Review
Microbiology
Stephen M. Matthews, Ian J. Groves, Christine M. O'Connor
Summary: Human cytomegalovirus (HCMV) is a betaherpesvirus that establishes lifelong infection in its host and can cause severe comorbidities in individuals with suppressed or compromised immune systems. The lifecycle of HCMV consists of lytic and latent phases, largely dependent upon the cell type infected and whether transcription from the major immediate early locus can ensue. Epigenetic regulation through chromatinization, chromatin modifiers, and transcription factor recruitment play important roles in controlling gene expression from the HCMV genome during infection.
Article
Virology
Anderson F. Brito, Guy Baele, Kanika D. Nahata, Nathan D. Grubaugh, John W. Pinney
Summary: As more herpesviral sequences became available, incongruences between host and viral phylogenies became more evident, with host switching and intrahost speciation being more common.
Article
Microbiology
Jean-Philippe Lavigne, Michel Hosny, Catherine Dunyach-Remy, Adeline Boutet-Dubois, Sophie Schuldiner, Nicolas Cellier, Alex Yahiaoui-Martinez, Virginie Molle, Bernard La Scola, Helene Marchandin, Albert Sotto
Summary: The study found a 25% rate of persistence of Staphylococcus aureus in patients with diabetic foot infections (DFI), with most cases having a relatively short persistence time. During persistent colonization, changes in bacterial genome content were observed, highlighting the low adaptive ability of S. aureus to the specific environment and stressful conditions of diabetic foot ulcers.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Declan L. Turner, Rachel M. Templin, Adele A. Barugahare, Brendan E. Russ, Stephen J. Turner, Georg Ramm, Rommel A. Mathias
Summary: UL34 is a viral protein expressed with leaky late kinetics and primarily located in the nucleus during infection. Deletion of UL34 from the HCMV genome did not stop viral spread, but significantly reduced the production of infectious virions by over 100-fold, indicating that UL34 is an augmenting gene in HCMV infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Pharmacology & Pharmacy
Tianyu Zhang, Theodore I. Potgieter, Erik Kosche, Jessica Rueckert, Eleonore Ostermann, Thomas Schulz, Martin Empting, Wolfram Brune
Summary: Human cytomegalovirus (HCMV, human herpesvirus 5) is a pathogen that causes serious disease in immunocompromised patients. The viral alkaline nuclease (AN) is identified as a potential drug target for anti-HCMV therapy. Researchers have discovered a thioxothiazolo[3,4-a]quinazoline derivative compound that inhibits AN activity and HCMV replication in vitro. The compound also shows activity against drug-resistant HCMVs and other herpesviruses.
ANTIVIRAL RESEARCH
(2023)
Article
Virology
Lindsey B. Crawford, Meaghan H. Hancock, Hillary M. Struthers, Daniel N. Streblow, Andrew D. Yurochko, Patrizia Caposio, Felicia D. Goodrum, Jay A. Nelson
Summary: This study demonstrates that CD34(+) progenitor cells derived from embryonic stem cells can serve as a model for HCMV latency, and the virus may either latently or persistently infect specific subpopulations of CD34(+) cells.
JOURNAL OF VIROLOGY
(2021)
Review
Immunology
Chuan Yu, Suna He, Wenwen Zhu, Penghui Ru, Xuemei Ge, Kavitha Govindasamy
Summary: Cancer is a major cause of death worldwide. Human cytomegalovirus (HCMV), a well-studied herpesvirus, has been implicated in various types of cancers. The complex interactions between the virus and the host can result in the transformation of normal cells. HCMV infection is usually asymptomatic but can cause severe health issues in immune-compromised individuals, including cancer patients. Studies have shown the presence of HCMV in different types of cancers, suggesting its importance in cancer progression. Importantly, HCMV is also associated with birth defects and abortion in pregnant women.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Chemistry, Physical
Nghi P. Nguyen, Brian L. Wadsworth, Daiki Nishiori, Edgar A. Reyes Cruz, Gary F. Moore
Summary: Understanding and controlling factors that restrict the rates of fuel-forming reactions are crucial for designing effective catalyst-modified semiconductors for solar-to-fuel applications. This study reveals two distinct mechanisms of photoelectrochemical hydrogen production and highlights diagnostic tools for better understanding these processes. The complex interplay between transport of photons, electrons, and chemical substrates in photoelectrosynthetic reactions is illustrated in this work.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Review
Virology
Kimberley Bruce, Jiawei Ma, Clara Lawler, Wanxiaojie Xie, Philip G. Stevenson, Helen E. Farrell
Summary: Animal models are crucial for understanding virus-host interactions in human infections. Recent studies on mouse cytomegalovirus (MCMV) have provided insights into the early events and spread of infection, as well as the tissue-specific mechanisms used by the virus to manipulate immune cells. These findings may have implications for the development of antivirals and vaccines against human cytomegalovirus (HCMV) infections.
