Review
Plant Sciences
Lorenzo N. Bizzio, Denise Tieman, Patricio R. Munoz
Summary: This review discusses the current state of research on fruit BCV biosynthesis from the perspective of molecular biology. The authors survey the diversity of BCV compounds identified in fruits and explore hypotheses regarding their biosynthesis. Additionally, insights from branched-chain precursor compound metabolism in non-plant organisms and potential avenues for future research are considered.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Antonio G. Cordente, Damian Espinase Nandorfy, Mark Solomon, Alex Schulkin, Radka Kolouchova, Ian Leigh Francis, Simon A. Schmidt
Summary: The study investigated the impact of higher alcohols on the aroma and flavor of wine, showing that they not only increase the concentration of 2-phenylethanol but also modulate the formation of other higher alcohols, highlighting the connections between yeast nitrogen and sulfur metabolism during fermentation. Additionally, the analysis of these compounds during wine storage and sensory properties revealed the differences produced by biologically modulating higher alcohols and the dynamic changes in wine flavor over aging.
Article
Pharmacology & Pharmacy
Tiangang Wu, Mengling Wang, Fengling Ning, Shilin Zhou, Xuetao Hu, Hong Xin, Svetlana Reilly, Xuemei Zhang
Summary: Fibrosis, characterized by excessive production of extracellular matrix, is a common pathological feature of organ diseases. Metabolic alterations, especially in the regulation of branched-chain amino acids (BCAAs), have been found to play significant roles in fibrogenesis. Dysregulation of BCAAs metabolism has been implicated in various diseases. This review summarizes the metabolic regulation of fibrosis, changes in BCAAs metabolism associated with fibrosis, and the effects and mechanisms of BCAAs intervention in hepatic, renal, and cardiac fibrosis, with a focus on liver fibrosis and associated hepatocellular carcinoma.
PHARMACOLOGICAL RESEARCH
(2023)
Review
Genetics & Heredity
Can Chen, Hassan Naveed, Keping Chen
Summary: This article introduces the important role of branched-chain amino acid aminotransferases in cellular metabolism, summarizes the related research in animals, plants, microorganisms, and humans, and analyzes the molecular mechanism. It has been found that disorders in branched-chain amino acid metabolism are closely related to various diseases, especially tumor development.
FRONTIERS IN GENETICS
(2023)
Article
Microbiology
Maria del Carmen Gonzalez-Jimenez, Juan Carlos Mauricio, Jaime Moreno-Garcia, Anna Puig-Pujol, Juan Moreno, Teresa Garcia-Martinez
Summary: Higher alcohols produced by yeast during fermentation significantly affect the smell and taste of wine. This study investigates the metabolic and proteomic changes of Saccharomyces cerevisiae under CO2 overpressure during secondary fermentation using proteomics and metabolomics. Results show differences in metabolic and proteomic profiles between pressure and no-pressure conditions, suggesting that CO2 overpressure may influence higher alcohol metabolism. These findings provide a basis for understanding the behavior of yeast during secondary fermentation in sparkling wine production.
Article
Chemistry, Multidisciplinary
Jia-yu Yu, Nancy Cao, Christoph D. Rau, Ro-Po Lee, Jieping Yang, Rachel J. Roth Flach, Lauren Petersen, Cansheng Zhu, Yea-Lyn Pak, Russell A. Miller, Yunxia Liu, Yibin Wang, Zhaoping Li, Haipeng Sun, Chen Gao
Summary: Parallel to changes in fatty acid and glucose metabolism, defects in branched-chain amino acid (BCAA) catabolism have been recognized as a metabolic hallmark and potential therapeutic target for heart failure. This study developed two mouse models to investigate the impact of BCAA catabolic defects in cardiomyocytes. The results showed that inactivation of the BCKDHA gene in cardiomyocytes led to loss of cardiac function and pathological changes, while inactivation of the BCKDK gene did not impact cardiac function. These findings establish the cell-autonomous role of BCAA catabolism in cardiac physiology and provide valuable models for studying BCAA-targeted therapy for heart failure.
