Article
Biology
Darren J. Walsh, David J. Bernard, Faith Pangilinan, Madison Esposito, Denise Harold, Anne Parle-McDermott, Lawrence C. Brody
Summary: The analysis of somatic variation in the mitochondrial genome requires deep sequencing of mitochondrial DNA. This study presents a PCR-free method for ultra-deep sequencing coverage of the mitochondrial genome, using isolated intact mitochondria and a sequence-independent approach. The method avoids false-heteroplasmy calls caused by long-range PCR amplification and enables researchers to identify low frequency heteroplasmy without introducing PCR biases or NUMT contamination.
COMMUNICATIONS BIOLOGY
(2022)
Article
Medicine, Research & Experimental
Jiayin Guo, Xiaoxu Chen, Zhiwei Liu, Haifeng Sun, Yu Zhou, Yichen Dai, Yu'e Ma, Lei He, Xuezhen Qian, Jianying Wang, Jie Zhang, Yichen Zhu, Jun Zhang, Bin Shen, Fei Zhou
Summary: The discovery of DddA-derived cytosine base editor (DdCBE) enables precise manipulation of mtDNA, holding potential for the treatment of mitochondrial disorders. In vivo testing using mouse cells and embryos demonstrated the effectiveness and accuracy of DdCBE in editing mtDNA.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Multidisciplinary Sciences
Yun Soo Hong, Stephanie L. Battle, Wen Shi, Daniela Puiu, Vamsee Pillalamarri, Jiaqi Xie, Nathan Pankratz, Nicole J. Lake, Monkol Lek, Jerome I. Rotter, Stephen S. Rich, Charles Kooperberg, Alex P. Reiner, Paul L. Auer, Nancy Heard-Costa, Chunyu Liu, Meng Lai, Joanne M. Murabito, Daniel Levy, Megan L. Grove, Alvaro Alonso, Richard Gibbs, Shannon Dugan-Perez, Lukasz P. Gondek, Eliseo Guallar, Dan E. Arking
Summary: Based on the study of participants in the UK Biobank, it was found that mitochondrial heteroplasmy is associated with increased risk of all-cause mortality and the prevalence and incidence of cancer, especially leukemia.
NATURE COMMUNICATIONS
(2023)
Article
Zoology
Guojun Zhang, Deqi Geng, Qiulin Guo, Wei Liu, Shufen Li, Wujun Gao, Yongfei Wang, Min Zhang, Yilin Wang, Yanzhen Bu, Hongxing Niu
Summary: The study systematically investigated and compared NUMTs in 23 bat genomes, revealing that NUMTs insertion in bat genomes is a common event with remarkable variations across species. NUMTs were mainly inserted into intergenic regions, but some were also found in functional genes, with evidence of coding function. Phylogenetic analysis highlighted clusters for Chiroptera, and polymorphic NUMTs showed distinct regional distribution patterns. The study provides novel insights into NUMT organization and features in bat genomes for further studying the evolution of bat species.
INTEGRATIVE ZOOLOGY
(2022)
Article
Surgery
Keshav K. Singh
Summary: The article discusses the genetic and environmental factors contributing to skin aging, highlighting the crucial role of mitochondria in this process. Research suggests that transplanting young mitochondria may potentially rejuvenate aging skin and hair.
PLASTIC AND RECONSTRUCTIVE SURGERY
(2021)
Article
Clinical Neurology
Ryan L. Davis, Kishore R. Kumar, Clare Puttick, Christina Liang, Kate E. Ahmad, Fabienne Edema-Hildebrand, Jin-Sung Park, Andre E. Minoche, Velimir Gayevskiy, Amali C. Mallawaarachchi, John Christodoulou, Deborah Schofield, Marcel E. Dinger, Mark J. Cowley, Carolyn M. Sue
Summary: Comprehensive bigenomic sequencing accurately detects causative genetic variants in affected mitochondrial disease patients, providing precise diagnosis, personalized treatment options, and information on genetic transmission risk.
