Article
Biotechnology & Applied Microbiology
Yongjian Wu, Xiaomin Cheng, Guangmin Jiang, Huishu Tang, Siqi Ming, Lantian Tang, Jiahai Lu, Cheng Guo, Hong Shan, Xi Huang
Summary: This study investigated the dynamics of oral and gut flora in 53 COVID-19 patients before and after the clearance of SARS-CoV-2, comparing them with 76 healthy individuals. The findings revealed a potential association between SARS-CoV-2 infection and alterations in the microbiome community, suggesting new dimensions for disease pathophysiology, potential microbial biomarkers, and treatment strategies for COVID-19.
NPJ BIOFILMS AND MICROBIOMES
(2021)
Article
Biochemical Research Methods
Borja Freire, Susana Ladra, Jose R. Parama, Leena Salmela
Summary: The study presents viaDBG, a fast and accurate de Bruijn graph-based tool for de novo assembly of viral quasispecies. By iteratively correcting sequencing errors, using large k-mers, and incorporating paired-end information in the graph, viaDBG achieves both accuracy and speed in assembling viral quasispecies.
Article
Immunology
Alvaro Lopez-Valinas, Marta Valle, Marta Perez, Ayub Darji, Chiara Chiapponi, Llilianne Ganges, Joaquim Segales, Jose I. Nunez
Summary: Influenza A viruses (IAVs) are constantly evolving, posing a threat to animal and human health. Vaccines can help reduce the spread of swine influenza viruses (SIAV) in farms, but they do not provide complete protection and may potentially favor viral evolution. A study on vaccinated and nonvaccinated pigs challenged with H1N2 SIAV showed that vaccinated animals had a higher proportion of virus mutations, indicating the potential for vaccine-driven evolution.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Microbiology
Sergio Ortega-del Campo, Luis Diaz-Martinez, Patricia Moreno, Esther Garcia-Rosado, M. Carmen Alonso, Julia Bejar, Ana Grande-Perez
Summary: NNV is a neurotropic virus that causes viral nervous necrosis disease in fish. It has a bisegmented (+) ssRNA genome and the variability of its genome may be associated with its virulence.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Xiaoli Jiao, Hiromi Imamichi, Brad T. Sherman, Rishub Nahar, Robin L. Dewar, H. Clifford Lane, Tomozumi Imamichi, Weizhong Chang
Summary: This study developed a tool called QuasiSeq, which utilizes a novel clustering method called SigClust, to analyze viral mixtures with high accuracy and sensitivity. QuasiSeq can correctly identify quasispecies and generate highly accurate quasispecies sequences, even with low-quality sequencing data. It has higher sensitivity and specificity compared to similar published software, and can handle large-scale sequencing data.
Article
Biotechnology & Applied Microbiology
Maria Artesi, Vincent Hahaut, Basiel Cole, Laurens Lambrechts, Fereshteh Ashrafi, Ambroise Marcais, Olivier Hermine, Philip Griebel, Natasa Arsic, Frank van der Meer, Arsene Burny, Dominique Bron, Elettra Bianchi, Philippe Delvenne, Vincent Bours, Carole Charlier, Michel Georges, Linos Vandekerckhove, Anne Van den Broeke, Keith Durkin
Summary: This study introduces a novel method, PCIP-seq, which uses long reads to accurately identify viral insertion sites and sequence their associated viral genomes. The method has significant potential applications in the research of virus-infected cells.
Article
Cell Biology
Jeff E. Mold, Laurent Modolo, Joanna Hard, Margherita Zamboni, Anton J. M. Larsson, Moa Stenudd, Carl-Johan Eriksson, Ghislain Durif, Patrik L. Stahl, Erik Borgstrom, Simone Picelli, Bjorn Reinius, Rickard Sandberg, Pedro Reu, Carlos Talavera-Lopez, Bjorn Andersson, Kim Blom, Johan K. Sandberg, Franck Picard, Jakob Michaelsson, Jonas Frisen
Summary: This study longitudinally tracked human CD8(+) T cell clones responding to yellow fever virus vaccination and found that clonal selection shapes the circulating memory repertoire during immune responses, with clones in the memory phase displaying biased differentiation trajectories. In secondary responses, specific CD8(+) T cell clones are poised to recapitulate skewed differentiation trajectories, highlighting the multifaceted human T cell response to acute viral infections.
