Biology最新文献 - Book学术

Raphanus sativus Linne Protects Human Nucleus Pulposus Cells against H2O2-Induced Damage by Inhibiting TREM2 油菜通过抑制 TREM2 保护人类核浆细胞免受 H2O2 引发的损伤

Biology Pub Date : 2024-08-09 DOI: 10.3390/biology13080602

Hyunseong Kim, C. Yeo, Jin Young Hong, Wanjin Jeon, Hyun Kim, Junseong Lee, Yoon Jae Lee, Seung Ho Baek, I. Ha

{"title":"Raphanus sativus Linne Protects Human Nucleus Pulposus Cells against H2O2-Induced Damage by Inhibiting TREM2","authors":"Hyunseong Kim, C. Yeo, Jin Young Hong, Wanjin Jeon, Hyun Kim, Junseong Lee, Yoon Jae Lee, Seung Ho Baek, I. Ha","doi":"10.3390/biology13080602","DOIUrl":"https://doi.org/10.3390/biology13080602","url":null,"abstract":"Intervertebral disc degeneration (IDD) progresses owing to damage and depletion of nucleus pulposus (NP) cells. Cytoprotection mitigates oxidative stress, nutrient deprivation, and mechanical stress, which lead to cell damage and necrosis. We aimed to examine the protective effect of Raphanus sativus Linne (RSL), common radish, against oxidative stress by H2O2 in human NP cells and whether the RSL extracts can inhibit triggering receptor expressed on myeloid cells 2 (TREM2), an inducer of apoptosis and degeneration in NP cells. We administered hydrogen peroxide (H2O2) to cultured human NP cells treated with RSL extracts. We used immunoblotting and quantitative PCR to investigate expression of the apoptosis-associated proteins in cultured cells. RSL significantly enhanced cell survival by suppressing the activation of cleaved caspase-3 and Bax. In contrast, RSL extract increased Bcl2 concentration to downregulate apoptosis. Additionally, RSL treatment notably enhanced the mRNA levels of ACAN and Col2a1 while significantly reducing those of ADAMTS-4, ADAMTS-5, MMP3, and MMP13, key genes involved in NP degeneration. While H2O2 elevated TREM2 expression, causing disc degeneration, RSL downregulated TREM2 expression. Thus, our findings imply that RSL supports human NP cells under oxidative stress and regulates the pathways underlying disc degeneration, particularly TREM2, and that RSL extracts may potentially prevent IDD.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"61 23","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141922593","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

The A226D Mutation of OmpC Leads to Increased Susceptibility to β-Lactam Antibiotics in Escherichia coli OmpC 的 A226D 突变导致大肠埃希菌对β-内酰胺类抗生素的敏感性增加

Biology Pub Date : 2024-08-09 DOI: 10.3390/biology13080600

Jiaming Zhu, Peng Guo, Yuting Zheng, Shiqing Xiang, Yang Zhao, Xinyu Liu, Chengzhang Fu, Youming Zhang, Hai Xu, Ling Li, Wenjia Wang, Mingyu Wang

{"title":"The A226D Mutation of OmpC Leads to Increased Susceptibility to β-Lactam Antibiotics in Escherichia coli","authors":"Jiaming Zhu, Peng Guo, Yuting Zheng, Shiqing Xiang, Yang Zhao, Xinyu Liu, Chengzhang Fu, Youming Zhang, Hai Xu, Ling Li, Wenjia Wang, Mingyu Wang","doi":"10.3390/biology13080600","DOIUrl":"https://doi.org/10.3390/biology13080600","url":null,"abstract":"Bacterial resistance to antibiotics can lead to long-lasting, hard-to-cure infections that pose significant threats to human health. One key mechanism of antimicrobial resistance (AMR) is to reduce the antibiotic permeation of cellular membranes. For instance, the lack of outer membrane porins (OMPs) can lead to elevated AMR levels. However, knowledge on whether mutations of OMPs can also influence antibiotic susceptibility is limited. This work aims to address this question and identified an A226D mutation in OmpC, a trimeric OMP, in Escherichia coli. Surveillance studies found that this mutation is present in 50 E. coli strains for which whole genomic sequences are available. Measurement of minimum inhibition concentrations (MICs) found that this mutation leads to a 2-fold decrease in MICs for β-lactams ampicillin and piperacillin. Further survival assays confirmed the role this mutation plays in β-lactam susceptibility. With molecular dynamics, we found that the A226D mutation led to increased overall flexibility of the protein, thus facilitating antibiotic uptake, and that binding with piperacillin was weakened, leading to easier antibiotic penetration. This work reports a novel mutation that plays a role in antibiotic susceptibility, along with mechanistic studies, and further confirms the role of OMPs in bacterial tolerance to antibiotics.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"56 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923772","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

