Functional & Integrative Genomics最新文献_第5页

Correction to: QTL-seq identifies genomic region associated with the crown root development under Jasmonic acid response Correction to：QTL-seq鉴定了茉莉酸反应下与冠根发育相关的基因组区域。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-10-02 DOI: 10.1007/s10142-024-01461-5

Tam Thi Thanh Tran, Liem Huu Minh Le, Trang Thi Nguyen, Thanh Chi Nguyen, Trang Thi Huyen Hoang, Phat Tien Do, Huong Thi Mai To

引用次数: 0

The role of lipoprotein‑associated phospholipase A2 in inflammatory response and macrophage infiltration in sepsis and the regulatory mechanisms 脂蛋白相关磷脂酶 A2 在败血症炎症反应和巨噬细胞浸润中的作用及其调控机制。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-30 DOI: 10.1007/s10142-024-01460-6

Li Jin, Mengxiao Jiang, Jun Qian, Zhihua Ge, Feng Xu, Wenjie Liao

{"title":"The role of lipoprotein‑associated phospholipase A2 in inflammatory response and macrophage infiltration in sepsis and the regulatory mechanisms","authors":"Li Jin, Mengxiao Jiang, Jun Qian, Zhihua Ge, Feng Xu, Wenjie Liao","doi":"10.1007/s10142-024-01460-6","DOIUrl":"10.1007/s10142-024-01460-6","url":null,"abstract":"<div><p>Lipoproteinassociated phospholipase A2 (Lp-PLA2), encoded by the phospholipase A2 group VII (<i>Pla2g7</i>) gene, has been pertinent to inflammatory responses. This study investigates the correlation between Lp-PLA2 and inflammatory injury in septic mice and explores its regulatory mechanism. Lp-PLA2 was found to be upregulated in the serum of septic mice induced by cecal ligation and puncture and in the culture supernatant of RAW264.7 cells following lipopolysaccharide and adenosine triphosphate treatments. The contents of Lp-PLA2 were positively correlated with increased concentrations of proinflammatory cytokines in patients with sepsis. Both animal and cellular models showed increased concentrations of proinflammatory cytokines. Spi-1 proto-oncogene (<i>Spi1</i>), highly expressed in these models, was found to activate <i>Pla2g7</i> transcription. Knockdown of <i>Pla2g7</i> or <i>Spi1</i> reduced the proinflammatory cytokine production, mitigated organ damage in mice, and suppressed macrophage migration in vitro. Retinoblastoma binding protein 6 (<i>Rbbp6</i>), poorly expressed in both models, was found to reduce Spi1 protein stability through ubiquitination modification. <i>Rbbp6</i> overexpression similarly suppressed inflammatory activation of RAW264.7 cells, which was counteracted by <i>Pla2g7</i> or <i>Spi1</i> upregulation. In summary, this study demonstrates that the <i>Pla2g7</i> loss and <i>Spi1</i> upregulation participate in inflammatory responses in sepsis by elevating the Lp-PLA2 levels.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the potential of nanomedicine for gene therapy across the physicochemical and cellular barriers 跨越物理化学和细胞障碍，探索纳米药物用于基因治疗的潜力。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-28 DOI: 10.1007/s10142-024-01459-z

Huma Hameed, Hafiz Shoaib Sarwar, Komel Younas, Muhammad Zaman, Muhammad Jamshaid, Ali Irfan, Maha Khalid, Muhammad Farhan Sohail

{"title":"Exploring the potential of nanomedicine for gene therapy across the physicochemical and cellular barriers","authors":"Huma Hameed, Hafiz Shoaib Sarwar, Komel Younas, Muhammad Zaman, Muhammad Jamshaid, Ali Irfan, Maha Khalid, Muhammad Farhan Sohail","doi":"10.1007/s10142-024-01459-z","DOIUrl":"10.1007/s10142-024-01459-z","url":null,"abstract":"<div><p>After COVID-19, a turning point in the way of pharmaceutical technology is gene therapy with beneficial potential to start a new medical era. However, commercialization of such pharmaceuticals would never be possible without the help of nanotechnology. Nanomedicine can fulfill the growing needs linked to safety, efficiency, and site-specific targeted delivery of Gene therapy-based pharmaceuticals. This review's goal is to investigate how nanomedicine may be used to transfer nucleic acids by getting beyond cellular and physicochemical barriers. Firstly, we provide a full description of types of gene therapy, their mechanism, translation, transcription, expression, type, and details of diseases with possible mechanisms that can only be treated with genes-based pharmaceuticals. Additionally, we also reviewed different types of physicochemical barriers, physiological and cellular barriers in nucleic acids (DNA/RNA) based drug delivery. Finally, we highlight the need and importance of cationic lipid-based nanomedicine/nanocarriers in gene-linked drug delivery and how nanotechnology can help to overcome the above-discussed barrier in gene therapy and their biomedical applications.</p><h3>Graphical abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Epigenetic gene silencing in plants: Insights from triplet repeat expansion in Arabidopsis 植物的表观遗传基因沉默：拟南芥三重重复扩增的启示

