Article
Plant Sciences
Shigekatsu Suzuki, Masanobu Kawachi, Chinatsu Tsukakoshi, Atsushi Nakamura, Kyoko Hagino, Isao Inouye, Ken-ichiro Ishida
Summary: The study reveals an unstable morphological, metabolic, and genetic relationship between B. bigelowii and its endosymbiont, including the nitrogen fixation role of the endosymbiont and the host's lack of expression of many essential genes associated with nitrogen compound uptake.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Engineering, Marine
Ansgar Gruber, Linda K. Medlin
Summary: Photosynthesis is a crucial process that converts inorganic carbon into organic biomass and contributes to the abundance of organic material on Earth. Oxygenic photosynthesis, particularly in cyanobacteria and eukaryotes, played a significant role in shaping the planet's atmosphere and enabling aerobic energy metabolism.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Gemma G. R. Murray, Jane Charlesworth, Eric L. Miller, Michael J. Casey, Catrin T. Lloyd, Marcelo Gottschalk, Alexander W. (Dan) Tucker, John J. Welch, Lucy A. Weinert
Summary: The study shows that genome reduction is consistently associated with pathogenicity in bacteria.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Nicolas Parisot, Carlos Vargas-Chavez, Clement Goubert, Patrice Baa-Puyoulet, Severine Balmand, Louis Beranger, Caroline Blanc, Aymeric Bonnamour, Matthieu Boulesteix, Nelly Burlet, Federica Calevro, Patrick Callaerts, Theo Chancy, Hubert Charles, Stefano Colella, Andre Da Silva Barbosa, Elisa Dell'Aglio, Alex Di Genova, Gerard Febvay, Toni Gabaldon, Mariana Galvao Ferrarini, Alexandra Gerber, Benjamin Gillet, Robert Hubley, Sandrine Hughes, Emmanuelle Jacquin-Joly, Justin Maire, Marina Marcet-Houben, Florent Masson, Camille Meslin, Nicolas Montagne, Andres Moya, Ana Tereza Ribeiro de Vasconcelos, Gautier Richard, Jeb Rosen, Marie-France Sagot, Arian F. A. Smit, Jessica M. Storer, Carole Vincent-Monegat, Agnes Vallier, Aurelien Vigneron, Anna Zaidman-Remy, Wael Zamoum, Cristina Vieira, Rita Rebollo, Amparo Latorre, Abdelaziz Heddi
Summary: The rice weevil, Sitophilus oryzae, is a significant agricultural pest with an intracellular symbiotic relationship with the bacterium Sodalis pierantonius. Its genome contains a large amount of transposable elements, which are associated with the insect's endosymbiotic state. Compared to other beetles, S. oryzae has undergone a high rate of gene expansion. Reconstruction of host-symbiont metabolic networks revealed that S. pierantonius relies on the host for essential substances.
Article
Plant Sciences
Sonja Repetti, Cintia Iha, Kavitha Uthanumallian, Christopher J. Jackson, Yibi Chen, Cheong Xin Chan, Heroen Verbruggen
Summary: This study aims to understand the genomic diversity in green algae and investigates lineage-specific gene evolution. The results show genome streamlining in Pedinophyceae and genome expansion in the UTC clade, which may contribute to their success in different habitats.
Article
Plant Sciences
Sophia V. Yudina, Mikhail I. Schelkunov, Lars Nauheimer, Darren Crayn, Sahut Chantanaorrapint, Michal Hrones, Michal Sochor, Martin Dancak, Shek-Shing Mar, Hong Truong Luu, Maxim S. Nuraliev, Maria D. Logacheva
Summary: This study investigates a diversity of plastid genomes in closely related non-photosynthetic plants, illustrating how gradual gene loss shapes the miniaturized plastomes of these plants and revealing the process of reductive evolution in heterotrophic plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Yixin Zhao, Guang-An Lu, Hao Yang, Pei Lin, Zhongqi Liufu, Tian Tang, Jin Xu
Summary: The Red Queen hypothesis suggests that new genes must evolve continuously to adapt to changing environments, or they will be eliminated. In an experiment with two Drosophila miRNAs, it was found that their fitness contributions differed in different species, supporting the predictions of the Red Queen hypothesis.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Martin Zoltner, Mark C. Field
Summary: Euglena gracilis is a robust photosynthetic flagellate with a large nuclear genome and multiple endosymbiotic/gene transfer events. Its extraordinary metabolic plasticity and mixotrophic lifestyle enable it to thrive in diverse environments and produce novel metabolites.
