Molecular omics最新文献_第3页

Outstanding Reviewers for Molecular Omics in 2023 2023 年 Molecular Omics 的杰出审稿人。

IF 3 4区生物学

Molecular omics Pub Date : 2024-09-05 DOI: 10.1039/D4MO90019G

引用次数: 0

Antimalarial mechanism of action of the natural product 9-methoxystrobilurin G† 天然产物 9-甲氧基石蒜碱 G 的抗疟作用机制

IF 3 4区生物学

Molecular omics Pub Date : 2024-08-29 DOI: 10.1039/D4MO00088A

Philip J. Shaw, Parichat Prommana, Chawanee Thongpanchang, Sumalee Kamchonwongpaisan, Darin Kongkasuriyachai, Yan Wang, Zhihua Zhou and Yiqing Zhou

{"title":"Antimalarial mechanism of action of the natural product 9-methoxystrobilurin G†","authors":"Philip J. Shaw, Parichat Prommana, Chawanee Thongpanchang, Sumalee Kamchonwongpaisan, Darin Kongkasuriyachai, Yan Wang, Zhihua Zhou and Yiqing Zhou","doi":"10.1039/D4MO00088A","DOIUrl":"10.1039/D4MO00088A","url":null,"abstract":"The natural product 9-methoxystrobilurin G (9MG) from Favolaschia spp basidiomycetes is a potent and selective antimalarial. The mechanism of action of 9MG is unknown. We induced 9MG resistance in Plasmodium falciparum 3D7 and Dd2 strains and identified mutations associated with resistance by genome sequencing. All 9MG-resistant clones possessed missense mutations in the cytochrome b (CYTB) gene, a key component of mitochondrial complex III. The mutations map to the quinol oxidation site of CYTB, which is also the target of antimalarials such as atovaquone. In a complementary approach to identify protein targets of 9MG, a photoactivatable derivative of 9MG was synthesized and applied in chemoproteomic-based target profiling. Three components of mitochondrial complex III (QCR7, QCR9, and COX15) were specifically enriched consistent with 9MG targeting CYTB and complex III function in P. falciparum. Inhibition of complex III activity by 9MG was confirmed by ubiquinone cytochrome c reductase assay using P. falciparum extract. The findings from this study may be useful for developing novel antimalarials targeting CYTB.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 9","pages":" 584-594"},"PeriodicalIF":3.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183150","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

Bacterial endosymbionts of a nitrogen-fixing yeast Rhodotorula mucilaginosa JGTA-S1 – insights into a yet unknown micro-ecosystem† 固氮酵母 Rhodotorula mucilaginosa JGTA-S1 的细菌内共生体--洞察一个未知的微生态系统

IF 3 4区生物学

Molecular omics Pub Date : 2024-08-28 DOI: 10.1039/D3MO00273J

Mayurakshi Nag, Janardhan Pallavi, Sandipan Chakraborty, Trina Roychoudhury, Sangita Mondal, Abhrajyoti Ghosh, Chinmay Saha, Manidipa Banerjee and Anindita Seal

