Multilocus Phylogenetic Study of the Scheffersomyces Yeast Clade and Characterization of the N-Terminal Region of Xylose Reductase Gene

Many of the known xylose-fermenting (X-F) yeasts are placed in the Scheffersomyces clade, a group of ascomycete yeasts that have been isolated from plant tissues and in association with lignicolous insects. We formally recognize fourteen species in this clade based on a maximum likelihood (ML) phylogenetic analysis using a multilocus dataset. This clade is divided into three subclades, each of which exhibits the biochemical ability to ferment cellobiose or xylose. New combinations are made for seven species of Candida in the clade, and three X-F taxa associated with rotted hardwood are described: Scheffersomyces illinoinensis (type strain NRRL Y-48827T  =  CBS 12624), Scheffersomyces quercinus (type strain NRRL Y-48825T  =  CBS 12625), and Scheffersomyces virginianus (type strain NRRL Y-48822T  =  CBS 12626). The new X-F species are distinctive based on their position in the multilocus phylogenetic analysis and biochemical and morphological characters. The molecular characterization of xylose reductase (XR) indicates that the regions surrounding the conserved domain contain mutations that may enhance the performance of the enzyme in X-F yeasts. The phylogenetic reconstruction using XYL1 or RPB1 was identical to the multilocus analysis, and these loci have potential for rapid identification of cryptic species in this clade

Post-genomic approaches to understanding interactions between fungi and their environment

Fungi inhabit every natural and anthropogenic environment on Earth. They have highly varied life-styles including saprobes (using only dead biomass as a nutrient source), pathogens (feeding on living biomass), and symbionts (co-existing with other organisms). These distinctions are not absolute as many species employ several life styles (e.g. saprobe and opportunistic pathogen, saprobe and mycorrhiza). To efficiently survive in these different and often changing environments, fungi need to be able to modify their physiology and in some cases will even modify their local environment. Understanding the interaction between fungi and their environments has been a topic of study for many decades. However, recently these studies have reached a new dimension. The availability of fungal genomes and development of post-genomic technologies for fungi, such as transcriptomics, proteomics and metabolomics, have enabled more detailed studies into this topic resulting in new insights. Based on a Special Interest Group session held during IMC9, this paper provides examples of the recent advances in using (post-)genomic approaches to better understand fungal interactions with their environments

A sociological dilemma: race, segregation, and US sociology

US sociology has been historically segregated in that, at least until the 1960s, there were two distinct institutionally organized traditions of sociological thought – one black and one white. For the most part, however, dominant historiographies have been silent on that segregation and, at best, reproduce it when addressing the US sociological tradition. This is evident in the rarity with which scholars such as WEB Du Bois, E Franklin Frazier, Oliver Cromwell Cox, or other ‘African American Pioneers of Sociology’, as Saint-Arnaud calls them, are presented as core sociological voices within histories of the discipline. This article addresses the absence of African American sociologists from the US sociological canon and, further, discusses the implications of this absence for our understanding of core sociological concepts. With regard to the latter, the article focuses in particular on the debates around equality and emancipation and discusses the ways in which our understanding of these concepts could be extended by taking into account the work of African American sociologists and their different interpretations of core themes

The Enigma of Soil Animal Species Diversity Revisited: The Role of Small-Scale Heterogeneity

Peer reviewedPublisher PD

Source identification and distribution reveals the potential of the geochemical Antarctic sea ice proxy IPSO25

The presence of a di-unsaturated highly branched isoprenoid (HBI) lipid biomarker (diene II) in Southern Ocean sediments has previously been proposed as a proxy measure of palaeo Antarctic sea ice. Here we show that a source of diene II is the sympagic diatom Berkeleya adeliensis Medlin. Furthermore, the propensity for B. adeliensis to flourish in platelet ice is reflected by an offshore downward gradient in diene II concentration in >100 surface sediments from Antarctic coastal and near-coastal environments. Since platelet ice formation is strongly associated with super-cooled freshwater inflow, we further hypothesize that sedimentary diene II provides a potentially sensitive proxy indicator of landfast sea ice influenced by meltwater discharge from nearby glaciers and ice shelves, and re-examination of some previous diene II downcore records supports this hypothesis. The term IPSO25-Ice Proxy for the Southern Ocean with 25 carbon atoms-is proposed as a proxy name for diene II

Efficient Network Reconstruction from Dynamical Cascades Identifies Small-World Topology of Neuronal Avalanches

Cascading activity is commonly found in complex systems with directed interactions such as metabolic networks, neuronal networks, or disease spreading in social networks. Substantial insight into a system's organization can be obtained by reconstructing the underlying functional network architecture from the observed activity cascades. Here we focus on Bayesian approaches and reduce their computational demands by introducing the Iterative Bayesian (IB) and Posterior Weighted Averaging (PWA) methods. We introduce a special case of PWA, cast in nonparametric form, which we call the normalized count (NC) algorithm. NC efficiently reconstructs random and small-world functional network topologies and architectures from subcritical, critical, and supercritical cascading dynamics and yields significant improvements over commonly used correlation methods. With experimental data, NC identified a functional and structural small-world topology and its corresponding traffic in cortical networks with neuronal avalanche dynamics

Thoracic spine pain in the general population: Prevalence, incidence and associated factors in children, adolescents and adults. A systematic review

