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The Role of AI-Driven De Novo Protein Design in the Exploration of the Protein Functional Universe. 人工智能驱动的从头蛋白质设计在蛋白质功能宇宙探索中的作用。
IF 3.5 3区 生物学
Biology-Basel Pub Date : 2025-09-15 DOI: 10.3390/biology14091268
Guohao Zhang, Chuanyang Liu, Jiajie Lu, Shaowei Zhang, Lingyun Zhu
{"title":"The Role of AI-Driven De Novo Protein Design in the Exploration of the Protein Functional Universe.","authors":"Guohao Zhang, Chuanyang Liu, Jiajie Lu, Shaowei Zhang, Lingyun Zhu","doi":"10.3390/biology14091268","DOIUrl":"10.3390/biology14091268","url":null,"abstract":"<p><p>The extraordinary diversity of protein sequences and structures gives rise to a vast protein functional universe with extensive biotechnological potential. Nevertheless, this universe remains largely unexplored, constrained by the limitations of natural evolution and conventional protein engineering. Substantial evidence further indicates that the known natural fold space is approaching saturation, with novel folds rarely emerging. AI-driven de novo protein design is overcoming these constraints by enabling the computational creation of proteins with customized folds and functions. This review systematically surveys the rapidly advancing field of AI-based de novo protein design, reviewing current methodologies and examining how cutting-edge computational frameworks accelerate discovery through three complementary vectors: (1) exploring novel folds and topologies; (2) designing functional sites de novo; (3) exploring sequence-structure-function landscapes. We highlight key applications across therapeutic, catalytic, and synthetic biology and discuss the persistent challenges. By fusing recent progress and the existing limitations, this review outlines how AI is not only accelerating the exploration of the protein functional universe but also fundamentally expanding the possibilities within protein engineering, paving the way for bespoke biomolecules with tailored functionalities.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12467925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145179754","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
Synergistic Effects of Gibberellic Acid, Forchlorfenuron, Thidiazuron, and Brassinosteroid Combinations on Seedless Berry Development and Quality Enhancement in 'Shine Muscat' and 'Red Muscat of Alexandria' Grapes. 赤霉素酸、氯吡脲、噻地唑隆和油菜素内酯组合对“亮麝香”和“亚历山大红麝香”葡萄无籽果实发育和品质提高的协同效应
IF 3.5 3区 生物学
Biology-Basel Pub Date : 2025-09-15 DOI: 10.3390/biology14091270
Pengcheng Yang, Zishu Wu, Boyang Liu, Lei Wang, Shiping Wang
{"title":"Synergistic Effects of Gibberellic Acid, Forchlorfenuron, Thidiazuron, and Brassinosteroid Combinations on Seedless Berry Development and Quality Enhancement in 'Shine Muscat' and 'Red Muscat of Alexandria' Grapes.","authors":"Pengcheng Yang, Zishu Wu, Boyang Liu, Lei Wang, Shiping Wang","doi":"10.3390/biology14091270","DOIUrl":"10.3390/biology14091270","url":null,"abstract":"<p><p>Plant growth regulators (PGRs) are widely used to enhance table grape quality, yet cultivar-specific responses and microstructural outcomes remain insufficiently resolved. We evaluated five PGRs-gibberellic acid (GA<sub>3</sub>), 24-epibrassinolide (EBR), forchlorfenuron (CPPU), thidiazuron (TDZ), and streptomycin (SM)-in 'Shine Muscat' and 'Red Muscat of Alexandria'. Twelve combinations were applied at full bloom (D0) and 14 days post-anthesis (D14), and morphological, physiological, and histological traits were monitored over 104 days. In 'Shine Muscat', GA<sub>3</sub> + TDZ and GA<sub>3</sub> + CPPU achieved nearly 100% seedlessness, while CPPU and TDZ markedly increased berry weight and size via cortical expansion. GA<sub>3</sub> increased berry weight but caused rachis thickening and reduced total soluble solids (TSS). EBR at concentrations ≥ 0.2 mg L<sup>-1</sup> inhibited berry growth, and SM reduced berry size and weight. Histology showed that TDZ and CPPU enlarged cortical area and epidermal thickness, potentially strengthening pericarp robustness, whereas GA<sub>3</sub> enlarged vascular bundle area. 'Red Muscat of Alexandria' showed generally weaker responses, reflecting differences between <i>Vitis vinifera</i> and hybrid backgrounds. These results demonstrate that combinatorial PGR strategies can be tailored to optimize berry development and quality through coordinated regulation of growth, metabolism, and microstructure. TDZ and CPPU exhibit strong production potential for enlargement, whereas GA<sub>3</sub> and EBR require careful dose optimization to balance benefits and quality risks.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12467870/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145179651","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