Article
Genetics & Heredity
Daniele Giannotti, Vittorio Boscaro, Filip Husnik, Claudia Vannini, Patrick J. Keeling
Summary: Comparing the genomes of 'Candidatus Nebulobacter' and Fastidiosibacter, two closely related bacteria with different ecological niches, revealed surprising similarities and suggested that only a few factors might be responsible for the establishment of obligate endosymbiosis in early stages.
MICROBIAL GENOMICS
(2022)
Article
Biology
Maeva Perez, Corinna Breusing, Bernard Angers, Roxanne A. Beinart, Yong-Jin Won, C. Robert Young
Summary: Vertical transmission of bacterial endosymbionts leads to gene loss and reduction in genome size. This study investigates the contributions of drift, recombination, and selection to genome evolution in two species of vesicomyid symbionts. The results suggest that drift is a significant force, while selection and interspecific recombination play critical roles in maintaining functional integrity and creating divergent patterns of gene conservation in the symbionts.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Barbara De Kegel, Colm J. Ryan
Summary: Genomic instability is a hallmark of cancer, and the dispensability of paralogs influences tumor genome evolution. It was found that genes with paralogs are more likely to be homozygously deleted, and paralogs that are essential in cancer cell lines are less frequently deleted in tumors.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Evolutionary Biology
Agusto R. Luzuriaga-Neira, Andrew M. Ritchie, Bryan L. Payne, Oliver Carrillo-Parramon, David A. Liberles, David Alvarez-Ponce
Summary: Highly abundant proteins tend to evolve slowly in a phenomenon called E-R anticorrelation. One hypothesis, the misfolding avoidance hypothesis, explains this by the toxic effects of protein misfolding. This hypothesis predicts that highly abundant proteins should exhibit high thermostability, but previous analyses have produced contradictory results. In this study, computational methods were used to compare the folding free energy of human-mouse orthologous proteins with different expression levels, finding that highly expressed proteins are often more thermostable.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Cell Biology
Arie Fridrich, Miguel Salinas-Saaverda, Itamar Kozlolvski, Joachim M. Surm, Eleni Chrysostomou, Abhinandan M. Tripathi, Uri Frank, Yehu Moran
Summary: The study reveals the importance of miR-2022 in initiating cell generation in Nematostella and its conservation across other cnidarian species.
Article
Microbiology
Diego Cortez, Gonzalo Neira, Carolina Gonzalez, Eva Vergara, David S. Holmes
Summary: The genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. In this study, a comparative genomics investigation of acidophilic bacteria was performed to examine the correlation between genome size reduction and decreasing pH. The results indicate that genome streamlining in acidophilic bacteria is supported by gene loss and reduced gene sizes, independent of other genome size constraints.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Nono S. C. Merleau, Sophie Penisson, Philip J. Gerrish, Santiago F. Elena, Matteo Smerlak
Summary: Viruses experience frequent population bottlenecks when transmitted to new hosts, leading to a fragile genetic structure as an evolutionary response. Increasing the fitness cost of mutations may lower the fixation probability of unfit mutants at each transmission, enhancing survival chances through multiple bottlenecks.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jose Francisco Munoz-Valle, Alberto Antony Venancio-Landeros, Rocio Sanchez-Sanchez, Karen Reyes-Diaz, Byron Galindo-Ornelas, Wendy Susana Hernandez-Monjaraz, Alejandra Garcia-Rios, Luis Fernando Garcia-Ortega, Jorge Hernandez-Bello, Marcela Pena-Rodriguez, Natali Vega-Magana, Luis Delaye, Mauricio Diaz-Sanchez, Octavio Patricio Garcia-Gonzalez
Summary: This study presents a faster and deeper SARS-CoV-2 surveillance method, from RT-qPCR screening to NGS analysis. The method identifies variants present in positive samples and classifies different viral populations based on relative abundance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Maria Jose Garzon, Mariana Reyes-Prieto, Rosario Gil
