Article
Biotechnology & Applied Microbiology
Christina M. Dauben, Maren J. Proll-Cornelissen, Esther M. Heuss, Anne K. Appel, Hubert Henne, Katharina Roth, Karl Schellander, Ernst Tholen, Christine Grosse-Brinkhaus
Summary: The study identified genomic regions associated with immune relevant traits in Landrace (LR) and Large White (LW) piglets, with differences between the two maternal pig lines and relevant candidate genes. The results partly align with previously identified quantitative trait loci (QTL) regions, and novel genomic regions were also identified for further analysis. The study suggests a polygenic and breed-specific background of immune relevant traits, providing insights for breeding-based modification of the porcine immune system.
Article
Biotechnology & Applied Microbiology
Katharina Roth, Maren Julia Proell-Cornelissen, Hubert Henne, Anne Kathrin Appel, Karl Schellander, Ernst Tholen, Christine Grosse-Brinkhaus
Summary: This study evaluated the joint genetic background of immune traits in Landrace and Large White pigs through the application of various univariate and multivariate genome-wide association study approaches. Compared to univariate methods, multivariate methodologies identified more significant associations, which might reflect the pleiotropic background of the immune system more accurately.
Article
Biochemistry & Molecular Biology
Sarah L. Fong, John A. Capra
Summary: The study revealed that simple enhancers are younger, more functionally diverse, and more active across species, while complex enhancers are older, less likely to associate with human traits and biochemical activity. Transposable-element-derived sequences contribute to enhancers of both architectures, with the majority found in simple enhancers.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Ulykbek Kairov, Askhat Molkenov, Aigul Sharip, Saule Rakhimova, Madina Seidualy, Arang Rhie, Ulan Kozhamkulov, Maxat Zhabagin, Jong-Il Kim, Joseph H. Lee, Joseph D. Terwilliger, Jeong-Sun Seo, Zhaxybay Zhumadilov, Ainur Akilzhanova
Summary: Kazakhstan, located along the Great Silk Road, has a rich history and a multiethnic population. By sequencing and analyzing the genomes of five ethnic Kazakhs, this study identified genetic variants associated with higher risks of diseases and demonstrated the importance of genotype-phenotype relations at the population level.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Zhiquan Yang, Chengfang Luo, Xinxin Pei, Shengbo Wang, Yiming Huang, Jiawei Li, Baohui Liu, Fanjiang Kong, Qing-Yong Yang, Chao Fang
Summary: This study collects and integrates a comprehensive set of multi-omics datasets to establish a user-friendly database called SoyMD. It provides efficient query options and analysis tools, highlighting its potential in soybean genetic breeding and functional genomics research.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Wei Liang Andre Tan, Laercio Ribeiro Porto Neto, Antonio Reverter, Michael McGowan, Marina Rufino Salinas Fortes
Summary: This study conducted genome-wide association analyses using sequence-level data targeting seven bull production and fertility traits in a multi-breed population of 6,422 tropically adapted bulls. The study identified genetic variants and candidate genes associated with these traits, highlighting the highly polygenic nature of the traits and significant results across the genome.
Article
Biotechnology & Applied Microbiology
Adepeju E. Onasanya, Charles El-Hage, Andres Diaz-Mendez, Paola K. Vaz, Alistair R. Legione, Glenn F. Browning, Joanne M. Devlin, Carol A. Hartley
Summary: This study analyzed the genome diversity and recombination mechanism of EHV2 virus. The results showed a high degree of genetic diversity and extensive recombination networks in EHV2 genomes. Recombination may be an important mechanism for EHV2 genome variation and evolution.
