Article
Immunology
Alex Olvera, Samandhy Cedeno, Anuska Llano, Beatriz Mothe, Jorge Sanchez, Gemma Arsequell, Christian Brander
Summary: Post-translational protein modifications, particularly glycosylation, may impact T cell epitope recognition presented by HLA molecules, but this aspect has been overlooked in HIV research. Studies demonstrated that glycosylation can affect T cell recognition of viral peptides in individuals with chronic HIV infection, indicating the potential importance of glyco-epitope specific T cell immunity in understanding host immune responses against viral infections. New methodologies are needed to accurately assess the role of glycosylation in altering T cell immunity to viral infections.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Medicine, General & Internal
Shishir K. Gupta, Oezge Osmanoglu, Rashmi Minocha, Sourish Reddy Bandi, Elena Bencurova, Mugdha Srivastava, Thomas Dandekar
Summary: This study successfully identified novel epitopes for vaccine design against C. auris using evolutionary information and reverse vaccinology approach. Two effective T-cell epitopes were found to have potential for the treatment of C. auris infection. In vivo experiments are needed to further test the efficacy of the designed vaccine.
FRONTIERS IN MEDICINE
(2022)
Article
Cell Biology
Parvin A. Barbhuiya, Arif Uddin, Supriyo Chakraborty
Summary: The study analyzed the codon usage patterns of mitochondrial ND genes in three amphibian groups, revealing differences in codon usage and significant variations in GC content among different groups. The results suggest that natural selection plays a predominant role in shaping codon usage bias of ND genes across orders.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Myeongji Cho, Xianglan Min, Hyeon S. Son
Summary: This study analyzed the gene sequences of HIV1, HIV2, and SIV to determine their codon usage patterns and explore their evolutionary and genetic characteristics. The results showed a bias towards "A" in the structural genes and a significant influence of selection pressure.
Review
Immunology
Arnaud John Kombe Kombe, Fleury Augustin Nsole Biteghe, Zelia Nelly Ndoutoume, Tengchuan Jin
Summary: Despite the effectiveness of antiviral drug repositioning, convalescent plasma, and current vaccines against SARS-CoV-2, the ongoing emergence of new variants of concern (VOCs) poses challenges in the global COVID-19 pandemic. These VOCs are characterized by mutations that enhance infectivity, evade immune responses, and have significant fatality rates.
FRONTIERS IN IMMUNOLOGY
(2022)
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
Virology
Dev Kumar Verma, Neeraj Sood, Anutosh Paria, T. R. Swaminathan, C. V. Mohan, K. V. Rajendran, P. K. Pradhan
Summary: The tilapia lake virus (TiLV), a highly infectious viral pathogen, poses a major threat to the global tilapia industry. This study investigated the genomic evolution of TiLV and found that reassortment, selection, and mutation play important roles in its evolution. The results highlight the dominant force of reassortment in the emergence of this highly infectious segmented RNA virus.
Article
Multidisciplinary Sciences
Alex McAvoy, John Wakeley
Summary: This study presents a method for studying evolutionary dynamics in populations with complex and heterogeneous structures. By using easily interpretable demographic measures, the long-term outcomes of evolution can be analyzed. The method can be applied to various evolutionary update mechanisms and extends the structure-coefficient theorem to better understand the mutation-selection balance under different conditions. The study applies this method to examine the production and distribution of social goods in spatially heterogeneous populations, revealing that the outcome of selection depends on the nature of the social good, spatial topology, and mutation frequency.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Biochemistry & Molecular Biology
Filip Ruzicka, Max Reuter
Summary: A new study in Drosophila serrata reveals the association between sexually antagonistic selection on cuticular hydrocarbons and a major-effect gene.
Article
Microbiology
Gregory A. Sowd, Christopher Aiken
Summary: Our study demonstrates that inositol phosphates, IP5 and IP6, play crucial roles in HIV-1 assembly and maturation. Depletion of IP5 and IP6 in T cells resulted in impaired viral particle assembly and reduced infectivity of produced virions. These findings suggest that targeting HIV-1 inositol phosphate binding pockets may inhibit distinct aspects of HIV-1 replication.
Article
Chemistry, Multidisciplinary
Natchaya Rasri, Lueacha Tabtimmai, Charoenkwan Kraiya, Montarop Yamabhai, Chomdao Sinthuvanich, Jatuporn Rattanasrisomporn, Kiattawee Choowongkomon
Summary: A feline IgG-bound scFv was selected and a scFv-AP platform was developed for feline infectious disease detection.
Article
Multidisciplinary Sciences
Lauren A. Choate, Gilad Barshad, Pierce W. McMahon, Iskander Said, Edward J. Rice, Paul R. Munn, James J. Lewis, Charles G. Danko
Summary: The study reveals potential human genome adaptation to anthrax disease and genetic signatures indicating recent positive selection on European-specific decrease in ANTXR2 expression. This suggests that humans adapted to anthrax disease due to early ecological changes associated with hunting and scavenging, and a second period of adaptation after the rise of modern agriculture.
NATURE COMMUNICATIONS
(2021)
Article
Immunology
E. Jane Homan, Robert D. Bremel
Summary: Most neoepitopes detected in tumor biopsies are not immunogenic due to the lack of T cells with neoepitope-cognate receptors. Mutations detected in tumors result in rare amino acid combinations that are less common in the human proteome and gastrointestinal microorganisms. Mutant amino acids in T cell exposed positions consistently generate less common amino acid motifs, and approximately 10% of the mutant amino acid motifs are absent from the human proteome. Cross-presentation of mutant exposed neoepitopes by MHC I and MHC II is particularly uncommon, and immunogenic epitopes have mutant amino acids exposed to the T cell receptor and present in the human and microbiome reference databases.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Cell Biology
Matthew A. Lawlor, Christopher E. Ellison
Summary: Transposable elements (TEs) are extremely common in eukaryotic species, and their persistence is attributed to their interactions with host genomes, including tolerance, evasion/antagonism, and cooperation. This review focuses on metazoan species and summarizes recent advances in understanding the harmful effects of TE insertions, such as epigenetic effects and TE-derived RNAs damaging host cells. It also explores new findings on the host pathways that silence TEs, including the piRNA pathway and the APOBEC3 and Kruppel-associated box zinc finger gene families. Additionally, it discusses novel strategies used by TEs to evade host silencing, such as utilizing the Y chromosome as a permissive niche for TE mobilization and employing counterdefense strategies against host silencing factors.
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2023)
Article
Microbiology
Jianglin Zhou, Yaling Xing, Zhe Zhou, Shengqi Wang
Summary: This study investigated the evolution and codon usage patterns of the Usutu virus (USUV). They found that USUV is influenced by various factors in its codon usage, including natural selection, mutation pressure, and dinucleotide abundance. The study also observed a complex interaction of codon usage between USUV and its host, suggesting a potential risk of cross-species transmission and subsequent outbreaks. Therefore, further epidemiologic surveys, diversity monitoring, and pathogenetic research are warranted.
FRONTIERS IN MICROBIOLOGY
(2023)
