keyword
https://read.qxmd.com/read/38535292/migrene-the-toolbox-for-microbial-and-individualized-gems-reactobiome-and-community-network-modelling
#1
JOURNAL ARTICLE
Gholamreza Bidkhori, Saeed Shoaie
Understanding microbial metabolism is crucial for evaluating shifts in human host-microbiome interactions during periods of health and disease. However, the primary hurdle in the realm of constraint-based modeling and genome-scale metabolic models (GEMs) pertaining to host-microbiome interactions lays in the efficient utilization of metagenomic data for constructing GEMs that encompass unexplored and uncharacterized genomes. Challenges persist in effectively employing metagenomic data to address individualized microbial metabolisms to investigate host-microbiome interactions...
February 21, 2024: Metabolites
https://read.qxmd.com/read/38534409/light-exposed-metabolic-responses-of-cordyceps-militaris-through-transcriptome-integrated-genome-scale-modeling
#2
JOURNAL ARTICLE
Panyawarin Soommat, Nachon Raethong, Ratchaprapa Ruengsang, Roypim Thananusak, Teeraphan Laomettachit, Kobkul Laoteng, Treenut Saithong, Wanwipa Vongsangnak
The genome-scale metabolic model (GSMM) of Cordyceps militaris provides a comprehensive basis of carbon assimilation for cell growth and metabolite production. However, the model with a simple mass balance concept shows limited capability to probe the metabolic responses of C. militaris under light exposure. This study, therefore, employed the transcriptome-integrated GSMM approach to extend the investigation of C. militaris 's metabolism under light conditions. Through the gene inactivity moderated by metabolism and expression (GIMME) framework, the i PS1474- ti GSMM model was furnished with the transcriptome data, thus providing a simulation that described reasonably well the metabolic responses underlying the phenotypic observation of C...
February 22, 2024: Biology
https://read.qxmd.com/read/38532295/pycomo-a-python-package-for-community-metabolic-model-creation-and-analysis
#3
JOURNAL ARTICLE
Michael Predl, Marianne Mießkes, Thomas Rattei, Jürgen Zanghellini
SUMMARY: PyCoMo is a python package for quick and easy generation of genome-scale compartmentalised community metabolic models that are compliant with current openCOBRA file formats. The resulting models can be used to predict (i) the maximum growth rate at a given abundance profile, (ii) the feasible community compositions at a given growth rate, and (iii) all exchange metabolites and cross-feeding interactions in a community metabolic model independent of the abundance profile; we demonstrate PyCoMo's capability by analysing methane production in a previously published simplified biogas community metabolic model (Koch et al...
March 26, 2024: Bioinformatics
https://read.qxmd.com/read/38522229/exposure-to-environmental-toxicants-is-associated-with-gut-microbiome-dysbiosis-insulin-resistance-and-obesity
#4
JOURNAL ARTICLE
Partho Sen, Yong Fan, Jennifer J Schlezinger, Stanislav D Ehrlich, Thomas F Webster, Tuulia Hyötyläinen, Oluf Pedersen, Matej Orešič
Environmental toxicants (ETs) are associated with adverse health outcomes. Here we hypothesized that exposures to ETs are linked with obesity and insulin resistance partly through a dysbiotic gut microbiota and changes in the serum levels of secondary bile acids (BAs). Serum BAs, per- and polyfluoroalkyl substances (PFAS) and additional twenty-seven ETs were measured by mass spectrometry in 264 Danes (121 men and 143 women, aged 56.6 ± 7.3 years, BMI 29.7 ± 6.0 kg/m2 ) using a combination of targeted and suspect screening approaches...
March 20, 2024: Environment International
https://read.qxmd.com/read/38517887/a-model-driven-approach-to-upcycling-recalcitrant-feedstocks-in-pseudomonas-putida-by-decoupling-pha-production-from-nutrient-limitation
#5
JOURNAL ARTICLE
Maria-Tsampika Manoli, Álvaro Gargantilla-Becerra, Carlos Del Cerro Sánchez, Virginia Rivero-Buceta, M Auxiliadora Prieto, Juan Nogales
Bacterial polyhydroxyalkanoates (PHAs) have emerged as promising eco-friendly alternatives to petroleum-based plastics since they are synthesized from renewable resources and offer exceptional properties. However, their production is limited to the stationary growth phase under nutrient-limited conditions, requiring customized strategies and costly two-phase bioprocesses. In this study, we tackle these challenges by employing a model-driven approach to reroute carbon flux and remove regulatory constraints using synthetic biology...
