Article
Oncology
Argun Akcakanat, Xiaofeng Zheng, Christian X. Cruz Pico, Tae-Beom Kim, Ken Chen, Anil Korkut, Aysegul Sahin, Vijaykumar Holla, Emily Tarco, Gopal Singh, Senthil Damodaran, Gordon B. Mills, Ana Maria Gonzalez-Angulo, Funda Meric-Bernstam
Summary: Molecular profiling in metastatic breast cancer patients revealed common and less frequent but potentially actionable alterations, demonstrating intertumoral heterogeneity and potential evolution of actionable targets with tumor progression. Further optimization of testing and integrated analysis for treatment selection is needed.
CLINICAL CANCER RESEARCH
(2021)
Article
Biology
Yuka Takemon, Joel M. Chick, Isabela Gerdes Gyuricza, Daniel A. Skelly, Olivier Devuyst, Steven P. Gygi, Gary A. Churchill, Ron Korstanje
Summary: By measuring mRNA and protein levels in genetically diverse mice at different ages, we found distinctive changes in mRNA and protein levels as age increases. These changes are associated with increased immune infiltration and decreased mitochondrial function. Proteins show a greater extent of change and reveal a wide array of biological processes affected, including unique features of aging in kidney. Most importantly, functionally important age-related protein changes were observed in the absence of corresponding mRNA changes, suggesting that mRNA profiling alone does not provide a complete picture of molecular aging in the kidney.
Article
Biochemistry & Molecular Biology
Wendell Albuquerque, Parviz Ghezellou, Leif Seidel, Johannes Burkert, Frank Will, Ralf Schweiggert, Bernhard Spengler, Holger Zorn, Martin Gand
Summary: This study presents the first comprehensive identification of proteome content from a white wine (cv. Silvaner). By using mass spectrometry-based proteomics, the wine protein composition was identified through in-solution and in-gel digestion methods after size exclusion chromatographic fractionation. A total of 154 characterized or uncharacterized proteins mainly from Vitis vinifera L. and Saccharomyces cerevisiae were identified, providing valuable information for wine authentication and understanding of organoleptic properties and stability.
Article
Biotechnology & Applied Microbiology
Simona Guerrini, Damiano Barbato, Lorenzo Guerrini, Eleonora Mari, Giacomo Buscioni, Silvia Mangani, Yuri Romboli, Viola Galli, Alessandro Parenti, Lisa Granchi
Summary: The study focuses on using indigenous Saccharomyces cerevisiae strains for wine fermentation, with a pilot-plant established in a winery to produce fresh yeast biomass efficiently. The wines produced with the indigenous strain exhibited unique flavors and characteristics compared to those made with commercial starters, demonstrating the effectiveness of the pilot-plant in enhancing enological performance.
FERMENTATION-BASEL
(2021)
Article
Biochemistry & Molecular Biology
Marine Gueugneau, Cecile Coudy-Gandilhon, Christophe Chambon, Julien Verney, Daniel Taillandier, Lydie Combaret, Cecile Polge, Stephane Walrand, Frederic Roche, Jean-Claude Barthelemy, Leonard Feasson, Daniel Bechet
Summary: The study found that healthy aging in old men is associated with upregulation of apoptosis and immune function, as well as downregulation of glycolysis and protein catabolism, while metabolic syndrome is mainly characterized by upregulation of proteolysis and downregulation of oxidative phosphorylation. This indicates potential muscle biomarkers for healthy aging and metabolic syndrome in old men.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Mei-hua Bao, Ruo-qi Zhang, Xiao-shan Huang, Ji Zhou, Zhen Guo, Bao-feng Xu, Rui Liu
Summary: Atherosclerosis is a chronic inflammatory disease with high prevalence and mortality, where plaque rupture is the main cause of clinical events. Analyzing the transcriptomic and proteomic profiles of stable and unstable plaques helps to prevent clinical manifestations. The study identified differentially expressed RNAs and proteins related to stress response, gene transcription, immune response, nervous system functions, hematologic activities, and the endocrine system, providing insights into regulating plaque stability.
FRONTIERS IN GENETICS
(2021)
Article
Food Science & Technology
Qian Zhang, Jian Ma, Yupei Yang, Jing Deng, Kaixian Zhu, Yuwen Yi, Junni Tang, Xiaole Jiang, Chenglin Zhu, Luca Laghi
Summary: Fermenting kiwifruit into kiwi wine can reduce economic losses, and this study evaluated the sensory characteristics and flavor profiles of kiwi wine fermented by different yeast strains, finding suitable strains for kiwi wine production.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Carmen Berbegal, Sergi Ferrer, Lucia Polo, Isabel Pardo, Maria Jose Garcia-Esparza, Lorena Andres, Inmaculada Alvarez, Victoria Lizama
Summary: The aim of this study was to isolate and characterize indigenous Saccharomyces cerevisiae yeasts from Cabernet Sauvignon grape must and investigate their impact on the final characteristics of the wines produced. The study was conducted at a Pago winery in Requena, Spain. Twenty-two yeasts were isolated from the grape must, and after molecular identification and typing, 11 different strains were identified. Laboratory-scale fermentations were performed to determine growth-related parameters and metabolic characteristics, while larger-scale fermentations were used to analyze the chemical and sensory attributes of the wines produced. Differences between strains in terms of growth and metabolism were observed. The goal was to identify the strains that would produce the highest concentrations of polyphenols and aromatics in the red Cabernet wines of the winery for future use.
