Molecular omics最新文献_第7页

TALKIEN: crossTALK IntEraction Network. A web-based tool for deciphering molecular communication through ligand–receptor interactions† TALKIN：跨TALK国际行动网络。一种基于网络的工具，用于通过配体-受体相互作用来破译分子通信。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-07-05 DOI: 10.1039/D3MO00049D

Ferran Moratalla-Navarro, Víctor Moreno and Rebeca Sanz-Pamplona

{"title":"TALKIEN: crossTALK IntEraction Network. A web-based tool for deciphering molecular communication through ligand–receptor interactions†","authors":"Ferran Moratalla-Navarro, Víctor Moreno and Rebeca Sanz-Pamplona","doi":"10.1039/D3MO00049D","DOIUrl":"10.1039/D3MO00049D","url":null,"abstract":"Molecular crosstalk, the dialogue between different cell types, is attracting more attention in cancer research. On the one hand, the communication between tumor and non-tumor cells in the microenvironment or between different tumor clones has influential consequences for the progression and spread of tumors and response to treatment. On the other hand, novel techniques such as single-cell sequencing or spatial transcriptomics provide detailed information that needs to be interpreted. TALKIEN: crossTALK IntEraction Network is a simple and intuitive online R/shiny application to visualize molecular crosstalk information through the construction and analysis of a protein–protein interaction network. Taking two or more lists of genes or proteins as input, which are representative of cell lineages, TALKIEN extracts information about ligand–receptor interactions, builds a network and analyzes it using systems biology techniques such as centrality measures and component analysis, among others. Moreover, it expands the network displaying pathways downstream receptors. The application allows users to select different graphical layouts, performs functional analysis and gives information about drugs targeting receptors. In conclusion, TALKIEN allows users to detect ligand–receptor interactions generating new in silico predictions of cell–cell communication thus providing a translational rationale for future experiments. It is freely available at https://www.odap-ico.org/talkien.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10128501","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

Integrated multi-omics analyses of microbial communities: a review of the current state and future directions 微生物群落的综合多组学分析：现状和未来方向综述。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-07-03 DOI: 10.1039/D3MO00089C

Muzaffer Arıkan and Thilo Muth

引用次数: 1

TarpiD, a database of putative and validated targets of piRNAs TarpiD，一个piRNA推定和验证靶点的数据库。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-06-27 DOI: 10.1039/D3MO00098B

Pooja Gupta, Gourab Das, Trisha Chattopadhyay, Zhumur Ghosh and Bibekanand Mallick

{"title":"TarpiD, a database of putative and validated targets of piRNAs","authors":"Pooja Gupta, Gourab Das, Trisha Chattopadhyay, Zhumur Ghosh and Bibekanand Mallick","doi":"10.1039/D3MO00098B","DOIUrl":"10.1039/D3MO00098B","url":null,"abstract":"Piwi-interacting RNAs (piRNAs) are a novel class of 18–36 nts long small non-coding single-stranded RNAs that play crucial roles in a wide array of critical biological activities besides maintaining genome integrity by transposon silencing. piRNAs influence biological processes and pathways by regulating gene expression at transcriptional and post-transcriptional level. Studies have reported that piRNAs silence various endogenous genes post-transcriptionally by binding to respective mRNAs through interaction with the PIWI proteins. Several thousands of piRNAs have been discovered in animals, but their functions remain largely undiscovered owing to a lack of proper guiding principles of piRNA targeting or diversity in targeting patterns amongst piRNAs from the same or different species. Identification of piRNA targets is essential for deciphering their functions. There are a few tools and databases on piRNAs, but there are no systematic and exclusive repositories to obtain information on target genes regulated by piRNAs and other related information. Hence, we developed a user-friendly database named TarpiD (Targets of piRNA Database) that offers comprehensive information on piRNA and its targets, including their expression, methodologies (high-throughput or low-throughput) for target identification/validation, cells/tissue types, diseases, target gene regulation types, target binding regions, and key functions driven by piRNAs through target gene interactions. The contents of TarpiD are curated from the published literature and enable users to search and download the targets of a particular piRNA or the piRNAs that target a specific gene for use in their research. This database harbours 28 682 entries of piRNA–target interactions supported by 15 methodologies reported in hundreds of cell types/tissues from 9 species. TarpiD will be a valuable resource for a better understanding of the functions and gene-regulatory mechanisms mediated by piRNAs. TarpiD is freely accessible for academic use at https://tarpid.nitrkl.ac.in/tarpid_db/.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10141048","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