Article
Agriculture, Multidisciplinary
Wang Kai, Wu Ping-xian, Chen De-juan, Zhou Jie, Yang Xi-di, Jiang An-an, Ma Ji-deng, Tang Qian-zi, Xioa Wei-hang, Jiang Yan-zhi, Zhu Li, Qiu Xiao-tian, Li Ming-zhou, Li Xue-wei, Tang Guo-qing
Summary: A genome-wide scan was performed to detect selection signatures in the domestication process of Landrace and Yorkshire pigs, revealing that genes associated with basic metabolism, disease resistance, body morphology, and organ control were subject to selection pressure. This study provides new insights into the potential genetic variation of phenotypic diversity in different pig breeds and helps understand the selection effects of modern breeding in these pigs.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2021)
Article
Biochemistry & Molecular Biology
Bryce Rowland, Sanan Venkatesh, Manuel Tardaguila, Jia Wen, Jonathan D. Rosen, Amanda L. Tapia, Quan Sun, Mariaelisa Graff, Dragana Vuckovic, Guillaume Lettre, Vijay G. Sankaran, Georgios Voloudakis, Panos Roussos, Jennifer E. Huffman, Alexander P. Reiner, Nicole Soranzo, Laura M. Raffield, Yun Li
Summary: Using transcriptome-wide association study, this research identified numerous gene-trait associations related to hematological traits and assigned these variants to putative target genes.
HUMAN MOLECULAR GENETICS
(2022)
Article
Hematology
Paola Leon-Mimila, Hugo Villamil-Ramirez, Luis R. Macias-Kauffer, Leonor Jacobo-Albavera, Blanca E. Lopez-Contreras, Rosalinda Posadas-Sanchez, Carlos Posadas-Romero, Sandra Romero-Hidalgo, Sofia Moran-Ramos, Mayra Dominguez-Perez, Marisol Olivares-Arevalo, Priscilla Lopez-Montoya, Roberto Nieto-Guerra, Victor Acuna-Alonzo, Gaston Macin-Perez, Rodrigo Barquera-Lozano, Blanca E. Del-Rio-Navarro, Israel Gonzalez-Gonzalez, Francisco Campos-Perez, Francisco Gomez-Perez, Victor J. Valdes, Alicia Sampieri, Juan G. Reyes-Garcia, Miriam Del C. Carrasco-Portugal, Francisco J. Flores-Murrieta, Carlos A. Aguilar-Salinas, Gilberto Vargas-Alarcon, Diana Shih, Peter J. Meikle, Anna C. Calkin, Brian G. Drew, Luis Vaca, Aldons J. Lusis, Adriana Huertas-Vazquez, Teresa Villarreal-Molina, Samuel Canizales-Quinteros
Summary: The study identified a genetic variant in the SIDT2 gene associated with HDL-C levels and cardiovascular risk in Mexicans, with implications for cholesterol and lipoprotein metabolism. The SIDT2/Val636Ile variant was more common in Native American populations and linked to lower LDL-C and ApoB levels. Further investigation showed that the variant affects cholesterol transport function, highlighting SIDT2 as a new player in human lipid metabolism.
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Long Chen, Jennie E. Pryce, Ben J. Hayes, Hans D. Daetwyler
Summary: Structural variants are large DNA segments that can explain only a small percentage of phenotypic variation in dairy cattle traits. While some structural variants showed significant association with production traits, their inclusion in genomic prediction models did not significantly improve accuracy. This suggests that SNP markers remain more reliable for predicting dairy cattle traits than structural variants.
Article
Microbiology
Mauricio Flores-Valdez, Miguel A. Ares, Roberto Rosales-Reyes, Javier Torres, Jorge A. Giron, Bart C. Weimer, Alfonso Mendez-Tenorio, Miguel A. De la Cruz
Summary: Klebsiella pneumoniae is a common nosocomial pathogen causing pneumonia, septicemia, and urinary tract infections, with an increasing acquisition of antibiotic-resistance genes. Whole-genome sequencing revealed beta-lactamase genes in all isolates, with bla(SHV) variant being the most prevalent. Multi-locus sequence typing identified 24 distinct sequence types, with ST76 and ST70 being the most frequent, and serotypes O1 and O3 being the most prevalent. Phylogenomic analysis showed correlation between virulence genes and virulent serotypes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Slim Karkar, Claire Dandine-Roulland, Jean-Francois Mangin, Yann Le Guen, Cathy Philippe, Jean-Francois Deleuze, Morgane Pierre-Jean, Edith Le Floch, Vincent Frouin
Summary: Neuroimaging-genetics cohorts combine brain imaging and genetic data to explore associations between genetic variants and brain features. A genome-wide haplotype analysis was conducted for brain sulcus opening values in this study, showing that such analysis is more sensitive than single-SNP approaches. The study highlights the importance of considering complex linkage disequilibrium structures in genetic analysis of brain features.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Taiana Cortez de Souza, Tatiana Cortez de Souza, Gregori Alberto Rovadoscki, Luiz Lehmann Coutinho, Gerson Barreto Mourao, Gregorio Miguel Ferreira de Camargo, Raphael Bermal Costa, Gleidson Giordano Pinto de Carvalho, Victor Breno Pedrosa, Luis Fernando Batista Pinto
Summary: GWAS was conducted on plasma urea concentration in Santa Ines sheep, identifying several genomic regions, candidate genes, and significant pathways that could potentially be used to improve performance and health of sheep and understand nitrogen utilization and excretion.
