Development of an integrative database with 499 novel microsatellite markers for Macaca fascicularis

<p>Abstract</p> <p>Background</p> <p>Cynomolgus macaques (<it>Macaca fascicularis</it>) are a valuable resource for linkage studies of genetic disorders, but their microsatellite markers are not sufficient. In genetic studies, a prerequisite for mapping genes is development of a genome-wide set of microsatellite markers in target organisms. A whole genome sequence and its annotation also facilitate identification of markers for causative mutations. The aim of this study is to establish hundreds of microsatellite markers and to develop an integrative cynomolgus macaque genome database with a variety of datasets including marker and gene information that will be useful for further genetic analyses in this species.</p> <p>Results</p> <p>We investigated the level of polymorphisms in cynomolgus monkeys for 671 microsatellite markers that are covered by our established Bacterial Artificial Chromosome (BAC) clones. Four hundred and ninety-nine (74.4%) of the markers were found to be polymorphic using standard PCR analysis. The average number of alleles and average expected heterozygosity at these polymorphic loci in ten cynomolgus macaques were 8.20 and 0.75, respectively.</p> <p>Conclusion</p> <p>BAC clones and novel microsatellite markers were assigned to the rhesus genome sequence and linked with our cynomolgus macaque cDNA database (QFbase). Our novel microsatellite marker set and genomic database will be valuable integrative resources in analyzing genetic disorders in cynomolgus macaques.</p

ACOUSTIC PERFORMANCE OF A SPLITTER DUCT SILENCER WITH ZIGZAG AIRWAYS

会議名称:The 28th International Congress and Exposition on Noise Control Engineering主催学会:INCE/US

Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence

BACKGROUND: In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues. RESULT: The full-insert sequences of 512 cDNA clones were determined. Ultimately we found 302 non-redundant cDNAs carrying open reading frames of 300 bp-length or longer. Among them, 89 cDNAs were found not to be annotated previously in the Ensembl human database. After searching against the Ensembl mouse database, we also found 69 putative coding sequences have no homologous cDNAs in the annotated human and mouse genome sequences in Ensembl. We subsequently designed a DNA microarray including 396 non-redundant cDNAs (with and without open reading frames) to examine the expression of the full-sequenced genes. With the testicular probe and a mixture of probes of 10 other tissues, 316 of 332 effective spots showed intense hybridized signals and 75 cDNAs were shown to be expressed very highly in the cynomolgus monkey testis, but not ubiquitously. CONCLUSIONS: In this report, we determined 302 full-insert sequences of cynomolgus monkey cDNAs with enough length of open reading frames to discover novel transcripts as human homologues. Among 302 cDNA sequences, human homologues of 89 cDNAs have not been predicted in the annotated human genome sequence in the Ensembl. Additionally, we identified 75 dominantly expressed genes in testis among the full-sequenced clones by using a DNA microarray. Our cDNA clones and analytical results will be valuable resources for future functional genomic studies

Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus

<p>Abstract</p> <p>Background</p> <p>Consolidating transcriptome data of non-human primates is essential to annotate primate genome sequences, and will facilitate research using non-human primates in the genomic era. <it>Macaca fascicularis </it>is a macaque monkey that is commonly used for biomedical and ecological research.</p> <p>Findings</p> <p>We constructed cDNA libraries of <it>Macaca fascicularis</it>, derived from tissues obtained from bone marrow, liver, pancreas, spleen, and thymus of a young male, and kidney of a young female. In total, 5'-end sequences of 56,856 clones were determined. Including the previously established cDNA libraries from brain and testis, we have isolated 112,587 cDNAs of <it>Macaca fascicularis</it>, which correspond to 56% of the curated human reference genes.</p> <p>Conclusion</p> <p>These sequences were deposited in the public sequence database as well as in-house macaque genome database <url>http://genebank.nibio.go.jp/qfbase/</url>. These data will become valuable resources for identifying functional parts of the genome of macaque monkeys in future studies.</p