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-28 DOI: 10.1007/s10142-024-01463-3

Jieni Gu, Iqra Noor, Xiaodong Yang, Hamza Sohail

引用次数: 0

LncRNAs orchestration of gastric cancer - particular emphasis on the etiology, diagnosis, and treatment resistance LncRNAs 与胃癌的关系--特别强调病因、诊断和耐药性。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-26 DOI: 10.1007/s10142-024-01450-8

Hanan Elimam, Rewan Moussa, Abdullah F. Radwan, Abdulrahman Hatawsh, Nourhan Elfar, Nora A. A. Alhamshry, Mai A. Abd-Elmawla, Nora M. Aborehab, Mohamed Bakr Zaki, Sherif S. Abdel Mageed, Osama A. Mohammed, Mustafa Ahmed Abdel-Reheim, Ahmed S. Doghish

{"title":"LncRNAs orchestration of gastric cancer - particular emphasis on the etiology, diagnosis, and treatment resistance","authors":"Hanan Elimam, Rewan Moussa, Abdullah F. Radwan, Abdulrahman Hatawsh, Nourhan Elfar, Nora A. A. Alhamshry, Mai A. Abd-Elmawla, Nora M. Aborehab, Mohamed Bakr Zaki, Sherif S. Abdel Mageed, Osama A. Mohammed, Mustafa Ahmed Abdel-Reheim, Ahmed S. Doghish","doi":"10.1007/s10142-024-01450-8","DOIUrl":"10.1007/s10142-024-01450-8","url":null,"abstract":"<div><p>Gastric cancer (GC) remains a major public health challenge worldwide. Long non-coding RNAs (lncRNAs) play important roles in the development, progression, and resistance to the treatment of GC, as shown by recent developments in molecular characterization. Still, an in-depth investigation of the lncRNA landscape in GC is absent. However, The objective of this systematic review is to evaluate our present understanding of the role that lncRNA dysregulation plays in the etiology of GC and treatment resistance, with a focus on the underlying mechanisms and clinical implications. Research that described the functions of lncRNA in angiogenesis, stemness, epigenetics, metastasis, apoptosis, development, and resistance to key treatments was given priority. In GC, it has been discovered that a large number of lncRNAs, including MALAT1, HOTAIR, H19, and ANRIL, are aberrantly expressed and are connected with disease-related outcomes. Through various methods such as chromatin remodeling, signal transduction pathways, and microRNA sponging, they modulate hallmark cancer capabilities. Through the activation of stemness programs, epithelial-mesenchymal transition (EMT), and survival signaling, LncRNAs also control resistance to immunotherapy, chemotherapy, and targeted therapies. By clarifying their molecular roles further, we may be able to identify new treatment targets and ways to overcome resistance. This article aims to explore the interplay between lncRNAs, and GC. Specifically, the focus is on understanding how lncRNAs contribute to the etiology of GC and influence treatment resistance in patients with this disease.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transcription factor YY1 adversely governs ovarian granulosa cell growth in PCOS by transcription activation-mediated CDKN1C upregulation 转录因子 YY1 通过转录激活介导的 CDKN1C 上调，对多囊卵巢综合征的卵巢颗粒细胞生长产生不利影响。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-25 DOI: 10.1007/s10142-024-01448-2

