Insights into the nuclear and mitochondrial genome of the Lemon shark < em > Negaprion brevirostris < /em > using low-coverage sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement
Gene. 2024 Feb 5;894:147939. doi: 10.1016/j.gene.2023.147939. Epub 2023 Oct 29.ABSTRACTThe Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ran...
Source: Gene - April 4, 2024 Category: Genetics & Stem Cells Authors: J Antonio Baeza Natalie C Stephens Alyssa Baker Andrew Lyons Bryan Franks Stacy Pirro Kevin A Feldheim Source Type: research
A positive selection at binding site 501 in the B.1 lineage might have triggered the highly infectious sub-lineages of SARS-CoV-2
This study sheds light on the evolutionary trajectory of the B lineage into highly infectious descendants in the recent past under the influence of positive and purifying selection exerted by natural immunity and vaccination of the host.PMID:38575097 | DOI:10.1016/j.gene.2024.148427 (Source: Gene)
Source: Gene - April 4, 2024 Category: Genetics & Stem Cells Authors: Basant K Tiwary Source Type: research
Splice site recognition - deciphering Exon-Intron transitions for genetic insights using Enhanced integrated Block-Level gated LSTM model
Gene. 2024 Apr 2:148429. doi: 10.1016/j.gene.2024.148429. Online ahead of print.ABSTRACTBioinformatics is a contemporary interdisciplinary area focused on analyzing the growing number of genome sequences. Gene variants are differences in DNA sequences among individuals within a population. Splice site recognition is a crucial step in the process of gene expression, where the coding sequences of genes are joined together to form mature messenger RNA (mRNA). These genetic variants that disrupt genes are believed to be the primary reason for neuro-developmental disorders like ASD (Autism Spectrum Disorder) is a neuro-developm...
Source: Gene - April 4, 2024 Category: Genetics & Stem Cells Authors: Mohemmed Sha Mohamudha Parveen Rahamathulla Source Type: research
Gene expression patterns of Sirtuin family members (SIRT1 TO SIRT7): Insights into pathogenesis and prognostic of myelodysplastic neoplasm
Gene. 2024 Apr 2:148428. doi: 10.1016/j.gene.2024.148428. Online ahead of print.ABSTRACTTo assess and validate the gene expression profile of SIRTs (SIRT1, SIRT2, SIRT3, SIRT4, SIRT5, SIRT6, and SIRT7) in relation to the pathogenesis and prognostic progression of Myelodysplastic neoplasm (MDS). Eighty bone marrow samples of patients with de novo MDS were diagnosed according to WHO 2022 and IPSS-R criteria. Ten bone marrow samples were obtained from elderly healthy volunteers and used as control samples. Gene expression levels of all SIRTs were assessed using RT-qPCR assays. Downregulation of SIRT2 (p = 0.009), SIRT3 (p = 0...
Source: Gene - April 4, 2024 Category: Genetics & Stem Cells Authors: Jo ão Vitor Caetano Goes Mateus de Aguiar Viana Leticia Rodrigues Sampaio Clarissa Brenda Alves Cavalcante Mayara Magna de Lima Melo Roberta Taiane Germano de Oliveira Daniela de Paula Borges Paola Gyuliane Gon çalves Ronald Feitosa Pinheiro Howard Lope Source Type: research
The vesicle trafficking gene, OsRab7, is critical for pollen development and male fertility in cytoplasmic male-sterility rice
Gene. 2024 Apr 2:148423. doi: 10.1016/j.gene.2024.148423. Online ahead of print.ABSTRACTRice cytoplasmic male sterility (CMS) provides an exceptional model for studying genetic interaction within plant nuclei given its inheritable trait of non-functional male gametophyte. Gaining a comprehensive understanding of the genes and pathways associated with the CMS mechanism is imperative for improving the vigor of hybrid rice agronomically, such as its productivity. Here, we observed a significant decrease in the expression of a gene named OsRab7 in the anther of the CMS line (SJA) compared to the maintainer line (SJB). OsRab7 i...