Article
Multidisciplinary Sciences
James de Villiers, Rensu Theart
Summary: This paper presents a novel method using neural networks to predict the occurrence and locations of mitochondrial fission, fusion, and depolarisation events in 3D. The accuracy achieved by the neural networks in predicting these events is relatively low, but it indicates their potential usefulness in the absence of time-lapse sequences. The results of this paper can serve as a baseline for future research in this area.
Article
Biochemical Research Methods
Caleb A. Lareau, Vincent Liu, Christoph Muus, Samantha D. Praktiknjo, Lena Nitsch, Pauline Kautz, Katalin Sandor, Yajie Yin, Jacob C. Gutierrez, Karin Pelka, Ansuman T. Satpathy, Aviv Regev, Vijay G. Sankaran, Leif S. Ludwig
Summary: The study developed a single-cell multi-omic approach called 'mtscATAC-seq' that enables simultaneous genotyping of mitochondrial DNA and profiling of accessible chromatin. By leveraging somatic mtDNA mutations, this method allows inference of clonal relationships among ex vivo-derived human cells. This technique provides a broadly applicable platform to map clonal relationships between cells in human tissues and enable additional modes of multi-omic discovery.
Article
Biochemistry & Molecular Biology
Sung-Ik Cho, Seonghyun Lee, Young Geun Mok, Kayeong Lim, Jaesuk Lee, Ji Min Lee, Eugene Chung, Jin-Soo Kim
Summary: Mitochondrial DNA editing is crucial for modeling mitochondrial genetic disorders and potential future treatments. This study presents a new editing enzyme called TALEDs, which efficiently induce A-to-G editing in human mitochondria.
Article
Multidisciplinary Sciences
Ching-Ching Wee, Nor Azlan Nor Muhammad, Vijay Kumar Subbiah, Masanori Arita, Yasukazu Nakamura, Hoe-Han Goh
Summary: This study reports the complete mitogenome of the Mesta variety of Garcinia mangostana L., which has great pharmaceutical potential. The mitogenome contains a total of 371,235 bp, with 1.7% possibly originating from plastid. The analysis of the mitogenome revealed various characteristics and evolutionary information about the Mesta variety.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Rahul K. Verma, Alena Kalyakulina, Cristina Giuliani, Pramod Shinde, Ajay Deep Kachhvah, Mikhail Ivanchenko, Sarika Jalan
Summary: Analysis revealed distinct co-occurrence motifs between high and low altitude regions, with some high altitude markers only co-occurring at high altitudes, suggesting a separate colonization route at high altitudes may have taken place.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Marcello Bellusci, Abraham J. Paredes-Fuentes, Eduardo Ruiz-Pesini, Beatriz Gomez, Miguel A. Martin, Julio Montoya, Rafael Artuch, MITOSPAIN Working Grp
Summary: This study provides nationwide epidemiological data for mitochondrial diseases (MD) in Spain, highlighting the incidence rates and genetic information related to the disease. Among pediatric patients, mutations in nuclear DNA genes were more common than mitochondrial DNA genes.
Review
Biochemistry & Molecular Biology
Carlos Jhovani Perez-Amado, Amellalli Bazan-Cordoba, Alfredo Hidalgo-Miranda, Silvia Jimenez-Morales
Summary: Analysis of mitochondrial genome is important in studying human diseases, including cancer, as mutations and variants in tumors impact tumor growth and invasion. Heteroplasmy-shifting is suggested to play a role in tumor progression and treatment response, but further research is needed to fully understand its clinical implications in treating human cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Patrizia Bottoni, Giulia Gionta, Roberto Scatena
Summary: Mitochondrial myopathies are a heterogeneous group of diseases caused by genetic mutations in proteins involved in mitochondrial oxidative metabolism. These myopathies show significant differences in their evolution, but some physiological and pathophysiological aspects of mitochondria reveal other potential molecular mechanisms that may play a significant role in their clinical progression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Pathology
Alina Nicolae, Justine Bouilly, Diane Lara, Virginie Fataccioli, Francois Lemonnier, Fanny Drieux, Marie Parrens, Cyrielle Robe, Elsa Poullot, Bettina Bisig, Celine Bossard, Audrey Letourneau, Edoardo Missiaglia, Christophe Bonnet, Vanessa Szablewski, Alexandra Traverse-Glehen, Marie-Helene Delfau-Larue, Laurence de Leval, Philippe Gaulard
Summary: This study examined the clinicopathological and molecular characteristics of nodal peripheral T-cell lymphoma, not otherwise specified (PTCL, NOS) with cytotoxic phenotype in Western patients. The findings revealed that this rare disease in the Western population is associated with aggressive behavior and impaired immunity.
