Article
Biochemical Research Methods
Hiroshi Mori, Hitoshi Ishikawa, Koichi Higashi, Yoshiaki Kato, Toshikazu Ebisuzaki, Ken Kurokawa
Summary: PZLAST is a rapid amino acid sequence similarity search tool that can search user sequences against public metagenomic data within a short period of time. Its fast search speed is achieved by utilizing the PEZY-SC2 processor and summarizing results based on the environmental distribution of similar sequences.
Article
Biochemical Research Methods
Giovanni Marques de Castro, Zandora Hastenreiter, Thiago Augusto Silva Monteiro, Thieres Tayroni Martins da Silva, Francisco Pereira Lobo
Summary: This article presents and validates a machine learning strategy to predict essential genes in insects using sequence-based intrinsic attributes and transcriptomic data. Even models trained using only intrinsic attributes can predict genes in other insect species, including lineage-specific essential genes. Furthermore, the inclusion of RNA-Seq data contributes to increased classifier performance.
Article
Biology
Gabrielle E. Scolaro, Edward L. Braun
Summary: The rates of amino acid substitution during evolutionary time are influenced by the chemical properties of amino acids. Different substitution rates reflect different evolutionary models, which can be shaped by both evolutionary history and environmental factors. This study provides evidence that both history and environment contribute to model differences in protein evolution.
Article
Biochemistry & Molecular Biology
Yuhua Fu, Hong Liu, Jingwen Dou, Yue Wang, Yong Liao, Xin Huang, Zhenshuang Tang, JingYa Xu, Dong Yin, Shilin Zhu, Yangfan Liu, Xiong Shen, Hengyi Liu, Jiaqi Liu, Xin Yang, Yi Zhang, Yue Xiang, Jingjin Li, Zhuqing Zheng, Yunxia Zhao, Yunlong Ma, Haiyan Wang, Xiaoyong Du, Shengsong Xie, Xuewen Xu, Haohao Zhang, Lilin Yin, Mengjin Zhu, Mei Yu, Xinyun Li, Xiaolei Liu, Shuhong Zhao
Summary: IAnimal is a cross-species, multi-omics knowledgebase that aims to improve the utilization of multi-omics data and simplify data integration for better understanding of gene regulation mechanisms and comprehensive analyses of biological systems.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Virology
Julia Kende, Massimiliano Bonomi, Sarah Temmam, Beatrice Regnault, Philippe Perot, Marc Eloit, Thomas Bigot
Summary: The improvement of knowledge about unknown viruses in the virosphere is crucial in virology. However, current evaluation methods for metagenomics tools do not consider their ability to detect novel or distant viruses. Simulating realistic evolutionary directions is essential for benchmarking and improving these tools. The Virus Pop pipeline is introduced here as a tool for simulating realistic protein sequences and expanding databases to better detect distant viruses. It has been demonstrated that Virus Pop is capable of generating simulated sequences that closely resemble real protein sequences and can identify novel pathogenic viruses not included in the databases.
Article
Mathematical & Computational Biology
Petr Rysavy, Filip Zelezny
Summary: In this paper, a tool for reference-free phylogeny is introduced, which can handle data without mature-level assembly. The tool calculates the Levenshtein distance between sequences, estimating the number of mutations between organisms. Novelty lies in the proposed combination of read and contig measures, a new method for read-contig mapping, and efficient embedding of contigs, compared to previous research.
Review
Cell Biology
Lon J. Van Winkle
Summary: Amino acid transport and metabolism play crucial roles in embryo development, with disturbances in these processes potentially leading to undesirable health outcomes in adults.
Article
Ecology
Barbara Bauer, Emilio Berti, Remo Ryser, Benoit Gauzens, Myriam R. Hirt, Benjamin Rosenbaum, Christoph Digel, David Ott, Stefan Scheu, Ulrich Brose
Summary: Research shows that while there is a correlation between species dissimilarity and food-web structures, much of the variation in food-web structure remains unexplained. Novel food-web assembly models demonstrate the importance of biotic filtering during community assembly, constraining the variability in food-web patterns across local communities.
