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So, let’s see what’s new in PLoS Genetics, PLoS Computational Biology, PLoS Pathogens and PLoS Neglected Tropical Diseases this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
Patterns of Positive Selection in Six Mammalian Genomes:

Populations evolve as mutations arise in individual organisms and, through hereditary transmission, gradually become “fixed” (shared by all individuals) in the population. Many mutations have essentially no effect on organismal fitness and can become fixed only by the stochastic process of neutral drift. However, some mutations produce a selective advantage that boosts their chances of reaching fixation. Genes in which new mutations tend to be beneficial, rather than neutral or deleterious, tend to evolve rapidly and are said to be under positive selection. Genes involved in immunity and defense are a well-known example; rapid evolution in these genes presumably occurs because new mutations help organisms to prevail in evolutionary “arms races” with pathogens. Many mammalian genes show evidence of positive selection, but open questions remain about the overall impact of positive selection in mammals. For example, which key differences between species can be attributed to positive selection? How have patterns of selection changed across the mammalian phylogeny? What are the effects of population size and gene expression patterns on positive selection? Here we attempt to shed light on these and other questions in a comprehensive study of ~16,500 genes in six mammalian genomes.

Engaging the Community: An Interview with Uche Amazigo:

Walking purposefully towards the shabby grey concrete structure that functions as the main health centre of Kyenjojo district in western Uganda, public health doctor Andrew Byamungu makes a trip he has done many times before since joining the vector control department of the Ugandan Ministry of Health. Fighting his way through the crowds of waiting patients and relatives, he greets the tired-looking health staff who, among their many other duties, are responsible for education and drug distribution in the country’s onchocerciasis control programme, which is one of the most advanced of the 19 country projects of the African Programme for Onchocerciasis Control (APOC).

H5N1 and 1918 Pandemic Influenza Virus Infection Results in Early and Excessive Infiltration of Macrophages and Neutrophils in the Lungs of Mice:

Patients who succumbed to influenza during the pandemic from 1918 to 1919 had severe lung pathology marked by extensive inflammatory infiltrate, indicating a robust immune response in the lung. Similar findings have been reported from H5N1-infected patients, raising the question as to why people expire in the presence of a strong immune response. We addressed this question by characterizing the immune cell populations in the mouse lung following infection with the 1918 pandemic virus and two H5N1 viruses isolated from fatal cases. We found that certain cells of the innate immune system, specifically macrophages and neutrophils, increase significantly early during infection but that the cells responsible for bridging the innate and adaptive immune responses, dendritic cells and the orchestrators of viral clearance, T cells, did not differ significantly between infection groups. Dendritic cells and mouse lung macrophages were shown to be susceptible to 1918 and H5N1 virus infection in vitro, suggesting a possible mechanism of pathogenesis. Our data shows excessive immune cell infiltration in the lungs contributing to severe consolidation and tissue architecture destruction in mice infected with highly pathogenic influenza viruses, supporting the histopathological observations of lung tissue from 1918 and H5N1 fatalities. Identification of the precise inflammatory cells associated with lung inflammation will be important for the development of treatments that could potentially enhance or modulate host innate immune responses.

Rise of the Machines:

Until recently, sequencing the entire genome of an organism was a major endeavor. New technologies are transforming this task into routine practice and launching a new assault on whole-genome sequencing.
It is more than 30 years since Sir Fred Sanger and colleagues published their method for sequencing DNA [1]. This Nobel Prize-winning work formed the basis of the vast majority of subsequent sequencing methodologies, albeit with some crucial technical innovations. Despite the great utility of Sanger sequencing, its scalability is inherently limited, and therefore the creation of warehouse-sized facilities was required to accomplish whole-genome sequencing projects. As a result, sequencing more than a few kilobases of DNA–a requirement for all but the simplest genomes–has long remained the province of a few dedicated sequencing centers. Within the last year, however, things have begun to change in dramatic ways. New sequencing technologies are emerging, announced in an assortment of reports, conference presentations, and press releases. In this issue of PLoS Genetics, Srivatsan et al. [2] report the resequencing of several genomes of the bacterium Bacillus subtilis using one of these new technologies. A new battle at the frontier of DNA sequencing has commenced.

