Frontiers in Genetics最新文献

{"title":"Phosphorus-solubilizing fungi promote the growth of <i>Fritillaria taipaiensis</i> P. Y. Li by regulating physiological and biochemical reactions and protecting enzyme system-related gene expression.","authors":"Yueheng Wang, Lin Yuan, Yuhan Wang, Jiaqi Lang, Mingyan Ye, Qingqiu Liu, Qiang Ma, Nong Zhou","doi":"10.3389/fgene.2024.1459191","DOIUrl":"10.3389/fgene.2024.1459191","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Introduction: &lt;/strong&gt;&lt;i&gt;Fritillaria taipaiensis&lt;/i&gt; P. Y. Li is a plant used to treat respiratory diseases such as pneumonia, bronchitis, and influenza. Its wild resources have become increasingly scarce, and the demand for efficient artificial cultivation has increased significantly in recent years. Phosphorus-solubilizing fungi can promote the dissolution of insoluble phosphate complex, which benefits plant nutrition. Another strategy for efficiently cultivating traditional Chinese medicine plants is to combine the soil with phosphorus-solubilizing fungi to provide nutrients and other desired features. This study aimed to investigate the effects of different phosphorus-solubilizing fungi and their combinations on photosynthesis, physiological and biochemical characteristics, and expression of protective enzyme system-related genes, and to find a reference strain suitable for the artificial cultivation and industrial development of &lt;i&gt;F. taipaiensis&lt;/i&gt; P. Y. Li. In this study, the phosphorus-solubilizing fungi isolated from the rhizosphere soil of &lt;i&gt;F. taipaiensis&lt;/i&gt; P. Y. Li were applied to the cultivation of &lt;i&gt;F. taipaiensis&lt;/i&gt; P. Y. Li for the first time.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;In this study, seven treatment groups (S1-S7) and one control group were set up using indoor pots as follows: S1 (inoculation with &lt;i&gt;Aspergillus tubingensis&lt;/i&gt;), S2 (inoculation with &lt;i&gt;A. niger&lt;/i&gt;), S3 (inoculation with &lt;i&gt;Aspergillus nigerfunigatus&lt;/i&gt;) and S4 (inoculation with &lt;i&gt;A. tubingensis&lt;/i&gt; and &lt;i&gt;A. niger&lt;/i&gt;), S5 (inoculation with &lt;i&gt;A. tubingensis&lt;/i&gt; and &lt;i&gt;A. nigerfunigatus&lt;/i&gt;), S6 (inoculation with &lt;i&gt;A. niger&lt;/i&gt; and &lt;i&gt;A. nigerfunigatus&lt;/i&gt;), S7 (inoculation with &lt;i&gt;A. tubingensis&lt;/i&gt;, &lt;i&gt;A. niger&lt;/i&gt;, and &lt;i&gt;A. nigerfunigatus&lt;/i&gt;), and CK (control group). These strains were inoculated into pots containing &lt;i&gt;F. taipaiensis&lt;/i&gt; P. Y. Li bulbs,and the effects of different phosphorus-solubilizing fungi and combinations on the photosynthetic characteristics, basic physiological and biochemical indicators, and differential gene expression of protective enzyme systems in &lt;i&gt;F. taipaiensis&lt;/i&gt; P. Y. Li leaves were determined.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Most growth indexes showed significant differences in the fungal treatment groups compared with the CK group (&lt;i&gt;P&lt;/i&gt; &lt; 0.05). The stem diameter and plant height in the S5 group were the highest, which were 58.23% and 62.49% higher than those in the CK group, respectively. The leaf area in the S7 group was the largest, which increased by 141.34% compared with that in the CK group. Except for intercellular CO&lt;sub&gt;2&lt;/sub&gt; concentration (Ci), the contents of photosynthetic pigments, photosynthetic parameters, and amounts of osmoregulatory substances increased to varying degrees in the fungal treatment groups (&lt;i&gt;P&lt;/i&gt; &lt; 0.05). Among these, the S5 group had the highest stomatal conductance index and soluble sugar and free proline contents, whereas S6 had the highest chlorophy","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1459191"},"PeriodicalIF":2.8,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11747862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004249","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}

