Article
Biochemistry & Molecular Biology
Ryan C. Vignogna, Sean W. Buskirk, Gregory Lang
Summary: Experimental evolution is a powerful tool for identifying genetic interactions, especially those involving non-loss-of-function mutations or mutations in essential genes. Researchers identified a strong positive genetic interaction between specific mutations in KEL1 and HSL7 in an experimentally evolved Saccharomyces cerevisiae population. By replaying the evolution of the population and performing whole-genome sequencing, they identified additional mutations with positive genetic interactions and validated these interactions through reconstruction experiments. This study highlights the ability of experimental evolution to uncover positive, allele-specific genetic interactions that are not easily detected by other methods, providing insights into unexplored areas of the yeast genetic interaction network.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Jose Gabriel Nino Barreat, Aris Katzourakis
Summary: This study provides new evidence supporting the viral nature of Mavericks and the potential existence of virions by conducting a phylogenomic analysis of Mavericks in hundreds of vertebrate genomes. It was found that Mavericks likely form an ancient lineage of aquatic dsDNA viruses, infecting osteichthyans for approximately 419 million years and undergoing frequent cross-species transmissions in cyprinid fish. All core genes of Mavericks are subject to strong purifying selection, suggesting their functional importance in some vertebrate lineages.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Virology
Mark D. Lee, Jack W. Creagh, Lance R. Fredericks, Angela M. Crabtree, Jagdish Suresh Patel, Paul A. Rowley
Summary: This study reports the first isolation of a double-stranded RNA virus, named PmV-L-A, from Pichia membranifaciens, indicating a shared ancestry with totiviruses that infect Saccharomycotina yeasts. Structural predictions of PmV-L-A proteins show conservation with Saccharomyces cerevisiae virus L-A. Additionally, possible mechanisms for RNA replication are provided based on similarities with RNA-dependent RNA polymerases of mammalian dsRNA viruses. Understanding the structure, function, and evolution of yeast totiviruses is crucial for our knowledge of animal diseases.
Article
Biochemistry & Molecular Biology
Pawel Blazej, Konrad Pawlak, Dorota Mackiewicz, Pawel Mackiewicz
Summary: This study investigates the evolutionary mechanisms of codon block structure in the genetic code through computer simulations. The results demonstrate that the reading system similar to that present in the standard genetic code (SGC) quickly dominates during evolution and possesses similar characteristics to the SGC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Lufeng Dan, Yuze Li, Shuhua Chen, Jingbo Liu, Yu Wang, Fangting Li, Xiangwei He, Lucas B. Carey
Summary: Most genetic changes have low reversion rates, but a study identified a rapid and reversible genetic variation mechanism that benefits adaptation to environmental fluctuations and evolutionary divergence.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Virology
Angelica Bravo, Leandro Fernandez-Garcia, Rodrigo Ibarra-Karmy, Gonzalo A. Mardones, Luis Mercado, Fernando J. Bustos, Robert J. Gifford, Gloria Arriagada
Summary: Endogenous viral elements (EVEs) are genomic DNA sequences derived from viruses and some of them can express proteins with physiological roles in their host. In this study, we found that DeRep, a protein encoded in an endogenous parvoviral element (EPV), demonstrated antiviral activity against an exogenous parvovirus in degu cells. This is the first time an EPV has been shown to have such activity.
Article
Biology
Alex J. Veglia, Kalia S. I. Bistolas, Christian R. Voolstra, Benjamin C. C. Hume, Hans-Joachim Ruscheweyh, Serge Planes, Denis Allemand, Emilie Boissin, Patrick Wincker, Julie Poulain, Clementine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Michel Flores, Didier Forcioli, Paola Furla, Pierre E. Galand, Eric Gilson, Fabien Lombard, Stephane Pesant, Stephanie Reynaud, Shinichi Sunagawa, Olivier P. Thomas, Romain Trouble, Didier Zoccola, Adrienne M. S. Correa, Rebecca L. Vega L. Thurber
Summary: A study on newly sequenced and publicly available metagenomes and genomes revealed the presence of endogenous +ssRNA viral elements within coral symbionts. These findings provide insight into the evolutionary history and hosts of contemporary viruses. This study highlights the importance of +ssRNA viruses in nested symbioses and their implications for host evolution, exaptation, and immunity in the context of reef health and disease.
