Article
Biochemistry & Molecular Biology
Kristina Grausa, Ivars Mozga, Karlis Pleiko, Agris Pentjuss
Summary: Genome-scale metabolic modeling is commonly used to study the effect of metabolism on organism phenotype. This article introduces a newly developed transcriptome analysis tool called IgemRNA, which has a user-friendly graphical interface, tackles software compatibility issues, and introduces novel algorithms for comparing different transcriptome datasets. Validation using publicly available transcriptome datasets showed that IgemRNA can validate transcriptome and environmental data on biochemical network topology.
Article
Agricultural Engineering
Jing Zhang, Qingru Li, Yanhong Lu, Xiaoyu Guan, Jiahuan Liu, Na Xu, Chunyu Cai, Xia Li, Bo Nan, Jingsheng Liu, Yuhua Wang
Summary: The study demonstrated that titanium dioxide (TiO2) stress significantly increased the astaxanthin yield of Phaffia rhodozyma PR106 by accelerating glucose uptake, promoting ethanol reuse, and shifting carbon flux to the astaxanthin synthesis pathway. This metabolic regulation under TiO2 stress improved the production of astaxanthin in PR106 strain, while not directly related to mRNA transcription and post-translational modifications regulation. Additionally, the regulation of ROS metabolism continued in the PR106 strain.
BIORESOURCE TECHNOLOGY
(2021)
Review
Oncology
Richard Miallot, Franck Galland, Virginie Millet, Jean-Yves Blay, Philippe Naquet
Summary: Metabolic rewiring presents new therapeutic opportunities in cancer, particularly in soft tissue sarcomas with their heterogeneous tissue origin and genetic history. Genetic alterations skew activation pathways and orient metabolic rewiring in sarcomas. The diverse metabolic landscapes in tumors condition the tumor microenvironment, immune responses, and prognosis, providing potential targets for metabolite-targeting drugs in controlling sarcoma growth.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2021)
Article
Environmental Sciences
Rajendran Velmurugan, Aran Incharoensakdi
Summary: There is a growing demand for biofuels worldwide, and cyanobacteria have unique characteristics that make them a promising candidate for biofuel production. Metabolic engineering and engineering of photosynthetic apparatus play crucial roles in developing economically feasible processes.
Article
Microbiology
Nevena Maslac, Chandni Sidhu, Hanno Teeling, Tristan Wagner
Summary: Some marine thermophilic methanogens are able to perform energy-consuming nitrogen fixation despite deriving only little energy from hydrogenotrophic methanogenesis. Researchers studied the process in Methanothermococcus thermolithotrophicus DSM 2095 and found that diazotrophic growth is dependent on molybdenum and involves upregulation of nitrogenase machinery and other genes. This research provides insights into how these organisms adapt to nitrogen and energy limitations.
Article
Biochemical Research Methods
Marzia Di Filippo, Dario Pescini, Bruno Giovanni Galuzzi, Marcella Bonanomi, Daniela Gaglio, Eleonora Mangano, Clarissa Consolandi, Lilia Alberghina, Marco Vanoni, Chiara Damiani
Summary: The authors introduce a computational pipeline called INTEGRATE that integrates transcriptomics and metabolomics data to predict the regulatory mechanisms of metabolic reactions. This pipeline has important implications in clinical treatment and various fields, such as cancer.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Endocrinology & Metabolism
Ming Gao, Minjian Chen, Qiuzhen Chen, Shuai Zhu, Hengjie Wang, Weizheng Yang, Xi Wang, Qiang Wang, Ling Gu
Summary: Well-controlled metabolism is crucial for optimal oocyte development. This study investigated the intrinsic regulation of oocyte maturation through metabolomics and transcriptomics analysis, revealing novel metabolic features during porcine oocyte meiosis. The findings provide a comprehensive data resource and potential molecular biomarkers for predicting and improving oocyte quality.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Cell Biology
Eunyong Ahn, Jueun Lee, Jisu Han, Seung-Min Lee, Ki-Sun Kwon, Geum-Sook Hwang
Summary: This study integrated metabolomic and transcriptomic data sets from young and old mice kidneys, revealing a defective renal glutathione metabolism as a signature of renal aging. The results suggest that restraining renal glutathione metabolism may alleviate or delay age-associated renal metabolic deterioration.
Review
Agricultural Engineering
Amandeep Brar, Manish Kumar, Twinkle Soni, V. Vivekanand, Nidhi Pareek
Summary: Microalgae have high biomass production rate and oil content, but low productivity and high cost hinder their use as biofuel resource. Genetic alterations and metabolic engineering could enhance microalgae's properties for biofuel production, promoting their economic commercialization.
BIORESOURCE TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Haein Lee, Jina Park, Seyun Kim
Summary: Acute stress response leads to various physiological changes in the brain, including altered gene expression and metabolic pathways. In this study, mice exposed to a brief water avoidance stress (WAS) showed aberrant expression of 60 genes and significant changes in 43 brain metabolites. Functional analysis revealed enrichment of genes involved in superoxide metabolism, while metabolomic profiling showed upregulation of lipolysis, eicosanoid biosynthesis, and endocannabinoid synthesis pathways. These findings provide valuable insights into the molecular events underlying acute stress and its impact on neural functions.