A Model of Stimulus-Specific Neural Assemblies in the Insect Antennal Lobe:

It has been proposed that synchronized neural assemblies in the antennal lobe of insects encode the identity of olfactory stimuli. In response to an odor, some projection neurons exhibit synchronous firing, phase-locked to the oscillations of the field potential, whereas others do not. Experimental data indicate that neural synchronization and field oscillations are induced by fast GABAA-type inhibition, but it remains unclear how desynchronization occurs. We hypothesize that slow inhibition plays a key role in desynchronizing projection neurons. Because synaptic noise is believed to be the dominant factor that limits neuronal reliability, we consider a computational model of the antennal lobe in which a population of oscillatory neurons interact through unreliable GABAA and GABAB inhibitory synapses. From theoretical analysis and extensive computer simulations, we show that transmission failures at slow GABAB synapses make the neural response unpredictable. Depending on the balance between GABAA and GABAB inputs, particular neurons may either synchronize or desynchronize. These findings suggest a wiring scheme that triggers stimulus-specific synchronized assemblies. Inhibitory connections are set by Hebbian learning and selectively activated by stimulus patterns to form a spiking associative memory whose storage capacity is comparable to that of classical binary-coded models. We conclude that fast inhibition acts in concert with slow inhibition to reformat the glomerular input into odor-specific synchronized neural assemblies.

High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies:

In this manuscript, we describe novel applications of the newly developed Solexa sequencing technology. We aim to provide insights into the following questions: (1) Can whole-genome sequencing, while rapidly surveying mega-bases of genome information, also reliably identify variations at the base-pair resolution? (2) Can it be used to identify the differences between isolates of the same laboratory strain and between different laboratory strains? (3) Can it be used as a genetic tool to predict phenotypes and identify suppressors? To this end, we performed whole-genome shotgun sequencing of several related strains of the widely studied model bacterium Bacillus subtilis, we identified genomic variations that potentially underlie strain-specific phenotypes, which occur frequently in biological studies, and we found multiple suppressor mutations within a single strain that are difficult to discern through traditional methods. We conclude that whole-genome sequencing can be directly used to guide genetic studies.

Searching For Shut Eye: Possible ‘Sleep Gene’ Identified:

While scientists and physicians know what happens if you don’t get six to eight hours of shut-eye a night, investigators have long been puzzled about what controls the actual need for sleep. Researchers at the University of Pennsylvania School of Medicine might have an answer, at least in fruit flies. In a recent study of fruit flies, they identified a gene that controls sleep.

Did Dinosaur Soft Tissues Still Survive? New Research Challenges Notion:

Paleontologists in 2005 hailed research that apparently showed that soft, pliable tissues had been recovered from dissolved dinosaur bones, a major finding that would substantially widen the known range of preserved biomolecules.

Lost An Appendage? Grow Another:

Cut off one finger from a salamander and one will grow back. Cut off two and two will grow back. It sounds logical, but how the salamander always regenerates the right number of fingers is still a biological mystery.

Fertility: Newly Discovered Proteins In Seminal Fluid Transferred During Mating May Affect Odds Of Producing Offspring:

Seminal fluid contains protein factors that, when transferred from a male to a female at mating, affect reproductive success. This is true of many different animals, from crickets to primates.

European Birds Flock To Warming Britain, While Some Northern Species Not Faring As Well:

Researchers at Durham, the RSPB and Cambridge University have found that birds such as the Cirl Bunting and Dartford Warbler are becoming more common across a wide range of habitats in Britain as temperatures rise.

The Buzz Of The Chase: Scientists Test Technique Used To Catch Serial Killers … On Bumblebees:

Scientists from Queen Mary, University of London are helping to perfect a technique used to catch serial killers, by testing it on bumblebees.

‘Chicken And Chips’ Theory Of Pacific Migration:

A new study of DNA from ancient and modern chickens has shed light on the controversy about the extent of pre-historic Polynesian contact with the Americas.

Life In A Bubble: Mathematicians Explain How Insects Breathe Underwater:

Hundreds of insect species spend much of their time underwater, where food may be more plentiful. MIT mathematicians have now figured out exactly how those insects breathe underwater.