Summary: This paper proposes a minimal translation machinery based on comparative and functional analysis of bacterial genomes, consisting of 142 genes, which can be applied in the design of synthetic cells.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Gilbert Smith, Alejandro Manzano-Marin, Mariana Reyes-Prieto, Catia Sofia Ribeiro Antunes, Victoria Ashworth, Obed Nanjul Goselle, Abdulhalem Abdulsamad A. Jan, Andres Moya, Amparo Latorre, M. Alejandra Perotti, Henk R. Braig
Summary: We propose that Demodex folliculorum represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Genome sequencing revealed extensive genome reduction and a decrease in the number of cells in the mite. This is the first evolutionary step in adopting a reductive, parasitic, or endosymbiotic lifestyle in an arthropod species.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Mathematics, Interdisciplinary Applications
I. Creus Marti, A. Moya, F. J. Santonja
Summary: This paper presents a Bayesian model for analyzing longitudinal gut microbiome data, taking into account compositional paradigm and principal balances. The proposed model is able to predict future dynamics of microbial community in the short term and analyze microbial interactions using estimated parameters. It is demonstrated to be useful through the analysis of six different datasets and comparison with four alternative models.
Article
Biochemistry & Molecular Biology
Francisco Gonzalez-Serrano, Cei Abreu-Goodger, Luis Delaye
Summary: Codon usage reflects the environment and evolutionary conditions of organisms. The R_ENC' index can better detect selection acting on codon usage and estimate the extent of selected codon usage bias. Gammaproteobacteria, Betaproteobacteria, Actinobacteria, and Firmicutes show more genomes with selected codon usage bias, indicating convergent evolution phenomenon.
JOURNAL OF MOLECULAR EVOLUTION
(2022)
Editorial Material
Biology
Andres Moya
PHYSICS OF LIFE REVIEWS
(2022)
Article
Infectious Diseases
Ricardo Garcia-Gamboa, Miguel Dominguez-Simi, Misael S. Gradilla-Hernandez, Jorge Bravo, Andres Moya, Blanca Ruiz-Alvarez, Marisela Gonzalez-Avila
Summary: This study evaluated the growth inhibition and antibiofilm activity of short-chain fatty acids and inulin-type fructans produced by Lacticaseibacillus rhamnosus and Pediococcus acidilactici against Candida albicans. The results showed significant growth inhibition and antibiofilm formation against a clinically isolated Candida albicans strain.
Article
Biology
Javier Falgueras-Cano, Juan Antonio Falgueras-Cano, Andres Moya
Summary: This study uses a cellular automaton to simulate the evolutionary dynamics of species and investigates the effects of different dispersal strategies on the interactions between digital organisms. The research finds that the distribution pattern significantly influences the dynamics, persistence, distribution, and abundance of populations. Aggregated distribution is crucial for predator-prey interactions and provides a straightforward explanation for the paradox of plankton and animal grouping. It is less efficient in preserving populations compared to uniform distribution, but it can enhance the evolutionary stability of certain biological interactions.
Article
Agriculture, Dairy & Animal Science
David Diaz-Reganon, Mercedes Garcia-Sancho, Alejandra Villaescusa, Angel Sainz, Beatriz Agulla, Mariana Reyes-Prieto, Antonio Rodriguez-Bertos, Fernando Rodriguez-Franco
Summary: Chronic inflammatory enteropathies are a common cause of chronic vomiting and diarrhea in dogs. This study aimed to characterize the intestinal bacterial microbiota in dogs with inflammatory bowel disease (IBD) using duodenal biopsies and fecal samples, and compare them to healthy dogs. The results showed significant differences in the gut microbiota of dogs with IBD compared to healthy dogs, with more pronounced changes in the fecal microbiota. Further investigations are needed to understand the functionality of the gut microbiome in canine IBD.
