Article
Multidisciplinary Sciences
Sarah Willkomm, Leonhard Jakob, Kevin Kramm, Veronika Graus, Julia Neumeier, Gunter Meister, Dina Grohmann
Summary: Human Argonaute 2 (hAgo2) plays a key role in the RNA interference pathway. Through single-molecule FRET measurements, this study provides detailed insights into the conformational states and dynamics of hAgo2 and its RNA complexes, revealing how their flexibility determines the function and fate of the ribonucleoprotein particle.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Dafni A. Glinos, Garrett Garborcauskas, Paul Hoffman, Nava Ehsan, Lihua Jiang, Alper Gokden, Xiaoguang Dai, Francois Aguet, Kathleen L. Brown, Kiran Garimella, Tera Bowers, Maura Costello, Kristin Ardlie, Ruiqi Jian, Nathan R. Tucker, Patrick T. Ellinor, Eoghan D. Harrington, Hua Tang, Michael Snyder, Sissel Juul, Pejman Mohammadi, Daniel G. MacArthur, Tuuli Lappalainen, Beryl Cummings
Summary: Regulation of transcript structure has a significant impact on transcript diversity and human disease. This study presents a large human long-read RNA-seq dataset, which allows for the analysis of the effects of genetic variation on transcript structure. Through allele-specific analysis of long reads, the researchers identified novel transcripts, characterized allele-specific expression and transcript structure events, and gained new insights into the impact of common and rare genetic variants on transcript alterations. The study also highlighted the regulatory effects modified by the cellular environment and enhanced variant interpretation for aberrant splicing patterns caused by rare variants.
Article
Multidisciplinary Sciences
Sergey Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche, Samantha Zarate, Pavel Avdeyev, Dylan J. Taylor, Kishwar Shafin, Alaina Shumate, Chunlin Xiao, Justin Wagner, Jennifer McDaniel, Nathan D. Olson, Michael E. G. Sauria, Mitchell R. Vollger, Arang Rhie, Melissa Meredith, Skylar Martin, Joyce Lee, Sergey Koren, Jeffrey A. Rosenfeld, Benedict Paten, Ryan Layer, Chen-Shan Chin, Fritz J. Sedlazeck, Nancy F. Hansen, Danny E. Miller, Adam M. Phillippy, Karen H. Miga, Rajiv C. McCoy, Megan Y. Dennis, Justin M. Zook, Michael C. Schatz
Summary: Compared to its predecessors, the Telomere-to-Telomere CHM13 genome has significant improvements in sequence length and structural accuracy, enabling more comprehensive study of the human genome. The application of the T2T-CHM13 reference has demonstrated improved accuracy in read mapping and variant calling for globally diverse samples, leading to the discovery of previously unresolved variants and the removal of false positives. These advancements position T2T-CHM13 as a potential replacement for GRCh38 as the dominant reference for human genetics.
Article
Engineering, Environmental
Wenshi Zhang, Hao Jiang, Wenjing Guo, Shen Li, Quanfa Zhang
Summary: This study integrated river isotopes, 15N pairing experiments, and qPCR to reveal the processes driving the high NO3- levels in a nearly pristine forest river on the Qinghai-Tibet Plateau. The river isotopes suggested that, at the catchment scale, NO3- removal was prevalent in summer, but weak in winter. The release of soil NO3- to the river was transport-limited in both seasons, which resulted in the consistently high NO3- levels.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Environmental Sciences
Federico Girolametti, Monica Panfili, Sabrina Colella, Emanuela Frapiccini, Anna Annibaldi, Silvia Illuminati, Mauro Marini, Cristina Truzzi
Summary: In this study, the total mercury (THg) levels were analyzed in European hake caught in the northern and central Adriatic Sea. The study found that there were no sex-related differences in THg levels in muscle, but significant season-related differences were observed in females. It also found a correlation between THg level and body size, sexual maturity, and lipid content. However, the THg concentration in hake fillets was consistently below the EU regulations, indicating that they are safe for human consumption.
