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New and Exciting in PLoS this week

Over the past week or so, PLoS IT/Web team made some serious upgrades to the site, including a much better, faster search – go and test it! Friday is also the time to point out cool new papers from four out of seven PLoS journals. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

Shearwater Foraging in the Southern Ocean: The Roles of Prey Availability and Winds:

Sooty (Puffinus griseus) and short-tailed (P. tenuirostris) shearwaters are abundant seabirds that range widely across global oceans. Understanding the foraging ecology of these species in the Southern Ocean is important for monitoring and ecosystem conservation and management. Tracking data from sooty and short-tailed shearwaters from three regions of New Zealand and Australia were combined with at-sea observations of shearwaters in the Southern Ocean, physical oceanography, near-surface copepod distributions, pelagic trawl data, and synoptic near-surface winds. Shearwaters from all three regions foraged in the Polar Front zone, and showed particular overlap in the region around 140°E. Short-tailed shearwaters from South Australia also foraged in Antarctic waters south of the Polar Front. The spatial distribution of shearwater foraging effort in the Polar Front zone was matched by patterns in large-scale upwelling, primary production, and abundances of copepods and myctophid fish. Oceanic winds were found to be broad determinants of foraging distribution, and of the flight paths taken by the birds on long foraging trips to Antarctic waters. The shearwaters displayed foraging site fidelity and overlap of foraging habitat between species and populations that may enhance their utility as indicators of Southern Ocean ecosystems. The results highlight the importance of upwellings due to interactions of the Antarctic Circumpolar Current with large-scale bottom topography, and the corresponding localised increases in the productivity of the Polar Front ecosystem.

Phylogenetic Relationships among Deep-Sea and Chemosynthetic Sea Anemones: Actinoscyphiidae and Actinostolidae (Actiniaria: Mesomyaria):

Sea anemones (Cnidaria, Actiniaria) are present in all marine ecosystems, including chemosynthetic environments. The high level of endemicity of sea anemones in chemosynthetic environments and the taxonomic confusion in many of the groups to which these animals belong makes their systematic relationships obscure. We use five molecular markers to explore the phylogenetic relationships of the superfamily Mesomyaria, which includes most of the species that live in chemosynthetic, deep-sea, and polar sea habitats and to test the monophyly of the recently defined clades Actinostolina and Chemosynthina. We found that sea anemones of chemosynthetic environments derive from at least two different lineages: one lineage including acontiate deep-sea taxa and the other primarily encompassing shallow-water taxa.

Trypanosoma brucei Modifies the Tsetse Salivary Composition, Altering the Fly Feeding Behavior That Favors Parasite Transmission:

Human African Trypanosomiasis, or sleeping sickness, is a devastating parasitic disease that is fatal if left untreated. Infections are acquired via the bite of an obligate blood feeding fly, the tsetse fly, that is exclusively present on the African continent. In this insect vector, the trypanosome parasite has a complex development ending in the salivary glands. In this experimental study we demonstrate that the Trypanosoma brucei parasites change the composition of the tsetse fly saliva making it less efficient to keep the blood fluid at the biting site in the mammalian host. This results in a more difficult blood feeding process and favors the fly biting activity on multiple hosts, thereby promoting the survival and circulation of the parasite within the natural host population. These findings give us a better understanding of how trypanosome infections in the human population can be maintained given the fact that only very few tsetse flies are actually carrying the parasite.

The Lagoon at Caroline/Millennium Atoll, Republic of Kiribati: Natural History of a Nearly Pristine Ecosystem:

A series of surveys were carried out to characterize the physical and biological parameters of the Millennium Atoll lagoon during a research expedition in April of 2009. Millennium is a remote coral atoll in the Central Pacific belonging to the Republic of Kiribati, and a member of the Southern Line Islands chain. The atoll is among the few remaining coral reef ecosystems that are relatively pristine. The lagoon is highly enclosed, and was characterized by reticulate patch and line reefs throughout the center of the lagoon as well as perimeter reefs around the rim of the atoll. The depth reached a maximum of 33.3 m in the central region of the lagoon, and averaged between 8.8 and 13.7 m in most of the pools. The deepest areas were found to harbor large platforms of Favia matthaii, which presumably provided a base upon which the dominant corals (Acropora spp.) grew to form the reticulate reef structure. The benthic algal communities consisted mainly of crustose coralline algae (CCA), microfilamentous turf algae and isolated patches of Halimeda spp. and Caulerpa spp. Fish species richness in the lagoon was half of that observed on the adjacent fore reef. The lagoon is likely an important nursery habitat for a number of important fisheries species including the blacktip reef shark and Napoleon wrasse, which are heavily exploited elsewhere around the world but were common in the lagoon at Millennium. The lagoon also supports an abundance of giant clams (Tridacna maxima). Millennium lagoon provides an excellent reference of a relatively undisturbed coral atoll. As with most coral reefs around the world, the lagoon communities of Millennium may be threatened by climate change and associated warming, acidification and sea level rise, as well as sporadic local resource exploitation which is difficult to monitor and enforce because of the atoll’s remote location. While the remote nature of Millennium has allowed it to remain one of the few nearly pristine coral reef ecosystems in the world, it is imperative that this ecosystem receives protection so that it may survive for future generations.