Article
Agriculture, Dairy & Animal Science
Zezhang Liu, Hong Li, Zhuxia Zhong, Siwen Jiang
Summary: By using high-depth genomic data, this study identified TBX3 gene and the Wnt signaling pathway as being associated with teat number-related traits in Chinese native Qingping pigs. Teat number plays an important role in sow's reproductive performance and piglet growth. This research provided useful molecular markers and candidate genes for improving teat number in sow breeding.
Article
Biotechnology & Applied Microbiology
Rosa Lundbye Allesoe, Agnete Troen Lundgaard, Ricardo Hernandez Medina, Alejandro Aguayo-Orozco, Joachim Johansen, Jakob Nybo Nissen, Caroline Brorsson, Gianluca Mazzoni, Lili Niu, Jorge Hernansanz Biel, Valentas Brasas, Henry Webel, Michael Eriksen Benros, Anders Gorm Pedersen, Piotr Jaroslaw Chmura, Ulrik Plesner Jacobsen, Andrea Mari, Robert Koivula, Anubha Mahajan, Ana Vinuela, Juan Fernandez Tajes, Sapna Sharma, Mark Haid, Mun-Gwan Hong, Petra B. Musholt, Federico De Masi, Josef Vogt, Helle Krogh Pedersen, Valborg Gudmundsdottir, Angus Jones, Gwen Kennedy, Jimmy Bell, E. Louise Thomas, Gary Frost, Henrik Thomsen, Elizaveta Hansen, Tue Haldor Hansen, Henrik Vestergaard, Mirthe Muilwijk, Marieke T. Blom, Leen M. T. Hart, Francois Pattou, Violeta Raverdy, Soren Brage, Tarja Kokkola, Alison Heggie, Donna McEvoy, Miranda Mourby, Jane Kaye, Andrew Hattersley, Timothy McDonald, Martin Ridderstrale, Mark Walker, Ian Forgie, Giuseppe N. Giordano, Imre Pavo, Hartmut Ruetten, Oluf Pedersen, Torben Hansen, Emmanouil Dermitzakis, Paul W. Franks, Jochen M. Schwenk, Jerzy Adamski, Mark McCarthy, Ewan Pearson, Karina Banasik, Simon Rasmussen, Soren Brunak
Summary: The application of multiple omics technologies in biomedical cohorts can reveal patient-level disease characteristics and individualized response to treatment. We developed a deep-learning-based framework, MOVE, to integrate and analyze multi-omics data from a cohort of newly diagnosed type 2 diabetes patients. By using in silico perturbations, we identified drug-omics associations in the multi-modal datasets with higher sensitivity than univariate statistical tests.
NATURE BIOTECHNOLOGY
(2023)
Article
Neurosciences
Burak Yulug, Ozlem Altay, Xiangyu Li, Lutfu Hanoglu, Seyda Cankaya, Simon Lam, Halil Aziz Velioglu, Hong Yang, Ebru Coskun, Ezgi Idil, Rahim Nogaylar, Ahmet Ozsimsek, Cemil Bayram, Ismail Bolat, Sena Oner, Ozlem Ozdemir Tozlu, Mehmet Enes Arslan, Ahmet Hacimuftuoglu, Serkan Yildirim, Muhammad Arif, Saeed Shoaie, Cheng Zhang, Jens Nielsen, Hasan Turkez, Jan Boren, Mathias Uhlen, Adil Mardinoglu
Summary: A clinical trial was conducted to study the effect of combined metabolic activators (CMA) on Alzheimer's disease (AD) patients. The results showed that CMA can improve cognitive functions and clinical parameters associated with AD. This study provides evidence for the use of CMA in the treatment of AD.
