A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state

<p>Abstract</p> <p>Background</p> <p>The serovars Enteritidis and Typhimurium of the Gram-negative bacterium <it>Salmonella enterica</it> are significant causes of human food poisoning. Fowl carrying these bacteria often show no clinical disease, with detection only established post-mortem. Increased resistance to the carrier state in commercial poultry could be a way to improve food safety by reducing the spread of these bacteria in poultry flocks. Previous studies identified QTLs for both resistance to carrier state and resistance to <it>Salmonella</it> colonization in the same White Leghorn inbred lines. Until now, none of the QTLs identified was common to the two types of resistance. All these analyses were performed using the F2 inbred or backcross option of the QTLExpress software based on linear regression. In the present study, QTL analysis was achieved using Maximum Likelihood with QTLMap software, in order to test the effect of the QTL analysis method on QTL detection. We analyzed the same phenotypic and genotypic data as those used in previous studies, which were collected on 378 animals genotyped with 480 genome-wide SNP markers. To enrich these data, we added eleven SNP markers located within QTLs controlling resistance to colonization and we looked for potential candidate genes co-localizing with QTLs.</p> <p>Results</p> <p>In our case the QTL analysis method had an important impact on QTL detection. We were able to identify new genomic regions controlling resistance to carrier-state, in particular by testing the existence of two segregating QTLs. But some of the previously identified QTLs were not confirmed. Interestingly, two QTLs were detected on chromosomes 2 and 3, close to the locations of the major QTLs controlling resistance to colonization and to candidate genes involved in the immune response identified in other, independent studies.</p> <p>Conclusions</p> <p>Due to the lack of stability of the QTLs detected, we suggest that interesting regions for further studies are those that were identified in several independent studies, which is the case of the QTL regions on chromosomes 2 and 3, involved in resistance to both <it>Salmonella</it> colonization and carrier state. These observations provide evidence of common genes controlling <it>S.</it> Typhimurium colonization and <it>S</it>. Enteritidis carrier-state in chickens.</p

Development of a high density 600K SNP genotyping array for chicken

Background: High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species.Results: We report here the development of a 600 K Affymetrix® Axiom® HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10-15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome (Gallus_gallus_4.0) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium (P < 0.00001) were excluded from the panel. The final array, designed on the basis of these analyses, consists of 580,954 SNPs and includes 21,534 coding variants. SNPs were selected to achieve an essentially uniform distribution based on genetic map distance for both broiler and layer lines. Due to a lower extent of LD in broilers compared to layers, as reported in previous studies, the ratio of broiler and layer SNPs in the array was kept as 3:2. The final panel was shown to genotype a wide range of samples including broilers and layers with over 100 K to 450 K informative SNPs per line. A principal component analysis was used to demonstrate the ability of the array to detect the expected population structure which is an important pre-investigation step for many genome-wide analyses.Conclusions: This Affymetrix® Axiom® array is the first SNP genotyping array for chicken that has been made commercially available to the public as a product. This array is expected to find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs and detection of copy number variants

Development of a high density 600K SNP genotyping array for chicken

Background High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species. Results We report here the development of a 600 K Affymetrix® Axiom® HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10–15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome (Gallus_gallus_4.0) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium (P < 0.00001) were excluded from the panel. The final array, designed on the basis of these analyses, consists of 580,954 SNPs and includes 21,534 coding variants. SNPs were selected to achieve an essentially uniform distribution based on genetic map distance for both broiler and layer lines. Due to a lower extent of LD in broilers compared to layers, as reported in previous studies, the ratio of broiler and layer SNPs in the array was kept as 3:2. The final panel was shown to genotype a wide range of samples including broilers and layers with over 100 K to 450 K informative SNPs per line. A principal component analysis was used to demonstrate the ability of the array to detect the expected population structure which is an important pre-investigation step for many genome-wide analyses. Conclusions This Affymetrix® Axiom® array is the first SNP genotyping array for chicken that has been made commercially available to the public as a product. This array is expected to find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs and detection of copy number variants.Additional co-authors: Georg Haberer, Steffen Weigend, Rudolf Preisinger, Mahmood Gholami, Saber Qanbari, Henner Simianer, Kellie A Watson, John A Woolliams & David W Bur

Decreased TNF-α synthesis by macrophages restricts cutaneous immunosurveillance by memory CD4+ T cells during aging

Immunity declines during aging, however the mechanisms involved in this decline are not known. In this study, we show that cutaneous delayed type hypersensitivity (DTH) responses to recall antigens are significantly decreased in older individuals. However, this is not related to CC chemokine receptor 4, cutaneous lymphocyte-associated antigen, or CD11a expression by CD4+ T cells or their physical capacity for migration. Instead, there is defective activation of dermal blood vessels in older subject that results from decreased TNF-α secretion by macrophages. This prevents memory T cell entry into the skin after antigen challenge. However, isolated cutaneous macrophages from these subjects can be induced to secrete TNF-α after stimulation with Toll-like receptor (TLR) 1/2 or TLR 4 ligands in vitro, indicating that the defect is reversible. The decreased conditioning of tissue microenvironments by macrophage-derived cytokines may therefore lead to defective immunosurveillance by memory T cells. This may be a predisposing factor for the development of malignancy and infection in the skin during aging

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Does Poor Dental Health Have a Role in the Emergence of Variant Creutzfeldt Jakob Disease in the United Kingdom?