{"title":"Bacterial endosymbionts of a nitrogen-fixing yeast Rhodotorula mucilaginosa JGTA-S1 – insights into a yet unknown micro-ecosystem†","authors":"Mayurakshi Nag, Janardhan Pallavi, Sandipan Chakraborty, Trina Roychoudhury, Sangita Mondal, Abhrajyoti Ghosh, Chinmay Saha, Manidipa Banerjee and Anindita Seal","doi":"10.1039/D3MO00273J","DOIUrl":"10.1039/D3MO00273J","url":null,"abstract":" Rhodotorula mucilaginosa JGTA-S1 is a yeast strain capable of fixing nitrogen and improving nitrogen nutrition in rice plants because of its nitrogen-fixing endobacteria, namely Stutzerimonas (Pseudomonas) stutzeri and Bradyrhizobium sp. To gain a deeper understanding of yeast endosymbionts, we conducted a whole-genome shotgun metagenomic analysis of JGTA-S1 cells grown under conditions of nitrogen sufficiency and deficiency. Our results showed that the endosymbiont population varied depending on the nitrogen regime. Upon mechanical disruption of yeast cells, we obtained endosymbionts in culturable form viz. Bacillus velezensis and Staphylococcus sp. under nitrogen-replete conditions and Lysinibacillus telephonicus., Brevibacillus sp., and Niallia circulans under nitrogen-depleted conditions. S. stutzeri and Bradyrhizobium sp. the previously reported endosymbionts remained unculturable. The culturable endosymbionts Staphylococcus sp. and Bacillus velezensis appear to possess genes for dissimilatory nitrate reduction (DNRA), an alternative pathway for ammonia synthesis. However, our findings suggest that these endosymbionts are facultative as they survive outside the host. The fitness of the yeast was not affected by curing of these microbes. Curing the yeast diazotrophic endosymbionts took a toll on its fitness. Our results also showed that the populations of S. stutzeri and B. velezensis increased significantly under nitrogen-depleted conditions compared to nitrogen-sufficient conditions. The importance of DNRA and nitrogen fixation is also reflected in the metagenomic reads of JGTA-S1.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 10","pages":" 630-641"},"PeriodicalIF":3.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183151","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

Proteomic analysis of peripheral blood mononuclear cells from OSCC patients reveals potential immune checkpoints to enable personalized treatment† 对 OSCC 患者外周血单核细胞的蛋白质组分析揭示了实现个性化治疗的潜在免疫检查点。

IF 3 4区生物学

Molecular omics Pub Date : 2024-08-23 DOI: 10.1039/D4MO00112E

Anjana Aravind, Rohan Thomas Mathew, Lepakshi Kuruba, Manavalan Vijayakumar and Thottethodi Subrahmanya Keshava Prasad

{"title":"Proteomic analysis of peripheral blood mononuclear cells from OSCC patients reveals potential immune checkpoints to enable personalized treatment†","authors":"Anjana Aravind, Rohan Thomas Mathew, Lepakshi Kuruba, Manavalan Vijayakumar and Thottethodi Subrahmanya Keshava Prasad","doi":"10.1039/D4MO00112E","DOIUrl":"10.1039/D4MO00112E","url":null,"abstract":"Oral squamous cell carcinoma (OSCC) is one of the most prevalent cancers worldwide, with high mortality and prevalence rates. OSCC is defined as an immunogenic tumor with the potential to be recognized and targeted by the immune system. It is characterized by the extensive infiltration of immune cells and plays a vital role in tumorigenesis. Peripheral blood mononuclear cells (PBMC) are a functional subset of immune cells readily accessible through minimally invasive procedures. The molecular characterization of immune cells aids in understanding their functional roles in various pathophysiological conditions. Proteomic analysis of PBMCs from cancer patients provides insight into the mechanism of immunoregulation and the role of immune cells in impeding tumor development and progression. Therefore, the present study investigated the immune cell proteome of a cancer control cohort within OSCC, leveraging data-independent acquisition analysis by mass spectrometry (DIA-MS). Among the differentially abundant proteins in OSCC, we identified promising molecular targets, including LMNB1, CTSB, CD14, CD177, and SPI1. Further exploration of the signaling pathways related to the candidate molecules demonstrated their involvement in cancer immunomodulation. Therefore, this study can serve as a platform for identifying new candidate proteins to further investigate their potential as immunotherapeutic targets and prognostic markers.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 8","pages":" 532-545"},"PeriodicalIF":3.0,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036374","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

Sequencing, assembly, and genomic annotation of Leucoagaricus gongylophorus LEU18496, a dikarya mutualistic species† Leucoagaricus gongylophorus LEU18496（一种迪卡里亚互生物种）的测序、组装和基因组注释。