MARINE POLLUTION BULLETIN
(2022)
Article
Endocrinology & Metabolism
Cecilia Legare, Andree-Anne Clement, Veronique Desgagne, Kathrine Thibeault, Frederique White, Simon-Pierre Guay, Benoit J. Arsenault, Michelle S. Scott, Pierre-Etienne Jacques, Patrice Perron, Renee Guerin, Marie-France Hivert, Luigi Bouchard
Summary: In this study, we identified 191 circulating miRNAs specific to pregnancy and 57 miRNAs that varied with gestational age during the first trimester. These miRNAs target biological pathways involved in fatty acid metabolism, ECM-receptor interaction, and TGF-beta signaling, indicating their role in maternal metabolic adaptation and fetal growth during pregnancy.
REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Michael Thane, Emmanouil Paisios, Torsten Stoeter, Anna-Rosa Krueger, Sebastian Glaess, Anne-Kristin Dahse, Nicole Scholz, Bertram Gerber, Dirk J. Lehmann, Michael Schleyer
Summary: This study introduces the IMBA, a tool for analyzing the behavior of individual larvae within groups. The authors use this tool to systematically describe the variability in locomotion of wild-type animals and how it is reduced by associative learning. They also report a novel locomotion phenotype of an adhesion GPCR mutant and investigate the modulation of locomotion by dopamine neurons and optogenetic activation of specific neurons.
Article
Multidisciplinary Sciences
Patrick F. Sullivan, Jennifer R. S. Meadows, Steven Gazal, BaDoi N. Phan, Xue Li, Diane P. Genereux, Michael X. Dong, Matteo Bianchi, Gregory Andrews, Sharadha Sakthikumar, Jessika Nordin, Ananya Roy, Matthew J. Christmas, Voichita D. Marinescu, Chao Wang, Ola Wallerman, James Xue, Shuyang Yao, Quan Sun, Jin Szatkiewicz, Jia Wen, Laura M. Huckins, Alyssa Lawler, Kathleen C. Keough, Zhili Zheng, Jian Zeng, Naomi R. Wray, Yun Li, Jessica Johnson, Jiawen Chen, Benedict Paten, Steven K. Reilly, Graham M. Hughes, Zhiping Weng, Katherine S. Pollard, Andreas R. Pfenning, Karin Forsberg-Nilsson, Elinor K. Karlsson, Kerstin Lindblad-Toh
Summary: Thousands of genomic regions associated with heritable human diseases are difficult to study due to a lack of understanding of which genomic positions are functionally important.
Article
Biochemistry & Molecular Biology
Jana M. Flury, Alexander Haas, Rafe M. Brown, Indraneil Das, Yong Min Pui, Kueh Boon-Hee, Ulrich Scheidt, Djoko T. Iskandar, Andre Jankowski, Stefan T. Hertwig
Summary: One of the most urgent tasks for taxonomists and evolutionary biologists today is to estimate the number of species on earth. The study on Occidozyga frogs in Southeast Asia revealed a surprisingly high level of genetic diversity, suggesting that species diversity in this group may have been underestimated. Further research is needed to understand the geographical structure and diversification in this amphibian clade.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Trevor N. Clark, Joelle Houriet, Warren S. Vidar, Joshua J. Kellogg, Daniel A. Todd, Nadja B. Cech, Roger G. Linington
Summary: Despite challenges in comparing untargeted metabolomics data between laboratories, this study found that data sets with low feature overlap can still yield similar qualitative descriptions using PCA. Differences in fragmentation, charge state, and adduct formation in the ionization source were identified as major factors causing discrepancies in the data sets.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Biochemistry & Molecular Biology
Margaux L. A. Hujoel, Maxwell A. Sherman, Alison R. Barton, Ronen E. Mukamel, Vijay G. Sankaran, Chikashi Terao, Po-Ru Loh
Summary: A computational approach leveraging haplotype sharing in biobank cohorts was developed to detect CNVs more sensitively, leading to insights into the genetic basis of human complex traits. Applied to UK Biobank, this approach identified multiple gene-trait relationships.
