Article
Virology
Ana Jordan-Paiz, Sandra Franco, Miguel Angel Martinez
Summary: Reducing the frequency of CpG dinucleotides in the HIV-1 envelope can enhance viral replication capacity and may be associated with differences in clinical progression rates in infected individuals.
Article
Biochemistry & Molecular Biology
Jacques Demongeot, Andres Moreira, Herve Seligmann
Summary: Theoretical minimal RNA rings are candidate primordial genes evolved for non-redundant coding of genetic code signals. These rings lack dinucleotide CG and gradually decrease towards its absence, which may have been influenced by feedback loops during evolution. This restructuring of the genetic code by CG mutability establishes itself as genetically encoded biological information.
Article
Biology
James A. deMayo, Reid S. Brennan, Melissa H. Pespeni, Michael Finiguerra, Lydia Norton, Gihong Park, Hannes Baumann, Hans G. Dam
Summary: Phenotypic plasticity and evolutionary adaptation can help populations cope with global change, but the limits and costs of adaptation under multiple stressors are not well understood. This study found that a copepod species, Acartia hudsonica, initially experienced a decline in fitness under the combined effects of ocean warming and acidification, but fully recovered within four generations, indicating an adaptive response and synergy between stressors. However, in the long term, the fitness of the adapted lineage was lower compared to the ambient conditions, suggesting a cost to producing phenotypes adapted to both warming and acidification. The study also found sustained phenotypic plasticity in the adapted lineage, even when exposed to different environments.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Infectious Diseases
Ping Wang, Hongou Wang, Cunwei Liu, Chengjie Feng, Qinghui Lu, Qinghua Zou
Summary: This study investigates the mechanism of tigecycline resistance in Acinetobacter baumannii by gradually culturing strains with different tigecycline susceptibilities. It is found that tigecycline resistance affects the susceptibility to other antibiotics and incurs fitness costs. Additionally, transposon insertion in the adeL gene is correlated with reduced sensitivity to tigecycline in A. baumannii.
Article
Virology
Mikhail Oliveira Leastro, David Villar-Alvarez, Juliana Freitas-Astua, Elliot Watanabe Kitajima, Vicente Pallas, Jesus angel Sanchez-Navarro
Summary: Competition experiments in transgenic tobacco plants showed the prevalence of the AMV construct carrying the CiLV-C2 MP. Analysis of AMV RNA 3 progeny revealed the presence of a mix of progeny with different variants, with MPS259F favoring cell-to-cell transport and MPS72F having a penalty in viral fitness.
Article
Biochemistry & Molecular Biology
Pablo Aledo, Juan Carlos Aledo
Summary: This study proposes a neutral continuous fitness-stability model inspired by the Arrhenius law to explain the observed amino acid substitution rates. The model suggests that the rate of substitution depends on a pre-exponential factor and an exponential term reflecting relative fitness. By analyzing stability changes in proteins and their disease-causing potential, the study found a significant positive correlation between energy values and the fitness effect of substitutions, supporting the validity of the model.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Shalini Nair, Xue Li, Grace A. Arya, Marina McDew-White, Marco Ferrari, Tim Anderson
Summary: Drug resistance mutations disrupt key physiological processes and carry fitness costs, affecting their spread in natural populations. Standardized culture medium used for measuring fitness may underestimate these costs. This study shows that fitness costs are significantly underestimated in rich culture medium and are strongly affected by the composition of the medium.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Microbiology
Nupur Biswas, Priyanka Mallick, Sujay Krishna Maity, Debaleena Bhowmik, Arpita Ghosh Mitra, Soumen Saha, Aviral Roy, Partha Chakrabarti, Sandip Paul, Saikat Chakrabarti
Summary: Identifying the genomic diversity and phylodynamic profiles of prevalent SARS-CoV-2 variants is crucial in understanding their evolution and spread. Genomic sequencing and analysis of variants collected in Kolkata, West Bengal, India revealed clade dynamics and potential associations between specific mutations and infection outcomes in Indian patients. Frequent mutations and co-mutations observed within major clades over time suggest the emergence of new mutations in the viral population.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Jie Yang, Esha Gupta, John R. Horton, Robert M. Blumenthal, Xing Zhang, Xiaodong Cheng
Summary: C>T somatic mutation is highly enriched in certain types of cancer, and it occurs most commonly via deamination of 5-methylcytosine to thymine. This study reveals the interaction between transcription factors and repair enzymes affects the occurrence of mutations, further highlighting the importance of DNA repair mechanisms.
