Biochemistry and Cell Biology最新文献_第5页

Evolution of techniques and tools for replication fork proteome and protein interaction studies. 复制叉蛋白质组和蛋白质相互作用研究技术和工具的演变。

IF 2.9 3区生物学

Biochemistry and Cell Biology Pub Date : 2024-04-01 Epub Date: 2023-12-19 DOI: 10.1139/bcb-2023-0215

Carla-Marie Jurkovic, François-Michel Boisvert

引用次数: 0

Optimized total RNA isolation from bovine sperm with enhanced sperm head lysis. 优化从牛精子中分离总RNA，增强精子头裂解。

IF 2.9 3区生物学

Biochemistry and Cell Biology Pub Date : 2024-04-01 Epub Date: 2023-11-10 DOI: 10.1139/bcb-2023-0231

Saurabh Tiwari, Abdallah Shahat, John Kastelic, Nehal Thakor, Jacob Thundathil

{"title":"Optimized total RNA isolation from bovine sperm with enhanced sperm head lysis.","authors":"Saurabh Tiwari, Abdallah Shahat, John Kastelic, Nehal Thakor, Jacob Thundathil","doi":"10.1139/bcb-2023-0231","DOIUrl":"10.1139/bcb-2023-0231","url":null,"abstract":"Increasing evidence of sperm RNA's role in fertilization and embryonic development has provided impetus for its isolation and thorough characterization. Sperm are considered tough-to-lyse cells due to the compact condensed DNA in sperm heads. Lack of consensus among bovine sperm RNA isolation protocols introduces experimental variability in transcriptome studies. Here, we describe an optimized method for total RNA isolation from bovine sperm using the TRIzol reagent. This study critically investigated the effects of various lysis conditions on sperm RNA isolation. Sperm suspended in TRIzol were subjected to a combination of mechanical treatments (sonication and passage through a 30G needle and syringe) and chemical treatments (supplementation with reducing agents 1,4-dithiothreitol and tris(2-carboxyethyl) phosphine hydrochloride (TCEP)). Microscopic evaluation of sperm lysis confirmed preferential sperm tail versus sperm head lysis. Interestingly, only TCEP-supplemented TRIzol (both mechanical treatments) had progressive sperm head lysis and consistently yielded total sperm RNA. Furthermore, RNA integrity was confirmed based on the electrophoresis profile and an absence of genomic DNA and somatic cells (e.g., epithelial cells, spermatids, etc.) with RT-qPCR. Our findings highlighted the importance of sperm lysis, specifically of the sperm head using TCEP with mechanical treatment, in total RNA isolation and presented a bovine-specific sperm RNA isolation method to reduce experimental variabilities.","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72208212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Protein arginine methyltransferase 1, a major regulator of biological processes. 蛋白质精氨酸甲基转移酶1，生物过程的主要调节因子。

IF 2.9 3区生物学

Biochemistry and Cell Biology Pub Date : 2024-04-01 Epub Date: 2023-11-03 DOI: 10.1139/bcb-2023-0212

Sadhana R N Sudhakar, Shahper N Khan, Ariel Clark, Thordur Hendrickson-Rebizant, Shrinal Patel, Ted M Lakowski, James R Davie

引用次数: 0

Identification of critical mitochondrial hub gene for facial nerve regeneration. 鉴定面部神经再生的关键线粒体枢纽基因

IF 2.9 3区生物学

Biochemistry and Cell Biology Pub Date : 2024-04-01 Epub Date: 2023-12-12 DOI: 10.1139/bcb-2023-0224

Xiaofang Cao, Yan Zhang, Yu Shi, Ying Li, Li Gao, Xiumei Wang, Liang Sun

{"title":"Identification of critical mitochondrial hub gene for facial nerve regeneration.","authors":"Xiaofang Cao, Yan Zhang, Yu Shi, Ying Li, Li Gao, Xiumei Wang, Liang Sun","doi":"10.1139/bcb-2023-0224","DOIUrl":"10.1139/bcb-2023-0224","url":null,"abstract":"Mitochondria play a critical role in nerve regeneration, yet the impact of gene expression changes related to mitochondria in facial nerve regeneration remains unknown. To address this knowledge gap, we analyzed the expression profile of the facial motor nucleus (FMN) using data obtained from the Gene Expression Omnibus (GEO) database (GSE162977). By comparing different time points in the data, we identified differentially expressed genes (DEGs). Additionally, we collected mitochondria-related genes from the Gene Ontology (GO) database and intersected them with the DEGs, resulting in the identification of mitochondria-related DEGs (MIT-DEGs). To gain further insights, we performed functional enrichment and pathway analysis of the MIT-DEGs. To explore the interactions among these MIT-DEGs, we constructed a protein-protein interaction (PPI) network using the STRING database and identified hub genes using the Degree algorithm of Cytoscape software. To validate the relevance of these genes to nerve regeneration, we established a rat facial nerve injury (FNI) model and conducted a series of experiments. Through these experiments, we confirmed three MIT-DEGs (Myc, Lyn, and Cdk1) associated with facial nerve regeneration. Our findings provide valuable insights into the transcriptional changes of mitochondria-related genes in the FMN following FNI, which can contribute to the development of new treatment strategies for FNI.","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138796361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ChestCovidNet: An Effective DL-based Approach for COVID-19, Lung Opacity, and Pneumonia Detection Using Chest Radiographs Images. ChestCovidNet：基于 DL 的有效方法，利用胸片图像检测 COVID-19、肺不张和肺炎

