Editorial Material
Cell Biology
Ina Kirmes, Steven Zuryn
Summary: The integrity of mitochondrial DNA is crucial for energy synthesis. A recent study reveals a vicious cycle of mtDNA replication within dysfunctional mitochondria that propagates genomes with deleterious mutations.
NATURE CELL BIOLOGY
(2022)
Article
Ecology
Thomas Lesaffre, Sylvain Billiard
Summary: This study investigates the higher levels of inbreeding depression in perennials compared to annuals in angiosperms. By combining a physiological growth model and multilocus population genetics approaches, the researchers explore the impact of mutations affecting growth or survival on inbreeding depression and mutation load. The study suggests that traits under strong selection, decreasing sharply with increasing life expectancy, may be responsible for generating high inbreeding depression in long-lived species.
AMERICAN NATURALIST
(2021)
Article
Multidisciplinary Sciences
Shinji Sasaki, Toshio Watanabe, Takayuki Ibi, Kiyotoshi Hasegawa, Yoichi Sakamoto, Shunsuke Moriwaki, Kazuhito Kurogi, Atsushi Ogino, Takanori Yasumori, Hiroyuki Wakaguri, Eiji Muraki, Youko Miki, Yuichi Yoshida, Yoshinobu Inoue, Ichiro Tabuchi, Ken Iwao, Taichi Arishima, Keisuke Kawashima, Manabu Watanabe, Sumio Sugano, Yoshikazu Sugimoto, Yutaka Suzuki
Summary: The intensive use of a few elite sires in cattle has led to an increased risk of deleterious recessive traits. By analyzing SNP array data and exome sequencing, researchers identified deleterious recessive haplotypes in Japanese Black cattle, some of which affect embryonic survival. The study found specific candidate mutations in genes like IARS, CDC45, and CLDN16 associated with these deleterious haplotypes.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Tong Li, Ruobing Guan, Yuqing Wu, Su Chen, Guohui Yuan, Xuexia Miao, Haichao Li
Summary: The study identified a novel virus, Agrotis ipsilon Nora virus (AINV), which can spread and infect different hosts, causing negative effects on Spodoptera frugiperda. Infection is mainly mediated by antiviral and amino acid metabolism pathways, resulting in prolonged larval period and reduced adult eclosion rate in the host species.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Peng Zuo, Chaoxin Zhang, Yupeng Gao, Lijunyi Zhao, Jiaxu Guo, Yonglin Yang, Qian Yu, Yunna Li, Zhipeng Wang, Hua Yang
Summary: Epistatic effects, an important part of the genetic effect in livestock, were studied in synthetic ewes from China. Genome-wide single nucleotide polymorphisms (SNPs) were used to identify SNP-SNP interactions associated with birth weight and weaning weight. Significant interactions were found for weaning weight, but not for one-yearling weight. The interactions of sheep body weight were dynamic and time-dependent. Transcription factors were found to play a role in explaining epistatic effects, and the target genes of transcription factors were also identified. The study provides insights into the genetic mechanism of weight development.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Biology
Piret Avila, Laurent Lehmann
Summary: This article explores the trade-off between germline maintenance and life history functions, and the impact of resource allocation on life history and deleterious mutation rate. The study shows that under higher exposure to environmental mutagens, selection favors allocating more resources to germline maintenance, even if it comes at the expense of life history functions, leading to a shift in allocation towards reproduction. Additionally, individuals with shorter lifespans and smaller body sizes at maturity are more common.
JOURNAL OF THEORETICAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Alexander Klug, Joachim Krug
Summary: Understanding the effects of recombination on populations evolving on neutral fitness landscapes with unfit genotypes is still an open problem. This study provides a comprehensive overview of the effects of recombination on evolvability and mutational robustness. The results show that some measures vary non-monotonically with the rates of mutation and recombination, and the presence of unfit genotypes alters the effects of recombination. A trade-off between evolvability and mutational robustness explains the conflicting trends induced by recombination.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
Changlong Chen, Shu Che, Zhou Dong, Jiayi Sui, Yu Tian, Yanyan Su, Meng Zhang, Wangwang Sun, Jiaqin Fan, Jianbo Xie, Hua Xie
Summary: Genome-wide association studies (GWAS) were conducted to identify the genetic basis of Pectobacterium spp. pathogenicity by analyzing genomic data and phenotypic measurements. The analysis revealed multiple loci associated with virulence and cellulase activity, as well as epistasis effects. This study provides valuable insights into the genetic mechanisms underlying Pectobacterium spp. pathogenicity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Changlong Chen, Shu Che, Zhou Dong, Jiayi Sui, Yu Tian, Yanyan Su, Meng Zhang, Wangwang Sun, Jiaqin Fan, Jianbo Xie, Hua Xie
Summary: This study used genome-wide association studies to identify genetic basis of pathogenicity in Pectobacterium spp. by integrating genomic data with virulence and cellulase activity phenotypes. The analysis discovered significant loci associated with Pectobacterium virulence and cellulase activity, as well as identified epistasis loci pairs. Furthermore, the study confirmed the epistasis effects of AraC transcriptional regulator and nutrient transport-related genes in contributing to the virulence phenotype.
