Review
Plant Sciences
Jason Sims, Fernando A. Rabanal, Christiane Elgert, Arndt Von Haeseler, Peter Schloegelhofer
Summary: Ribosomal RNA genes are organized in large domains of hundreds of rDNA units, with stable inheritance crucial for survival. During meiosis, rDNA loci are embedded within the nucleolus favoring non-homologous end joining as a repair mechanism, while rare homologous recombination events dynamically change rDNA unit numbers. The sequence heterogeneity and size stability of rDNA clusters in Arabidopsis thaliana show potential functional implications and drive further research into the mechanisms maintaining their metastable state.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Microbiology
Yang-Yang Fan, Qiang Tang, Yang Li, Feng-He Li, Jing-Hang Wu, Wen-Wei Li, Han-Qing Yu
Summary: The study introduces a novel genetic device iEditing for rapid and efficient genome editing in Shewanella oneidensis MR-1, with the combination of Red or RecET recombination system achieving an editing efficiency of up to 100%. The iEditing device is eliminated simultaneously during genome editing, eliminating the need for follow-up removal of the encoding system.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Usman N. Ikumapayi, Golam Sarwar, Catherine Okoi, Peggy-Estelle Maguiagueu Tientcheu, Marianne Defernez, Justin O'Grady, Martin Antonio, Mark J. Pallen
Summary: The study reveals the genomic diversity of Escherichia coli in asymptomatic children from rural Gambia, with 56 genotypes identified and an average of 2.7 genotypes per host. Most diversity is attributed to immigration events, while a minority arises from within-host evolution. Many isolates carry virulence factors and resistance genes, indicating a potential reservoir for these genes. The study also highlights the importance of immigration and strain establishment in generating diversity, with only a minor role played by within-host evolution.
Article
Biochemical Research Methods
Ruiyan Guo, Weiyu Zhao, Linhua Wei, Shoutao Zhang, Lijie Feng, Yanan Guo
Summary: The SLiCE cloning method, which utilizes cell lysates from Escherichia coli, enables seamless DNA cloning and is more cost-effective than commercial kits. The study found that SLiCE extracts could easily be prepared using various simple and low-cost methods without affecting DNA cloning efficiency. This highlights the efficiency of the SLiCE cloning method for seamless DNA cloning in vitro.
JOURNAL OF MICROBIOLOGICAL METHODS
(2022)
Article
Microbiology
Qiu-Yun Zhao, Jia-Hang Zhu, Run-Mao Cai, Xing-Run Zheng, Li-Juan Zhang, Man-Xia Chang, Yue-Wei Lu, Liang-Xing Fang, Jian Sun, Hong-Xia Jiang
Summary: Carbapenem resistance in Enterobacteriaceae is a major challenge in treating nosocomial infections. The bla(NDM) carbapenemase genes, expressed by NDM-producing Escherichia coli, have been found in various sources worldwide, including farm animals. This study investigates the dynamic evolution of blaNDM genetic contexts and bla(NDM)-harboring plasmids, with a focus on the role of IS26 elements in multi drug-resistant regions (MRRs) formation and the dissemination of blaNDM. The findings emphasize the importance of monitoring and limiting the transmission of NDM-producing isolates from food animals to humans.
Article
Biochemistry & Molecular Biology
Katrin Bartke, Linnea Garoff, Douglas L. Huseby, Gerrit Brandis, Diarmaid Hughes
Summary: Integrating E. coli DNA into the Salmonella chromosome through conjugation resulted in hybrids with reduced growth rate, but some hybrids showed no significant decrease in growth fitness. This suggests that barriers to creating high-fitness interspecies hybrids may be lower than previously thought.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Yu Kang, Lina Yuan, Xing Shi, Yanan Chu, Zilong He, Xinmiao Jia, Qiang Lin, Qin Ma, Jian Wang, Jingfa Xiao, Songnian Hu, Zhancheng Gao, Fei Chen, Jun Yu
Summary: This study investigates genome-wide recombination within a species using a dataset of Escherichia coli genomes. The research highlights extensive within-clade recombination and a sharp decline in between-clade recombination, establishing a genetic barrier between clades as phylogenetic distance increases. Recombination plays a critical role in early speciation by optimizing genes and alleles for physiological activities and shaping genetic diversity within populations.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Oncology
Simone N. Koole, Philip C. Schouten, Jan Hauke, Roel J. C. Kluin, Petra Nederlof, Lisa K. Richters, Gabriele Krebsbach, Karolina Sikorska, Maartje Alkemade, Mark Opdam, Jules H. Schagen van Leeuwen, Henk W. R. Schreuder, Ralph H. M. Hermans, Ignace H. J. T. de Hingh, Constantijne H. Mom, Henriette J. G. Arts, Maaike van Ham, Peter van Dam, Peter Vuylsteke, Joyce Sanders, Hugo M. Horlings, Koen K. van de Vijver, Eric Hahnen, Willemien J. van Driel, Rita Schmutzler, Gabe S. Sonke, Sabine C. Linn
Summary: The addition of hyperthermic intraperitoneal chemotherapy (HIPEC) with cisplatin to interval cytoreductive surgery improves recurrence-free and overall survival in patients with stage III ovarian cancer. HRD ovarian tumors, especially HRD/BRCAwt and non-HRD/BRCAwt tumors, respond best to treatment with HIPEC.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Virology
Alvin Crespo-Bellido, J. Steen Hoyer, Divya Dubey, Ronica B. Jeannot, Siobain Duffy
Summary: Begomoviruses significantly impact crop production and food security worldwide by emerging new genotypes through high mutation frequencies and recombination. Recombination has driven speciation in the cassava mosaic begomovirus species complex, significantly impacting genetic diversity. CMD caused by these viruses poses a significant threat to cassava production in Africa and Asia.
