Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215.

Background: A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern.

Transcriptional signatures measured in whole blood correlate with protection against tuberculosis in inbred and outbred mice.

Although BCG has been used for almost 100 years to immunize against Mycobacterium tuberculosis, TB remains a global public health threat. Numerous clinical trials are underway studying novel vaccine candidates and strategies to improve or replace BCG, but vaccine development still lacks a well-defined set of immune correlates to predict vaccine-induced protection against tuberculosis. This study aimed to address this gap by examining transcriptional responses to BCG vaccination in C57BL/6 inbred mice, coupled with protection studies using Diversity Outbred mice.

Enhanced secretion of satiety-promoting gut hormones in healthy humans after consumption of white bread enriched with cellular chickpea flour: A randomized crossover study.

Background: Dietary intake of pulses is associated with beneficial effects on body weight management and cardiometabolic health, but some of these effects are now known to depend on integrity of plant cells, which are usually disrupted by flour milling. Novel cellular flours preserve the intrinsic dietary fiber structure of whole pulses and provide a way to enrich preprocessed foods with encapsulated macronutrients.

Objectives: This study aimed to determine the effects of replacing wheat flour with cellular chickpea flour on postprandial gut hormones, glucose, insulin, and satiety responses to white bread.

In Silico Identification of Potential Thyroid Hormone System Disruptors among Chemicals in Human Serum and Chemicals with a High Exposure Index.

Data on toxic effects are at large missing the prevailing understanding of the risks of industrial chemicals. Thyroid hormone (TH) system disruption includes interferences of the life cycle of the thyroid hormones and may occur in various organs. In the current study, high-throughput screening data available for 14 putative molecular initiating events of adverse outcome pathways, related to disruption of the TH system, were used to develop 19 in silico models for identification of potential thyroid hormone system-disrupting chemicals.

A genome-wide test for paternal indirect genetic effects on lifespan in .

Exposing sires to various environmental manipulations has demonstrated that paternal effects can be non-trivial also in species where male investment in offspring is almost exclusively limited to sperm. Whether paternal effects also have a genetic component (i.e.

Structure-function studies of chickpea and durum wheat uncover mechanisms by which cell wall properties influence starch bioaccessibility.

Positive health effects of dietary fibre have been established; however, the underpinning mechanisms are not well understood. Plant cell walls are the predominant source of fibre in the diet. They encapsulate intracellular starch and delay digestive enzyme ingress, but food processing can disrupt the structure.

The impact of replacing wheat flour with cellular legume powder on starch bioaccessibility, glycaemic response and bread roll quality: A double-blind randomised controlled trial in healthy participants.

The global rise in obesity and type 2 diabetes has generated significant interest in regulating the glycaemic impact of staple foods. Wheat breads (white or wholemeal) are popular staples, but have a high-glycaemic index, due to the highly digestible wheat starch. Reducing the glycaemic potency of white bread is challenging because the bread-making conditions are mostly conducive to starch gelatinisation.

Comparison of Methods for Feature Selection in Clustering of High-Dimensional RNA-Sequencing Data to Identify Cancer Subtypes.

Cancer subtype identification is important to facilitate cancer diagnosis and select effective treatments. Clustering of cancer patients based on high-dimensional RNA-sequencing data can be used to detect novel subtypes, but only a subset of the features (e.g.

Combining epigenetic and clinicopathological variables improves specificity in prognostic prediction in clear cell renal cell carcinoma.

Background: Metastasized clear cell renal cell carcinoma (ccRCC) is associated with a poor prognosis. Almost one-third of patients with non-metastatic tumors at diagnosis will later progress with metastatic disease. These patients need to be identified already at diagnosis, to undertake closer follow up and/or adjuvant treatment.

Centralization Within Sub-Experiments Enhances the Biological Relevance of Gene Co-expression Networks: A Plant Mitochondrial Case Study.

Unlabelled: Gene co-expression networks (GCNs) can be prepared using a variety of mathematical approaches based on data sampled across diverse developmental processes, tissue types, pathologies, mutant backgrounds, and stress conditions. These networks are used to identify genes with similar expression dynamics but are prone to introducing false-positive and false-negative relationships, especially in the instance of large and heterogenous datasets. With the aim of optimizing the relevance of edges in GCNs and enhancing global biological insight, we propose a novel approach that involves a data-centering step performed simultaneously per gene and per sub-experiment, called centralization within sub-experiments (CSE).

Vaccine-Mediated Mechanisms Controlling SCHU S4 Growth in a Rat Co-Culture System.

causes the severe disease tularemia. In the present study, the aim was to identify correlates of protection in the rat co-culture model by investigating the immune responses using two vaccine candidates conferring distinct degrees of protection in rat and mouse models. The immune responses were characterized by use of splenocytes from naïve or Live vaccine strain- (LVS) or ∆∆-immunized Fischer 344 rats as effectors and bone marrow-derived macrophages infected with the highly virulent strain SCHU S4.

An mRNA-mRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria monocytogenes.

Bacterial pathogens often employ RNA regulatory elements located in the 5' untranslated regions (UTRs) to control gene expression. Using a comparative structural analysis, we examine the structure of 5' UTRs at a global scale in the pathogenic bacterium Listeria monocytogenes under different conditions. In addition to discovering an RNA thermoswitch and detecting simultaneous interaction of ribosomes and small RNAs with mRNA, we identify structural changes in the 5' UTR of an mRNA encoding the post-translocation chaperone PrsA2 during infection conditions.

