Article
Biotechnology & Applied Microbiology
Reihaneh Bashiri, Thomas P. Curtis, Irina D. Ofiteru
Summary: This study evaluates the capability of several protein public databases and scanning tools for identifying lipolytic features in cold-adapted bacterial lipase sequences. The findings show that there is a lack of information in public protein databases about bacterial lipase sequences, but the integration of AlphaFold within InterPro can significantly improve lipase identification and classification.
JOURNAL OF BIOTECHNOLOGY
(2022)
Article
Microbiology
Valerian Lupo, Paola Sandra Mercuri, Jean-Marie Frere, Bernard Joris, Moreno Galleni, Denis Baurain, Frederic Kerff
Summary: Bacterial genes encoding antibiotic resistance, especially beta-lactamases, are a major concern for combating bacterial pathogens. This study surveyed a reference database of genomes and identified a large variety of beta-lactamases, highlighting the diversity of these enzymes. It was also found that environmental bacteria serve as a reservoir for resistance genes that can be transferred to clinical strains.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Benoit Morel, Pierre Barbera, Lucas Czech, Ben Bettisworth, Lukas Huebner, Sarah Lutteropp, Dora Serdari, Evangelia-Georgia Kostaki, Ioannis Mamais, Alexey M. Kozlov, Pavlos Pavlidis, Dimitrios Paraskevis, Alexandros Stamatakis
Summary: Inferring reliable phylogenies from virus sequence data is difficult due to the large number of sequences and low number of mutations; rooting the inferred phylogeny with external outgroups or applying novel computational methods is not credible; automatic classification of current sequences into subclasses for molecular species delimitation is also not possible due to sequences being too closely related.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Physics, Multidisciplinary
Borja Vargas, David Cuesta-Frau, Paula Gonzalez-Lopez, Maria-Jose Fernandez-Cotarelo, Oscar Vazquez-Gomez, Ana Colas, Manuel Varela
Summary: This study applies three time series entropy calculation methods to body temperature records and finds that Slope Entropy is a stable and robust method with higher sensitivity in clinical thermometry.
Article
Biochemistry & Molecular Biology
Rajender Kumar
Summary: Lipases have diverse substrate specificity and can be modulated at the structural and functional level for improved versions. The structural analysis of microbial lipases provides insights into the characteristics of alkaliphilic and thermophilic lipases, such as conformational changes and solvent exposure of the active site. The integration of stability features from thermophilic lipases into alkaliphilic lipases can lead to the design of novel thermo-alkaliphilic lipases.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Mohamad Farihan Afnan Mohd Rozi, Raja Noor Zaliha Raja Abd Rahman, Adam Thean Chor Leow, Mohd Shukuri Mohamad Ali
Summary: This study investigates the evolutionary process of bacterial lipases from family I.3 and reconstructs the last universal common ancestor (LUCA) sequence through phylogenetic tree inference and ancestral sequence reconstruction (ASR) technique. The purified LUCA exhibits high temperature and pH adaptability, as well as tolerance towards metal ions and organic solvents. The findings contribute to the understanding of temperature and environment during ancient times, and the reconstructed ancestral enzymes have improved properties for industrial applications using ASR technique as a general enzyme engineering technique.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Arnaud Chatonnet, Michel Perochon, Eric Velluet, Pascale Marchot
Summary: The ESTHER database provides online access to a classification of proteins harboring the alpha/beta hydrolase fold and their relatives. It offers information on sequences, structures, ligands, and functions of these proteins, as well as related literature and databases. The database is important for biotechnological applications and new research in the field.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Chemistry, Medicinal
Matthias Fellner, Annabel Walsh, Stephen Dela Ahator, Nadia Aftab, Ben Sutherland, Eng W. Tan, Alexander T. Bakker, Nathaniel I. Martin, Mario van der Stelt, Christian S. Lentz
Summary: The development of new treatment options for bacterial infections requires the identification of new targets for antibiotics and antivirulence strategies. In this study, the authors characterized a serine hydrolase called FphH in Staphylococcus aureus and found its functional role in stress responses and potential connection with the ribosome rescue system. The atomic characterization of FphH will facilitate the development of specific inhibitors and probes to further understand its physiological role and validity as a drug target.