Shitao Dong, Youbin Liu, Zhimin Yang

{"title":"Transcription factor YY1 adversely governs ovarian granulosa cell growth in PCOS by transcription activation-mediated CDKN1C upregulation","authors":"Shitao Dong, Youbin Liu, Zhimin Yang","doi":"10.1007/s10142-024-01448-2","DOIUrl":"10.1007/s10142-024-01448-2","url":null,"abstract":"<div><h3>Background</h3><p>Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disease in women of childbearing age, making it imperative to explore more biomarkers for PCOS. Furthermore, previous studies have reported that cyclin dependent kinase inhibitor 1 C (CDKN1C) might be associated with PCOS progression. However, the molecular mechanism of CDKN1C involved in PCOS is poorly defined.</p><h3>Methods</h3><p>CDKN1C and Yin-Yang-1 (YY1) expression levels were determined using real-time quantitative polymerase chain reaction (RT-qPCR) and Western blot assay. Cell viability, proliferation, cell cycle progression, and cell apoptosis were analyzed using 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT), 5-ethynyl-2’-deoxyuridine (EdU), and flow cytometry assays. Caspase 3 activity was examined using a commercial kit. Binding between YY1 and CDKN1C promoter was predicted by JASPAR and verified using Chromatin immunoprecipitation (ChIP) and dual-luciferase reporter assays.</p><h3>Results</h3><p>CDKN1C and YY1 were highly expressed in PCOS granulosa cells (GCs). Furthermore, CDKN1C silencing could promote cell proliferation and cell cycle process and repress cell apoptosis in human ovarian granulosa cell line KGN cells. For mechanistic analysis, YY1 is directly bound to the promoter of CDKN1C and transcriptional-regulated CDKN1C expression.</p><h3>Conclusion</h3><p>YY1-activated CDKN1C might block KGN cell proliferation and induce cell apoptosis, providing a possible therapeutic target for PCOS treatment.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to: Identification of predictors for neurological outcome after cardiac arrest in peripheral blood mononuclear cells through integrated bioinformatics analysis and machine learning 更正：通过综合生物信息学分析和机器学习，确定外周血单核细胞中心脏骤停后神经功能预后的预测因子。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-25 DOI: 10.1007/s10142-024-01440-w

Zhonghao Li, Ying Qin, Xiaoyu Liu, Jie Chen, Aling Tang, Shengtao Yan, Guoqiang Zhang

引用次数: 0

Hybrid-genome sequence analysis of Enterobacter cloacae FACU and morphological characterization: insights into a highly arsenic-resistant strain 衣腔肠杆菌 FACU 的杂交基因组序列分析和形态特征：对高砷抗性菌株的认识。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-25 DOI: 10.1007/s10142-024-01441-9

Abdelhadi A. Abdelhadi, Nagwa I. Elarabi, Saifeldeen M. Ibrahim, Mostafa A. Abdel-Maksoud, Heba A. R. Abdelhaleem, Saeedah Almutairi, Abdul Malik, Bushra Hafeez Kiani, Ahmed R. Henawy, Asmaa A. Halema

{"title":"Hybrid-genome sequence analysis of Enterobacter cloacae FACU and morphological characterization: insights into a highly arsenic-resistant strain","authors":"Abdelhadi A. Abdelhadi, Nagwa I. Elarabi, Saifeldeen M. Ibrahim, Mostafa A. Abdel-Maksoud, Heba A. R. Abdelhaleem, Saeedah Almutairi, Abdul Malik, Bushra Hafeez Kiani, Ahmed R. Henawy, Asmaa A. Halema","doi":"10.1007/s10142-024-01441-9","DOIUrl":"10.1007/s10142-024-01441-9","url":null,"abstract":"<div><p>Many organisms have adapted to survive in environments with high levels of arsenic (As), a naturally occurring metalloid with various oxidation states and a common element in human activities. These organisms employ diverse mechanisms to resist the harmful effects of arsenic compounds. Ten arsenic-resistant bacteria were isolated from contaminated wastewater in this study. The most efficient bacterial isolate able to resist 15,000 ppm Na<sub>2</sub>HAsO<sub>4</sub>·7H<sub>2</sub>O was identified using the <i>16S rRNA</i> gene and whole genome analysis as <i>Enterobacter cloacae</i> FACU. The arsenic <i>E. cloacae</i> FACU biosorption capability was analyzed. To further unravel the genetic determinants of As stress resistance, the whole genome sequence of <i>E. cloacae</i> FACU was performed. The FACU complete genome sequence consists of one chromosome (5.7 Mb) and two plasmids, pENCL 1 and pENCL 2 (755,058 and 1155666 bp, respectively). 7152 CDSs were identified in the <i>E. cloacae</i> FACU genome. The genome consists of 130 genes for tRNA and 21 for rRNAs. The average G + C content was found to be 54%. Sequencing analysis annotated 58 genes related to resistance to many heavy metals, including 16 genes involved in arsenic efflux transporter and arsenic reduction (five <i>arsRDABC</i> genes) and 42 genes related to lead, zinc, mercury, nickel, silver, copper, cadmium and chromium in FACU. Scanning electron microscopy (SEM) confirmed the difference between the morphological responses of the As-treated FACU compared to the control strain. The study highlights the genes involved in the mechanism of As stress resistance, metabolic pathways, and potential activity of <i>E. cloacae</i> FACU at the genetic level.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

m6A methylation in myocardial tissue of septic mice analyzed using MeRIP/m6A-sequencing and RNA-sequencing 使用 MeRIP/m6A 测序和 RNA 测序分析脓毒症小鼠心肌组织中的 m6A 甲基化。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-25 DOI: 10.1007/s10142-024-01452-6