Correlation Analysis Between Time Awareness and Morningness-Eveningness Preference

The circadian clock is adjusted by light inputs via the retinohypothalamic tract. Because environmental light is controllable for modern humans at the individual’s preference although under social schedules, individual differences in time-related psychology and behavior may be associated with morningness-eveningness preference (M-E preference). To examine this hypothesis, we used the Time Management Scale and Time Anxiety Scale to quantify time-related psychology and behavior. These scales aim to evaluate “awareness of effective time management and utilization” and “anxiety about uncontrollable time schedule and unexpected time-related outcome”, respectively. According to our correlation analysis using mid-sleep time as a marker for M-E preference, we obtained results supporting our hypothesis in the correlation between the M-E preference values and the Time Management Scale scores, with larger “time estimation” and “taking each moment as it comes” scores associated with more morningness and eveningness, respectively. Considering that modern humans likely become night owls under artificial light conditions, it appears plausible that lower awareness of time management leads to more eveningness

On acoustic performance of a splitter duct silencer with zigzag cahnnels.

会議名称:The 28th International Congress and Exposition on Noise Control Engineering主催学会:INCE/US

ヒト歯肉線維芽細胞における酸化ストレスに対するレスベラトロール，ケルセチン，及びN-アセチルシステインの生物学的影響

In periodontitis, production of reactive oxygen species (ROS) by neutrophils induces oxidative stress and deteriorates surrounding tissues. Antioxidants reduce damage caused by ROS and are used to treat diseases involving oxidative stress. This study summarizes the different effects of resveratrol, quercetin, and N-acetylcysteine (NAC) on human gingival fibroblasts (HGFs) under oxidative stress induced by hydrogen peroxide. Real-time cytotoxicity analyses reveals that resveratrol and quercetin enhanced cell proliferation even under oxidative stress. Of the antioxidants tested, resveratrol is the most effective at inhibiting ROS production. HGFs incubated with resveratrol and quercetin up-regulate the transcription of type I collagen gene after 3 h, but only resveratrol sustained this up-regulation for 24 h. A measurement of the oxygen consumption rate (OCR, mitochondrial respiration) shows that resveratrol generates the highest maximal respiratory capacity, followed by quercetin and NAC. Simultaneous measurement of OCR and the extracellular acidification rate (non-mitochondrial respiration) reveals that resveratrol and quercetin induce an increase in mitochondrial respiration when compared with untreated cells. NAC treatment consumes less oxygen and enhances more non-mitochondrial respiration. In conclusion, resveratrol is the most effective antioxidant in terms of real-time cytotoxicity analysis, reduction of ROS production, and enhancement of type I collagen synthesis and mitochondrial respiration in HGFs

GWAS of mosaic loss of chromosome Y highlights genetic effects on blood cell differentiation

Abstract: Mosaic loss of chromosome Y (mLOY) is frequently observed in the leukocytes of ageing men. However, the genetic architecture and biological mechanisms underlying mLOY are not fully understood. In a cohort of 95,380 Japanese men, we identify 50 independent genetic markers in 46 loci associated with mLOY at a genome-wide significant level, 35 of which are unreported. Lead markers overlap enhancer marks in hematopoietic stem cells (HSCs, P ≤ 1.0 × 10−6). mLOY genome-wide association study signals exhibit polygenic architecture and demonstrate strong heritability enrichment in regions surrounding genes specifically expressed in multipotent progenitor (MPP) cells and HSCs (P ≤ 3.5 × 10−6). ChIP-seq data demonstrate that binding sites of FLI1, a fate-determining factor promoting HSC differentiation into platelets rather than red blood cells (RBCs), show a strong heritability enrichment (P = 1.5 × 10−6). Consistent with these findings, platelet and RBC counts are positively and negatively associated with mLOY, respectively. Collectively, our observations improve our understanding of the mechanisms underlying mLOY