ACS INFECTIOUS DISEASES
(2023)
Article
Biochemical Research Methods
Sean M. Solari, Remy B. Young, Vanessa R. Marcelino, Samuel C. Forster
Summary: Shotgun metagenomic sequencing provides unprecedented resolution for understanding microbial community structure and function. However, current analytical methods focused on taxonomic classifications may obscure functional relationships. This paper presents expam, a taxonomy agnostic tool based on a tree structure, for identifying biologically relevant clades from shotgun metagenomic sequencing.
Article
Biochemistry & Molecular Biology
Xiaoyu Yang, Ting Guo, Juan Li, Zhong Chen, Bin Guo, Xinmin An
Summary: The study identified 152 PtrMYBRs in Populus, divided into six major subgroups, showing different expression patterns in various tissues and stress conditions. The MYB-related proteins are likely involved in plant development and stress responses in Populus, playing crucial roles in antioxidant defense system and signaling pathways regulation. The findings provide valuable information for understanding the functions of MYB-related proteins and genetic improvement of Populus.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Fang Wang, Ke Wang, Lei Cai, Mingjun Zhao, Paul M. Kirk, Guomei Fan, Qinglan Sun, Bo Li, Shuai Wang, Zhengfei Yu, Dong Han, Juncai Ma, Linhuan Wu, Yijian Yao
Summary: Fungal taxonomy is a complex and rapidly changing field, posing challenges for taxonomists in naming fungi. Fungal Names is a registration platform with a standardized and integrated database, providing powerful tools for research in fungal taxonomy. It encompasses a vast collection of taxon names and specimen records since 1596, along with other related information, serving as a summary of the history and recent advances in fungal taxonomy.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Jing Xu, Suming Dai, Xue Wang, Alessandra Gentile, Zhuo Zhang, Qingxiang Xie, Yajun Su, Dazhi Li, Bing Wang
Summary: Through studying the ADF gene family in sweet orange, seven CsADFs were identified and found to have potential impact on the development of sweet oranges under biotic or abiotic stress. Among them, CsADF4 was significantly up-regulated at 4 days post-infection and localized in both the nucleus and cytoplasm. Overexpression of CsADF4 enhanced the sensitivity of sweet orange leaves to pathogens.
Article
Microbiology
Anastasia A. A. Karlsen, Vera S. S. Kichatova, Karen K. K. Kyuregyan, Mikhail I. I. Mikhailov
Summary: HEV-3 and HEV- 4 show stable transmission patterns in deer species, indicating they may be true hosts. However, swine are the primary source of infection for deer and other ruminants. Further understanding of HEV-3 and HEV-4 circulation in wildlife requires complete genomic sequences from different regions.
Article
Mathematical & Computational Biology
Shalini Chaudhary, Yibing Wu, Doug Strongman, Yan Wang
Summary: CIGAF is a digital database focused on Trichomycete fungi, providing curated collection records from 1929 to 2022. It offers an interactive web interface for exploring field collection data, including insect host information, collection site coordinates, and climatic measures. CIGAF serves as a comprehensive resource hub for further research in mycology, entomology, symbiosis, and biogeography.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Biochemistry & Molecular Biology
Swati Verma, Gautam Kumar Meghwanshi, Rajender Kumar
Summary: Microbial lipases are widely used biocatalysts for environmental and industrial applications. Extremophile lipases exhibit higher activity and diversity, allowing for the design of biotransformation reactions with higher yields and less byproducts. Additionally, novel lipases can be discovered through analysis of unexplored nucleotide/metagenomic databases.