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Cristina Ramos, Rogelio Hernandez-Tamayo, Maria Lopez-Sanz, Begona Carrasco, Ester Serrano, Juan C. Alonso, Peter L. Graumann, Silvia Ayora
Summary: This study explores the role of RecD2 in DNA replication and its interaction with RecA. The results demonstrate that RecD2 counteracts the inhibition of leading and lagging strand synthesis by physically interacting with RecA. Additionally, RecD2 overcomes replicative stress by modulating RecA-mediated DNA strand exchange and branch migration.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Obstetrics & Gynecology
Wuzhou Yuan, Jing Ni, Hao Wen, Weijie Shi, Xuejun Chen, Hongwei Huang, Xiaotian Zhang, Xuan Lu, Changbin Zhu, Hua Dong, Shuang Yang, Xiaohua Wu, Xiaoxiang Chen
Summary: This study developed a novel machine learning-based algorithm called the Genomic Scar Score (GSS) for predicting homologous recombination deficiency (HRD) events. The GSS model displayed high sensitivity in detecting BRCA-deficient events and identified patients who could benefit from poly(ADP-ribose) polymerase inhibitors (PARPi) treatment. Additionally, the GSS showed high concordance among different NGS panels, indicating its robustness.
BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY
(2022)
Review
Oncology
Elisa Taiana, Maria Eugenia Gallo Cantafio, Vanessa Katia Favasuli, Cecilia Bandini, Giuseppe Viglietto, Roberto Piva, Antonino Neri, Nicola Amodio
Summary: Genomic instability (GI) plays a critical role in the pathobiology of multiple myeloma (MM) by promoting the acquisition of tumor hallmarks. Non-coding RNA molecules are emerging as key players in GI pathways in MM, providing new opportunities for therapeutic interventions. The dysregulation of non-coding RNAs in MM adds another layer of complexity to understanding the molecular determinants of GI in this disease.
Article
Biochemistry & Molecular Biology
Camille Henry, Neema Mbele, Michael M. Cox
Summary: In bacteria, the repair of post-replication gaps by homologous recombination requires the action of RecF, RecO and RecR proteins. However, it is still unclear how RecF targets the system to appropriate sites. The hypothesis of specific RecF binding to gap ends was tested by examining RecF and RecFR binding to more than 40 DNA substrates, but no specific DNA binding was observed. The results suggest that factors other than RecF or RecFR may be involved in targeting post-replication gaps, possibly through interactions with additional proteins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Gastroenterology & Hepatology
Talia Golan, Grainne M. O'Kane, Robert E. Denroche, Maria Raitses-Gurevich, Robert C. Grant, Spring Holter, Yifan Wang, Amy Zhang, Gun Ho Jang, Chani Stossel, Dikla Atias, Sharon Halperin, Raanan Berger, Yulia Glick, J. Patrick Park, Adeline Cuggia, Laura Williamson, Hui-Li Wong, David F. Schaeffer, Daniel J. Renouf, Ayelet Borgida, Anna Dodd, Julie M. Wilson, Sandra E. Fischer, Faiyaz Notta, Jennifer J. Knox, George Zogopoulos, Steven Gallinger
Summary: By analyzing whole genome sequencing data of PDAC patients, HRD-PDAC can be better identified, and patients without BRCA/PALB2 mutations may also benefit from DNA damage response agents.