IF 2.9 3区生物学

Biochemistry and Cell Biology Pub Date : 2024-02-02 DOI: 10.1139/bcb-2023-0265

Naeem Ullah, Javed Ali Khan, Sultan Almakdi, Mohammed S Alshehri, Mimonah Al Qathrady, Muhammad Shahid Anwar, Ikram Syed

{"title":"ChestCovidNet: An Effective DL-based Approach for COVID-19, Lung Opacity, and Pneumonia Detection Using Chest Radiographs Images.","authors":"Naeem Ullah, Javed Ali Khan, Sultan Almakdi, Mohammed S Alshehri, Mimonah Al Qathrady, Muhammad Shahid Anwar, Ikram Syed","doi":"10.1139/bcb-2023-0265","DOIUrl":"https://doi.org/10.1139/bcb-2023-0265","url":null,"abstract":"Currently used lung disease screening tools are expensive in terms of money and time. Therefore, chest radiograph images (CRIs) are employed for prompt and accurate COVID-19 identification. Recently, many researchers have applied Deep learning (DL) based models to detect COVID-19 automatically. However, their model could have been more computationally expensive and less robust, i.e., its performance degrades when evaluated on other datasets. This study proposes a trustworthy, robust, and lightweight network (ChestCovidNet) that can detect COVID-19 by examining various CRIs datasets. The ChestCovidNet model has only 11 learned layers, eight convolutional (Conv) layers, and three fully connected (FC) layers. The framework employs both the Conv and group Conv layers, Leaky Relu activation function, shufflenet unit, Conv kernels of 3×3 and 1×1 to extract features at different scales, and two normalization procedures that are cross-channel normalization and batch normalization. We used 9013 CRIs for training whereas 3863 CRIs for testing the proposed ChestCovidNet approach. Furthermore, we compared the classification results of the proposed framework with hybrid methods in which we employed DL frameworks for feature extraction and support vector machines (SVM) for classification. The study's findings demonstrated that the embedded low-power ChestCovidNet model worked well and achieved a classification accuracy of 98.12% and recall, F1-score, and precision of 95.75%.","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139671221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SUMO-3 promotes the ubiquitin-dependent turnover of TRIM55. SUMO-3促进TRIM55的泛素依赖性周转。

IF 2.9 3区生物学

Biochemistry and Cell Biology Pub Date : 2024-02-01 Epub Date: 2023-09-13 DOI: 10.1139/bcb-2023-0153

Nour-El-Houda Hammami, Natacha Mérindol, Mélodie B Plourde, Tara Maisonnet, Sophie Lebel, Lionel Berthoux

{"title":"SUMO-3 promotes the ubiquitin-dependent turnover of TRIM55.","authors":"Nour-El-Houda Hammami, Natacha Mérindol, Mélodie B Plourde, Tara Maisonnet, Sophie Lebel, Lionel Berthoux","doi":"10.1139/bcb-2023-0153","DOIUrl":"10.1139/bcb-2023-0153","url":null,"abstract":"Human muscle-specific RING fingers (MURFs) are members of the tripartite motif (TRIM) family of proteins characterized by their C-terminal subgroup one signature domain. MURFs play a role in sarcomere formation and microtubule dynamics. It was previously established that some TRIMs undergo post-translational modification by small ubiquitin-like modifier (SUMO). In this study, we explored the putative SUMOylation of MURF proteins as well as their interactions with SUMO. MURF proteins (TRIM54, TRIM55, and TRIM63) were not found to be SUMOylated. However, TRIM55 turnover by proteasomal and lysosomal degradation was higher upon overexpression of SUMO-3 but not of SUMO-1. Furthermore, it is predicted that TRIM55 contains two potential SUMO-interacting motifs (SIMs). We found that SIM1- and SIM2-mutated TRIM55 were more stable than the wild-type (WT) protein partly due to decreased degradation. Consistently, SIM-mutated TRIM55 was less polyubiquitinated than the WT protein, despite similar monoubiquitination levels. Using IF microscopy, we observed that SIM motifs influenced TRIM55 subcellular localization. In conclusion, our results suggest that SUMO-3 or SUMO-3-modified proteins modulate the localization, stability, and RING ubiquitin ligase activity of TRIM55.","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10228876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LncRNAs: the good, the bad, and the unknown. lncRNA：好的、坏的和未知的。

IF 2.9 3区生物学

Biochemistry and Cell Biology Pub Date : 2024-02-01 Epub Date: 2023-08-14 DOI: 10.1139/bcb-2023-0155