Article
Multidisciplinary Sciences
Wouter Steyaert, Lonneke Haer-Wigman, Rolph Pfundt, Debby Hellebrekers, Marloes Steehouwer, Juliet Hampstead, Elke de Boer, Alexander Stegmann, Helger Yntema, Erik-Jan Kamsteeg, Han Brunner, Alexander Hoischen, Christian Gilissen
Summary: This paper presents a method called "Chameleolyser" that accurately identifies variants in duplicated genomic regions. Application of this method to a large cohort of exome samples led to the identification of a significant number of rare variants, including those that resulted in direct molecular diagnoses for previously undiagnosed patients.
NATURE COMMUNICATIONS
(2023)
Article
Meteorology & Atmospheric Sciences
Dapeng Zhang, Yanyan Huang, BoTao Zhou, Huijun Wang
Summary: The study found that the South Asian high (SAH) has weakened after the late 1970s, a trend also observed in observational data. The weakening of the SAH is associated with a southward shift of the East Asian westerly jet, increased ascending motion over the Yangtze River valley, and increased descending motion over North China.
JOURNAL OF CLIMATE
(2021)
Article
Zoology
Brian L. Sidlauskas, Fernando M. Assega, Bruno F. Melo, Claudio Oliveira, Jose L. O. Birindelli
Summary: The Anostomidae family is one of the most diverse families of Neotropical freshwater fishes, and the genus Anostomoides has recently been revised to include two valid species with different phylogenetic histories.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Multidisciplinary Sciences
Vivek K. Bajpai, Tomek Swigut, Jaaved Mohammed, Sahin Naqvi, Martin Arreola, Josh Tycko, Tayne C. Kim, Jonathan K. Pritchard, Michael C. Bassik, Joanna Wysocka
Summary: This study identified 169 genes associated with skin pigmentation, 135 of which were previously unknown. These genes are up-regulated in melanocytes from darkly pigmented individuals and are involved in melanosome biogenesis, endosomal transport, and gene regulation. The study also revealed the functions of KLF6 and COMMD3 in melanosome maturation and melanosomal pH regulation.
Article
Biochemistry & Molecular Biology
Macarena Lopez-Sanchez, Carlos Loucera, Maria Pena-Chilet, Joaquin Dopazo
Summary: Recent studies have shown the importance of host genetics in the prognosis of COVID-19. This study used a mathematical mechanistic model to identify potential interactions between rare disease genes and the COVID-19 infection process. Out of the analyzed disease genes, 254 genes directly affect the COVID-19 molecular disease mechanism and 207 genes have an indirect effect. These findings suggest the potential for preventive measures in some rare diseases based on the links between disease genes and COVID-19 hallmarks.
HUMAN MOLECULAR GENETICS
(2022)
Article
Multidisciplinary Sciences
Katharina Dulias, M. George B. Foody, Pierre Justeau, Marina Silva, Rui Martiniano, Gonzalo Oteo-Garcia, Alessandro Fichera, Simao Rodrigues, Francesca Gandini, Alison Meynert, Kevin Donnelly, Timothy J. Aitman, Andrew Chamberlain, Olivia Lelong, George Kozikowski, Dominic Powlesland, Clive Waddington, Valeria Mattiangeli, Daniel G. Bradley, Jaroslaw Bryk, Pedro Soares, James F. Wilson, Graeme Wilson, Hazel Moore, Maria Pala, Ceiridwen J. Edwards, Martin B. Richards
Summary: During the Neolithic period, Orkney was a major cultural center with flourishing farming and long-range contacts. New genomic evidence shows significant inward migration during the Bronze Age, but most of the male lineages originated from the local Neolithic period. Meanwhile, there is evidence of continuity in the female line of descent from the Mesolithic period to the present day.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Mathematical & Computational Biology
Pelin Gundogdu, Carlos Loucera, Inmaculada Alamo-Alvarez, Joaquin Dopazo, Isabel Nepomuceno
Summary: In this study, a pathway-driven neural network was proposed to successfully solve cell-type related problems at single-cell resolution and provide a biologically meaningful representation of scRNA-seq data. The integration of pathways and deep neural networks resulted in a superior performance compared to other similar approaches. The use of pathways within the network structure also allowed for easy interpretability of the results.
