Friday - when four out of seven PLoS journals publish new articles. Check them out. And 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:
Protected areas are fundamental to biodiversity conservation, but there is growing recognition of the need to extend beyond protected areas to meet the ecological requirements of species at larger scales. Landscape-scale conservation requires an evaluation of management impact on biodiversity under different land-use strategies; this is challenging and there exist few empirical studies. In a conservation landscape in northern Republic of Congo we demonstrate the application of a large-scale monitoring program designed to evaluate the impact of conservation interventions on three globally threatened species: western gorillas, chimpanzees and forest elephants, under three land-use types: integral protection, commercial logging, and community-based natural resource management. We applied distance-sampling methods to examine species abundance across different land-use types under varying degrees of management and human disturbance. We found no clear trends in abundance between land-use types. However, units with interventions designed to reduce poaching and protect habitats - irrespective of land-use type - harboured all three species at consistently higher abundance than a neighbouring logging concession undergoing no wildlife management. We applied Generalized-Additive Models to evaluate a priori predictions of species response to different landscape processes. Our results indicate that, given adequate protection from poaching, elephants and gorillas can profit from herbaceous vegetation in recently logged forests and maintain access to ecologically important resources located outside of protected areas. However, proximity to the single integrally protected area in the landscape maintained an overriding positive influence on elephant abundance, and logging roads - even subject to anti-poaching controls - were exploited by elephant poachers and had a major negative influence on elephant distribution. Chimpanzees show a clear preference for unlogged or more mature forests and human disturbance had a negative influence on chimpanzee abundance, in spite of anti-poaching interventions. We caution against the pitfalls of missing and confounded co-variables in model-based estimation approaches and highlight the importance of spatial scale in the response of different species to landscape processes. We stress the importance of a stratified design-based approach to monitoring species status in response to conservation interventions and advocate a holistic framework for landscape-scale monitoring that includes smaller-scale targeted research and punctual assessment of threats.
The Fine Tuning of Pain Thresholds: A Sophisticated Double Alarm System:
Two distinctive features characterize the way in which sensations including pain, are evoked by heat: (1) a thermal stimulus is always progressive; (2) a painful stimulus activates two different types of nociceptors, connected to peripheral afferent fibers with medium and slow conduction velocities, namely Aδ- and C-fibers. In the light of a recent study in the rat, our objective was to develop an experimental paradigm in humans, based on the joint analysis of the stimulus and the response of the subject, to measure the thermal thresholds and latencies of pain elicited by Aδ- and C-fibers. For comparison, the same approach was applied to the sensation of warmth elicited by thermoreceptors. A CO2 laser beam raised the temperature of the skin filmed by an infrared camera. The subject stopped the beam when he/she perceived pain. The thermal images were analyzed to provide four variables: true thresholds and latencies of pain triggered by heat via Aδ- and C-fibers. The psychophysical threshold of pain triggered by Aδ-fibers was always higher (2.5-3°C) than that triggered by C-fibers. The initial skin temperature did not influence these thresholds. The mean conduction velocities of the corresponding fibers were 13 and 0.8 m/s, respectively. The triggering of pain either by C- or by Aδ-fibers was piloted by several factors including the low/high rate of stimulation, the low/high base temperature of the skin, the short/long peripheral nerve path and some pharmacological manipulations (e.g. Capsaicin). Warming a large skin area increased the pain thresholds. Considering the warmth detection gave a different picture: the threshold was strongly influenced by the initial skin temperature and the subjects detected an average variation of 2.7°C, whatever the initial temperature. This is the first time that thresholds and latencies for pain elicited by both Aδ- and C-fibers from a given body region have been measured in the same experimental run. Such an approach illustrates the role of nociception as a "double level" and "double release" alarm system based on level detectors. By contrast, warmth detection was found to be based on difference detectors. It is hypothesized that pain results from a CNS build-up process resulting from population coding and strongly influenced by the background temperatures surrounding at large the stimulation site. We propose an alternative solution to the conventional methods that only measure a single "threshold of pain", without knowing which of the two systems is involved.
One Bacterial Cell, One Complete Genome:
While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200-900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.
