Article
Biochemistry & Molecular Biology
Jin-fang Wang, Hai-yan Yu, Shao-bo Ma, Qiang Lin, Da-zhi Wang, Xin Wang
Summary: This study analyzed the mitochondrial genomes of three lampriform species and inferred a time-calibrated phylogeny, revealing the mitogenomic structure variation and functional substitutions associated with adaptive radiation. It provides important insights into the systematic taxonomy and adaptive evolution studies of Lampriformes species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Xiaohan Shu, Ruizhong Yuan, Zhilin Xia, Gui Gao, Lei Yang, Zhirong Sun, Qing Mu, Pu Tang, Xuexin Chen
Summary: This study sequenced and annotated three mitogenomes of Meteorus species, revealing rich and diverse tRNA gene rearrangements. Compared to the ancestral organization, only seven tRNAs were conserved and trnG had its own unique location. The phylogenetic analysis showed that Meteorus species formed a clade within the subfamily Euphorinae and were closely related to Zele. The tRNA rearrangement patterns matched the phylogenetic relationships, indicating that tRNA rearrangements provide insights into mitochondrial genome evolution at the genus/species levels in insects.
FRONTIERS IN GENETICS
(2023)
Article
Genetics & Heredity
Jiayang Xue, Wenjun Wang, Jing Shao, Xiangming Dai, Zhouyong Sun, Jacob D. Gardner, Liang Chen, Xiaoning Guo, Nan Di, Xuesong Pei, Xiaohong Wu, Ganyu Zhang, Can Cui, Peng Cao, Feng Liu, Qingyan Dai, Xiaotian Feng, Ruowei Yang, Wanjing Ping, Lizhao Zhang, Nu He, Qiaomei Fu
Summary: This study sequenced 172 complete mitochondrial genomes from individuals related to the Shimao culture and Taosi culture in the Middle Yellow River basin. The results showed close genetic connections between the populations inhabiting Shimao City and the earlier Yangshao culture population in northern Shaanxi Province. The Shimao-related populations also had the closest maternal affinity with the contemporaneous Taosi populations and shared more affinity with present-day northern Han populations.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Xing Zhang, Liu Yang, Lingyun Hou, Hua Li, Hai Xiang, Xingbo Zhao
Summary: This study confirms that approximately 4,000-year-old bovines from North China were taurine cattle, originating from the Near East. Ancient Chinese cattle had a genetic contribution to the taurine cattle of South China. There was a rapid decrease in the female effective population size of Chinese taurine cattle around 4.65 thousand years ago.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Noemi Borbely, Orsolya Szekely, Bea Szeifert, Daniel Gerber, Istvan Mathe, Elek Benko, Balazs Gusztav Mende, Balazs Egyed, Horolma Pamjav, Anna Szecsenyi-Nagy
Summary: In this study, we analyzed 115 whole mitogenomes and 92 Y-chromosomal STR and SNP profiles from the Szekely ethnic group in southeast Transylvania. The results showed that the Szekelys have a predominantly local uniparental make-up with limited admixture from neighboring populations. Phylogenetic analysis also revealed an eastern origin for certain maternal and paternal lineages, which could be linked to ancient DNA data.
Article
Biochemistry & Molecular Biology
Epifania Arango-Isaza, Marco Rosario Capodiferro, Maria Jose Aninao, Hiba Babiker, Simon Aeschbacher, Alessandro Achilli, Cosimo Posth, Roberto Campbell, Felipe I. Martinez, Paul Heggarty, Scott Sadowsky, Kentaro K. Shimizu, Chiara Barbieri
Summary: This study analyzes the genetic ancestry of the Mapuche, one of the largest indigenous groups in South America. The findings reveal significant differences between the Mapuche ancestors and those in the Far South, with no further migration waves from the north. Additionally, there is evidence of gene flow between the Central and Southern Andes, suggesting the southward spread of cultural traits. The study also emphasizes the importance of integrating genetic narrative with indigenous knowledge and perspectives.
Article
Genetics & Heredity
Pille Hallast, Anastasia Agdzhoyan, Oleg Balanovsky, Yali Xue, Chris Tyler-Smith
Summary: The genomes of present-day humans outside Africa originated almost entirely from a single out-migration similar to 50,000-70,000 years ago, followed by mixture with Neanderthals contributing similar to 2% to all non-Africans. Phylogenetic analyses of Y chromosome sequences point to East/Southeast Asia as the origin of all known surviving non-African male lineages.