Olfactory Fine-tuning Helps Fruit Flies Find Their Mates:

Fruit flies fine-tune their olfactory systems by recalibrating the sensitivity of different odor channels in response to changing concentrations of environmental cues, a new study has shown. Disable this calibration system, and flies have trouble finding a mate, the researchers found.

There are 62 new articles in PLoS ONE this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
Diurnal and Circadian Rhythms in the Tomato Transcriptome and Their Modulation by Cryptochrome Photoreceptors:

Circadian clocks are internal molecular time-keeping mechanisms that provide living organisms with the ability to adjust their growth and physiology and to anticipate diurnal environmental changes. Circadian clocks, without exception, respond to light and, in plants, light is the most potent and best characterized entraining stimulus. The capacity of plants to respond to light is achieved through a number of photo-perceptive proteins including cryptochromes and phytochromes. There is considerable experimental evidence demonstrating the roles of photoreceptors in providing light input to the clock. In order to identify genes regulated by diurnal and circadian rhythms, and to establish possible functional relations between photoreceptors and the circadian clock in tomato, we monitored the temporal transcription pattern in plants entrained to long-day conditions, either by large scale comparative profiling, or using a focused approach over a number of photosensory and clock-related genes by QRT-PCR. In parallel, focused transcription analyses were performed in cry1a- and in CRY2-OX tomato genotypes. We report a large series of transcript oscillations that shed light on the complex network of interactions among tomato photoreceptors and clock-related genes. Alteration of cryptochrome gene expression induced major changes in the rhythmic oscillations of several other gene transcripts. In particular, over-expression of CRY2 had an impact not only on day/night fluctuations but also on rhythmicity under constant light conditions. Evidence was found for widespread diurnal oscillations of transcripts encoding specific enzyme classes (e.g. carotenoid biosynthesis enzymes) as well as for post-transcriptional diurnal and circadian regulation of the CRY2 transcript.

Postglacial Colonisation Patterns and the Role of Isolation and Expansion in Driving Diversification in a Passerine Bird:

Pleistocene glacial cycles play a major role in diversification and speciation, although the relative importance of isolation and expansion in driving diversification remains debated. We analysed mitochondrial DNA sequence data from 15 great reed warbler (Acrocephalus arundinaceus) populations distributed over the vast Eurasian breeding range of the species, and revealed unexpected postglacial expansion patterns from two glacial refugia. There were 58 different haplotypes forming two major clades, A and B. Clade A dominated in Western Europe with declining frequencies towards Eastern Europe and the Middle East, but showed a surprising increase in frequency in Western and Central Asia. Clade B dominated in the Middle East, with declining frequencies towards north in Central and Eastern Europe and was absent from Western Europe and Central Asia. A parsimonious explanation for these patterns is independent postglacial expansions from two isolated refugia, and mismatch distribution analyses confirmed this suggestion. Gene flow analyses showed that clade A colonised both Europe and Asia from a refugium in Europe, and that clade B expanded much later and colonised parts of Europe from a refugium in the Middle East. Great reed warblers in the eastern parts of the range have slightly paler plumage than western birds (sometimes treated as separate subspecies; A. a. zarudnyi and A. a. arundinaceus, respectively) and our results suggest that the plumage diversification took place during the easterly expansion of clade A. This supports the postglacial expansion hypothesis proposing that postglacial expansions drive diversification in comparatively short time periods. However, there is no indication of any (strong) reproductive isolation between clades and our data show that the refugia populations became separated during the last glaciation. This is in line with the Pleistocene speciation hypothesis invoking that much longer periods of time in isolation are needed for speciation to occur.

