Article
Plant Sciences
Changyu Li, Yaoyao Li, Guangshu Song, Di Yang, Zhanchao Xia, Changhe Sun, Yuelei Zhao, Mei Hou, Mingyue Zhang, Zhi Qi, Baobao Wang, Haiyang Wang
Summary: In this study, we conducted phenotypic and gene expression analyses for 137 elite inbred lines of maize from different breeding eras in China. We identified four yield-related traits that significantly improved during modern maize breeding and identified several candidate genes associated with these traits. Our results demonstrate the effectiveness of our combined approaches for uncovering key candidate regulatory genes and functional variation underlying the improvement of important agronomic traits during modern maize breeding.
Article
Plant Sciences
Huan Zheng, Yang Dong, Huilan Nong, Liyuan Huang, Jing Liu, Xin Yu, Yaguan Zhang, Lina Yang, Ben Hong, Wu Wang, Jianmin Tao
Summary: Fruit shape is an important agronomic feature in crops. The VvSUN gene plays a crucial role in controlling fruit shape through coordination with the auxin pathway and plant hormone signal transduction. VvSUN affects the anisotropic growth of the fruit by regulating cell number and endogenous auxin levels.
HORTICULTURE RESEARCH
(2022)
Article
Physics, Multidisciplinary
Samarendra Das, Shesh N. Rai
Summary: Genome-wide expression study is a powerful tool for quantifying gene expression dynamics, and gene set analysis is commonly used for gaining insights into the underlying biology of diseases or stresses. However, existing methods may have limitations when analyzing specific traits in plant biology. Therefore, a new statistical approach, GSQSeq, was developed to perform robust and successful trait-specific gene set analysis by integrating gene expression data with QTL data.
Article
Plant Sciences
Niraj Khemka, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Summary: Integrated transcriptome data analysis identified candidate long non-coding RNAs (lncRNAs) associated with QTLs and involved in miRNA-mediated seed size/weight determination in chickpea seed development. The study provides a comprehensive resource and identifies potential lncRNAs that play important roles in chickpea seed development and seed size/weight determination.
Article
Biochemical Research Methods
Jiajun Yang, Dongyang Wang, Yanbo Yang, Wenqian Yang, Weiwei Jin, Xiaohui Niu, Jing Gong
Summary: This study comprehensively evaluated the impact of eight commonly used normalization methods on eQTL identification using RNA-seq and genotype data from different cancer samples. Our results showed that different methods could cause 20-30% differences in the final results, with TMM identified as the optimal normalization method.
The combination of methods was found to not only identify more cis-eQTLs, but also improve the performance of the ROC curve, suggesting the potential benefits of considering pairwise combinations of normalization methods in eQTL analysis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Xinpeng Guo, Jinyu Han, Yafei Song, Zhilei Yin, Shuaichen Liu, Xuequn Shang
Summary: This study aims to address some challenges in multi-omics analysis and proposes a classification model that considers internal correlations, achieving high accuracy and easy interpretability in genotype-phenotype association analysis.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Pingchuan Deng, Tao Yan, Wanquan Ji, Guoping Zhang, Liang Wu, Dezhi Wu
Summary: Genetic variation is an important factor in gene transcription and contributes to functional and phenotypic diversity. This study investigated the transcriptome variation of barley under cadmium exposure and identified significant changes in gene expression and alternative splicing. A genome-wide association study revealed numerous expression and splicing quantitative trait loci that affect a large percentage of genes, including metal transporter genes. Additionally, a correlation was found between genetic variants affecting gene expression and alternative splicing and cadmium accumulation traits. This study highlights the role of genetic effects on gene expression and splicing in cadmium accumulation and provides insights into understanding genetic variation and phenotypic diversity.
Article
Genetics & Heredity
Helene Ruffieux, Benjamin P. Fairfax, Isar Nassiri, Elena Vigorito, Chris Wallace, Sylvia Richardson, Leonardo Bottolo
Summary: EPISPOT is a joint framework that enhances molecular QTL mapping by utilizing large panels of epigenetic annotations, improving statistical power and shedding light on the regulatory basis of trans-acting genetic variants.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Sulev Koks, Abigail L. Pfaff, Vivien J. Bubb, John P. Quinn
Summary: Transposable elements (TEs) play a crucial role in regulating gene expression by influencing the presence or absence of polymorphic TEs, which can alter the expression of genes or gene clusters with potentially large effects on genetic networks. The study highlights the significant regulatory function of TEs in shaping the transcriptome and provides insights into their impact on complex traits and missing heritability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Jing Chen, Lindsey J. Leach, Zewei Luo
Summary: Mapping quantitative trait loci (QTL) in autotetraploid species is a timely and challenging task. Two papers by Wu and his colleagues proposed statistical methods for QTL mapping in these species, but have been criticized for fundamental conceptual errors from statistical and genetic perspectives.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Agriculture, Dairy & Animal Science
Beining Kang, Junjie Wang, Hongfu Zhang, Wei Shen, Othman El-Mahdy Othman, Yong Zhao, Lingjiang Min
Summary: This study explored DNA methylation status in ovaries of high and low litter size goats, finding global differences and many differentially methylated region-related genes. Enrichment analysis indicated involvement of these genes in gamete development, reproductive system development, WNT signaling pathways, and MAPK signaling pathways. The study suggests that DNA methylation in goat ovaries may be important for folliculogenesis, oocyte ovulation rate, and litter size.