ACTA PHARMACOLOGICA SINICA
(2023)
Article
Cell Biology
Sonia Ravanelli, Qiaochu Li, Andrea Annibal, Aleksandra Trifunovic, Adam Antebi, Thorsten Hoppe
Summary: Using genetics and multi-omics analyses, researchers have found a link between branched-chain amino acid metabolism and the regulation of the ubiquitin-proteasome system. This sheds light on the role of branched-chain amino acids in the aging process and opens up possibilities for future therapeutic interventions.
Article
Agronomy
Di Gong, Yang Bi, Yuanyuan Zong, Yongcai Li, Edward Sionov, Dov Prusky
Summary: The study revealed that infection with Penicillium expansum significantly increased the accumulation of amino acids in apple fruits, leading to enhanced biosynthesis of branched-chain volatile compounds.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2021)
Review
Oncology
Er Xu, Bangju Ji, Ketao Jin, Yefeng Chen
Summary: Branched-chain amino acids (BCAAs) play a crucial role in tumorigenesis and can influence tumor growth and progression. Increased levels of BCAAs have been associated with tumor growth inhibition, while a deficiency in BCAAs can promote tumor metastasis. BCAAs serve as nitrogen donors, contributing to the synthesis of macromolecules crucial for cancer cell growth. This review discusses the dual role of BCAAs in cancer and provides insights into their potential as therapeutic interventions.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemical Research Methods
Catarina Pereira, Davide Mendes, Thomas Dias, Raquel Garcia, Marco Gomes da Silva, Maria Joao Cabrita
Summary: The importance of yeasts in aroma production during wine fermentation is crucial for wine producers aiming to improve complexity and enhance specific characteristics. This study aimed to investigate the impact of different Saccharomyces-type yeasts on the AAs composition and volatile profile of Arinto white wines. Results showed significant differences in AAs content and volatile profile among the Arinto wines, with Native yeast resulting in wines with a volatile profile richer in esters compared to other samples.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Nutrition & Dietetics
Seonghee Park, Minjeong Chae, Hyoungsu Park, Kyong Park
Summary: The study aimed to investigate the association between BCAA intake and handgrip strength in Korean older adults, finding a positive correlation between leucine intake and handgrip strength, which is beneficial for maintaining muscle health.
Article
Microbiology
Joel T. Steyer, Damien J. Downes, Cameron C. Hunter, Pierre A. Migeon, Richard B. Todd
Summary: The study focuses on genes related to leucine biosynthesis in Aspergillus nidulans, identifying key enzyme-coding genes and investigating their contribution to BCAA biosynthesis. The research reveals that gene expression is regulated by leucine availability, which is crucial for pathogenic fungi to cause disease in hosts.
Article
Endocrinology & Metabolism
Deirdre K. Tobias, Samia Mora, Subodh Verma, Filio Billia, Julie E. Buring, Patrick R. Lawler
Summary: The study found that fasting was associated with lower plasma BCAA levels in women without metabolic syndrome or T2D, but had no significant impact on women with Type 2 diabetes. These results suggest that impaired BCAA metabolism may be related to the pathophysiology of T2D.
METABOLISM-CLINICAL AND EXPERIMENTAL
(2021)
Article
Biochemistry & Molecular Biology
Bo Zhang, Yan Chen, Xiaolei Shi, Mi Zhou, Lei Bao, Kimmo J. Hatanpaa, Toral Patel, Ralph J. DeBerardinis, Yingfei Wang, Weibo Luo
Summary: This study reveals that hypoxia induces upregulation of the BCAA transporter LAT1 and the BCAA metabolic enzyme BCAT1 in human glioblastoma cells through the mediation of HIF-1 and HIF-2. HIF-1α plays a critical role in hypoxia-induced BCAT1 expression, and knockout of HIFs reduces glutamate labeling from BCAAs in GBM cells. Inhibition of BCAT1 inhibits GBM cell growth under hypoxia, highlighting a previously unrecognized HIF-dependent metabolic pathway.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Valeryia Mikalayeva, Monika Pankeviciute, Vaidotas Zvikas, V. Arvydas Skeberdis, Sergio Bordel
Summary: The degradation of branched chain amino acids serves as an important energy and carbon source for the proliferation of some cancer cells, providing a potential therapeutic target.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Erica T. Prates, Michael R. Garvin, Mirko Pavicic, Piet Jones, Manesh Shah, Omar Demerdash, B. Kirtley Amos, Armin Geiger, Daniel Jacobson
Summary: Although SARS-CoV and SARS-CoV-2 possess highly similar protein arsenals, they have spread among humans at extremely different rates. Through proteome-wide comparative structural analysis, unique molecular elements in the SARS-CoV-2 proteome which may explain the differing consequences have been identified, including nonconservative substitutions in key functional regions such as the spike glycoprotein, nsp1, and nsp3. The conservation of functional protein regions within the two taxa is also notable.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Mirko Pavicic, Kirk Overmyer, Attiq Ur Rehman, Piet Jones, Daniel Jacobson, Kristiina Himanen
Summary: Image-based symptom scoring is a powerful tool for associating disease resistance with plant genotypes. This study presents two strategies for assessing severity and symptom progression of Botrytis infection in Arabidopsis leaves using pixel classification and chlorophyll fluorescence imaging. Both strategies provide robust and sensitive methods for tracking disease progression over time.
