Genomics最新文献_第6页

Integrated analyses provide insights into the seed dormancy mechanisms of the endangered plant Sinojackia sarcocarpa 综合分析有助于深入了解濒危植物荆芥种子休眠机制。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-21 DOI: 10.1016/j.ygeno.2025.110991

Yao Yang, Tingting Feng, Xianzhe Zheng, Huifang Zheng, Hao Tang, Xiaobo Yu

{"title":"Integrated analyses provide insights into the seed dormancy mechanisms of the endangered plant Sinojackia sarcocarpa","authors":"Yao Yang, Tingting Feng, Xianzhe Zheng, Huifang Zheng, Hao Tang, Xiaobo Yu","doi":"10.1016/j.ygeno.2025.110991","DOIUrl":"10.1016/j.ygeno.2025.110991","url":null,"abstract":"<div><div><em>Sinojackia sarcocarpa</em>, an endangered ornamental plant endemic to China, faces germination challenges that contribute to its endangered status. The mechanisms of its seed dormancy are not well understood. This study used morphological, physiological, transcriptomic, and gene function analyses to investigate these mechanisms. Our research shows that seed dormancy in <em>Sinojackia sarcocarpa</em> involves both physical and physiological factors. We found that removing the hard endocarp and applying gibberellic acid can effectively break dormancy. Transcriptomic analysis identified 2218 up-regulated and 374 down-regulated genes during germination. Notably, DOG1-domain genes <em>SsDOGL4</em>, <em>SsTGA9</em>, and <em>SsTGA10</em> were significantly downregulated, while <em>SsDOG1</em> was not. Additionally, overexpression of <em>SsDOGL4</em> in <em>Arabidopsis</em> endosperm was found to enhance seed dormancy. Collectively, these findings offer significant insights into the mechanisms underlying seed dormancy in this endangered plant species.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110991"},"PeriodicalIF":3.4,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 serum small non-coding RNA as biomarkers for endometrial receptivity 血清小分子非编码RNA作为子宫内膜容受性生物标志物的鉴定。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-21 DOI: 10.1016/j.ygeno.2025.111002

Shaoyuan Xu , Dongling Hu , Yanqin Ye , Yanli Mu , Yao Xiong , Yuanzhen Zhang

{"title":"Identification of serum small non-coding RNA as biomarkers for endometrial receptivity","authors":"Shaoyuan Xu , Dongling Hu , Yanqin Ye , Yanli Mu , Yao Xiong , Yuanzhen Zhang","doi":"10.1016/j.ygeno.2025.111002","DOIUrl":"10.1016/j.ygeno.2025.111002","url":null,"abstract":"<div><h3>Background</h3><div>Current endometrial receptivity analysis is invasive, preventing embryo transfer during the biopsy cycle. This study aims to screen serum sncRNAs as non-invasive biomarkers for ERA tests.</div></div><div><h3>Methods</h3><div>The study included 12 infertile patients undergoing IVF-ET and ERA, whose serum samples were collected for high-energy sequencing technology to detect sncRNA expression profiles. We overexpressed and knocked down tsRNA-35:73-Asp-GTC-1 in the decidualized Immortalized Human Eutopic Endometrial Stromal Cells (HESC) model cultured in vitro to further investigate the its effect on decidualization. The predicted tsRNA-35:73-Asp-GTC-1 target gene was verified by PCR analysis.</div></div><div><h3>Results</h3><div>We screened 286 differentially expressed tsRNAs, 46 miRNAs, and 106 piRNAs. KEGG analysis indicated that differentially expressed tsRNAs were associated with pathways such as ‘Calcium signaling pathway,’ ‘Sphingolipid signaling pathway,’ etc. The results of RT-qPCR validation showed that the trends of four significantly differentially expressed tsRNAs in serum and endometrium were consistent with sequencing results. ROC curves demonstrated that these four tsRNAs have good predictive value for endometrial receptivity. Overexpression of tsRNA-35:73-Asp-GTC-1 affected the morphology of decidualized cells, and the decidualization indicators also showed a decreasing trend. While knocking down tsRNA-35:73-Asp-GTC-1 had the opposite effect. The RT-qPCR results showed that tsRNA-35:73-Asp-GTC-1 was associated with the Wnt3 target gene.</div></div><div><h3>Conclusion</h3><div>Serum sncRNA analysis shows potential for studying the molecular mechanisms of endometrial receptivity. Four serum tsRNAs can serve as novel biomarkers for non-invasive endometrial receptivity detection. TsRNA-35:73-Asp-GTC-1 may further regulate endometrial receptivity by targeting Wnt3.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111002"},"PeriodicalIF":3.4,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Genome-wide DNA methylation analysis of sorghum leaves following foreign GA3 exposure under salt stress 盐胁迫下外源GA3暴露后高粱叶片全基因组DNA甲基化分析