Evolutionary Fate of the Opine Synthesis Genes in the Arachis L. Genomes 罂粟基因组中鸦片碱合成基因的进化命运

Biology Pub Date : 2024-08-09 DOI: 10.3390/biology13080601

Olesja D. Bogomaz, V. D. Bemova, Nikita A. Mirgorodskii, T. Matveeva

{"title":"Evolutionary Fate of the Opine Synthesis Genes in the Arachis L. Genomes","authors":"Olesja D. Bogomaz, V. D. Bemova, Nikita A. Mirgorodskii, T. Matveeva","doi":"10.3390/biology13080601","DOIUrl":"https://doi.org/10.3390/biology13080601","url":null,"abstract":"Naturally transgenic plants are plants that have undergone Agrobacterium-mediated transformation under natural conditions without human involvement. Among Arachis hypogaea L., A. duranensis Krapov. & W.C. Greg, A. ipaensis Krapov. & W.C. Greg, A. monticola Krapov. & Rigoni, and A. stenosperma Krapov. & W.C. Greg are known to contain sequences derived from the T-DNA of “Agrobacterium”. In the present study, using molecular genetics and bioinformatic methods, we characterized natural transgenes in 18 new species from six sections of the genus Arachis. We found that small fragments of genes for enzymes of the agropine synthesis pathway were preserved only in some of the studied samples and were lost in the majority of the species during evolution. At the same time, genes, similar to cucumopine synthases (cus-like), remained intact in almost all of the investigated species. In cultivated peanuts, they are expressed in a tissue-specific manner. We demonstrated the intraspecific variability of the structure and expression of the cus-like gene in cultivated peanuts. The described diversity of gene sequences horizontally transferred from Agrobacterium to plants helps to shed light on the phylogeny of species of the genus Arachis and track possible hybridization events. Data on the ability of certain species to hybridize are useful for planning breeding schemes aimed at transferring valuable traits from wild species into cultivated peanuts.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"80 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141922185","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

Hypoxia-Induced Adaptations of Embryonic Fibroblasts: Implications for Developmental Processes 缺氧诱导的胚胎成纤维细胞适应性：对发育过程的影响

Biology Pub Date : 2024-08-08 DOI: 10.3390/biology13080598

Zeyu Li, Delong Han, Zhenchi Li, Lingjie Luo

{"title":"Hypoxia-Induced Adaptations of Embryonic Fibroblasts: Implications for Developmental Processes","authors":"Zeyu Li, Delong Han, Zhenchi Li, Lingjie Luo","doi":"10.3390/biology13080598","DOIUrl":"https://doi.org/10.3390/biology13080598","url":null,"abstract":"Animal embryonic development occurs under hypoxia, which can promote various developmental processes. Embryonic fibroblasts, which can differentiate into bone and cartilage and secrete various members of the collagen protein family, play essential roles in the formation of embryonic connective tissues and basement membranes. However, the adaptations of embryonic fibroblasts under hypoxia remain poorly understood. In this study, we investigated the effects of hypoxia on mouse embryonic fibroblasts (MEFs). We found that hypoxia can induce migration, promote metabolic reprogramming, induce the production of ROS and apoptosis, and trigger the activation of multiple signaling pathways of MEFs. Additionally, we identified several hypoxia-inducible genes, including Proser2, Bean1, Dpf1, Rnf128, and Fam71f1, which are regulated by HIF1α. Furthermore, we demonstrated that CoCl2 partially mimics the effects of low oxygen on MEFs. However, we found that the mechanisms underlying the production of ROS and apoptosis differ between hypoxia and CoCl2 treatment. These findings provide insights into the complex interplay between hypoxia, fibroblasts, and embryonic developmental processes.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141926169","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

Impact of BMI and Cardiorespiratory Fitness on Oxidative Stress in Plasma and Circulating Exosomes Following Acute Exercise 急性运动后体重指数和心肺功能对血浆和循环外泌体中氧化应激的影响

Biology Pub Date : 2024-08-08 DOI: 10.3390/biology13080599

Aaron L. Slusher, Nishant P Visavadiya, Brandon G. Fico, Brisamar Estébanez, Edmund O. Acevedo, Chun-Jung Huang

