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GBMPhos: A Gating Mechanism and Bi-GRU-Based Method for Identifying Phosphorylation Sites of SARS-CoV-2 Infection. GBMPhos:识别 SARS-CoV-2 感染磷酸化位点的门控机制和基于 Bi-GRU 的方法
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2024-10-06 DOI: 10.3390/biology13100798
Guohua Huang, Runjuan Xiao, Weihong Chen, Qi Dai
{"title":"GBMPhos: A Gating Mechanism and Bi-GRU-Based Method for Identifying Phosphorylation Sites of SARS-CoV-2 Infection.","authors":"Guohua Huang, Runjuan Xiao, Weihong Chen, Qi Dai","doi":"10.3390/biology13100798","DOIUrl":"https://doi.org/10.3390/biology13100798","url":null,"abstract":"<p><p>Phosphorylation, a reversible and widespread post-translational modification of proteins, is essential for numerous cellular processes. However, due to technical limitations, large-scale detection of phosphorylation sites, especially those infected by SARS-CoV-2, remains a challenging task. To address this gap, we propose a method called GBMPhos, a novel method that combines convolutional neural networks (CNNs) for extracting local features, gating mechanisms to selectively focus on relevant information, and a bi-directional gated recurrent unit (Bi-GRU) to capture long-range dependencies within protein sequences. GBMPhos leverages a comprehensive set of features, including sequence encoding, physicochemical properties, and structural information, to provide an in-depth analysis of phosphorylation sites. We conducted an extensive comparison of GBMPhos with traditional machine learning algorithms and state-of-the-art methods. Experimental results demonstrate the superiority of GBMPhos over existing methods. The visualization analysis further highlights its effectiveness and efficiency. Additionally, we have established a free web server platform to help researchers explore phosphorylation in SARS-CoV-2 infections. The source code of GBMPhos is publicly available on GitHub.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505089/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sexual Dimorphism in Sex Hormone Metabolism in Human Skeletal Muscle Cells in Response to Different Testosterone Exposure. 不同睾酮暴露下人体骨骼肌细胞性激素代谢的性别二态性
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2024-10-05 DOI: 10.3390/biology13100796
Paolo Sgrò, Cristina Antinozzi, Christopher W Wasson, Francesco Del Galdo, Ivan Dimauro, Luigi Di Luigi
{"title":"Sexual Dimorphism in Sex Hormone Metabolism in Human Skeletal Muscle Cells in Response to Different Testosterone Exposure.","authors":"Paolo Sgrò, Cristina Antinozzi, Christopher W Wasson, Francesco Del Galdo, Ivan Dimauro, Luigi Di Luigi","doi":"10.3390/biology13100796","DOIUrl":"https://doi.org/10.3390/biology13100796","url":null,"abstract":"<p><p>Muscle tissue is an important target of sex steroids, and particularly, testosterone plays essential roles in muscle cell metabolism. Wide ranges of studies have reported sex differences in basal muscle steroidogenesis, and recently several genes have been identified to be regulated by androgen response elements that show innate sex differences in muscle. However, studies accounting for and demonstrating cell sexual dimorphism in vitro are still scarce and not well characterized. Here, we demonstrated the ability of 46XX and 46XY human primary skeletal muscle cells to differently activate steroidogenesis in vitro, likely related to sex-chromosome onset, and to differently induce hormone release after increasing doses of testosterone exposure. Cells were treated with testosterone at concentrations of 0.5, 2, 5, 10, 32, and 100 nmol/L for 24 h. Variations in 17β-HSD, 5α-R2, CYP-19 expression, DHT, estradiol, and androstenedione release, as well as IL6 and IL8 release, were analyzed, respectively, by RT-PCR, ELISA, and luminex-assay. Following testosterone treatments, and potentially at any concentration level, an increase in the expression of 17β-HSD, 5α-R2, and CYP-19 was observed in 46XY cells, accompanied by elevated levels of DHT, androstenedione, and IL6/IL8 release. Following the same treatment, 46XX cells exhibited an increase in 5α-R2 and CYP-19 expression, a conversion of androgens to estrogens, and a reduction in IL6 and IL8 release. In conclusion, this study demonstrated that sex-chromosome differences may influence in vitro muscle cell steroidogenesis and hormone homeostasis, which are pivotal for skeletal muscle metabolism.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phylogeography of the Sinica Group of Macaques in the Himalayas: Taxonomic and Evolutionary Implications. 喜马拉雅山西尼卡猕猴群的系统地理学:分类学和进化的意义。