Cutaneous Bacteria of the Redback Salamander Prevent Morbidity Associated with a Lethal Disease:

Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), is an infectious disease that causes population declines of many amphibians. Cutaneous bacteria isolated from redback salamanders, Plethodon cinereus, and mountain yellow-legged frogs, Rana muscosa, inhibit the growth of Bd in vitro. In this study, the bacterial community present on the skin of P. cinereus individuals was investigated to determine if it provides protection to salamanders from the lethal and sub-lethal effects of chytridiomycosis. When the cutaneous bacterial community was reduced prior to Bd exposure, salamanders experienced a significantly greater decrease in body mass, which is a symptom of the disease, when compared to infected individuals with a normal bacterial community. In addition, a greater proportion of infected individuals with a reduced bacterial community experienced limb-lifting, a behavior seen only in infected individuals. Overall, these results demonstrate that the cutaneous bacterial community of P. cinereus provides protection to the salamander from Bd and that alteration of this community can change disease resistance. Therefore, symbiotic microbes associated with this species appear to be an important component of its innate skin defenses.

Activation of AMPA Receptors in the Suprachiasmatic Nucleus Phase-Shifts the Mouse Circadian Clock In Vivo and In Vitro:

The glutamatergic neurotransmission in the suprachiasmatic nucleus (SCN) plays a central role in the entrainment of the circadian rhythms to environmental light-dark cycles. Although the glutamatergic effect operating via NMDAR (N-methyl D-aspartate receptor) is well elucidated, much less is known about a role of AMPAR (α-amino-3-hydroxy-5-methylisoxazole-4-p​ropionic acid receptor) in circadian entrainment. Here we show that, in the mouse SCN, GluR2 and GluR4 AMPAR subtypes are abundantly expressed in the retinorecipient area. In vivo microinjection of AMPA in the SCN during the early subjective night phase-delays the behavioral rhythm. In the organotypic SCN slice culture, AMPA application induces phase-dependent phase-shifts of core-clock gene transcription rhythms. These data demonstrate that activation of AMPAR is capable of phase-shifting the circadian clock both in vivo and in vitro, and are consistent with the hypothesis that activation of AMPA receptors is a critical step in the transmission of photic information to the SCN.

Use of Genome-Wide Expression Data to Mine the “Gray Zone” of GWA Studies Leads to Novel Candidate Obesity Genes:

Obesity has a strong genetic component and an estimated 45%-85% of the variation in adult relative weight is genetically determined. Many genes have recently been identified in genome-wide association studies. The individual effects of the identified genes, however, have been very modest, and their identification required very large sample sizes. New approaches are therefore needed to uncover further genetic variants that contribute to the development of obesity and related conditions. Much can be learned from studying the expression of genes in adipose tissue of obese and non-obese subjects, but it is very difficult to distinguish which genes’ expression differences represent reactions to obesity from those related to causal processes. We studied monozygotic twin pairs discordant for obesity and contrasted the gene expression profiles of obese and lean co-twins (controlling for genetic variation) to those from unrelated individuals to try to discern the cause-and-effect relationships of the identified changes in gene expression in fat. Testing the identified genes in 21,000 individuals identified numerous new genes with possible roles in the development of obesity. Among the top findings was a gene involved in blood coagulation (Factor XIIIA1), possibly linking obesity with known complications including deep vein thrombosis, heart attack, and stroke.

Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families:

Metagenomics provides a unique opportunity to sample the gene content of microbial communities adapted to specific environments and for the study of the correlations between the presence or absence of gene families that occur in organisms within that environment. Such studies provide detailed information about the adaptation of microbes to a given environment and, indirectly, provide clues about the most important molecular processes that are specific for that environment. Having performed such an analysis for the community of the human distal gut, we report many new protein families and identify many others that are highly specific for this particular environment. The function of most of these proteins is unknown, which illustrates the extent of our ignorance about the organisms within this environment that are so important for human health and well being.

Internet Treatment for Generalized Anxiety Disorder: A Randomized Controlled Trial Comparing Clinician vs. Technician Assistance:

