Article
Agronomy
Ramon G. Leon, Jeffrey C. Dunne, Fred Gould
Summary: The evolution of resistance to multiple herbicides and non-target site resistance often involves multiple genes, leading to a polygenic control of weed adaptation. Advances in whole-genome sequencing and bioinformatic tools have enabled a better understanding of genetic control of resistance and other important traits in weed adaptation, allowing for predictions of responses to selection pressure by herbicides and other environmental factors. The use of tools such as quantitative trait loci mapping and genomic prediction will help in explaining how pests adapt to control tools and how specific genotypes thrive and spread.
PEST MANAGEMENT SCIENCE
(2021)
Article
Evolutionary Biology
William R. Shoemaker, Daisy Chen, Nandita R. Garud
Summary: Genetic variation in the human gut microbiome plays a crucial role in various phenotypes. However, our understanding of its origins and maintenance is limited. By comparing evolutionary processes across different species, we can identify universal trends and deviations. The human gut microbiome offers unparalleled potential for comparative population genomics studies.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Stephen P. Wooding, Vicente A. Ramirez
Summary: This study analyzed the diversity of human bitter taste receptors (TAS2Rs) on a global scale and found variations among different genes and relatively small differences among populations. This suggests a relaxation of selective pressure on TAS2Rs during human evolution.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Leo Speidel, Lara Cassidy, Robert W. Davies, Garrett Hellenthal, Pontus Skoglund, Simon R. Myers
Summary: The study introduces a fast and scalable approach, Colate, for inferring ancestral relationships between low-coverage genomes without requiring phasing or imputation. The method leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. By applying this approach to modern and ancient DNA samples, the research identifies dynamic population structure and gene flow between early farmers and European hunter-gatherer groups.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Editorial Material
Microbiology
Nandita Garud
Summary: Microbes can evolve rapidly to adapt to selection pressures, but our understanding of the adaptation in microbiomes is still incomplete. Advances in modeling complex populations and scenarios will help us better understand adaptation in microbiomes and other natural populations experiencing similar complexities.
Article
Biochemistry & Molecular Biology
Remi Matthey-Doret
Summary: SimBit is a high-performance population genetics simulator that can simulate various selection, demographic and mating scenarios, track QTLs and model ecological relationships among multiple species. It comes with a convenient R wrapper for project management and outperforms other simulators in most benchmarks.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Microbiology
Guihong Zhao, Rui Su, Meng Yuan, Hongkun Ma, Taidong Bo, Hao Jiang, Chen Wu, Yanjun Li
Summary: The study investigated streptomycin-resistant mutants of Corynebacterium glutamicum with rpsL K43 mutations, finding that a single rpsL(K43) mutation did not confer resistance to multiple antibiotics, suggesting additional mutations are needed. Nine mutants were constructed and found to exhibit different growth and enhanced green fluorescent protein (eGFP) expression under different culture conditions.
CURRENT MICROBIOLOGY
(2022)
Article
Hematology
Llucia Alberti-Servera, Sofie Demeyer, Inge Govaerts, Toon Swings, Jolien De Bie, Olga Gielen, Marco Brociner, Lucienne Michaux, Johan Maertens, Anne Uyttebroeck, Kim De Keersmaecker, Nancy Boeckx, Heidi Segers, Jan Cools
Summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive leukemia characterized by chromosomal rearrangements and somatic mutations in protein-coding regions. Most T-ALL cases have activating mutations in NOTCH1 and other genes related to signaling and regulation. Single-cell DNA sequencing reveals clonal architecture and evolution in T-ALL, showing major and minor clones at diagnosis and during treatment.
Article
Ophthalmology
Asrin Rasul, Laura Roos, Kristian Groth, Per Riise, Daniella Bach-Holm, Line Kessel
Summary: This retrospective cohort study describes the causes of ectopia lentis (EL) and the outcomes after surgery in a Danish population. The study found that Marfan syndrome was the main cause of EL, and surgery improved visual acuity. The most common complication after surgery was ocular hypertension, and there were no cases of postoperative retinal detachment.
JOURNAL OF CATARACT AND REFRACTIVE SURGERY
(2022)
Article
Oncology
Haiyue Li, Yongjun He, Li Wang, Shishi Xing, Linna Peng, Dongya Yuan, Tianbo Jin
Summary: The investigation of CYP2J2 mutations in Chinese Uyghurs revealed new mutations, different genotypes and alleles, which were compared with other ethnic groups. These findings provide valuable insights into the genetic characteristics of CYP2J2 in different populations and its impact on drug metabolism.