Article
Multidisciplinary Sciences
Wu Zuo, Guangming Chen, Zhimei Gao, Shuai Li, Yanyan Chen, Chenhui Huang, Juan Chen, Zhengjun Chen, Ming Lei, Qian Bian
Summary: During meiosis, chromosomes undergo significant changes in morphology and intranuclear positioning. A study using Hi-C mapping in mouse spermatogenesis revealed the roles of transcriptional activity and mechanical force in homolog alignment and recombination.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Kshitij Srivastava, Anne-Sophie Fratzscher, Bo Lan, Willy Albert Flegel
Summary: This study identified long reference sequences by analyzing homozygous genomic regions in the 1000 Genomes Project database. A total of 902 ACKR1 haplotypes of varying lengths were confirmed, with the longest being 80,584 nucleotides and the shortest being 1,901 nucleotides. The approach of using tracts of homozygosity for definitive reference sequences is scalable and can be applied to any gene.
BMC BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Min-Ah Sun, Hyun Min Sung, Jisun Kim, Jae-Hee Lee, Sungbo Shim, Young-Hwa Byun
Summary: The East Asian summer monsoon is expected to increase in precipitation and duration under future global warming levels, with a higher frequency of strong rainfall events. This has implications for water management and climate policies in the region.
Article
Geosciences, Multidisciplinary
Ningyuan Zhao, Lingyun Ji, Wenting Zhang, Xiaoxue Xu, Jinshuo Wang
Summary: In recent years, frequent earthquakes of high seismic hazard have been occurring on the southeastern edge of the Tibetan Plateau. Due to its remote location, there have been no high-resolution geodetic measurements of the Ganzi-Yushu fault zone. This study used InSAR and GNSS data to analyze the deformation field, fault slip rate, and seismic hazard of the area, highlighting the high slip deficit and strain rate anomalies in the Dangjiang and Dengke segments.
FRONTIERS IN EARTH SCIENCE
(2023)
Article
Genetics & Heredity
Shicheng Chen, Ting Yu, Nicolas Terrapon, Bernard Henrissat, Edward D. Walker
Summary: Asaia bacteria play a key role in the microbiome of many mosquito species, potentially delivering antimalaria or antivirus effectors through paratransgenesis. Strain W12 has the largest genome size among Asaia species, with more glycoside hydrolase-encoding genes and predicted regulatory protein components, indicating its potential for plant biomass degradation and adaptation to environmental changes in the mosquito gut. Additionally, Asaia sp. W12 carries genes involved in the production of 2,3-butandiol and inositol, possibly contributing to biofilm formation and stress tolerance.
Article
Metallurgy & Metallurgical Engineering
Peng LI, Qi-Feng Guo, Mei-Feng Cai, Sheng-Jun Miao
Summary: To investigate the present-day state of tectonic stress and tectonization in a coastal gold mine area, three different stress measurement methods were used, and 49 groups of stress data were determined. The results show that horizontal tectonic stress dominates the present-day stress field, favoring thrust and strike-slip faulting. The stress level is relatively high, posing challenges for underground excavations. The contemporary stress field is the result of dynamic action and tectonic movement in various geological periods.
TRANSACTIONS OF NONFERROUS METALS SOCIETY OF CHINA
(2023)
Article
Biotechnology & Applied Microbiology
Youli Li, Min Gu, Xuanzhe Liu, Jianna Lin, Huier Jiang, Huiyun Song, Xingcui Xiao, Wei Zhou
Summary: This study sequenced and compared the mitochondrial genomes of Toona sinensis and Toona ciliata, and analyzed their repetitive sequences in comparison with the chloroplast genome. Phylogenetic analysis revealed the evolutionary relationship between these two species.
Article
Microbiology
J. F. Freitas, D. F. L. Silva, B. S. Silva, J. N. F. Castro, M. B. M. C. Felipe, R. C. B. Silva-Portela, C. F. Minnicelli, L. F. Agnez-Lima
Summary: In this study, nine isolates with the ability to grow with petroleum as the only carbon source and emulsify kerosene were identified as a new subspecies of Acinetobacter baumannii. These isolates possess the potential to degrade hydrocarbons and produce biosurfactants or bioemulsifiers, which could be deployed for bioremediation strategies.
