Mapping of novel loci involved in lung and colon tumor susceptibility by the use of genetically selected mouse strains

Two non-inbred mouse lines, phenotypically selected for maximal (AIRmin) and minimal (AIRmax) acute inflammatory response, show differential susceptibility/resistance to the development of several chemically-induced tumor types. An intercross pedigree of these mice was generated and treated with the chemical carcinogen dimethylhydrazine, which induces lung and intestinal tumors. Genome wide high-density genotyping with the Restriction Site-Associated DNA genotyping (2B-RAD) technique was used to map genetic loci modulating individual genetic susceptibility to both lung and intestinal cancer. Our results evidence new common quantitative trait loci (QTL) for those phenotypes and provide an improved understanding of the relationship between genomic variation and individual genetic predisposition to tumorigenesis in different organs.

Population Genetics of New Zealand Pagrus auratus and Genetic Variation of an Aquaculture Broodstock

<p>Fisheries and aquaculture are major contributors of nutrition and animal protein worldwide. Understanding the genetic variation and differentiation within and between wild populations is important for both sustainable fisheries management and selection of aquaculture broodstock. This study determined the genetic variation and differentiation of New Zealand Pagrus auratus based on mitochondrial DNA control region sequencing and microsatellite DNA genotyping. Low but significant differentiation was measured between several sample sites, but otherwise the population was genetically panmictic. The M-ratio test and Fu’s Fs statistics indicate that there may have been historical bottlenecks at all sample sites and a more recent bottleneck in the Tasman Bay. Two South Island sites were identified that had not been through recent bottlenecks and were not significantly differentiated from the Tasman Bay, which may provide a source of gene flow to aid its genetic recovery. Comparison of the broodstock and wild genetic variation indicate that the broodstock represented most of the genetic variation found in high frequency in wild populations, but further wild-caught individuals may be needed, based on the criteria used in several previous studies. Simulations indicate that adding approximately 20 and 48 wild-caught individuals from multiple populations to the current broodstock was needed to represent all genetic variation above a target frequency of 0.05 in the Tasman Bay and all sample sites, respectively.</p>

Population Genetics of New Zealand Pagrus auratus and Genetic Variation of an Aquaculture Broodstock

<p>Fisheries and aquaculture are major contributors of nutrition and animal protein worldwide. Understanding the genetic variation and differentiation within and between wild populations is important for both sustainable fisheries management and selection of aquaculture broodstock. This study determined the genetic variation and differentiation of New Zealand Pagrus auratus based on mitochondrial DNA control region sequencing and microsatellite DNA genotyping. Low but significant differentiation was measured between several sample sites, but otherwise the population was genetically panmictic. The M-ratio test and Fu’s Fs statistics indicate that there may have been historical bottlenecks at all sample sites and a more recent bottleneck in the Tasman Bay. Two South Island sites were identified that had not been through recent bottlenecks and were not significantly differentiated from the Tasman Bay, which may provide a source of gene flow to aid its genetic recovery. Comparison of the broodstock and wild genetic variation indicate that the broodstock represented most of the genetic variation found in high frequency in wild populations, but further wild-caught individuals may be needed, based on the criteria used in several previous studies. Simulations indicate that adding approximately 20 and 48 wild-caught individuals from multiple populations to the current broodstock was needed to represent all genetic variation above a target frequency of 0.05 in the Tasman Bay and all sample sites, respectively.</p>

Whole-Blood Methylation Analysis Reveals Respiratory Environmental Functional Pathways Involved in Severity Following SARS-CoV-2 Infection

SARS-CoV-2 causes a severe inflammatory syndrome called COVID-19 that primarily affects the lungs leading, in many cases, to bilateral pneumonia, severe dyspnea and in ~5% of the cases, death. The mechanisms through which this occurs are still being elucidated. A strong relationship between COVID-19 progression and autoimmune disorder pathogenesis has been identified as an exacerbated interferon immune response or an inflammatory condition mediated by an increase of pro-inflammatory cytokine production, among other. DNA methylation is known to regulate immune response processes, thus COVID-19 progression might be also conditioned by DNA methylation changes not studied in depth, yet. Thus, here an epigenome-wide DNA methylation analysis combined with DNA genotyping for 101 and 473 SARS-CoV-2 negative and positive lab tested individuals, respectively, from two different clinical centers is presented in order to evaluate the implications of the epigenetic regulation in the course of COVID-19 disease. The results reveal the existence of an epigenome regulation of functional pathways associated with the COVID-19 progression, such as innate interferon responses, hyperactivation of B and T lymphocytes, phagocytosis and innate C-type lectin DC-SIGN. These DNA methylation changes were found to be regulated by genetic loci associated with COVID-19 susceptibility and autoimmune disease. In mild COVID-19 patients hypomethylation of CpGs regulating genes within the AKT signaling pathway, and the hypermethylation of a group of CpGs related to environmental traits regulating IL-6 expression via the transcription factor CEBP, discriminate these individuals from those who develop the most critical outcomes of the disease. Thus, the analysis points out to an environmental contribution that mediated by DNA methylation changes in SARS-CoV-2 positive patients, might be playing a role in triggering the cytokine storm described in the most severe cases. In addition, important differences were found in terms of epigenetic regulation between severe and mild cases when compared with systemic autoimmune diseases.

THE TESTING OF SSR MARKERS OF GENES CONTROLLING RESISTANCE TO P. HALSTEDII AND THE SELECTION OF OPTIMAL CONDITIONS FOR PCR

Downy mildew is one of the most harmful diseases of sunflower. The most effective measure of this disease control is the development of resistant varieties and hybrids. The use of molecular markers, in particular DNA markers, allows to control the presence of dominant resistance genes at each stage of breeding. We carried out the selection of the optimal method for the isolation of sunflower DNA and the selection of the optimal temperature regimes of amplification for 10 pairs of primers developed to mark the Pl6, Pl8, Pl13, and PlArg genes. Preliminary, we identified 13 allelic variants that are suitable for DNA genotyping of Helianthus annuus by these loci.