Source: Gene - April 4, 2024 Category: Genetics & Stem Cells Authors: Suping Ying Yunting Tang Wei Yang Zhao Hu Ruifeng Huang Jie Ding Xiangyun Yi Jiawei Niu Zihan Chen Ting Wang Wei Liu Xiaojue Peng Source Type: research
Dynamic analysis of SARS-CoV-2 evolution based on different countries
In conclusion, our study not only sheds light on the evolutionary trajectory of SARS-CoV-2 but also underscores the urgency for robust, continuous global data collection and sharing. It highlights the necessity for rapid adaptations in medical countermeasures, including vaccine development, to stay ahead of pathogen evolution. This research provides valuable insights for future pandemic preparedness and response strategies.PMID:38575101 | DOI:10.1016/j.gene.2024.148426 (Source: Gene)
Source: Gene - April 4, 2024 Category: Genetics & Stem Cells Authors: Binghan Xiao Linhuan Wu Qinlan Sun Chang Shu Songnian Hu Source Type: research
Advances in the evolution research and genetic breeding of peanut
Gene. 2024 Apr 2:148425. doi: 10.1016/j.gene.2024.148425. Online ahead of print.ABSTRACTPeanut is an important cash crop used in oil, food and feed in our country. The rapid development of sequencing technology has promoted the research on the related aspects of peanut genetic breeding. This paper reviews the research progress of peanut origin and evolution, genetic breeding, molecular markers and their applications, genomics, QTL mapping and genome selection techniques. The main problems of molecular genetic breeding in peanut research worldwide include: the narrow genetic resources of cultivated species, unstable genetic...
Source: Gene - April 4, 2024 Category: Genetics & Stem Cells Authors: Hui Zhang Yueyi Tang Yunlai Yue Yong Chen Source Type: research
Insights into the nuclear and mitochondrial genome of the Lemon shark < em > Negaprion brevirostris < /em > using low-coverage sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement
Gene. 2024 Feb 5;894:147939. doi: 10.1016/j.gene.2023.147939. Epub 2023 Oct 29.ABSTRACTThe Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ran...
Source: Gene - April 4, 2024 Category: Genetics & Stem Cells Authors: J Antonio Baeza Natalie C Stephens Alyssa Baker Andrew Lyons Bryan Franks Stacy Pirro Kevin A Feldheim Source Type: research
Exploring non-coding genetic variability in ACE2: Functional annotation and in vitro validation of regulatory variants
Gene. 2024 Apr 1:148422. doi: 10.1016/j.gene.2024.148422. Online ahead of print.ABSTRACTThe surge in human whole-genome sequencing data has facilitated the study of non-coding region variations, yet understanding their biological significance remains a challenge. We used a computational workflow to assess the regulatory potential of non-coding variants, with a particular focus on the Angiotensin Converting Enzyme 2 (ACE2) gene. This gene is crucial in physiological processes and serves as the entry point for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing coronavirus disease 19 (COVID-19). I...
Source: Gene - April 3, 2024 Category: Genetics & Stem Cells Authors: Agnese Giovannetti Sara Lazzari Manuel Mangoni Alice Traversa Tommaso Mazza Chiara Parisi Viviana Caputo Source Type: research
GPCR-mediated regulation of beige adipocyte formation: Implications for obesity and metabolic health
Gene. 2024 Mar 30;915:148421. doi: 10.1016/j.gene.2024.148421. Online ahead of print.ABSTRACTObesity and its associated complications pose a significant burden on health. The non-shivering thermogenesis (NST) and metabolic capacity properties of brown adipose tissue (BAT), which are distinct from those of white adipose tissue (WAT), in combating obesity and its related metabolic diseases has been well documented. However, beige adipose tissue, the third and relatively novel type of adipose tissue, which emerges in extensive presence of WAT and shares similar favorable metabolic properties with BAT, has garnered considerabl...
