Catalogue Search | MBRL
Are you sure you want to remove the book from the shelf?
{{itemTitle}}
1,087
result(s) for
"Ishikawa, Akira"
Sort by:
Identification of a Putative Quantitative Trait Gene for Resistance to Obesity in Mice Using Transcriptome Analysis and Causal Inference Tests
It is still challenging to identify causal genes governing obesity. Pbwg1.5, a quantitative trait locus (QTL) for resistance to obesity, was previously discovered from wild Mus musculus castaneus mice and was fine-mapped to a 2.1-Mb genomic region of mouse chromosome 2, where no known gene with an effect on white adipose tissue (WAT) has been reported. The aim of this study was to identify a strong candidate gene for Pbwg1.5 by an integration approach of transcriptome analysis (RNA-sequencing followed by real-time PCR analysis) and the causal inference test (CIT), a statistical method to infer causal relationships between diplotypes, gene expression and trait values. Body weight, body composition and biochemical traits were measured in F2 mice obtained from an intercross between the C57BL/6JJcl strain and a congenic strain carrying Pbwg1.5 on the C57BL/6JJcl background. The F2 mice showed significant diplotype differences in 12 traits including body weight, WAT weight and serum cholesterol/triglyceride levels. The transcriptome analysis revealed that Ly75, Pla2r1, Fap and Gca genes were differentially expressed in the liver and that Fap, Ifih1 and Grb14 were differentially expressed in WAT. However, CITs indicated statistical evidence that only the liver Ly75 gene mediated between genotype and WAT. Ly75 expression was negatively associated with WAT weight. The results suggested that Ly75 is a putative quantitative trait gene for the obesity-resistant Pbwg1.5 QTL discovered from the wild M. m. castaneus mouse. The finding provides a novel insight into a better understanding of the genetic basis for prevention of obesity.
Journal Article
Correction: Identification of a Putative Quantitative Trait Gene for Resistance to Obesity in Mice Using Transcriptome Analysis and Causal Inference Tests
[This corrects the article DOI: 10.1371/journal.pone.0170652.].
Journal Article
Gastric Adenocarcinoma with Enteroblastic Differentiation Resected through Endoscopic Submucosal Dissection: A Case Report
Abstract
Introduction: Gastric adenocarcinoma with enteroblastic differentiation (GAED) is a rare histological type of gastric adenocarcinoma that occurs in the stomach and is known for its aggressive behavior. GAED is diagnosed histopathologically and is often advanced at the time of diagnosis. Case Presentation: We report the case of a 70-year-old male with a 20-mm superficial depressed lesion on the anterior wall of the antrum. Histological examination of the endoscopic submucosal dissection specimen revealed that the tumor was composed of dilated or slit-like branching tubules; additionally, the tumor cells had clear cytoplasm resembling that of the fetal digestive tract. Immunohistochemically, the tumor cells were positive for Glypican-3 and alpha-fetoprotein. A pathological diagnosis of GAEDs was established. GAED was found in approximately 30% of all the tumor cells and showed lymphatic invasion. The patient has been under recurrence-free follow-up for approximately 1 year after the endoscopic submucosal dissection. Conclusion: In order to detect a large number of cases, immunostaining should be aggressively performed if morphological findings are suspicious for GAED.
Journal Article
A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis
Large numbers of quantitative trait loci (QTL) affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs) for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.
Journal Article
New Candidate Genes for a Chicken Pectoralis Muscle Weight QTL Identified by a Hypothesis-Free Integrative Genetic Approach
Background/Objectives: Identifying candidate genes underlying quantitative trait loci (QTL) in poultry has traditionally required labor-intensive positional cloning. Previous studies using an F2 population derived from native Japanese Nagoya (NAG) and White Plymouth Rock (WPR) breeds revealed a major QTL on chromosome 2 affecting 3-week body weight and 4-week pectoralis muscle weight. This study aimed to identify candidate genes for this QTL using a hypothesis-free integrative genetic approach. Methods: We employed a multi-step analytical framework combining QTL remapping, transcriptome analysis, gene enrichment analysis, haplotype frequency comparison, and correlation analysis. QTL remapping was performed using individual traits and their first principal component (PC1) in 239 F2 chickens. RNA-sequencing (RNA-seq) of liver tissue was conducted for F2 individuals with extreme PC1 scores, followed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) validation. Results: QTL remapping refined the 95% confidence interval to a chromosome 2 region containing 329 genes. RNA-seq analysis identified 23 differentially expressed genes (DEGs) within this interval. Although gene enrichment analysis initially highlighted GATA binding protein 6 (GATA6) as a potential candidate, RT-qPCR in NAG, WPR, and F1 chickens showed no significant expression differences, excluding GATA6. Haplotype frequency and correlation analyses prioritized cadherin-17 (CDH17) as the strongest candidate gene and ring finger protein 151 (RNF151) as a secondary candidate. Conclusions: Our hypothesis-free integrative approach effectively refined candidate genes for a chromosome 2 QTL influencing early growth and pectoralis muscle weight. CDH17 and RNF151 represent promising targets for functional validation and may support marker-assisted selection to improve muscle-related traits in chickens.
