Article
Biochemical Research Methods
Dan Wang, Fei-Liao Lai, Feng Gao
Summary: A novel pipeline, Ori-Finder 3, based on the Z-curve methodology is presented for computational prediction of replication origins in Saccharomyces cerevisiae. The pipeline can predict ARS at the single-nucleotide level with 83% and 60% of the top 100 and top 300 predictions matching known ARS records.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Xiang Meng, Alan Reed, Sandie Lai, Juraj Szavits-Nossan, John E. G. McCarthy
Summary: Gene expression stochasticity is an inherent feature of biological systems, creating non-genetic cellular variation and influencing various processes. In this study, the researchers discovered a distinct form of non-transcriptional noise associated with the translation machinery and mRNA 5'UTR of the GCN4 gene in yeast. They characterized the heterogeneity of translation initiation mediated by GCN4-5'UTR using different techniques and found a subpopulation of cells that consistently exhibited enhanced GCN4 translation under non-starvation conditions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Wenhao Fu, Xiuling Cao, Tingting An, Huihui Zhao, Jie Zhang, Danqi Li, Xuejiao Jin, Beidong Liu
Summary: Our study screened a yeast non-essential gene-deletion library with NH4Cl and identified 61 NH4Cl-sensitive deletion mutants. Among them, 34 were confirmed through drop test analysis. Enrichment analysis of these 34 genes revealed that biosynthesis metabolism, mitophagy, MAPK signaling, and other pathways may play important roles in NH4Cl resistance. Transcriptome analysis under NH4Cl stress showed significant upregulation of 451 genes and significant downregulation of 835 genes. These genes are mainly enriched in nitrogen compound metabolic process, cell wall, MAPK signaling pathway, mitophagy, and glycine, serine and threonine metabolism.
Article
Cell Biology
Sevan Arabaciyan, Michael Saint-Antoine, Cathy Maugis-Rabusseau, Jean-Marie Francois, Abhyudai Singh, Jean-Luc Parrou, Jean-Pascal Capp
Summary: Single-cell variability of growth, especially in microbial cells, has been a focus of recent research. A new methodological pipeline was developed to investigate the influence of initial protein levels on microcolony growth rates, showing that the initial Tsl1 expression level did not affect growth rates. Further analysis on the natural variations of TPS1 expression did not reveal any correlations either.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
William M. Shaw, Lucie Studena, Kyler Roy, Piotr Hapeta, Nicholas S. McCarty, Alicia E. Graham, Tom Ellis, Rodrigo Ledesma-Amaro
Summary: CRISPR gene activation and inhibition is a powerful synthetic tool for influencing gene expression, with applications in foundational studies, cellular reprogramming, and metabolic engineering. The authors developed a method for inducible expression of multiple gRNAs, increasing the capacity for CRISPR gene activation and inhibition and enhancing flexibility in target gene manipulation. They also created a highly regulated and user-friendly CRISPR toolkit in yeast, enabling simultaneous activation and repression of 11 genes in central metabolism, resulting in a significant increase in succinic acid production.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Xiuling Cao, Tingting An, Wenhao Fu, Jie Zhang, Huihui Zhao, Danqi Li, Xuejiao Jin, Beidong Liu
Summary: This study identified the cellular pathways and key genes that respond to NaHCO3 stress through genome-wide screening using a Saccharomyces cerevisiae deletion mutant library. Bioinformatics and transcriptomic analysis revealed the specific cellular genes and pathways involved in NaHCO3 resistance.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Christoph B. Messner, Vadim Demichev, Julia Muenzner, Simran K. Aulakh, Natalie Barthel, Annika Roehl, Lucia Herrera-Dominguez, Anna-Sophia Egger, Stephan Kamrad, Jing Hou, Guihong Tan, Oliver Lemke, Enrica Calvani, Lukasz Szyrwiel, Michael Muelleder, Kathryn S. Lilley, Charles Boone, Georg Kustatscher, Markus Ralser
Summary: Functional genomic strategies are crucial for gene function annotation and regulatory network analysis. In this study, we integrated functional genomics with proteomics to quantify protein abundances in a large-scale knockout library of Saccharomyces cerevisiae using data-independent acquisition mass spectrometry. Our findings indicate that global protein expression is influenced by a complex interplay of biological and functional properties, and functional proteomics can complement current gene annotation strategies. This study provides insights into the principles governing protein expression and offers a valuable resource for functional annotation.