Outstanding Reviewers for Molecular Omics in 2022 2022年分子组学杰出审稿人

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-06-26 DOI: 10.1039/D3MO90017G

引用次数: 0

Proteomic analysis reveals mechanisms underlying increased efficacy of bleomycin by photochemical internalization in bladder cancer cells† 蛋白质组学分析揭示了博莱霉素通过光化学内在化在膀胱癌症细胞中提高疗效的机制。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-06-22 DOI: 10.1039/D2MO00337F

Odrun A. Gederaas, Animesh Sharma, Saide Mbarak, Bjørnar Sporsheim, Anders Høgset, Vanya Bogoeva, Geir Slupphaug and Lars Hagen

{"title":"Proteomic analysis reveals mechanisms underlying increased efficacy of bleomycin by photochemical internalization in bladder cancer cells†","authors":"Odrun A. Gederaas, Animesh Sharma, Saide Mbarak, Bjørnar Sporsheim, Anders Høgset, Vanya Bogoeva, Geir Slupphaug and Lars Hagen","doi":"10.1039/D2MO00337F","DOIUrl":"10.1039/D2MO00337F","url":null,"abstract":"Photochemical internalization (PCI) is a promising new technology for site-specific drug delivery, developed from photodynamic therapy (PDT). In PCI, light-induced activation of a photosensitizer trapped inside endosomes together with e.g. chemotherapeutics, nucleic acids or immunotoxins, allows cytosolic delivery and enhanced local therapeutic effect. Here we have evaluated the photosensitizer meso-tetraphenyl chlorine disulphonate (TPCS2a/fimaporfin) in a proteome analysis of AY-27 rat bladder cancer cells in combination with the chemotherapeutic drug bleomycin (BML). We find that BLMPCI attenuates oxidative stress responses induced by BLM alone, while concomitantly increasing transcriptional repression and DNA damage responses. BLMPCI also mediates downregulation of bleomycin hydrolase (Blmh), which is responsible for cellular degradation of BLM, as well as several factors known to be involved in fibrotic responses. PCI-mediated delivery might thus allow reduced dosage of BLM and alleviate unwanted side effects from treatment, including pulmonary fibrosis.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2023/mo/d2mo00337f?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10022014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 2

Protein network analysis links the NSL complex to Parkinson’s disease via mitochondrial and nuclear biology† 蛋白质网络分析通过线粒体和核生物学将NSL复合体与帕金森病联系起来

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-06-14 DOI: 10.1039/D2MO00325B

