Review
Virology
Xuan Xu, Qing-Ye Zhang, Xin-Yi Chu, Yuan Quan, Bo-Min Lv, Hong-Yu Zhang
Summary: The article summarizes the genetic, subcellular location, and evolutionary features of human genes that have been successfully used as antiviral targets. These features are then used to screen novel druggable antiviral targets and find potential antiviral drugs, aiming to promote the discovery of new antiviral drugs.
Article
Biochemistry & Molecular Biology
Isaac Overcast, Victor Noguerales, Emmanouil Meramveliotakis, Carmelo Andujar, Paula Arribas, Thomas J. Creedy, Brent C. Emerson, Alfried P. Vogler, Anna Papadopoulou, Helene Morlon
Summary: Understanding the contributions of ecological and evolutionary processes to ecological communities is important for predicting their responses to future changes. Metabarcoding methods provide data on genetic variation and community dynamics. A new simulation model is presented that predicts species abundance, genetic variation, and phylogenetic relationships under different parameter settings. The model is applied to soil microarthropod metabarcoding data to reveal the effects of neutral and non-neutral processes on community structure.
Article
Genetics & Heredity
Renjuan Qian, Youju Ye, Qingdi Hu, Xiaohua Ma, Jian Zheng
Summary: Gladiolus gandavensis, an important ornamental plant, has only been found in Cangnan County, Zhejiang Province, China. The chloroplast genome sequencing revealed its structural characteristics and high homology with Crocus cartwrightianus and Crocus sativus. These findings suggest that G. gandavensis may have originated from South Africa.
Article
Evolutionary Biology
Hannes Svardal, Walter Salzburger, Milan Malinsky
Summary: Evolutionary radiations have contributed significantly to the variation in biodiversity in Cichlid fishes, with low nucleotide diversity within species and a large proportion of shared variation among species. Population genetics provides a suitable conceptual framework for evolutionary genomic studies of Cichlid radiations. Hybridization plays an important role in shaping patterns of genetic variation and promoting species diversification in Cichlids.
ANNUAL REVIEW OF ANIMAL BIOSCIENCES, VOL 9, 2021
(2021)
Editorial Material
Biochemistry & Molecular Biology
Lars Opgenoorth, Christian Rellstab
Summary: The study of drought resistance in white spruce utilized multiple data sources and analytical approaches to identify candidate genes involved in growth and resistance to extreme drought events, showcasing how diverse datasets can provide complementary evidence to overcome challenges in the research field.
Article
Biochemistry & Molecular Biology
Ryan A. York, Luke E. Brezovec, Jenn Coughlan, Steven Herbst, Avery Krieger, Su-Yee Lee, Brandon Pratt, Ashley D. Smart, Eugene Song, Anton Suvorov, Daniel R. Matute, John C. Tuthill, Thomas R. Clandinin
Summary: This study investigates the evolution of walking behavior in fruit flies. Through capturing the movement of multiple species and strains, the researchers find that walking can be represented in a universal behavior space with evolutionarily conserved structure. However, specific movements and transitions have evolved rapidly, leading to convergent evolution in the temporal structure of locomotion.
Article
Microbiology
Yunha Hwang, Peter R. Girguis
Summary: This study investigated the population-level genetic diversity of marine microbes and found differences in genetic diversification between different ocean basins, potentially due to variations in nutrient availability and environmental fluctuations.
News Item
Multidisciplinary Sciences
Diana Kwon
Summary: Drugs that silence faulty genes could potentially treat brain diseases, but a halted clinical trial has posed a setback in this field.
Editorial Material
Multidisciplinary Sciences
Conrad O. Iyegbe, Paul F. O'Reilly
Summary: Rare and common genetic variants associated with schizophrenia provide convergent clues about the underlying biology of this complex disorder.
