Article
Biochemistry & Molecular Biology
Jade Sales-Lee, Daniela S. Perry, Bradley A. Bowser, Jolene K. Diedrich, Beiduo Rao, Irene Beusch, John R. Yates, Scott W. Roy, Hiten D. Madhani
Summary: The study identified that certain conserved spliceosomal proteins affect splicing efficiency and suppress splice errors in intron-rich fungi, potentially through kinetic proofreading mechanisms, facilitating greater intron diversity.
Article
Biochemistry & Molecular Biology
Damilare D. Akintade, Bhabatosh Chaudhuri
Summary: Apoptosis is a genetically regulated cell death process, with Bax playing a key role in programmed cell death. Research suggests that enhancing vesicular membrane trafficking can obstruct Bax-induced apoptosis in yeast, potentially through membrane repair mechanisms. Maintaining membrane integrity is crucial to prevent ion leakage and ultimately cell death from reactive oxygen species.
Article
Multidisciplinary Sciences
Davier Gutierrez-Gongora, Fouad Raouf-Alkadhimi, Ryan S. S. Prosser, Jennifer Geddes-McAlister
Summary: Extracts from mollusk species showed inhibitory effects on the growth and virulence factor production of Cryptococcus neoformans. The compounds derived from natural sources have the potential to inhibit virulence factor production in this fungal pathogen.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Alexander Kroll, Yvan Rousset, Xiao-Pan Hu, Nina A. Liebrand, Martin J. Lercher
Summary: Researchers developed a general model that can predict turnover numbers of enzyme-catalyzed reactions, even for dissimilar enzymes. This model outperforms existing models and provides a valuable tool for understanding enzyme efficiency and cellular physiology. The development of accurate computational prediction methods for turnover numbers is highly desirable due to the lack of experimental estimates.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Muhammad Nabeel Asim, Muhammad Ali Ibrahim, Muhammad Imran Malik, Andreas Dengel, Sheraz Ahmed
Summary: Predicting protein-protein interactions (PPI) is crucial for understanding the functions of proteins and their involvement in diseases. This paper introduces an AI-based approach that utilizes transfer learning to generate statistical representation of protein sequences, and proposes the ADH-PPI classifier that outperforms existing methods in predictive performance.
Article
Multidisciplinary Sciences
Naser Faraji, Seyed Shahriar Arab, Alireza Doustmohammad, Norelle L. Daly, Ahmad Yari Khosroushahi
Summary: ApInAPDB is a database containing 818 apoptosis-inducing anticancer peptides, providing peptide-related information and structural information calculation and presentation. Users can search through three user-friendly tools. This is of great significance for research in peptide design and cancer therapy.
SCIENTIFIC REPORTS
(2022)
Article
Agriculture, Dairy & Animal Science
Xue Yang, Chao Yang, Defu Tang, Qunli Yu, Li Zhang
Summary: This study investigated the effects of dietary selenium yeast and jujube powder on mitochondrial oxidative damage and cell apoptosis during postmortem aging of broilers. The findings suggest that different doses of selenium yeast and jujube powder can inhibit mitochondrial oxidation to varying degrees, providing protection against cell apoptosis.
Article
Fisheries
Zhixiong Xu, Junru Hu, Yufan Zhang, Lirong Bai
Summary: The objective of this study was to investigate the effects of selenium yeast on the growth, histomorphology, antioxidant capacity and apoptosis of largemouth bass. The results showed that the addition of 1.5 and 2.0 mg/kg of selenium yeast significantly reduced weight gain rate and specific growth rate, and disorganized the structure of liver cells in largemouth bass. However, the supplementation of 1.0 mg/kg selenium yeast increased the activities of glutathione peroxidase and superoxide dismutase in serum.
AQUACULTURE REPORTS
(2023)
Review
Biotechnology & Applied Microbiology
Darren K. Lam, Gavin Sherlock
Summary: The discovery of Yca1 metacaspase's role in regulating apoptosis in Saccharomyces cerevisiae has shed light on understanding apoptotic mechanisms in yeast. Furthermore, recent studies have revealed the involvement of Yca1 and other metacaspase proteins in various cellular processes, such as cellular proteostasis and cell cycle regulation. This minireview presents recent findings on Yca1, which will facilitate further research on the multifunctionality of metacaspases and novel apoptosis pathways in yeast and other non-metazoans. Additionally, advancements in high-throughput screening technologies are discussed, offering potential solutions for exploring the apoptotic and nonapoptotic functions of metacaspase proteins across different species.
FEMS YEAST RESEARCH
(2023)
Article
Endocrinology & Metabolism
Shan-Shan Dong, Dong-Li Zhu, Xiao-Rong Zhou, Yu Rong, Mengqi Zeng, Jia-Bin Chen, Feng Jiang, Xiao-Mei Tuo, Zhihui Feng, Tie-Lin Yang, Yan Guo
Summary: This study revealed the molecular mechanisms of an SNP (rs12454712) in the genome for central obesity and demonstrated its potential as a promising target for developing appropriate therapies.
Article
Biochemistry & Molecular Biology
Meiling Zhang, Zhe Jiang, Yichen Ma, Wenqing Liu, Yuan Zhuang, Bo Lu, Kai Li, Jinying Peng, Chengqi Yi
Summary: In this study, a method called "PRAISE" was developed to quantitatively assess the abundance of pseudouridine (psi) in the human transcriptome. The approach involved selective chemical labeling of psi with bisulfite, which induced a nucleotide deletion signature during reverse transcription. The results revealed a median modification level of about 10% for 2,209 confident psi sites in HEK293T cells. The method was also used to identify differential mRNA targets of pseudouridine synthases and quantified pseudouridine sites in mitochondrial mRNA catalyzed by PUS1.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Tiantian Han, Yingchun Zhou, Danhua Li
Summary: This study identified 199 common genes between HCC and depression, with GO term enrichment analysis showing association with cell death and apoptosis, and KEGG enrichment analysis showing pathways related to inflammatory response. Some genes exhibited statistical differences in expression and survival rates in HCC, possibly linked to associated drugs.
