Review
Immunology
Christian A. Devaux, Pierre Pontarotti, Sephora Nehari, Didier Raoult
Summary: Adaptive immunity is a sophisticated form of immune response that retains molecular memory of a great diversity of non-self target antigens. It is highly evolved and complements innate immunity, which is a relatively non-specific defense mechanism.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Patrick C. F. Buchholz, Bert van Loo, Bernard D. G. Eenink, Erich Bornberg-Bauer, Juergen Pleiss
Summary: Protein family evolutionary relationships can be characterized either by networks or by trees. Ancestral protein sequences in networks act as bridges and share close similarity with extant sequences. Some reconstructed ancestor sequences can also be interpreted as yet-to-be-identified homologues or consensus sequences.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2021)
Article
Biology
Lam Si Tung Ho, Edward Susko
Summary: Likelihood-based methods are considered the best approaches for reconstructing ancestral states, but consistency issues may arise when the tree topology and edge lengths are unknown. Consistency is proven under symmetric models and a simple consistent estimator is found under non-symmetric models.
JOURNAL OF MATHEMATICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Joana Damas, Marco Corbo, Jaebum Kim, Jason Turner-Maier, Marta Farre, Denis M. Larkin, Oliver A. Ryder, Cynthia Steiner, Marlys L. Houck, Shaune Hall, Lily Shiue, Stephen Thomas, Thomas Swale, Mark Daly, Jonas Korlach, Marcela Uliano-Silva, Camila J. Mazzoni, Bruce W. Birren, Diane P. Genereux, Jeremy Johnson, Kerstin Lindblad-Toh, Elinor K. Karlsson, Martin T. Nweeia, Rebecca N. Johnson, Harris A. Tewin
Summary: Decrypting the rearrangements that drive mammalian chromosome evolution is crucial for understanding speciation, adaptation, and disease susceptibility. By computationally reconstructing ancestral karyotypes and syntenic relationships, the study reveals the chromosome structure and evolutionary history of the mammalian ancestors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Lucas C. Wheeler, Michael J. Harms
Summary: The study suggests that ancestral proteins may have been less specific than modern proteins, but when interactions with random peptide targets are considered, the picture becomes more complex. It demonstrates that altered biological specificity does not necessarily indicate altered intrinsic specificity.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Andrii Mazur, Pavel Grinkevich, Radka Chaloupkova, Petra Havlickova, Barbora Kascakova, Michal Kuty, Jiri Damborsky, Ivana Kuta Smatanova, Tatyana Prudnikova
Summary: Haloalkane dehalogenases are key enzymes in hydrolytic degradation of halogenated compounds, with ancestral sequence reconstruction being a powerful tool for studying molecular evolution and designing robust proteins for enzyme technologies. The newly characterized ancestral enzyme AncLinB-DmbA has unique structural features compared to its descendant enzymes, offering insights into the evolution of this enzyme family.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Letter
Biochemistry & Molecular Biology
Roberto Del Amparo, Miguel Arenas
Summary: Selecting the best-fitting substitution model is recommended for accurately reconstructing ancestral sequences.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Hussein A. Hejase, Ziyi Mo, Leonardo Campagna, Adam Siepel
Summary: A novel method called SIA was developed to detect and quantify positive selection using the ancestral recombination graph and deep learning. Extensive benchmarking showed its effectiveness in simulations and real data, revealing novel signals of selection in European populations and confirming selection signals in genes related to human phenotypes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Isabel Nocedal, Michael T. Laub
Summary: Gene duplication is important for generating new signaling pathways during evolution. In this study, the researchers used ancestral sequence reconstruction to resurrect a bacterial two-component signaling system that duplicated in alpha-proteobacteria. They determined the interaction specificities of the signaling proteins before and after the duplication event and identified key mutations responsible for establishing specificity in the two systems. These findings suggest that protein-protein interactions with latent potential may be easily duplicated and diverged.