Article
Genetics & Heredity
Maria Gonzalez-del Pozo, Elena Fernandez-Suarez, Nereida Bravo-Gil, Cristina Mendez-Vidal, Marta Martin-Sanchez, Enrique Rodriguez-de la Rua, Manuel Ramos-Jimenez, Maria Jose Morillo-Sanchez, Salud Borrego, Guillermo Antinolo
Summary: This study aims to define a WGS-based algorithm for interpreting variants in inherited retinal dystrophies (IRD). Through data analysis and filtering, the optimal tool combinations were identified and a candidate gene was successfully identified. This translational strategy is essential for the advancement of personalized medicine.
NPJ GENOMIC MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Pilar Puerto-Camacho, Juan Diaz-Martin, Joaquin Olmedo-Pelayo, Alfonso Bolado-Carrancio, Carmen Salguero-Aranda, Carmen Jordan-Perez, Marina Esteban-Medina, Inmaculada Alamo-Alvarez, Daniel Delgado-Bellido, Laura Lobo-Selma, Joaquin Dopazo, Ana Sastre, Javier Alonso, Thomas G. P. Gruenewald, Carmelo Bernabeu, Adam Byron, Valerie G. Brunton, Ana Teresa Amaral, Enrique De Alava
Summary: This study found that the expression of endoglin (ENG) and matrix metalloproteinase 14 (MMP14) is significantly associated with poor prognosis in Ewing sarcoma (ES) patients. Further experiments demonstrated the key role of ENG and MMP14 in cell mechanotransduction and their impact on migration and adhesion in ES cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Biochemical Research Methods
Salvador Capella-Gutierrez, Eva Alloza, Laura Rubinat-Ripoll, Ana Conesa, Alfonso Valencia
Article
Immunology
Nadia Madrid-Elena, Sergio Serrano-Villar, Carolina Gutierrez, Beatriz Sastre, Matias Morin, Laura Luna, Laura Martin, Javier Santoyo-Lopez, Maria Rosa Lopez-Huertas, Elena Moreno, Maria Laura Garcia-Bermejo, Miguel Angel Moreno-Pelayo, Santiago Moreno
Summary: This study demonstrates that modulation of miRNA expression in T cells enhances specific cytotoxic immune responses to HIV, providing a new approach for achieving HIV remission.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Lynne Hocking, Claire Andrews, Christine Armstrong, Morad Ansari, David Baty, Jonathan Berg, Therese Bradley, Caroline Clark, Austin Diamond, Jill Doherty, Anne Lampe, Ruth McGowan, David Moore, Dawn O'Sullivan, Andrew Purvis, Javier Santoyo-Lopez, Paul Westwood, Michael Abbott, Nicola J. Williams, Zosia Scottish Genomes Partnership, Timothy Aitman, Zosia Miedzybrodzka
Summary: Scottish NHS genetics centres investigated the diagnostic utility of the Genomics England 100,000 Genomes Project for rare, inherited conditions. Genome sequencing with gene panel filtering and reporting showed improved diagnostic yield compared to previous testing, but not compared to routine trio-exome sequence tests. Re-interpretation of genomic data using updated gene panels modestly increased diagnostic yield. Efficient methods for analyzing structural variation or decreased costs are needed to justify the additional expense of genome sequencing over exome sequencing.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Cankut Cubuk, Carlos Loucera, Maria Pena-Chilet, Joaquin Dopazo
Summary: Reprogramming metabolism is a key feature of cancer, and recent research suggests that metabolites may play a crucial role in regulating signaling pathways. Mechanistic models were used to analyze the metabolic and signaling pathway activities of Breast invasive Carcinoma (BRCA), and Gaussian Processes combined with SHapley Additive exPlanations (SHAP) were employed to identify potential causal relationships between metabolite production and signaling pathway regulation. A total of 317 metabolites were found to significantly impact signaling circuits, revealing a complex crosstalk between signaling and metabolic pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Pharmacology & Pharmacy
Rocio Nunez-Torres, Guillermo Pita, Maria Pena-Chilet, Daniel Lopez-Lopez, Jorge Zamora, Gema Roldan, Belen Herraez, Nuria Alvarez, Maria Rosario Alonso, Joaquin Dopazo, Anna Gonzalez-Neira
Summary: The implementation of pharmacogenetics (PGx) is a significant milestone for achieving safer and more effective therapies in precision medicine. However, the adoption of PGx diagnostics is slow and unequal worldwide, partly due to the lack of ethnic-specific PGx information. Genetic data from 3006 Spanish individuals were analyzed, revealing allele frequencies and putative deleterious variants for main PGx genes. A comparison of high-throughput diagnostic techniques indicated that genotyping with the PGx HT array is the most suitable solution. The integrated information is made available through the Collaborative Spanish Variant Server for the scientific community.