Article
Agriculture, Dairy & Animal Science
Alvaro Navarro-Castilla, Mario Garrido, Hadas Hawlena, Isabel Barja
Summary: The study validated an enzyme immunoassay for measuring fecal corticosterone metabolites in three wild gerbil species, showing its suitability as a reliable indicator of adrenocortical activity in these species and revealing different responses to stressors among closely related species and individuals within the same species.
Article
Microbiology
Ron Flatau, Michal Segoli, Hadas Hawlena
Summary: The study examined three common mechanisms for endosymbiont persistence in arthropod host populations and found that none of them fully support the continual presence of endosymbionts. Future research should focus on other directions to better understand the persistence of endosymbionts in fleas and other model systems with extreme sex differences.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Mario Garrido, Snir Halle, Ron Flatau, Carmit Cohen, Alvaro Navarro-Castilla, Isabel Barja, Hadas Hawlena
Summary: This study investigated the relationship between species diversity and disease risk using a model system of rodents and Mycoplasma pathogens. The results suggest that one host acts as a pathogen amplifier while the other two hosts serve as diluters, reducing the overall number of infected hosts by clearing the infection faster. This highlights the importance of experimental studies exploring different aspects of host-pathogen interactions in multiple hosts in diversity-disease research.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Ecology
Shimon Bershtein, Daniel Kleiner, Dan Mishmar
Summary: Recent advances in AI-based 3D protein structure prediction have the potential to address health-related questions and impact evolution. Integration of structural predictions with functional genomic studies is emphasized for a comprehensive understanding of protein properties and their effects on fitness.
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Ecology
Snir Halle, Mario Garrido, Klil Noy, Irit Messika, Hadar Kedem, Carmit Cohen, Koren Ytzhak, Zehava Siegal, Georgy Shenbrot, Zvika Abramsky, Yaron Ziv, Arnon Karnieli, Hadas Hawlena
Summary: The study found that spatial heterogeneity in sand biocrusts in the desert is closely related to differences in host community structure, and that the stabilization of sand can affect pathogen occurrence through changes in host community structure and vector burdens. Changes in the structure of the same host community can simultaneously amplify and dilute the effects of different pathogens.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2022)
Review
Ecology
Mario Garrido, Scott K. Hansen, Rami Yaari, Hadas Hawlena
Summary: The study recommends a formal model selection approach (MSA) using information criteria and compares it with two traditional methods using numerical simulations. MSA-SEM shows superior and unbiased results under suboptimal realistic conditions typical in ecological studies. A roadmap for MSA-SEM is provided along with a demonstration through a case study.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Hadar Medini, Amit Zirman, Dan Mishmar
Summary: Mitochondrial dysfunction has been found to play a central role in COVID-19, with significantly reduced mtDNA gene expression in patients observed, suggesting a potential link to the disease. Additionally, elevated expression of ROS-response genes and glycolysis enzymes in patients may indicate a shift towards glycolysis, creating conditions beneficial for SARS-CoV-2 replication.