Dissociable Neural Systems for Timing: Evidence from Subjects with Basal Ganglia Lesions:
The neural basis of timing remains poorly understood. Although controversy persists, many lines of evidence, including studies in animals, functional imaging studies in humans and lesion studies in humans and animals suggest that the basal ganglia are important for temporal processing [1]. We report data from a wide range of timing tasks from two subjects with disabling neurologic deficits caused by bilateral lesions of the basal ganglia. Both subjects perform well on tasks assessing time estimation, reproduction and production tasks. Additionally, one subject performed normally on psychophysical tasks requiring the comparison of time intervals ranging from milliseconds to seconds; the second subject performed abnormally on the psychophysical task with a 300ms standard but did well with 600ms, 2000ms and 8000ms standards. Both subjects performed poorly on an isochronous rhythm production task on which they are required to maintain rhythmic tapping. As studies of subjects with brain lesions permit strong inferences regarding the necessity of brain structures, these data demonstrate that the basal ganglia are not crucial for many sub- or supra-second timing operations in humans but are needed for the timing procedures that underlie the production of movements. This dissociation suggests that distinct and dissociable processes may be employed to measure time intervals. Inconsistencies in findings regarding the neural basis of timing may reflect the availability of multiple temporal processing routines that are flexibly implemented in response to task demands.
Population variation in the degree of seasonal polymorphism is rare in birds, and the genetic basis of this phenomenon remains largely undescribed. Both sexes of Scandinavian and Scottish Willow grouse (Lagopus lagopus) display marked differences in their winter phenotypes, with Scottish grouse retaining a pigmented plumage year-round and Scandinavian Willow grouse molting to a white morph during winter. A widely studied pathway implicated in vertebrate pigmentation is the melanin system, for which functional variation has been characterised in many taxa. We sequenced coding regions from four genes involved in melanin pigmentation (DCT, MC1R, TYR and TYRP1), and an additional control involved in the melanocortin pathway (AGRP), to investigate the genetic basis of winter plumage in Lagopus. Despite the well documented role of the melanin system in animal coloration, we found no plumage-associated polymorphism or evidence for selection in a total of ~2.6 kb analysed sequence. Our results indicate that the genetic basis of alternating between pigmented and unpigmented seasonal phenotypes is more likely explained by regulatory changes controlling the expression of these or other loci in the physiological pathway leading to pigmentation.
Innate Recognition of Fungal Cell Walls:
The emergence of fungal infections as major causes of morbidity and mortality in immunosuppressed individuals has prompted studies into how the host recognizes fungal pathogens. Fungi are eukaryotes and as such share many similarities with mammalian cells. The most striking difference, though, is the presence of a cell wall that serves to protect the fungus from environmental stresses, particularly osmotic changes [1]. This task is made challenging because the fungus must remodel itself to allow for cell growth and division, including the conversion to different morphotypes, such as occurs during germination of spherical spores into filamentous hyphae. The cell wall also connects the fungus with its environment by triggering intracellular signaling pathways and mediating adhesion to other cells and extracellular matrices. Here, important facts and concepts critical for understanding innate sensing of the fungal cell wall by mammalian pathogens are reviewed.
Genome-wide association studies (GWAS) have successfully contributed to the detection of genetic variants involved in body-weight regulation. We jointly analysed two GWAS for early-onset extreme obesity in 2,258 individuals of European origin and followed-up the findings in 3,141 individuals. Evidence for association of markers in two new genetic loci was shown (SDCCAG8 on chromosome 1q43-q44 and between TNKS/MSRA on chromosome 8p23.1). We also re-identified variants in or near FTO, MC4R, and TMEM18 to be associated with extreme obesity. In addition, we assessed the effect of the markers in 31,182 obese, lean, normal weight, and unselected individuals from population-based samples and showed that the variants near FTO, MC4R, TMEM18, and SDCCAG8 were consistently associated with obesity. For variants of TNKS/MSRA, the obesity association was limited to children and adolescents. In summary, we detected two new obesity loci and confirmed that the currently known major common variants related to obesity overlap to a substantial degree between children and adults.
A Reaction-Diffusion Model of Human Brain Development:
The anatomical variability of the human brain folds remains an unclear and challenging issue. However it is clear that this variability is the product of the brain development. Several hypotheses coexist for explaining the rapid development of cortical sulci and it is of the highest interest that understanding their variability would improve the comparison of anatomical and functional data across cohorts of subjects. In this article we propose to extend a model of cortical folding based on interactions between growth factors that shape the cortical surface. First the originality of our approach lies in the fact that the surface on which these mechanisms take place is deformed iteratively and engenders geometric patterns that can be linked to cortical sulci. Secondly we show that some statistical properties of our model can reflect the reproducibility and the variability of sulcal structures. At the end we compare different patterns produced by the model to different pathologies of brain development.
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