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2024-10-04 DOI: 10.3390/biology13100795
Laxman Khanal, Xueyou Li, Asmit Subba, Sapana Ulak, Randall C Kyes, Xue-Long Jiang
{"title":"Phylogeography of the <i>Sinica</i> Group of Macaques in the Himalayas: Taxonomic and Evolutionary Implications.","authors":"Laxman Khanal, Xueyou Li, Asmit Subba, Sapana Ulak, Randall C Kyes, Xue-Long Jiang","doi":"10.3390/biology13100795","DOIUrl":"https://doi.org/10.3390/biology13100795","url":null,"abstract":"<p><p>Owing to the taxonomic incongruence between the morphological features and genetic relationships of the <i>sinica</i> group of macaques (genus <i>Macaca</i>), the taxonomy of this macaque group has remained inconclusive. We aimed to resolve the taxonomic quandary and improve our understanding of the historical biogeography of the group by including macaque DNA samples from previously unsampled areas in the Himalayas. We sequenced and analyzed three mitochondrial DNA loci [cytochrome b (CYTB), cytochrome oxidase subunit 1 (COI) and D-loop; 2898 bp] for sequence polymorphism, phylogenetics, species delimitation, and ancestral area reconstruction. We confirmed the occurrence of Arunachal macaque (<i>Macaca munzala</i>) on the southern slopes of the Eastern Himalayas in the Xizang Zizhiqu (Tibet Autonomous Region) of China. The results revealed that the <i>sinica</i> group of macaques is a parapatric species group composed of seven distinct species. Phylogenetic and species delimitation analyses revealed that the two previously considered subspecies of Assamese macaques (the eastern subspecies <i>M. assamensis assamensis</i> and the western subspecies <i>M. a. pelops</i>) are two distinct species. The eastern Assamese macaque is a sister species to the Tibetan macaque, whereas the western Assamese macaque and Arunachal macaque are the closest genetic sister species. The <i>sinica</i> group of macaques underwent five vicariance and seven dispersal radiations in the past, which mainly coincided with the Quaternary climatic oscillations between the late Pliocene and the late Pleistocene. By integrating our phylogenetic and ancestral area reconstruction results with findings from previous paleontological and molecular studies, we propose a robust hypothesis about the phylogeography of the <i>sinica</i> group of macaques.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of Cuproptosis-Associated Prognostic Gene Expression Signatures from 20 Tumor Types. 从 20 种肿瘤类型中鉴定杯突相关预后基因表达特征
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2024-10-03 DOI: 10.3390/biology13100793
Ednah Ooko, Nadeen T Ali, Thomas Efferth
{"title":"Identification of Cuproptosis-Associated Prognostic Gene Expression Signatures from 20 Tumor Types.","authors":"Ednah Ooko, Nadeen T Ali, Thomas Efferth","doi":"10.3390/biology13100793","DOIUrl":"https://doi.org/10.3390/biology13100793","url":null,"abstract":"<p><p>We investigated the mRNA expression of 124 cuproptosis-associated genes in 7489 biopsies from 20 different tumor types of The Cancer Genome Atlas (TCGA). The KM plotter algorithm has been used to calculate Kaplan-Meier statistics and false discovery rate (FDR) corrections. Interaction networks have been generated using Ingenuity Pathway Analysis (IPA). High mRNA expression of 63 out of 124 genes significantly correlated with shorter survival times of cancer patients across all 20 tumor types. IPA analyses revealed that their gene products were interconnected in canonical pathways (e.g., cancer, cell death, cell cycle, cell signaling). Four tumor entities showed a higher accumulation of genes than the other cancer types, i.e., renal clear cell carcinoma (<i>n</i> = 21), renal papillary carcinoma (<i>n</i> = 13), kidney hepatocellular carcinoma (<i>n</i> = 13), and lung adenocarcinoma (<i>n</i> = 9). These gene clusters may serve as prognostic signatures for patient survival. These signatures were also of prognostic value for tumors with high mutational rates and neoantigen loads. Cuproptosis is of prognostic significance for the survival of cancer patients. The identification of specific gene signatures deserves further exploration for their clinical utility in routine diagnostics.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Dynamics of Heart Rate Asymmetry and Situational Sleepiness from Evening to Night: The Role of Daytime Sleepiness. 从傍晚到夜晚的心率不对称和情境性嗜睡的动态变化:白天嗜睡的作用