Genetic Diversity, Genetic Structure and Demographic History of the Leaf Beetle Platycorynus peregrinus (Herbst, 1783) (Coleoptera: Chrysomelidae) from Thailand. 泰国叶甲虫(Platycorynus peregrinus, Herbst, 1783)的遗传多样性、遗传结构和种群历史(鞘翅目:金甲科)。
IF 3.5 3区 生物学
Biology-Basel Pub Date : 2025-09-13 DOI: 10.3390/biology14091266
Satakoon Kaewmungkoon, Nakorn Pradit, Warayutt Pilap, Salakjit Ninlaphay, Takan Chatiwong, Jatupon Saijuntha, Chavanut Jaroenchaiwattanachote, Wittaya Tawong, Warong Suksavate, Pairot Pramual, Chairat Tantrawatpan, Weerachai Saijuntha
{"title":"Genetic Diversity, Genetic Structure and Demographic History of the Leaf Beetle <i>Platycorynus peregrinus</i> (Herbst, 1783) (Coleoptera: Chrysomelidae) from Thailand.","authors":"Satakoon Kaewmungkoon, Nakorn Pradit, Warayutt Pilap, Salakjit Ninlaphay, Takan Chatiwong, Jatupon Saijuntha, Chavanut Jaroenchaiwattanachote, Wittaya Tawong, Warong Suksavate, Pairot Pramual, Chairat Tantrawatpan, Weerachai Saijuntha","doi":"10.3390/biology14091266","DOIUrl":"10.3390/biology14091266","url":null,"abstract":"<p><p><i>Platycorynus peregrinus</i> (Herbst, 1783) is a leaf beetle of agricultural importance, yet its genetic diversity and population structure remain poorly understood. We analyzed mitochondrial cytochrome c oxidase subunit I (<i>COI</i>) sequences from 147 individuals across 19 populations in Thailand. Forty-five haplotypes were identified, showing high haplotype diversity (0.942) and moderate nucleotide diversity (0.00562). Significant genetic differentiation (Φ<sub>ST</sub> = 0.0000-0.7857) was strongly associated with geographical distance, and this population structure was further supported by AMOVA (<i>F</i><sub>CT</sub> = 0.21925, <i>p</i> < 0.001). Neutrality tests and mismatch distribution analyses revealed signals of population expansion, alongside evidence of localized differentiation. The substantial genetic variability observed suggests high dispersal ability and possible cryptic lineages. These insights not only advance understanding of the evolutionary dynamics of <i>P. peregrinus</i> but also provide valuable guidance for developing sustainable pest management strategies.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12467580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145179638","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
Hepatocyte-Specific Transcriptional Responses to Liver-Targeted Delivery of a Soluble Epoxide Hydrolase Inhibitor in a Mouse Model of Alcohol-Associated Liver Disease. 在酒精相关性肝病小鼠模型中,肝脏靶向递送可溶性环氧化物水解酶抑制剂的肝细胞特异性转录反应
IF 3.5 3区 生物学
Biology-Basel Pub Date : 2025-09-13 DOI: 10.3390/biology14091267
Dennis R Warner, Jeffrey B Warner, Josiah E Hardesty, Yasmeen Abdelfadil, Chirag Soni, Philip Bauer, Claudio Maldonado, Craig J McClain, Irina A Kirpich
{"title":"Hepatocyte-Specific Transcriptional Responses to Liver-Targeted Delivery of a Soluble Epoxide Hydrolase Inhibitor in a Mouse Model of Alcohol-Associated Liver Disease.","authors":"Dennis R Warner, Jeffrey B Warner, Josiah E Hardesty, Yasmeen Abdelfadil, Chirag Soni, Philip Bauer, Claudio Maldonado, Craig J McClain, Irina A Kirpich","doi":"10.3390/biology14091267","DOIUrl":"10.3390/biology14091267","url":null,"abstract":"<p><p>Alcohol-associated liver disease (ALD) is a chronic condition caused by excessive alcohol consumption, with limited effective pharmacological treatments currently available. The inhibition of soluble epoxide hydrolase (s-EH) has emerged as a promising therapeutic strategy in experimental ALD. In this study, we developed a novel liver-targeted formulation of the s-EH inhibitor <i>t</i>-TUCB, encapsulated in fusogenic lipid vesicles (FLVs), and tested its