MICROBIOLOGY SPECTRUM
(2023)
Article
Plant Sciences
Guogen Zhang, Zhiyuan Bi, Jing Jiang, Jingbing Lu, Keyang Li, Di Bai, Xinchen Wang, Xueyu Zhao, Min Li, Xiuqin Zhao, Wensheng Wang, Jianlong Xu, Zhikang Li, Fan Zhang, Yingyao Shi
Summary: By utilizing genome-wide association and epistasis analysis (GWAES), the genetic basis of rice saline-alkali tolerance was studied. A total of 165 main-effect quantitative trait nucleotides (QTNs) and 124 additional epistatic QTNs were identified, explaining a significant portion of the phenotypic variation of saline-alkali tolerance. Most of these QTNs were located in genomic regions associated with saline-alkali tolerance or known genes. The finding of candidate genes and favorable haplotypes provides valuable information for genetic improvement of rice saline-alkali tolerance.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Ecology
Brian MacPherson, Ryan Scott, Robin Gras
Summary: The prevalence of sexual reproduction in most animal species despite its considerable costs is still a puzzle in evolutionary theory. The hypothesis of purifying selection suggests that sexual reproduction helps eliminate deleterious alleles through selecting reduced function mutations. This hypothesis is tested in a computer simulation study using EcoSim program.
ECOLOGICAL COMPLEXITY
(2021)
Article
Biochemistry & Molecular Biology
Stefano Castellana, Tommaso Biagini, Francesco Petrizzelli, Luca Parca, Noemi Panzironi, Viviana Caputo, Angelo Luigi Vescovi, Massimo Carella, Tommaso Mazza
Summary: MitImpact's third major release expands its collection of genomic, clinical, and functional annotations of all non-synonymous substitutions of the human mitochondrial genome, providing new information on putative Compensated Pathogenic Deviations and co-varying amino acid sites of the Respiratory Chain subunits, as well as evidence of energetic and structural residue compensation through techniques of molecular dynamics simulation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Leo Speidel, Lara Cassidy, Robert W. Davies, Garrett Hellenthal, Pontus Skoglund, Simon R. Myers
Summary: The study introduces a fast and scalable approach, Colate, for inferring ancestral relationships between low-coverage genomes without requiring phasing or imputation. The method leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. By applying this approach to modern and ancient DNA samples, the research identifies dynamic population structure and gene flow between early farmers and European hunter-gatherer groups.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Public, Environmental & Occupational Health
Shiqi Lin, Xingjian Gao, Frauke Degenhardt, Yu Qian, Tianzi Liu, Xavier Farre Ramon, Syed Sibte Hadi, Manuel Romero-Gomez, Javier Fernandez, Agustin Albillos, Maria Buti Ferret, Luis Bujanda, Antonio Julia, Rafael de Cid, Rosanna Asselta, Andre Franke, Fan Liu
Summary: This study conducted a genome-wide epistasis study of COVID-19 severity and identified three significant interactions between different genes. The most significant interaction was found between rs9792388 upstream of PDGFRL and rs3025892 downstream of SNAP25, indicating a possible molecular mechanism by which SARS-CoV-2 affects the nervous system.
EUROPEAN JOURNAL OF EPIDEMIOLOGY
(2023)
Article
Cell Biology
Pramod Shinde, Harry J. Whitwell, Rahul Kumar Verma, Mikhail Ivanchenko, Alexey Zaikin, Sarika Jalan
Summary: Investigating human mitochondrial genome variations can provide insights into human history and natural selection. Analysis of 24,167 human mt-genome samples from five continents revealed different co-mutation patterns among populations, with a stronger COX gene co-mutation bias in Asian and American populations. The study also showed a hierarchical modularity in the co-mutation networks and mutations clustered preferentially in known mitochondrial haplogroups.
