Comparative genomics of Toll-like receptor signalling in five species

<p>Abstract</p> <p>Background</p> <p>Over the last decade, several studies have identified quantitative trait loci (QTL) affecting variation of immune related traits in mammals. Recent studies in humans and mice suggest that part of this variation may be caused by polymorphisms in genes involved in Toll-like receptor (TLR) signalling. In this project, we used a comparative approach to investigate the importance of TLR-related genes in comparison with other immunologically relevant genes for resistance traits in five species by associating their genomic location with previously published immune-related QTL regions.</p> <p>Results</p> <p>We report the genomic localisation of <it>TLR1-10 </it>and ten associated signalling molecules in sheep and pig using <it>in-silico </it>and/or radiation hybrid (RH) mapping techniques and compare their positions with their annotated homologues in the human, cattle and mouse whole genome sequences. We also report medium-density RH maps for porcine chromosomes 8 and 13. A comparative analysis of the positions of previously published relevant QTLs allowed the identification of homologous regions that are associated with similar health traits in several species and which contain TLR related and other immunologically relevant genes. Additional evidence was gathered by examining relevant gene expression and association studies.</p> <p>Conclusion</p> <p>This comparative genomic approach identified eight genes as potentially causative genes for variations of health related traits. These include susceptibility to clinical mastitis in dairy cattle, general disease resistance in sheep, cattle, humans and mice, and tolerance to protozoan infection in cattle and mice. Four TLR-related genes (<it>TLR1</it>, <it>6</it>, <it>MyD88</it>, <it>IRF3</it>) appear to be the most likely candidate genes underlying QTL regions which control the resistance to the same or similar pathogens in several species. Further studies are required to investigate the potential role of polymorphisms within these genes.</p

Transplanting rejuvenated blood stem cells extends lifespan of aged immunocompromised mice

One goal of regenerative medicine is to rejuvenate tissues and extend lifespan by restoring the function of endogenous aged stem cells. However, evidence that somatic stem cells can be targeted in vivo to extend lifespan is still lacking. Here, we demonstrate that after a short systemic treatment with a specific inhibitor of the small RhoGTPase Cdc42 (CASIN), transplanting aged hematopoietic stem cells (HSCs) from treated mice is sufficient to extend the healthspan and lifespan of aged immunocompromised mice without additional treatment. In detail, we show that systemic CASIN treatment improves strength and endurance of aged mice by increasing the myogenic regenerative potential of aged skeletal muscle stem cells. Further, we show that CASIN modifies niche localization and H4K16ac polarity of HSCs in vivo. Single-cell profiling reveals changes in HSC transcriptome, which underlie enhanced lymphoid and regenerative capacity in serial transplantation assays. Overall, we provide proof-of-concept evidence that a short systemic treatment to decrease Cdc42 activity improves the regenerative capacity of different endogenous aged stem cells in vivo, and that rejuvenated HSCs exert a broad systemic effect sufficient to extend murine health- and lifespan

Adapting Agriculture to Climate Change: A Synopsis of Coordinated National Crop Wild Relative Seed Collecting Programs across Five Continents

The Adapting Agriculture to Climate Change Project set out to improve the diversity, quantity, and accessibility of germplasm collections of crop wild relatives (CWR). Between 2013 and 2018, partners in 25 countries, heirs to the globetrotting legacy of Nikolai Vavilov, undertook seed collecting expeditions targeting CWR of 28 crops of global significance for agriculture. Here, we describe the implementation of the 25 national collecting programs and present the key results. A total of 4587 unique seed samples from at least 355 CWR taxa were collected, conserved ex situ, safety duplicated in national and international genebanks, and made available through the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture (Plant Treaty). Collections of CWR were made for all 28 targeted crops. Potato and eggplant were the most collected genepools, although the greatest number of primary genepool collections were made for rice. Overall, alfalfa, Bambara groundnut, grass pea and wheat were the genepools for which targets were best achieved. Several of the newly collected samples have already been used in pre-breeding programs to adapt crops to future challenges.info:eu-repo/semantics/publishedVersio

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Social Safety Nets for Food and Nutritional Security in India

This paper brings together existing literature on the Mahatma Gandhi National Rural Employment Guarantee Act (MGNRGEA) and the Public Distribution System (PDS) in India, offering a narrative review of the evidence on impacts on food security, health and nutrition of beneficiaries. Both programs operate on a large scale and have the capacity to impact the factors leading to undernutrition. It is evident that despite the deficiencies in implementation, both the MGNREGA and the PDS are inclusive and reach the poor and the marginalized who are likely to also experience greater undernutrition and poor health. Data challenges have however prevented researchers from conducting studies that assess the ultimate impact of these two large-scale programs on health and nutrition. The evidence that exists suggests largely positive impacts indicating a clear potential to make these programs more nutrition sensitive not just by incorporating elements that would explicitly address nutritional concerns but also by directing specific attention to innovations that strengthen critical complementarities and synergies that exist between the two programs