Article
Biotechnology & Applied Microbiology
S. Kalra, R. Peyser, J. Ho, C. Babbin, N. Bohan, A. Cortes, J. Erley, M. Fatima, J. Flinn, E. Horwitz, R. Hsu, W. Lee, V. Lu, A. Narch, D. Navas, I. Kalu, E. Ouanemalay, S. Ross, F. Sowole, E. Specht, J. Woo, K. Yu, J. D. Coolon
Summary: Precise regulation of transcription is crucial for normal organism form and function, and minor alterations in gene expression can lead to phenotypic variation and disease. In this study, we investigated the response of target genes to systematic reduction of RAP1 expression in Saccharomyces cerevisiae. Our results revealed that Rap1 acts as an activator for more target genes than as a repressor and functions differently in different gene groups. These findings expand our understanding of this important transcriptional regulator.
Article
Multidisciplinary Sciences
Ignacio Belda, Thomas C. Williams, Miguel de Celis, Ian T. Paulsen, Isak S. Pretorius
Summary: Synthetic metagenomics has the potential to reveal the complexity of microbial ecosystems by showing the simplicity of microbial communities captured in a single cell. Conceptually, a yeast cell carrying a representative synthetic metagenome could uncover the complexity of interactions between multiple species, as illustrated here with wine ferments.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Roger M. Pallares, David Faulkner, Dahlia D. An, Solene Hebert, Alex Loguinov, Michael Proctor, Jonathan A. Villalobos, Kathleen A. Bjornstad, Chris J. Rosen, Christopher Vulpe, Rebecca J. Abergel
Summary: Lanthanides, a group of critical elements widely used in various industries, have been found to potentially impact human health. This study used a functional toxicogenomics approach in baker's yeast to assess the toxicity mechanisms of lanthanides, revealing different trends and effects on cellular responses. The research highlighted the disruption of vesicle-mediated transport and biosynthetic pathways as key functions affected by lanthanides, with implications for potential targeting of human orthologs by these elements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Agricultural Engineering
Fengguang Zhao, Yaping Zhang, Jian Hu, Ce Shi, Xiang Ao, Shengding Wang, Ying Lin, Zhongwei Sun, Shuangyan Han
Summary: A haploid gene-deletion library was screened to identify 22 vanillin-tolerant mutants and investigate the tolerance mechanisms. The deleted genes in these mutants were found to be involved in phosphate and inositol polyphosphate metabolism and intracellular sterol transport. Activation of the phosphate signaling pathway was unfavorable for yeast under vanillin pressure, while inositol polyphosphates played a role in altering vanillin tolerance by regulating phosphate metabolism. Additionally, reducing sterol transport from the plasma membrane enhanced tolerance to vanillin. Two representative yeast deletions, pho84 Delta and lam3 Delta, showed good growth performance and rapid ethanol production in the presence of vanillin.