TRANSLATIONAL NEURODEGENERATION
(2023)
Article
Mathematical & Computational Biology
Bouchra Ezzamouri, Dorines Rosario, Gholamreza Bidkhori, Sunjae Lee, Mathias Uhlen, Saeed Shoaie
Summary: The human gut microbiome plays a significant role in metabolic disorders, such as type 2 diabetes mellitus. This study investigates the mechanistic role of the gut microbiome in response to metformin treatment, using metagenomics data and genome-scale metabolic modeling. The results demonstrate the commensal and competing behavior of key bacterial species in response to metformin and highlight the impact of different nutritional environments.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Article
Medical Laboratory Technology
Franklin Ducatez, Carine Pilon, Justine Ferey, Stephane Marret, Soumeya Bekri, Abdellah Tebani
Summary: This study evaluated the impact of different hematocrit levels and punching positions on the assessment of enzyme activity in dried blood spot (DBS) samples. The results showed that hematocrit, punching position, and the use of different sampling methods did not affect the assessment of enzyme activity, indicating the reliability of DBS in this test.
CLINICA CHIMICA ACTA
(2023)
Article
Biochemistry & Molecular Biology
Maria Grazia Andreassi, Nadia Haddy, Mats Harms-Ringdahl, Jonica Campolo, Andrea Borghini, Francois Chevalier, Jochen M. Schwenk, Brice Fresneau, Stephanie Bolle, Manuel Fuentes, Siamak Haghdoost
Summary: The Health Effects of Cardiac Fluoroscopy and Modern Radiotherapy (photon and proton) in Pediatrics (HARMONIC) is a five-year project funded by the European Commission with the aim of improving understanding of long-term ionizing radiation risks for pediatric patients. This paper provides a detailed overview of the project's rationale, design, and methods for the biological aspect, with objectives to understand the molecular pathways and identify potential biomarkers involved in long-term health risks. Biological samples will be collected at three time points, and state-of-the-art analytical methods will be used to assess biomarker levels and explore proteomics and miRNA transcriptomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ilana B. Kotliar, Emilie Ceraudo, Kevin Kemelmakher-Liben, Deena A. Oren, Emily Lorenzen, Tea Dodig-Crnkovic, Mizuho Horioka-Duplix, Thomas Huber, Jochen M. Schwenk, Thomas P. Sakmar
Summary: The interaction between MRGPRX4 and RAMP2 can regulate the signaling pathway and cell surface expression of cholestatic itch, suggesting potential therapeutic implications for future drug development in treating cholestatic itch.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Andreas Hober, Mirela Rekanovic, Bjorn Forsstrom, Sara Hansson, David Kotol, Andrew J. Percy, Mathias Uhlen, Jan Oscarsson, Fredrik Edfors, Tasso Miliotis
Summary: This study presents a novel quantitative approach to determine the absolute concentration of apo(a) in two microliters of plasma using proteotypic peptides, which meets the requirements for targeted proteomics assays. The assay parameters were optimized, and the LC-SRM/MS results were compared with a commercially available immunoassay.
Article
Multidisciplinary Sciences
Leo Dahl, Ilana B. Kotliar, Annika Bendes, Tea Dodig-Crnkovic, Samuel Fromm, Arne Elofsson, Mathias Uhlen, Thomas P. Sakmar, Jochen M. Schwenk
Summary: A multiplexed immunoassay was developed to test the selectivity of over 400 anti-GPCR antibodies. The results showed that about 61% of the antibodies were selective, 11% bound off-target, and 28% did not bind to any GPCR. It was also found that on-target antibodies had longer, more disordered antigens and were less buried in the interior of GPCR proteins compared to other antibodies.
