Metabolite Profile of Cervicovaginal Fluids from Early Pregnancy Is Not Predictive of Spontaneous Preterm Birth.

In our study, we used a mass spectrometry-based metabolomic approach to search for biomarkers that may act as early indicators of spontaneous preterm birth (sPTB). Samples were selected as a nested case-control study from the Screening for Pregnancy Endpoints (SCOPE) biobank in Auckland, New Zealand. Cervicovaginal swabs were collected at 20 weeks from women who were originally assessed as being at low risk of sPTB.

Comparison of Illumina de novo assembled and Sanger sequenced viral genomes: A case study for RNA viruses recovered from the plant pathogenic fungus Sclerotinia sclerotiorum.

The advent of 'next generation sequencing' (NGS) technologies has led to the discovery of many novel mycoviruses, the majority of which are sufficiently different from previously sequenced viruses that there is no appropriate reference sequence on which to base the sequence assembly. Although many new genome sequences are generated by NGS, confirmation of the sequence by Sanger sequencing is still essential for formal classification by the International Committee for the Taxonomy of Viruses (ICTV), although this is currently under review. To empirically test the validity of de novo assembled mycovirus genomes from dsRNA extracts, we compared the results from Illumina sequencing with those from random cloning plus targeted PCR coupled with Sanger sequencing for viruses from five Sclerotinia sclerotiorum isolates.

Equation-free analysis of spike-timing-dependent plasticity.

Spike-timing-dependent plasticity is the process by which the strengths of connections between neurons are modified as a result of the precise timing of the action potentials fired by the neurons. We consider a model consisting of one integrate-and-fire neuron receiving excitatory inputs from a large number-here, 1000-of Poisson neurons whose synapses are plastic. When correlations are introduced between the firing times of these input neurons, the distribution of synaptic strengths shows interesting, and apparently low-dimensional, dynamical behaviour.

Data for chromosome contacts and matched transcription profiles at three cell cycle phases in the fission yeast.

The data described in this article pertains to Grand et al. (2014), "Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure" [1]. Temperature sensitive Schizosaccharomyces pombe cell division cycle (cdc) mutants, which are induced by a shift in temperature to 36 °C, were chosen for the analysis of genome structure in the G1 phase, G2 phase and mitotic anaphase of the cell cycle.

Foods, macronutrients and fibre in the diet of blue sheep (Psuedois nayaur) in the Annapurna Conservation Area of Nepal.

Food resources are often critical regulating factors affecting individual fitness and population densities. In the Himalayan Mountains, Bharal "blue sheep" (Pseudois nayaur) are the main food resource for the endangered snow leopard (Panthera uncia), as well as being preyed upon by other predators. Blue sheep, however, may face a number of challenges including food resource competition with other wild and domestic ungulates, and hunting pressure.

Climate Change-Induced Range Expansion of a Subterranean Rodent: Implications for Rangeland Management in Qinghai-Tibetan Plateau.

Disturbances, both human-induced and natural, may re-shape ecosystems by influencing their composition, structure, and functional processes. Plateau zokor (Eospalax baileyi) is a typical subterranean rodent endemic to Qinghai-Tibetan Plateau (QTP), which are considered ecosystem engineers influencing the alpine ecosystem function. It is also regarded as a pest aggravating the degradation of overgrazed grassland and subject to regular control in QTP since 1950s.

Simultaneous Estimation of Additive and Mutational Genetic Variance in an Outbred Population of Drosophila serrata.

How new mutations contribute to genetic variation is a key question in biology. Although the evolutionary fate of an allele is largely determined by its heterozygous effect, most estimates of mutational variance and mutational effects derive from highly inbred lines, where new mutations are present in homozygous form. In an attempt to overcome this limitation, middle-class neighborhood (MCN) experiments have been used to assess the fitness effect of new mutations in heterozygous form.

Quantum heat baths satisfying the eigenstate thermalization hypothesis.

A class of autonomous quantum heat baths satisfying the eigenstate thermalization hypothesis (ETH) criteria is proposed. We show that such systems are expected to cause thermal relaxation of much smaller quantum systems coupled to one of the baths local observables. The process of thermalization is examined through residual fluctuations of local observables of the bath around their thermal values predicted by ETH.

Large orb-webs adapted to maximise total biomass not rare, large prey.

Spider orb-webs are the ultimate anti-ballistic devices, capable of dissipating the relatively massive kinetic energy of flying prey. Increased web size and prey stopping capacity have co-evolved in a number orb-web taxa, but the selective forces driving web size and performance increases are under debate. The rare, large prey hypothesis maintains that the energetic benefits of rare, very large prey are so much greater than the gains from smaller, more common prey that smaller prey are irrelevant for reproduction.

Solutions to an advanced functional partial differential equation of the pantograph type.

A model for cells structured by size undergoing growth and division leads to an initial boundary value problem that involves a first-order linear partial differential equation with a functional term. Here, size can be interpreted as DNA content or mass. It has been observed experimentally and shown analytically that solutions for arbitrary initial cell distributions are asymptotic as time goes to infinity to a certain solution called the steady size distribution.

