Engineering a xylose fermenting yeast for lignocellulosic ethanol production.

Lignocellulosic ethanol is produced by yeast fermentation of lignocellulosic hydrolysates generated by chemical pretreatment and enzymatic hydrolysis of plant cell walls. The conversion of xylose into ethanol in hydrolysates containing microbial inhibitors is a major bottleneck in biofuel production. We identified sodium salts as the primary yeast inhibitors, and evolved a Saccharomyces cerevisiae strain overexpressing xylose catabolism genes in xylose or glucose-mixed medium containing sodium salts.

Delineation of chicken immune markers in the era of omics and multicolor flow cytometry.

Multiparameter flow cytometry is a routine method in immunological studies incorporated in biomedical, veterinary, agricultural, and wildlife research and routinely used in veterinary clinical laboratories. Its use in the diagnostics of poultry diseases is still limited, but due to the continuous expansion of reagents and cost reductions, this may change in the near future. Although the structure and function of the avian immune system show commonalities with mammals, at the molecular level, there is often low homology across species.

Chicken intestinal organoids: a novel method to measure the mode of action of feed additives.

There is a rapidly growing interest in how the avian intestine is affected by dietary components and feed additives. The paucity of physiologically relevant models has limited research in this field of poultry gut health and led to an over-reliance on the use of live birds for experiments. The development of complex 3D intestinal organoids or "mini-guts" has created ample opportunities for poultry research in this field.

Phenotypic and genomic characterisation of performance of tropically adapted chickens raised in smallholder farm conditions in Ethiopia.

Background: In sub-Saharan Africa, 80% of poultry production is on smallholder village farms, where chickens are typically reared outdoors in free-ranging conditions. There is limited knowledge on chickens' phenotypic characteristics and genetics under these conditions.

Objective: The present is a large-scale study set out to phenotypically characterise the performance of tropically adapted commercial chickens in typical smallholder farm conditions, and to examine the genetic profile of chicken phenotypes associated with growth, meat production, immunity, and survival.

Discrimination of distinct chicken M cell subsets based on CSF1R expression.

In mammals, a subset of follicle-associated epithelial (FAE) cells, known as M cells, conduct the transcytosis of antigens across the epithelium into the underlying lymphoid tissues. We previously revealed that M cells in the FAE of the chicken lung, bursa of Fabricius (bursa), and caecum based on the expression of CSF1R. Here, we applied RNA-seq analysis on highly enriched CSF1R-expressing bursal M cells to investigate their transcriptome and identify novel chicken M cell-associated genes.

Mapping and identifying service models for community-based services for children with intellectual disabilities and behaviours that challenge in England.

Background: One in five children with an intellectual disability in the UK display behaviours that challenge. Despite associated impacts on the children themselves, their families, and services, little research has been published about how best to design, organise, and deliver health and care services to these children. The purpose of this study was to describe how services are structured and organised ("service models") in England for community-based health and care services for children with intellectual disability who display behaviours that challenge.

Distribution and spatiotemporal development of organised lymphoid tissues in the chicken intestinal tract.

Chickens exhibit a distinct immune architecture characterised by the absence of draining lymph nodes and the presence of a well-developed mucosa-associated lymphoid tissue. The structure and spatiotemporal development of chicken lymphoid tissues in the intestine are poorly documented. The macroscopically indistinct structure of chicken Peyer's patches has impeded studies into their development.

Disentangling the innate immune responses of intestinal epithelial cells and lamina propria cells to Typhimurium infection in chickens.

serovar Typhimurium (STm) is a major foodborne pathogen and poultry are a key reservoir of human infections. To understand the host responses to early stages of infection in poultry, we infected 2D and 3D enteroids, the latter of which contains leukocytes, neurons, and mesenchymal cells that are characteristic of the lamina propria. We infected these enteroids with wild-type (WT STm), a non-invasive mutant lacking the gene (Δ STm), or treated them with STm lipopolysaccharide (LPS) and analyzed the expression of innate immune related genes by qPCR at 4 and 8 h.

