Genes to cells : devoted to molecular & cellular mechanisms最新文献

Potential negative effect of total parenteral nutrition on the human circadian clock. 全肠外营养对人体生物钟的潜在负面影响。

IF 2.1

Genes to cells : devoted to molecular & cellular mechanisms Pub Date : 2022-10-01 Epub Date: 2022-08-03 DOI: 10.1111/gtc.12976

Muneto Tatsumoto, Ritsuko Matsumura, Takuyuki Endo, Isao T Tokuda, Koichi Node, Makoto Akashi

引用次数: 1

Machine learning approach identifies prominent codons from different degenerate groups influencing gene expression in bacteria. 机器学习方法从影响细菌基因表达的不同退化群中识别出突出的密码子。

IF 2.1

Genes to cells : devoted to molecular & cellular mechanisms Pub Date : 2022-10-01 Epub Date: 2022-08-22 DOI: 10.1111/gtc.12977

Piyali Sen, Annushree Kurmi, Suvendra Kumar Ray, Siddhartha Sankar Satapathy

{"title":"Machine learning approach identifies prominent codons from different degenerate groups influencing gene expression in bacteria.","authors":"Piyali Sen, Annushree Kurmi, Suvendra Kumar Ray, Siddhartha Sankar Satapathy","doi":"10.1111/gtc.12977","DOIUrl":"https://doi.org/10.1111/gtc.12977","url":null,"abstract":"Unequal usage of synonymous codons is known as codon usage bias (CUB), which is generally different between the high-expression genes (HEG) and low-expression genes (LEG) in organisms is not yet adequately reported across different bacteria. In this study, a machine learning-based approach was implemented initially to find out codons that are significantly different between the HEG and LEG in Escherichia coli. It identified Cys codons such as UGU and UGC, Lys codons such as AAA and AAG that were least influenced by gene expression. Codons such as UCU (Ser), CUG (Leu), GGG (Gly), CGG (Arg) etc. were identified to be influenced maximum by the gene expression. The study was extended to analyze codon usage in 683 other bacterial species. Cys (UGU/UGC) and Ser (AGU/AGC) codons were identified being the least different between the two groups of genes across these bacterial species. Codons such as CGA, CUG, GGG, GCC, ACC, AUA, and AUC were identified to be influenced by the gene expression across majority of these species. This study supports the role of CUB on gene expression across bacteria and demonstrates a commonality among bacteria regarding behavior of certain codons with regard to gene expression.","PeriodicalId":520630,"journal":{"name":"Genes to cells : devoted to molecular & cellular mechanisms","volume":" ","pages":"591-601"},"PeriodicalIF":2.1,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40419547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Involvement of the centrosomal protein 55 (cep55) gene in zebrafish head formation. 中心体蛋白55 (cep55)基因参与斑马鱼头部形成。

IF 2.1

Genes to cells : devoted to molecular & cellular mechanisms Pub Date : 2019-10-01 Epub Date: 2019-09-01 DOI: 10.1111/gtc.12715

Kanoko Yanagi, Ryota Sone, Rie Ohga, Atsuo Kawahara

引用次数: 3

miR-214 and hypoxia down-regulate Necl-2/CADM1 and enhance ErbB2/ErbB3 signaling. miR-214和缺氧下调Necl-2/CADM1，增强ErbB2/ErbB3信号。

IF 2.1

Genes to cells : devoted to molecular & cellular mechanisms Pub Date : 2013-03-01 Epub Date: 2013-01-10 DOI: 10.1111/gtc.12027

Kenji Momose, Akihiro Minami, Yohei Shimono, Kiyohito Mizutani, Kentaro Nobutani, Takeshi Azuma, Yoshimi Takai

引用次数: 20

C. elegans Rassf homolog, rasf-1, is functionally associated with rab-39 Rab GTPase in oxidative stress response. 秀丽隐杆线虫Rassf同源物rasf-1在氧化应激反应中与Rab -39 Rab GTPase功能相关。

IF 2.1

Genes to cells : devoted to molecular & cellular mechanisms Pub Date : 2013-03-01 Epub Date: 2013-01-07 DOI: 10.1111/gtc.12028

Motohiko Takenaka, Hideki Inoue, Atsushi Takeshima, Tomonori Kakura, Toshiyuki Hori