Article
Ecology
Yue Cai, Yong Nie, Yang Gao, Bo Huang
Summary: This study investigated the sexual reproductive potential and phylogenetic diversity of B. bassiana natural populations in China through the collection and molecular identification of isolates. Five phylogenetic species of B. bassiana from different geographic origins were discovered, and the presence of sexual and asexual isolates was found in some collection sites. These results provide insights into the ecological conditions of sexual reproduction in B. bassiana natural populations and shed light on the potential for sexual reproduction in other supposedly 'asexual' fungi.
Article
Anthropology
Luis J. Sanchez-Martinez, Candela L. Hernandez, Juan N. Rodriguez, Jean M. Dugoujon, Andrea Novelletto, Paloma Ropero, Luisa Pereira, Rosario Calderon
Summary: The study in western Andalusia, Spain reveals a restricted spectrum of beta-thalassemia mutations, with certain specificities supporting a distinct structure of some specific beta-thalassemia alleles. IVSI-1 (G > A) shows strong regionalization, and spatial correlogram reflects a narrow wave structure possibly linked to genetic isolation and drift. The historical context of endemic malaria, high consanguinity rates, and unique demographic features help in understanding the molecular portrait of beta-thalassemia in western Andalusia.
ANNALS OF HUMAN BIOLOGY
(2021)
Article
Infectious Diseases
Shelby M. Hutton, Adelaide Miarinjara, Nathan E. Stone, Fara N. Raharimalala, Annick O. Raveloson, Ravo Rakotobe Harimanana, Mireille Harimalala, Soanandrasana Rahelinirina, Ryelan F. Mcdonough, Abbe D. Ames, Crystal Hepp, Minoarisoa Rajerison, Joseph D. Busch, David M. Wagner, Romain Girod
Summary: The study revealed the presence of two different mutations in the voltage-gated sodium channel gene of the oriental rat flea populations in Madagascar, which are associated with resistance to synthetic pyrethroids. The research also developed a rapid detection assay for these resistance mutations. This study provides important information for the control of fleas and the prevention of plague transmission in Madagascar.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Virology
Derek W. Wright, William T. Harvey, Joseph Hughes, MacGregor Cox, Thomas P. Peacock, Rachel Colquhoun, Ben Jackson, Richard Orton, Morten Nielsen, Nienyun Sharon Hsu, Ewan M. Harrison, Thushan de Silva, Andrew Rambaut, Sharon J. Peacock, David L. Robertson, Alessandro M. Carabelli
Summary: COG-UK Mutation Explorer is a web resource that provides knowledge and analysis on SARS-CoV-2 virus genome mutations and variants in the UK. It focuses on antigenic amino acid replacements that have immunological significance. The resource curates data from over 2 million genome sequences and cross-references them with experimental data from the literature. It tracks mutations that could impact the neutralizing activity of antibodies and vaccines, as well as changes in T cell epitopes and resistance to antiviral drugs.
Article
Biochemistry & Molecular Biology
Guy Ling, Danielle Miller, Rasmus Nielsen, Adi Stern
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Biochemistry & Molecular Biology
Talia Kustin, Adi Stern
Summary: RNA viruses exhibit a trend towards A-rich coding sequences during evolution, mainly influenced by selection pressures, which contribute to the advancement of genome evolution. Research findings suggest that single-stranded RNA viruses undergo selective pressure resulting in the presence of A-rich coding sequences in their genomes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Moran Meir, Noam Harel, Danielle Miller, Maoz Gelbart, Avigdor Eldar, Uri Gophna, Adi Stern
Article
Virology
Maoz Gelbart, Adi Stern
Article
Genetics & Heredity
Alison F. Feder, Pleuni S. Pennings, Dmitri A. Petrov
Summary: This paper demonstrates the use of time series data to bound evolutionary parameters, complementing and informing traditional population genetic approaches. By studying drug-induced resistance evolution in HIV, we show new evidence that early HIV treatment failure was driven by soft sweeps.
Article
Biology
Florian Mattenberger, Victor Latorre, Omer Tirosh, Adi Stern, Ron Geller
Summary: This study comprehensively defines the effects of mutations on the capsid of a human picornavirus, identifying key structural and sequence determinants that predict mutational fitness effects. It also introduces a bioinformatic approach for identifying host proteins targeted by viral proteases based on capsid-encoded protease cleavage sites, shedding light on important aspects of viral biology, evolution, and host interactions.