therapeutic efficacy in a mouse model of ALD. This formulation achieved high encapsulation efficiency and targeted primarily hepatocytes. Male C57BL/6J mice were fed an ethanol-containing liquid diet for 10 days, followed by a single ethanol binge on day 11. A subset of mice received a single intraperitoneal dose of <i>t</i>-TUCB-FLVs two hours before the binge. <i>t</i>-TUCB-FLVs significantly attenuated liver injury as assessed by multiple endpoints, including decreased plasma ALT levels and hepatocyte cell death. Spatial transcriptomic analysis revealed that <i>t</i>-TUCB-FLV treatment modulated gene expression in hepatocytes across multiple key pathways, including xenobiotic metabolism, carbohydrate and lipid metabolism, bile acid homeostasis, inflammation, energy balance, and circadian rhythm. Collectively, these findings support liver-specific s-EH inhibition as a potentially effective therapeutic approach for ALD.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12467949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145179577","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
Integrated miRNA-mRNA Atlas Reveals Temperature-Graded Brain Neuroendocrine Adaptation to Cold Stress in Silvery Pomfret (Pampus argenteus). 综合miRNA-mRNA图谱揭示了银鲳鱼对冷胁迫的温度梯度脑神经内分泌适应。
IF 3.5 3区 生物学
Biology-Basel Pub Date : 2025-09-13 DOI: 10.3390/biology14091265
Danqing Yin, Xianhui Ning
{"title":"Integrated miRNA-mRNA Atlas Reveals Temperature-Graded Brain Neuroendocrine Adaptation to Cold Stress in Silvery Pomfret (<i>Pampus argenteus</i>).","authors":"Danqing Yin, Xianhui Ning","doi":"10.3390/biology14091265","DOIUrl":"10.3390/biology14091265","url":null,"abstract":"<p><p>Temperature stress is a major cause of mortality in aquaculture, yet the molecular mechanisms underlying cold adaptation in commercially important fish such as the silver pomfret (<i>Pampus argenteus</i>) remain poorly understood. In this study, we used integrated miRNA and mRNA transcriptomics to analyze brain tissue responses of silver pomfret under gradient cold exposure conditions (28 °C control, 18 °C moderate, 13 °C extreme). We identified 85 differentially expressed miRNAs (DEmiRs), with 22 altered under moderate cold and 68 altered in extreme cold, demonstrating that miRNA regulatory activity intensifies with decreasing temperature. Combined miRNA target prediction and expression correlation analysis revealed 8 and 247 differentially expressed target genes (DETGs), which formed cold-adaptive regulatory networks with corresponding DEmiRs. Functional analysis showed enrichment of pathways related to circadian rhythm (e.g., PER targeted by miR-429-y and miR-181-z), immunity (e.g., JUN-miR-10545-x cluster), and endocrine function (e.g., NHERF1-miR-181-z). Notably, miR-181-z was identified as a central regulatory hub, interacting with 13.2% nodes in BE network. Our study provides the first comprehensive miRNA-mRNA network resource for cold stress response in silver pomfret, offering valuable molecular biomarkers for breeding cold-resilient strains and enhancing sustainable aquaculture practices.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12467872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145179605","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
Ethnobotanical Heritage of Edible Plants Species in Mueang District, Yasothon Province, Northeastern Thailand. 泰国东北部亚索松省Mueang地区食用植物物种的民族植物学遗产。
IF 3.5 3区 生物学
Biology-Basel Pub Date : 2025-09-13 DOI: 10.3390/biology14091264
Piyaporn Saensouk, Surapon Saensouk, Thawatphong Boonma, Yuefeng Zhang, Lingling Lv, Tammanoon Jitpromma