Katie Kelly, Patrick A. Lewis, Helene Plun-Favreau and Claudia Manzoni

{"title":"Protein network analysis links the NSL complex to Parkinson’s disease via mitochondrial and nuclear biology†","authors":"Katie Kelly, Patrick A. Lewis, Helene Plun-Favreau and Claudia Manzoni","doi":"10.1039/D2MO00325B","DOIUrl":"https://doi.org/10.1039/D2MO00325B","url":null,"abstract":"Whilst the majority of Parkinson’s Disease (PD) cases are sporadic, much of our understanding of the pathophysiological basis of the disease can be traced back to the study of rare, monogenic forms of PD. In the past decade, the availability of genome-wide association studies (GWAS) has facilitated a shift in focus, toward identifying common risk variants conferring increased risk of developing PD across the population. A recent mitophagy screening assay of GWAS candidates has functionally implicated the non-specific lethal (NSL) complex in the regulation of PINK1-mitophagy. Here, a bioinformatics approach has been taken to investigate the proteome of the NSL complex, to unpick its relevance to PD pathogenesis. The NSL interactome has been built, using 3 online tools: PINOT, HIPPIE and MIST, to mine curated, literature-derived protein–protein interaction (PPI) data. We built (i) the ‘mitochondrial’ NSL interactome exploring its relevance to PD genetics and (ii) the PD-oriented NSL interactome to uncover biological pathways underpinning the NSL/PD association. In this study, we find the mitochondrial NSL interactome to be significantly enriched for the protein products of PD-associated genes, including the Mendelian PD genes LRRK2 and VPS35. In addition, we find nuclear processes to be amongst those most significantly enriched within the PD-associated NSL interactome. These findings strengthen the role of the NSL complex in sporadic and familial PD, mediated by both its mitochondrial and nuclear functions.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2023/mo/d2mo00325b?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49995153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Biochemical and metabolic signatures are fundamental to drought adaptation in PGPR Enterobacter bugandensis WRS7† 生物化学和代谢特征是布甘肠杆菌WRS7†干旱适应的基础

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-05-29 DOI: 10.1039/D3MO00051F

Saumya Arora, Piyoosh K Babele and Prabhat Nath Jha

{"title":"Biochemical and metabolic signatures are fundamental to drought adaptation in PGPR Enterobacter bugandensis WRS7†","authors":"Saumya Arora, Piyoosh K Babele and Prabhat Nath Jha","doi":"10.1039/D3MO00051F","DOIUrl":"https://doi.org/10.1039/D3MO00051F","url":null,"abstract":"Drought alone causes more annual loss in crop yield than the sum of all other environmental stresses. There is growing interest in harnessing the potential of stress-resilient PGPR in conferring plant resistance and enhancing crop productivity in drought-affected agroecosystems. A detailed understanding of the complex physiological and biochemical responses will open up the avenues to stress adaptation mechanisms of PGPR communities under drought. It will pave the way for rhizosphere engineering through metabolically engineered PGPR. Therefore, to reveal the physiological and metabolic networks in response to drought-mediated osmotic stress, we performed biochemical analyses and applied untargeted metabolomics to investigate the stress adaptation mechanisms of a PGPR Enterobacter bugendensis WRS7 (Eb WRS7). Drought caused oxidative stress and resulted in slower growth rates in Eb WRS7. However, Eb WRS7 could tolerate drought stress and did not show changes in cell morphology under stress conditions. Overproduction of ROS caused lipid peroxidation (increment in MDA) and eventually activated antioxidant systems and cell signalling cascades, which led to the accumulation of ions (Na+, K+, and Ca2+), osmolytes (proline, exopolysaccharides, betaine, and trehalose), and modulated lipid dynamics of the plasma membranes for osmosensing and osmoregulation, suggesting an osmotic stress adaption mechanism in PGPR Eb WRS7. Finally, GC–MS-based metabolite profiling and deregulated metabolic responses highlighted the role of osmolytes, ions, and intracellular metabolites in regulating Eb WRS7 metabolism. Our results suggest that understanding the role of metabolites and metabolic pathways can be exploited for future metabolic engineering of PGPR and developing bio inoculants for plant growth promotion under drought-affected agroecosystems.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49995152","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

Integrated network pharmacology and fecal metabolomic analysis of the combinational mechanisms of Shexiang Baoxin Pill against atherosclerosis† 综合网络药理学和粪便代谢组学分析麝香保心丸抗动脉粥样硬化的联合机制。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-05-24 DOI: 10.1039/D3MO00067B

