Article
Multidisciplinary Sciences
Alejandro V. Cano, Hana Rozhonova, Arlin Stoltzfus, David M. McCandlish, Joshua L. Payne
Summary: This study investigates the influence of mutation spectrum on the spectrum of adaptive substitutions, demonstrating that the mutation spectrum has a proportional influence on the spectrum of adaptive substitutions in all three species, but the predictive power of the model differs substantially between the species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Swarnendu Tripathi, Nikita R. Dsouza, Angela J. Mathison, Elise Leverence, Raul Urrutia, Michael T. Zimmermann
Summary: This study reports computational scores for interpreting disease-associated genomic variation in the RAS family of genes. By using a combination of experimental datasets and computational methods, the research found a high correlation between 3D structure-based scores and experimental measures, indicating the impact of biochemical scores on the functional behavior of variants.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Genetics & Heredity
Philip Ruelens, J. Arjan G. M. de Visser
Summary: Experimental evolution studies show that in very small populations, mutant clones with higher mutation rates can adapt faster by acquiring beneficial mutations, while wild-type populations have limited adaptive potential with inactivating mutations.
Article
Ecology
Daniel S. S. Park, Yingying Xie, Hanna T. T. Thammavong, Rima Tulaiha, Xiao Feng
Summary: The study assessed highly recurring coordinates in biodiversity data and identified artificial hotspots that are mainly caused by imperfect data management and georeferencing. The Artificial Hotspot Occurrence Inventory (AHOI) can improve accuracy of biodiversity assessments, estimate uncertainty associated with records from artificial hotspots, and identify problems in biodiversity informatics workflows.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Biochemistry & Molecular Biology
Christopher A. Klebanoff, Smita S. Chandran
Summary: PIK3CA gain-of-function mutations are common in human solid cancers. Using SIFT-seq, a panel of TCRs that bind a mutant PI3K alpha shared neoantigen was identified, including a potential clinical candidate that interacts with cancer cells through a distinctive CDR3 beta loop.
Article
Mathematics, Interdisciplinary Applications
Ricardo Simao
Summary: In one-dimensional heterogeneous models of hard-particle flux, system dynamics strongly depend on the behavior of the leading particle. Models meeting certain criteria show a link between traffic theory and graph theory, simplifying the analysis of driving style spreading. Evolutionary dynamics transform quenched disorders into dynamical disorders in heterogeneous systems.
CHAOS SOLITONS & FRACTALS
(2021)
Article
Biochemistry & Molecular Biology
Natan Nagar, Jerome Tubiana, Gil Loewenthal, Haim J. Wolfson, Nir Ben Tal, Tal Pupko
Summary: MSAs are important tools in molecular evolution and structural biology research, allowing inference of tolerated amino acids at each site during protein evolution. EvoRator2, a deep-learning algorithm trained on protein structures, can predict tolerated amino acids at any given site based on protein structural information. It shows satisfying results for position-weighted scoring matrices (PSSM) prediction and near state-of-the-art performance in predicting mutation effects in deep mutation scanning (DMS) experiments.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Wouter A. C. van Amsterdam, Joost J. C. Verhoeff, Netanja Harlianto, Gijs A. Bartholomeus, Aahlad Manas Puli, Pim A. de Jong, Tim Leiner, Anne S. R. van Lindert, Marinus J. C. Eijkemans, Rajesh Ranganath
Summary: Randomized Controlled Trials (RCT) are the gold standard for estimating treatment effects, but in certain situations, treatment effect estimates from observational data are needed. PROTECT is a method developed to estimate treatment effects from observational data when there are unobserved confounders, but proxy measurements of these confounders exist. In an observational cohort of 504 stage III non-small cell lung cancer (NSCLC) patients, PROTECT provided credible treatment effect estimates, unlike conventional confounding adjustment methods which seemed to overestimate the treatment effect.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
James S. Horton, Louise M. Flanagan, Robert W. Jackson, Nicholas K. Priest, Tiffany B. Taylor
Summary: Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Experiments in bacteria reveal that a powerfully deterministic genetic hotspot can be built and broken by a handful of silent mutations, highlighting an underappreciated role for silent genetic variation in determining adaptive outcomes.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Zhaogeng Lu, Jiawen Cui, Li Wang, Nianjun Teng, Shoudong Zhang, Hon-Ming Lam, Yingfang Zhu, Siwei Xiao, Wensi Ke, Jinxing Lin, Chenwu Xu, Biao Jin
Summary: The study reveals that long-term elevated temperatures significantly increase mutation rates in plants with distinctive mutational spectra, occurring mainly in intergenic regions, coding regions, and transposable elements. Additionally, mutations are more likely to accumulate in genes associated with defense responses, DNA repair, and signaling under elevated temperatures.