Review
Infectious Diseases
Shiu-Jau Chen, Shao-Cheng Wang, Yuan-Chuan Chen
Summary: Human cytomegalovirus (HCMV) is a widespread virus that poses a serious threat to human health. Traditional antiviral drugs have limited efficacy due to various issues, but novel drugs and gene-targeting approaches show promise in treating HCMV infections. Cell therapy has also been explored as a potential treatment. However, further research is needed to overcome challenges and develop more effective strategies.
TROPICAL MEDICINE AND INFECTIOUS DISEASE
(2022)
Review
Medicine, General & Internal
Manuele Biazzo, Gabriele Deidda
Summary: The human gut microbiota plays a crucial role in various human pathologies. Restoring the balance and composition of the gut microbiota through pre/probiotic supplementation or fecal microbiota transplantation shows promising therapeutic potential for a wide range of conditions, including gastrointestinal disorders, liver diseases, cancer, and brain disorders. This review examines the preparation methods, clinical trial evidence, and the importance of donor selection in fecal microbiota transplantation, aiming to stimulate discussion and explore new therapeutic perspectives.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Immunology
Caroline L. Ashley, Brian P. McSharry, Hamish E. G. McWilliam, Richard J. Stanton, Ceri A. Fielding, Rommel A. Mathias, David P. Fairlie, James McCluskey, Jose A. Villadangos, Jamie Rossjohn, Allison Abendroth, Barry Slobedman
Summary: This study reveals that human cytomegalovirus (HCMV) inhibits the MR1 pathway and disrupts the MR1:MAIT cell axis through the viral protein gpUS9. The interaction between this virus and MAIT cells in the context of viral infection is not well characterized.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Virology
Melissa A. A. Moy, Donna Collins-McMillen, Lindsey Crawford, Christopher Parkins, Sebastian Zeltzer, Katie Caviness, Syed Shujaat Ali Zaidi, Patrizia Caposio, Felicia Goodrum
Summary: Human cytomegalovirus (HCMV) is a significant human pathogen that can establish a lifelong latent infection. This study reveals an epistatic relationship between the viral genes UL136p33 and UL135 in controlling virus reactivation from latency. Stabilizing UL136p33 can compensate for the loss of UL135 and promote increased viral replication in hematopoietic progenitor cells and humanized mouse models.
JOURNAL OF VIROLOGY
(2023)
Article
Engineering, Multidisciplinary
Yang DaPeng, Liu Hong
Summary: Despite the thriving market for dexterous hand prostheses with multiple degrees of freedom, user demand for intuitive operation remains largely unmet, leading to low acceptance rates. Shared control methods integrating myoelectric control and artificial intelligence offer a new conceptual solution for intuitive operation of dexterous prostheses. By dividing complex tasks into subtasks and utilizing different strategies, control issues can potentially be addressed.
SCIENCE CHINA-TECHNOLOGICAL SCIENCES
(2021)
Article
Virology
Luwanika Mlera, Donna Collins-McMillen, Sebastian Zeltzer, Jason C. Buehler, Melissa Moy, Kristen Zarrella, Katie Caviness, Louis Cicchini, David J. Tafoya, Felicia Goodrum
Summary: Herpesviruses, including HCMV, which infects the majority of the population worldwide, establish lifelong latent infections and pose a risk for diseases, especially in immunocompromised individuals. We demonstrate that the cellular E3 ligase IDOL targets HCMV UL136p33 protein for degradation, which plays a key role in reactivation. This work provides important insights into the mechanisms of HCMV replication and latency.