Article
Biology
Alison F. Feder, Kristin N. Harper, Chanson J. Brumme, Pleuni S. Pennings
Summary: Triple-drug therapies have transformed HIV from a fatal condition to a chronic one, significantly reducing the risk of drug resistance evolution, but not eliminating it entirely.
Article
Clinical Neurology
Miri Gelbart, Elhanan Nahum, Maoz Gelbart, Eytan Kaplan, Gili Kadmon, Amir Kershenovich, Helen Toledano, Avichai Weissbach
Summary: Hyperlactatemia is common in children following craniotomy for brain tumor resection, but not associated with hemodynamic impairment or longer length of stay.
CHILDS NERVOUS SYSTEM
(2022)
Article
Biotechnology & Applied Microbiology
Alessio D. Nahmad, Cicera R. Lazzarotto, Natalie Zelikson, Talia Kustin, Mary Tenuta, Deli Huang, Inbal Reuveni, Daniel Nataf, Yuval Raviv, Miriam Horovitz-Fried, Iris Dotan, Yaron Carmi, Rina Rosin-Arbesfeld, David Nemazee, James E. Voss, Adi Stern, Shengdar Q. Tsai, Adi Barzel
Summary: In vivo engineering of B cells to secrete anti-HIV antibodies is a safe, potent, and scalable method that can be used for the treatment of infectious and noncommunicable diseases.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sheri Harari, Maayan Tahor, Natalie Rutsinsky, Suzy Meijer, Danielle Miller, Oryan Henig, Ora Halutz, Katia Levytskyi, Ronen Ben-Ami, Amos Adler, Yael Paran, Adi Stern
Summary: In immunocompromised patients with chronic SARS-CoV-2 infection, adaptive evolution occurs and some mutations may lead to the emergence of variants of concern. However, certain mutations associated with global transmission are absent in chronic infections. The study also found a strong correlation between viral rebound and antibody evasion. The findings suggest a tradeoff between antibody evasion and transmissibility, highlighting the importance of monitoring chronic infections for understanding the emergence of variants of concern.
Article
Multidisciplinary Sciences
Danielle Miller, Adi Stern, David Burstein
Summary: In this study, the authors propose a concept to reveal the function of uncharacterized genes using deep learning methods adopted from natural language processing. By repurposing NLP algorithms to model gene semantics, they are able to predict functional categories for genes and demonstrate the potential of combining microbial genomics and language models to discover gene functions in microbes.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Maya A. A. Lewinsohn, Trevor Bedford, Nicola F. F. Mueller, Alison F. F. Feder
Summary: A Bayesian state-dependent evolutionary phylodynamic model (SDevo) is used to quantify the difference in division rates between tumour cells at the periphery and interior. This model accurately infers spatially varying birth rates of tumors and outperforms existing methods in analyzing differential sequence evolution. Clinical data shows evidence of higher division rates on the tumor edge. The use of high-resolution, multi-region sequencing can further help investigate spatial growth restrictions and other factors that influence tumor progression.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Pediatrics
Miri Gelbart, Efraim Bilavsky, Oded Scheurman, Gabriel Chodick, Maoz Gelbart, Liat Ashkenazi-Hoffnung
Summary: This study aimed to describe the incidence, characteristics, and associated factors of recurrent mastoiditis in hospitalized children. It was found that the incidence of recurrent mastoiditis was 6.3%, with a median interval of 3 months between episodes. The first episodes of recurring cases were more common in children with atopic dermatitis and a history of percutaneous abscess drainage. The second episode of acute mastoiditis had a milder clinical course and shorter durations compared to the first episode.
PEDIATRICS INTERNATIONAL
(2023)
Article
Virology
Itamar Caspi, Moran Meir, Nadav Ben Nun, Reem Abu Rass, Uri Yakhini, Adi Stern, Yoav Ram
Summary: RNA viruses have high genetic diversity due to mutation and natural selection, but separating these forces is challenging. This study developed a method to infer the mutation rate and selection parameters from full haplotype sequences using neural networks. Applying this method to MS2 bacteriophage data, a mutation rate of approximately 0.2 mutations per genome per replication cycle was estimated. Additionally, evidence of reciprocal sign epistasis between beneficial mutations was found. In summary, this study provides insights into the mutation rate and selection parameters of RNA viruses using a novel approach.
Article
Microbiology
Maoz Gelbart, Sheri Harari, Ya'ara Ben-Ari, Talia Kustin, Dana Wolf, Michal Mandelboim, Orna Mor, Pleuni S. Pennings, Adi Stern