Review
Genetics & Heredity
Jianzhi Zhang
Summary: Genomics, a interdisciplinary field of biology, has revolutionized various subdisciplines of life sciences by providing large amount of data, introducing high-throughput technologies, and offering new approaches to biology. In this review, the author describes what they have learned from genomics, mainly focusing on variation, interaction, and selection, which are central topics in evolutionary biology. The author expects that the most important contributions of genomics to evolutionary biology in the future will include providing genome sequences of almost all known species on Earth, facilitating high-throughput phenotyping of natural variants and mutants, and assisting in the determination of causality in evolutionary processes using experimental evolution.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Pierre Baduel, Basile Leduque, Amandine Ignace, Isabelle Gy, Jose Gil, Olivier Loudet, Vincent Colot, Leandro Quadrana
Summary: This study reveals that transposable element (TE) mobilization is a major driver of genetic variation in A. thaliana, regulated by genetic and environmental factors. TE insertions occur at a similar rate to base substitutions, with individual TE families showing varying mobilization activities. High rates of transposition seem to be positively selected at the edge of the species' ecological niche.
Article
Biochemistry & Molecular Biology
J. Andrew DeWoody, Avril M. Harder, Samarth Mathur, Janna R. Willoughby
Summary: The importance of genetic diversity in conservation biology cannot be overstated, as it is closely tied to evolutionary fitness and crucial for conservation efforts. In the Anthropocene, responsible management should prioritize the conservation of ecosystems, communities, populations, individuals, and their underlying genetic diversity.
Article
Multidisciplinary Sciences
Daniel L. Barabasi, Daniel Czegel
Summary: This passage discusses a method of network connection based on identity-dependent compatibility rules, deriving from genetic principles to generate specific topologies and various network structures. It also explores the characteristics of Random Genetic networks and their behavior under targeted attacks, serving as a relevant null-model for social and biological systems.
SCIENTIFIC REPORTS
(2021)
Editorial Material
Multidisciplinary Sciences
Samira Asgari, Lionel A. Pousaz
Summary: An individual's genetics play a role in their susceptibility to infectious diseases and the severity of symptoms. A recent international study has identified specific regions of the human genome that can impact the risk of severe COVID-19.
Editorial Material
Biology
Suzanne E. McGaugh, Aaron J. Lorenz, Lex E. Flagel
Summary: Genomic prediction methods, based on contributions from many loci of small effect, have been used in plant and animal breeding for almost two decades to predict breeding value for an individual. However, the application of these techniques in evolutionary genomics studies has been slow, with challenges still remaining to be overcome.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Sarah M. Huecker, Zachary Ardern, Tatyana Goldberg, Andrea Schafferhans, Michael Bernhofer, Gisle Vestergaard, Chase W. Nelson, Michael Schloter, Burkhard Rost, Siegfried Scherer, Klaus Neuhaus
Article
Multidisciplinary Sciences
Sonja Vanderhaeghen, Barbara Zehentner, Siegfried Scherer, Klaus Neuhaus, Zachary Ardern
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Alina Glaub, Christopher Huptas, Klaus Neuhaus, Zachary Ardern
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Chase W. Nelson, Zachary Ardern, Xinzhu Wei
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Microbiology
Barbara Zehentner, Zachary Ardern, Michaela Kreitmeier, Siegfried Scherer, Klaus Neuhaus
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Zachary Ardern, Klaus Neuhaus, Siegfried Scherer
FRONTIERS IN MOLECULAR BIOSCIENCES
(2020)
Article
Biology
Chase W. Nelson, Zachary Ardern, Tony L. Goldberg, Chen Meng, Chen-Hao Kuo, Christina Ludwig, Sergios-Orestis Kolokotronis, Xinzhu Wei
Article
Virology
Irwin Jungreis, Chase W. Nelson, Zachary Ardern, Yaara Finkel, Nevan J. Krogan, Kei Sato, John Ziebuhr, Noam Stern-Ginossar, Angelo Pavesi, Andrew E. Firth, Alexander E. Gorbalenya, Manolis Kellis
Summary: A proposal for standardized naming of at least six small ORFs overlapping well-characterized SARS-CoV-2 genes, emphasizing the importance of avoiding confusion caused by different names. Additionally, authors are recommended to provide lengths and coordinates when referring to these ORFs to reduce ambiguity.
Article
Biotechnology & Applied Microbiology
Stefan Wichmann, Siegfried Scherer, Zachary Ardern
Summary: The construction of overlapping genes is found to be less constrained than expected, with many constructed sequences indistinguishable from typical sequences in their protein family. Virus domains are actually less suitable for designing overlapping genes compared to bacterial or eukaryotic domains, contrary to previous beliefs. This study sheds light on the creation of overlapping genes and highlights the potential for synthetic biology in understanding genetic elements across different life forms.