Article
Biochemistry & Molecular Biology
Delyana P. Vasileva, Jared C. Streich, Leah H. Burdick, Dawn M. Klingeman, Hari B. Chhetri, Christa M. Brelsford, J. Christopher Ellis, Dan M. Close, Daniel A. Jacobson, Joshua K. Michener
Summary: This study demonstrates the impact of restriction-modification systems on the distribution of recombination in bacteria, regardless of genome features. It also shows that recombination occurs uniformly across the bacterial genome and is not influenced by species-level genetic distance.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Natasha Alethea Luyt, Sandra Beaufort, Benoit Divol, Mathabatha Evodia Setati, Patricia Taillandier, Florian Franz Bauer
Summary: The study investigates the negative interaction between Saccharomyces cerevisiae and Lachancea thermotolerans during wine fermentations. Direct physical contact between these two yeast species reduces the culturability and viability of Lachancea thermotolerans, leading to earlier cell death, while also impacting the culturability of Saccharomyces cerevisiae. This interaction does not significantly affect major fermentation metabolites but does influence the production of some volatile compounds.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Microbiology
Lethiwe L. Mbuyane, Florian F. Bauer, Audrey Bloem, Carole Camarasa, Anne Ortiz-Julien, Benoit Divol
Summary: This study aimed to evaluate the influence of specific fatty acid and sterol mixtures on non-Saccharomyces yeast fermentation rates and the production of primary fermentation metabolites. The results showed that different lipid mixtures had species-dependent effects, which may be linked to variations in lipid profile and divergent metabolic activities. These findings suggest that species-specific lipid adjustments could optimize yeast metabolic footprint and wine organoleptic properties.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Food Science & Technology
Samantha C. Fairbairn, Ana Rita Monforte, Jeanne Brand, Antonio C. Silva Ferreira, Florian F. Bauer
Summary: This study explores the impact of yeast metabolic activity on producing wine-like aroma and finds that the de novo synthesis of aromatic compounds by yeast largely contributes to the sensory recognition of a product as wine. Furthermore, grape-derived volatile compounds are not necessary for creating a wine-like sensation.
Article
Microbiology
C. G. Conacher, R. K. Naidoo-Blassoples, D. Rossouw, F. F. Bauer
Summary: Nonlinear ecological interactions within microbial ecosystems, especially in eukaryotic microorganisms, remain understudied. This study investigated the transcriptomic response of Saccharomyces cerevisiae to pairwise versus tri-species culture and revealed the presence of higher-order interactions in the more complex setting, highlighting stress response and metabolic adaptation mechanisms.
Article
Microbiology
Jordi Tronchoni, Mathabatha Evodia Setati, Daniela Fracassetti, Federica Valdetara, David Maghradze, Roberto Foschino, Jose Antonio Curiel, Pilar Morales, Ramon Gonzalez, Ileana Vigentini, Florian Franz Bauer
Summary: Microbial diversity in vineyards and grapes influences the health and character of wine. The drivers of microbial diversity in vineyards and grapes are influenced by soil, climate, and viticultural practices. This study provides evidence for a grape core microbial consortium and suggests the existence of country-specific and cultivar-specific microbial fingerprints.