Article
Biology
Mirko Treccani, Elena Locatelli, Ristina Patuzzo, Giovanni Malerba
Summary: The need for significant results in genomic big data has led to the use of a large number of genetic markers in genome-wide association studies. Genotype imputation, a statistical and inferential procedure based on a known reference panel, has served this purpose since the beginning. It allows for association analysis of a greater number of polymorphic sites that have not been previously tested by the used technology. This review provides an overview of genotype imputation process, highlighting the most popular methods and discussing its usage in the current genomic landscape, as well as future developments and investigation areas.
Article
Virology
Alexandre Flageul, Pierrick Lucas, Edouard Hirchaud, Fabrice Touzain, Yannick Blanchard, Nicolas Eterradossi, Paul Brown, Beatrice Grasland
Summary: The bioinformatic pipeline VVV was developed to analyze viral populations in given samples from NGS data, making data processing and result analysis more accessible to non-bioinformaticians. VVV generated consensus sequences and identified viral genetic variants, validated by comparing wild-type and cloned virus populations in different animal coronaviruses. This pipeline simplifies the study of viral genetic evolution and increases understanding among biologists.
Article
Biodiversity Conservation
Malgorzata Bacmaga, Jadwiga Wyszkowska, Jan Kucharski
Summary: The study aimed to evaluate the impact of tebuconazole on bacterial population numbers, diversity, structure, and soil enzymatic activity. Tebuconazole caused changes in bacterial population numbers and diversity, stimulated the proliferation of organotrophic bacteria, and inhibited actinobacteria growth. Additionally, it altered the structure of bacterial communities and influenced soil enzymatic activities.
ECOLOGICAL INDICATORS
(2021)
Article
Fisheries
Natsuko Nakayama, Masami Hamaguchi
Summary: This study demonstrates the genetic diversity of HcRNAV in natural sediments using clone library and Next Generation Sequencing (NGS) analysis. The diversity of HcRNAV sequences varies with time and location, suggesting a process of natural selection. To effectively utilize HcRNAV for bloom control, it is necessary to collect and pool sediments containing HcRNAV from multiple local sites.
Article
Biochemical Research Methods
Xuecong Fu, Haoyun Lei, Yifeng Tao, Russell Schwartz
Summary: In this study, a tumor phylogeny method called TUSV-ext was developed, which integrates single-nucleotide variants (SNVs), copy number alterations (CNAs), and structural variations (SVs) into a single inference framework. The accuracy and usability of the method were demonstrated through simulations and application to real tumor data, revealing the evolutionary tree and clonal structure of the tumor.
Article
Gastroenterology & Hepatology
Huei-Ru Cheng, Hung-Chih Yang, Su-Ru Lin, Ta-Yu Yang, You-Yu Lin, Tung-Hung Su, Tai-Chung Tseng, Chun-Jen Liu, Jia-Horng Kao
Summary: The diversity of viral quasispecies and the concentration of HBcrAg at the end of treatment can predict virological relapse within 1 year after stopping therapy. Low baseline viral nucleotide diversity and high HBcrAg concentration are associated with a higher risk of relapse.
HEPATOLOGY INTERNATIONAL
(2021)
Review
Oncology
Salvatore Nicola Bertuccio, Laura Anselmi, Riccardo Masetti, Annalisa Lonetti, Sara Cerasi, Sara Polidori, Salvatore Serravalle, Andrea Pession
Summary: Despite improvements in therapeutic protocols and risk stratification, AML remains a major cause of childhood leukemic mortality, with high rates of relapse and poor response to conventional chemotherapy in pediatric patients. Research focuses on the genetic heterogeneity of pediatric AML, its association with clonal evolution leading to relapse, and innovative tools for enhanced diagnosis and drug screening. The ultimate goal is targeted therapy to improve prognosis and reduce toxic side effects of current treatments for pediatric AML.
Article
Biochemistry & Molecular Biology
Solenn Stoeckel, Ronan Becheler, Ekaterina Bocharova, Dominique Barloy
Summary: Autopolyploidy is common and important in eukaryotes. The emergence of new genotyping methods allows for accurate calculation of allele dosage, facilitating the study of autopolyploid populations and species. GenAPoPop is a user-friendly solution that calculates population genetic indices and provides graphical representations for the analysis of autopolyploid populations.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Infectious Diseases
Cristina Andres, Alejandra Gonzalez-Sanchez, Moraima Jimenez, Ester Marquez-Algaba, Maria Pinana, Candela Fernandez-Naval, Juliana Esperalba, Narcis Saubi, Josep Quer, Ariadna Rando-Segura, Marta Miarons, Maria Gema Codina, Isabel Ruiz-Camps, Tomas Pumarola, Pau Abrisqueta, Andres Anton
Summary: This study aimed to monitor the early emergence of genetic mutations related to reduced susceptibility to monoclonal antibody (mAb)-based treatment in immunocompromised patients with long-term viral excretion. The results showed that most cases were infected with the Omicron variant, and mutations associated with mAb therapy resistance were detected in some patients. This highlights the importance of monitoring for drug resistance mutations in immunocompromised patients and the community.