Source: Gene - April 1, 2024 Category: Genetics & Stem Cells Authors: Yuanxu Cui Hugo Auclair Rong He Qiang Zhang Source Type: research
GPCR-mediated regulation of beige adipocyte formation: implications for obesity and metabolic health
Gene. 2024 Mar 30:148421. doi: 10.1016/j.gene.2024.148421. Online ahead of print.ABSTRACTObesity and its associated complications pose a significant burden on health. The non-shivering thermogenesis (NST) and metabolic capacity properties of brown adipose tissue (BAT), which are distinct from those of white adipose tissue (WAT), in combating obesity and its related metabolic diseases has been well documented. However, beige adipose tissue, the third and relatively novel type of adipose tissue, which emerges in extensive presence of WAT and shares similar favorable metabolic properties with BAT, has garnered considerable at...
Source: Gene - April 1, 2024 Category: Genetics & Stem Cells Authors: Yuanxu Cui Hugo Auclair Rong He Qiang Zhang Source Type: research
Corrigendum to "Comparative analysis of the difference in flavonoid metabolic pathway during coloring between red-yellow and red sweet cherry (Prunus avium L.)" [Gene 880 (2023) 147602]
Gene. 2024 Mar 30;914:148408. doi: 10.1016/j.gene.2024.148408. Online ahead of print.NO ABSTRACTPMID:38555698 | DOI:10.1016/j.gene.2024.148408 (Source: Gene)
Source: Gene - March 31, 2024 Category: Genetics & Stem Cells Authors: Liwei Chu Wei Zheng Jiao Wang Zhen Wang Wei Zhao Baixia Zhao Guohui Xu Min Xiao Xin Lou Fengrong Pan Yongbin Zhou Source Type: research
Effect of MSX1 on the cellular function of cardiomyocytes
In this study, we used AC16 cell culture, real-time fluorescence quantitative PCR (qPCR), protein blotting (Western blot), flow cytometry apoptosis assay and lactate dehydrogenase (LDH) ELISA (Enzyme-Linked Immunosorbnent Assay) to investigate the effect of the MSX1 gene on cardiomyocyte function. The results showed that MSX1 plays a protective role against hypoxia of cardiomyocytes. However, further studies are required to fully understand the role of MSX1 in the regulation of LDH expression in different cell types and under different conditions.PMID:38556116 | DOI:10.1016/j.gene.2024.148419 (Source: Gene)
Source: Gene - March 31, 2024 Category: Genetics & Stem Cells Authors: Huang Linhuan Zhong Liangying Lin Shaobin Zhu Caixia Cai Danlei Huang Siqi Hong Peiming Kong Shu Xie Yingjun Luo Yanmin Source Type: research
Chronic sleep fragmentation reduces left ventricular contractile function and alters gene expression related to innate immune response and circadian rhythm in the mouse heart
In this study, we aimed to investigate the effects of SF interventions at various life stages on cardiac structure and function, as well as to identify genes associated with SF-induced cardiac dysfunction. To achieve this, we established mouse models of chronic SF and two-week sleep recovery (SR).Our results revealed that chronic SF significantly compromised left ventricular contractile function across different life stages, leading to alterations in cardiac structure and ventricular remodeling, particularly during early life stages. Moreover, microarray analysis of mouse heart tissue identified two significant modules and...
Source: Gene - March 31, 2024 Category: Genetics & Stem Cells Authors: Ling Zhong Jie Zhang Jielin Yang Bo Li Xinghao Yi John R Speakman Shan Gao Ming Li Source Type: research
Corrigendum to "Comparative analysis of the difference in flavonoid metabolic pathway during coloring between red-yellow and red sweet cherry (Prunus avium L.)" [Gene 880 (2023) 147602]
Gene. 2024 Mar 30;914:148408. doi: 10.1016/j.gene.2024.148408. Online ahead of print.NO ABSTRACTPMID:38555698 | DOI:10.1016/j.gene.2024.148408 (Source: Gene)
Source: Gene - March 31, 2024 Category: Genetics & Stem Cells Authors: Liwei Chu Wei Zheng Jiao Wang Zhen Wang Wei Zhao Baixia Zhao Guohui Xu Min Xiao Xin Lou Fengrong Pan Yongbin Zhou Source Type: research