Evolution of Skull and Mandible Shape in Cats (Carnivora: Felidae):

The felid family consists of two major subgroups, the sabretoothed and the feline cats, to which all extant species belong, and are the most anatomically derived of all carnivores for predation on large prey with a precision killing bite. There has been much controversy and uncertainty about why the skulls and mandibles of sabretoothed and feline cats evolved to become so anatomically divergent, but previous models have focused on single characters and no unifying hypothesis of evolutionary shape changes has been formulated. Here I show that the shape of the skull and mandible in derived sabrecats occupy entirely different positions within overall morphospace from feline cats, and that the evolution of skull and mandible shape has followed very different paths in the two subgroups. When normalised for body-size differences, evolution of bite forces differ markedly in the two groups, and are much lower in derived sabrecats, and they show a significant relationship with size and cranial shape, whereas no such relationship is present in feline cats. Evolution of skull and mandible shape in modern cats has been governed by the need for uniform powerful biting irrespective of body size, whereas in sabrecats, shape evolution was governed by selective pressures for efficient predation with hypertrophied upper canines at high gape angles, and bite forces were secondary and became progressively weaker during sabrecat evolution. The current study emphasises combinations of new techniques for morphological shape analysis and biomechanical studies to formulate evolutionary hypotheses for difficult groups.

Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms:

A scanning electron microscope survey was initiated to determine if the previously reported findings of “dinosaurian soft tissues” could be identified in situ within the bones. The results obtained allowed a reinterpretation of the formation and preservation of several types of these “tissues” and their content. Mineralized and non-mineralized coatings were found extensively in the porous trabecular bone of a variety of dinosaur and mammal species across time. They represent bacterial biofilms common throughout nature. Biofilms form endocasts and once dissolved out of the bone, mimic real blood vessels and osteocytes. Bridged trails observed in biofilms indicate that a previously viscous film was populated with swimming bacteria. Carbon dating of the film points to its relatively modern origin. A comparison of infrared spectra of modern biofilms with modern collagen and fossil bone coatings suggests that modern biofilms share a closer molecular make-up than modern collagen to the coatings from fossil bones. Blood cell size iron-oxygen spheres found in the vessels were identified as an oxidized form of formerly pyritic framboids. Our observations appeal to a more conservative explanation for the structures found preserved in fossil bone.

From Plants to Birds: Higher Avian Predation Rates in Trees Responding to Insect Herbivory:

An understanding of the evolution of potential signals from plants to the predators of their herbivores may provide exciting examples of co-evolution among multiple trophic levels. Understanding the mechanism behind the attraction of predators to plants is crucial to conclusions about co-evolution. For example, insectivorous birds are attracted to herbivore-damaged trees without seeing the herbivores or the defoliated parts, but it is not known whether birds use cues from herbivore-damaged plants with a specific adaptation of plants for this purpose. We examined whether signals from damaged trees attract avian predators in the wild and whether birds could use volatile organic compound (VOC) emissions or net photosynthesis of leaves as cues to detect herbivore-rich trees. We conducted a field experiment with mountain birches (Betula pubescens ssp. czerepanovii), their main herbivore (Epirrita autumnata) and insectivorous birds. Half of the trees had herbivore larvae defoliating trees hidden inside branch bags and half had empty bags as controls. We measured predation rate of birds towards artificial larvae on tree branches, and VOC emissions and net photosynthesis of leaves. The predation rate was higher in the herbivore trees than in the control trees. This confirms that birds use cues from trees to locate insect-rich trees in the wild. The herbivore trees had decreased photosynthesis and elevated emissions of many VOCs, which suggests that birds could use either one, or both, as cues. There was, however, large variation in how the VOC emission correlated with predation rate. Emissions of (E)-DMNT [(E)-4,8-dimethyl-1,3,7-nonatriene], β-ocimene and linalool were positively correlated with predation rate, while those of highly inducible green leaf volatiles were not. These three VOCs are also involved in the attraction of insect parasitoids and predatory mites to herbivore-damaged plants, which suggests that plants may not have specific adaptations to signal only to birds.