CLINICAL MICROBIOLOGY AND INFECTION
(2023)
Article
Biochemistry & Molecular Biology
Nuria Estanyol-Torres, Cristina Domenech-Coca, Raul Gonzalez-Dominguez, Antonio Minarro, Ferran Reverter, Jose Antonio Moreno-Munoz, Jesus Jimenez, Manel Martin-Palomas, Pol Castellano-Escuder, Hamza Mostafa, Santi Garcia-Vallve, Nerea Abasolo, Miguel A. Rodriguez, Helena Torrell, Josep M. del Bas, Alex Sanchez-Pla, Antoni Caimari, Anna Mas-Capdevila, Cristina Andres-Lacueva, Anna Crescenti
Summary: The study aimed to evaluate the effects of a mixture of four dietary fibers on obese rats. The results showed that the fiber mixture significantly reduced body weight, adiposity, HbA1c, and HDL-cholesterol levels in the rats. It also improved energy expenditure, fat oxidation, and intestinal health, while reducing adiponectin and LPS levels. The intervention effect was observed at the metabolomic, metagenomic, and transcriptomic levels.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2023)
Article
Infectious Diseases
Maria Pinana, Jorgina Vila, Cristina Andres, Jordi Saura, Alejandra Gonzalez-Sanchez, Anna Creus-Costa, Narcis Saubi, Juliana Esperalba, Ariadna Rando, Manuel Jesus Iglesias-Cabezas, Josep Quer, Antoni Soriano-Arandes, Pere Soler-Palacin, Tomas Pumarola, Andres Anton
Summary: The prevalence, molecular epidemiology, and clinical manifestations of human bocavirus (HBoV) in patients at a tertiary hospital in Barcelona, Spain were described in this study. Respiratory specimens from pediatric patients were collected for laboratory confirmation of respiratory viruses. Phylogenetic analysis of HBoV was performed and clinical features were studied retrospectively.
Article
Biochemistry & Molecular Biology
Josep Gregori, Marta Ibanez-Lligona, Josep Quer
Summary: The rapid evolution of a viral quasispecies in a host, especially during treatment, is compared to the slow evolution of a natural ecosystem. Methods to quantify the evolution of a quasispecies are introduced and simulated examples are given. The correlation between the proposed indices is also discussed and a clinical case is used to demonstrate the efficacy of the proposed methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Gastroenterology & Hepatology
Joel Flores-Arriaga, Maria C. Aso, Arantzazu Izagirre, Ami D. Sperber, Olafur S. Palsson, Shrikant I. Bangdiwala, Angel Lanas, Luis Bujanda, Beatriz Lobo, Carmen Alonso-Cotoner, Alex Sanchez-Pla, Javier Santos
Summary: The study used data from the Rome Foundation Global Epidemiology Study to assess the prevalence and burden of gut-brain disorders in Spain. The survey, completed by 2072 participants, revealed that 43.6% of respondents met diagnostic criteria for at least one disorder, with functional constipation being the most prevalent. The study highlights the need for specialized training and future research in this area.
NEUROGASTROENTEROLOGY AND MOTILITY
(2023)
Review
Virology
Marta Ibanez-Lligona, Sergi Colomer-Castell, Alejandra Gonzalez-Sanchez, Josep Gregori, Carolina Campos, Damir Garcia-Cehic, Cristina Andres, Maria Pinana, Tomas Pumarola, Francisco Rodriguez-Frias, Andres Anton, Josep Quer
Summary: Viruses are the major cause of epidemics and pandemics, and high-throughput next-generation sequencing technologies based on metagenomics can detect new infectious genomes and properly diagnose certain diseases. However, these techniques require a large amount of genetic material and involve complex bioinformatic analyses.