{"title":"Mapping the use of cardiovascular genetic services in pediatric clinical care: challenges and opportunities for improvement.","authors":"Kerstin Hundal, Courtney L Scherr, Hoda Fakhari, Sanjana Ramesh, Lisa Dellefave-Castillo, Deb Duquette, Sara Cherny, Elizabeth M McNally, Gregory Webster, Laura J Rasmussen-Torvik","doi":"10.3389/fgene.2024.1476466","DOIUrl":"10.3389/fgene.2024.1476466","url":null,"abstract":"<p><strong>Purpose: </strong>Clinical genetic testing is increasingly integrated in managing and diagnosing cardiac conditions and disease. It is important to identify ongoing challenges. This study aimed to better understand how genetic testing is integrated into pediatric cardiac care and identify barriers and opportunities for improvement.</p><p><strong>Methods: </strong>We conducted qualitative interviews with pediatric cardiology clinicians (N = 12). Following a journey mapping approach to data analysis, we described genetic testing workflow phases, participants' thoughts and behaviors within each phase, and barriers and opportunities for improvement.</p><p><strong>Results: </strong>Participants described several challenges across the genetic testing workflow, from identifying patients for testing to disclosing results to the patients. Testing logistics, decision-making, and collaboration emerged as the most prominent challenges. Variation remains in the utilization of genetic testing, partially driven by case complexity and type of testing and attributable to other factors, like the level of interaction with genetics experts and inconsistent processes within the electronic medical record.</p><p><strong>Conclusion: </strong>Clinical genetic pediatric cardiology requires more systematic integration of genetic testing and transparent processes. Major opportunities include the interplay between clinicians, genetic experts, and the EMR. Incorporating process mapping results into clinical logistics may eradicate some barriers experienced by pediatric cardiologists and increase clinical efficiency.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1476466"},"PeriodicalIF":2.8,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11747378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004178","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}

{"title":"Dual disease co-expression analysis reveals potential roles of estrogen-related genes in postmenopausal osteoporosis and Parkinson's disease.","authors":"Dongdong Yu, Jian Kang, Chengguo Ju, Qingyan Wang, Ye Qiao, Long Qiao, Dongxiang Yang","doi":"10.3389/fgene.2024.1518471","DOIUrl":"10.3389/fgene.2024.1518471","url":null,"abstract":"<p><strong>Introduction: </strong>The deficiency of estrogen correlates with a range of diseases, notably Postmenopausal osteoporosis (PMO) and Parkinson's disease (PD). There is a possibility that PMO and PD may share underlying molecular mechanisms that are pivotal in their development and progression. The objective of this study was to identify critical genes and potential mechanisms associated with PMO by examining co-expressed genes linked to PD.</p><p><strong>Methods: </strong>Initially, pertinent data concerning PMO and PD were obtained from the GWAS database, followed by conducting a Bayesian colocalization analysis. Subsequently, co-expressed genes from the PMO dataset (GSE35956) and the PD dataset (GSE20164) were identified and cross-referenced with estrogen-related genes (ERGs). Differentially expressed genes (DEGs) among PMO, PD, and ERGs were subjected to an array of bioinformatics analyses, including Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses, in addition to protein-protein interaction (PPI) network analysis. The study also involved constructing TF-gene interactions, TF-microRNA coregulatory networks, interactions of hub genes with diseases, and validation through quantitative reverse transcription polymerase chain reaction (qRT-PCR).</p><p><strong>Results: </strong>The colocalization analysis uncovered shared genetic variants between PD and osteoporosis, with a posterior probability of colocalization (PPH4) measured at 0.967. Notably, rs3796661 was recognized as a shared genetic variant. A total of 11 genes were classified as DEGs across PMO, PD, and ERGs. Five principal KEGG pathways were identified, which include the p53 signaling pathway, TGF-beta signaling pathway, cell cycle, FoxO signaling pathway, and cellular senescence. Additionally, three hub genes-WT1, CCNB1, and SMAD7-were selected from the PPI network utilizing Cytoscape software. These three hub genes, which possess significant diagnostic value for PMO and PD, were further validated using GEO datasets. Interactions between transcription factors and genes, as well as between microRNAs and hub genes, were established. Ultimately, the expression trends of the identified hub genes were confirmed through qRT-PCR validation.</p><p><strong>Conclusions: </strong>This study is anticipated to offer innovative approaches for identifying potential biomarkers and important therapeutic targets for both PMO and PD.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1518471"},"PeriodicalIF":2.8,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11747517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004348","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}

