Article
Biochemistry & Molecular Biology
Yuanyuan Cheng, Catherine Grueber, Carolyn J. Hogg, Katherine Belov
Summary: The major histocompatibility complex (MHC) is crucial for the vertebrate immune system, but accurately characterizing MHC genetic diversity in non-model species is technically challenging due to gene duplication and diversification. A new long-read based MHC typing method has been developed to address these challenges and provide better solutions for high accuracy MHC typing in research. This approach allows for population-scale MHC typing in various species, revealing new insights into genetic diversity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Jicong Cao, Eva Maria Novoa, Zhizhuo Zhang, William C. W. Chen, Dianbo Liu, Gigi C. G. Choi, Alan S. L. Wong, Claudia Wehrspaun, Manolis Kellis, Timothy K. Lu
Summary: By using a high-throughput screening approach on 5'UTR libraries, this study identified three synthetic 5'UTRs that outperformed commonly used non-viral gene therapy plasmids in expressing protein payloads. This finding has important implications for engineered cell and gene therapies.
NATURE COMMUNICATIONS
(2021)
Article
Computer Science, Information Systems
Hossein Estiri, Zachary H. Strasser, Shawn N. Murphy
Summary: This study aimed to develop a high-throughput phenotyping method leveraging temporal sequential patterns from electronic health records. Using temporal sequences for phenotyping resulted in superior classification performance compared to standard representations, and transitive sequences offered more accurate phenotype characterization.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2021)
Article
Biochemical Research Methods
Andrzej Zielezinski, Sebastian Deorowicz, Adam Gudys
Summary: The Phage-Host Interaction Search Tool (PHIST) is a tool that predicts prokaryotic hosts of viruses based on exact matches between viral and host genomes. It improves host prediction accuracy at the species level and is significantly faster than other alignment-based tools, making it suitable for metagenomics studies.
Article
Genetics & Heredity
Jing Li, Bertrand Llorente, Gianni Liti, Jia-Xing Yue
Summary: Meiotic recombination ensures chromosome segregation and promotes allele shuffling. RecombineX is a computational framework that automates the analysis of tetrad sequencing data, allowing for marker identification, genotyping, and recombination profiling. It can analyze data based on reference genomes or parental assemblies, and includes features for copy number variation profiling and missing genotype inference. RecombineX also includes a simulation module for hypothesis testing. It has been demonstrated to be accurate and robust for organisms with small and large genomes.
Review
Plant Sciences
Yunus Emre Arvas, Sevgi Marakli, Yilmaz Kaya, Ruslan Kalendar
Summary: The use of molecular markers is crucial in various fields of molecular genetics, such as gene identification, plant breeding, and genetic characterization. Transposable elements, particularly retrotransposons, are widely used as molecular markers due to their presence in eukaryotic genomes and ability to integrate into dispersed chromosomal locations. The ongoing development of molecular marker technologies is closely linked to high-throughput genotype sequencing platforms, making this research highly significant.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Veterinary Sciences
Hee-Chun Chung, Van Giap Nguyen, Yong-ho Park, Bong-Kyun Park
Summary: PCV3 has been reported in multiple countries from 2015 to 2018, with six strains detected in this study through PCR methods. The study reassembled PCV3 genes at the nucleotide sequence level, generating 16 new sequences. A combination model of replicase, ORF3, and capsid protein coding genes was selected for genotyping, allowing classification into three genotypes and several subtypes.
VETERINARY MEDICINE AND SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Artur Gurgul, Igor Jasielczuk, Tomasz Szmatola, Sebastian Sawicki, Ewelina Semik-Gurgul, Boguslawa Dlugosz, Monika Bugno-Poniewierska
Summary: A genotyping strategy based on Nanopore sequencing was developed for simple and cost-efficient genome-wide analysis in horses. The method generated 28,426 highly accurate polymorphisms, which can be improved by increasing sequencing depth.