News Item
Microbiology
Zachary Ardern
Summary: This article discusses how technological advancements have allowed for the identification of short protein-coding open reading frames, leading to the discovery of previously hidden small proteins.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Michaela Kreitmeier, Zachary Ardern, Miriam Abele, Christina Ludwig, Siegfried Scherer, Klaus Neuhaus
Summary: The discovery of overlapping genes with significant coding overlaps has revolutionized our understanding of genomic complexity. In this study, two unusually long antisense open reading frames were found in a pathogenic bacterium, and their transcription and translation were confirmed. Proteomics analysis revealed regulation of protein abundances, suggesting biological functionality. These findings highlight a potentially unexplored dimension of prokaryotic genomes.
Review
Microbiology
Zachary Ardern, Sagarika Chakraborty, Florian Lenk, Anne-Kristin Kaster
Summary: Annotating protein sequences is crucial for understanding microbial diversity and potential applications, but traditional methods are limited by the vast amount of 'omics' data. Hypothetical proteins (HPs) are a knowledge gap with hidden potential. Artificial intelligence (AI) and machine learning algorithms offer opportunities to leverage 'Big Data' for comprehensive genome annotations. This review explores the aims, methods, and recent research examples of protein annotation, with a focus on machine and deep learning algorithms.
FEMS MICROBIOLOGY REVIEWS
(2023)
Review
Biochemistry & Molecular Biology
Zachary Ardern
Summary: Protein-coding DNA sequences can produce different amino acid sequences by shifting nucleotide triplets or translating codons from the opposite strand. These alternative reading frames contribute to the evolution of novel proteins. Recent studies have demonstrated this phenomenon in various organisms. These sequences provide more opportunities for the creation of new genes and have unique properties that may facilitate gene origin. The implications of these findings are significant in molecular biology, including genome annotation, structural biology, and evolutionary genomics.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Editorial Material
Biochemistry & Molecular Biology
Zachary Ardern, Md Hassan uz-Zaman
Summary: A recent study in Cell Systems uncovers a substantial translatome that lacks significant evolutionary constraint but plays an active role in various cellular systems.
Article
Biology
Theodoros Kyriazos, Mary Poga
Summary: This paper explores the innovative intersection of quantum mechanics and psychology, examining the potential impact of quantum principles on human emotions, cognition, and consciousness. By drawing parallels between quantum phenomena and psychological counterparts, a quantum-psychological model is proposed, reimagining the characteristics of emotional states, cognitive breakthroughs, interpersonal relationships, and the nature of consciousness. Computational models and simulations are used to explore the implications and applications of this interdisciplinary fusion, highlighting its potential benefits and inherent challenges. Approaching this emerging framework with both enthusiasm and skepticism is crucial, and rigorous empirical validation is necessary to fully realize its potential in research and therapeutic contexts.
Article
Biology
Abir U. Igamberdiev
Summary: Biological systems strive to maximize self-maintenance and adaptability by establishing stable non-equilibrium states that organize the fluxes of matter and energy and control metabolic processes. These states are realized in autopoietic structures that operate based on biological codes. The principle of thermodynamic buffering optimizes metabolic fluxes, and in developing systems, the principle transforms into increasing external work. Bauer's concept of the stable non-equilibrium state places thermodynamics within the framework of internal biological causality, providing a relational theory of biological thermodynamics.
Article
Biology
Oleg Gaidai, Vladimir Yakimov, Yuhao Niu, Zirui Liu
Summary: This study presents a new methodology for assessing pandemic risks in a national health system. The suggested approach addresses the highdimensionality and complex cross-correlations between regional observations, enabling accurate epidemiological risk forecasts for multi-regional biological and health systems.
Article
Biology
Amirreza Khalili Golmankhaneh, Suemeyye Tunc, Agnieszka Matylda Schlichtinger, Dachel Martinez Asanza, Alireza Khalili Golmankhaneh
Summary: This article introduces important concepts such as fractal calculus and fractal analysis, the calculation of squared residuals, and the determination of Aikaike's information criterion for fitting cancer-related data. The study also investigates the double-size cancer in the fractal temporal dimension with respect to various mathematical models.