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-20 DOI: 10.1016/j.ygeno.2025.111000

Yanqing Wu , Jiao Liu , Lu Zhao , Guisheng Zhou , Yuhan Tang

{"title":"Genome-wide DNA methylation analysis of sorghum leaves following foreign GA3 exposure under salt stress","authors":"Yanqing Wu , Jiao Liu , Lu Zhao , Guisheng Zhou , Yuhan Tang","doi":"10.1016/j.ygeno.2025.111000","DOIUrl":"10.1016/j.ygeno.2025.111000","url":null,"abstract":"<div><div>Sorghum is an increasingly popular topic of research in elucidating survival and adaptation approaches to augmented salinity. Nonetheless, little is known about the outcome and modulatory networks involved in the gibberellic acid (GA3)-induced salt stress alleviation in sorghum. Here, we identified 50 mg/L GA3 as the optimal concentration for sorghum (‘Jitian 3’) development under salt stress. Based on genome-wide DNA methylation analysis, CpG sites displayed the most abundant methylation statuses among all stages, with a mean value of 68.2 %, then CHG (57.9 %), and CHH (21.2 %). We identified 18,032 differentially methylated regions (DMRs) in the GA3-exposed groups. In particular, we recognized 5943 DMR genes and 269 DMR-promoter genes. Using conjoint transcriptome and DNA methylation analyses, we identified 337 important methylated-genes, which were involved in “phenylpropanoid biosynthesis”, “arginine and proline metabolism” and “tyrosine metabolism”. Together, the aforementioned data provides an in-depth understanding of the epigenetic modulation of gene expression during GA3 treatment.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111000"},"PeriodicalIF":3.4,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143022948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells WDR26缺失改变了哺乳动物细胞的染色质可及性和基因表达谱。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-19 DOI: 10.1016/j.ygeno.2025.111001

Gabriel Onea , Alireza Ghahramani , Xu Wang , Haider M. Hassan , Nathalie G. Bérubé , Caroline Schild-Poulter

{"title":"WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells","authors":"Gabriel Onea , Alireza Ghahramani , Xu Wang , Haider M. Hassan , Nathalie G. Bérubé , Caroline Schild-Poulter","doi":"10.1016/j.ygeno.2025.111001","DOIUrl":"10.1016/j.ygeno.2025.111001","url":null,"abstract":"<div><div>WD-repeat containing protein 26 (WDR26) is an essential component of the CTLH E3 ligase complex. Mutations in <em>WDR26</em> lead to Skraban-Deardorff, an intellectual disability syndrome with clinical features resembling other disorders arising from defects in transcriptional regulation and chromatin structure. However, the role of WDR26 and its associated CTLH complex in regulating chromatin or transcription has not been elucidated. Here, we assessed how loss of WDR26 affects chromatin accessibility and gene expression. Transcriptome analysis of WDR26 knockout HeLa cells revealed over 2000 differentially expressed genes, while ATAC-Seq analysis showed over 32,000 differentially accessible chromatin regions, the majority mapping to intergenic and intronic regions and 13 % mapping to promoters. Above all, we found that WDR26 loss affected expression of genes regulated by AP-1 and NF-1 transcription factors and resulted in dramatic changes in their chromatin accessibility. Overall, our analyses implicate WDR26 and the CTLH complex in chromatin regulation.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111001"},"PeriodicalIF":3.4,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Huc-MSC-derived exosomes alleviates alcohol-induced osteonecrosis of the femoral head through targeting the miR-25-3p/GREM1 axis huc - msc衍生的外泌体通过靶向miR-25-3p/GREM1轴减轻酒精诱导的股骨头骨坏死。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-16 DOI: 10.1016/j.ygeno.2025.110996

Zhifang Tang , Xiaoyan Xu , Wei Shi , Xianzhen Ren , Huan Luo , Yongqing Xu , Chuan Li