Molecular mechanisms of xylose utilization by Pseudomonas fluorescens: overlapping genetic responses to xylose, xylulose, ribose and mannitol.

Bacterial degradation of xylose is sequentially mediated by two enzymes - an isomerase (XutA) and a xylulokinase (XutB) - with xylulose as an intermediate. Pseudomonas fluorescens SBW25, though capable of growth on xylose as a sole carbon source, encodes only one degradative enzyme XutA at the xylose utilization (xut) locus. Here, using site-directed mutagenesis and transcriptional assays, we have identified two functional xylulokinase-encoding genes (xutB1 and xutB2) and further show that expression of xutB1 is specifically induced by xylose.

The Gcn2 Regulator Yih1 Interacts with the Cyclin Dependent Kinase Cdc28 and Promotes Cell Cycle Progression through G2/M in Budding Yeast.

The Saccharomyces cerevisiae protein Yih1, when overexpressed, inhibits the eIF2 alpha kinase Gcn2 by competing for Gcn1 binding. However, deletion of YIH1 has no detectable effect on Gcn2 activity, suggesting that Yih1 is not a general inhibitor of Gcn2, and has no phenotypic defect identified so far. Thus, its physiological role is largely unknown.

Successive Generations in a Rat Model Respond Differently to a Constant Obesogenic Environment.

Research has shown that if a mother experiences a transitory perturbation to her environment during pregnancy or lactation, there are transgenerational consequences often involving a disordered metabolic phenotype in first generation offspring with recovery across subsequent generations. In contrast, little is known about the nature of the transgenerational response of offspring when a mother experiences a perturbation that is not transitory but instead persists across generations. Our study, using a rat model, subjected the parental generation to a change in environment and concomitant shift from a grain-based to obesogenic diets to generate an adipose phenotype in first generation offspring emulating a common scenario in human urbanisation and migration.

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.

Classically or alternatively activated macrophages (M1 and M2, respectively) play distinct and important roles for microbiocidal activity, regulation of inflammation and tissue homeostasis. Despite this, their transcriptional regulatory dynamics are poorly understood. Using promoter-level expression profiling by non-biased deepCAGE we have studied the transcriptional dynamics of classically and alternatively activated macrophages.

Analysing avian eggshell pigments with Raman spectroscopy.

Avian eggshells are variable in appearance, including coloration. Here, we demonstrate that Raman spectroscopy can provide accurate diagnostic information about major eggshell constituents, including the pigments biliverdin and protoporphyrin IX. Eggshells pigmented with biliverdin showed a series of pigment-diagnostic Raman peaks under 785 nm excitation.

Coral reefs. Limited scope for latitudinal extension of reef corals.

An analysis of present-day global depth distributions of reef-building corals and underlying environmental drivers contradicts a commonly held belief that ocean warming will promote tropical coral expansion into temperate latitudes. Using a global data set of a major group of reef corals, we found that corals were confined to shallower depths at higher latitudes (up to 0.6 meters of predicted shallowing per additional degree of latitude).

Integration over song classification replicates: song variant analysis in the hihi.

Human expert analyses are commonly used in bioacoustic studies and can potentially limit the reproducibility of these results. In this paper, a machine learning method is presented to statistically classify avian vocalizations. Automated approaches were applied to isolate bird songs from long field recordings, assess song similarities, and classify songs into distinct variants.

Deciphering β-Lactoglobulin Interactions at an Oil-Water Interface: A Molecular Dynamics Study.

Protein adsorption at liquid-liquid interfaces is of immense relevance to many biological processes and dairy-based functional foods. Due to experimental limitations, however, there is still a remarkable lack of understanding of the adsorption mechanism, particularly at a molecular level. In this study, atomistic molecular dynamics simulations were used to elucidate the approach and adsorption mechanism of β-lactoglobulin (β-LG) at a decane-water interface.

Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection.

Basic leucine zipper transcription factor Batf2 is poorly described, whereas Batf and Batf3 have been shown to play essential roles in dendritic cell, T cell, and B cell development and regulation. Batf2 was drastically induced in IFN-γ-activated classical macrophages (M1) compared with unstimulated or IL-4-activated alternative macrophages (M2). Batf2 knockdown experiments from IFN-γ-activated macrophages and subsequent expression profiling demonstrated important roles for regulation of immune responses, inducing inflammatory and host-protective genes Tnf, Ccl5, and Nos2.

Biochar in co-contaminated soil manipulates arsenic solubility and microbiological community structure, and promotes organochlorine degradation.

We examined the effect of biochar on the water-soluble arsenic (As) concentration and the extent of organochlorine degradation in a co-contaminated historic sheep-dip soil during a 180-d glasshouse incubation experiment. Soil microbial activity, bacterial community and structure diversity were also investigated. Biochar made from willow feedstock (Salix sp) was pyrolysed at 350 or 550°C and added to soil at rates of 10 g kg-1 and 20 g kg-1 (representing 30 t ha-1 and 60 t ha-1).

Nine challenges for deterministic epidemic models.

Deterministic models have a long history of being applied to the study of infectious disease epidemiology. We highlight and discuss nine challenges in this area. The first two concern the endemic equilibrium and its stability.