BIORESOURCE TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Mark Boltengagen, Daan Verhagen, Michael Roland Wolff, Elisa Oberbeckmann, Matthias Hanke, Ulrich Gerland, Philipp Korber, Felix Mueller-Planitz
Summary: In this study, the organization of nucleosomes in Saccharomyces cerevisiae was investigated using the Fiber-Seq technique. The results revealed deviations from the stereotypical nucleosome organization, including long linker DNAs between nucleosomes, missing nucleosomes in gene bodies, cell-to-cell heterogeneity in nucleosome occupancy, heterogeneous phasing of arrays, and irregular nucleosome spacing. These findings provide valuable information for understanding the chromatin structure and function.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Paul Cachera, Helen Olsson, Hilde Coumou, Mads L. Jensen, Benjamin J. Sanchez, Tomas Strucko, Marcel van den Broek, Jean-Marc Daran, Michael K. Jensen, Nikolaus Sonnenschein, Michael Lisby, Uffe H. Mortensen
Summary: CRI-SPA allows simple and rapid transfer of chromosomal genetic features between different strains of Saccharomyces cerevisiae. It is highly efficient and reproducible, and even allows marker-free transfer of genetic features. The simplicity, speed, and reliability of CRI-SPA make it a versatile tool for studying biological processes at a systems level.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jia-Hsin Huang, You-Rou Liao, Tzu-Chieh Lin, Cheng-Hung Tsai, Wei-Yun Lai, Yang-Kai Chou, Jun-Yi Leu, Huai-Kuang Tsai, Cheng-Fu Kao
Summary: iTARGEX, a new association framework, can identify novel regulators involved in biological traits without prior functional annotations. Experimental validation of the novel candidates provides solid evidence for their roles in the respective traits, converting genome-wide observations into causal gene function predictions. Further application of iTARGEX is expected to facilitate the discovery of new regulators and provide observations for novel mechanistic hypotheses regarding different biological traits and phenotypes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Li Cheng, Xuetong Yue, Zhaoyu Qin, Xiaogang Sun, Fuchu He, Junbiao Dai, Chen Ding
Summary: This study reports a genome-wide quantitative proteomic system that uses unique code peptides to achieve precise protein quantification. By systematically tagging and decoding 40 yeast proteins using mass spectrometry, the researchers successfully recovered all code peptides with a large and consistent quantitative dynamic range. Additionally, they verified the alterations in glucose and galactose metabolism pathways in yeast under different carbon source conditions.
Article
Critical Care Medicine
Jingjing Li, Kun-Hsing Yu, John Oehlert, Laura L. Jeliffe-Pawlowski, Jeffrey B. Gould, David K. Stevenson, Michael Snyder, Gary M. Shaw, Hugh M. O'Brodovich
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2015)
Article
Medicine, Research & Experimental
Xiaofeng Xin, Wei Dai, Jie Wu, Liping Fang, Ming Zhao, Pengpeng Zhang, Min Chen
EXPERIMENTAL AND THERAPEUTIC MEDICINE
(2016)
Article
Multidisciplinary Sciences
Pamela Milani, Renan Escalante-Chong, Brandon C. Shelley, Natasha L. Patel-Murray, Xiaofeng Xin, Miriam Adam, Berhan Mandefro, Dhruv Sareen, Clive N. Svendsen, Ernest Fraenkel
SCIENTIFIC REPORTS
(2016)
Article
Immunology
Pengpeng Zhang, Xiaofeng Xin, Liping Fan, Hao Jiang, Xiaoyong Xu, Xin Su, Yi Shi
INTERNATIONAL IMMUNOPHARMACOLOGY
(2017)
Article