Article
Multidisciplinary Sciences
Brian J. Caldwell, Andrew S. Norris, Caroline F. Karbowski, Alyssa M. Wiegand, Vicki H. Wysocki, Charles E. Bell
Summary: Some bacteriophages encode a recombinase that catalyzes single-stranded DNA annealing (SSA). In this study, a Red beta homolog from a prophage of Listeria innocua in complex with two complementary DNA strands was determined using cryo-electron microscopy. The structure revealed a helical protein filament bound to an extended and unwound DNA duplex. The protein shares similarity in fold and single-stranded DNA-binding mode with RAD52, providing insights into the mechanism of protein-catalyzed SSA.
NATURE COMMUNICATIONS
(2022)
Article
Endocrinology & Metabolism
Matti O. Ruuskanen, Pande P. Erawijantari, Aki S. Havulinna, Yang Liu, Guillaume Meric, Jaakko Tuomilehto, Michael Inouye, Pekka Jousilahti, Veikko Salomaa, Mohit Jain, Rob Knight, Leo Lahti, Teemu J. Niiranen
Summary: This study examined the long-term association between gut microbiome composition and incident type 2 diabetes. The findings identified specific species and clusters of bacteria that were consistently associated with incident diabetes and suggested potential therapeutic targets for the disease.
Article
Genetics & Heredity
Denis Volk, Fan Yang-Turner, Xavier Didelot, Derrick W. Crook, David Wyllie
Summary: Researchers have developed a software tool called Catwalk that can quickly detect highly similar sequences in large collections of microbial genomes. The tool performs well and can rapidly identify close relatives of SARS-CoV-2 and Mycobacterium tuberculosis genomes among millions of samples.
MICROBIAL GENOMICS
(2022)
Article
Biology
Jake Carson, Alice Ledda, Luca Ferretti, Matt Keeling, Xavier Didelot
Summary: The bounded coalescent model, which represents the origin of individuals from a common ancestor after a certain date, has important applications in various fields. This study introduces a new algorithm for simulating this model directly, demonstrating its computational efficiency compared to rejection sampling. The study also presents a method for calculating the probability of the last common ancestor occurring after a given date, which is crucial for analyzing phylogenetic data under the bounded coalescent model.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Allergy
Yang Liu, Shu Mei Teo, Guillaume Meric, Howard H. F. Tang, Qiyun Zhu, Jon G. Sanders, Yoshiki Vazquez-Baeza, Karin Verspoor, Ville A. Vartiainen, Pekka Jousilahti, Leo Lahti, Teemu Niiranen, Aki S. Havulinna, Rob Knight, Veikko Salomaa, Michael Inouye
Summary: This study found significant associations between gut microbiome and incident asthma and COPD in a population-based cohort of 7115 adults. Machine learning models demonstrated the predictive capabilities of baseline gut microbiome abundance for asthma and COPD, outperforming individual conventional risk factors. The integration of gut microbiome and conventional risk factors further improved prediction capacities.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Review
Urology & Nephrology
Joanne A. O'Donnell, Tenghao Zheng, Guillaume Meric, Francine Z. Marques
Summary: A large body of evidence has shown that the gut microbiome plays a role in regulating blood pressure through various mechanisms, including changes in gene pathways and the production of beneficial or detrimental metabolites. Dysbiosis in the gut microbiome can result in inflammation and disruption of the intestinal barrier, activating mechanisms associated with blood pressure regulation. Challenges in gut microbiome research include minimizing confounding factors and establishing causality, but new approaches such as clinical trials and computational methods offer potential for leveraging the microbiome to lower blood pressure.
NATURE REVIEWS NEPHROLOGY
(2023)
Article
Microbiology
Sadaf Rasheed Mughal, Sadia Ambreen Niazi, Thuy Do, Steven C. Gilbert, Xavier Didelot, David R. Radford, David Beighton
Summary: The aim of this study was to use high-throughput sequencing techniques to investigate the taxonomy of Actinomyces naeslundii and its closely related species. The strains were classified as A. naeslundii and A. oris based on MLST data analysis. Whole genome sequencing was performed on selected strains of A. oris and A. naeslundii, and comparative genomic analysis was carried out. The results showed that A. oris forms six distinct groups, while A. naeslundii forms three. The correct designation of isolates will help in the identification of clinical Actinomyces isolates found in dental plaque and accelerate further research on the biochemical characterization and pathogenesis of this group of microorganisms.