IF 3 4区生物学

Molecular omics Pub Date : 2024-08-20 DOI: 10.1039/D4MO00108G

Freddy Castillo-Alfonso, Cecilio Valadez-Cano, Gabriela Cejas-Añón, José Utrilla, Juan-Carlos Sigala Alanis, Sylvie Le Borgne, Alfonso Mauricio Sales-Cruz, Gabriel Vigueras-Ramírez and Roberto Olivares-Hernández

{"title":"Sequencing, assembly, and genomic annotation of Leucoagaricus gongylophorus LEU18496, a dikarya mutualistic species†","authors":"Freddy Castillo-Alfonso, Cecilio Valadez-Cano, Gabriela Cejas-Añón, José Utrilla, Juan-Carlos Sigala Alanis, Sylvie Le Borgne, Alfonso Mauricio Sales-Cruz, Gabriel Vigueras-Ramírez and Roberto Olivares-Hernández","doi":"10.1039/D4MO00108G","DOIUrl":"10.1039/D4MO00108G","url":null,"abstract":"The basidiomycete fungus Leucoagaricus gongylophorus is able to grow in the fungus garden of leaf-cutter ants. This mutualistic interaction has driven the evolutionary adaptation of L. gongylophorus, shaping its metabolism to produce enzymes adept at lignocellulosic biomass degradation. In this study, we undertook the comprehensive sequencing, assembly, and functional annotation of the genome of L. gongylophorus strain LEU18496, mutualistic fungus of the Atta mexicana. Our genomic analyses revealed a distinctive bimodal nature to the genome: a predominant region characterized by AT enrichment and low genetic density, alongside a smaller region exhibiting higher GC content and higher genetic density. The presence of transposable elements (TEs) within the AT-enriched region suggests genomic compartmentalization, facilitating differential evolutionary rates. With a gene count of 6748, the assembled genome of L. gongylophorus LEU18496 surpasses previous reports for this fungal species. Inspection of genes associated with central metabolism unveiled a remarkable abundance of carbohydrate-active enzymes (CAZymes) and fungal oxidative lignin enzymes (FOLymes), underscoring their pivotal roles in the life cycle of this fungus.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 8","pages":" 524-531"},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004865","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

YAP activation is robust to dilution† YAP 的活化对稀释作用很强

IF 3 4区生物学

Molecular omics Pub Date : 2024-08-14 DOI: 10.1039/D4MO00100A

Ian Jones, Mar Arias-Garcia, Patricia Pascual-Vargas, Melina Beykou, Lucas Dent, Tara Pal Chaudhuri, Theodoros Roumeliotis, Jyoti Choudhary, Julia Sero and Chris Bakal

{"title":"YAP activation is robust to dilution†","authors":"Ian Jones, Mar Arias-Garcia, Patricia Pascual-Vargas, Melina Beykou, Lucas Dent, Tara Pal Chaudhuri, Theodoros Roumeliotis, Jyoti Choudhary, Julia Sero and Chris Bakal","doi":"10.1039/D4MO00100A","DOIUrl":"10.1039/D4MO00100A","url":null,"abstract":"The concentration of many transcription factors exhibits high cell-to-cell variability due to differences in synthesis, degradation, and cell size. Whether the functions of these factors are robust to fluctuations in concentration, and how this may be achieved, is poorly understood. Across two independent panels of breast cancer cells, we show that the average whole cell concentration of YAP decreases as a function of cell area. However, the nuclear concentration distribution remains constant across cells grouped by size, across a 4–8 fold size range, implying unperturbed nuclear translocation despite the falling cell wide concentration. Both the whole cell and nuclear concentration was higher in cells with more DNA and CycA/PCNA expression suggesting periodic synthesis of YAP across the cell cycle offsets dilution due to cell growth and/or cell spreading. The cell area – YAP scaling relationship extended to melanoma and RPE cells. Integrative analysis of imaging and phospho-proteomic data showed the average nuclear YAP concentration across cell lines was predicted by differences in RAS/MAPK signalling, focal adhesion maturation, and nuclear transport processes. Validating the idea that RAS/MAPK and cell cycle regulate YAP translocation, chemical inhibition of MEK or CDK4/6 increased the average nuclear YAP concentration. Together, this study provides an example case, where cytoplasmic dilution of a protein, for example through cell growth, does not limit a cognate cellular function. Here, that same proteins translocation into the nucleus.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 9","pages":" 554-569"},"PeriodicalIF":3.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/mo/d4mo00100a?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183152","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