Medicine, Research & Experimental
Peng-Peng Zhang, Xiao-Feng Xin, Xiao-Yong Xu, Li-Ping Fang, Jie Wu, Yi Shi
EXPERIMENTAL AND THERAPEUTIC MEDICINE
(2017)
Article
Medicine, Research & Experimental
Liping Fang, Jie Wu, Tao Huang, Pengpeng Zhang, Xiaofeng Xin, Yi Shi
EXPERIMENTAL AND THERAPEUTIC MEDICINE
(2018)
Article
Cell Biology
Anthony R. Soltis, Norman J. Kennedy, Xiaofeng Xin, Feng Zhou, Scott B. Ficarro, Yoon Sing Yap, Bryan J. Matthews, Douglas A. Lauffenburger, Forest M. White, Jarrod A. Marto, Roger J. Davis, Ernest Fraenkel
Article
Immunology
Fang Zhang, Xin Su, Gang Huang, Xiao-Feng Xin, E-Hong Cao, Yi Shi, Yong Song
JOURNAL OF IMMUNOLOGY RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Jingjing Li, Minyi Shi, Zhihai Ma, Shuchun Zhao, Ghia Euskirchen, Jennifer Ziskin, Alexander Urban, Joachim Hallmayer, Michael Snyder
MOLECULAR SYSTEMS BIOLOGY
(2014)
Article
Multidisciplinary Sciences
Fang Zhang, Xin Su, Gang Huang, Xiao-Feng Xin, E-Hong Cao, Yi Shi, Yong Song
SCIENTIFIC REPORTS
(2017)
Article
Oncology
Ming Zhao, Xiao-Feng Xin, Huan Hu, Xian-Hui Pan, Tang-Feng Lv, Hong-Bing Liu, Jian-Ya Zhang, Yong Song
TRANSLATIONAL LUNG CANCER RESEARCH
(2019)
Article
Oncology
Ming Zhao, Xiao-Feng Xin, Jian-Ya Zhang, Wei Dai, Tang-Feng Lv, Yong Song
Article
Multidisciplinary Sciences
Xiaojia Zhu, Yuwei Wang, Yujie Xiao, Qianwen Gao, Li Gao, Wenhui Zhang, Xiaofeng Xin, Kesu Chen, Ujala Srivastava, Vamsi Krishna Murthy Ginjupalli, Michael Cupelli, Pietro Enea Lazzerini, Pier Leopoldo Capecchi, Long Chen, Mohamed Boutjdir
Summary: Inflammatory diseases like COVID-19 are associated with a cytokine storm characterized by high levels of interleukin-6 (IL-6). This study aims to understand the electrophysiological basis of inflammation-associated arrhythmic risk with the presence of azithromycin (AZM) and hydroxychloroquine (HCQ). The results show that IL-6 alone or in combination with AZM and HCQ can cause mild to moderate reductions in heart rate, PR-interval, and corrected QT (QTc). IL-6 alone is more potent in affecting these measurements compared to the combination of drugs. Additionally, the combination of IL-6, AZM, and HCQ can lead to severe bradycardia, conduction abnormalities, and QTc prolongation. These abnormalities can be attenuated by tocilizumab (TCZ), a monoclonal antibody against IL-6 receptor, and are attributed to changes in action potentials and ion-currents. Inflammation poses a greater risk for arrhythmia than the drug combination therapy.
SCIENTIFIC REPORTS
(2022)
Article
Cardiac & Cardiovascular Systems
Pietro Enea Lazzerini, Riccardo Accioli, Maurizio Acampa, Wen-Hui Zhang, Decoroso Verrengia, Alessandra Cartocci, Maria Romana Bacarelli, Xiaofeng Xin, Viola Salvini, Ke-Su Chen, Fabio Salvadori, Antonio D'errico, Stefania Bisogno, Gabriele Cevenini, Tommaso Marzotti, Matteo Capecchi, Franco Laghi-Pasini, Long Chen, Pier Leopoldo Capecchi, Mohamed Boutjdir
Summary: This study investigates the short-term impact of IL-6 elevation on QTc in patients with severe COVID-19 and explores the underlying mechanisms. The findings demonstrate that IL-6 elevation can promote QTc prolongation through ventricular electric remodeling. These findings highlight the importance of anti-inflammatory treatment in COVID-19.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Proceedings Paper
Automation & Control Systems
Degao Hou, Xiaofeng Xin, Jiyu Qian
PROCEEDINGS OF THE SEVENTH ASIA INTERNATIONAL SYMPOSIUM ON MECHATRONICS, VOL II
(2020)