Article
Biochemistry & Molecular Biology
Tal Cohen, Hadar Medini, Chen Mordechai, Alal Eran, Dan Mishmar
Summary: By analyzing a large number of RNA-seq samples, we found that modifications in mt-RNA are negatively correlated with mtDNA gene expression levels, and this correlation varies across different tissues. Additionally, we observed that environmental factors can affect the impact of these modifications on gene expression.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Keyla Carstens Marques de Sousa, Ricardo Gutierrez, Dayana Yahalomi, Tali Shalit, Barak Markus, Yaarit Nachum-Biala, Hadas Hawlena, Evgeniya Marcos-Hadad, Einat Hazkani-Covo, Haroldo Henrique de Rezende Neves, Shay Covo, Shimon Harrus
Summary: This study focused on the genetic diversity of a genetically diverse Bartonella species, Bartonella krasnovii, which circulates among gerbils and their associated fleas. The researchers found structural diversity in the genomes of this species, with a large proportion of the structural variations associated with prophages. Further analysis revealed that most of the structural variations and prophage insertions were found at the chromosome replication termination site, suggesting this site as a plastic zone of the B. krasnovii chromosome. These findings demonstrate the extensive genomic diversity harbored by wild B. krasnovii strains and suggest that its diversification is initially promoted by structural changes, probably driven by phages.
Review
Biochemistry & Molecular Biology
Ruth Rodriguez-Pastor, Yarden Shafran, Nadav Knossow, Ricardo Gutierrez, Shimon Harrus, Luis Zaman, Richard E. Lenski, Jeffrey E. Barrick, Hadas Hawlena
Summary: This article introduces laboratory experiments on the evolution of blood-borne parasitic microbes in animal hosts, offering guidelines for designing such experiments. The importance of selecting appropriate ancestral genotypes, treatments, replicates, controls, variables, covariates, and timing for checkpoints is emphasized, along with recommended preliminary experiments for quantification and transmission methods. Despite their technical nature, these methodological considerations also have conceptual implications.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Idit Gunther, Hadas Hawlena, Lior Azriel, Dan Gibor, Olaf Berke, Eyal Klement
Summary: This article examines the effectiveness of trap-neuter-return/release (TNR) in controlling the population of domestic cats and suggests a management approach that emphasizes high intensity, continuity, and geographic contiguity. The study finds that TNR has some effectiveness in reducing the cat population, but the rebound increase in reproduction and longevity of cats limits the population reduction. To enhance management effectiveness and mitigate compensatory effects, the article recommends integrating TNR with complementary methods.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Ecology
Hadas Hawlena
Summary: Coexistence theories have advanced rapidly in the field of ecology, surpassing their experimental testing. This article discusses the reasons for this gap, calls for interdisciplinary researchers to construct a roadmap for coexistence research, and recommends actions to be implemented.
ECOLOGY AND EVOLUTION
(2022)
Review
Ecology
Hadas Hawlena, Mario Garrido, Carmit Cohen, Snir Halle, Shahar Cohen
Summary: Coexistence theories have rapidly developed in the field of ecology, but they suffer from interdisciplinary gaps and a lack of universality. The modern coexistence theory (MCT) aims to address these deficiencies by formulating universal conditions for coexistence. However, despite its mechanistic foundation, it has been rarely used to determine the exact mechanisms that govern competitive outcomes. Recent theoretical developments have made MCT more accessible to experimentalists, but practical challenges remain. This study proposes that a comprehensive understanding of species co-occurrence patterns in nature can be achieved by combining the phenomenological approach with the mechanistic view of MCT and coexistence experiments focusing on specific mechanisms.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biology
Noam Shtolz, Dan Mishmar
Summary: By analyzing mtDNAs from about 8000 metazoans, it was found that most metazoans have highly conserved gene content and codon preferences in their mtDNA. However, gene order (MGO) is selectively constrained within but not between phyla, and certain gene stretches are highly conserved across metazoans. The analysis of RNA-seq data from 53 metazoans suggests that mtDNA rearrangements impact mtDNA regulation.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biology
Adam Z. Hasik, Kayla C. King, Hadas Hawlena
Summary: We examine the potential influence of interspecific host competition on the evolution of virulence. Host natural mortality, body mass changes, population density, and community diversity are identified as factors affecting virulence evolution. A conceptual framework is proposed to explain how these factors, which change during host competition, can drive the evolution of virulence through impacts on life-history trade-offs. The complexity of interspecific host competition and virulence evolution requires further investigation to understand contrasting mechanisms. Additionally, different transmission strategies of parasites should be taken into account. A comprehensive approach focusing on interspecific host competition is crucial for understanding the evolution of virulence.