Article
Biochemical Research Methods
Henry Wang, Olivier Julien
Summary: CaspSites is a free-to-use database and web application that provides experimentally observed human caspase substrates using N-terminomics. It stores cleavage site information for caspases 1-9 in human lysates and apoptotic cells, collected from published studies. The database can be queried, viewed, and exported using the search page of the web application. CaspSites updates regularly with new experimental findings for understudied caspases, offering insights into the roles of human caspases in cellular processes.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Mengyi Sun, Jianzhi Zhang
Summary: In this study, direct evidence for the translational accuracy hypothesis (TAH) of codon usage bias is presented through analyzing proteomic data from Escherichia coli. The experimentally measured codon-specific translational accuracies validate a sequence-based proxy and support the TAH across various taxa. The relative translational accuracies of synonymous codons vary among taxa and are strongly correlated with the amounts of cognate transfer RNAs (tRNAs) relative to those of near-cognate tRNAs, suggesting coevolution between codon usage bias and the tRNA pool.
Article
Biochemistry & Molecular Biology
Wen-Chuan Hsieh, Benjamin M. Sutter, Holly Ruess, Spencer D. Barnes, Venkat S. Malladi, Benjamin P. Tu
Summary: Acetyl-CoA is a key intermediate that plays a critical role in coordinating gene expression with metabolic state. High levels of acetyl-CoA activate genes involved in cell growth or tumorigenesis through histone acetylation, but the role of histone acetylation under low levels of acetyl-CoA is not well understood. In a yeast starvation model, we observed a significant shift in the global occupancy of histone acetylation following carbon starvation. Histone acetylation marks relocate from growth-promoting genes to genes involved in gluconeogenesis and fat metabolism. This reallocation is mediated by the histone deacetylase Rpd3p and the acetyltransferase Gcn5p.
Article
Cell Biology
Kwanjeera Wanichthanarak, Nutvadee Wongtosrad, Dina Petranovic
MECHANISMS OF AGEING AND DEVELOPMENT
(2015)
Article
Multidisciplinary Sciences
Mingtao Huang, Yunpeng Bai, Staffan L. Sjostrom, Bjorn M. Hallstrom, Zihe Liu, Dina Petranovic, Mathias Uhlen, Haakan N. Joensson, Helene Andersson-Svahn, Jens Nielsen
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Correction
Biotechnology & Applied Microbiology
J. L. Martinez, D. Petranovic, J. Nielsen
Article
Neurosciences
Ana Joyce Munoz-Arellano, Xin Chen, Andrea Molt, Eugenio Meza, Dina Petranovic
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2018)
Article
Biotechnology & Applied Microbiology
Keith E. J. Tyo, Zihe Liu, Ylva Magnusson, Dina Petranovic, Jens Nielsen
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2014)
Article
Biotechnology & Applied Microbiology
Jose L. Martinez, Lifang Liu, Dina Petranovic, Jens Nielsen
BIOTECHNOLOGY AND BIOENGINEERING
(2015)
Review
Biotechnology & Applied Microbiology
Mario G. Mirisola, Ralf J. Braun, Dina Petranovic
FEMS YEAST RESEARCH
(2014)
Article
Biotechnology & Applied Microbiology
Jin Hou, Hongting Tang, Zihe Liu, Tobias Osterlund, Jens Nielsen, Dina Petranovic
FEMS YEAST RESEARCH
(2014)
Article
Biotechnology & Applied Microbiology
Lifang Liu, Jose L. Martinez, Zihe Liu, Dina Petranovic, Jens Nielsen
METABOLIC ENGINEERING
(2014)
Article
Biotechnology & Applied Microbiology
Hongting Tang, Jiajing Wang, Shenghuan Wang, Yu Shen, Dina Petranovic, Jin Hou, Xiaoming Bao
MICROBIAL CELL FACTORIES
(2018)
Article
Multidisciplinary Sciences
Luis Caspeta, Yun Chen, Payam Ghiaci, Amir Feizi, Steen Buskov, Bjorn M. Hallstrom, Dina Petranovic, Jens Nielsen
Article
Mathematical & Computational Biology
Kwanjeera Wanichthanarak, Intawat Nookaew, Dina Petranovic
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2014)
Article
Biotechnology & Applied Microbiology
Olena P. Ishchuk, August T. Frost, Facundo Muniz-Paredes, Saki Matsumoto, Nathalie Laforge, Nelida Leiva Eriksson, Jose L. Martinez, Dina Petranovic
Summary: By modifying the genes of Saccharomyces cerevisiae, researchers were able to reduce the degradation of human hemoglobin and increase its production to record levels during glucose fermentation. This increased production was accompanied by higher oxygen consumption rate and glycerol yield, indicating the yeast's response to rebalance its NADH levels under conditions of oxygen limitation and increased protein production.
METABOLIC ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Lifang Liu, Yiming Zhang, Zihe Liu, Dina Petranovic, Jens Nielsen
FEMS YEAST RESEARCH
(2015)
Article
Biotechnology & Applied Microbiology
Xin Chen, Dina Petranovic
FEMS YEAST RESEARCH
(2015)