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2024-10-03 DOI: 10.3390/biology13100794
Valeriia Demareva
{"title":"The Dynamics of Heart Rate Asymmetry and Situational Sleepiness from Evening to Night: The Role of Daytime Sleepiness.","authors":"Valeriia Demareva","doi":"10.3390/biology13100794","DOIUrl":"https://doi.org/10.3390/biology13100794","url":null,"abstract":"<p><p>The relationship between daytime sleepiness and heart rate asymmetry (HRA) during the transition from evening to night is crucial for understanding autonomic regulation and its implications for alertness. This study aims to investigate how daytime sleepiness influences HRA dynamics from evening to night and how situational sleepiness correlates with HRA metrics. HRA metrics were calculated at 8 P.M., 9 P.M., and 10 P.M. in 50 participants, categorized into 'Lower Normal' and 'Higher Normal' daytime sleepiness groups based on Epworth Sleepiness Scale (ESS) scores. Situational sleepiness was assessed using the Karolinska Sleepiness Scale (KSS) and Stanford Sleepiness Scale (SSS). The results demonstrated that individuals with 'Higher Normal' daytime sleepiness exhibited lower HRA metrics at 10 P.M. compared to those with 'Lower Normal' daytime sleepiness, supporting the suggestion that higher daytime sleepiness correlates with reduced parasympathetic activity and diminished autonomic responsiveness. Significant negative correlations between situational sleepiness and HRA metrics were observed in the 'Higher Normal' group, particularly with the SSS. Therefore, increased daytime sleepiness affects HRA dynamics by decreasing parasympathetic activity and altering autonomic regulation at the beginning of the biological night (10 P.M.). These findings suggest potential applications for enhancing drowsiness detection and managing fatigue in safety-critical environments.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504512/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Physiological Mechanisms of Transcranial Direct Current Stimulation to Enhance Motor Performance: A Narrative Review. 经颅直流电刺激提高运动表现的生理机制:叙述性综述。
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2024-10-02 DOI: 10.3390/biology13100790
Shuo Qi, Lei Cao, Qingchun Wang, Yin Sheng, Jinglun Yu, Zhiqiang Liang
{"title":"The Physiological Mechanisms of Transcranial Direct Current Stimulation to Enhance Motor Performance: A Narrative Review.","authors":"Shuo Qi, Lei Cao, Qingchun Wang, Yin Sheng, Jinglun Yu, Zhiqiang Liang","doi":"10.3390/biology13100790","DOIUrl":"https://doi.org/10.3390/biology13100790","url":null,"abstract":"<p><p>Transcranial direct current stimulation (tDCS) is a non-invasive neuromodulation technique that applies a stable, low-intensity (1-2 mA) direct current to modulate neuronal activity in the cerebral cortex. This technique is effective, simple to operate, affordable, and widely employed across various fields. tDCS has been extensively used in clinical and translational research, with growing applications in military and competitive sports domains. In recent years, the use of tDCS in sports science has garnered significant attention from researchers. Numerous studies have demonstrated that tDCS can enhance muscle strength, explosive power, and aerobic metabolism, reduce fatigue, and improve cognition, thereby serving as a valuable tool for enhancing athletic performance. Additionally, recent research has shed light on the physiological mechanisms underlying tDCS, including its modulation of neuronal resting membrane potential to alter cortical excitability, enhancement of synaptic plasticity to regulate long-term potentiation, modulation of neurovascular coupling to improve regional cerebral blood flow, and improvement of cerebral network functional connectivity, which activates and reinforces specific brain regions. tDCS also enhances the release of excitatory neurotransmitters, further regulating brain function. This article, after outlining the role of tDCS in improving physical performance, delves into its mechanisms of action to provide a deeper understanding of how tDCS enhances athletic performance and offers novel approaches and perspectives for physical performance enhancement.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Change Rate of the Fbxl21 Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental Mammals. 胎盘哺乳动物 Fbxl21 基因的变化率及其蛋白质的氨基酸组成与特定物种的寿命有关