FERMENTATION-BASEL
(2023)
Article
Biochemistry & Molecular Biology
Peng Lu, Jiaqiao Zhou, Sibo Wei, Konosuke Takada, Hayato Masutani, Suguru Okuda, Ken Okamoto, Michio Suzuki, Tomoya Kitamura, Kentaro Masujin, Takehiro Kokuho, Hideaki Itoh, Koji Nagata
Summary: African swine fever (ASF) is a devastating disease caused by the African swine fever virus (ASFV) that threatens the pig industry and food security worldwide. This study identified potential vaccine targets for developing a broad-spectrum defense against ASFV by analyzing genomic and transcriptomic data of different ASFV strains. The results provide valuable candidate ORFs for ASF vaccine development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Food Science & Technology
Cintia Rompkovksi, Bruna Carla Agustini, Flavia Deffert, Maria Goreti Amboni Stadtlober, Debora Brand, Gildo Almeida da Silva, Tania Maria Bordin Bonfim
Summary: The use of non-Saccharomyces yeast strains in winemaking is gaining popularity as consumers demand new and healthier wine styles. However, scaling up these strains for industrial fermentation poses challenges. Current research focuses on expanding laboratory inoculations within winery environments to confirm viability and analyze resveratrol content in the final wines.
JOURNAL OF FOOD SCIENCE AND TECHNOLOGY-MYSORE
(2022)
Article
Food Science & Technology
Magdalena A. Mann, Lisa M. Frisch, Rudi F. Vogel, Ludwig Niessen
Summary: Research indicated significant differences in PAU5 production among different yeast strains and under varied fermentation conditions, highlighting the potential impact on the gushing potential of sparkling wines.
FOOD RESEARCH INTERNATIONAL
(2021)
Article
Food Science & Technology
Vanesa Postigo, Paula Sanz, Margarita Garcia, Teresa Arroyo
Summary: The use of non-Saccharomyces yeasts in brewing can improve the sensory profile of beers and produce low-alcohol functional beers. This study evaluated the capacity of non-Saccharomyces strains isolated from Madrid agriculture in brewing. The results showed the potential of these strains in producing low-alcohol beers and enhancing flavors in sequential fermentation.
Article
Environmental Sciences
Zhen Qin, Qianqian Ge, Jiajia Wang, Mingdong Li, Ping Liu, Jian Li, Jitao Li
Summary: The study investigated the alkalinity adaptation mechanism of the ridgetail white prawn through integrated analysis of gill-specific transcriptome and proteome. The results revealed up-regulated genes and proteins related to ion transport at 12 hours, as well as enriched pathways related to carbohydrate metabolism and immune response at 36 hours after alkalinity exposure. This comprehensive analysis sheds light on the molecular response to alkalinity stress in shrimp.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Biochemical Research Methods
Xinyue Liu, Jiaming Li, Steven P. Gygi, Joao A. Paulo
Summary: Saccharomyces cerevisiae is widely used for studying biological functions and pathways. In this study, the yeast proteome was analyzed using sample multiplexing, uncovering protein networks and gene ontology classifications. The dataset provides a valuable resource for future investigations and serves as a template for network analysis using yeast deletion strain collections.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Microbiology
Giovana Girardi-Piva, Erick Casalta, Jean-Luc Legras, Thibault Nidelet, Martine Pradal, Faiza Macna, David Ferreira, Anne Ortiz-Julien, Catherine Tesniere, Virginie Galeote, Jean-Roch Mouret
Summary: Sterols play an essential role in wine yeast fermentation, promoting yeast growth, metabolism, and viability, as well as resistance to stress. Ergosterol has a greater impact on yeast metabolism and cell viability compared to phytosterols.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Food Science & Technology
Marianne McKay, Florian F. Bauer, Valeria Panzeri, Astrid Buica
Summary: The study confirms that work related to wine matrices can be carried out with PM rather than DA, suggesting that the limitations of DA can be addressed through careful choice of evaluation method. It also emphasizes the importance of carefully considering the composition of the matrix when determining and comparing olfactory perceptual interactions in wine and when evaluating the effects of treatments on wine aroma.
JOURNAL OF SENSORY STUDIES
(2021)
Review
Food Science & Technology
Lethiwe Lynett Mbuyane, Florian Franz Bauer, Benoit Divol
Summary: This review article provides an extensive evaluation of the biosynthesis, accumulation, metabolism and regulation of fatty acids and sterols in yeasts, discussing the implications of yeast lipid content on stress resistance and performance during alcoholic fermentation, with a particular emphasis on non-Saccharomyces yeasts.
FOOD RESEARCH INTERNATIONAL
(2021)
Review
Biotechnology & Applied Microbiology
C. G. Conacher, N. A. Luyt, R. K. Naidoo-Blassoples, D. Rossouw, M. E. Setati, F. F. Bauer
Summary: The general interest in microbial ecology has surged in the past decade, driven by technological advances and the recognition of the fundamental services provided by these ecosystems. In biotechnology, ecosystems offer more functionalities than single species, but their complexity and interactions limit their applications. Research shows that next generation sequencing can accurately map microbiomes, but functional microbiomics is needed to bridge the gap between mapping and understanding.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
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
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)