Whole genome profiling refines a panel of correlates to predict vaccine efficacy against Mycobacterium tuberculosis.

New vaccines are needed to combat the public health threat posed by M. tuberculosis (M. tb), but no correlates have been defined to aid vaccine development.

Plant Cell Walls: Impact on Nutrient Bioaccessibility and Digestibility.

Cell walls are important structural components of plants, affecting both the bioaccessibility and subsequent digestibility of the nutrients that plant-based foods contain. These supramolecular structures are composed of complex heterogeneous networks primarily consisting of cellulose, and hemicellulosic and pectic polysaccharides. The composition and organization of these different polysaccharides vary depending on the type of plant tissue, imparting them with specific physicochemical properties.

Cluster analysis on high dimensional RNA-seq data with applications to cancer research - An evaluation study.

Background: Clustering of gene expression data is widely used to identify novel subtypes of cancer. Plenty of clustering approaches have been proposed, but there is a lack of knowledge regarding their relative merits and how data characteristics influence the performance. We evaluate how cluster analysis choices affect the performance by studying four publicly available human cancer data sets: breast, brain, kidney and stomach cancer.

Gene expression profiles define molecular subtypes of prostate cancer bone metastases with different outcomes and morphology traceable back to the primary tumor.

Bone metastasis is the lethal end-stage of prostate cancer (PC), but the biology of bone metastases is poorly understood. The overall aim of this study was therefore to explore molecular variability in PC bone metastases of potential importance for therapy. Specifically, genome-wide expression profiles of bone metastases from untreated patients (n = 12) and patients treated with androgen-deprivation therapy (ADT, n = 60) were analyzed in relation to patient outcome and to morphological characteristics in metastases and paired primary tumors.

A panel of correlates predicts vaccine-induced protection of rats against respiratory challenge with virulent Francisella tularensis.

There are no defined correlates of protection for any intracellular pathogen, including the bacterium Francisella tularensis, which causes tularemia. Evaluating vaccine efficacy against sporadic diseases like tularemia using field trials is problematic, and therefore alternative strategies to test vaccine candidates like the Francisella Live Vaccine Strain (LVS), such as testing in animals and applying correlate measurements, are needed. Recently, we described a promising correlate strategy that predicted the degree of vaccine-induced protection in mice given parenteral challenges, primarily when using an attenuated Francisella strain.

Temporal and long-term gut microbiota variation in allergic disease: A prospective study from infancy to school age.

Background: Compositional changes in the early-life gut microbiota have been implicated in IgE-associated allergic diseases, but there is lack of longitudinal studies. We examined gut microbiota development from infancy to school age in relation to onset of IgE-associated allergic diseases. At 8 years of age, we also examined the relationship between gut microbiota and T-cell regulation, estimated as responses to polyclonal T-cell activation.

Vaccine-Mediated Mechanisms Controlling Replication of in Human Peripheral Blood Mononuclear Cells Using a Co-culture System.

Cell-mediated immunity (CMI) is normally required for efficient protection against intracellular infections, however, identification of correlates is challenging and they are generally lacking. is a highly virulent, facultative intracellular bacterium and CMI is critically required for protection against the pathogen, but how this is effectuated in humans is poorly understood. To understand the protective mechanisms, we established an co-culture assay to identify how control of infection of is accomplished by human cells and hypothesized that the model will mimic immune mechanisms.

Bioethanol production from spent mushroom compost derived from chaff of millet and sorghum.

Background: In Uganda, the chaff remaining from threshed panicles of millet and sorghum is a low value, lignocellulose-rich agricultural by-product. Currently, it is used as a substrate for the cultivation of edible Oyster mushrooms (). The aim of this study was to assess the potential to exploit the residual post-harvest compost for saccharification and fermentation to produce ethanol.

SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts.

Autosomal recessive osteopetrosis (ARO) is a heterogeneous disorder, characterized by defective osteoclastic resorption of bone that results in increased bone density. We have studied nine individuals with an intermediate form of ARO, from the county of Västerbotten in Northern Sweden. All afflicted individuals had an onset in early infancy with optic atrophy, and in four patients anemia was present at diagnosis.

A statistically compiled test battery for feasible evaluation of knee function after rupture of the Anterior Cruciate Ligament - derived from long-term follow-up data.

Purpose: Clinical test batteries for evaluation of knee function after injury to the Anterior Cruciate Ligament (ACL) should be valid and feasible, while reliably capturing the outcome of rehabilitation. There is currently a lack of consensus as to which of the many available assessment tools for knee function that should be included. The present aim was to use a statistical approach to investigate the contribution of frequently used tests to avoid redundancy, and filter them down to a proposed comprehensive and yet feasible test battery for long-term evaluation after ACL injury.

A new concept and a comprehensive evaluation of SYSMEX UF-1000i flow cytometer to identify culture-negative urine specimens in patients with UTI.

Urinary tract infections (UTIs) are among the most common bacterial infections in men and urine culture is gold standard for diagnosis. Considering the high prevalence of culture-negative specimens, any method that identifies such specimens is of interest. The aim was to evaluate a new screening concept for flow cytometry analysis (FCA).

High-risk regions and outbreak modelling of tularemia in humans.

Sweden reports large and variable numbers of human tularemia cases, but the high-risk regions are anecdotally defined and factors explaining annual variations are poorly understood. Here, high-risk regions were identified by spatial cluster analysis on disease surveillance data for 1984-2012. Negative binomial regression with five previously validated predictors (including predicted mosquito abundance and predictors based on local weather data) was used to model the annual number of tularemia cases within the high-risk regions.