{"title":"C. elegans Rassf homolog, rasf-1, is functionally associated with rab-39 Rab GTPase in oxidative stress response.","authors":"Motohiko Takenaka, Hideki Inoue, Atsushi Takeshima, Tomonori Kakura, Toshiyuki Hori","doi":"10.1111/gtc.12028","DOIUrl":"https://doi.org/10.1111/gtc.12028","url":null,"abstract":"The Ras association domain family (Rassf) is one of the Ras effectors, which can bind to several GTP-charged Ras-like GTPases. The Rassf proteins are widely conserved beyond species from nematode to human. To explore the novel functions of Rassf proteins, we took advantage of nematode C. elegans as a model animal with only one Rassf homolog, T24F1.3 (rasf-1). The rasf-1-mutant as well as rasf-1-knockdown animals were found to be more sensitive to oxidative stress of arsenite than in wild type, indicating that rasf-1 is involved in oxidative stress response. We next screened for proteins that interact with RASF-1 by the yeast two-hybrid system and identified RAB-39 Rab GTPase as an interacting partner of RASF-1. We not only confirmed specific binding between these molecules but also demonstrated that RASF-1 binds to GTP-bound form but not GDP-bound form of RAB-39. Importantly, rab-39 mutant animals were also sensitive to oxidative stress, which was dependent on rasf-1 according to the epistasis analysis. Moreover, Rassf1 and Rab39, mammalian homologs of rasf-1 and rab-39, respectively, were shown to interact with each other in vitro. These results indicate that the RASF-1 functionally interacts with RAB-39 and that the interaction between their homologs is conserved in mammals.","PeriodicalId":520630,"journal":{"name":"Genes to cells : devoted to molecular & cellular mechanisms","volume":" ","pages":"203-10"},"PeriodicalIF":2.1,"publicationDate":"2013-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/gtc.12028","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40216414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Transcriptionally active nuclei are selective in mature multinucleated osteoclasts. 转录活性核在成熟的多核破骨细胞中具有选择性。

IF 2.1

Genes to cells : devoted to molecular & cellular mechanisms Pub Date : 2010-10-01 Epub Date: 2010-09-10 DOI: 10.1111/j.1365-2443.2010.01441.x

Min-Young Youn, Ichiro Takada, Yuuki Imai, Hisataka Yasuda, Shigeaki Kato

{"title":"Transcriptionally active nuclei are selective in mature multinucleated osteoclasts.","authors":"Min-Young Youn, Ichiro Takada, Yuuki Imai, Hisataka Yasuda, Shigeaki Kato","doi":"10.1111/j.1365-2443.2010.01441.x","DOIUrl":"https://doi.org/10.1111/j.1365-2443.2010.01441.x","url":null,"abstract":"Multinucleation is indispensable for the bone-resorbing activity of mature osteoclasts. Although multinucleation is evident in mature osteoclasts and certain other cell types, putative regulatory networks among nuclei remain poorly characterized. To address this issue, transcriptional activity of each nucleus in a multinucleated osteoclast was assessed by detecting the distributions of nuclear proteins by immunocytochemistry and primary transcripts by RNA FISH. Patterns of epigenetic histone markers governing transcription as well as localization of tested nuclear receptor proteins appeared indistinguishable among nuclei in differentiated Raw264 cells and mouse mature osteoclasts. However, RNAPII-Ser5P/2P and NFATc1 proteins were selectively distributed in certain nuclei in the same cell. Similarly, the distributions of primary transcripts for osteoclast-specific genes (Nfatc1, Ctsk and Acp5) as well as a housekeeping gene (beta-tubulin) were limited in certain nuclei within individual cells. By fusing two Raw264 cell lines that stably expressed ZsGreen-NLS and DsRed-NLS proteins, transmission of nuclear proteins across all of the nuclei in a cell could be observed, presumably through the shared cytoplasm. Taken together, we conclude that although nuclear proteins are diffusible among nuclei, only certain nuclei within a multinucleated osteoclast are transcriptionally active.","PeriodicalId":520630,"journal":{"name":"Genes to cells : devoted to molecular & cellular mechanisms","volume":" ","pages":"1025-35"},"PeriodicalIF":2.1,"publicationDate":"2010-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/j.1365-2443.2010.01441.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40060784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 26