If Land Temperatures Increase 4 Degrees Celsius:

Scientists from the Mediterranean Institute for Advanced Studies* have formulated a universal rule that explains the equilibrium of plant communities, showing how plants assure the survival of their species whether their lives last a day or are prolonged over centuries.

There are 28 new articles up on PLoS ONE today. As always, I offer you my own picks, but you go there and look at all of them, then read, rate, comment and annotate:
Living with the Past: Nutritional Stress in Juvenile Males Has Immediate Effects on their Plumage Ornaments and on Adult Attractiveness in Zebra Finches:

The environmental conditions individuals experience during early development are well known to have fundamental effects on a variety of fitness-relevant traits. Although it is evident that the earliest developmental stages have large effects on fitness, other developmental stages, such as the period when secondary sexual characters develop, might also exert a profound effect on fitness components. Here we show experimentally in male zebra finches, Taeniopygia guttata, that nutritional conditions during this later period have immediate effects on male plumage ornaments and on their attractiveness as adults. Males that had received high quality food during the second month of life, a period when secondary sexual characteristics develop, were significantly more attractive as adults in mate choice tests than siblings supplied with standard food during this period. Preferred males that had experienced better nutritional conditions had larger orange cheek patches when nutritional treatments ended than did unpreferred males. Sexual plumage ornaments of young males thus are honest indicators of nutritional conditions during this period. The mate choice tests with adult birds indicate that nutritional conditions during the period of song learning, brain and gonad development, and moult into adult plumage have persisting effects on male attractiveness. This suggests that the developmental period following nutritional dependence from the parents is just as important in affecting adult attractiveness as are much earlier developmental periods. These findings thus contribute to understanding the origin and consequences of environmentally determined fitness components.

More under the fold….

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There is new cool stuff published last night in PLoS Biology and PLoS Medicine, including:

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