{"title":"Impact of BMI and Cardiorespiratory Fitness on Oxidative Stress in Plasma and Circulating Exosomes Following Acute Exercise","authors":"Aaron L. Slusher, Nishant P Visavadiya, Brandon G. Fico, Brisamar Estébanez, Edmund O. Acevedo, Chun-Jung Huang","doi":"10.3390/biology13080599","DOIUrl":"https://doi.org/10.3390/biology13080599","url":null,"abstract":"The impact of cardiorespiratory fitness (VO2max) and obesity on indices of oxidative stress in plasma and circulating exosome-like extracellular vesicles (ELVs) were examined following acute exercise. Indices of oxidative stress in plasma and isolated plasma ELVs were examined in aerobically trained (NW-Tr; n = 15) and untrained (NW-UTr; n = 18) normal-weight individuals and aerobically untrained individuals with obesity (Ob-Utr; n = 10) prior to and immediately following acute maximal treadmill running. Following exercise, ELV flotillin-1 expression (p = 0.008) and plasma total antioxidant capacity (TAC; p = 0.010) increased more in NW-UTr compared to NW-Tr and Ob-UTr participants, whereas plasma protein carbonyls (PC) decreased more in Ob-UTr compared to NW-Tr and NW-UTr groups. ELV glutathione (GSH) concentrations decreased more in NW-Tr compared to NW-UTr and Ob-UTr participants (p = 0.009), whereas lipid peroxidase (LPO) concentrations increased more in Ob-UTr compared to NW-Tr and NW-UTr participants (p = 0.003). Body mass index (BMI) was associated negatively with plasma TAC and PC (p < 0.05) and positively with ELV LPO concentration responses (p = 0.009). Finally, plasma-to-total (plasma + ELV) GSH ratios decreased in Ob-UTr compared to NW-Tr and NW-UTr participants (p = 0.006), PC ratios increased in NW-Tr and NW-UTr compared to Ob-UTr subjects (p = 0.008), and reactive oxygen/nitrogen species ratios increased in NW-UTr and decreased in Ob-UTr participants (p < 0.001). BMI, independently of VO2max, differentially regulates indices of oxidative stress within plasma and circulating ELVs prior to and immediately following acute maximal treadmill exercise.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"55 36","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141928951","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

Schisandrin A Attenuates Diabetic Nephropathy via EGFR/AKT/GSK3β Signaling Pathway Based on Network Pharmacology and Experimental Validation 基于网络药理学和实验验证的五味子素 A 通过表皮生长因子受体/AKT/GSK3β 信号通路缓解糖尿病肾病

Biology Pub Date : 2024-08-08 DOI: 10.3390/biology13080597

Pengyu Wang, Qing Lan, Qi Huang, Ruyi Zhang, Shuo Zhang, Leiming Yang, Yan Song, Tong Wang, Guandi Ma, Xiufen Liu, Xiying Guo, Youzhi Zhang, Chao Liu

{"title":"Schisandrin A Attenuates Diabetic Nephropathy via EGFR/AKT/GSK3β Signaling Pathway Based on Network Pharmacology and Experimental Validation","authors":"Pengyu Wang, Qing Lan, Qi Huang, Ruyi Zhang, Shuo Zhang, Leiming Yang, Yan Song, Tong Wang, Guandi Ma, Xiufen Liu, Xiying Guo, Youzhi Zhang, Chao Liu","doi":"10.3390/biology13080597","DOIUrl":"https://doi.org/10.3390/biology13080597","url":null,"abstract":"Diabetic nephropathy (DN) is one of the common complications of diabetes and the main cause of end-stage renal disease (ESRD) in clinical practice. Schisandrin A (Sch A) has multiple pharmacological activities, including inhibiting fibrosis, reducing apoptosis and oxidative stress, and regulating immunity, but its pharmacological mechanism for the treatment of DN is still unclear. In vivo, streptozotocin (STZ) and a high-fat diet were used to induce type 2 diabetic rats, and Sch A was administered for 4 weeks. At the same time, protein–protein interaction (PPI) networks were established to analyze the overlapping genes of DN and Sch A. Subsequently, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were performed to determine the hub pathway. In addition, molecular docking was used to preliminarily verify the affinity of hub proteins and Sch A. Further, H&E staining, Sirius red staining, immunohistochemistry, immunofluorescence, and western blot analysis were used to detect the location and expression of related proteins in DN. This study revealed the multi-target and multi-pathway characteristics of Sch A in the treatment of DN. First, Sch A could effectively improve glucose tolerance, reduce urine microprotein and urine creatinine levels, and alleviate renal pathological damage in DN rats. Second, EGFR was the hub gene screened in overlapping genes (43) of Sch A (100) and DN (2524). Finally, it was revealed that Sch A could inhibit the protein expression levels of EGFR and PTRF and reduced the expression of apoptosis-related proteins, and this effect was related to the modulation of the AKT/GSK-3β signaling pathway. In summary, Sch A has a protective effect in DN rats, EGFR may be a potential therapeutic target, throughout modulating AKT/GSK-3β pathway.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"9 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141927355","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