{"title":"The analysis of gene co-expression network and immune infiltration revealed biomarkers between triple-negative and non-triple negative breast cancer.","authors":"Yao Yi, Yu Zhong, Lianhua Xie, Shuxian Lu, Yifeng Zhang","doi":"10.3389/fgene.2024.1505011","DOIUrl":"10.3389/fgene.2024.1505011","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Triple-negative breast cancer (TNBC) is a heterogeneous disease with a worse prognosis. Despite ongoing efforts, existing therapeutic approaches show limited success in improving early recurrence and survival outcomes for TNBC patients. Therefore, there is an urgent need to discover novel and targeted therapeutic strategies, particularly those focusing on the immune infiltrate in TNBC, to enhance diagnosis and prognosis for affected individuals.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;The gene co-expression network and gene ontology analyses were used to identify the differential modules and their functions based on the GEO dataset of GSE76275. The Weighted Gene Co-Expression Network Analysis (WGCNA) was used to describe the correlation patterns among genes across multiple samples. Subsequently, we identified key genes in TNBC by assessing genes with an absolute correlation coefficient greater than 0.80 within the eigengene of the enriched module that were significantly associated with breast cancer subtypes. The diagnostic potential of these key genes was evaluated using receiver operating characteristic (ROC) curve analysis with three-fold cross-validation. Furthermore, to gain insights into the prognostic implications of these key genes, we performed relapse-free survival (RFS) analysis using the Kaplan-Meier plotter online tool. CIBERSORT analysis was used to characterize the composition of immune cells within complex tissues based on gene expression data, typically derived from bulk RNA sequencing or microarray datasets. Therefore, we explored the immune microenvironment differences between TNBC and non-TNBC by leveraging the CIBERSORT algorithm. This enabled us to estimate the immune cell compositions in the breast cancer tissue of the two subtypes. Lastly, we identified key transcription factors involved in macrophage infiltration and polarization in breast cancer using transcription factor enrichment analysis integrated with orthogonal omics.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;The gene co-expression network and gene ontology analyses revealed 19 modules identified using the dataset GSE76275. Of these, modules 5, 11, and 12 showed significant differences between in breast cancer tissue between TNBC and non-TNBC. Notably, module 11 showed significant enrichment in the WNT signaling pathway, while module 12 demonstrated enrichment in lipid/fatty acid metabolism pathways. Subsequently, we identified SHC4/KCNK5 and ABCC11/ABCA12 as key genes in module 11 and module 12, respectively. These key genes proved to be crucial in accurately distinguishing between TNBC and non-TNBC, as evidenced by the promising average AUC value of 0.963 obtained from the logistic regression model based on their combinations. Furthermore, we found compelling evidence indicating the prognostic significance of three key genes, KCNK5, ABCC11, and ABCA12, in TNBC. Finally, we also identified the immune cell compositions in breast cancer tissue between","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1505011"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004255","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}

{"title":"Exploring the prognostic significance of lactate-mitochondria-related genes in prostate cancer.","authors":"Yuan Wang, Ronghui Chen, Feng-Le Jiang, Xin Jiang, Yuehong Zhou, Yingying Zhou, Xinyi Hong, Chaoying Lin, Wei-Jia Wang, Sufang Qiu","doi":"10.3389/fgene.2024.1515045","DOIUrl":"10.3389/fgene.2024.1515045","url":null,"abstract":"<p><p>Prostate cancer (PCa) is a common and serious health issue among older men globally. Metabolic reprogramming, particularly involving lactate and mitochondria, plays a key role in PCa progression, but studies linking these factors to prognosis are limited. To identify novel prognostic markers of PCa based on lactate-mitochondria-related genes (LMRGs), RNA sequencing data and clinical information of PCa from The Cancer Genome Atlas (TCGA) and the cBioPortal database were used to construct a lactate-mitochondria-related risk signature. Here, we established a novel nine-LMRG risk signature for PCa, and Kaplan-Meier curves confirmed a worse prognosis for high-risk subgroups in the TCGA dataset. Meanwhile, a nomogram that effectively predicts the prognosis of PCa patients was also constructed. Next, close associations between the lactate-mitochondria-related signature and the immune microenvironment were examined to clarify the role of LMRGs in shaping the immune landscape. Furthermore, as the only lactate-related gene among the nine key prognostic risk genes, myeloperoxidase (MPO) was identified as a key factor that mediates lactate production <i>in vitro</i> and <i>in vivo</i> through attenuation of the glycolytic pathway. More importantly, MPO significantly inhibited PCa cell migration, invasion, and epithelial-mesenchymal transition (EMT), indicating its potential as an anticancer gene. Additionally, PCa with high MPO expression is highly sensitive to chemotherapeutic agents and mitochondrial inhibitors, highlighting its potential as an improved therapeutic strategy for PCa management.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1515045"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003611","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}