MICROBIOLOGICAL RESEARCH
(2023)
Article
Genetics & Heredity
Alejandro Blanco-Verea, Brais Pineiro, Rocio Gil, Eva Ramos-Luis, Maria Alvarez-Barredo, Bernardo Lopez-Abel, Beatriz Sobrino, Jorge Amigo, Jose Ramon Gonzalez-Juanatey, Angel Carracedo, Maria Brion
Summary: This study used a cardiac gene panel for sequencing and ExomeDepth software for copy number variation (CNV) detection. After a rigorous prioritization process, three real CNVs were confirmed in five individuals in the MYH11, FBN1, and PDMI7 genes. Based on Bayes factors, BF values above 60 were established as the threshold for considering real CNVs in the calling process carried out by ExomeDepth on our gene panel.
MOLECULAR DIAGNOSIS & THERAPY
(2023)
Review
Geriatrics & Gerontology
Laura Navarro, Alberto Gomez-Carballa, Sara Pischedda, Julian Montoto-Louzao, Sandra Viz-Lasheras, Alba Camino-Mera, Thomas Hinault, Federico Martinon-Torres, Antonio Salas
Summary: This study systematically reviewed the state-of-the-art of neuroscience and cognitive sciences research on music and Alzheimer's disease (AD) and found that music has beneficial effects on patients with neurodegenerative diseases, especially in memory and cognition. Transcriptomic and epigenomic data analysis also revealed connections between music-related genes and AD. These findings provide a new roadmap for genetic research and musical interventions in AD and other neurodegenerative conditions.
FRONTIERS IN AGING NEUROSCIENCE
(2023)
Article
Pediatrics
Benno Kohlmaier, Manuel Leitner, Nienke N. Hagedoorn, Dorine M. Borensztajn, Ulrich von Both, Enitan D. Carrol, Marieke Emonts, Michiel van der Flier, Ronald de Groot, Jethro Herberg, Michael Levin, Emma Lim, Ian K. Maconochie, Federico Martinon-Torres, Ruud G. Nijman, Marko Pokorn, Irene Rivero-Calle, Chantal D. Tan, Maria Tsolia, Clementien L. Vermont, Joany M. Zachariasse, Dace Zavadska, Henriette A. Moll, Werner Zenz
Summary: This study investigated febrile children with petechial rashes who presented to European emergency departments and found that children with a combination of fever and petechial rash were more likely to have sepsis, meningitis, bacterial infections, and require immediate life-saving interventions and intensive care unit admissions. Therefore, the combination of fever and petechial rash is still an important warning sign for childhood sepsis and meningitis.
Article
Pediatrics
Ruud G. Nijman, Chantal D. Tan, Nienke N. Hagedoorn, Daan Nieboer, Jethro Adam Herberg, Anda Balode, Ulrich von Both, Enitan D. Carrol, Irini Eleftheriou, Marieke Emonts, Michiel van der Flier, Ronald de Groot, Benno Kohlmaier, Emma Lim, Federico Martinon-Torres, Marko Pokorn, Franc Strle, Maria Tsolia, Shunmay Yeung, Joany M. Zachariasse, Dace Zavadska, Werner Zenz, Michael Levin, Clementien L. Vermont, Henriette A. Moll, Ian K. Maconochie
Summary: This study aimed to describe the characteristics and clinical outcomes of children with fever lasting >= 5 days presenting to emergency departments. The study found that children with prolonged fever have a higher risk of serious bacterial infection (SBI). However, warning signs of SBI were observed infrequently, highlighting the need for careful clinical assessment and diagnostic workup.
ARCHIVES OF DISEASE IN CHILDHOOD
(2023)
Letter
Respiratory System
Sonia Ares-Gomez, Narmeen Mallah, Jacobo Pardo-Seco, Victoria Nartallo-Penas, Susana Miras-Carballal, Carmen Rodriguez-Tenreiro-Sanchez, Irene Rivero-Calle, Marta Pineiro-Sotelo, Carmen Duran-Parrondo, Federico Martinon-Torres
ARCHIVOS DE BRONCONEUMOLOGIA
(2023)
Review
Respiratory System
Federico Martinon-Torres, Jose Antonio Navarro-Alonso, Maria Garces-Sanchez, Antoni Soriano-Arandes
Summary: This article summarizes the efforts being made across the globe to accommodate new RSV immunization options and provides recommendations organized around five priorities. Spain has been a notable example of converting RSV prevention into a national desideratum.