{"title":"Ethnobotanical Heritage of Edible Plants Species in Mueang District, Yasothon Province, Northeastern Thailand.","authors":"Piyaporn Saensouk, Surapon Saensouk, Thawatphong Boonma, Yuefeng Zhang, Lingling Lv, Tammanoon Jitpromma","doi":"10.3390/biology14091264","DOIUrl":"10.3390/biology14091264","url":null,"abstract":"<p><p>Traditional knowledge of edible plants is essential for food security, nutrition, and cultural identity in rural communities, yet many regions, including Mueang District, Yasothon Province (MY), remain underexplored in ethnobotanical studies. The lack of systematic documentation of local plant diversity and uses in MY presents a significant gap in understanding how these resources contribute to the sustainability of local food systems. This study addresses this gap by providing a comprehensive ethnobotanical survey of edible plants in Mueang District, Northeastern Thailand. Documenting 170 species across 60 families, the study reveals a rich plant diversity reflecting a dynamic interplay of native and introduced species, as well as cultivated and wild-harvested resources that sustain local food security, nutrition, and cultural traditions. Fabaceae emerged as the most species-rich family, while staple cereals such as <i>Oryza sativa</i> L. and <i>Zea mays</i> L. dominate use-value rankings. Quantitative indices, including Species Use Value (SUV), Relative Frequency of Citation (RFC), Cultural Food Significance Index (CFSI), and Fidelity Level (%FL), elucidate nuanced patterns of plant utilization, highlighting multifunctional species that bridge food and medicine. High cultural consensus on key medicinal plants underscores the deep integration of traditional healthcare within local food systems. The diversity of edible plant uses-from beverages and condiments to medicinal foods-illustrates adaptive strategies that enhance dietary diversity and ecological resilience. These findings contribute to the understanding of biocultural diversity and underscore the importance of conserving both plant biodiversity and indigenous knowledge to promote sustainable, locally adapted food systems. The study also identifies priority species for future pharmacological and agronomic research to support climate-resilient food sovereignty.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12467265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145179700","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
Expression Dynamics of Neurotransmitter System Genes in Early Sea Urchin Embryos: Insights from a Four-Species Comparative Transcriptome Analysis. 早期海胆胚胎中神经递质系统基因的表达动态:来自四种比较转录组分析的见解。
IF 3.5 3区 生物学
Biology-Basel Pub Date : 2025-09-12 DOI: 10.3390/biology14091262
Yuri B Shmukler, Nina M Alyoshina, Yulia O Nikishina, Denis A Nikishin
{"title":"Expression Dynamics of Neurotransmitter System Genes in Early Sea Urchin Embryos: Insights from a Four-Species Comparative Transcriptome Analysis.","authors":"Yuri B Shmukler, Nina M Alyoshina, Yulia O Nikishina, Denis A Nikishin","doi":"10.3390/biology14091262","DOIUrl":"10.3390/biology14091262","url":null,"abstract":"<p><p>Transmitters such as serotonin, dopamine, noradrenaline, and acetylcholine act as regulators or triggers of numerous processes in the early embryo, including in sea urchins. However, the identity of these mechanisms relative to mature nervous systems remains controversial. The aim of this study was to comprehensively characterize the transcriptomic basis of these as well as glutamatergic, GABAergic and histaminergic systems by comparing publicly available RNA-Seq data across four sea urchin species <i>(Mesocentrotus franciscanus</i>, <i>Lytechinus variegatus</i>, <i>Paracentrotus lividus</i>, <i>Strongylocentrotus purpuratus</i>) during early development (egg to early gastrula). Transcript abundance was normalized using the geometric mean of housekeeping genes (GHG) to facilitate comparative analysis and to use the universal significance threshold. We detected mRNA transcripts encoding numerous components (enzymes, receptors, transporters) for all seven transmitter systems from the earliest stages, suggesting a complex signaling potential prior to neurogenesis. The expression of multiple mRNAs of receptors for the same transmitter indirectly supports our earlier notion of the possibility of simultaneous regulation of different processes by this transmitter even in the single-cell embryo. Notably, transcripts for key synthesis enzymes (TPH, DBH) were often low, indicating limited de novo synthesis, while transcripts for degradation enzymes (MAO, AChE) were abundant. Consistent expression across species was observed for specific receptors such as HTR6, D1-like dopamine, β-adrenergic receptors and the α7 subunit of nicotinic AChR. However, the expression profiles of many components, particularly glutamatergic receptors and metabolic enzymes, showed considerable interspecies variability. These findings indicate that multiple transmitter systems are transcriptionally represented early in development, suggesting substantial molecular overlap with mature systems, while the diversity between species points to possible evolutionary plasticity. This comparative transcriptomic dataset provides a basis for targeted functional studies of the role and interactions of these pre-nervous transmitter pathways in orchestrating embryogenesis.