Journal Article
Effects of root-colonizing fungi on pioneer Pinus thunbergii seedlings in primary successional volcanic mudflow on Kuchinoerabu Island, Japan
Root-colonizing fungi, such as mycorrhizal fungi and dark septate endophyte fungi, are often found on pioneer plant species during early primary succession. However, little is known about which fungal species are responsible for the establishment of pioneer plants when these symbionts colonize simultaneously. We investigated the root-colonizing fungal communities of Pinus thunbergii that established prior to lichens, bryophytes, and short-lived herbaceous plants in a primary successional volcanic mudflow site on Kuchinoerabu Island, Japan. We collected a total of 54 current-year and 1- to 2-year-old seedlings. The colonization of root fungi was evaluated by direct observation of key structures (e.g., mantle, arbuscule, microsclerotia, and hyphae) and molecular analysis. Of the 34 current-year seedlings collected, only 12 individuals were colonized by ectomycorrhizal (ECM) fungi. By contrast, all 1- to 2-year-old seedlings were colonized by ECM fungi. Seedlings colonized by pine-specific ECM fungi, specifically Rhizopogon roseolus and Suillus granulatus, showed higher nitrogen and phosphorus contents in their needles compared to non-ECM seedlings. Arbuscular mycorrhizal fungi and dark septate endophyte fungi were found in only two and three individuals, respectively. The high density of mycophagous deer on Kuchinoerabu-jima may contribute to the favored dispersal of ECM fungi over other root-colonizing fungi. In conclusion, the seedling establishment of P. thunbergii at the volcanic mudflow may be largely supported by ECM fungi, with negligible effects of arbuscular mycorrhizal fungi and dark septate endophytes.
Journal Article
Genetic Architecture of Innate Fear Behavior in Chickens
The genetic architecture of innate fear behavior in chickens is poorly understood. Here, we performed quantitative trait loci (QTL) analysis of innate responses to tonic immobility (TI) and open field (OF) fears in 242 newly hatched chicks of an F2 population between the native Japanese Nagoya breed and the White Leghorn breed using 881 single nucleotide polymorphism markers obtained by restriction site-associated DNA sequencing. At genome-wide 5% significance levels, four QTL for TI traits were revealed on chromosomes 1–3 and 24. Two of these loci had sex-specific effects on the traits. For OF traits, three QTL were revealed on chromosomes 2, 4 and 7. The TI and OF QTL identified showed no overlaps in genomic regions and different modes of inheritance. The three TI QTL and one OF QTL exerted antagonistic effects on the traits. The results demonstrated that context-dependent QTL underlie the variations in innate TI and OF behaviors.
Journal Article
Fine-grained interplanetary dust input during the Turonian (Late Cretaceous): evidence from osmium isotope and platinum group elements
The Turonian age (~ 90–94 Ma) was the hottest geological interval in the Cretaceous and also marked by the K3 event, a pronounced enrichment of
3
He in pelagic sediments (i.e., massive input of extraterrestrial materials). Here, we present Os isotopic (
187
Os/
188
Os) and platinum group element (PGE) data from Turonian sedimentary records. After a sharp unradiogenic shift during the end-Cenomanian oceanic anoxic event 2, the
187
Os/
188
Os ratios declined continuously throughout the Turonian, which could be ascribed to the formations of several large igneous provinces (LIPs). Because the interval with the most unradiogenic
187
Os/
188
Os ratios (i.e., enhanced LIP volcanism) does not correspond to the warmest interval during the mid-Cretaceous, additional sources of CO
2
, such as subduction zone volcanism or the kimberlite formation, may explain the Cretaceous Thermal Maximum. As Os isotope ratios do not show any sharp unradiogenic shifts and PGE concentrations do not exhibit a pronounced enrichment, an influx of fine-grained cosmic dust to the Earth’s surface, possibly from the long-period comet showers, can be inferred at the time of the
3
He enrichment during the mid-Turonian K3 event. Our findings highlight the different behaviors of
3
He and PGE information in the sedimentary rocks during the input of fined-grained extraterrestrial materials.
Journal Article
Exploring the relationship between personal and cohabiting family members’ COVID-19 infection experiences and fear of COVID-19: a longitudinal study based on the Japan COVID-19 and Society Internet Survey (JACSIS)
ObjectivesThis study aims to explore the relationship between the combined experiences of COVID-19 infection in individuals and their family members and the resulting fear of COVID-19, with a focus on the severity of symptoms and various sociodemographic factors.DesignLongitudinal survey study.SettingThe Japan COVID-19 and Society Internet Survey (JACSIS), a large-scale web panel survey administered in Japan.ParticipantsAnalysis was based on responses from 15 542 individuals who participated in all three waves of JACSIS conducted between 2020 and 2022.Main outcome measuresThe primary measure was the fear of COVID-19, assessed using the Fear of COVID-19 Scale. The study employed a two-way analysis of variance without repetition, Games-Howell post hoc tests and ordinary least-squares linear regression analysis, with time points treated as fixed effects.ResultsThe study revealed significant differences in fear levels based on the combined COVID-19 infection experiences of respondents and their family members, with variations observed across different time points. Mild symptoms in either the respondents or their family members correlated with reduced fear (β=−0.584, SE=0.181, p=0.001), while severe symptoms were associated with increased fear (β=1.244, SE=0.217, p<0.001). Gender, age, marital status and a history of respiratory disease or mental illness were also significant factors. For instance, females reported higher fear levels compared with males (β=0.707, SE=0.049, p<0.001), and those with a history of respiratory diseases showed increased fear (β=1.632, SE=0.286, p<0.001). Over time, the general fear of COVID-19 decreased, with the sharpest decline observed at T3 compared with T1 (β=−1.399, SE=0.061, p<0.001).ConclusionThe study highlights the significant influence of the combined COVID-19 infection experiences of individuals and their family members (the severity of symptoms, in particular) on the fear of COVID-19. These results underscore the need for tailored mental health interventions that consider both personal and familial infection experiences, as well as other sociodemographic factors. The findings also reflect the evolving public response to the changing dynamics of the pandemic.
Journal Article