COMMUNICATIONS BIOLOGY
(2023)
Article
Virology
Juan F. Cornejo-Franco, Robert A. Alvarez-Quinto, Dimitre Mollov, Diego F. Quito-Avila
Summary: The complete genomic sequence of a previously uncharacterized virus named Bursera graveolens associated totivirus 1 (BgTV-1) was obtained from the palo santo tree in Ecuador. Phylogenetic analysis confirmed that BgTV-1 belongs to the genus Totivirus. Based on its distinct host and low sequence similarity with its closest relatives, this virus represents a new member of the genus.
ARCHIVES OF VIROLOGY
(2023)
Article
Biology
Erika Alden DeBenedictis, Dieter Soll, Kevin M. Esvelt
Summary: This study investigates the tolerance of the Escherichia coli genetic code to tRNA mutations and found that while most tRNAs can be converted to a quadruplet form, only nine aminoacyl tRNA synthetases can tolerate quadruplet anticodons. This limits the chemical alphabet available for an all-quadruplet code.
Article
Genetics & Heredity
Antoinette C. van der Kuyl
Summary: This study provides evidence for the adaptation of SERV retroviruses to germ line reproduction through sequence analysis of 81 SERV proviruses from Cercopithecinae Old World monkey genomes.
Review
Plant Sciences
Joris Macquet, Shantala Mounichetty, Sylvain Raffaele
Summary: Plants and pathogens engage in a coevolutionary arms race, leading to diversification and specialization of genes involved in resistance and virulence. Major innovations in plant-pathogen interactions have emerged through the expansion of gene function. Understanding these molecular mechanisms is crucial for the functional and predictive biology of plant-pathogen interactions.
TRENDS IN PLANT SCIENCE
(2022)
Article
Virology
Fatima Boulanouar, Stephane Ranque, Anthony Levasseur
Summary: This study conducted mycovirome studies on Malassezia and discovered three new mycoviruses, providing insights into their impact on clinical skin disorders.
Article
Multidisciplinary Sciences
Diogo M. Ribeiro, Simone Rubinacci, Anna Ramisch, Robin J. Hofmeister, Emmanouil T. Dermitzakis, Olivier Delaneau
Summary: The study reveals that local gene co-expression occurs in a significant percentage of genes across different human tissues. By integrating various molecular assays, the researchers estimate the mechanisms and identify expression quantitative trait loci associated with co-expressed gene pairs. These eQTLs are more likely to affect multiple human traits and provide insights into trait pleiotropy and functional interpretation of genetic findings.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Michael Yarus
Summary: The evolution of the Standard Genetic Code (SGC) is quantitatively modeled in multiple coding environments. The study reveals that unselective code division is more conducive to rapid evolution compared to selective code division. By combining different types of code division, fusion, independent environmental coding tables, and wobble coding, 32 possible pathways for SGC evolution are identified. Some pathways evolve quickly and achieve high code accuracy. The most likely routes to the SGC involve a combination of fusion and division, with the only difference being fusion with independent environmental codes. Code fusion can unite multiple codon assignment mechanisms. However, code division and fusion can lead to the emergence of an SGC from a single primary origin via familiar cellular events.