March 21, 2024: Cell Reports
https://read.qxmd.com/read/38517169/design-of-a-proteolytic-module-for-improved-metabolic-modeling-of-bacteroides-caccae
#6
JOURNAL ARTICLE
Amandine Paulay, Ghjuvan M Grimaud, Raphaël Caballero, Béatrice Laroche, Marion Leclerc, Simon Labarthe, Emmanuelle Maguin
The gut microbiota plays a crucial role in health and is significantly modulated by human diets. In addition to Western diets which are rich in proteins, high-protein diets are used for specific populations or indications, mainly weight loss. In this study, we investigated the effect of protein supplementation on Bacteroides caccae , a Gram-negative gut symbiont. The supplementation with whey proteins led to a significant increase in growth rate, final biomass, and short-chain fatty acids production. A comprehensive genomic analysis revealed that B...
March 22, 2024: MSystems
https://read.qxmd.com/read/38500406/genome-scale-metabolic-modeling-of-thraustochytrium-sp-rt2316-16-effects-of-nutrients-on-metabolism
#7
JOURNAL ARTICLE
Carolina Shene, Allison Leyton, Liset Flores, Daniela Chavez, Juan A Asenjo, Yusuf Chisti
Marine thraustochytrids produce metabolically important lipids such as the long-chain omega-3 polyunsaturated fatty acids, carotenoids, and sterols. The growth and lipid production in thraustochytrids depends on the composition of the culture medium that often contains yeast extract as a source of amino acids. This work discusses the effects of individual amino acids provided in the culture medium as the only source of nitrogen, on the production of biomass and lipids by the thraustochytrid Thraustochytrium sp...
March 18, 2024: Biotechnology and Bioengineering
https://read.qxmd.com/read/38496672/local-patterns-of-genetic-sharing-challenge-the-boundaries-between-neuropsychiatric-and-insulin-resistance-related-conditions
#8
Giuseppe Fanelli, Barbara Franke, Chiara Fabbri, Josefin Werme, Izel Erdogan, Ward De Witte, Geert Poelmans, I Hyun Ruisch, Lianne Maria Reus, Veerle van Gils, Willemijn J Jansen, Stephanie J B Vos, Kazi Asraful Alam, Aurora Martinez, Jan Haavik, Theresa Wimberley, Søren Dalsgaard, Ábel Fóthi, Csaba Barta, Fernando Fernandez-Aranda, Susana Jimenez-Murcia, Simone Berkel, Silke Matura, Jordi Salas-Salvadó, Martina Arenella, Alessandro Serretti, Nina Roth Mota, Janita Bralten
UNLABELLED: The co-occurrence of insulin resistance (IR)-related metabolic conditions with neuropsychiatric disorders is a complex public health challenge. Evidence of the genetic links between these phenotypes is emerging, but little is currently known about the genomic regions and biological functions that are involved. To address this, we performed Local Analysis of [co]Variant Association (LAVA) using large-scale (N=9,725-933,970) genome-wide association studies (GWASs) results for three IR-related conditions (type 2 diabetes mellitus, obesity, and metabolic syndrome) and nine neuropsychiatric disorders...
March 8, 2024: medRxiv
https://read.qxmd.com/read/38492006/a-dynamic-model-of-growth-phase-of-bio-conversion-of-methane-to-polyhydroxybutyrate-using-dynamic-flux-balance-analysis
#9
JOURNAL ARTICLE
Mohadeseh Nasershariat, Mahmoud Reza Pishvaie, Ramin Bozorgmehry Boozarjomehry, Steffen Waldherr
Biological conversion of waste methane to biodegradable plastics is a way of reducing their production cost. This study addresses the computational modeling of the growth phase reactor of the process of polyhydroxybutyrate production. The model was used for investigating the effect of gas recycling and inlet gas retention time on the reactor performance. The model was run by the use of a genome-scale metabolic network of Methylocystis hirsuta in a dynamic flux balance analysis framework. The reactor has been modeled for two separate feeding scenarios: a pure methane feed and a biogas feed...
March 16, 2024: Bioprocess and Biosystems Engineering
https://read.qxmd.com/read/38485510/identification-of-novel-mammalian-viruses-in-tree-shrews-tupaia-belangeri-chinensis
#10
JOURNAL ARTICLE
Hong Zhou, Ren-Rong Tian, Xiu-Rong Wang, Jin-Xuan Yang, Yun-Xiao Wang, Ming-Liang Zhao, Xu-Dong Zhang, Yu-Hua Ma, Long-Bao Lv, Edward C Holmes, Yong-Tang Zheng, Wei-Feng Shi
The Chinese tree shrew ( Tupaia belangeri chinensis ), a member of the mammalian order Scandentia, exhibits considerable similarities with primates, including humans, in aspects of its nervous, immune, and metabolic systems. These similarities have established the tree shrew as a promising experimental model for biomedical research on cancer, infectious diseases, metabolic disorders, and mental health conditions. Herein, we used meta-transcriptomic sequencing to analyze plasma, as well as oral and anal swab samples, from 105 healthy asymptomatic tree shrews to identify the presence of potential zoonotic viruses...