Article
Chemistry, Multidisciplinary
Baiqing Li, Shimin Su, Chan Zhu, Jie Lin, Xinyue Hu, Lebin Su, Zhunzhun Yu, Kuangbiao Liao, Hongming Chen
Summary: In recent years, artificial intelligence (AI) has revolutionized chemical synthesis, but the lack of suitable representation methods for chemical reactions and scarcity of reaction data hinder the wider application of AI in reaction prediction. This study introduces a novel reaction representation called GraphRXN, which uses a universal graph-based neural network framework to encode chemical reactions directly from two-dimensional reaction structures. The GraphRXN model demonstrates comparable or superior performance to other baseline models when evaluated on three publicly available chemical reaction datasets. Wet-lab experiments were conducted to generate reaction data for further evaluation of the effectiveness of GraphRXN. The model achieved decent accuracy (R-2 of 0.712) when built on high-throughput experimentation data, suggesting its potential for deployment in an integrated workflow combining robotics and AI technologies for forward reaction prediction.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Christian M. Gallardo, Shiyi Wang, Daniel J. Montiel-Garcia, Susan J. Little, Davey M. Smith, Andrew L. Routh, Bruce E. Torbett
Summary: This study overcomes technical challenges in RNA virus sequencing by developing a nanopore-based method to accurately sequence viral genomes from clinical samples. The method can detect rare viral genomes at <1% frequency, facilitating the study of genetic resistance to antiviral therapy and immune pressure.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Stefano Capomaccio, Michela Ablondi, Daniele Colombi, Cristina Sartori, Andrea Giontella, Katia Cappelli, Enrico Mancin, Vittoria Asti, Roberto Mantovani, Alberto Sabbioni, Maurizio Silvestrelli
Summary: In this study, the current status of the modern Italian gene pool was described. The results show that some native Italian breeds preserve distinct gene pools, potentially due to adaptation to different geographical contexts. However, comparisons with international breeds reveal strong gene flow from renowned breeds into several Italian breeds, likely due to historical introgression. Some breeds also show unique characteristics based on their breeding history. Lastly, certain breeds exist more for cultural, traditional, and geographical reasons rather than genetic distinctiveness.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Sayantan Sarkar, Avat Shekoofa, Angela McClure, Jason D. Gillman
Summary: This study evaluated the drought-tolerance trait of transpiration rate limitation (TRlim) in soybean using a high-throughput technique with an aquaporin inhibitor. Genetic analysis identified QTLs associated with TRlim and leaf temperature, and candidate genes related to enhanced tolerance to abiotic stress were also identified. These findings provide valuable insights for the development of drought-tolerant soybean varieties.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Diane Gleeson, Debarati Sethi, Radka Platte, Jonathan Burvill, Daniel Barrett, Shaheen Akhtar, Michaela Bruntraeger, Joanna Bottomley, James Bussell, Edward Ryder
Summary: Genotyping of knockout alleles in mice can be performed using endpoint PCR, qPCR, or NGS, with NGS being highly scalable and applicable to various allele types. One challenge is locating unique areas of the genome, especially when dealing with gene families or regions of high homology.
Article
Chemistry, Multidisciplinary
Marta Napiorkowska, Luzius Pestalozzi, Sven Panke, Martin Held, Steven Schmitt
Summary: A high-throughput platform for optimizing microbial protein production is described, using droplet microfluidics and flow cytometry. The platform successfully cultures several industrially relevant bacterial and yeast strains and isolates strains with superior production titers by detecting peptides or proteins released from the cell via autolysis or secretion.
Article
Biochemistry & Molecular Biology
Marzia Rossato, Luca Marcolungo, Luca De Antoni, Giulia Lopatriello, Elisa Bellucci, Gaia Cortinovis, Giulia Frascarelli, Laura Nanni, Elena Bitocchi, Valerio Di Vittori, Leonardo Vincenzi, Filippo Lucchini, Kirstin E. Bett, Larissa Ramsay, David James Konkin, Massimo Delledonne, Roberto Papa
Summary: High-throughput genotyping allows for the analysis of genetic diversity in large populations and genome-wide association studies. In this study, the researchers used CRISPR-Cas9 technology to remove repetitive elements in the lentil genome, thus focusing the sequencing data on coding and regulatory regions. This method significantly increased genotyping accuracy and the number of genotyped bases compared to non-depleted libraries.