JOURNAL OF VIROLOGY
(2023)
Review
Ecology
Ana Y. Morales-Arce, Susanna J. Sabin, Anne C. Stone, Jeffrey D. Jensen
Summary: Recent genomic sequencing of patient samples has revealed low levels of genetic diversity within Mycobacterium tuberculosis (M.TB), attributed to various factors. This emerging evolutionary framework is forming a new paradigm for studying within-host pathogen evolution.
Article
Biochemistry & Molecular Biology
Parul Johri, Kellen Riall, Hannes Becher, Laurent Excoffier, Brian Charlesworth, Jeffrey D. Jensen
Summary: Current methods for inferring population history assume neutrality, but neglect the effects of direct and background selection. The study shows that background selection can lead to mis-inferences of population growth, especially with increasing strength of purifying selection and density of directly selected sites.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Florian Clemente, Martina Unterlaender, Olga Dolgova, Carlos Eduardo G. Amorim, Francisco Coroado-Santos, Samuel Neuenschwander, Elissavet Ganiatsou, Diana I. Cruz Davalos, Lucas Anchieri, Frederic Michaud, Laura Winkelbach, Jens Bloecher, Yami Ommar Arizmendi Cardenas, Barbara Sousa da Mota, Eleni Kalliga, Angelos Souleles, Ioannis Kontopoulos, Georgia Karamitrou-Mentessidi, Olga Philaniotou, Adamantios Sampson, Dimitra Theodorou, Metaxia Tsipopoulou, Ioannis Akamatis, Paul Halstead, Kostas Kotsakis, Dushka Urem-Kotsou, Diamantis Panagiotopoulos, Christina Ziota, Sevasti Triantaphyllou, Olivier Delaneau, Jeffrey D. Jensen, J. Victor Moreno-Mayar, Joachim Burger, Vitor C. Sousa, Oscar Lao, Anna-Sapfo Malaspinas, Christina Papageorgopoulou
Summary: The Cycladic, Minoan, and Helladic cultures mark Greece's Bronze Age, characterized by urbanism, complex social structures, craft specialization, and early writing. Early Bronze Age populations in Greece are homogeneous and primarily derive from Neolithic Aegeans, contradicting previous hypotheses. In contrast, Middle Bronze Age individuals in northern Greece show significant Pontic-Caspian Steppe-related ancestry, contributing to shaping modern Greek genomes.
Review
Virology
Hsuan-Yuan Wang, Sarah M. Valencia, Susanne P. Pfeifer, Jeffrey D. Jensen, Timothy F. Kowalik, Sallie R. Permar
Summary: HCMV is one of the most prevalent viruses globally, causing common morbidity and mortality for immunocompromised individuals. Clinical observations suggest that mixed strain infections are common and may lead to more severe disease progression. This genetic variation in glycoproteins could be an important resource for future efforts to combat HCMV infections.
Article
Ecology
Ana Y. Morales-Arce, Parul Johri, Jeffrey D. Jensen
Summary: The study presents an analysis pipeline for inferring the distribution of fitness effects from viral populations, accounting for non-standard population dynamics. The approach is demonstrated through two illustrative applications and potential applications to virus evolution research are discussed.
Article
Genetics & Heredity
Susanna Sabin, Ana Y. Morales-Arce, Susanne P. Pfeifer, Jeffrey D. Jensen
Summary: This study compares the evolutionary dynamics of the recombining M. canettii with the nonrecombining M. tuberculosis complex using whole-genome sequencing data and population genomic models. The authors discuss differences in observed genomic diversity and highlight the potential mis-inference caused by neglecting common model violations.
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
Parul Johri, Wolfgang Stephan, Jeffrey D. Jensen
Summary: This study raises concerns about recent publications in PLOS Genetics that argue for the statistical identifiability and pervasive evolutionary role of soft selective sweeps in Drosophila and HIV populations. The results highlight the dangers of fitting evolutionary models without considering competing models and the tendency to view positive selection as a foregone conclusion in certain research areas.