Ganesan Arunkumar

引用次数: 0

RNA-binding protein NOVA1 promotes acute T-lymphocyte leukemia progression by stabilizing USP44 mRNA. RNA结合蛋白NOVA1通过稳定USP44mRNA促进急性T淋巴细胞白血病的进展。

IF 2.9 3区生物学

Biochemistry and Cell Biology Pub Date : 2024-02-01 Epub Date: 2023-10-10 DOI: 10.1139/bcb-2023-0092

Bin Zhang, Ruowen Sun, Min Gu, Zehui Jiang, Ye Wang, Linlin Zhang, Xiaoyang Liu, Zuofei Chi

{"title":"RNA-binding protein NOVA1 promotes acute T-lymphocyte leukemia progression by stabilizing USP44 mRNA.","authors":"Bin Zhang, Ruowen Sun, Min Gu, Zehui Jiang, Ye Wang, Linlin Zhang, Xiaoyang Liu, Zuofei Chi","doi":"10.1139/bcb-2023-0092","DOIUrl":"10.1139/bcb-2023-0092","url":null,"abstract":"Acute T-lymphocyte leukemia (T-ALL) is a malignant tumor disease. RNA-binding protein neotumor ventral antigen-1 (NOVA1) is highly expressed in bone marrow mononuclear cells of T-ALL patients, while the role of NOVA1 in T-ALL progression remains unknown. The gain- and loss-of-function studies for NOVA1 were performed in Jurkat and CCRF-CEM cells. NOVA1 overexpression promoted cell proliferation and cell cycle progression. NOVA1 knockdown increased the apoptosis rate of T-ALL cells. Ubiquitin-specific protease 44 (USP44), a nuclear protein with deubiquitinase catalytic activity, has been reported to play an oncogene role in human T-cell leukemia. USP44 expression was positively associated with NOVA1, and RNA immunoprecipitation assay verified the binding of NOVA1 to the mRNA of USP44. USP44 knockdown partially abolished NOVA1-induced cell proliferation and inhibition of apoptosis. The in vivo xenograft experiment was performed by injection of T-ALL tumor cells into the tail vein of NOD/SCID mice. The knockdown of NOVA1 had lower tumorigenicity. NOVA1 knockdown alleviated pathological changes in lung and spleen tissues, and increased the overall survival period and the weight of T-ALL mice. Thus, NOVA1 acts as an accelerator in T-ALL, and its function might be achieved by binding to and stabilizing USP44 mRNA.","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41189736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The 3' terminal region of Zika virus RNA contains a conserved G-quadruplex and is unfolded by human DDX17. 寨卡病毒RNA的3'末端区域包含一个保守的G-四链体，并由人类DDX17展开。

IF 2.9 3区生物学

Biochemistry and Cell Biology Pub Date : 2024-02-01 Epub Date: 2023-09-29 DOI: 10.1139/bcb-2023-0036

Dannielle L Gemmill, Corey R Nelson, Maulik D Badmalia, Higor S Pereira, Liam Kerr, Michael T Wolfinger, Trushar R Patel

{"title":"The 3' terminal region of Zika virus RNA contains a conserved G-quadruplex and is unfolded by human DDX17.","authors":"Dannielle L Gemmill, Corey R Nelson, Maulik D Badmalia, Higor S Pereira, Liam Kerr, Michael T Wolfinger, Trushar R Patel","doi":"10.1139/bcb-2023-0036","DOIUrl":"10.1139/bcb-2023-0036","url":null,"abstract":"Zika virus (ZIKV) infection remains a worldwide concern, and currently no effective treatments or vaccines are available. Novel therapeutics are an avenue of interest that could probe viral RNA-human protein communication to stop viral replication. One specific RNA structure, G-quadruplexes (G4s), possess various roles in viruses and all domains of life, including transcription and translation regulation and genome stability, and serves as nucleation points for RNA liquid-liquid phase separation. Previous G4 studies on ZIKV using a quadruplex forming G-rich sequences Mapper located a potential G-quadruplex sequence in the 3' terminal region (TR) and was validated structurally using a 25-mer oligo. It is currently unknown if this structure is conserved and maintained in a large ZIKV RNA transcript and its specific roles in viral replication. Using bioinformatic analysis and biochemical assays, we demonstrate that the ZIKV 3' TR G4 is conserved across all ZIKV isolates and maintains its structure in a 3' TR full-length transcript. We further established the G4 formation using pyridostatin and the BG4 G4-recognizing antibody binding assays. Our study also demonstrates that the human DEAD-box helicases, DDX3X132-607 and DDX17135-555, bind to the 3' TR and that DDX17135-555 unfolds the G4 present in the 3' TR. These findings provide a path forward in potential therapeutic targeting of DDX3X or DDX17's binding to the 3' TR G4 region for novel treatments against ZIKV.","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41106050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Note of appreciation. 感谢信

IF 2.9 3区生物学

Biochemistry and Cell Biology Pub Date : 2024-02-01 DOI: 10.1139/bcb-2023-0272

引用次数: 0