Article
Virology
Martin Pirkl, Joachim Buech, Carole Devaux, Michael Boehm, Anders Sonnerborg, Francesca Incardona, Ana Abecasis, Anne-Mieke Vandamme, Maurizio Zazzi, Rolf Kaiser, Thomas Lengauer
Summary: Human immunodeficiency virus (HIV) can develop resistance to all antiretroviral drugs, but multidrug resistance is rare. The accumulation of resistance mutations follows a predetermined order rather than being acquired randomly and simultaneously. Understanding this order can help elucidate the mechanisms of multidrug resistance.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Virology
Annabel Rector, Mandy Bloemen, Marijn Thijssen, Leen Delang, Joren Raymenants, Jonathan Thibaut, Bram Pussig, Lore Fondu, Bert Aertgeerts, Marc Van Ranst, Chris Van Geet, Jef Arnout, Elke Wollants
Summary: Wastewater surveillance is crucial in managing the global COVID-19 pandemic, serving as an early warning system for outbreaks and a tool to track the circulation of specific variants. This study used various wastewater collection points in Leuven to investigate the application of wastewater surveillance. Wastewater samples were collected and analyzed using RT-qPCR to quantify SARS-CoV-2 RNA, and specific mutations were detected to identify circulating variants. The study found that wastewater SARS-CoV-2 concentration preceded peaks in positive cases and detected the presence of different variants simultaneously during the transition period. Wastewater-based surveillance is a valuable tool for monitoring virus circulation and variants in larger populations.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Clinical Neurology
Matteo Riva, Roxanne Wouters, David Nittner, Jolien Ceusters, Edmond Sterpin, Roberto Giovannoni, Uwe Himmelreich, Willy Gsell, Marc Van Ranst, An Coosemans
Summary: This study aimed to analyze the effects of optimizing radiotherapy schedules in combination with radioimmunotherapy on the tumor microenvironment of experimental high-grade gliomas. The results showed that radiation dosage and fractionation significantly influenced the survival, tumor immunity, and glioma stem cells in experimental high-grade gliomas. These findings should be considered when designing more synergistic and effective radioimmunotherapy combinations.
JOURNAL OF NEUROSURGICAL SCIENCES
(2023)
Article
Virology
Sharonjit K. Dhillon, Cindy Simoens, Lize Cuypers, Jannes Bode, Jesper Bonde, Philippe Corbisier, Clementina E. Cocuzza, Marc Van Ranst, Marc Arbyn
Summary: The study protocol VALCOR was conducted to evaluate the performance of Aptima SARS-CoV-2 assay using clinical samples. The results showed that Aptima had excellent performance in sensitivity, specificity, and overall agreement, with the ability to detect clinical samples at a low limit of detection. This highlights the importance of evaluating diagnostic assays for reliable test outcomes.
Article
Microbiology
Marijn Thijssen, Frank Tacke, Lore Van Espen, David Cassiman, Mahmoud Naser Aldine, Frederik Nevens, Marc Van Ranst, Jelle Matthijnssens, Mahmoud Reza Pourkarim
Summary: This study aimed to characterize the longitudinal plasma virome dynamics in chronic hepatitis B virus (HBV) infected patients. The virome was primarily composed of members of the Anello-, Flavi-, and Hepadnaviridae (HBV) families. The study found no correlation between virome structure and dynamics with the different stages of chronic HBV infection or antiviral therapy. The analysis of viruses observed in multiple timepoints revealed the presence of a dynamic community.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Public, Environmental & Occupational Health
Justin Carrico, Claire E. Mellott, Sandra E. Talbird, Andre Bento-Abreu, Barbara Merckx, Jessica Vandenhaute, Damia Benchabane, Nicolas Dauby, Olivier Ethgen, Philippe Lepage, Jeroen Luyten, Marc Raes, Steven Simoens, Marc Van Ranst, Amanda Eiden, Mawuli K. Nyaku, Goran Bencina
Summary: In this study, the public health impact and return on investment of Belgium's pediatric immunization program (PIP) were evaluated. The PIP was found to prevent infections and deaths, as well as save costs in both the healthcare sector and society. Continued investment in the PIP is recommended to sustain its positive impact.
