Article
Virology
Katherine Li, Connor Lowey, Paul Sandstrom, Hezhao Ji
Summary: CAVES is a tool for comparing epitopes of closely related pathogens, providing fast analysis results and reducing user workload and time. It uses a two-level analysis approach and utilizes positional sequence data to improve accuracy and speed. CAVES is an open-source software that runs through a graphical user interface on Windows systems.
Article
Multidisciplinary Sciences
Jared L. Johnson, Tomer M. Yaron, Emily M. Huntsman, Alexander Kerelsky, Junho Song, Amit Regev, Ting-Yu Lin, Katarina Liberatore, Daniel M. Cizin, Benjamin M. Cohen, Neil Vasan, Yilun Ma, Konstantin Krismer, Jaylissa Torres Robles, Bert van de Kooij, Anne E. van Vlimmeren, Nicole Andree-Busch, Norbert F. Kaeufer, Maxim Dorovkov, Alexey G. Ryazanov, Yuichiro Takagi, Edward R. Kastenhuber, Marcus D. Goncalves, Benjamin D. Hopkins, Olivier Elemento, Dylan J. Taatjes, Alexandre Maucuer, Akio Yamashita, Alexei Degterev, Mohamed Uduman, Jingyi Lu, Sean D. Landry, Bin Zhang, Ian Cossentino, Rune Linding, John Blenis, Peter Hornbeck, Benjamin E. Turk, Michael B. Yaffe, Lewis C. Cantley
Summary: Protein phosphorylation is a common post-translational modification, and thousands of phosphorylated sites have been associated with human diseases and biological processes. However, the responsible protein kinases for most phosphorylation events are currently unknown. This study used synthetic peptide libraries to profile the substrate specificity of 303 Ser/Thr kinases and identified the kinases capable of phosphorylating reported phosphorylation sites.
Article
Biochemical Research Methods
Alexis Dereeper, Marilyne Summo, Damien F. Meyer
Summary: PanExplorer is a web application that provides various genomic analyses and reports, aiding in the better understanding of bacterial pan-genomes.
Article
Environmental Sciences
Qiang Wang, Min Zhang, Rongrong Li
Summary: The outbreak of the COVID-19 pandemic has worsened plastic pollution worldwide and has also changed the research trends in this field. The number of publications on plastic pollution has increased significantly since the pandemic began, and developing countries have become more involved in research on plastic pollution. Additionally, the focus of research has shifted towards solutions for plastic pollution, particularly in relation to microplastics. However, there is currently no effective solution for plastic pollution caused by COVID-19.
ENVIRONMENTAL RESEARCH
(2022)
Article
Genetics & Heredity
Pedram Rajaei, Khadijeh Hoda Jahanian, Amin Beheshti, Shahab S. Band, Abdollah Dehzangi, Hamid Alinejad-Rokny
Summary: Bioinformatics and computational biology contribute significantly to generating vast knowledge in biology. VIRMOTIF is a user-friendly comprehensive tool that integrates different functionalities for analyzing DNA sequences comprehensively, including computing motifs, visualizing data, and clustering analysis.
Article
Biochemical Research Methods
Margaret R. Woodhouse, Shatabdi Sen, David Schott, John L. Portwood, Michael Freeling, Justin W. Walley, Carson M. Andorf, James C. Schnable
Summary: RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. The comparative gene expression tool qTeller has been revamped to take advantage of the growing number of public RNA-Seq datasets, enabling users to evaluate gene expression data in a defined genomic interval and perform two-gene comparisons across multiple user-chosen tissues. The updated qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets, along with support for additional data formats and a modernized interface.
Article
Biochemical Research Methods
Patrick Adelberger, Klaus Eckelt, Markus J. Bauer, Marc Streit, Christian Haslinger, Thomas Zichner
Summary: A main task in computational cancer analysis is to identify patient subgroups based on metadata attributes or genomic markers, and the web-based cohort analysis tool Coral is designed to support this task by allowing users to interactively create, refine, and compare cohorts. Coral also visualizes the evolution of cohorts and provides intuitive access to prevalence information, as well as the ability to store, share, and reproduce findings. It is pre-loaded with data from over 128,000 samples from various cancer research projects.