Xue Liang, Xiaotong Hu, Jiao Li, Boyang Zhang, Tianshu Gu, Hualing Wang, Mingzhong Zhang, Xiaodong Xia, Siyu Guan, Wenfeng Shangguan, Shuai Miao, Weiding Wang, Hao Zhang, Zhiqiang Zhao, Lijun Wang

{"title":"m6A methylation in myocardial tissue of septic mice analyzed using MeRIP/m6A-sequencing and RNA-sequencing","authors":"Xue Liang, Xiaotong Hu, Jiao Li, Boyang Zhang, Tianshu Gu, Hualing Wang, Mingzhong Zhang, Xiaodong Xia, Siyu Guan, Wenfeng Shangguan, Shuai Miao, Weiding Wang, Hao Zhang, Zhiqiang Zhao, Lijun Wang","doi":"10.1007/s10142-024-01452-6","DOIUrl":"10.1007/s10142-024-01452-6","url":null,"abstract":"<div><p>Septic cardiomyopathy is a secondary myocardial injury caused by sepsis. N6-methyl-adenosine (m6A) modification is involved in the pathological progression of septic cardiomyopathy; however, the pathological mechanism remains unclear. In this study, we identified the overall m6A modification pattern in septic myocardial injury and determined its potential interactions with differentially expressed genes (DEGs). A sepsis mouse model exhibiting septic symptoms and myocardial tissue damage was induced by lipopolysaccharide (LPS). LPS-induced septic myocardial tissues and control myocardial tissues were subjected to methylated RNA immunoprecipitation sequencing and RNA sequencing to screen for differentially expressed m6A peaks and DEGs. We identified 859 significantly m6A-modified genes in septic myocardial tissues, including 432 upregulated and 427 downregulated genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to explore the biological importance of differentially expressed m6A methylated genes and DEGs. Differentially expressed m6A methylated genes were enriched in immune- and inflammation-related pathways. Conjoint analysis revealed co-expression of differentially expressed m6A genes and DEGs, including genes that were upregulated or downregulated and those showing opposite trends. High expression of m6A-related genes (<i>WTAP</i> and <i>IGF2BP2</i>), interleukin-17, and interleukin-17 pathway-related genes (<i>MAPK11</i> and <i>TRAF3IP2</i>) was verified using reverse transcription-quantitative PCR. We confirmed the presence of m6A modification of the transcriptome and m6A-mediated gene expression in septic myocardial tissues.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular analyses of the tubby-like protein gene family and their response to salt and high temperature in the foxtail millet (Setaria italica) 狐尾黍（Setaria italica）类管蛋白基因家族及其对盐和高温反应的分子分析。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-09-25 DOI: 10.1007/s10142-024-01458-0

Zhuanzhuan Jiang, Xiaoqi Chen, Lingling Ruan, Yan Xu, Ke Li

{"title":"Molecular analyses of the tubby-like protein gene family and their response to salt and high temperature in the foxtail millet (Setaria italica)","authors":"Zhuanzhuan Jiang, Xiaoqi Chen, Lingling Ruan, Yan Xu, Ke Li","doi":"10.1007/s10142-024-01458-0","DOIUrl":"10.1007/s10142-024-01458-0","url":null,"abstract":"<div><p>Tubby-like proteins (TLPs) are a group of proteins found in both eukaryotes and prokaryotes. They are significant in various physiological and biochemical processes, especially in plants’ response to abiotic stress. However, the role of TLP in foxtail millet (<i>Setaria italica</i>) remains unclear. The millet genome has 16 members of the TLP family with typical Tub domains, which can be sorted into five subgroups based on gene structure, motif, and protein domain distribution. <i>SiTLPs</i> were discovered to be predominantly located in the nucleus and also had extracellular distribution. The interspecific evolutionary analysis indicated that <i>SiTLPs</i> had a closer evolutionary relationship with monocots and were consistent with the morphological classification of foxtail millet. When subjected to salt stress, the abundance of <i>SiTLP</i> was affected, and qRT-PCR results showed that the expression levels of certain <i>SiTLP</i> members were induced by salt stress while others remained unresponsive. Except for <i>SiTLP14</i>, all other <i>SiTLP</i> genes were up-regulated in response to high-temperature stress, implying a potentially crucial role for <i>SiTLP</i> in mitigating high-temperature-induced damage. This study provides valuable insights into understanding the functional significance of the <i>TLP</i> gene family in foxtail millet.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0