Malignant neoplasm of lacrimal gland with pulmonary metastasis.

Adenoid cystic carcinomas (ACC) make up 3%-5% of head and neck malignancies. They have a high propensity to metastasise, in particular to the lungs. A 65-year-old male diagnosed with a right lacrimal gland ACC T2N0M0 (surgically resected 12 years prior) presented with an incidentally noted 1.

Chicken CSF2 and IL-4-, and CSF2-dependent bone marrow cultures differentiate into macrophages over time.

Chicken bone marrow-derived macrophages (BMMΦ) and dendritic cells (BMDC) are utilized as models to study the mononuclear phagocytic system (MPS). A widely used method to generate macrophages and DC is to culture bone marrow cells in the presence of colony-stimulating factor-1 (CSF1) to differentiate BMMΦ and granulocyte-macrophage-CSF (GM-CSF, CSF2) and interleukin-4 (IL-4) to differentiate BMDC, while CSF2 alone can lead to the development of granulocyte-macrophage-CSF-derived DC (GMDC). However, in chickens, the MPS cell lineages and their functions represented by these cultures are poorly understood.

Establishment of bovine 3D enteroid-derived 2D monolayers.

Three-dimensional (3D) intestinal enteroids are powerful in vitro models for studying intestinal biology. However, due to their closed structure direct access to the apical surface is impeded, limiting high-throughput applications of exogenous compounds and pathogens. In this study, we describe a method for generating confluent 2D enteroids from single-cell suspensions of enzymatically-dissociated ileum-derived bovine 3D enteroids.

Novel chicken two-dimensional intestinal model comprising all key epithelial cell types and a mesenchymal sub-layer.

The intestinal epithelium plays a variety of roles including providing an effective physical barrier and innate immune protection against infection. Two-dimensional models of the intestinal epithelium, 2D enteroids, are a valuable resource to investigate intestinal cell biology and innate immune functions and are suitable for high throughput studies of paracellular transport and epithelial integrity. We have developed a chicken 2D enteroid model that recapitulates all major differentiated cell lineages, including enterocytes, Paneth cells, Goblet cells, enteroendocrine cells and leukocytes, and self-organises into an epithelial and mesenchymal sub-layer.

Avian Pathogenic (APEC) Strain-Dependent Immunomodulation of Respiratory Granulocytes and Mononuclear Phagocytes in -Reporter Transgenic Chickens.

Avian pathogenic (APEC) cause severe respiratory and systemic disease in chickens, commonly termed colibacillosis. Early immune responses after initial infection are highly important for the outcome of the infection. In this study, the early interactions between -expressing APEC strains of serotypes O1:K1:H7 and O2:K1:H5 and phagocytic cells in the lung of -reporter transgenic chickens were investigated.

Antigen Sampling -Expressing Epithelial Cells Are the Functional Equivalents of Mammalian M Cells in the Avian Follicle-Associated Epithelium.

The follicle-associated epithelium (FAE) is a specialized structure that samples luminal antigens and transports them into mucosa-associated lymphoid tissues (MALT). In mammals, transcytosis of antigens across the gut epithelium is performed by a subset of FAE cells known as M cells. Here we show that colony-stimulating factor 1 receptor (CSF1R) is expressed by a subset of cells in the avian bursa of Fabricius FAE.

Visualisation and characterisation of mononuclear phagocytes in the chicken respiratory tract using CSF1R-transgenic chickens.

The respiratory tract is a key organ for many avian pathogens as well as a major route for vaccination in the poultry industry. To improve immune responses after vaccination of chickens through increased uptake of vaccines and targeting to antigen presenting cells, a better understanding of the avian respiratory immune system is required. Transgenic MacReporter birds were used expressing a reporter gene (eGFP or mApple) under the control of the CSF1R promoter and enhancer in cells of the mononuclear phagocyte (MNP) lineage to visualize the ontogeny of the lymphoid tissue, macrophages and dendritic cells, in the trachea, lung and air sac of birds from embryonic day 18-63 weeks of age.