March 18, 2024: Zoological Research
https://read.qxmd.com/read/38478777/prediction-of-essential-proteins-of-klebsiella-pneumoniae-using-integrative-bioinformatics-and-systems-biology-approach-unveiling-new-avenues-for-drug-discovery
#11
JOURNAL ARTICLE
Gnanasekar Pranavathiyani, Archana Pan
Klebsiella pneumoniae is an opportunistic multidrug-resistant bacterial pathogen responsible for various health care-associated infections. The prediction of proteins that are essential for the survival of bacterial pathogens can greatly facilitate the drug development and discovery pipeline toward target identification. To this end, the present study reports a comprehensive computational approach integrating bioinformatics and systems biology-based methods to identify essential proteins of K. pneumoniae involved in vital processes...
March 13, 2024: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/38475720/tracing-vitamins-on-the-long-non-coding-lane-of-the-transcriptome-vitamin-regulation-of-lncrnas
#12
REVIEW
Fatemeh Yazarlou, Fatemeh Alizadeh, Leonard Lipovich, Roberta Giordo, Soudeh Ghafouri-Fard
A major revelation of genome-scale biological studies in the post-genomic era has been that two-thirds of human genes do not encode proteins. The majority of non-coding RNA transcripts in humans are long non-coding RNA (lncRNA) molecules, non-protein-coding regulatory transcripts with sizes greater than 500 nucleotides. LncRNAs are involved in nearly every aspect of cellular physiology, playing fundamental regulatory roles both in normal cells and in disease. As result, they are functionally linked to multiple human diseases, from cancer to autoimmune, inflammatory, and neurological disorders...
March 12, 2024: Genes & Nutrition
https://read.qxmd.com/read/38468344/prediction-of-metabolites-associated-with-somatic-mutations-in-cancers-by-using-genome-scale-metabolic-models-and-mutation-data
#13
JOURNAL ARTICLE
GaRyoung Lee, Sang Mi Lee, Sungyoung Lee, Chang Wook Jeong, Hyojin Song, Sang Yup Lee, Hongseok Yun, Youngil Koh, Hyun Uk Kim
BACKGROUND: Oncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate developing treatment strategies for cancers, but is challenging due to the large number of metabolites in a cell and the presence of multiple genes associated with cancer development. RESULTS: Here we report the development of a computational workflow that predicts metabolite-gene-pathway sets...
March 11, 2024: Genome Biology
https://read.qxmd.com/read/38468098/a-machine-learning-approach-for-predicting-essentiality-of-metabolic-genes
#14
JOURNAL ARTICLE
Lilli J Freischem, Diego A Oyarzún
The identification of essential genes is a key challenge in systems and synthetic biology, particularly for engineering metabolic pathways that convert feedstocks into valuable products. Assessment of gene essentiality at a genome scale requires large and costly growth assays of knockout strains. Here we describe a strategy to predict the essentiality of metabolic genes using binary classification algorithms. The approach combines elements from genome-scale metabolic models, directed graphs, and machine learning into a predictive model that can be trained on small knockout data...
2024: Methods in Molecular Biology
https://read.qxmd.com/read/38467625/an-organism-wide-atlas-of-hormonal-signaling-based-on-the-mouse-lemur-single-cell-transcriptome
#15
JOURNAL ARTICLE
Shixuan Liu, Camille Ezran, Michael F Z Wang, Zhengda Li, Kyle Awayan, Jonathan Z Long, Iwijn De Vlaminck, Sheng Wang, Jacques Epelbaum, Christin S Kuo, Jérémy Terrien, Mark A Krasnow, James E Ferrell
Hormones mediate long-range cell communication and play vital roles in physiology, metabolism, and health. Traditionally, endocrinologists have focused on one hormone or organ system at a time. Yet, hormone signaling by its very nature connects cells of different organs and involves crosstalk of different hormones. Here, we leverage the organism-wide single cell transcriptional atlas of a non-human primate, the mouse lemur (Microcebus murinus), to systematically map source and target cells for 84 classes of hormones...