Article
Microbiology
Manuela Parra, Rosa de los angeles Bayas-Rea, Teresa Guerrero, Stuart Torres, Giuseppe D'Auria, Mariana Reyes-Prieto, Sonia Zapata
Summary: This study describes the isolation of two lytic Salmonella bacteriophages, whose genomes show similarity to the lytic phage NBSal001 in the Drexlerviridae family. These bacteriophages provide an option to reduce the presence of Salmonella.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Mycology
Alene Alder-Rangel, Alexandre Melo Bailao, Alfredo Herrera-Estrella, Amanda E. A. Rangel, Attila Gacser, Audrey P. Gasch, Claudia B. L. Campos, Christina Peters, Francine Camelim, Fulvia Verde, Geoffrey Michael Gadd, Gerhard Braus, Iris Eisermann, Janet Quinn, Jean-Paul Latge, Jesus Aguirre, Joan W. Bennett, Joseph Heitman, Joshua D. Nosanchuk, Laila P. Partida-Martinez, Martine Bassilana, Mavis A. Acheampong, Meritxell Riquelme, Michael Feldbruegge, Nancy P. Keller, Nemat O. Keyhani, Nina Gunde-Cimerman, Raquel Nascimento, Robert A. Arkowitz, Rosa Reyna Mourino-Perez, Sehar Afshan Naz, Simon Avery, Thiago Olitta Basso, Ulrich Terpitz, Xiaorong Lin, Drauzio E. N. Rangel
Summary: The fourth International Symposium on Fungal Stress (ISFUS) and the XIII International Fungal Biology Conference were held in Sao Jose dos Campos, SP, Brazil in September 2022. The event featured 33 renowned speakers from 12 countries and contributed to international scientific cooperation and research in Brazil.
Review
Biology
Rebeca de la Fuente, Wladimiro Diaz-Villanueva, Vicente Arnau, Andres Moya
Summary: Genomic signature refers to characteristics associated with DNA sequences, which can be used to analyze genotype-phenotype patterns, identify gene expression profiles, or study statistical properties of DNA sequences. This review performs a bibliometric analysis to identify the main genomic signatures and categorizes them according to their conceptual meanings. It highlights the importance of genomic signatures in evolutionary biology.
Article
Biochemical Research Methods
Luis Delaye
Summary: The SARS-CoV-2 virus has the highest number of sequenced genomes ever recorded, with millions of copies stored in the GISAID database. This presents challenges in analyzing the evolution of the virus due to the need for accurate geographical information. However, errors and inconsistencies can occur when researchers manually input metadata, making the correction process time-consuming. To address this, a suite of Perl scripts, called CurSa, is provided to curate and sample genome sequences from specific locations, facilitating the preparation of files for evolutionary studies. The CurSa scripts can be accessed at: https://github.com/luisdelaye/CurSa/.
BIOLOGY METHODS & PROTOCOLS
(2023)
Article
Microbiology
Cecilio Valadez-Cano, Roberto Olivares-Hernandez, Astrid N. Espino-Vazquez, Laila P. Partida-Martinez
Summary: We constructed and calculated a Genome-Scale Model of a fungal-bacterial-viral holobiont, and found that changes in the lipid and nucleotide metabolism of the host are crucial for the functionality of the holobiont. Glycerol plays a pivotal role in the fungal-bacterial metabolic interaction, while Narnavirus does not impact the symbiotic relationship.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Mycology
Jose Francisco Cabrera-Rangel, Judit Valeria Mendoza-Servin, Gonzalo Cordova-Lopez, Raul Alcalde-Vazquez, Raymundo Saul Garcia-Estrada, Robert Winkler, Laila P. Partida-Martinez
Summary: This study analyzed the symbiotic and toxinogenic potential of Rhizopus species derived from agricultural soils in Mexico. The findings revealed a more diverse symbiotic relationship between Rhizopus and Mycetohabitans than anticipated.
FRONTIERS IN FUNGAL BIOLOGY
(2022)