Article
Veterinary Sciences
Mostafa Y. Abdel-Glil, Helmut Hotzel, Herbert Tomaso, Xavier Didelot, Christian Brandt, Christian Seyboldt, Joerg Linde, Stefan Schwarz, Heinrich Neubauer, Hosny El-Adawy
Summary: Campylobacter fetus subsp. venerealis (Cfv) is the cause of bovine genital campylobacteriosis (BGC), which is a trade-relevant disease listed by the World Organization for Animal Health (WOAH). This study aimed to investigate the genomic diversity of German Cfv strains isolated from different federal states in Germany. Whole-genome sequencing and phylogenetic analysis were conducted on 63 Cfv strains collected between 1985 and 2015, and compared with international Cfv isolates. The results showed a genetically conserved Cfv population in Germany, with a lineage that emerged in the nineteenth century and diversified over time. The control interventions in Germany have been successful, as no outbreaks have been reported since 2015.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Microbiology
Kate E. Dingle, Jane Freeman, Xavier Didelot, T. Phuong Quan, David W. Eyre, Jeremy Swann, William D. Spittal, Emma V. Clark, Keith A. Jolley, A. Sarah Walker, Mark H. Wilcox, Derrick W. Crook
Summary: Clostridioides difficile is a significant cause of healthcare-associated infections, with multidrug-resistant strains causing high-mortality outbreaks. Cephalosporin treatment is a known risk factor, and antimicrobial stewardship is important for control. This study investigated the correlation between cephalosporin MICs, amino acid substitutions in penicillin binding proteins, and fluoroquinolone resistance in C. difficile.
Article
Multidisciplinary Sciences
Michelle Kendall, Daphne Tsallis, Chris Wymant, Andrea Di Francia, Yakubu Balogun, Xavier Didelot, Luca Ferretti, Christophe Fraser
Summary: The NHS COVID-19 app, launched in England and Wales in September 2020, had a Bluetooth-based contact tracing functionality to reduce the transmission of SARS-CoV-2. The study shows that user engagement and the app's impact on the epidemic varied based on social and epidemic characteristics. The authors also discuss the interaction and complementarity of manual and digital contact tracing approaches.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Matthew O. Macaulay, Aaron Darling, Mathieu O. Fourment
Summary: Bayesian inference is widely used in phylogenetics to compute distributions of phylogenies. This paper explores the use of hyperbolic space as a low dimensional representation for tree-like data. The authors embed genomic sequences in hyperbolic space and perform hyperbolic Markov Chain Monte Carlo for Bayesian inference. They demonstrate the effectiveness of this method on eight data sets and investigate the impact of embedding dimension and hyperbolic curvature on performance. The results show that hyperbolic space is suitable for phylogenetic inference.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Sidaswar Krishnan, Matthew DeMaere, Dominik Beck, Martin Ostrowski, Justin Seymour, Aaron Darling
Summary: Rhometa is a new software package that can determine recombination rates from shotgun sequencing reads of metagenomes. It extends the composite likelihood approach and enables the analysis of modern short-read datasets. Rhometa offers a comprehensive solution for determining population recombination rates from contemporary metagenomic read datasets.
Article
Infectious Diseases
Luis Roger Esquivel Gomez, Cyril Savin, Voahangy Andrianaivoarimanana, Soloandry Rahajandraibe, Lovasoa Nomena Randriantseheno, Zhemin Zhou, Arthur Kocher, Xavier Didelot, Minoarisoa Rajerison, Denise Kuehnert
Summary: Plague reappeared in the city of Mahajanga, Madagascar in 1991 after a plague-free period of over 60 years. This study used a phylogeographic model to analyze the genome sequences of Yersinia pestis and identified two migrations from the Central Highlands that caused the outbreaks in the 1990s. The pathogen likely survived in wild reservoirs before spillover to humans.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Multidisciplinary Sciences
David Helekal, Matt Keeling, Yonatan H. Grad, Xavier Didelot
Summary: Increasing levels of antibiotic resistance pose a major threat to public health. Understanding the costs and benefits of resistance can lead to better use of antibiotics and prevent the spread of resistance.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Virology
Xavier Didelot, Vinicius Franceschi, Simon D. W. Frost, Ann Dennis, Erik M. Volz
Summary: Inference of effective population size from genomic data can provide insights into demographic history and epidemiological dynamics. A nonparametric approach based on latent process models is developed to estimate the population size dynamics, optimizing parameters using out-of-sample prediction accuracy. The methodology is demonstrated using simulation experiments and applied to HIV-1 and SARS-CoV-2 datasets to estimate the impact of interventions on epidemic dynamics.
Article
Biochemical Research Methods
Xavier Didelot, David Helekal, Michelle Kendall, Paolo Ribeca
Summary: The ability to distinguish imported cases from locally acquired cases is important for selecting public health control strategies. This study proposes an alternative approach using genomic data from a specific location to detect imported cases by comparing them with previous cases from the same location.