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12467107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145179169","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
Decapod Crustaceans in a Transitional River System: Insights from the Ribeira de Iguape Ecoregion, Brazil. 过渡河流系统中的十足甲壳类动物:来自巴西Ribeira de Iguape生态区的见解。
IF 3.5 3区 生物学
Biology-Basel Pub Date : 2025-09-12 DOI: 10.3390/biology14091255
Esthephany Konesuk Santos Miranda, Maria Rosa Roque Santana Gomes, Luis Carlos Ferreira de Almeida, Giovana Bertini
{"title":"Decapod Crustaceans in a Transitional River System: Insights from the Ribeira de Iguape Ecoregion, Brazil.","authors":"Esthephany Konesuk Santos Miranda, Maria Rosa Roque Santana Gomes, Luis Carlos Ferreira de Almeida, Giovana Bertini","doi":"10.3390/biology14091255","DOIUrl":"10.3390/biology14091255","url":null,"abstract":"<p><p>Freshwater ecosystems are essential for biodiversity conservation but face increasing threats from human activities. This study assessed the species richness, diversity, and spatial and temporal distribution of decapod crustaceans (Caridea and Brachyura) in the lower Ribeira de Iguape River, southeastern Brazil, a globally recognized freshwater ecoregion. Monthly sampling took place over one year at three sites using both active and passive capture methods. Environmental parameters were measured in the field, and multivariate analyses (correspondence analysis, PERMANOVA, and multiple regression) were applied to explore species-environment relationships and community structure. A total of 42,897 individuals were recorded, including eight Caridea and four Brachyura species. Carideans accounted for over 97 percent of the total, with <i>Potimirim</i> spp. and <i>Macrobrachium acanthurus</i> as the most abundant. The site nearest the river mouth showed the highest species richness and diversity, likely due to its transitional characteristics and moderate salinity variation. Environmental variables such as dissolved oxygen and salinity influenced species occurrence, although biological interactions may also contribute. Seasonal changes in abundance appeared most evident during winter and spring, driven by shifts in dominant taxa. The presence of the non-native <i>Macrobrachium rosenbergii</i> suggests early establishment and reinforces the need for long-term ecological monitoring in transitional freshwater environments.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12467917/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145179492","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-Genome Analysis of a Novel Multidrug-Resistant Escherichia coli Strain from Dairy Calves in Northeast China: Mechanisms of Antibiotic Resistance and Biofilm Formation. 东北地区一株新型多药耐药奶牛大肠杆菌的全基因组分析:抗生素耐药机制和生物膜形成
IF 3.5 3区 生物学
Biology-Basel Pub Date : 2025-09-12 DOI: 10.3390/biology14091257
Xuanpan Ding, Qiuyue An, Huijie Kang, Siyao Li, Shuai Zhang, Haotian Yang, Xinyi Dou, Yaxin Ji, Yuan Zhao, Honggang Fan
{"title":"Whole-Genome Analysis of a Novel Multidrug-Resistant <i>Escherichia coli</i> Strain from Dairy Calves in Northeast China: Mechanisms of Antibiotic Resistance and Biofilm Formation.","authors":"Xuanpan Ding, Qiuyue An, Huijie Kang, Siyao Li, Shuai Zhang, Haotian Yang, Xinyi Dou, Yaxin Ji, Yuan Zhao, Honggang Fan","doi":"10.3390/biology14091257","DOIUrl":"10.3390/biology14091257","url":null,"abstract":"<p><p>The use of antibiotics is so widespread in animal husbandry, but negligent management and lack of policies often lead to the massive use of antibiotics on farms. In this study, we collected cases of epidemic calf diarrhea in northeastern China and isolated a new strain of multidrug-resistant <i>Escherichia coli</i> (MDR-<i>E. coli</i>). In