Article
Biochemical Research Methods
Lang Zhou, Tingze Feng, Shuangbin Xu, Fangluan Gao, Tommy T. Lam, Qianwen Wang, Tianzhi Wu, Huina Huang, Li Zhan, Lin Li, Yi Guan, Zehan Dai, Guangchuang Yu
Summary: The identification of conserved and variable regions in multiple sequence alignment is crucial for accelerating gene function understanding. ggmsa, an R package, provides various display methods to mine comprehensive sequence features, supports correlation analysis, and offers a new visualization method for genome alignment, aiding researchers in discovering MSA patterns and making decisions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Mathematical & Computational Biology
Raphael Flores, Cecile Huneau, Laura Burlot, Mathilde Laine, Erik Kimmel, Cyril Pommier, Michael Alaux, Anne-Francoise Adam-Blondon, Caroline Pont, Hadi Quesneville, Jerome Salse
Summary: SyntenyViewer is a web-based tool that provides comparative genomics data and a reservoir of conserved genes for studying plant evolution and conducting translational research.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Multidisciplinary Sciences
Philippe Bardou, Sandrine Laguerre, Sarah Maman Haddad, Sabrina Legoueix Rodriguez, Elisabeth Laville, Claire Dumon, Gabrielle Potocki-Veronese, Christophe Klopp
Summary: Functional metagenomics is a classical way to discover genes responsible for specific metabolic functions from uncultured bacteria, with hundreds of sequences already published in public databases. The MINTIA software package enables biologists to easily generate and analyze large metagenomic sequence sets retrieved after activity-based screening, improving research efficiency.
Article
Ecology
Ruifeng Fan, Wei Ma, Shilei Liu, Qingyang Huang
Summary: The study sequenced and compared the chloroplast genomes of several ferns, identifying highly variable loci and confirming the typical quadripartite structures of chloroplast genomes in ferns. The results also showed the relationships among these ferns in terms of their phylogenetic classification.
ECOLOGY AND EVOLUTION
(2021)
Article
Materials Science, Multidisciplinary
Zean Tian, Zhongyang Zhang, Xiao Jiang, Feng Wei, Shen Ping, Fan Wu
Summary: In the past few decades, numerous visualization software has been developed for structural analysis of disordered/complex systems. However, ensuring the uniqueness and correctness of structural quantification remains challenging. This paper introduces LaSCA, a visualization analysis tool that meets the essential requirements for general structural analysis and provides various functionalities for analyzing complex systems. With efficient hardware acceleration and special algorithms, LaSCA is capable of processing large numbers of atoms and tracking their structural evolutions, making it robust and cost-effective.
Article
Biochemistry & Molecular Biology
Emidio Capriotti, Piero Fariselli
Summary: One of the major challenges in human genetics is determining the functional impact of different types of genetic variations. CADD is a widely used algorithm that predicts the effects of genome variations by combining sequence conservation and functional features. We developed a machine-learning tool called PhD-SNPg, which relies solely on sequence-based features and is easy to install and use. The updated version of PhD-SNPg can also predict the impact of insertion and deletion variations, and performs similarly to CADD, making it useful for rapid genome interpretation and tool development benchmarking.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Anabelle Laurent, Xiaodan Lyu, Peter Kyveryga, David Makowski, Heike Hofmann, Fernando Miguez
Summary: The concept of on-farm research networks allows farmers to test new agricultural management practices with support from local researchers, aiming to increase crop productivity and profitability. ISOFAST, an interactive web tool developed using R Shiny, simplifies interpretation of multi-site and multi-year summaries of trial results, generating new knowledge for farmers and agronomists.
RESEARCH SYNTHESIS METHODS
(2021)
Article
Biochemistry & Molecular Biology
Peng Zhou, Li Wang, Hai Liu, Chunyan Li, Zhimin Li, Jinxiang Wang, Xiaoming Tan
Summary: CyanoOmicsDB is a database aiming to provide comprehensive functional information for cyanobacterial genes, with over 8 million entries from 928 genomes. It integrates transcriptional and translational profiles, gene function predictions, protein sequences, homologs, and more, offering researchers in this field a convenient way to access functional information on cyanobacterial genes. Compared to other existing databases, CyanoOmicsDB stands out for its extensive datasets and comprehensive functional information.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Pharmacology & Pharmacy
Timothy R. Baffi, Ksenya Cohen-Katsenelson, Alexandra C. Newton
Summary: While protein kinases have been successfully targeted for diseases, protein phosphatases have not been utilized as therapeutic targets due to incomplete understanding of their effects on signaling networks. PHLPP, a relatively new player in cell signaling, has roles in cell survival, proliferation, and apoptosis, and recent research suggests it may have opposing effects in promoting cell survival. Additionally, PHLPP has been identified as a critical mediator of transcriptional programs in cancer and inflammation.
ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 61, 2021
(2021)
Editorial Material
Biochemical Research Methods
Claire E. Eyers
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Lauren J. Tomlinson, Matthew Batchelor, Joscelyn Sarsby, Dominic P. Byrne, Philip J. Brownridge, Richard Bayliss, Patrick A. Eyers, Claire E. Eyers
Summary: Protein kinase inhibitors are effective in treating diseases driven by aberrant kinase signaling and can help understand the cellular roles of kinase signaling complexes. This study characterizes the conformational changes and stability of protein kinase Aurora A (Aur A) caused by binding of the physiological activator TPX2 or small molecule inhibitors using gas-phase ion-mobility mass spectrometry (IM-MS). The results show that inhibitor binding induces more compact configurations of Aur A, leading to the stabilization of active Aur A.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemical Research Methods
Anton Kalyuzhnyy, Patrick A. Eyers, Claire E. Eyers, Emily Bowler-Barnett, Maria J. Martin, Zhi Sun, Eric W. Deutsch, Andrew R. Jones
Summary: This study profiles the human phosphoproteome to estimate the false discovery rate of phosphosites and predict a more realistic count of true identifications. It highlights significant potential of false-positive data in phosphorylation databases and emphasizes the importance of quality control for such data.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Multidisciplinary Sciences
Laura Marr, Dipsikha Biswas, Leonard A. Daly, Christopher Browning, Sarah C. M. Vial, Daniel P. Maskell, Catherine Hudson, Jay A. Bertrand, John Pollard, Neil A. Ranson, Heena Khatter, Claire E. Eyers, Kei Sakamoto, Elton Zeqiraj
Summary: The study describes the structural basis of glycogen synthase (GS) regulation, specifically its inactivation mechanism through phosphorylation. The findings provide insights into glycogen synthesis regulation and facilitate research on glycogen-related diseases.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Mitchell H. Omar, Dominic P. Byrne, Kiana N. Jones, Tyler M. Lakey, Kerrie B. Collins, Kyung-Soon Lee, Leonard A. Daly, Katherine A. Forbush, Ho-Tak Lau, Martin Golkowski, G. Stanley McKnight, David T. Breault, Anne-Marie Lefrancois-Martinez, Antoine Martinez, Claire E. Eyers, Geoffrey S. Baird, Shao-En Ong, F. Donelson Smith, Patrick A. Eyers, John D. Scott
Summary: Mutations in protein kinase A catalytic subunit lead to adrenal Cushing's syndrome, and the mutants are excluded from kinase-anchoring protein signaling islands, resulting in excessive cortisol production. Incorporating the mutants into kinase-anchoring protein complexes restores normal endocrine function. Each mutant activates a different signaling pathway, contributing to the development of the disease.
Article
Biochemistry & Molecular Biology
Jill E. Hunter, Amy E. Campbell, Scott Kerridge, Callum Fraser, Nicola L. Hannaway, Saimir Luli, Iglika Ivanova, Philip J. Brownridge, Jonathan Coxhead, Leigh Taylor, Peter Leary, Megan S. R. Hasoon, Claire E. Eyers, Neil D. Perkins
Summary: In this study, we discovered the up-regulation of multiple bypass pathways in lymphomas with mutant NF-kappa B subunits, and demonstrated that drugs targeting these pathways could potentially be used to aid the successful clinical application of CHK1 inhibitors.
BIOCHEMICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Jill E. Hunter, Amy E. Campbell, Jacqueline A. Butterworth, Helene Sellier, Nicola L. Hannaway, Saimir Luli, Achilleas Floudas, Niall S. Kenneth, Adam J. Moore, Philip J. Brownridge, Huw D. Thomas, Jonathan Coxhead, Leigh Taylor, Peter Leary, Megan S. R. Hasoon, Andrew M. Knight, Michelle D. Garrett, Ian Collins, Claire E. Eyers, Neil D. Perkins
Summary: DNA replication stress is a common feature of cancer cells, and ATR/CHK1 signaling pathway is an attractive target for anti-cancer therapies. This study reveals the critical role of RelA NF-xB subunit in MYC induced DNA replication stress, suggesting its potential as a therapeutic target.
BIOCHEMICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Jill E. Hunter, Amy E. Campbell, Nicola L. Hannaway, Scott Kerridge, Saimir Luli, Jacqueline A. Butterworth, Helene Sellier, Reshmi Mukherjee, Nikita Dhillon, Praveen D. Sudhindar, Ruchi Shukla, Philip J. Brownridge, Hayden L. Bell, Jonathan Coxhead, Leigh Taylor, Peter Leary, Megan S. R. Hasoon, Ian Collins, Michelle D. Garrett, Claire E. Eyers, Neil D. Perkins
Summary: The study found that deleting c-Rel results in earlier onset of lymphoma, contrary to the expected function of this NF-xB subunit. E mu-Myc/cRel-/- lymphomas were shown to have a major defect in the CHK1 pathway, involving a loss of CHK1 protein expression and resistance to CHK1 inhibitor treatment.
BIOCHEMICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Dominic P. Byrne, Safal Shrestha, Leonard A. Daly, Vanessa Marensi, Krithika Ramakrishnan, Claire E. Eyers, Natarajan Kannan, Patrick A. Eyers
Summary: Pseudokinases lack conserved amino acids for catalytic activity and have diverse biological functions. Human PSKH2 is a pseudokinase closely related to the canonical kinase PSKH1. Species-level adaptations have led to the appearance of PSKH2 variants alongside PSKH1 in vertebrate genomes. PSKH2 lacks protein phosphotransferase activity and its N-terminal domain is required for stable expression and localization to the mitochondrial fraction. PSKH2 is part of a mitochondrial protein network and its expression is regulated through the HSP90/Cdc37 chaperone system.
BIOCHEMICAL JOURNAL
(2023)
Editorial Material
Biochemical Research Methods
John R. Yates, Ileana M. Cristea, Meng-Qui Dong, Claire E. Eyers, Joshua LaBaer, Jia V. Li, Jeremy K. Nicholson, Christopher M. Overall, Magnus Palmblad, Nikolai Slavov
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Leandro Xavier Neves, R. Alan Wilson, Philip Brownridge, Stephen W. W. Holman, Victoria M. M. Harman, Claire E. E. Eyers, Robert J. J. Beynon, William Castro-Borges
Summary: In this study, a detailed method for preserving the proteome of adult Schistosoma mansoni worms was described in order to enrich the tissues associated with the parasite's alimentary tract. The methodology employed label-free and QconCAT-based absolute quantification to detect S. mansoni oesophageal gland products. By stabilizing the proteome and minimizing sample degradation during dissection, the hidden proteome of target tissues, which are not readily available from total lysates due to their small volumes, could be accessed. This protocol can be used for the discovery of proteins with potential diagnostic and therapeutic utility in other Schistosoma species lacking quantitative proteomics characterization of specialized tissues.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Leonard A. Daly, Dominic P. Byrne, Simon Perkins, Philip J. Brownridge, Euan Mcdonnell, Andrew R. Jones, Patrick A. Eyers, Claire E. Eyers
Summary: In this study, a MS-based workflow for sY-peptide characterization was developed, allowing systematic investigation of the sulfome. The key for distinguishing sulfated peptides from phosphopeptides was low collision energy-induced neutral loss. Applying this workflow identified 21 new sulfotyrosine-containing proteins and revealed new interplay between enzymes relevant to both protein and glycan sulfation.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Allen Po, Claire Eyers
Summary: Top-down proteomics aims to identify and analyze intact proteoforms extracted from biological samples. However, defining and pinpointing post-translational modifications on intact proteins remains a challenge. This is crucial for understanding the specific roles and structure-function relationships of proteins.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Chemistry, Multidisciplinary
Leonard A. Daly, Christopher J. Clarke, Allen Po, Sally O. Oswald, Claire E. Eyers
Summary: The article focuses on the application of mass spectrometry in the identification and quantification of protein modifications, specifically phosphorylation and sulfation. It discusses the challenges associated with discriminating and pinpointing the sites of these modifications on polypeptide chains. The article showcases various approaches for enrichment and site localisation of phosphorylated and sulfated peptides, as well as modification analysis in intact proteins. It also discusses the use of native ion-mobility MS to explore the effects of these modifications on protein structure and ligand binding. The article provides insights into the current strategies and future directions in studying phosphorylation and sulfation using mass spectrometry.
CHEMICAL COMMUNICATIONS
(2023)