AMERICAN JOURNAL OF TRANSLATIONAL RESEARCH
(2021)
Editorial Material
Multidisciplinary Sciences
David Enard
Summary: DNA analysis of humans from the Middle Ages reveals that survivors of the bubonic plague experienced rapid natural selection, potentially leading to an increased risk of autoimmune diseases in their descendants.
News Item
Multidisciplinary Sciences
Ewen Callaway
Summary: Ancient DNA from closely related individuals provides new insight into the lives and social structures of Neanderthals.
Biographical-Item
Multidisciplinary Sciences
Bert Holldobler
Summary: This article introduces a naturalist, conservationist and synthesizer who founded sociobiology.
News Item
Multidisciplinary Sciences
Ewen Callaway, Heidi Ledford
Summary: Svante Paabo's discoveries using ancient DNA have had a significant impact on our understanding of human evolution and have played a key role in the development of the field of palaeogenomics.
Article
Microbiology
Laura C. Jacques, Angharad E. Green, Thomas E. Barton, Murielle Baltazar, Julia Aleksandrowicz, Rong Xu, Erwan Trochu, Aras Kadioglu, Daniel R. Neill
Summary: The short generation time of bacterial pathogens allows for the accumulation of de novo mutations during routine culture procedures, which can influence genetic diversity and virulence characteristics. This study demonstrates how laboratory handling of Streptococcus pneumoniae can lead to changes in the genetic structure and virulence of bacterial populations.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Catarina Pinto, Rita Melo-Miranda, Isabel Gordo, Ana Sousa
Summary: The lac operon is a well-known gene regulatory circuit in bacteria, providing a competitive advantage in the mouse gut by as much as 11%, contingent on diet and other gut microbiota. Despite lactose being absent in most mammals during adulthood, the selective pressure for maintaining the lac operon may be weak, explaining the polymorphism observed in E. coli.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Tanja Dapa, Ricardo Serotte Ramiro, Miguel Filipe Pedro, Isabel Gordo, Karina Bivar Xavier
Summary: Switching from a low-fat and high-fiber diet to a Western-style high-fat and high-sugar diet can cause imbalances in the gut microbiota, leading to various pathological conditions. This study investigated the mutations in Bacteroides thetaiotaomicron in the gut under different dietary regimens and found that periodic dietary changes caused fluctuations in mutation frequency, accompanied by metabolic shifts.
CELL HOST & MICROBE
(2022)
Article
Evolutionary Biology
Dragan Stajic, Claudia Bank, Isabel Gordo
Summary: Epigenetic regulation of gene expression allows for the emergence of distinct phenotypic states within the clonal population, and these states can switch in a stochastic manner between generations. This study shows that under fluctuating environmental conditions, rapid epigenetic switching provides an advantage, while genetic mutations are favored in stable environments.
GENOME BIOLOGY AND EVOLUTION
(2022)
Editorial Material
Ecology
Isabel Gordo
Summary: The rate of fixation of different antibiotic-resistance mutation types demonstrates a trade-off influenced by population size.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Debanjan Mukherjee, Angelo Ferreira Chora, Jean-Christophe Lone, Ricardo S. Ramiro, Birte Blankenhaus, Karine Serre, Mario Ramirez, Isabel Gordo, Marc Veldhoen, Patrick Varga-Weisz, Maria M. Mota
Summary: This study reveals that the microbiota colonizing the lung can promote respiratory distress syndrome and mortality during malaria infections. Parasite sequestration in the lung results in sustained immune activation and production of anti-inflammatory cytokine compromises microbial control, leading to severe lung disease. Clearance of bacteria prevents MA-ARDS-associated lethality. Hence, the balance between the host's anti-inflammatory response and microbial control should be considered when intervening against respiratory complications.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
N. Frazao, A. Konrad, M. Amicone, E. Seixas, D. Guleresi, M. Laessig, I Gordo
Summary: By monitoring evolution for more than six thousand generations in the mouse gut, the authors show that a colonizing bacterial strain evolves through two modes: one involving metabolic mutations and the other involving the domestication of bacteriophages. The study demonstrates the importance of the microbiota diversity and the presence of related strains in the colonization success of Escherichia coli. The research also highlights the rapid formation of ecotypes and phage domestication in the mammalian gut.