ARCHIVOS DE BRONCONEUMOLOGIA
(2023)
Article
Infectious Diseases
T. Pumarola, J. Diez-Domingo, F. Martinon-Torres, E. Redondo Margueello, R. Ortiz de Lejarazu Leonardo, M. Carmo, G. Bizouard, G. Drago, J. L. Lopez-Belmonte, H. Bricout, C. De Courville, A. Gil-de-Miguel
Summary: This study estimated the clinical and economic burden of severe influenza in Spain using statistical models. The results showed that there is a significant under-detected burden of influenza, especially in the elderly population. The average annual cost of influenza-related hospitalizations was 45.7 million euros, and the average annual mortality rate due to influenza was 27.7 per 100,000 people.
BMC INFECTIOUS DISEASES
(2023)
Article
Medicine, General & Internal
Timo Hess, Carlo Maj, Jan Gehlen, Oleg Borisov, Stephan L. Haas, Ines Gockel, Michael Vieth, Guillaume Piessen, Hakan Alakus, Yogesh Vashist, Carina Pereira, Michael Knapp, Vitalia Schueller, Alexander Quaas, Heike I. Grabsch, Jessica Trautmann, Ewa Malecka-Wojciesko, Anna Mokrowiecka, Jan Speller, Andreas Mayr, Julia Schroeder, Axel M. Hillmer, Dominik Heider, Florian Lordick, Angeles Perez-Aisa, Rafael Campo, Jesus Espinel, Fernando Geijo, Concha Thomson, Luis Bujanda, Federico Sopena, Angel Lanas, Maria Pellise, Claudia Pauligk, Thorsten Oliver Goetze, Carolin Zelck, Julian Reingruber, Emadeldin Hassanin, Peter Elbe, Sandra Alsabeah, Mats Lindblad, Magnus Nilsson, Nicole Kreuser, Rene Thieme, Francesca Tavano, Roberta Pastorino, Dario Arzani, Roberto Persiani, Jin-On Jung, Henrik Nienhueser, Katja Ott, Ralf R. Schumann, Oliver Kumpf, Susen Burock, Volker Arndt, Anna Jakubowska, Malgorzta Lawniczak, Justyna Dabrowska, Olivier Cussenot, Anne Boland-Auge, Delphine Daian, Jean-Francois Deleuze, Erika Salvi, Maris Teder-Laving, Gianluca Tomasello, Margherita Ratti, Chiara Senti, Valli De Re, Agostino Steffan, Arnulf H. Hoelscher, Katharina Messerle, Christiane Josephine Bruns, Armands Sivins, Inga Bogdanova, Jurgita Skieceviciene, Justina Arstikyte, Markus Moehler, Hauke Lang, Peter P. Grimminger, Martin Kruschewski, Nikolaos Vassos, Claus Schildberg, Philipp Lingohr, Karsten Ridwelski, Hans Lippert, Nadine Fricker, Peter Krawitz, Per Hoffmann, Markus M. Noethen, Lothar Veits, Jakob R. Izbicki, Adrianna Mostowska, Federico Martinon-Torres, Daniele Cusi, Rolf Adolfsson, Geraldine Cancel-Tassin, Aksana Hoeblinger, Ernst Rodermann, Monika Ludwig, Gisela Keller, Andres Metspalu, Hermann Brenner, Joerg Heller, Markus Neef, Michael Schepke, Franz Ludwig Dumoulin, Lutz Hamann, Renato Cannizzaro, Michele Ghidini, Dominik Plassmann, Michael Geppert, Peter Malfertheiner, Olivier Gehlen, Tomasz Skoczylas, Marek Majewski, Jan Lubinski, Orazio Palmieri, Stefania Boccia, Anna Latiano, Nuria Aragones, Thomas Schmidt, Mario Dinis-Ribeiro, Rui Medeiros, Salah-Eddin Al-Batran, Marcis Leja, Juozas Kupcinskas, Maria A. Garcia-Gonzalez, Marino Venerito, Johannes Schumachera
Summary: This study characterized the genetic risk architecture of gastric cancer (GC) and its subtypes, and found that GC is genetically heterogenous. It also revealed the shared genetic aetiology between cardia GC and oesophageal adenocarcinoma (OAC) and its precursor lesion Barrett's oesophagus (BO).