Article
Multidisciplinary Sciences
Smit Chetan Doshi, Gerrit Lohmann, Monica Ionita
Summary: This study identifies highly correlated significant pairs of compound climate events in Europe on a monthly scale. The findings show high combined risks between different hazard pairs and highlight the vulnerability of agricultural and coastal areas to compound events over the last few decades.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Jianglin Zhou, Xuejun Wang, Zhe Zhou, Shengqi Wang
Summary: The exceptional outbreak of monkeypox in 100 non-endemic countries since 2022 poses a major public health concern. Analysis of codon usage patterns in the 2022 outbreak strains of monkeypox virus revealed unique evolutionary features, with codon usage bias predominantly determined by mutation pressure. The virus also showed adaptation to various primate hosts, including humans, indicating the importance of sustained monitoring.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Medicinal
Feng-Xu Wu, Jing-Fang Yang, Long-Can Mei, Fan Wang, Ge-Fei Hao, Guang-Fu Yang
Summary: Protein-protein interactions are crucial in biological processes, and studying the mutational effects of hotspots helps understand protein binding. The PIIMS web server integrates molecular dynamics simulation and free energy perturbation to further evaluate the impact of different mutations on hotspot residues.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Editorial Material
Multidisciplinary Sciences
Linda Nordling
Summary: The viral disease is commonly spread across the continent, yet many countries lack the necessary resources to increase public awareness and provide treatment for patients.
Article
Oncology
Lisa M. Allinson, Aaron Potts, Angharad Goodman, Nick Bown, Matthew Bashton, Dean Thompson, Nermine O. Basta, Alem S. Gabriel, Michael McCorkindale, Antony Ng, Richard J. Q. McNally, Deborah A. Tweddle
Summary: ALK is the most commonly mutated oncogene in neuroblastoma, and its mutation frequency increases at relapse. This study reports the loss of ALK mutations in two neuroblastoma patients at relapse and in a neuroblastoma cell line. This highlights the spatial and temporal heterogeneity within tumors and emphasizes the importance of confirming the persistence of ALK mutations detected at diagnosis in clones leading to relapse.
GENES CHROMOSOMES & CANCER
(2022)
Review
Plant Sciences
Britt Koskella, Tiffany B. Taylor
ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 56
(2018)
Article
Ecology
Antonio M. M. Rodrigues, Tiffany B. Taylor
JOURNAL OF EVOLUTIONARY BIOLOGY
(2018)
Article
Multidisciplinary Sciences
Anastasia V. Wass, George Butler, Tiffany B. Taylor, Philip R. Dash, Louise J. Johnson
ROYAL SOCIETY OPEN SCIENCE
(2020)
Article
Biology
Lucy J. Bock, Philip M. Ferguson, Maria Clarke, Vichayanee Pumpitakkul, Matthew E. Wand, Paul-Enguerrand Fady, Leanne Allison, Roland A. Fleck, Matthew J. Shepherd, A. James Mason, J. Mark Sutton
Summary: The adaptation of Pseudomonas aeruginosa to the antiseptic octenidine is characterized by synergistic changes in efflux and plasma membrane composition, primarily through mutations in SmvR, SmvA, PssA, and PgsA. This adaptation leads to significantly increased octenidine tolerance in both laboratory and simulated clinical settings, with stable mutations and specific gene deletions associated with higher level, synergistic tolerance.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
James S. Horton, Louise M. Flanagan, Robert W. Jackson, Nicholas K. Priest, Tiffany B. Taylor
Summary: Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Experiments in bacteria reveal that a powerfully deterministic genetic hotspot can be built and broken by a handful of silent mutations, highlighting an underappreciated role for silent genetic variation in determining adaptive outcomes.
NATURE COMMUNICATIONS
(2021)
Review
Microbiology
Tiffany B. Taylor, Matthew J. Shepherd, Robert W. Jackson, Mark W. Silby
Summary: At the gene level, mutation is the raw material for natural selection, while at the gene regulatory network (GRN) level, crosstalk provides opportunities for genetic innovation and adaptation. Various genetic and environmental features can increase the potential for crosstalk and rewiring of GRNs, which can be selected if they provide fitness benefits. This article identifies factors that facilitate crosstalk and rewiring, and discusses the impact of GRN features on evolution.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Biology
James S. S. Horton, Shani U. P. Ali, Tiffany B. B. Taylor
Summary: Predicting population navigation of genotype-phenotype landscape requires consideration of selection and mutation bias. Transient mutation bias can influence the navigability by biasing mutational trajectory early in the adaptive walk. This study investigates whether transient mutation bias can reliably and predictably place populations on a mutational trajectory to the strongest selective phenotype or usher populations to realize inferior phenotypic outcomes.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Microbiology
Louise M. Flanagan, James S. Horton, Tiffany B. Taylor
Summary: The observed mutational spectrum of adaptive outcomes can be constrained by factors such as mutational biases and complex environments. In this study, we investigated the impact of nutrient environments on the evolution of motility in Pseudomonas fluorescens and found that the mutational spectrum and phenotype strength were influenced by the nutrient environment.
Article
Biochemistry & Molecular Biology
Matthew J. Shepherd, Aidan P. Pierce, Tiffany B. Taylor
Summary: The survival of a population during environmental shifts depends on the rate of phenotypic adaptation keeping up with changing conditions. This study explores the rewiring of gene regulatory network connections to facilitate novel interactions and transcription factor innovation. The research identifies three key properties that enable transcription factor innovation: high activation, high expression, and pre-existing low-level affinity for novel target genes. The ease of acquiring these properties is constrained by the preexisting GRN architecture.