Article
Plant Sciences
Lucio D'Andrea, Nicolas Sierro, Sonia Ouadi, Tomas Hasing, Elijah Rinaldi, Nikolai V. Ivanov, Aureliano Bombarely
Summary: In this study, the researchers analyzed the plastidial and nuclear genes of several Nicotiana diploid species and found that Nicotiana section Suaveolentes is a polyploid tobacco species that originated in Australia through hybridization between diploid relatives.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Chang-Hwa Chiang, Troy Wymore, Attabey Rodriguez Benitez, Azam Hussain, Janet L. Smith, Charles L. Brooks, Alison R. H. Narayan
Summary: Controlling the selectivity of a reaction is crucial for targeted synthesis. Achieving complementary selectivity profiles is challenging in biocatalytic reactions due to enzymes' intrinsic single selectivity preferences. Therefore, understanding the structural features that control selectivity in biocatalytic reactions is critical for achieving tunable selectivity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Abayomi S. Olabode, Mitchell J. Mumby, Tristan A. Wild, Laura Munoz-Baena, Jimmy D. Dikeakos, Art F. Y. Poon
Summary: Nef is a unique accessory protein in primate HIV-1, HIV-2, and SIV lentiviruses that interacts with multiple host proteins to evade the immune response and enhance virion infectivity. This study reconstructed ancestral viral proteins and showed that the ability of Nef to downregulate CD4 evolved gradually, while the downregulation of SERINC5 was abruptly recovered in the HIV-1/M ancestor. This framework provides insights into the functional changes of viral proteins throughout evolutionary history.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Agriculture, Multidisciplinary
Jiamin Hu, Xiaoyu Chen, Lu Zhang, Jieyu Zhou, Guochao Xu, Ye Ni
Summary: By employing ancestral sequence reconstruction and consensus sequence analysis, the researchers engineered the thermostability of a novel Dcarbamoylase derived from Nitratireductor indicus. They obtained a mutant with significantly increased thermostability, which showed improved catalytic activity and stability in the hydantoinase process. This study provides a valuable resource for industrial synthesis of optically pure natural and non-natural amino acids.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Editorial Material
Engineering, Electrical & Electronic
Keiji Tanaka, Norimitsu Yoshida
Summary: Photoconductive methods are commonly used to evaluate the photo-electronic responses in semiconductors. However, these methods may be influenced by bolometric effects caused by temperature rises, which have been overlooked in many studies. We emphasize that in semiconductors with narrower bandgap energies (<0.5 eV) and shorter carrier lifetimes (<1 ns), photo-thermal currents tend to dominate over photo-currents. We also discuss some ideas for evaluating photoconductivity in such materials.
JOURNAL OF MATERIALS SCIENCE-MATERIALS IN ELECTRONICS
(2023)
Article
Biotechnology & Applied Microbiology
Michael C. U. Hammond-Kosack, Robert King, Kostya Kanyuka, Kim E. Hammond-Kosack
Summary: The study found that most gene promoters are highly conserved, with multiple haplotypes and some being identical to a reference variety. These data are valuable for gene function studies and wheat breeding.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Miguel Arenas
Summary: In this study, a computational framework called ProteinEvolverABC is presented to jointly estimate recombination and substitution rates from alignments of protein sequences. The framework utilizes the approximate Bayesian computation approach and can accurately coestimate recombination and substitution rates under diverse evolutionary scenarios.
Article
Biochemistry & Molecular Biology
Filipa Moreira, Miguel Arenas, Arnaldo Videira, Filipe Pereira
Summary: This study reveals the evolutionary history and genetic variations of TOPIIA in animals, showing that it is highly conserved in Metazoa. The origins of TOPIIA paralogues differ between jawed and jawless vertebrates, possibly due to tetraploidization events. The specialized role of TOP2B in postmitotic cells may have driven its stronger purifying selection compared to TOP2A. Positive selection was detected in the variable C-terminal domain (CTD) of TOPIIA, suggesting its adaptation to cellular interactions. Amino acid substitutions in TOP2A CTD were found between modern and archaic humans, indicating its potential contribution to human evolution. Six residues conferring resistance to chemotherapy were identified between TOP2A and TOP2B, which could be targeted for the development of TOP2A-specific inhibitors. Overall, this research provides insights into the origin, diversification, and selection pressures of animal TOPIIA.
JOURNAL OF MOLECULAR EVOLUTION
(2022)
Article
Oncology
Joao M. Alves, Sonia Prado-Lopez, Laura Tomas, Monica Valecha, Nuria Estevez-Gomez, Pilar Alvarino, Dominik Geisel, Dominik Paul Modest, Igor M. Sauer, Johann Pratschke, Nathanael Raschzok, Christine Sers, Soulafa Mamlouk, David Posada
Summary: This study analyzed the evolutionary history of recurrent hepatic lesions in a patient with metastatic colorectal cancer (mCRC) using single-cell whole-genome sequencing data, revealing the impact of treatment on the genetic and evolutionary determinants.
Article
Biotechnology & Applied Microbiology
Joao M. Alves, Nuria Estevez-Gomez, Monica Valecha, Sonia Prado-Lopez, Laura Tomas, Pilar Alvarino, Roberto Pineiro, Laura Muinelo-Romay, Patricia Mondelo-Macia, Mercedes Salgado, Agueda Iglesias-Gomez, Laura Codesido-Prada, Joaquin Cubiella, David Posada
Summary: The study compared the genomic profiles of CTC pools from mCRC patients using different enrichment strategies and found that Parsortix and some CellSearch CTC pools closely matched the genomic features of primary tumor samples, while FACS CTC pools contained more sequencing artifacts.