order to explore the information of this pathogen in detail, we used whole-genome sequencing to determine the genome sequence, and explored in detail the resistance, pathogenicity, genetic evolution and other biological processes of the strain through bioinformatics analysis. The results showed that the <i>E. coli</i> isolated in this study was a new multidrug-resistant strain with a large number of drug resistance genes (77) and virulence genes (84), including a circular chromosome and five circular plasmids, which are basically impossible to treat by currently commonly used antibiotics. The findings of this study suggest that the prolonged misuse of antibiotics in agricultural settings may contribute to the development of antibiotic-resistant strains of <i>E. coli</i>. This, in turn, has the potential to trigger outbreaks of antibiotic-resistant bacterial diarrhea, leading to substantial economic losses and posing significant public health risks. These results underscore the necessity for the judicious use of antibiotics and will inform the development of pertinent policies and regulations.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12467046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145179624","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
Chromosomal Instability and Periodontal Disease in Idiopathic Infertility: Evidence of a Possible Association. 特发性不孕患者的染色体不稳定性与牙周病:一种可能关联的证据。
IF 3.5 3区 生物学
Biology-Basel Pub Date : 2025-09-12 DOI: 10.3390/biology14091256
Cristina-Crenguţa Albu, Ştefan-Dimitrie Albu, Claudia Florina Bogdan-Andreescu, Cristian-Viorel Poalelungi, Constantin Marian Damian, Alexandru Burcea, Andreea-Mariana Bănățeanu, Emin Cadar, Dan Alexandru Slăvescu, Anca Daniela Brăila
{"title":"Chromosomal Instability and Periodontal Disease in Idiopathic Infertility: Evidence of a Possible Association.","authors":"Cristina-Crenguţa Albu, Ştefan-Dimitrie Albu, Claudia Florina Bogdan-Andreescu, Cristian-Viorel Poalelungi, Constantin Marian Damian, Alexandru Burcea, Andreea-Mariana Bănățeanu, Emin Cadar, Dan Alexandru Slăvescu, Anca Daniela Brăila","doi":"10.3390/biology14091256","DOIUrl":"10.3390/biology14091256","url":null,"abstract":"<p><strong>Background: </strong>Chromosomal instability (CIN) may underlie a subset of idiopathic infertility, and chronic periodontitis could contribute to genomic fragility. We tested whether periodontal status is associated with cytogenetic instability in adults with idiopathic infertility.</p><p><strong>Methods: </strong>This was a cross-sectional study of 60 adults aged 20-40 years, comprising idiopathic infertility (<i>n</i> = 30) and fertile controls (<i>n</i> = 30), each with 18 women and 12 men. Significant exclusions included systemic inflammatory disease, pregnancy/lactation, recent antibiotics/NSAIDs, and periodontal therapy within 6 months. Periodontal examination recorded probing depth (PD), clinical attachment loss (CAL), and bleeding on probing (BOP). Cytogenetic testing used mitomycin C-induced chromosomal breakage to derive the Breakage Index (BI); CIN was defined as BI ≥ 4.0. Analyses compared infertile with CIN (<i>n</i> = 19), infertile without CIN (<i>n</i> = 11), and controls (<i>n</i> = 30).</p><p><strong>Results: </strong>Infertile participants with CIN had a higher periodontitis burden compared to infertile participants without CIN and to controls (moderate-severe: 89.5% vs. 54.5% vs. 26.7%); mean BI also differed (5.2 ± 0.9 vs. 1.3 ± 0.5 vs. 0.4 ± 0.2). Periodontal measures followed the same gradient, with greater CAL and PD in CIN-positive infertility.</p><p><strong>Conclusions: </strong>In idiopathic infertility, CIN was cross-sectionally associated with more severe periodontitis, and the BI correlated with CAL, PD, and BOP. Causality cannot be inferred and residual confounding cannot be excluded. Periodontal screening is a feasible adjunct that may help identify a modifiable inflammatory burden; prospective and interventional studies are warranted.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12467813/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145179470","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}
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