Essential Role of Polarity Protein Par3 for Epidermal Homeostasis through Regulation of Barrier Function, Keratinocyte Differentiation, and Stem Cell Maintenance

Partitioning-defective (Par) proteins contribute to multiprotein complexes that drive cell polarity and fate in invertebrates. Of these, the ternary Par3-atypical protein kinase C-Par6 polarity complex mediates asymmetry in various systems, whereas Par3 and aPKC/Par6 can also act independently. aPKC-lambda has recently been implicated in epidermal differentiation and stem cell fate; however, whether Par3 contributes to the homeostasis of adult stratified epithelia is currently unknown. Here, we provide functional evidence that epidermal Par3 loss disturbed the inside-out skin barrier, coinciding with altered expression and localization of principle tight junction components, and that epidermal differentiation and thickness were increased. Moreover, Par3 inactivation caused an initial expansion and later decline of hair follicle bulge stem cells, accompanied by an enrichment of committed progenitors, formation of hypertrophic sebaceous glands, and increased epidermal differentiation, suggesting aberrant cell fate decisions. Importantly, and opposite to aPKC lambda deletion, Par3 loss did not enhance perpendicular cell divisions. Instead, in Par3-deficient hair follicles, spindles were shifted toward planar orientation, indicating that abnormal differentiation after Par3 inactivation is unlikely to be attributed to increased perpendicular spindle orientation. Collectively, mammalian Par3 controls the epidermal barrier, differentiation, and stem cell maintenance in the pilosebaceous unit, which are all essential for the homeostasis of an important barrier-forming epithelium

Developing a decision instrument to guide abdominal-pelvic imaging of blunt trauma patients: Methodology and protocol of the NEXUS abdominal-pelvic imaging study

Although computed tomography (CT) of the abdomen and pelvis (A/P) can provide crucial information for managing blunt trauma patients, liberal and indiscriminant imaging is expensive, can delay critical interventions, and unnecessarily exposes patients to ionizing radiation. Currently no definitive recommendations exist detailing which adult blunt trauma patients should receive A/P CT imaging and which patients may safely forego CT. Considerable benefit could be realized by identifying clinical criteria that reliably classify the risk of abdominal and pelvic injuries in blunt trauma patients. Patients identified as “very low risk” by such criteria would be free of significant injury, receive no benefit from imaging and therefore could be safely spared the expense and radiation exposure associated with A/P CT. The goal of this two-phase nationwide multicenter observational study is to derive and validate the use of clinical criteria to stratify the risk of injuries to the abdomen and pelvis among adult blunt trauma patients. We estimate that nation-wide implementation of a rigorously developed decision instrument could safely reduce CT imaging of adult blunt trauma patients by more than 20%, and reduce annual radiographic charges by $180 million, while simultaneously expediting trauma care and decreasing radiation exposure with its attendant risk of radiation-induced malignancy. Prior to enrollment we convened an expert panel of trauma surgeons, radiologists and emergency medicine physicians to develop a consensus definition for clinically significant abdominal and pelvic injury. In the first derivation phase of the study, we will document the presence or absence of preselected candidate criteria, as well as the presence or absence of significant abdominal or pelvic injuries in a cohort of blunt trauma victims. Using recursive partitioning, we will examine combinations of these criteria to identify an optimal “very low risk” subset that identifies injuries with a sensitivity exceeding 98%, excludes injury with a negative predictive value (NPV) greater than 98%, and retains the highest possible specificity and potential to decrease imaging. In Phase 2 of the study we will validate the performance of a decision rule based on these criteria among a new cohort of patients to ensure that the criteria retain high sensitivity, NPV and optimal specificity. Validating the sensitivity of the decision instrument with high statistical precision requires evaluations on 317 blunt trauma patients who have significant abdominal-pelvic injuries, which will in turn require evaluations on approximately 6,340 blunt trauma patients. We will estimate potential reductions in CT imaging by counting the number of abdominal-pelvic CT scans performed on “very low risk” patients. Reductions in charges and radiation exposure will be determined by respectively summing radiographic charges and lifetime decreases in radiation morbidity and mortality for all “very low risk” cases. Trial registration: Clinicaltrials.gov trial registration number: NCT04937868