Estimation of Genetic Parameters, and Genetic and Environmental Effects on Progeny Carcass Traits of a Nucleus Breeding Population in Japanese Black Cattle

Genetic parameters of body weight at the start of fattening (BSF), carcass weight (CWT), subcutaneous fat thickness (SFT), rib thickness (RBT), meat quality grade (MQG), beef marbling score (BMS) and rib eye area (REA) in Japanese Black cattle were estimated. The effects of genetic and environmental factors on fattening performance and carcass quality traits of the progeny were also analyzed. The averages of BSF, CWT, SFT, RBT and REA were 189 kg, 408 kg, 24.9 mm, 69.3 mm and 47.5 cm^2, respectively. CWT was significantly affected (p<0.01) by sire, while BSF (p<0.01), CWT (p<0.01), SFT (p<0.01), RBT (p<0.01) and REA (p<0.05) were significantly affected by dam, indicating the scope of the applicability of selective breeding for improving the dam population for producing beef cattle with greater genetic ability to carcass traits. The sex of the calf had a significant (p<0.01 or p<0.05) effect on all the traits studied except REA. BSF, RBT, MQG and BMS were significantly (p<0.01) affected by the year and season of the birth of calves. The fattening farm exerted a significant influence (p<0.01) on BSF, CWT, MQG and BMS. The heritability estimates for BMS, CWT, RBT, BSF and MQG were 0.36, 0.34, 0.31, 0.26 and 0.23, respectively. Genetically, REA correlated negatively with BSF (-0.57) and SFT (-0.69), as did BMS with CWT (-0.35), SFT (-0.50) and RBT (-0.44). All the other traits correlated positively with one another

Bilateral Chronic Subdural Hematoma in the Posterior Fossa Treated with a Burr Hole Irrigation: A Case Report and Review of the Literature

Chronic subdural hematoma (CSH) in the posterior fossa is extremely rare. The surgical strategy is still controversial. We report a case of bilateral CSH in the posterior fossa successfully treated with a single-burr hole surgery. A 74-year-old man under anticoagulation and antiplatelet therapy developed headache and nausea during observation for an asymptomatic supratentorial CSH. Radiological examinations revealed appearance of bilateral CSH in the posterior fossa associated with hydrocephalus. Upon rapid deterioration of the patient’s consciousness, an urgent treatment was required. A burr hole was made near the transverse-sigmoid junction on the left side to access the hematoma. No ventricular drainage was placed as his consciousness improved during the decompression of the hematoma. Postoperative computed tomography showed that bilateral CSH and hydrocephalus had been successfully treated. In bilateral CSH in the posterior fossa, there may be a connection between each side. CSH in the posterior fossa, when urgent, can be treated under local anesthesia with a unilateral burr hole irrigation

Intradural Lipoma at the Craniocervical Junction Presenting with Progressing Hemiparesis: A Case Report

Intradural spinal lipomas are rare in an adult population. They are mostly asymptomatic and usually associated with spinal dysraphism in a pediatric population. We report a rare case of spinal lipoma without dysraphism and with progressing hemiparesis. A 60-year-old woman had incidental lipoma at the craniocervical junction observed for more than 5 years. Recently, she developed right-sided hemiparesis and sensory disturbance. Radiological studies revealed a large lipoma compressing the dorsal medulla and C1–C2 spinal cord. Standard midline suboccipital craniotomy and C1 laminectomy were performed, and the lipoma was removed subtotally. The lipoma showed severe adhesion to the dorsal medulla and C1 spinal cord; therefore, the excision was limited as internal debulking. Her neurological deficit subsided within 6 months after the decompressive surgery. Considering the benign nature of lipoma, internal decompression is a reasonable management for this lesion

Microbial diversity in deep-sea methane seep sediments presented by SSU rRNA gene tag sequencing

http://www.godac.jamstec.go.jp/darwin/cruise/yokosuka/yk06-03/

Isolation and characterization of a thermophilic, obligately anaerobic and heterotrophic marine Chloroflexi bacterium from a Chloroflexi dominated microbial community associated with a Japanese shallow hydrothermal system, and proposal for Thermomarinilinea lacunofontalis gen. nov., sp. nov.