{"title":"Marfan syndrome: insights from animal models.","authors":"Yuanyuan Jiang, Ping Jia, Xiaoying Feng, Dingding Zhang","doi":"10.3389/fgene.2024.1463318","DOIUrl":"10.3389/fgene.2024.1463318","url":null,"abstract":"<p><p>Marfan syndrome (MFS) is an inherited disorder that affects the connective tissues and mainly presents in the bones, eyes, and cardiovascular system, etc. Aortic pathology is the leading cause of death in patients with Marfan syndrome. The fibrillin-1 gene (<i>FBN1</i>) is a major gene involved in the pathogenesis of MFS. It has been shown that the aortic pathogenesis of MFS is associated with the imbalances of the transforming growth factor-beta (TGF-β) signaling pathway. However, the exact molecular mechanism of MFS is unclear. Animal models may partially mimic MFS and are vital to the study of MFS. Several species of animals have been used for MFS studies, including chicks, cattle, mice, pigs, zebrafishes, <i>Caenorhabditis elegans</i>, and rabbits. These models were developed spontaneously or in combination with genetic engineering techniques. This review is to describe the TGF-β signaling pathway in MFS and the potential application of animal models to provide new therapeutic strategies for patients with MFS.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1463318"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004200","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}

{"title":"TransferBAN-Syn: a transfer learning-based algorithm for predicting synergistic drug combinations against echinococcosis.","authors":"Haitao Li, Yuanyuan Chu, Liyuan Jiang, Lei Li, GuoDong Lv, Yuansheng Liu, Chunhou Zheng, Yansen Su","doi":"10.3389/fgene.2024.1465368","DOIUrl":"10.3389/fgene.2024.1465368","url":null,"abstract":"<p><p>Echinococcosis is a zoonotic parasitic disease caused by the larvae of echinococcus tapeworms infesting the human body. Drug combination therapy is highly valued for the treatment of echinococcosis because of its potential to overcome resistance and enhance the response to existing drugs. Traditional methods of identifying drug combinations via biological experimentation is costly and time-consuming. Besides, the scarcity of existing drug combinations for echinococcosis hinders the development of computational methods. In this study, we propose a transfer learning-based model, namely TransferBAN-Syn, to identify synergistic drug combinations against echinococcosis based on abundant information of drug combinations against parasitic diseases. To the best of our knowledge, this is the first work that leverages transfer learning to improve prediction accuracy with limited drug combination data in echinococcosis treatment. Specifically, TransferBAN-Syn contains a drug interaction feature representation module, a disease feature representation module, and a prediction module, where the bilinear attention network is employed in the drug interaction feature representation module to deeply extract the fusion feature of drug combinations. Besides, we construct a special dataset with multi-source information and drug combinations for parasitic diseases, including 21 parasitic diseases and echinococcosis. TransferBAN-Syn is designed and initially trained on the abundant data from the 21 parasitic diseases, which serves as the source domain. The parameters in the feature representation modules of drug interactions and diseases are preserved from this source domain, and those in the prediction module are then fine-tuned to specifically identify the synergistic drug combinations for echinococcosis in the target domain. Comparison experiments have shown that TransferBAN-Syn not only improves the accuracy of predicting echinococcosis drug combinations but also enhances generalizability. Furthermore, TransferBAN-Syn identifies potential drug combinations that hold promise in the treatment of echinococcosis. TransferBAN-Syn not only offers new synergistic drug combinations for echinococcosis but also provides a novel approach for predicting potential drug pairs for diseases with limited combination data.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1465368"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004258","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}