FRONTIERS IN PUBLIC HEALTH
(2023)
Article
Infectious Diseases
Ana Cecilia Ribeiro Cruz, Leonardo Henrique Almeida Hernandez, Carine Fortes Aragao, Thito Yan Bezerra da Paz, Sandro Patroca da Silva, Fabio Silva da Silva, Ana Alice de Aquino, Glennda Juscely Galvao Pereira Cereja, Bruna Lais Sena do Nascimento, Jose Wilson Rosa Junior, Carmeci Natalina Elias, Cristiano Gomes Nogueira, Daniel Garkauskas Ramos, Vagner Fonseca, Marta Giovanetti, Luiz Carlos Junior Alcantara, Bruno Tardelli Diniz Nunes, Pedro F. da Costa Vasconcelos, Livia Caricio Martins, Joaquim Pinto Nunes-Neto
Summary: The largest outbreak of sylvatic yellow fever virus (YFV) in Brazil between 2016-2018 was reported, and entomo-virological surveillance was considered important for monitoring YFV. Mosquitoes were collected from six Brazilian states and tested for YFV using RT-qPCR. YFV infection was detected in various mosquito species, including Ae. albopictus, indicating the potential for urban YFV re-emergence. The study highlights the need to strengthen YFV surveillance, vaccination coverage, and vector control measures in Brazil.
TROPICAL MEDICINE AND INFECTIOUS DISEASE
(2023)
Article
Cardiac & Cardiovascular Systems
Stefaan Six, Peter Theuns, Pieter Libin, Ann Nowe, Luigi Pannone, Bart Bogaerts, Simon Jaxy, Catharina Olsen, Gudrun Pappaert, Isel Grau, Juan Sieira, Sonia Van Dooren, Esther Scheirlynck, Julie Nekkebroeck, Marina Mallefroy, Carlo de Asmundis, Johan Bilsen
Summary: This study aimed to assess the psychosocial outcomes of Brugada syndrome (BrS) patients and propose tailored psychosocial care. The results showed that BrS patients had higher levels of mental distress and a higher prevalence of Type D personality compared to the general population.
Article
Immunology
Isabel Leroux-Roels, Marc Van Ranst, Corinne Vandermeulen, Carline Vanden Abeele, Nathalie De Schrevel, Bruno Salaun, Celine Verheust, Marie-Pierre David, Shady Kotb, Veronica Hulstrom
Summary: This study evaluated the safety and immune responses of a third dose of an investigational vaccine against respiratory syncytial virus (RSV) in older adults aged 60-80 years. The results showed that the third dose of the vaccine was well tolerated and induced a good immune response in older adults.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Urology & Nephrology
Evert Cleenders, Priyanka Koshy, Elisabet Van Loon, Katrien Lagrou, Kurt Beuselinck, Graciela Andrei, Marta Crespo, Katrien De Vusser, Dirk Kuypers, Evelyne Lerut, Kris Mertens, Olga Mineeva-Sangwo, Parmjeet Randhawa, Aleksandar Senev, Robert Snoeck, Ben Sprangers, Claire Tinel, Amaryllis Van Craenenbroeck, Jan van den Brand, Marc Van Ranst, Geert Verbeke, Maarten Coemans, Maarten Naesens
Summary: This study aimed to investigate the value of performing a biopsy at the time of BKPyV-DNAemia in distinguishing presumptive and proven PyVAN. The results showed that plasma viral load had good predictive value for SV40 positivity, while the dichotomy of SV40 immunohistochemistry did not predict viral clearance. Therefore, the distinction between presumptive and proven PyVAN based on SV40 immunohistochemistry has limited clinical value.
KIDNEY INTERNATIONAL
(2023)
Article
Genetics & Heredity
Nikola Sklenovska, Mandy Bloemen, Valentijn Vergote, Anne-Sophie Logist, Bert Vanmechelen, Lies Laenen, Emmanuel Andre, Jean-Jacques Muyembe-Tamfum, Elke Wollants, Marc Van Ranst, Piet Maes, Tony Wawina-Bokalanga
Summary: Monkeypox is a viral zoonosis with circulation in animals and humans in some African countries. Despite the long-known identification of monkeypox virus (MPXV) as a human pathogen, the availability of accurate diagnostic assays and comparative performance studies remains limited. In this study, we developed a real-time PCR test and evaluated its performance against a commercial detection assay. Our results demonstrate the validity and accuracy of the developed test for confirming MPXV infection.