A novel marine thermophilic and heterotrophic Anaerolineae bacterium in the phylum Chloroflexi, strain SW7T, was isolated from an in situ colonization system deployed in the main hydrothermal vent of the Taketomi submarine hot spring field located on the southern part of Yaeyama Archipelago, Japan. The microbial community associated with the hydrothermal vent was predominated by thermophilic heterotrophs such as Thermococcaceae and Anaerolineae, and the next dominant population was thermophilic sulfur oxidizers. Both aerobic and anaerobic hydrogenotrophs including methanogens were detected as minor populations. During the culture-dependent viable count analysis in this study, an Anaerolineae strain SW7T was isolated from an enrichment culture at a high dilution rate. Strain SW7T was an obligately anaerobic heterotroph grew with fermentation, and non-motile thin rods 3.5-16.5 μm in length and 0.2 μm in width constituting multicellular filament. Growth was observed between 37-65 ℃ (optimum 60℃), pH 5.5-7.3 (optimum pH 6.0), 0.5-3.5% (w/v) NaCl concentration (optimum 1.0%). Based on physiological and phylogenetic features of a new isolate, we propose a new species representing a novel genus Thermomarinilinea: the type strain of Thermomarinilinea lacunofontalis sp. nov., is SW7T (= JCM15506T = KCTC5908T)

Distribution and Niche Separation of Planktonic Microbial Communities in the Water Columns from the Surface to the Hadal Waters of the Japan Trench under the Eutrophic Ocean

The Japan Trench is located under the eutrophic Northwestern Pacific while the Mariana Trench that harbors the unique hadal planktonic biosphere is located under the oligotrophic Pacific. Water samples from the sea surface to just above the seafloor at a total of 11 stations including a trench axis station, were investigated several months after the Tohoku Earthquake in March 2011. High turbidity zones in deep waters were observed at most of the sampling stations. The small subunit (SSU) rRNA gene community structures in the hadal waters (water depths below 6000 m) at the trench axis station were distinct from those in the overlying meso-, bathy and abyssopelagic waters (water depths between 200 and 1000 m, 1000 and 4000 m and 4000 and 6000 m, respectively), although the SSU rRNA gene sequences suggested that potential heterotrophic bacteria dominated in all of the waters. Potential niche separation of nitrifiers, including ammonia-oxidizing archaea (AOA), was revealed by quantitative PCR analyses. It seems likely that Nitrosopumilus-like AOAs respond to a high flux of electron donors and dominate in several zones of water columns including shallow and very deep waters. This study highlights the effects of suspended organic matter, as induced by seafloor deformation, on microbial communities in deep waters and confirm the occurrence of the distinctive hadal biosphere in global trench environments hypothesized in the previous study.http://www.godac.jamstec.go.jp/darwin/cruise/mirai/mr11-03/ehttp://www.godac.jamstec.go.jp/darwin/cruise/yokosuka/yk11-e03/ehttp://www.godac.jamstec.go.jp/darwin/cruise/yokosuka/yk11-e04_leg2/

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

publication en ligne. Article dans revue scientifique avec comité de lecture. nationale.National audienceThe human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

Evaluation of the section modulus for tree-stem cross sections of irregular shape

The effect of section modulus as estimated for tree stems of irregular cross section with hollow trunks on windthrow resistance was discussed. The sample trees were 12 aged poplar trees growing along the roadside in Sapporo. Binarized bitmap images of photographs of the crosscut surface of the sample tree stems were used to calculate numerical solutions for section moduli. The error for image resolution was simulated to less than 1% under the condition in which the image was divided into more than 400 pixels. The coefficient of variation in section modulus concerning six neutral axis directions in a horizontal plane was 11-14%. The reduction in section modulus caused by decay or hollow trunk was 36-56% of the full cross section. The effect of section modulus on critical wind velocity was found to be considerable. The critical wind velocity calculated for some of the sample trees was less than 40 m/s, and these trees were considered to be in danger of bending failure of the stems