{"title":"Huc-MSC-derived exosomes alleviates alcohol-induced osteonecrosis of the femoral head through targeting the miR-25-3p/GREM1 axis","authors":"Zhifang Tang , Xiaoyan Xu , Wei Shi , Xianzhen Ren , Huan Luo , Yongqing Xu , Chuan Li","doi":"10.1016/j.ygeno.2025.110996","DOIUrl":"10.1016/j.ygeno.2025.110996","url":null,"abstract":"<div><div>Osteonecrosis of the femoral head (ONFH) is a destructive bone disease, and overuse of alcohol is one of the major contributing factors. Although mesenchymal stem cells (MSCs) and their exosomes have been reported to attenuate ONFH, the potential mechanisms of alcohol-induced ONFH (AONFH) are unclear. Here, we isolated and identified human umbilical cord MSCs-derived exosomal (hucMSCs-exos) miR-25-3p. We observed that hucMSCs-exos transferred miR-25-3p into bone marrow stem cells (BMSCs). HucMSCs-exos miR-25-3p increased cell viability, osteogenic differentiation, and inhibited apoptosis of alcohol-treated BMSCs and AONFH rat model. Mechanically, hucMSCs-exos upregulated miR-25-3p expression in BMSCs by repressing miR-25-3p DNA methylation, and DNA methylation inhibitor 5-Aza-2-deoxycytidine (DAC) ameliorated AONFH. Besides, miR-25-3p suppressed gremlin 1 (GREM1) expression, and upregulation of GREM1 restored the inhibition of hucMSCs-exos on AONFH. Therefore, we determined that hucMSCs-exos miR-25-3p alleviated AONFH by inhibiting miR-25-3p DNA methylation and GREM1 expression, which may help identify novel biomarkers, diagnostic and therapeutic targets.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110996"},"PeriodicalIF":3.4,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

scRNA-seq reveals involvement of monocytes in immune response in SLE patients scRNA-seq揭示单核细胞参与SLE患者的免疫应答。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-14 DOI: 10.1016/j.ygeno.2025.110994

Guoying Wang , Huihui Tao , Lingling Zhou , Junning Zhang , Wenjun Pu , Tiantian Xu , Chunmei Wen , Yali Peng , Mengyao Wu , Xuejia Zheng , Yong Dai

{"title":"scRNA-seq reveals involvement of monocytes in immune response in SLE patients","authors":"Guoying Wang , Huihui Tao , Lingling Zhou , Junning Zhang , Wenjun Pu , Tiantian Xu , Chunmei Wen , Yali Peng , Mengyao Wu , Xuejia Zheng , Yong Dai","doi":"10.1016/j.ygeno.2025.110994","DOIUrl":"10.1016/j.ygeno.2025.110994","url":null,"abstract":"<div><h3>Background</h3><div>Systemic Lupus Erythematosus (SLE) is a typical autoimmune disease characterized by a complex pathogenesis and a strong genetic predisposition. The study of inflammatory response in SLE monocytes is not very clear, and exploring the inflammatory factors of monocytes is beneficial to discover new diagnostic targets.</div></div><div><h3>Results</h3><div>Using scRNA-seq technology, we obtained the quantitative changes in circulating immune cells and various cellular immune metabolic profiles between SLE patients and healthy volunteers. A significant increase in monocytes was observed in peripheral blood of SLE patients. Flow cytometry was employed to validate the types and quantities of circulating immune cells in SLE, corroborating the scRNA-seq results. Monocyte highly expressed IRF1 (interferon regulatory factor 1) in SLE. Previous research proves that IRF1 is widely involved in immune regulation and inflammatory response, and can promote the transcription of a variety of pro-inflammatory cytokines. Additionally, Inflammatory factors secreted by monocytes in serum were measured. The results demonstrated a significant upregulation of IFN-γ, TNF-α, IL-2, IL-6, IL-8, IL-10, IL-1β in the sera of SLE patients compared to healthy controls.</div></div><div><h3>Conclusion</h3><div>Our results demonstrate upregulation of monocyte inflammation in circulating immune cells in SLE patients and expands the current understanding of circulating immune cells in SLE.</div><div>Our study provides a blueprint for future exploration of SLE monocytes, revealing the pathogenesis and inventing new immunotherapies.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110994"},"PeriodicalIF":3.4,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets 母体日粮纤维含量的差异影响胎儿和仔猪基因表达模式和染色质可及性。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-13 DOI: 10.1016/j.ygeno.2025.110995

Smahane Chalabi , Linda Loonen , Jos Boekhorst , Houcheng Li , Lingzhao Fang , Peter W. Harrison , Wassim Lakhal , Jerome Lluch , Alexey Sokolov , Sarah Djebali , Andrea Rau , Elisabetta Giuffra , Jerry Wells