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2024-10-02 DOI: 10.3390/biology13100792
Vassily A Lyubetsky, Gregory A Shilovsky, Jian-Rong Yang, Alexandr V Seliverstov, Oleg A Zverkov
{"title":"The Change Rate of the <i>Fbxl21</i> Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental Mammals.","authors":"Vassily A Lyubetsky, Gregory A Shilovsky, Jian-Rong Yang, Alexandr V Seliverstov, Oleg A Zverkov","doi":"10.3390/biology13100792","DOIUrl":"https://doi.org/10.3390/biology13100792","url":null,"abstract":"<p><p>This article proposes a methodology for establishing a relationship between the change rate of a given gene (relative to a given taxon) together with the amino acid composition of the proteins encoded by this gene and the traits of the species containing this gene. The methodology is illustrated based on the mammalian genes responsible for regulating the circadian rhythms that underlie a number of human disorders, particularly those associated with aging. The methods used are statistical and bioinformatic ones. A systematic search for orthologues, pseudogenes, and gene losses was performed using our previously developed methods. It is demonstrated that the least conserved <i>Fbxl21</i> gene in the Euarchontoglires superorder exhibits a statistically significant connection of genomic characteristics (the median of <i>dN</i>/<i>dS</i> for a gene relative to all the other orthologous genes of a taxon, as well as the preference or avoidance of certain amino acids in its protein) with species-specific lifespan and body weight. In contrast, no such connection is observed for <i>Fbxl21</i> in the Laurasiatheria superorder. This study goes beyond the protein-coding genes, since the accumulation of amino acid substitutions in the course of evolution leads to pseudogenization and even gene loss, although the relationship between the genomic characteristics and the species traits is still preserved. The proposed methodology is illustrated using the examples of circadian rhythm genes and proteins in placental mammals, e.g., longevity is connected with the rate of <i>Fbxl21</i> gene change, pseudogenization or gene loss, and specific amino acid substitutions (e.g., asparagine at the 19th position of the CRY-binding domain) in the protein encoded by this gene.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Spatiotemporal Variation and Ecological Evaluation of Macroinvertebrate Functional Feeding Groups in the Upper Yellow River. 黄河上游大型无脊椎动物功能取食群的时空变异与生态学评价
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2024-10-02 DOI: 10.3390/biology13100791
Peilun Li, Shuhan Xiong, Jiacheng Liu, Tai Wang, Yanbin Liu, Kai Liu, Yongjie Wang, Jilong Wang
{"title":"The Spatiotemporal Variation and Ecological Evaluation of Macroinvertebrate Functional Feeding Groups in the Upper Yellow River.","authors":"Peilun Li, Shuhan Xiong, Jiacheng Liu, Tai Wang, Yanbin Liu, Kai Liu, Yongjie Wang, Jilong Wang","doi":"10.3390/biology13100791","DOIUrl":"https://doi.org/10.3390/biology13100791","url":null,"abstract":"<p><p>Against the backdrop of hydropower development in the upper Yellow River, comprehending the spatiotemporal variation and ecological evaluation of macroinvertebrate functional feeding groups (FFGs) is paramount for the conservation and restoration of aquatic biological resources in watersheds. Detailed surveys of macroinvertebrates were conducted in the gorge and plain areas of the upper Yellow River in July 2022 and March, May, and October 2023, culminating in the identification of 65 taxonomic units (genus or species) spanning 4 phyla, 14 orders, and 35 families. Of these, 41 taxonomic units were discovered in the gorge areas and 57 in the plain areas. Among the FFGs of macroinvertebrates in the upper Yellow River, collector-gatherers were overwhelmingly dominant, followed by scrapers, collector-filterers, predators, and shredders. Concerning river section types, dominant species in the gorge areas included <i>Gammarus</i> sp., <i>Limnodrilus hoffmeisteri</i>, and <i>Polypedilum</i> sp. among collector-gatherers, while in the plain areas, dominant species included <i>Ecdyonurus</i> sp. among scrapers, <i>Hydropsyche</i> sp. among collector-filterers, and <i>Gammarus</i> sp., <i>Limnodrilus hoffmeisteri</i>, and <i>Chironomus</i> sp. among collector-gatherers. A Mantel test revealed that dissolved oxygen, conductivity, and orthophosphate were the primary