Article
Health Care Sciences & Services
Zhebin Yu, Sandra Ekstrom, Tom Bellander, Petter Ljungman, Goeran Pershagen, Kristina Eneroth, Inger Kull, Anna Bergstrom, Antonios Georgelis, Massimo Stafoggia, Olena Gruzieva, Erik Melen
Summary: There is an association between air pollution exposure and long COVID in young adults in Sweden. A survey conducted from October 2021 to February 2022 found that 15.4% of participants reported experiencing long COVID symptoms. The study suggests that long-term exposure to PM2.5 and other air pollutants may increase the risk of long COVID in young adults.
LANCET REGIONAL HEALTH-EUROPE
(2023)
Article
Medical Laboratory Technology
Abdellah Tebani, Frederic Barbey, Olivier Dormond, Franklin Ducatez, Stephane Marret, Albina Nowak, Soumeya Bekri
Summary: Fabry disease is an X-linked lysosomal rare disease caused by a deficiency of α-galactosidase A activity. The accumulation of glycosphingolipids affects the kidney, heart, and central nervous system, reducing life expectancy. A deep plasma proteomic profiling identified proteomic profiles that could distinguish FD patients from controls, highlighting the involvement of pro-inflammatory cytokines and extracellular matrix remodeling in FD pathogenesis. These findings will contribute to better understanding of the molecular mechanisms in FD and future diagnostic and therapeutic advancements.
TRANSLATIONAL RESEARCH
(2023)
Review
Biotechnology & Applied Microbiology
Mathias Uhlen, Stephen R. Quake
Summary: The impact of next-generation sequencing (NGS) is of great significance in the field of life science, contributing to our understanding of human health, disease, biology, and ecology. The majority of NGS systems are based on the concept of 'sequencing by synthesis' (SBS), which uses engineered DNA polymerase for sequential detection of nucleotide incorporation. This review discusses some key concepts leading to the development of NGS technology.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Oncology
David Kotol, Jakob Woessmann, Andreas Hober, Maria Bueno Alvez, Khue Hua Tran Minh, Fredrik Ponten, Linn Fagerberg, Mathias Uhlen, Fredrik Edfors
Summary: This study utilized mass spectrometry to study proteins in the blood samples of cancer patients and identified potential markers for diagnosing multiple myeloma. By using machine learning and differential expression analysis, a high-accuracy diagnostic model was established, which has significant implications for diagnostic tools in cancer research.
Article
Cardiac & Cardiovascular Systems
Senka Sendic, Ladan Mansouri, Mun-Gwan Hong, Jochen M. Schwenk, Maria J. Eriksson, Britta Hylander, Joachim Lundahl, Stefan H. Jacobson
Summary: Elevated levels of circulating sCD14 and OPG in patients with CKD stages 2-3 were significantly associated with ABI, a measure of arterial stiffness. An increase in sCD14 over time in CKD stages 2-3 patients was associated with a corresponding increase in ABI.
CARDIORENAL MEDICINE
(2023)
Article
Endocrinology & Metabolism
Adem Y. Dawed, Andrea Mari, Andrew Brown, Timothy J. McDonald, Lin Li, Shuaicheng Wang, Mun-Gwan Hong, Sapna Sharma, Neil R. Robertson, Anubha Mahajan, Xuan Wang, Mark Walker, Stephen Gough, Leen M. 't Hart, Kaixin Zhou, Ian Forgie, Hartmut Ruetten, Imre Pavo, Pallav Bhatnagar, Angus G. Jones, Ewan R. Pearson, for the D. I. R. E. C. T. consortium DIRECT consortium
Summary: This study identified genetic variants associated with the response to GLP-1 receptor agonist treatment in patients with type 2 diabetes, which provides valuable insights for clinical decision making and personalized medicine.
LANCET DIABETES & ENDOCRINOLOGY
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Sarah Snanoudj, Celine Derambure, Celine Lesueur, Lenaig Donval, Stephane Marret, Soumeya Bekri, Abdellah Tebani
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)