{"title":"Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets","authors":"Smahane Chalabi , Linda Loonen , Jos Boekhorst , Houcheng Li , Lingzhao Fang , Peter W. Harrison , Wassim Lakhal , Jerome Lluch , Alexey Sokolov , Sarah Djebali , Andrea Rau , Elisabetta Giuffra , Jerry Wells","doi":"10.1016/j.ygeno.2025.110995","DOIUrl":"10.1016/j.ygeno.2025.110995","url":null,"abstract":"<div><div>This study investigates the impact of maternal gestation diets with varying fiber contents on gene expression and chromatin accessibility in fetuses and piglets fed a low fiber diet post weaning. High-fiber maternal diets, enriched with sugar beet pulp or pea internal fiber, were compared to a low-fiber maternal diet to evaluate their effects on liver and muscle tissues. The findings demonstrate that maternal high-fiber diets significantly alter chromatin accessibility, predicted transcription factor activity and transcriptional landscape in both fetuses and piglets. A gene set enrichment analysis revealed over-expression of gene ontology terms related to metabolic processes and under-expression of those linked to immune responses in piglets from sows given the high-fiber diets during gestation. This suggests better metabolic health and immune tolerance of the fetus and offspring, in line with the documented epigenetic effects of short chain fatty acids on immune and metabolic pathways. A deconvolution analysis of the bulk RNA-seq data was performed using cell-type specific markers from a single cell transcriptome atlas of adult pigs. These results confirmed that the transcriptomic and chromatin accessibility data do not reflect different cell type compositions between maternal diet groups but rather phenotypic changes triggered by maternal nutrition in shaping the epigenetic and transcriptional environment of fetus and offspring. Our findings have implications for improving animal health and productivity as well as broader implications for human health, suggesting that optimizing maternal diet with high-fiber content could enhance metabolic health and immune function in the formative years after birth and potentially to adulthood.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110995"},"PeriodicalIF":3.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Decoding gene expression dynamics during seed development in sesame (Sesamum indicum L.) through RNA-Seq analysis 通过RNA-Seq分析解码芝麻种子发育过程中的基因表达动态。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-12 DOI: 10.1016/j.ygeno.2025.110997

Bantayehu Bekele , Mebeaselassie Andargie , Miguel Gallach , Dereje Beyene , Kassahun Tesfaye

{"title":"Decoding gene expression dynamics during seed development in sesame (Sesamum indicum L.) through RNA-Seq analysis","authors":"Bantayehu Bekele , Mebeaselassie Andargie , Miguel Gallach , Dereje Beyene , Kassahun Tesfaye","doi":"10.1016/j.ygeno.2025.110997","DOIUrl":"10.1016/j.ygeno.2025.110997","url":null,"abstract":"<div><div>Sesame (<em>Sesamum indicum</em> L., 2n = 2× = 26) from the Pedaliaceae family is primarily grown for its high oil content, rich in unsaturated fatty acids like linoleic acid (LA) and alpha-linolenic acid (ALA). However, the molecular mechanisms of sesame oil accumulation remain poorly understood. This study analyzed transcriptomes at two seed development stages: Young Stage (YS, pods 1.5–2.5 cm) and Mature Stage (MS, brown pods >2.5 cm), to explore regulatory mechanisms and identify key genes involved in lipid biosynthesis.</div><div>From 25,173 genes, 18,820 with expression values >10 CPM in at least 70 % of replicates were included in differential expression (DE) analysis. Active expression (LFC > 0) was observed in 9372 and 9448 genes at YS and MS, respectively. DEGs were annotated, revealing roles in various biological processes, (e.g., mRNA metabolic process, reproduction-related developmental processes, seed development), molecular functions (e.g., aminoacyltransferase activity, ubiquitin-like protein and ubiquitin-protein transferase activities), and cellular components (e.g., peroxisome, microbody, lipid droplet).</div><div>KEGG analysis highlighted genes involved in fatty acid synthesis (e.g., <em>fabG</em>, <em>fabZ</em>), TAG biosynthesis (<em>DGAT1</em>, <em>GPAT</em>), and alpha-linolenic acid metabolism (<em>AOS</em>, <em>LCAT3</em>). Key genes upregulated at MS included <em>SIN_1025205</em> (protein transport), <em>SIN_1006853</em> (acetylajmalan esterase), and <em>SIN_1003267</em> (gamma-cadinene synthase). The study generated a valuable transcriptome dataset and gene list for seed development and lipid biosynthesis, which will be validated through functional studies. An interactive webpage is provided for data exploration.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110997"},"PeriodicalIF":3.4,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Further insights into the molecular mechanisms underlying tobacco straw cultivation of Pleurotus ostreatus by comparative transcriptome analyses 通过比较转录组分析进一步了解平菇烟草秸秆栽培的分子机制。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-10 DOI: 10.1016/j.ygeno.2025.110992