Internet-based cognitive behavioural therapy (iCBT) for generalized anxiety disorder (GAD) has been shown to be effective when guided by a clinician. The present study sought to replicate this finding, and determine whether support from a technician is as effective as guidance from a clinician. Randomized controlled non-inferiority trial comparing three groups: Clinician-assisted vs. technician-assisted vs. delayed treatment. Community-based volunteers applied to the VirtualClinic (www.virtualclinic.org.au) research program and 150 participants with GAD were randomized. Participants in the clinician- and technician-assisted groups received access to an iCBT program for GAD comprising six online lessons, weekly homework assignments, and weekly supportive contact over a treatment period of 10 weeks. Participants in the clinician-assisted group also received access to a moderated online discussion forum. The main outcome measures were the Penn State Worry Questionnaire (PSWQ) and the Generalized Anxiety Disorder-7 Item (GAD-7). Completion rates were high, and both treatment groups reduced scores on the PSWQ (p<0.001) and GAD-7 (p<0.001) compared to the delayed treatment group, but did not differ from each other. Within group effect sizes on the PSWQ were 1.16 and 1.07 for the clinician- and technician-assisted groups, respectively, and on the GAD-7 were 1.55 and 1.73, respectively. At 3 month follow-up participants in both treatment groups had sustained the gains made at post-treatment. Participants in the clinician-assisted group had made further gains on the PSWQ. Approximately 81 minutes of clinician time and 75 minutes of technician time were required per participant during the 10 week treatment program. Both clinician- and technician-assisted treatment resulted in large effect sizes and clinically significant improvements comparable to those associated with face-to-face treatment, while a delayed treatment/control group did not improve. These results provide support for large scale trials to determine the clinical effectiveness and acceptability of technician-assisted iCBT programs for GAD. This form of treatment has potential to increase the capacity of existing mental health services.

Optimal Drug Synergy in Antimicrobial Treatments:

The use of antibiotics against bacterial infections has led to the emergence of multi-drug resistant pathogens such as tuberculosis and MRSA. In order to control resistance, clinicians have increasingly turned to multi-antibiotic therapies. The common wisdom is to use combinations of drugs that act synergistically to kill the infection, but the impact of drug synergy on the evolution of resistance is unclear. Using mathematical simulations of an in vivo infection model, we asked what level of drug synergy would minimize the risk of multi-drug resistance while preserving the efficacy of treatment. We found that synergy may increase or decrease the risk of multi-drug resistance in a given treatment, depending on infection properties such as mutation rate and the availability of resources. Surprisingly, under conditions of strong competition for resources within the host, we found that maximal synergy–currently favored in clinical settings–can actually increase the risk of multi-drug resistance. Our results identify conditions under which drug synergy exacerbates the problem of multi-drug resistance, and offer guidelines for the selection of drug pairs that suppress it.

Optimality of Mutation and Selection in Germinal Centers:

The antibodies in our immune system could efficiently improve their abilities in recognizing new antigens. This is done with the help of proliferation, mutation and selection of B cells which carry antibodies, but we have difficulties in developing a quantitative description of this adaptation process which is consistent with the various aspects of experimental observations. Based on the knowledge from experiments, here we present a theoretical model to calculate the numbers of B cells with different antigen recognizing abilities all the time, and look for the best possible design that improves the antigen recognizing ability most efficiently. We find that the best possible design is consistent with the experimental observations, pointing to the conclusion that the immune system has been optimized in evolution. We then study the trade-offs leading to the optimization of the design. The results will not only improve our understanding of the functions in immune system, but also reveal the design principles behind the details. In addition, the study enhances our understanding of the population dynamics in evolution.

Within- and Among-Population Variation in Chytridiomycosis-Induced Mortality in the Toad Alytes obstetricans:

Chytridiomycosis is a fungal disease linked to local and global extinctions of amphibians. Susceptibility to chytridiomycosis varies greatly between amphibian species, but little is known about between- and within-population variability. However, this kind of variability is the basis for the evolution of tolerance and resistance evolution to disease. In a common garden experiment, we measured mortality after metamorphosis of Alytes obstetricans naturally infected with Batrachochytrium dendrobatidis. Mortality rates differed significantly among populations and ranged from 27 to 90%. Within populations, mortality strongly depended on mass at and time through metamorphosis. Although we cannot rule out that the differences observed resulted from differences in skin microbiota, different pathogen strains or environmental effects experienced by the host or the pathogen prior to the start of the experiment, we argue that genetic differences between populations are a likely source of at least part of this variation. To our knowledge, this is the first study showing differences in survival between and within populations under constant laboratory conditions. Assuming that some of this intraspecific variation has a genetic basis, this may suggest that there is the potential for the evolution of resistance or tolerance, which might allow population persistence.

Evolution of DNA Replication Protein Complexes in Eukaryotes and Archaea:

The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA), replication factor C (RFC), and the minichromosome maintenance (MCM) complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best. While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex–all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea. This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota.

SUBTLEX-CH: Chinese Word and Character Frequencies Based on Film Subtitles:

Word frequency is the most important variable in language research. However, despite the growing interest in the Chinese language, there are only a few sources of word frequency measures available to researchers, and the quality is less than what researchers in other languages are used to. Following recent work by New, Brysbaert, and colleagues in English, French and Dutch, we assembled a database of word and character frequencies based on a corpus of film and television subtitles (46.8 million characters, 33.5 million words). In line with what has been found in the other languages, the new word and character frequencies explain significantly more of the variance in Chinese word naming and lexical decision performance than measures based on written texts. Our results confirm that word frequencies based on subtitles are a good estimate of daily language exposure and capture much of the variance in word processing efficiency. In addition, our database is the first to include information about the contextual diversity of the words and to provide good frequency estimates for multi-character words and the different syntactic roles in which the words are used. The word frequencies are freely available for research purposes.