Heterogeneous Evolution of Breast Cancer Cells—An Endogenous Molecular-Cellular Network Study 乳腺癌细胞的异质进化--内源性分子-细胞网络研究

Biology Pub Date : 2024-07-26 DOI: 10.3390/biology13080564

Tianqi Li, Yong-Cong Chen, Ping Ao

{"title":"Heterogeneous Evolution of Breast Cancer Cells—An Endogenous Molecular-Cellular Network Study","authors":"Tianqi Li, Yong-Cong Chen, Ping Ao","doi":"10.3390/biology13080564","DOIUrl":"https://doi.org/10.3390/biology13080564","url":null,"abstract":"Breast cancer heterogeneity presents a significant challenge in clinical therapy, such as over-treatment and drug resistance. These challenges are largely due to its obscure normal epithelial origins, evolutionary stability, and transitions on the cancer subtypes. This study aims to elucidate the cellular emergence and maintenance of heterogeneous breast cancer via quantitative bio-process modeling, with potential benefit to therapeutic strategies for the disease. An endogenous molecular–cellular hypothesis posits that both pathological and physiological states are phenotypes evolved from and shaped by interactions among a number of conserved modules and cellular factors within a biological network. We hereby developed a model of core endogenous network for breast cancer in accordance with the theory, quantifying its intrinsic dynamic properties with dynamic modeling. The model spontaneously generates cell states that align with molecular classifications at both the molecular and modular level, replicating four widely recognized molecular subtypes of the cancer and validating against data extracted from the TCGA database. Further analysis shows that topologically, a singular progression gateway from normal breast cells to cancerous states is identified as the Luminal A-type breast cancer. Activated positive feedback loops are found to stabilize cellular states, while negative feedback loops facilitate state transitions. Overall, more routes are revealed on the cellular transition between stable states, and a traceable count explains the origin of breast cancer heterogeneity. Ultimately, the research intended to strength the search for therapeutic targets.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"19 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141801405","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

Sprint Interval Training Improves Brain-Derived Neurotropic Factor-Induced Benefits in Brain Health—A Possible Molecular Signaling Intervention 短跑间歇训练可提高脑源性神经营养因子对大脑健康的益处--一种可能的分子信号干预措施

Biology Pub Date : 2024-07-26 DOI: 10.3390/biology13080562

Xueqiang Zhu, Wenjia Chen, A. Thirupathi

{"title":"Sprint Interval Training Improves Brain-Derived Neurotropic Factor-Induced Benefits in Brain Health—A Possible Molecular Signaling Intervention","authors":"Xueqiang Zhu, Wenjia Chen, A. Thirupathi","doi":"10.3390/biology13080562","DOIUrl":"https://doi.org/10.3390/biology13080562","url":null,"abstract":"Physical exercise can significantly impact our bodies, affecting our functional capacity, structure establishment, and molecular makeup. The magnitude of these changes depends on the specific exercise protocols used. For instance, low-to-moderate-intensity exercise can activate important molecular targets in the short term, such as BDNF-mediated signaling, while high-intensity exercise can maintain these signaling molecules in the active state for a longer term. This makes it challenging to recommend specific exercises for obtaining BDNF-induced benefits. Additionally, exercise-induced molecular signaling targets can have positive and negative effects, with some exercises blunting these targets and others activating them. For example, increasing BDNF concentration through exercise can be beneficial for brain health, but it may also have a negative impact on conditions such as bipolar disorder. Therefore, a deeper understanding of a specific exercise-mediated mechanistic approach is required. This review will delve into how the sprint exercise-mediated activation of BDNF could help maintain brain health and explore potential molecular interventions.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"35 24","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141800474","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