{"title":"A genome-wide association study identified candidate regions and genes for commercial traits in a Landrace population.","authors":"Guojian Ma, Xihong Tan, Ying Yan, Tianyang Zhang, Jianhua Wang, Xiaoling Chen, Jingya Xu","doi":"10.3389/fgene.2024.1505197","DOIUrl":"10.3389/fgene.2024.1505197","url":null,"abstract":"<p><p>Backfat thickness (BFT) and feed conversion ratio (FCR) are important commercial traits in the pig industry. With the increasing demand for human health and meat production, identifying functional genomic regions and genes associated with these commercial traits is critical for enhancing production efficiency. In this research, we conducted a genome-wide association study (GWAS) on a Landrace population comprising 4,295 individuals with chip data for BFT and FCR. Our analysis revealed a total of 118 genome-wide significant signals located on chromosomes SSC1, SSC2, SSC7, SSC12, and SSC13, respectively. Furthermore, we identified 10 potential regions associated with the two traits and annotated the genes within these regions. In addition, enrichment analysis was also performed. Notably, candidate genes such as <i>SHANK2</i>, <i>KCNQ1</i>, and <i>ABL1</i> were found to be associated with BFT, whereas <i>NAP1L4</i>, <i>LSP1</i>, and <i>PPFIA1</i> genes were related to the FCR. Our findings provide valuable insights into the genetic architecture of these two traits and offer guidance for future pig breeding efforts.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1505197"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004401","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}

{"title":"S-DCNN: prediction of ATP binding residues by deep convolutional neural network based on SMOTE.","authors":"Sixi Hao, Cai-Yan Li, Xiuzhen Hu, Zhenxing Feng, Gaimei Zhang, Caiyun Yang, Huimin Hu","doi":"10.3389/fgene.2024.1513201","DOIUrl":"10.3389/fgene.2024.1513201","url":null,"abstract":"<p><strong>Background: </strong>The realization of many protein functions requires binding with ligands. As a significant protein-binding ligand, ATP plays a crucial role in various biological processes. Currently, the precise prediction of ATP binding residues remains challenging.</p><p><strong>Methods: </strong>Based on the sequence information, this paper introduces a method called S-DCNN for predicting ATP binding residues, utilizing a deep convolutional neural network (DCNN) enhanced with the synthetic minority over-sampling technique (SMOTE).</p><p><strong>Results: </strong>The incorporation of additional feature parameters such as dihedral angles, energy, and propensity factors into the standard parameter set resulted in a significant enhancement in prediction accuracy on the ATP-289 dataset. The S-DCNN achieved the highest Matthews correlation coefficient value of 0.5031 and an accuracy rate of 97.06% on an independent test set. Furthermore, when applied to the ATP-221 and ATP-388 datasets for validation, the S-DCNN outperformed existing methods on ATP-221 and performed comparably to other methods on ATP-388 during independent testing.</p><p><strong>Conclusion: </strong>Our experimental results underscore the efficacy of the S-DCNN in accurately predicting ATP binding residues, establishing it as a potent tool in the prediction of ATP binding residues.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1513201"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004253","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}

{"title":"Differential regulation of apoptosis-related genes during long-term culture and differentiation of canine adipose-derived stem cells - a functional bioinformatical analysis.","authors":"Maurycy Jankowski, Katarzyna Stefańska, Michał Suchodolski, Claudia Dompe, Grzegorz Wąsiatycz, Bartosz Kempisty, Michał Nowicki, Magdalena Roszak","doi":"10.3389/fgene.2024.1515778","DOIUrl":"10.3389/fgene.2024.1515778","url":null,"abstract":"<p><strong>Introduction: </strong>Stem cells derived from adipose tissue are gaining popularity in the field of regenerative medicine due to their adaptability and clinical potential. Their rapid growth, ability to differentiate, and easy extraction with minimal complications make adipose-derived stem cells (ADSCs) a promising option for many treatments, particularly those targeting bone-related diseases. This study analyzed gene expression in canine ADSCs subjected to long-term culture and osteogenic differentiation.</p><p><strong>Methods: </strong>ADSCs were isolated from discarded surgical waste and cultured for 14 days with and without differentiation media to assess osteogenic changes. RNA sequencing (RNA-seq) and bioinformatical analysis were performed to obtain comprehensive transcriptomic data. A total of 17793 genes were detected and GO enrichment analysis was performed on the differentially expressed genes to identify significantly up- and downregulated Biological Process (BP) GO terms across each comparison.</p><p><strong>Results: </strong>The upregulation of apoptosis-regulating genes and genes related to circulatory system development suggest an induction of these processes, while the downregulation of neurogenesis and gliogenesis genes points to reciprocal regulation during osteogenic differentiation of canine ADSCs.</p><p><strong>Discussion: </strong>These findings underscore the potential of ADSCs in bone regeneration and offer valuable insights for advancing tissue engineering, however further studies, including proteomic analyses, are needed to confirm these patterns and their biological significance.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1515778"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743971/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004438","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}