Article
Biochemistry & Molecular Biology
Roberto Del Amparo, Luis Daniel Gonzalez-Vazquez, Laura Rodriguez-Moure, Ugo Bastolla, Miguel Arenas
Summary: Genetic recombination is a common evolutionary mechanism that contributes to molecular diversity. However, its impact on protein folding stability has been less studied compared to point mutations. This study found that although recombination can affect multiple protein sites, it does not significantly increase the elimination of proteins due to insufficient stability compared to mutation events. Recombination disrupts epistatic interactions but does not reduce the overall stability of recombinant proteins. Instead, it amplifies the difference in stability between recombined proteins, leading to phenotypic diversity.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Filipa Moreira, Miguel Arenas, Arnaldo Videira, Filipe Pereira
Summary: Type IB topoisomerases are important targets for anticancer drugs as they relax the torsional stress associated with DNA metabolism. TOP1 and TOP1MT are two types of topoisomerases specific to the nucleus and mitochondria respectively, and their origin and evolution in chordates remain unknown.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Article
Marine & Freshwater Biology
Manuel Mendoza, Sara Rocha, Jesus Troncoso, David Posada, Carlos Canchaya
JOURNAL OF MOLLUSCAN STUDIES
(2023)
Review
Genetics & Heredity
Luis Daniel Gonzalez-Vazquez, Miguel Arenas
Summary: SARS-CoV-2 has produced various molecular variants during its expansion in humans, leading to different transmissibility, disease severity, and resistance to treatments. Recent studies have investigated the molecular evolution of the virus and found that it evolves at a moderate rate with fluctuations over time. Recombination events between related coronaviruses were infrequent, and molecular adaptation varied among SARS-CoV-2 genes. Monitoring the molecular evolution of the virus is crucial for predicting phenotypic consequences and designing effective treatments.
Article
Genetics & Heredity
Roberto Del Amparo, Miguel Arenas
Summary: Probabilistic phylogenetic tree reconstruction has traditionally been performed by selecting the best-fitting substitution model of molecular evolution. Recent studies have proposed that this step is unnecessary, leading to a debate in the field. However, in the case of protein sequences, the selection of a substitution model has a significant influence on phylogenetic tree reconstruction. Our analysis of real and simulated data shows that phylogenetic trees reconstructed using the best-fitting substitution model of protein evolution are the most accurate in terms of topology and branch lengths.
Article
Environmental Sciences
Noelia Trigo-Tasende, Juan A. Vallejo, Soraya Rumbo-Feal, Kelly Conde-Perez, Manuel Vaamonde, Angel Lopez-Oriona, Ines Barbeito, Mohammed Nasser-Ali, Ruben Reif, Bruno K. Rodino-Janeiro, Elisa Fernandez-Alvarez, Iago Iglesias-Corras, Borja Freire, Javier Tarrio-Saavedra, Laura Tomas, Pilar Gallego-Garcia, David Posada, German Bou, Ignacio Lopez-de-Ullibarri, Ricardo Cao, Susana Ladra, Margarita Poza
Summary: The wastewater-based epidemiology program COVIDBENS in A Coruna, Spain, monitored viral load and detected SARS-CoV-2 mutations in wastewater using RT-qPCR and Illumina sequencing. It successfully predicted community outbreaks and identified new variants, providing early warning to local authorities and health managers.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Correction
Biochemical Research Methods
Mohammadamin Edrisi, Monica V. Valecha, Sunkara B. Chowdary, Sergio Robledo, Huw A. Ogilvie, David Posada, Hamim Zafar, Luay Nakhleh
Article
Cell Biology
Nico Borgsmueller, Monica Valecha, Jack Kuipers, Niko Beerenwinkel, David Posada
Summary: This study developed a statistical test called the Poisson Tree test to detect varying evolutionary rates among cell lineages. The application of this test on healthy and cancer samples revealed that the evolutionary rates of cell lineages are not always constant, but can vary.
Article
Virology
David Ferreiro, Ruqaiya Khalil, Maria J. Gallego, Nuno S. Osorio, Miguel Arenas
Summary: This study investigates the stability evolution of the human immunodeficiency virus (HIV-1) protease (PR) and finds that the PR has a wide structural plasticity to accommodate mutations without affecting overall stability evolution.
Article
Biotechnology & Applied Microbiology
Senbai Kang, Nico Borgsmueller, Monica Valecha, Jack Kuipers, Joao M. Alves, Sonia Prado-Lopez, Debora Chantada, Niko Beerenwinkel, David Posada, Ewa Szczurek
Summary: This article presents a statistical method called SIEVE for the joint inference of somatic variants and cell phylogeny from single-cell DNA sequencing. The SIEVE method utilizes raw read counts for all nucleotides and corrects acquisition bias of branch lengths. It outperforms other methods in phylogenetic reconstruction and variant calling accuracy, especially for homozygous variants. When applied to three datasets, including triple-negative breast cancer and colorectal cancer samples, SIEVE finds that double mutant genotypes are rare in colorectal cancer but unexpectedly frequent in triple-negative breast cancer.
Article
Public, Environmental & Occupational Health
Paloma Noelia Trigo-Tasende, Manuel Vaamonde, Kelly Conde-Perez, Angel Lopez-Oriona, Elisa F. Alvarez, Borja Freire, Mohammed Nasser-Ali, Ines Barbeito, Soraya Rumbo-Feal, Ruben Reif, Bruno K. Rodinos, Jose Parama, Laura Tomas, Pili Gallego, German Bou, Javier Tarrio-Saavedra, Iago I. Corras, David Posada, Ignacio Lopez de Ulibarri, Juan A. Vallejo, Susana Ladra, Ricardo Cao, Margarita Poza
REVISTA DE SALUD AMBIENTAL
(2022)