Article
Fisheries
Jian Sun, Wenyi Wu, Hong Ji
Summary: Different tissues exhibit distinct glucose and lipid metabolisms during overwintering. Lipolysis was activated in adipose tissue, triglycerides were utilized in hepatopancreas, and muscle primarily utilized glycogen followed by triglycerides as energy substrates.
Article
Biotechnology & Applied Microbiology
Vivienne Mol, Martyn Bennett, Benjamin J. Sanchez, Beata K. Lisowska, Markus J. Herrgard, Alex Toftgaard Nielsen, David J. Leak, Nikolaus Sonnenschein
Summary: This study presents p-thermo, the most comprehensive genome-scale model to date of Parageobacillus thermoglucosidasius NCIMB 11955, which accurately predicts the metabolism of this bacteria and resolves an uncharacterized bottleneck in anaerobic metabolism.
METABOLIC ENGINEERING
(2021)
Review
Biotechnology & Applied Microbiology
Marc Scherer, Sarel J. Fleishman, Patrik R. Jones, Thomas Dandekar, Elena Bencurova
Summary: In order to ensure a sustainable supply of chemicals, innovative biotechnological solutions are essential to replace reliance on fossil resources. The lack of efficient and specific biocatalysts has hindered the commercialization of biotechnological processes for renewable chemical manufacturing. To address this challenge, researchers propose utilizing computational tools to streamline the identification and optimization of enzyme variants for use in the biotechnological industry.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Environmental Sciences
Jiahui OuYang, Yangchun Gao, Yufeng Wei, Huangping Huang, Yan Ge, Jun Zhao, Shiping Gong
Summary: The yellow pond turtle is cultured for various purposes in China. Cold stress can lead to disease outbreaks and mortality, but the underlying mechanism is still unclear.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Mario Lorenz, Raphaela Fritsche-Guenther, Cornelia Bartsch, Angelika Vietzke, Alina Eisenberger, Karl Stangl, Verena Stangl, Jennifer A. Kirwan
Summary: Periods of low energy supply pose challenges for organisms and cells. In this study, we examined the metabolic changes in human umbilical vein endothelial cells (HUVECs) during serum starvation. The results showed decreased levels of metabolites involved in glycolysis, the TCA cycle, and the glycerol pathway, while amino acid levels increased. Metabolic flux analysis revealed faster incorporation of labeled glucose and glutamine into cellular metabolism after serum starvation, suggesting increased metabolic activity to cope with energy deficiency.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Ryan K. Fritts, Breah LaSarre, Ari M. Stoner, Amanda L. Posto, James B. McKinlay
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2017)
Article
Microbiology
Breah LaSarre, David T. Kysela, Barry D. Stein, Adrien Ducret, Yves V. Brun, James B. McKinlay
Article
Biotechnology & Applied Microbiology
Alexandra L. McCully, Megan G. Behringer, Jennifer R. Gliessman, Evgeny V. Pilipenko, Jeffrey L. Mazny, Michael Lynch, D. Allan Drummond, James B. McKinlay
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2018)
Article
Microbiology
Heidi S. Schindel, Jonathan A. Karty, James B. McKinlay, Carl E. Bauer
JOURNAL OF BACTERIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Sara E. Jones-Burrage, Timothy A. Kremer, James B. McKinley
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Alekhya Govindaraju, James B. McKinlay, Breah LaSarre
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Microbiology
Alexandra L. McCully, Maureen C. Onyeziri, Breah LaSarre, Jennifer R. Gliessman, James B. McKinlay
Article
Biotechnology & Applied Microbiology
Breah LaSarre, Adam M. Deutschbauer, Crystal E. Love, James B. McKinlay
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Ecology
Ryan K. Fritts, Jordan T. Bird, Megan G. Behringer, Anna Lipzen, Joel Martin, Michael Lynch, James B. McKinlay
Editorial Material
Environmental Sciences
James B. McKinlay
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2021)
Review
Microbiology
Ryan K. Fritts, Alexandra L. McCully, James B. McKinlay
Summary: The transfer of nutrients between cells, known as cross-feeding, is a crucial aspect of microbial communities that impacts health and global biogeochemical cycles. Externalized molecules play a diverse role in promoting cross-feeding relationships, which can be characterized by a mix of cooperation and competition. The interplay between microbial physiology, environmental factors, and extracellular molecules shape the dynamics of cross-feeding interactions.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2021)
Article
Microbiology
Brittany E. E. Mazny, Olivia F. F. Sheff, Breah LaSarre, Anastasia McKinlay, James B. B. McKinlay
Summary: This article presents a new genome sequence for the derivative strain CGA0092 of Rhodopseudomonas palustris CGA009, which is a versatile model purple nonsulfur bacterium used for both fundamental and applied research.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Biotechnology & Applied Microbiology
Breah LaSarre, Ryan Morlen, Gina C. Neumann, Caroline S. Harwood, James B. McKinlay
Summary: Partial denitrifiers can still be regulated by denitrification intermediates that they cannot use.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Amee A. Sangani, Alexandra L. McCully, Breah LaSarre, James B. McKinlay
FEMS MICROBIOLOGY LETTERS
(2019)
Article
Microbiology
Fredrick J. Lee, Kayla Miller, James B. McKinlay, Irene L. G. Newton
FEMS MICROBIOLOGY ECOLOGY
(2018)