Extraction and untargeted analysis of metabolome from undemineralised cortical bone matrix† 从未脱矿皮质骨基质中提取代谢组并进行非靶向分析

IF 3 4区生物学

Molecular omics Pub Date : 2024-07-22 DOI: 10.1039/D4MO00015C

Andrea Bonicelli, George Taylor and Noemi Procopio

{"title":"Extraction and untargeted analysis of metabolome from undemineralised cortical bone matrix†","authors":"Andrea Bonicelli, George Taylor and Noemi Procopio","doi":"10.1039/D4MO00015C","DOIUrl":"10.1039/D4MO00015C","url":null,"abstract":"Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) untargeted metabolomics has become the gold standard for the profiling of low-molecular-weight compounds. Recently, this discipline has raised great interest in forensic sciences, especially in the field of toxicology and for post-mortem interval estimation. The current study aims at evaluating three extraction protocols and two LC-MS/MS assays run in both positive and negative modes, to identify the most suitable method to conduct post-mortem metabolomic profiling of bone tissue. A fragment of the anterior tibia of a 82 years-old male sampled from a human taphonomy facility was powdered via freeze-milling. The powdered sub-samples were extracted in five replicates per protocol. Methods tested were (I) a biphasic chloroform–methanol–water protocol, (II) a single phase methanol–water protocol, and (III) a single phase methanol–acetonitrile–water protocol. LC-MS/MS analyses were carried out via high performance liquid chromatography, either on hydrophilic interaction (HILIC) or on reversed-phase (C18) columns in both positive and negative ionisation modes, coupled with a Q-TOF mass spectrometer. Results suggest that the highest consistency between replicates and quality control samples was obtained with the single phase extractions (i.e., methanol–acetonitrile–water), whilst the ideal combination of instrumental set up HILIC chromatography in positive ionisation mode and of C18 chromatography in negative ionisation mode. For the purpose of forensic investigations, a combination of a single phase extraction and the two aforementioned chromatographic and mass spectrometry modes could represent an ideal set up for obtaining bone metabolomic profiles from taphonomically altered bones.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 8","pages":" 517-523"},"PeriodicalIF":3.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/mo/d4mo00015c?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141737538","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

Discovery of candidate biomarkers from plasma-derived extracellular vesicles of patients with cirrhosis and hepatocellular carcinoma: an exploratory proteomic study† 从肝硬化和肝细胞癌患者的血浆源性细胞外囊泡中发现候选生物标记物：一项探索性蛋白质组学研究。

IF 3 4区生物学

Molecular omics Pub Date : 2024-07-16 DOI: 10.1039/D4MO00043A

Cecilia Zertuche-Martínez, Juan Manuel Velázquez-Enríquez, Karina González-García, Jovito Cesar Santos-Álvarez, María de los Ángeles Romero-Tlalolini, Socorro Pina-Canseco, Laura Pérez-Campos Mayoral, Pablo Muriel, Saúl Villa-Treviño, Rafael Baltiérrez-Hoyos, Jaime Arellanes-Robledo and Verónica Rocío Vásquez-Garzón