Article
Virology
Marijn Thijssen, Gholamreza Khamisipour, Mohammad Maleki, Timothy Devos, Guangdi Li, Marc Van Ranst, Jelle Matthijnssens, Mahmoud Reza Pourkarim
Summary: Blood transfusion safety is crucial for public health. Studies have shown the presence of a virome in the blood of healthy individuals, which could be missed by current screening techniques. This study characterized the virome in Iranian multiple-transfused patients and healthy blood donors, revealing the presence of various viruses, with Anelloviridae and Flaviviridae being the most common families.
Article
Virology
Larissa Domingues Castilho de Arruda, Marta Giovanetti, Vagner Fonseca, Marina Castilhos Souza Umaki Zardin, Gislene Garcia de Castro Lichs, Silvia Asato, Ana Olivia Pascoto Esposito, Miriam Tokeshi Mueller, Joilson Xavier, Hegger Fritsch, Mauricio Lima, Carla de Oliveira, Elaine Vieira Santos, Livia de Mello Almeida Maziero, Danila Fernanda Rodrigues Frias, Danielle Ahad das Neves, Liliane Ferreira da Silva, Ellen Caroline Rodrigues Barretos, Paulo Eduardo Tsuha Oshiro, Bianca Modafari Goday, Jessica Klener Lemos dos Santos, Simone Kashima, Carlos F. C. de Albuquerque, Rodrigo Fabiano do Carmo Said, Alexander Rosewell, Luiz Henrique Ferraz Demarchi, Julio Croda, Luiz Carlos Junior Alcantara, CrhistinneCavalheiro Maymone Goncalves
Summary: Since its discovery in early 1916, dengue fever has caused extensive urban outbreaks in Brazil, posing a serious threat to public health. A genomic surveillance training program was conducted in collaboration with local health authorities, resulting in the generation of 177 DENV genome sequences collected during a period of high dengue fever cases. The study identified the co-circulation of different dengue serotypes and diverse viral lineages, indicating multiple introduction events of viral strains in the region. The findings highlight the complex and changing dynamics of DENV transmission and emphasize the value of ongoing surveillance activities in informing public health actions.
Article
Microbiology
Danitza Xiomara Romero-Calle, Francisnei Pedrosa-Silva, Luiz Marcelo Ribeiro Tome, Vagner Fonseca, Raquel Guimaraes Benevides, Leila Thaise Santana de Oliveira Santos, Tulio de Oliveira, Mateus Matiuzzi da Costa, Luiz Carlos Junior Alcantara, Vasco Ariston de Carvalho Azevedo, Bertram Brenig, Thiago M. Venancio, Craig Billington, Aristoteles Goes-Neto
Summary: Despite the use of new treatments, antimicrobial resistance is still increasing, calling for novel strategies. Bacteriophages have the potential to control bacterial pathogens like Salmonella. A Salmonella phage, Wara, was isolated from water samples in the Subae River Basin in Brazil. Its genome was sequenced using Oxford Nanopore Technologies and Illumina HiSeq, and assembly was carried out using Racon and Unicycler. Wara was found to be a member of the Tequintavirus genus and has therapeutic and biocontrol potential against Salmonella in healthcare and agriculture.
Article
Microbiology
Anielly Sarana da Silva, Gabriel Montenegro de Campos, Marcia Guimaraes Villanova, Rafael dos Santos Bezerra, Luciana Maria Mendes Santiago, Rodrigo Haddad, Dimas Tadeu Covas, Marta Giovanetti, Luiz Carlos Junior Alcantara, Maria Carolina Elias, Sandra Coccuzzo Sampaio, Simone Kashima, Svetoslav Nanev Slavov
Summary: This study evaluated the frequency, molecular features, and circulating genotypes of Human pegivirus-1 (HPgV-1) in patients with fulminant hepatitis. The results showed that 44.4% of the collected plasma samples were positive for HPgV-1, with all positive samples belonging to genotype 2. Further research is needed to understand the impact of HPgV-1 on diseases.