Assessment of the feasibility and clinical value of further research to evaluate the management options for children with Down syndrome and otitis media with effusion: a feasibility study.

Background: There is clinical uncertainty of the benefits and costs of different treatment options for children with Down syndrome who have glue ear. This study was designed to assess the extent of this lack of knowledge and determine if pursuing further information would be practical, beneficial and cost-effective.

Objectives: To assess the level and practical effect of current uncertainty around treatment options for children with Down syndrome and glue ear.

Detection of somatic mutations in tumors using unaligned clonal sequencing data.

Most cancers arise and evolve as a consequence of somatic mutations. These mutations influence tumor behavior and clinical outcome. Consequently, there is considerable interest in identifying somatic variants within specific genes (such as BRAF, KRAS and EGFR) so that chemotherapy can be tailored to the patient's tumor genotype rather than using a generic treatment based on histological diagnosis alone.

Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution.

Current methods for resolving genetically distinct subclones in tumor samples require somatic mutations to be clustered by allelic frequencies, which are determined by applying a variant calling program to next-generation sequencing data. Such programs were developed to accurately distinguish true polymorphisms and somatic mutations from the artifactual nonreference alleles introduced during library preparation and sequencing. However, numerous variant callers exist with no clear indication of the best performer for subclonal analysis, in which the accuracy of the assigned variant frequency is as important as correctly indicating whether the variant is present or not.

Mutation detection by clonal sequencing of PCR amplicons and grouped read typing is applicable to clinical diagnostics.

We describe a sensitive technique for mutation detection using clonal sequencing. We analyzed DNA extracted from 13 cancer cell lines and 35 tumor samples and applied a novel approach to identify disease-associated somatic mutations. By matching reads against an index of known variants, noise can be dramatically reduced, enabling the detection and quantification of those variants, even when they are present at less than 1% of the total sequenced population; this is comparable to, or better than, current diagnostic methods.

Diffuse noxious inhibitory control function in women with provoked vestibulodynia.

Objectives: The objective of the study was to assess diffuse noxious inhibitory control (DNIC) function in women with provoked vestibulodynia (PVD) compared with healthy controls through the use of 2 different methodologies. Furthermore, the study aimed to assess whether pain characteristics correlate with DNIC in women with PVD.

Methods: Twenty-three healthy control women and 23 women diagnosed with PVD by the study gynecologist participated in the study.

To lube or not to lube: experiences and perceptions of lubricant use in women with and without dyspareunia.

Introduction: There are few studies examining the relationship between lubricant use and sexual functioning, and no studies have examined this relationship in women with dyspareunia. Vaginal dryness is a prevalent complaint among women of all ages. There is an association between vaginal dryness and painful intercourse; therefore, women with dyspareunia represent a particularly relevant sample of women in which to investigate lubricant use.

Ceramic materials as bearing surfaces for total hip arthroplasty.

During the past decade, advances in total hip arthroplasty component design have produced implants with reliable clinical results in regard to fixation. The foremost unresolved challenge has been the development of bearing surfaces that can withstand the higher demands of younger and more active patients. New alternative bearings with superior wear characteristics that minimize debris include ceramic-on-ceramic, metal-on-metal, and highly cross-linked polyethylenes in combination with ceramic or metal.

Bearings of the future for total hip arthroplasty.

In the last decade or so, newer hip bearings such as ceramic-on-ceramic, metal-on-metal, and metal-on-highly cross-linked polyethylene were introduced into clinical practice in attempts to reduce the debris load released to the tissues after total hip arthroplasty. Present clinical evidence suggests that these newer bearings reduce both abrasive wear and the incidence of osteolysis at up to 10 years clinical follow-up. As further efforts to reduce abrasive wear may meet decreasing returns, we suggest that other bearing issues remain unresolved.