Article
Nutrition & Dietetics
Hamza Mostafa, Tomas Merono, Antonio Minarro, Alex Sanchez-Pla, Fabian Lanuza, Raul Zamora-Ros, Agnetha Linn Rostgaard-Hansen, Nuria Estanyol-Torres, Marta Cubedo-Cullere, Anne Tjonneland, Rikard Landberg, Jytte Halkjaer, Cristina Andres-Lacueva
Summary: This observational study explored the association between anthocyanin intake and cardiometabolic risk. Results revealed specific associations between anthocyanins and certain plasma metabolites, some of which were inversely correlated with visceral adipose tissue. These findings suggest a potential link between anthocyanin intake and cardiometabolic health benefits.
Article
Endocrinology & Metabolism
Marta Corral-Pujol, Berta Arpa, Estela Rosell-Mases, Leire Egia-Mendikute, Conchi Mora, Thomas Stratmann, Alex Sanchez, Anna Casanovas, Josep Enric Esquerda, Didac Mauricio, Marta Vives-Pi, Joan Verdaguer
Summary: During the development of autoimmune diabetes, an autoimmune attack occurs against the peripheral nervous system. A study on NOD mice revealed the formation of cytoplasmic vacuoles and alterations in gene transcription which may be involved in the development of the disease.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Microbiology
Brenda Martinez-Gonzalez, Isabel Gallego, Josep Gregori, Maria Eugenia Soria, Pilar Somovilla, Ana Isabel de Avila, Carlos Garcia-Crespo, Antoni Duran-Pastor, Carlos Briones, Jordi Gomez, Josep Quer, Esteban Domingo, Celia Perales
Summary: In this study, we report the mild mutagenic activity of sofosbuvir (SOF) for hepatitis C virus (HCV). Serial passages of HCV in the presence of SOF led to increased C & RARR; U transitions in the mutant spectra, indicating its potential as a mild mutagen. This activity was dependent on the fitness of the HCV population and may contribute to its antiviral efficacy.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Review
Immunology
Francisco Rodriguez-Frias, Ariadna Rando-Segura, Josep Quer
Summary: Hepatitis is a complex inflammation of the liver, primarily caused by hepatotropic viruses, but can also be influenced by other pathogens, metabolic disorders, or autoimmune reactions. In 2022, an unknown etiology of severe acute hepatitis in previously healthy young children, with cases requiring liver transplantation, drew global attention. The co-occurrence with COVID-19 may be a contributing factor to this acute hepatitis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Immunology
Nicolas Fissolo, Laura Calvo-Barreiro, Herena Eixarch, Ursula Boschert, Luisa M. Villar, Lucienne Costa-Frossard, Mireia Ferrer, Alex Sanchez, Eva Borras, Eduard Sabido, Carmen Espejo, Xavier Montalban, Manuel Comabella
Summary: This study characterized the transcriptomic and proteomic profiles induced by cladribine in blood cells, and identified potential treatment response biomarkers to cladribine in patients with multiple sclerosis.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Meritxell Llorens-Revull, Brenda Martinez-Gonzalez, Josep Quer, Juan Ignacio Esteban, Gonzalo Nunez-Moreno, Pablo Minguez, Idoia Burgui, Ricardo Ramos-Ruiz, Maria Eugenia Soria, Angie Rico, Mar Riveiro-Barciela, Silvia Sauleda, Maria Piron, Irene Corrales, Francesc E. Borras, Francisco Rodriguez-Frias, Ariadna Rando, Clara Ramirez-Serra, Silvia Camos, Esteban Domingo, Marta Bes, Celia Perales, Maria Isabel Costafreda
Summary: MicroRNAs (miRNAs) encapsulated in extracellular vesicles (EVs) have potential as diagnostic and prognostic biomarkers. This study aimed to find a reliable EV isolation method for miRNA sequencing, suitable for clinical applications. Results showed that SEC yielded the highest amount of EVs with good reproducibility, while GRAD and SEC+GRAD resulted in purer EV preparations. The NEBNext library exhibited the highest reproducibility in miRNA recovery and diversity. Therefore, combining GRAD EV isolation with NEBNext library preparation is suitable for miRNA detection using plasma samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, General & Internal
Jesus Rivera-Esteban, Alba Jimenez-Masip, Sergio Munoz-Martinez, Salvador Augustin, Rafael A. Guerrero, Pablo Gabriel-Medina, Roser Ferrer-Costa, Francisco Rodriguez-Frias, Elisabet Turu, Andres Marco, Juan M. Pericas
Summary: Metabolic disorders, including MASLD, are highly prevalent among inmates. The prevalence of significant fibrosis seems notably higher than that of the general population, underscoring the need for targeted screening programs and therapeutic interventions in the incarcerated population.
JOURNAL OF CLINICAL MEDICINE
(2023)