March 11, 2024: Nature Communications
https://read.qxmd.com/read/38460783/revealing-the-dynamics-and-mechanisms-of-bacterial-interactions-in-cheese-production-with-metabolic-modelling
#16
JOURNAL ARTICLE
Maxime Lecomte, Wenfan Cao, Julie Aubert, David James Sherman, Hélène Falentin, Clémence Frioux, Simon Labarthe
Cheese taste and flavour properties result from complex metabolic processes occurring in microbial communities. A deeper understanding of such mechanisms makes it possible to improve both industrial production processes and end-product quality through the design of microbial consortia. In this work, we caracterise the metabolism of a three-species community consisting of Lactococcus lactis, Lactobacillus plantarum and Propionibacterium freudenreichii during a seven-week cheese production process. Using genome-scale metabolic models and omics data integration, we modeled and calibrated individual dynamics using monoculture experiments, and coupled these models to capture the metabolism of the community...
March 7, 2024: Metabolic Engineering
https://read.qxmd.com/read/38448908/differentiated-adaptative-genetic-architecture-and-language-related-demographical-history-in-south-china-inferred-from-619-genomes-from-56-populations
#17
JOURNAL ARTICLE
Qiuxia Sun, Mengge Wang, Tao Lu, Shuhan Duan, Yan Liu, Jing Chen, Zhiyong Wang, Yuntao Sun, Xiangping Li, Shaomei Wang, Liuyi Lu, Liping Hu, Libing Yun, Junbao Yang, Jiangwei Yan, Shengjie Nie, Yanfeng Zhu, Gang Chen, Chuan-Chao Wang, Chao Liu, Guanglin He, Renkuan Tang
BACKGROUND: The underrepresentation of human genomic resources from Southern Chinese populations limited their health equality in the precision medicine era and complete understanding of their genetic formation, admixture, and adaptive features. Besides, linguistical and genetic evidence supported the controversial hypothesis of their origin processes. One hotspot case was from the Chinese Guangxi Pinghua Han people (GPH), whose language was significantly similar to Southern Chinese dialects but whose uniparental gene pool was phylogenetically associated with the indigenous Tai-Kadai (TK) people...
March 6, 2024: BMC Biology
https://read.qxmd.com/read/38448436/integration-of-graph-neural-networks-and-genome-scale-metabolic-models-for-predicting-gene-essentiality
#18
JOURNAL ARTICLE
Ramin Hasibi, Tom Michoel, Diego A Oyarzún
Genome-scale metabolic models are powerful tools for understanding cellular physiology. Flux balance analysis (FBA), in particular, is an optimization-based approach widely employed for predicting metabolic phenotypes. In model microbes such as Escherichia coli, FBA has been successful at predicting essential genes, i.e. those genes that impair survival when deleted. A central assumption in this approach is that both wild type and deletion strains optimize the same fitness objective. Although the optimality assumption may hold for the wild type metabolic network, deletion strains are not subject to the same evolutionary pressures and knock-out mutants may steer their metabolism to meet other objectives for survival...
March 6, 2024: NPJ Systems Biology and Applications
https://read.qxmd.com/read/38445018/metabolic-collaboration-between-cells-in-the-tumor-microenvironment-has-a-negligible-effect-on-tumor-growth
#19
JOURNAL ARTICLE
Johan Gustafsson, Fariba Roshanzamir, Anders Hagnestål, Sagar M Patel, Oseeyi I Daudu, Donald F Becker, Jonathan L Robinson, Jens Nielsen
The tumor microenvironment is composed of a complex mixture of different cell types interacting under conditions of nutrient deprivation, but the metabolism therein is not fully understood due to difficulties in measuring metabolic fluxes and exchange of metabolites between different cell types in vivo . Genome-scale metabolic modeling enables estimation of such exchange fluxes as well as an opportunity to gain insight into the metabolic behavior of individual cell types. Here, we estimated the availability of nutrients and oxygen within the tumor microenvironment using concentration measurements from blood together with a metabolite diffusion model...
March 4, 2024: The innovation
https://read.qxmd.com/read/38444371/genome-scale-metabolic-models-in-translational-medicine-the-current-status-and-potential-of-machine-learning-in-improving-the-effectiveness-of-the-models
#20
REVIEW
Beste Turanli, Gizem Gulfidan, Ozge Onluturk Aydogan, Ceyda Kula, Gurudeeban Selvaraj, Kazim Yalcin Arga
The genome-scale metabolic model (GEM) has emerged as one of the leading modeling approaches for systems-level metabolic studies and has been widely explored for a broad range of organisms and applications. Owing to the development of genome sequencing technologies and available biochemical data, it is possible to reconstruct GEMs for model and non-model microorganisms as well as for multicellular organisms such as humans and animal models. GEMs will evolve in parallel with the availability of biological data, new mathematical modeling techniques and the development of automated GEM reconstruction tools...
March 6, 2024: Molecular Omics
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