Article
Biochemistry & Molecular Biology
Elias Primetis, Spyridon Chavlis, Pavlos Pavlidis
Summary: In this study, amino acid interactions and substitutions were investigated, revealing that substitutions are associated with the spatial neighborhoods of amino acid residuals, providing insights into the amino acid substitution process.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Wei-Ting Liu, Cheng-Chen Chen, Dar-Der Ji, Wu-Chun Tu
Summary: This study aimed to investigate whether the cecropin-prophenoloxidase regulatory mechanism is a cross-species physiological function among mosquitoes. The results showed that three mosquito cecropin Bs play crucial roles in cuticle formation during pupal development via the regulation of prophenoloxidase 3. The effects of cecropin B knockdown were rescued in a cross-species manner by injecting synthetic cecropin B peptide into pupae. Further investigations revealed that these cecropin B peptides bind to specific motifs within the PPO 3 DNA fragments obtained from the mosquitoes. These findings suggest the existence of similar cecropin-prophenoloxidase regulatory mechanisms in multiple mosquito species.
Article
Chemistry, Multidisciplinary
Liang Ai, Jie Feng, Yu Hua Yao
Summary: In this paper, a new fast alignment-free method is proposed for protein sequence similarity and evolutionary analysis. The method clusters the 20 natural amino acids into 6 groups based on their physicochemical properties and constructs a 12-dimensional vector for each reduced amino acid sequence. The Euclidean distance is then used to measure the similarity and evolutionary distance between protein sequences. Experimental results on three datasets demonstrate the effectiveness of the proposed method in accurately clustering protein sequences.
MATCH-COMMUNICATIONS IN MATHEMATICAL AND IN COMPUTER CHEMISTRY
(2023)
Article
Plant Sciences
Tian Wan, Bai-xue Qiao, Jing Zhou, Ke-sen Shao, Liu-yi Pan, Feng An, Xu-sheng He, Tao Liu, Ping-ke Li, Yu-liang Cai
Summary: This study reports the chloroplast genome sequences of 11 Cerasus species to investigate the evolution of their plastome. The results reveal the typical quadripartite circular structure of Cerasus chloroplast genomes and the presence of 115 unique genes. Several genes were found to have high nucleotide diversity and more polymorphic sites, including matK, rps16, and rbcL. The phylogenetic analysis sheds light on the relationships between different Cerasus species, providing insights for further research on their phylogenetics and phylogeography.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Chemistry, Physical
Anna Zmich, Lydia J. Perkins, Craig Bingman, Justin F. Acheson, Andrew R. Buller
Summary: Pyridoxal phosphate (PLP)-dependent enzymes provide access to a variety of non-canonical amino acids (ncAAs), which are crucial for building complex bioactive molecules. The vinylglycineketimine (VGK) subfamily of PLP-dependent enzymes, known for its role in sulfur metabolism, includes both desirable synthases and lyases that break down ncAAs. Through substrate multiplexed screening, we identified a thermostable and highly expressive & gamma;-synthase from Caldicellulosiruptorhydrothermalis (CahyGS) that enables preparative-scale synthesis of thioether-containing ncAAs.
Article
Biodiversity Conservation
Ramiro Martin-Devasa, Sara Martinez-Santalla, Carola Gomez-Rodriguez, Rosa M. Crujeiras, Andres Baselga
Summary: This study aimed to assess the dependence between the form of the decrease in biological similarity with distance (distance-decay) and species range size, and introduced the use of a sigmoidal model, the Gompertz function, for fitting distance-decay models. The results showed that the functional form of distance-decay patterns depends on species range size, and the Gompertz function accommodates different frequency distributions of species range size.
DIVERSITY AND DISTRIBUTIONS
(2022)
Article
Biochemistry & Molecular Biology
Wenyue Huang, Xiaona Hu, Yanlin Ren, Minggui Song, Chuang Ma, Zhenyan Miao
Summary: The advent of high-throughput sequencing technologies has led to the production of a significant amount of omics data in plants. However, the lack of comprehensive platforms providing evolutionary annotation information and multi-species multi-omics data has hindered systematic and efficient analysis on specific genes. In order to address this issue, an advanced plant multi-omics platform, IPOP, has been established, which collects and analyzes various types of data and provides tools to facilitate evolutionary and functional analysis. This platform offers valuable insights and data for cross-species comparison and evolutionary research in the plant sciences community.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)