Editorial Material
Immunology
Siddhartha Sankar Datta, Federico Martinon-Torres, Nino Berdzuli, Niyazi Cakmak, Michael Edelstein, Simon Cottrell, Mark Muscat
Summary: Universal immunization greatly reduces the incidence and mortality of vaccine-preventable diseases. However, routine immunization coverage varies significantly between countries, populations, and districts, and has even declined in some cases. Insufficient immunization coverage leads to susceptible individuals and outbreaks of vaccine-preventable diseases. The European Immunization Agenda 2030 aims to promote equity in immunization and assist stakeholders in addressing local challenges to improve overall health in the WHO European Region.
Article
Medicine, General & Internal
Harsita Patel, Amalia Sintou, Rasheda A. Chowdhury, Stephen Rothery, Alma Octavia Iacob, Sanjay Prasad, Peter P. Rainer, Federico Martinon-Torres, Vanessa Sancho-Shimizu, Chisato Shimizu, Kirsten Dummer, Adriana H. Tremoulet, Jane C. Burns, Susanne Sattler, Michael Levin
Summary: This study investigated the presence of anticardiac autoantibodies in MIS-C or COVID-19 vaccine-induced myocarditis and found no evidence of antibody binding to cardiac tissue in these conditions. This suggests that the cardiac pathology in MIS-C and vaccine-induced myocarditis is unlikely to be driven by direct anticardiac antibody-mediated mechanisms.
Article
Ethics
Fabian J. S. van der Velden, Emma Lim, Lily Gills, Jasmin Broadey, Louise Hayes, Eve Roberts, Jack Courtney, Joanne Ball, Jethro Herberg, Rachel Galassini, Marieke Emonts, DIAMONDS consortium
Summary: This study explores the views and knowledge of children and young people in the UK regarding biobanking and consent. The findings suggest that most children accept prospective and deferred consent, and prefer to reconsent when cognitively mature enough. Additionally, children wanted to be informed about the reuse of their biobanked biospecimens.
BMC MEDICAL ETHICS
(2023)
Article
Biotechnology & Applied Microbiology
Antonio Salas, Irene Rivero-Calle, Federico Martinon-Torres
Summary: Vaccine hesitancy is considered a top global health threat by the WHO. This study investigates the ability of the AI chatbot ChatGPT to generate opinions on vaccine hesitancy by examining its response to prevalent false information, contraindications, and myths about vaccine safety circulating on the internet. The findings suggest that while ChatGPT's default responses may be incomplete, they are generally satisfactory and have the potential to guide users towards scientifically aligned information, though it cannot replace experts or scientific evidence itself.
HUMAN VACCINES & IMMUNOTHERAPEUTICS
(2023)
Article
Multidisciplinary Sciences
Esther Willems, Jolein Gloerich, Anouk Suppers, Michiel van der Flier, Lambert P. van den Heuvel, Nicole van de Kar, Ria H. L. A. Philipsen, Maurice van Dael, Myrsini Kaforou, Victoria J. Wright, Jethro A. Herberg, Federico Martinon Torres, Michael Levin, Ronald de Groot, Alain J. van Gool, Dirk J. Lefeber, Hans J. C. T. Wessels, Marien I. de Jonge
Summary: Mechanisms of infection and pathogenesis have mainly focused on differential gene or protein expression, with less emphasis on posttranslational modifications. In this study, a novel glycoproteomics approach was applied to investigate systemic proteome-wide glycosylation in response to infection. Through characterization of site-specific protein glycosylation in plasma samples from controls and patients, a glycopeptide signature was identified that could significantly differentiate between bacterial and viral infections. Additionally, machine learning algorithm-based analysis demonstrated the ability to identify the causative pathogens based on distinct host blood plasma glycopeptide signatures. These findings highlight the potential of glycoproteomics as an innovative approach to enhance the interpretation of relevant biological changes during infection.
Article
Genetics & Heredity
Daniel Lopez-Lopez, Gema Roldan, Jose Fernandez-Rueda, Gerrit Bostelmann, Rosario Carmona, Virginia Aquino, Javier Perez-Florido, Francisco Ortuno, Guillermo Pita, Rocio Nunez-Torres, Anna Gonzalez-Neira, Maria Pena-Chilet, Joaquin Dopazo
Summary: SPACNACS is a collaborative database that collects copy number variation data from more than 400 genomes and exomes of unrelated Spanish individuals. It provides detailed information on the local genetic variability and can be used for disease gene discovery and pharmacogenomics research.