NATURE COMMUNICATIONS
(2022)
Review
Microbiology
Jorge Moura de Sousa, Marta Lourenco, Isabel Gordo
Summary: Horizontal gene transfer is a crucial driver of bacterial diversity and the rapid spread of antibiotic resistance in host-associated microbiomes. Recent studies have greatly enhanced our understanding of horizontal gene transfer mechanisms, the ecological complexities of bacterial interactions and mobile elements, and the impact of host physiology on genetic exchanges. Detecting and quantifying genetic exchanges in vivo pose fundamental challenges, but novel computational approaches and theoretical models combined with experimental methods are helping to overcome these challenges. Integration of these approaches with studies on multiple strains and transfer elements in both in vivo and controlled host-associated environments is essential.
CELL HOST & MICROBE
(2023)
Review
Microbiology
Hugo C. Barreto, Isabel Gordo
Summary: A large number of microorganisms continuously divide in the guts of animals and humans, allowing for real-time observation of microbial evolution. Recent studies have revealed that natural selection shapes within-host evolution in the intestines of mice and humans, with the gut microbiota being highly dynamic and influenced by species diversity. Genetic and bioinformatics tools can help quantify the selection strength on mutations and transfer events in gut ecosystems, providing insights into the drivers and functional consequences of gut evolution. Understanding the rules of intrahost microbiota evolution is crucial for the development of effective microbiota therapies.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Biology
Ana-Hermina Ghenu, Andre Amado, Isabel Gordo, Claudia Bank
Summary: Predicting mutational effects is crucial for antibiotic resistance control, but it becomes difficult due to G x E, G x G, or G x G x E interactions. This study quantified G x G x E effects in Escherichia coli and assessed the predictability of fitness landscapes across different environments. The results showed the dominance of ABR genotypes over gene knock-outs in the presence of antibiotics, indicating the predictability of evolution in adverse environments.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Nelson Frazao, Isabel Gordo
Summary: Social networks can shape the species composition of the gut microbiome by influencing the ecology of gut bacteria. In an experimental evolution study in mice, it was found that there is a transmission rate of 7% (& PLUSMN;3% 2SE) of E. coli cells per day between hosts living in the same household. The results also showed that hosts with similar diets and habits are expected to have similar microbiome species compositions and evolutionary dynamics.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Respiratory System
Sara Melo-Dias, Miguel Cabral, Andreia Furtado, Sara Souto-Miranda, Maria Aurora Mendes, Joao Cravo, Catarina Rodrigues Almeida, Alda Marques, Ana Sousa
Summary: Pulmonary rehabilitation (PR) can alter the composition of oral microbiota, which is associated with the effectiveness of PR for COPD management. It increases the abundance of beneficial bacteria Prevotella melaninogenica and decreases harmful bacteria Streptococcus and Lautropia.
RESPIRATORY RESEARCH
(2023)
Correction
Respiratory System
Sara Melo-Dias, Carla Valente, Lilia Andrade, Alda Marques, Ana Sousa
RESPIRATORY RESEARCH
(2022)
Article
Medicine, Research & Experimental
Vitor Borges, Joana Isidro, Nidia Sequeira Trovao, Silvia Duarte, Helena Cortes-Martins, Hugo Martiniano, Isabel Gordo, Ricardo Leite, Luis Vieira, Raquel Guiomar, Joao Paulo Gomes
Summary: Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented in collaboration with over 50 laboratories distributed nationwide. The study detected at least 277 independent introductions of SARS-CoV-2, mostly from European countries, highlighting the importance of early measures in minimizing the spread of the virus.
COMMUNICATIONS MEDICINE
(2022)
Article
Evolutionary Biology
Massimo Amicone, Vitor Borges, Maria Joao Alves, Joana Isidro, Libia Ze-Ze, Silvia Duarte, Luis Vieira, Raquel Guiomar, Joao Paulo Gomes, Isabel Gordo
Summary: By conducting experimental evolution with two strains of SARS-CoV-2 in Vero cells, researchers estimated a high rate of mutation accumulation, particularly in the strain carrying the D614G mutation.
EVOLUTION MEDICINE AND PUBLIC HEALTH
(2022)
Article
Respiratory System
Sara Melo-Dias, Carla Valente, Lilia Andrade, Alda Marques, Ana Sousa
Summary: Individuals with COPD have been found to have a distinct oral microbiota composition, with differences in bacterial profiles compared to healthy individuals. Salivary bacteria show associations with COPD, particularly in relation to severe exacerbations, suggesting the potential use of saliva as a non-invasive specimen for future studies on respiratory diseases like COPD.
RESPIRATORY RESEARCH
(2022)