Review
Evolutionary Biology
Brian Charlesworth, Jeffrey D. Jensen
Summary: This article discusses the genetic, demographic, and selective forces that limit the observed levels of DNA sequence variation in natural populations, and highlights the potentially important role of population size change in this process.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Parul Johri, Adam Eyre-Walker, Ryan N. Gutenkunst, Kirk E. Lohmueller, Jeffrey D. Jensen
Summary: This article discusses the challenges of disentangling the effects of natural selection and population history on genome-wide variation in population genetics. It highlights the theoretical and computational challenges that still need to be addressed, as well as the difficulties in dealing with model complexity and violations, and offers thoughts on potentially fruitful next steps.
GENOME BIOLOGY AND EVOLUTION
(2022)
Editorial Material
Biochemistry & Molecular Biology
Brian Charlesworth, Jeffrey D. Jensen
Summary: This article addresses recent claims regarding the importance of indirect selection, arguing that it is not a new or poorly studied phenomenon and that alternative explanations exist for the patterns described by the authors.
Article
Multidisciplinary Sciences
Emily R. Hager, Olivia S. Harringmeyer, T. Brock Wooldridge, Shunn Theingi, Jacob T. Gable, Sade McFadden, Beverly Neugeboren, Kyle M. Turner, Jeffrey D. Jensen, Hopi E. Hoekstra
Summary: This study characterized the genetic basis of trait variation in different ecotypes of deer mice and identified a chromosomal inversion linked to tail length and coat color. The frequency of the inversion was high in the forest ecotype, decreased across a habitat transition, and was absent in the prairie ecotype. Divergent selection was implicated in maintaining the inversion at observed frequencies despite high levels of gene flow, and the study explored the fitness benefits arising from suppressed recombination within the inversion.
Article
Biochemistry & Molecular Biology
Parul Johri, Charles F. Aquadro, Mark Beaumont, Brian Charlesworth, Laurent Excoffier, Adam Eyre-Walker, Peter D. Keightley, Michael Lynch, Gil McVean, Bret A. Payseur, Susanne P. Pfeifer, Wolfgang Stephan, Jeffrey D. Jensen
Summary: The field of population genomics has grown rapidly, but there is a tendency to focus on specific models at the expense of exploring underlying evolutionary processes. We need to pay more attention to statistical inference and theory and establish relevant baseline models for each analysis.
Article
Genetics & Heredity
Fabian B. Freund, Elise Kerdoncuff, Sebastian Matuszewski, Marguerite Lapierre, Marcel Hildebrandt, Jeffrey Jensen, Luca Ferretti, Amaury Lambert, Timothy Sackton, Guillaume Achaz
Summary: The standard neutral model of molecular evolution has often been used as a reference for population genomics. However, our study shows that alternative genealogical models, such as multiple merger coalescent models, may provide a better fit to observed allele frequency data. This has important implications for population genomic studies and related fields.
Review
Microbiology
John W. Terbot, Parul Johri, Schuyler W. Liphardt, Vivak Soni, Susanne P. Pfeifer, Brandon S. Cooper, Jeffrey M. Good, Jeffrey D. Jensen
Summary: In the past 3 years, the SARS-CoV-2 virus has caused a global health crisis with multiple waves of spread. Genomic surveillance efforts have increased to track and anticipate the virus's evolution, resulting in a large number of patient isolates available in public databases. However, accurately quantifying the emergence of adaptive viral variants is challenging due to various co-occurring and interacting evolutionary processes. This study outlines the critical components of an evolutionary baseline model for SARS-CoV-2, including mutation rates, recombination rates, fitness effects, infection dynamics, and compartmentalization, and discusses the current understanding of these parameters. Recommendations for future clinical sampling, model construction, and statistical analysis are also provided.
Article
Evolutionary Biology
John W. Terbot II, Brandon S. Cooper, Jeffrey M. Good, Jeffrey D. Jensen
Summary: This study develops a simulation framework to study the intrahost evolutionary dynamics of SARS-CoV-2 and establish a baseline model for improved virus data analysis. The study finds that the evolution of SARS-CoV-2 is influenced by severe infection bottlenecks, low levels of reproductive skew, and strongly deleterious mutations.
GENOME BIOLOGY AND EVOLUTION
(2023)