Zhicong Wang, Qianqian Wan, Bin Xie, Zifan Zhu, Xike Xu, Peng Fu and Runhui Liu

{"title":"Integrated network pharmacology and fecal metabolomic analysis of the combinational mechanisms of Shexiang Baoxin Pill against atherosclerosis†","authors":"Zhicong Wang, Qianqian Wan, Bin Xie, Zifan Zhu, Xike Xu, Peng Fu and Runhui Liu","doi":"10.1039/D3MO00067B","DOIUrl":"10.1039/D3MO00067B","url":null,"abstract":"Shexiang Baoxin Pill (SBP) has an excellent therapeutic effect on atherosclerosis (AS), but the combinational mechanisms of SBP against AS remain unclear. This study aimed to investigate the combinational mechanisms of SBP against AS by comprehensive network pharmacology and fecal metabolomic analysis. Bufonis venenum, one of the adjuvant medicines in SBP, is an animal medicine with a narrow therapeutic window. Considering animal protection, we evaluated the anti-AS effect of SBP without BV (SBP-BV) using ApoE−/− mouse models, culture cells, and metabolomic methods. Our data suggested that SBP showed remarkable anti-atherosclerotic effects through multiple targets and multiple pathways, while each component in SBP played different roles in their synergistic effect. Notably, SBP-BV showed comparable effects with SBP in the treatment of AS. Both SBP and SBP-BV could reduce cholesterol uptake in RAW264.7 cells and prevent the occurrence and development of AS in WD-induced ApoE−/− mice by attenuating the atherosclerotic plaque area, and reducing inflammatory cytokines and cholesterol levels in vivo. Our finding might provide new insights into the research and development of new anti-atherosclerosis drugs.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9686673","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: Analysis of N-glycosylation protein of Kashin–Beck disease chondrocytes derived from induced pluripotent stem cells based on label-free strategies with LC-MS/MS 更正:基于无标记策略的LC-MS/MS对诱导多能干细胞来源的大骨节病软骨细胞n -糖基化蛋白的分析

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-05-24 DOI: 10.1039/D3MO90016A

Sen Wang, Peilin Meng, Linlin Yuan and Xiong Guo

引用次数: 0

Butyrate promotes C2C12 myoblast proliferation by activating ERK/MAPK pathway† 丁酸盐通过激活ERK/MAPK通路†促进C2C12成肌细胞增殖

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-05-19 DOI: 10.1039/D2MO00256F

Li Guan, Ziyi Cao, Ziyue Pan, Chao Zhao, Mengjuan Xue, Fan Yang and Jie Chen

{"title":"Butyrate promotes C2C12 myoblast proliferation by activating ERK/MAPK pathway†","authors":"Li Guan, Ziyi Cao, Ziyue Pan, Chao Zhao, Mengjuan Xue, Fan Yang and Jie Chen","doi":"10.1039/D2MO00256F","DOIUrl":"10.1039/D2MO00256F","url":null,"abstract":"Sarcopenia has garnered considerable interest in recent years as ageing-associated diseases constitute a significant worldwide public health burden. Nutritional supplements have received much attention as potential tools for managing sarcopenia. However, the specific nutrients responsible are still under-investigated. In the current study, we first determined the levels of short chain fatty acids (SCFAs) and intestinal flora in the feces of elderly sarcopenia subjects and elderly healthy individuals by ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS). Then cell viability detection, flow cytometry and transcriptome analysis were adopted to experimentally evaluate the effect and the underlying mechanism of SCFA on C2C12 cells proliferation in vitro. The results suggested that patients with sarcopenia exhibited decreased levels of butyrate. And butyrate may stimulate C2C12 myocyte proliferation via promoting G1/S cell cycle transition. Transcriptomic analyses pointed to upregulation of the Mitogen-activated protein kinase (MAPK) signaling pathway in butyrate-treated cells. In addition, the above proliferative phenotypes could be suppressed by the combination of ERK/MAPK inhibitor. A combined transcriptomic and metabolomic approach was applied in our study to investigate the potential effect of microbiota-derived butyrate yield on muscular proliferation which may indicate a protective effect of nutritional supplements.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2023/mo/d2mo00256f?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9984225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 2