Review
Biochemistry & Molecular Biology
Marija Rosandic, Vladimir Paar
Summary: Through 10 years of investigation and research, we have discovered the Supersymmetry Genetic Code table which utilizes double mirror symmetry and Watson-Crick pairing. This table is built with 2 x 8 codon boxes, quadruplet DNA symmetries, and the classification of trinucleotides/codons. We also found that single-stranded RNA contains the complete code of life and instructions for DNA development through Watson-Crick pairing. The symmetries between the genetic code and DNA quadruplet are highly conserved throughout evolution even between distant organisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Evolutionary Biology
Matthew J. Ballinger, Ryan M. R. Gawryluk, Steve J. Perlman
GENOME BIOLOGY AND EVOLUTION
(2019)
Review
Biology
Matthew J. Ballinger, Steve J. Perlman
CURRENT OPINION IN INSECT SCIENCE
(2019)
Article
Multidisciplinary Sciences
Alexey A. Kotov, Derek J. Taylor
SCIENTIFIC REPORTS
(2019)
Article
Multidisciplinary Sciences
Elena I. Zuykova, Nickolai A. Bochkarev, Derek J. Taylor, Alexey A. Kotov
Article
Multidisciplinary Sciences
Derek J. Taylor, Sandra J. Connelly, Alexey A. Kotov
SCIENTIFIC REPORTS
(2020)
Article
Zoology
Alexey A. Kotov, Petr G. Garibian, Eugeniya Bekker, Derek J. Taylor, Dmitry P. Karabanov
Summary: This study investigated the phylogeography, rates of evolution, and taxonomic status of different clades within the Daphnia curvirostris complex, revealing an eastern Palaearctic clade with at least four species having diagnostic morphological characters. Convergent morphological characters were also detected within the complex, providing insights into species boundaries. Divergence time estimates suggested an ancient origin for the Daphnia korovchinskyi group, but were complicated by the limited number of calibration points.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Article
Multidisciplinary Sciences
Petr G. Garibian, Anna N. Neretina, Derek J. Taylor, Alexey A. Kotov
Article
Zoology
Jukka Salmela, Oskari Harma, Derek J. Taylor
Summary: Chaoborus flavicans is a complex of at least four species, with three named in the study. These species are found in lakes, ponds, and northern European regions. A synapomorphy of the Chaoborus flavicans species complex is the position of the larval subordinate mandibular tooth.
Article
Multidisciplinary Sciences
Petr G. Garibian, Dmitry P. Karabanov, Anna N. Neretina, Derek J. Taylor, Alexey A. Kotov
Summary: The study revealed that the species Bosminopsis deitersi actually includes a cryptic species widely distributed in the Old World called Bosminopsis zernowi, with significant genetic divergence between the two. Samples indicated low genetic differentiation in Bosminopsis zernowi, and molecular clock and biogeographic analysis suggested a Mesozoic origin for this species group. This evidence contradicts the single species hypothesis for Bosminopsis deitersi and supports the existence of an ancient species group with marked morphological conservation.
Article
Marine & Freshwater Biology
Keonho Kim, Derek J. Taylor
Summary: This study investigated the thermal plasticity of Daphnia galeata, a freshwater zooplankton, focusing on the rigid setae of its second limb. The results showed that temperature had a significant effect on the length ratios of the rigid setae, indicating thermal plasticity. Allometry, the relationship between body size and setae length, also differed significantly among different temperatures. The study concluded that rapid thermal plasticity in non-filtering limbs is more important than previously thought for Daphnia.
JOURNAL OF PLANKTON RESEARCH
(2022)
Article
Environmental Sciences
Dmitry P. Karabanov, Eugeniya I. Bekker, Petr G. Garibian, Russell J. Shiel, Tsuyoshi Kobayashi, Derek J. Taylor, Alexey A. Kotov
Summary: Biotic introductions continue to disrupt ecosystems, and this study assesses recent introductions of the Chydorus sphaericus group in Australia, suggesting that recent cross-hemisphere dispersal is more common than previously believed.
Article
Multidisciplinary Sciences
Alexey A. Kotov, Derek J. Taylor
Summary: The Daphnia longispina complex contains several key freshwater species, and this study identified a new species, Daphnia japonica sp. nov. Recognizing the local and subalpine diversity in this group is crucial due to ongoing anthropogenic disturbance and its potential impacts on introductions, local extirpations, and hybridization.
Article
Virology
Matthew J. Ballinger, Rebecca C. Christian, Logan D. Moore, Derek J. Taylor, Afsoon Sabet
Summary: This study investigates the diversity and persistence of inherited virome in an insect species using geographical isolation. They identify eight novel RNA viruses and find evidence of vertical transmission. The small interfering RNA pathway targets the inherited virome, but the Piwi-mediated RNA silencing pathway does not function as a general antiviral defense in this insect.
Article
Virology
Matthew J. Ballinger, Derek J. Taylor
Article
Biotechnology & Applied Microbiology
Matthew J. Ballinger, Logan D. Moore, Steve J. Perlman
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2018)