Article
Plant Sciences
Spela Tomaz, Marko Petek, Tjasa Lukan, Karmen Pogacar, Katja Stare, Erica Teixeira Prates, Daniel A. Jacobson, Jan Zrimec, Gregor Bajc, Matej Butala, Marusa Pompe Novak, Quentin Dudley, Nicola Patron, Ajda Taler-Vercic, Aleksandra Usenik, Dusan Turk, Salome Prat, Anna Coll, Kristina Gruden
Summary: This study identified a novel potato transcription factor, StTGA2.1, which plays a crucial role in hormone-mediated immune responses by interacting with other transcription factors. The study also revealed the molecular mechanisms of StTGA2.1 and its regulation of key genes involved in plant immune response.
Article
Food Science & Technology
Micha Horacek, Helene Nieuwoudt, Florian F. Bauer, Bahareh Bagheri, Mathabatha E. Setati
Summary: Geographic origin and terroir greatly affect the price of wine. Measures for control are needed due to intentional incorrect declarations. This study compares the stable isotope pattern of South African wine with Central European/Austrian wine and shows that discrimination between the two regions is generally straightforward. However, exceptionally hot and dry summers in Europe may reduce this differentiation.
Article
Biochemistry & Molecular Biology
Jaclyn M. Noshay, Tyler Walker, William G. Alexander, Dawn M. Klingeman, Jonathon Romero, Angelica M. Walker, Erica Prates, Carrie Eckert, Stephan Irle, David Kainer, Daniel A. Jacobson
Summary: Empirical rules-of-thumb for sgRNA efficiency are limited, and this study introduces a new feature set and public resource for interpreting and predicting sgRNA efficiency using quantum chemical tensors. The study identifies important traits for sgRNA design in bacterial species and captures intricate interactions in local and neighboring nucleotides of the target DNA by encoding quantitative attributes of position-specific sequences using quantum descriptors. These novel encodings enhance our understanding of the quantum biological processes involved in CRISPR-Cas9 machinery.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Thaddeus J. Kunkel, Alice Townsend, Kyle A. Sullivan, Jean Merlet, Edward H. Schuchman, Daniel A. Jacobson, Andrew P. Lieberman
Summary: The study reveals that the deficiency of the intracellular cholesterol transporter NPC1 in Npc1(-/-) mice leads to impaired oligodendrocyte lineage cell differentiation and developmental myelination through disrupted epigenetic regulation. The researchers also identify potential therapeutic targets, such as the use of H3K27 demethylase inhibitors, to rescue this phenotype. These findings highlight the importance of NPC1 in oligodendrocyte development and provide insights for targeted therapeutic interventions.
NATURE COMMUNICATIONS
(2023)
Proceedings Paper
Computer Science, Artificial Intelligence
Jean Merlet, John Lagergren, Veronica G. Melesse Vergara, Mikaela Cashman, Christopher Bradburne, Raina Plowright, Emily Gurley, Wayne Joubert, Daniel Jacobson
Summary: This study developed an exhaustive vector comparison method to classify SARS-CoV-2 genome sequences and found that the distribution of Omicron variants differed spatially across countries.
PROCEEDINGS OF THE PLATFORM FOR ADVANCED SCIENTIFIC COMPUTING CONFERENCE, PASC 2023
(2023)
Article
Biotechnology & Applied Microbiology
Eleonore Pourcelot, Cleo Conacher, Therese Marlin, Florian Bauer, Virginie Galeote, Thibault Nidelet
Summary: This study provides fundamental insights into the microbial dynamics in early fermentation and contributes to the understanding of more complex consortia encompassing multiple yeast strains. The results show that yeast species and strains play different roles in population dynamics, with strains having a greater impact on the strength of interactions.
FEMS YEAST RESEARCH
(2023)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Kshitij Mehta, Ashley Cliff, Frederic Suter, Angelica M. Walker, Matthew Wolf, Daniel Jacobson, Scott Klasky
Summary: The increasing volumes of scientific data and the popularity of ensemble workflows have led to new challenges for existing workflow management systems when scaling to extreme sizes. This paper describes the experience of scaling an ensemble workflow and proposes capabilities and abstractions for executing workflow at extreme scale.
2022 IEEE 18TH INTERNATIONAL CONFERENCE ON E-SCIENCE (ESCIENCE 2022)
(2022)