<p>Abstract</p> <p>Background</p> <p>Thoracic spine pain (TSP) is experienced across the lifespan by healthy individuals and is a common presentation in primary healthcare clinical practice. However, the epidemiological characteristics of TSP are not well documented compared to neck and low back pain. A rigorous evaluation of the prevalence, incidence, correlates and risk factors needs to be undertaken in order for epidemiologic data to be meaningfully used to develop evidence-based prevention and treatment recommendations for TSP.</p> <p>Methods</p> <p>A systematic review method was followed to report the evidence describing prevalence, incidence, associated factors and risk factors for TSP among the general population. Nine electronic databases were systematically searched to identify studies that reported either prevalence, incidence, associated factors (cross-sectional study) or risk factors (prospective study) for TSP in healthy children, adolescents or adults. Studies were evaluated for level of evidence and method quality.</p> <p>Results</p> <p>Of the 1389 studies identified in the literature, 33 met the inclusion criteria for this systematic review. The mean (SD) quality score (out of 15) for the included studies was 10.5 (2.0). TSP prevalence data ranged from 4.0–72.0% (point), 0.5–51.4% (7-day), 1.4–34.8% (1-month), 4.8–7.0% (3-month), 3.5–34.8% (1-year) and 15.6–19.5% (lifetime). TSP prevalence varied according to the operational definition of TSP. Prevalence for any TSP ranged from 0.5–23.0%, 15.8–34.8%, 15.0–27.5% and 12.0–31.2% for 7-day, 1-month, 1-year and lifetime periods, respectively. TSP associated with backpack use varied from 6.0–72.0% and 22.9–51.4% for point and 7-day periods, respectively. TSP interfering with school or leisure ranged from 3.5–9.7% for 1-year prevalence. Generally, studies reported a higher prevalence for TSP in child and adolescent populations, and particularly for females. The 1 month, 6 month, 1 year and 25 year incidences were 0–0.9%, 10.3%, 3.8–35.3% and 9.8% respectively. TSP was significantly associated with: concurrent musculoskeletal pain; growth and physical; lifestyle and social; backpack; postural; psychological; and environmental factors. Risk factors identified for TSP in adolescents included age (being older) and poorer mental health.</p> <p>Conclusion</p> <p>TSP is a common condition in the general population. While there is some evidence for biopsychosocial associations it is limited and further prospectively designed research is required to inform prevention and management strategies.</p

Thoracic spine pain in the general population: Prevalence, incidence and associated factors in children, adolescents and adults. A systematic review

<p>Abstract</p> <p>Background</p> <p>Thoracic spine pain (TSP) is experienced across the lifespan by healthy individuals and is a common presentation in primary healthcare clinical practice. However, the epidemiological characteristics of TSP are not well documented compared to neck and low back pain. A rigorous evaluation of the prevalence, incidence, correlates and risk factors needs to be undertaken in order for epidemiologic data to be meaningfully used to develop evidence-based prevention and treatment recommendations for TSP.</p> <p>Methods</p> <p>A systematic review method was followed to report the evidence describing prevalence, incidence, associated factors and risk factors for TSP among the general population. Nine electronic databases were systematically searched to identify studies that reported either prevalence, incidence, associated factors (cross-sectional study) or risk factors (prospective study) for TSP in healthy children, adolescents or adults. Studies were evaluated for level of evidence and method quality.</p> <p>Results</p> <p>Of the 1389 studies identified in the literature, 33 met the inclusion criteria for this systematic review. The mean (SD) quality score (out of 15) for the included studies was 10.5 (2.0). TSP prevalence data ranged from 4.0–72.0% (point), 0.5–51.4% (7-day), 1.4–34.8% (1-month), 4.8–7.0% (3-month), 3.5–34.8% (1-year) and 15.6–19.5% (lifetime). TSP prevalence varied according to the operational definition of TSP. Prevalence for any TSP ranged from 0.5–23.0%, 15.8–34.8%, 15.0–27.5% and 12.0–31.2% for 7-day, 1-month, 1-year and lifetime periods, respectively. TSP associated with backpack use varied from 6.0–72.0% and 22.9–51.4% for point and 7-day periods, respectively. TSP interfering with school or leisure ranged from 3.5–9.7% for 1-year prevalence. Generally, studies reported a higher prevalence for TSP in child and adolescent populations, and particularly for females. The 1 month, 6 month, 1 year and 25 year incidences were 0–0.9%, 10.3%, 3.8–35.3% and 9.8% respectively. TSP was significantly associated with: concurrent musculoskeletal pain; growth and physical; lifestyle and social; backpack; postural; psychological; and environmental factors. Risk factors identified for TSP in adolescents included age (being older) and poorer mental health.</p> <p>Conclusion</p> <p>TSP is a common condition in the general population. While there is some evidence for biopsychosocial associations it is limited and further prospectively designed research is required to inform prevention and management strategies.</p

Regulation of inflammation in Japanese encephalitis

Uncontrolled inflammatory response of the central nervous system is a hallmark of severe Japanese encephalitis (JE). Although inflammation is necessary to mount an efficient immune response against virus infections, exacerbated inflammatory response is often detrimental. In this context, cells of the monocytic lineage appear to be important forces driving JE pathogenesis