Article
Infectious Diseases
Sarah K. Buddenborg, Lijing Bu, Si-Ming Zhang, Faye D. Schilkey, Gerald M. Mkoji, Eric S. Loker
PLOS NEGLECTED TROPICAL DISEASES
(2017)
Article
Biochemistry & Molecular Biology
Jonathan H. Schultz, Lijing Bu, Coen M. Adema
MOLECULAR IMMUNOLOGY
(2018)
Article
Multidisciplinary Sciences
Si-Ming Zhang, Lijing Bu, Martina R. Laidemitt, Lijun Lu, Martin W. Mutuku, Gerald M. Mkoji, Eric S. Loker
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Melissa C. Sanchez, Pauline M. Cupit, Lijing Bu, Charles Cunningham
MOLECULAR AND BIOCHEMICAL PARASITOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Guohua Yin, Yuliang Zhang, Maojie Fu, Sui Sheng T. Hua, Qixing Huang, Kayla K. Pennerman, Guangxi Wu, Wayne M. Jurick, Samantha Lee, Lijing Bu, Hui Zhao, Joan W. Bennett
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2019)
Article
Infectious Diseases
Sarah K. Buddenborg, Bishoy Kamel, Ben Hanelt, Lijing Bu, Si-Ming Zhang, Gerald M. Mkoji, Eric S. Loker
PLOS NEGLECTED TROPICAL DISEASES
(2019)
Article
Biotechnology & Applied Microbiology
Lijun Lu, Eric S. Loker, Si-Ming Zhang, Sarah K. Buddenborg, Lijing Bu
Article
Infectious Diseases
Lijun Lu, Eric S. Loker, Coen M. Adema, Si-Ming Zhang, Lijing Bu
PLOS NEGLECTED TROPICAL DISEASES
(2020)
Article
Multidisciplinary Sciences
Kimberly A. Morrissey, Marcin Wegrecki, T. Praveena, Victoria L. Hansen, Lijing Bu, Komagal Kannan Sivaraman, Samuel Darko, Daniel C. Douek, Jamie Rossjohn, Robert D. Miller, Jerome Le Nours
Summary: The study describes a unique population of γμTCRs found exclusively in non-eutherian mammals, with restricted diversity in the Vγ and Vμj domains and highly diverse unpaired Vμ domain. Crystal structures of two distinct γμTCRs reveal the structural basis of the association and suggest a major antigen recognition determinant in the CDR3μ loop of the Vμ domain. This defines the molecular basis underlying the assembly of a third TCR lineage, the γμTCR.
Article
Microbiology
Guohua Yin, Hui Zhao, Kayla K. Pennerman, Wayne M. Jurick, Maojie Fu, Lijing Bu, Anping Guo, Joan W. Bennett
Summary: Blue mold of apple is caused by various Penicillium species, with P. expansum being the most aggressive while P. solitum is weak in infecting apple fruit. Genomic analyses of different Penicillium species showed differences in mycotoxin production and toxin emitting capabilities. The study provides insights into the genetic bases of mycotoxins and toxic volatile organic compounds in Penicillium spp.
Article
Microbiology
Erika T. Ebbs, Eric S. Loker, Lijing Bu, Sean A. Locke, Vasyl V. Tkach, Ramesh Devkota, Veronica R. Flores, Hudson A. Pinto, Sara Brant
Summary: This study utilized targeted sequence capture of ultra-conserved elements (UCEs) to generate a phylogenomic dataset for the estimation of schistosomatid interrelationships. The resulting family-level phylogeny provided resolution to several long-standing uncertainties within the Schistosomatidae, highlighting the role of host-switching in diversification.
Article
Biology
Lijing Bu, Daibin Zhong, Lijun Lu, Eric S. Loker, Guiyun Yan, Si-Ming Zhang
Summary: This study compares the genomes of two homozygous lines of the freshwater snail to identify genomic differences related to resistance and susceptibility to the parasite Schistosoma mansoni. By constructing a genetic map and identifying quantitative trait loci associated with snail resistance/susceptibility and body pigmentation, the study provides insights into the genetic mechanisms of compatibility between the snail and the parasite. It offers valuable genomic resources for understanding vector snail biology and developing innovative control strategies.
COMMUNICATIONS BIOLOGY
(2022)
Article
Infectious Diseases
Lijing Bu, Lijun Lu, Martina Laidemitt, Si-Ming Zhang, Martin Mutuku, Gerald Mkoji, Michelle Steinauer, Eric S. Loker
Summary: This study provides genomic resources for the African schistosome vector, Biomphalaria pfeifferi, including its genome size, comparison with other snail vectors, and expansion of gene families. These resources will contribute to a better understanding of the dependence of schistosomes on snails and offer potential targets for more specific snail control programs.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Microbiology
Guohua Yin, Yuliang Zhang, Sui Sheng T. Hua, Jiujiang Yu, Lijing Bu, Kayla K. Pennerman, Qixing Huang, Anping Guo, Joan W. Bennett
GENOME ANNOUNCEMENTS
(2017)
Article
Genetics & Heredity
Jonathan H. Schultz, Lauren M. Bansbach, Jarrett A. Bremmer, Kirsten E. Dimmler, Quinn A. Forde, Elisa M. Gagliano, Elizabeth M. Glenn, Chance M. Greengrass, Joe P. Hayes, Aurora L. Kraus, Lewis Larsen, Erin Lucero, Matthew T. McClendon, Heather L. Mercer, Karen C. Mims, Kajal N. Patel, Fotios Patsalis, Dianne E. Peterson, Jarrod M. Platero, Mohammed M. Rizvi, Kassandra Serna, Tyler E. Steele, Nicholas L. Turner, Lijing Bu, Lijun Lu, Coen M. Adema
MITOCHONDRIAL DNA PART B-RESOURCES
(2018)