Introduction: Variant creutzfeldt jakob disease (vCJD) is the hu-man neurological disease known to be caused by the same proteinaceous infectious agent (“prion”) that causes Bovine Spongiform Encephalopathy or "Mad Cow Disease". Two un-usual and unexplained characteristics of the vCJD epidemic are its geographical distribution within the UK (about twice as frequent in Scotland and Northern England) and its median age of onset of 26 years that has remained unchanged over the fifteen years of the epidemic.The hypothesis: Infection via the dental route as a consequence of poor dental health, most probably the presence of untreated decay may account for the geographical distribution of vCJD in the UK and offer an explanation for the constant median age of onset of the dis-ease by representing a fixed stage in development.Evaluation of the hypothesis: Analysis of existing data indicates that vCJD incidence by region and an index of dental health by region are positively correlated (r=0.737, p= 0.015). The hypothesis that infection via the dental route may explain the constant median age of onset and geographical distribution of vCJD could be investigated further with a case control study based on individual dental records and by further animal experiments to confirm the biological plausibility of this route

Identification, cloning and characterisation of interleukin-1F5 (IL-36RN) in the chicken

The human IL-1 family contains eleven genes encoded at three separate loci. Nine, including IL-36 receptor antagonist (IL-36RN), also known as IL-1F5, are present at a single locus on chromosome 2, whereas IL-18 and IL-33 lie on chromosomes 11 and 9 respectively. There are currently only three known orthologues in the chicken - IL-1β, IL-18 and IL-1RN - which are encoded on chromosomes 22, 24 and unplaced, respectively. A novel chicken IL-1 family sequence representing IL-36RN (IL-1F5) was initially identified from an expressed sequence tag (EST) library by its similarity to both chicken IL-1RN and chicken IL-1β. Following isolation of the cDNA from the liver of an uninfected bird, a number of unique sequence features were identified. The predicted protein has a longer NH ₂-terminus than the human protein; however, as in mammals, this region contains neither a prodomain nor a signal peptide. A putative nuclear export sequence is also apparent, yet a similar motif is absent in mammalian IL-36RN. Although chIL-36RN exhibits low homology with its mammalian orthologues, it encodes a predicted β-trefoil structure whose β-strands are conserved with those of the mouse sequence.Unlike in mammals, chIL-36RN expression was constitutive in all tissues and cell subsets examined. In response to viral infection, expression was significantly downregulated in a line of birds which are susceptible to the virus.Chicken IL-36RN, like chIL-1RN, is not encoded at the chIL-1β locus, further emphasising the genomic fragmentation of the large IL-1 gene cluster found in mammals. This suggests differential evolution of this cytokine family since the divergence of birds and mammals from a common ancestor, and underlines the difficulty of determining the full repertoire of chIL-1 family members

Identification, cloning, and functional characterization of the IL-1 receptor antagonist in the chicken reveal important differences between the Chicken and mammals

The human IL-1 family contains 11 genes encoded at three separate loci. Nine, including IL-1R antagonist (IL-1RN), are present at a single locus on chromosome 2, whereas IL-18 and IL-33 lie on chromosomes 11 and 9, respectively. There are currently only two known orthologs in the chicken, IL-1β and IL-18, which are encoded on chromosomes 22 and 24, respectively. Two novel chicken IL-1 family sequences were identified from expressed sequence tag libraries, representing secretory and intracellular (icIL-1RN) structural variants of the IL-1RN gene, as seen in mammals. Two further putative splice variants (SVs) of both chicken IL-1RN (chIL-1RN) structural variants were also isolated. Alternative splicing of human icIL-1RN gives three different transcripts; there are no known SVs for human secretory IL-1RN. The chicken icIL-1RN SVs differ from those found in human icIL-1RN in terms of the rearrangements involved. In mammals, IL-1RN inhibits IL-1 activity by physically occupying the IL-1 type I receptor. Both full-length structural variants of chIL-1RN exhibited biological activity similar to their mammalian orthologs in a macrophage cell line bioassay. The four SVs, however, were not biologically active. The chicken IL-1 family is more fragmented in the genome than those of mammals, particularly in that the large multigene locus seen in mammals is absent. This suggests differential evolution of the family since the divergence of birds and mammals from a common ancestor, and makes determination of the full repertoire of chicken IL-1 family members more challenging

Direct measurement of porto-systemic gradient in a failing fontan circulation

We describe the case history of a 42-year-old man with cardiac cirrhosis, portal hypertension, and life-threatening variceal bleeding after Fontan revision surgery. Direct pressure measurements in the portal vein, though high, demonstrated only a modest portosystemic gradient (PSG), 9 mm Hg. A transjugular intrahepatic portosystemic shunt procedure was performed. This reduced the PSG (3 mm Hg). His bleeding was controlled. The patient's histopathological findings were identical to that previously documented in Fontan patients, raising the question of whether these subdiaphragmatic hemodynamics are representative of the broader failing Fontan population.<br/