Article
Biology
Pelin Gundogdu, Inmaculada Alamo, Isabel A. Nepomuceno-Chamorro, Joaquin Dopazo, Carlos Loucera
Summary: Single-cell data enables the study of cell dynamics at unprecedented resolution. SigPrimedNet is a data-driven solution that identifies cells and learns the functional summarization of signaling measurements.
Article
Biochemistry & Molecular Biology
Miriam Paya-Milans, Maria Pena-Chilet, Carlos Loucera, Marina Esteban-Medina, Joaquin Dopazo
Summary: Soft tissue sarcoma is a group of rare and difficult-to-treat cancers, and the study shows that computational analysis of gene expression data can reveal the importance of signaling pathways in patient survival. Thirteen signaling circuits were identified as predictors of patient survival, and the protective role of the immune system in the tumor microenvironment and potential therapeutic strategies were also described.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Anthony M. Vandersteen, Ruwan A. Weerakkody, David A. Parry, Christina Kanonidou, Daniel J. Toddie-Moore, Jana Vandrovcova, Rebecca Darlay, Javier Santoyo-Lopez, Alison Meynert, Hanadi NIHR BioResource, Hanadi Kazkaz, Rodney Grahame, Carole Cummings, Marion Bartlett, Neeti Ghali, Angela F. Brady, F. Michael Pope, Fleur S. van Dijk, Heather J. Cordell, Timothy J. Aitman
Summary: Through the clinical application of large panel-based sequencing and WES, we are able to distinguish rare subtypes of complex EDS, LDS, and related syndromes, and identify novel candidate genes and pathways for hEDS and HTAD.
JOURNAL OF MEDICAL GENETICS
(2023)
Article
Virology
Carlos Loucera, Rosario Carmona, Marina Esteban-Medina, Gerrit Bostelmann, Dolores Munoyerro-Muniz, Roman Villegas, Maria Pena-Chilet, Joaquin Dopazo
Summary: This study utilized data from the Andalusian Population Health Database to investigate the relationship between prior drug consumption and patient outcomes in COVID-19. It identified 21 drugs associated with better patient survival and effectively controlled covariates.
Article
Biochemistry & Molecular Biology
Javier Perez-Florido, Carlos S. Casimiro-Soriguer, Francisco Ortuno, Jose L. Fernandez-Rueda, Andrea Aguado, Maria Lara, Cristina Riazzo, Manuel A. Rodriguez-Iglesias, Pedro Camacho-Martinez, Laura Merino-Diaz, Inmaculada Pupo-Ledo, Adolfo de Salazar, Laura Vinuela, Ana Fuentes, Natalia Chueca, Federico Garcia, Joaquin A. Dopazo, Jose Lepe
Summary: Recombination is an evolutionary strategy to acquire new viral properties quickly. The Andalusian genomic surveillance strategy has revealed a high number of co-infections, providing an ideal setting for the emergence of new recombinants. Whole genome sequencing of SARS-CoV-2 has been conducted, detecting three novel recombinant variants with two break points. The increased frequency of co-infection and recombination raises the risk of recombinant variants with increased transmissibility and pathogenicity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)