Arabidopsis BTB-A2s Play a Key Role in Drought Stress 拟南芥 BTB-A2 在干旱胁迫中发挥关键作用

Biology Pub Date : 2024-07-26 DOI: 10.3390/biology13080561

Guohua Cai, Yunxiao Zang, Zhongqian Wang, Shuoshuo Liu, Guodong Wang

{"title":"Arabidopsis BTB-A2s Play a Key Role in Drought Stress","authors":"Guohua Cai, Yunxiao Zang, Zhongqian Wang, Shuoshuo Liu, Guodong Wang","doi":"10.3390/biology13080561","DOIUrl":"https://doi.org/10.3390/biology13080561","url":null,"abstract":"Drought stress significantly impacts plant growth, productivity, and yield, necessitating a swift fine-tuning of pathways for adaptation to harsh environmental conditions. This study explored the effects of Arabidopsis BTB-A2.1, BTB-A2.2, and BTB-A2.3, distinguished by their exclusive possession of the Broad-complex, Tramtrack, and Bric-à-brac (BTB) domain, on the negative regulation of drought stress mediated by abscisic acid (ABA) signaling. Promoter analysis revealed the presence of numerous ABA-responsive and drought stress-related cis-acting elements within the promoters of AtBTB-A2.1, AtBTB-A2.2, and AtBTB-A2.3. The AtBTB-A2.1, AtBTB-A2.2, and AtBTB-A2.3 transcript abundances increased under drought and ABA induction according to qRT-PCR and GUS staining. Furthermore, the Arabidopsis btb-a2.1/2/3 triple mutant exhibited enhanced drought tolerance, supporting the findings from the overexpression studies. Additionally, we detected a decrease in the stomatal aperture and water loss rate of the Arabidopsis btb-a2.1/2/3 mutant, suggesting the involvement of these genes in repressing stomatal closure. Importantly, the ABA signaling-responsive gene levels within Arabidopsis btb-a2.1/2/3 significantly increased compared with those in the wild type (WT) under drought stress. Based on such findings, Arabidopsis BTB-A2s negatively regulate drought stress via the ABA signaling pathway.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"15 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141801993","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

D-sORF: Accurate Ab Initio Classification of Experimentally Detected Small Open Reading Frames (sORFs) Associated with Translational Machinery D-sORF：对实验检测到的与转译机制相关的小开放阅读框（sORF）进行精确的 Ab Initio 分类

Biology Pub Date : 2024-07-26 DOI: 10.3390/biology13080563

Nikos Perdikopanis, Antonis Giannakakis, Ioannis Kavakiotis, A. Hatzigeorgiou

{"title":"D-sORF: Accurate Ab Initio Classification of Experimentally Detected Small Open Reading Frames (sORFs) Associated with Translational Machinery","authors":"Nikos Perdikopanis, Antonis Giannakakis, Ioannis Kavakiotis, A. Hatzigeorgiou","doi":"10.3390/biology13080563","DOIUrl":"https://doi.org/10.3390/biology13080563","url":null,"abstract":"Small open reading frames (sORFs; <300 nucleotides or <100 amino acids) are widespread across all genomes, and an increasing variety of them appear to be translating from non-genic regions. Over the past few decades, peptides produced from sORFs have been identified as functional in various organisms, from bacteria to humans. Despite recent advances in next-generation sequencing and proteomics, accurate annotation and classification of sORFs remain a rate-limiting step toward reliable and high-throughput detection of small proteins from non-genic regions. Additionally, the cost of computational methods utilizing machine learning is lower than that of biological experiments, and they can be employed to detect sORFs, laying the groundwork for biological experiments. We present D-sORF, a machine-learning framework that integrates the statistical nucleotide context and motif information around the start codon to predict coding sORFs. D-sORF scores directly for coding identity and requires only the underlying genomic sequence, without incorporating parameters such as the conservation, which, in the case of sORFs, may increase the dispersion of scores within the significantly less conserved non-genic regions. D-sORF achieves 94.74% precision and 92.37% accuracy for small ORFs (using the 99 nt medium length window). When D-sORF is applied to sORFs associated with ribosomes, the identification of transcripts producing peptides (annotated by the Ensembl IDs) is similar to or superior to experimental methodologies based on ribosome-sequencing (Ribo-Seq) profiling. In parallel, the recognition of putative negative data, such as the intron-containing transcripts that associate with ribosomes, remains remarkably low, indicating that D-sORF could be efficiently applied to filter out false-positive sORFs from Ribo-Seq data because of the non-productive ribosomal binding or noise inherent in these protocols.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"35 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141800606","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