{"title":"Discovery of candidate biomarkers from plasma-derived extracellular vesicles of patients with cirrhosis and hepatocellular carcinoma: an exploratory proteomic study†","authors":"Cecilia Zertuche-Martínez, Juan Manuel Velázquez-Enríquez, Karina González-García, Jovito Cesar Santos-Álvarez, María de los Ángeles Romero-Tlalolini, Socorro Pina-Canseco, Laura Pérez-Campos Mayoral, Pablo Muriel, Saúl Villa-Treviño, Rafael Baltiérrez-Hoyos, Jaime Arellanes-Robledo and Verónica Rocío Vásquez-Garzón","doi":"10.1039/D4MO00043A","DOIUrl":"10.1039/D4MO00043A","url":null,"abstract":"Extracellular vesicles (EVs) represent an attractive source of biomarkers due to their biomolecular cargo. The aim of this study was to identify candidate protein biomarkers from plasma-derived EVs of patients with liver cirrhosis (LC) and hepatocellular carcinoma (HCC). Plasma-derived EVs from healthy participants (HP), LC, and HCC patients (eight samples each) were subjected to label-free quantitative proteomic analysis using LC-MS/MS. A total of 248 proteins were identified, and differentially expressed proteins (DEPs) were obtained after pairwise comparison. We found that DEPs mainly involve complement cascade activation, coagulation pathways, cholesterol metabolism, and extracellular matrix components. By choosing a panel of up- and down-regulated proteins involved in cirrhotic and carcinogenesis processes, TGFBI, LGALS3BP, C7, SERPIND1, and APOC3 were found to be relevant for LC patients, while LRG1, TUBA1C, TUBB2B, ACTG1, C9, HP, FGA, FGG, FN1, PLG, APOB and ITIH2 were associated with HCC patients, which could discriminate both diseases. In addition, we identified the top shared proteins in both diseases, which included LCAT, SERPINF2, A2M, CRP, and VWF. Thus, our exploratory proteomic study revealed that these proteins might play an important role in the disease progression and represent a panel of candidate biomarkers for the prognosis and diagnosis of LC and HCC.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 7","pages":" 483-495"},"PeriodicalIF":3.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141620465","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

Identification of autophagy-related signatures in nonalcoholic fatty liver disease and correlation with non-parenchymal cells of the liver† 鉴定非酒精性脂肪肝中的自噬相关特征以及与非肝实质细胞的相关性。

IF 3 4区生物学

Molecular omics Pub Date : 2024-07-10 DOI: 10.1039/D4MO00060A

Kaiwei Chen, Ling Wei, Shengnan Yu, Ningning He and Fengjuan Zhang

{"title":"Identification of autophagy-related signatures in nonalcoholic fatty liver disease and correlation with non-parenchymal cells of the liver†","authors":"Kaiwei Chen, Ling Wei, Shengnan Yu, Ningning He and Fengjuan Zhang","doi":"10.1039/D4MO00060A","DOIUrl":"10.1039/D4MO00060A","url":null,"abstract":"Non-alcoholic fatty liver disease (NAFLD) is a chronic hepatic disease. The incidence and prevalence of NAFLD have increased greatly in recent years, and there is still a lack of effective drugs. Autophagy plays an important role in promoting liver metabolism and maintaining liver homeostasis, and defects in autophagy levels are considered to be related to the development of NAFLD. However, the molecular mechanisms of autophagy in NAFLD still remain unknown. In this study, we identified 6 autophagy-associated hub genes using gene expression profiles obtained from the GSE48452 and GSE89632 datasets. Biomarkers were screened according to gene significance (GS) and module membership (MM) using weighted gene co-expression network analysis (WGCNA), and the immune infiltration landscape of the liver in NAFLD patients was explored using the CIBERSORT algorithm. Subsequently, we analyzed the relationship between liver non-parenchymal cells and autophagy-related hub genes using scRNA-seq data (GSE129516). Finally, we separated the NAFLD patients into two groups based on 6 hub genes by consensus clustering and screened 10 potential autophagy-related small molecules based on the cMAP database.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 7","pages":" 469-482"},"PeriodicalIF":3.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141563889","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

Integrating host and microbiome biology using holo-omics 利用整体组学整合宿主和微生物组生物学。

IF 3 4区生物学

Molecular omics Pub Date : 2024-07-04 DOI: 10.1039/D4MO00017J

Carl M. Kobel, Jenny Merkesvik, Idun Maria Tokvam Burgos, Wanxin Lai, Ove Øyås, Phillip B. Pope, Torgeir R. Hvidsten and Velma T. E. Aho

引用次数: 0