Xinran Li, Liu Luo, Xuying Wang , Miao Zhu

{"title":"Further insights into the molecular mechanisms underlying tobacco straw cultivation of Pleurotus ostreatus by comparative transcriptome analyses","authors":"Xinran Li, Liu Luo, Xuying Wang , Miao Zhu","doi":"10.1016/j.ygeno.2025.110992","DOIUrl":"10.1016/j.ygeno.2025.110992","url":null,"abstract":"<div><div>Cultivation of edible mushrooms on straw can significantly reduce production costs, provide notable environmental and ecological benefits. However, the molecular mechanisms via which mushrooms utilize straw are not well understood. We conducted a comparative transcriptomic analysis of oyster mushrooms cultivated on two different biomass substrates, namely, corncob and tobacco straw at various developmental stages. The results revealed that the biomass substrates induced distinct transcriptomic changes during mycelium and fruiting body development. Straw affected the metabolism of pyruvate and acetyl-CoA, with significant downregulation of pyruvate decarboxylase expression, and upregulation of acetyl-CoA hydrolase during mycelial growth. Genes associated with cell wall and carbohydrate metabolism were significantly upregulated, and the PLD-PA-mTOR pathway was activated during the fruiting body development stage in mushrooms grown on straw. These findings reveal the transcriptomic adaptations of oyster mushrooms to tobacco straw, and enhance our understanding of the molecular mechanisms underlying biomass conversion by edible fungi using straw.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110992"},"PeriodicalIF":3.4,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 aberrant plasma vesicles containing AAK1 and CCDC18-AS1 in adolescents with major depressive disorder and preliminary exploration of treatment efficacy 青少年重度抑郁障碍中含有AAK1和CCDC18-AS1的异常血浆囊泡的鉴定及治疗效果的初步探讨

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-09 DOI: 10.1016/j.ygeno.2025.110993

Yifan Xu , Rong Zhang , Xinzhe Du , Yangxi Huang , Yao Gao , Yujiao Wen , Dan Qiao , Ning Sun , Zhifen Liu

{"title":"Identification of aberrant plasma vesicles containing AAK1 and CCDC18-AS1 in adolescents with major depressive disorder and preliminary exploration of treatment efficacy","authors":"Yifan Xu , Rong Zhang , Xinzhe Du , Yangxi Huang , Yao Gao , Yujiao Wen , Dan Qiao , Ning Sun , Zhifen Liu","doi":"10.1016/j.ygeno.2025.110993","DOIUrl":"10.1016/j.ygeno.2025.110993","url":null,"abstract":"<div><h3>Background</h3><div>Major depressive disorder (MDD) during adolescence significantly jeopardizes both mental and physical health. However, the etiology underlying MDD in adolescents remains unclear.</div></div><div><h3>Methods</h3><div>A total of 74 adolescents with MDD and 40 health controls (HCs) who underwent comprehensive clinical and cognitive assessments were enrolled. Differential expression analysis was conducted on plasma extracellular vesicles (EVs) carrying long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) by microarray analysis. Two possible lncRNA-miR-mRNA networks were established and candidate regulatory axes were generated using the StarBase, miRDB, and TargetScan bioinformatics databases. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the candidate molecules and signaling axes in a clinical cohort.</div></div><div><h3>Results</h3><div>A total of 3752 dysregulated lncRNAs and 1789 dysfunctional mRNAs were identified. Two candidate regulatory axes (AC156455.1/miR-126-5p/AAK1 and CCDC18-AS1/miR-6835-5p/CCND2) with potential connections with MDD were selected. The candidate molecules exhibit differential expression patterns among adolescents with MDD and HCs, as well as before and after treatment with sertraline in adolescents with MDD. Furthermore, AAK1, CCDC18-AS1, and miR-6835-5p expressions exhibited significant differences between the response and non-response groups. Baseline expression of CCDC18-AS1, miR-6835-5p, and CCND2 could predict the therapeutic effect of sertraline, which may be associated with reducing suicidal ideation and improving cognitive function.</div></div><div><h3>Conclusion</h3><div>Our study may provide insights into the understanding of the underlying pathological mechanisms in adolescents with MDD.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110993"},"PeriodicalIF":3.4,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142969795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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