Temperature-Dependent Sex Determination in Fish Revisited: Prevalence, a Single Sex Ratio Response Pattern, and Possible Effects of Climate Change:

In gonochoristic vertebrates, sex determination mechanisms can be classified as genotypic (GSD) or temperature-dependent (TSD). Some cases of TSD in fish have been questioned, but the prevalent view is that TSD is very common in this group of animals, with three different response patterns to temperature. We analyzed field and laboratory data for the 59 fish species where TSD has been explicitly or implicitly claimed so far. For each species, we compiled data on the presence or absence of sex chromosomes and determined if the sex ratio response was obtained within temperatures that the species experiences in the wild. If so, we studied whether this response was statistically significant. We found evidence that many cases of observed sex ratio shifts in response to temperature reveal thermal alterations of an otherwise predominately GSD mechanism rather than the presence of TSD. We also show that in those fish species that actually have TSD, sex ratio response to increasing temperatures invariably results in highly male-biased sex ratios, and that even small changes of just 1-2°C can significantly alter the sex ratio from 1:1 (males:females) up to 3:1 in both freshwater and marine species. We demonstrate that TSD in fish is far less widespread than currently believed, suggesting that TSD is clearly the exception in fish sex determination. Further, species with TSD exhibit only one general sex ratio response pattern to temperature. However, the viability of some fish populations with TSD can be compromised through alterations in their sex ratios as a response to temperature fluctuations of the magnitude predicted by climate change.

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Piecing Together An Extinct Lemur, Large As A Big Baboon:

Penn State researchers have used computed tomography (CT) technology to virtually glue newly-discovered skull fragments of a rare extinct lemur back into its partial skull, which was discovered over a century ago. Alan Walker, Evan Pugh Professor of Anthropology and Biology at Penn State, and Research Associate in Anthropology Timothy Ryan, led the research. The different fragments of this lemur’s skull are separated by thousands of miles, with the partial skull in Vienna and the pieces of frontal bone in the United States.

Insect Biodiversity In Amazon May Be Result Of Ice Age Climate Change And Ancient Flooding, Not River Barriers:

Ice age climate change and ancient flooding–but not barriers created by rivers–may have promoted the evolution of new insect species in the Amazon region of South America, a new study suggests.

Unexpected Key To Flowering Plants’ Diversity:

What began with an off-the-cuff curiosity eventually led Joe Williams to hang from the limbs of a tree 80 feet above the soil of northeastern Australia. The things Williams, a University of Tennessee, Knoxville, researcher found there may help explain the amazing diversity in the world’s flowering plants, a question that has puzzled scientists from the time of Charles Darwin to today.

Uncertain Future For Elephants Of Thailand:

Worries over the future of Thailand’ s famous elephants have emerged following an investigation by a University of Manchester team.

Endangered European Wild Cat May Protected By Proposed Network Of Corridors:

For the first time an international researcher team has developed a model, which identifies potential habitats and corridors for the European wildcat (Felis silvestris silvestris). Using Rheinland-Pfalz as an example, it was demonstrated that almost half of this German federal state could be suitable for wildcats, enabling a maximum population of 1600 females.

What’s new in PLoS Biology and PLoS Medicine this week? Among else:

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Birdsong Not Just For The Birds: Bio-acoustic Method Also Hears Nature’s Cry For Help:

Switch on the mike, start the recording, the stage is set for the local fauna!

Explosion In Marine Biodiversity Explained By Climate Change:

A global change in climate could explain the explosion in marine biodiversity that took place 460 million years ago. Researchers from Lyon (1) and Canberra (Australia) (2) have found evidence of a progressive ocean cooling of about 15°C over a period of 40 million years during the Ordovician (3). Until now, this geologic period had been associated with a “super greenhouse effect” on our planet.

Plant Steroids Offer New Paradigm For How Hormones Work:

Steroids bulk up plants just as they do human athletes, but the playbook of molecular signals that tell the genes to boost growth and development in plant cells is far more complicated than in human and animal cells.

Acidification Of The Sea Hampers Reproduction Of Marine Species: Decreasing pH The Biggest Threat To Marine Animal Life For Thousands Of Years:

By absorbing carbon dioxide from the atmosphere, and from the human use of fossil fuels, the world’s seas function as a giant buffer for the Earth’s life support system. The chemical balance of the sea has long been regarded as immovable.

Bacteria Reveal Secret Of Adaptation At Evolution Canyon:

Bacteria living on opposite sides of a canyon have evolved to cope with different temperatures by altering the make-up of their ‘skin’, or cell membranes. Scientists have found that bacteria change these complex and important structures to adapt to different temperatures by looking at the appearance of the bacteria as well as their genes. The researchers hope their study, published in the August issue of Microbiology, will start a new trend in research.