environmental factors affecting the FFGs of macroinvertebrates in the upper Yellow River, with variations observed in their effects across different months. The evaluation results of the Hilsenhoff Biological Index and Shannon-Wiener Index indicate that the water quality of the upper Yellow River is at a moderate level. An assessment of the upper Yellow River ecosystem using FFG parameters demonstrated that macroinvertebrate biomass progressively increased from upstream (gorge areas) to downstream (plain areas) spatially, accompanied by increasing habitat stability, with cascade hydropower development identified as a key factor impacting habitat stability. These findings provide pertinent data and a theoretical foundation for the protection of aquatic biological resources and watershed management in the upper Yellow River.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505124/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Whole-Transcriptome Analysis Reveals Potential CeRNA Regulatory Mechanism in Takifugu rubripes against Cryptocaryon irritans Infection. 全转录组分析揭示了泷蛙抗隐翅虫感染的潜在 CeRNA 调控机制
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2024-10-01 DOI: 10.3390/biology13100788
Yuqing Xia, Xiaoqing Yu, Zhen Yuan, Yi Yang, Ying Liu
{"title":"Whole-Transcriptome Analysis Reveals Potential CeRNA Regulatory Mechanism in <i>Takifugu rubripes</i> against <i>Cryptocaryon irritans</i> Infection.","authors":"Yuqing Xia, Xiaoqing Yu, Zhen Yuan, Yi Yang, Ying Liu","doi":"10.3390/biology13100788","DOIUrl":"https://doi.org/10.3390/biology13100788","url":null,"abstract":"<p><p><i>Cryptocaryon irritans</i> (<i>C. irritans</i>) is a proto-ciliate parasite that infects marine fishes, including the cultured species <i>Takifugu rubripes</i> (<i>T. rubripes</i>), causing disease and potential mortality. In host organisms, infection by parasites triggers an immune response that is modulated by regulatory elements including proteins and non-coding RNAs. In this study, the whole transcriptome RNA sequencing of <i>T. rubripes</i> gill tissue before and after infection with <i>C. irritans</i> was performed to reveal the competitive endogenous RNA (ceRNA) regulatory network. Histomorphology revealed gill segment swelling and parasitic invasion in the infected group. The analysis identified 18 differentially expressed miRNAs (DEMs), 214 lncRNAs (DELs), 2501 genes (DEGs), and 7 circRNAs (DECs) in the infected group. Gene Ontology (GO) enrichment analysis revealed that these genes were notably enriched in the Wnt signaling pathway and mTOR signaling pathway. The co-expression networks (lncRNA/circRNA-miRNA-mRNA) were constructed based on correlation analysis of the differentially expressed RNAs. Further analysis suggested that the LOC105418663-circ_0000361-fru-miR-204a-<i>fzd3a</i> ceRNA axis was potentially involved in the regulation of immune responses against <i>C. irritans</i> infection. Finally, the expression levels of DEG, DEL, and DEM were validated. This study reveals the regulatory mechanism of a candidate ceRNA network, providing insights into the potential mechanism of <i>T. rubripes</i>' infection with <i>C. irritans</i>.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evolution of Media Supporting the Development of Mammalian Preimplantation Embryos In Vitro. 支持哺乳动物植入前胚胎体外发育的培养基的演变。
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2024-10-01 DOI: 10.3390/biology13100789
Hongsheng Men
{"title":"Evolution of Media Supporting the Development of Mammalian Preimplantation Embryos In Vitro.","authors":"Hongsheng Men","doi":"10.3390/biology13100789","DOIUrl":"https://doi.org/10.3390/biology13100789","url":null,"abstract":"<p><p>Assisted reproductive technology has revolutionized our ability to genetically manipulate, maintain and rederive laboratory animals of biomedical importance; manipulate animal reproduction or genetics to boost production of farm animals; and improve human reproductive health. The media for in vitro manipulation and the culture of embryos play a critical role in the development of assisted reproductive technology. In this review, the evolution of culture media supporting embryo development in vitro from selected animal species, laboratory animals (mice and rats) and farm animals (pigs and cattle), will be discussed with a focus on the development of chemically defined media.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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