JOURNAL OF ANIMAL PHYSIOLOGY AND ANIMAL NUTRITION
(2022)
Article
Biochemistry & Molecular Biology
Jian Chen, Xiangbo Zhang, Fei Yi, Xiang Gao, Weibin Song, Haiming Zhao, Jinsheng Lai
Summary: MP3RNA-seq is a highly efficient method for transcriptome sequencing, suitable for large-scale experiments. Application to double haploid lines of maize demonstrated its high accuracy and sensitivity in high-throughput gene expression profiling and genotyping.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Immunology
Yuri F. van der Heijden, Fernanda Maruri, Amondrea Blackman, Robert Morrison, Yan Guo, Timothy R. Sterling
Summary: Genomic and gene expression data of 27 clinical fluoroquinolone-resistant Mycobacterium tuberculosis isolates with different responses to an efflux pump inhibitor were compared. The gene Rv0191 showed increased gene expression and significance in expression quantitative trait loci analysis. This study provides evidence for the importance of Rv0191 in the evaluation of efflux-mediated fluoroquinolone resistance in Mycobacterium tuberculosis.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Cardiac & Cardiovascular Systems
Akhilesh Kumar Bajpai, Qingqing Gu, Buyan-Ochir Orgil, Fuyi Xu, Carolina Torres-Rojas, Wenyuan Zhao, Chen Chen, Athena Starlard-Davenport, Byron Jones, Djamel Lebeche, Jeffrey A. Towbin, Enkhsaikhan Purevjav, Lu Lu, Wenjing Zhang
Summary: Copper (Cu) is necessary for the functioning of enzymes involved in cellular and physiological processes. Variations in cardiac Cu content can lead to cardiac pathologies and imbalance in systemic Cu metabolism. This study identified significant correlations between cardiac Cu concentration and left ventricular size and LV hypertrophy in BXD mice. Six QTLs and 21 candidate genes, including Prex1 and Irx3, were identified as regulators of cardiac Cu levels.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2023)
Article
Multidisciplinary Sciences
Himadri Shekhar Roy, Amrit Kumar Paul, Ranjit Kumar Paul
Summary: This study utilized an integrated hierarchical Bayesian model to identify cis- and trans-eQTLs in barley and mice, and discovered corresponding eQTL hotspots.
Article
Microbiology
Daniel Sepulveda-Crespo, Ana Trevino-Nakoura, Jose M. Bellon, Maria A. Jimenez-Sousa, Pablo Ryan, Isidoro Martinez, Amanda Fernandez-Rodriguez, Salvador Resino
Summary: The standard algorithm for diagnosing hepatitis C virus (HCV) infection involves an HCV antibody test for screening and a nucleic acid amplification test (NAAT) for confirmation. The accuracy of the Abbott ARCHITECT HCV Ag assay was evaluated in people living with HIV/AIDS (PLWHA), showing good performance in high-prevalence settings but poor in low-prevalence settings. It was excellent in excluding active HCV infection.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Medicine, Research & Experimental
Sergio Salguero, Oscar Brochado-Kith, Ana Virseda Verdices, Juan Berenguer, Juan Gonzalez-Garcia, Isidoro Martinez, Cristina Diez, Victor Hontanon, Leire Perez-Latorre, Amanda Fernandez-Rodriguez, Maria Angeles Jimenez-Sousa, Salvador Resino
Summary: We identified a gene expression signature associated with advanced cirrhosis with high risk for clinically significant portal hypertension (CSPH) in HIV/HCV coinfected patients through analyzing the gene expression profile of peripheral blood mononuclear cells (PBMCs). A cross-sectional study on 68 patients was conducted, and liver stiffness measurement (LSM) was used for stratification. We found 60 differentially expressed transcripts between patients with LSM < 12.5 kPa and >= 25 kPa, and two of them were validated in a different cohort.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Medicine, Research & Experimental
Violeta Lara-Aguilar, Daniel Valle-Millares, Celia Crespo-Bermejo, Sergio Grande-Garcia, Manuel Llamas-Adan, Maria Engracia Cortijo-Alfonso, Luz Martin-Carbonero, Lourdes Dominguez, Pablo Ryan, Ignacio de los Santos, Sofia Bartolome-Sanchez, Erick Joan Vidal-Alcantara, Maria Angeles Jimenez-Sousa, Amanda Fernandez-Rodriguez, Veronica Briz
Summary: This study examined the senescence profiles in people living with HIV who have acute or chronic Hepatitis C. The results showed that the profiles improved after HCV elimination, either spontaneously or with direct-acting antivirals.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Multidisciplinary Sciences
Erola Pairo-Castineira, Konrad Rawlik, Andrew D. Bretherick, Ting Qi, Yang Wu, Isar Nassiri, Glenn A. McConkey, Marie Zechner, Lucija Klaric, Fiona Griffiths, Wilna Oosthuyzen, Athanasios Kousathanas, Anne Richmond, Jonathan Millar, Clark D. Russell, Tomas Malinauskas, Ryan Thwaites, Kirstie Morrice, Sean Keating, David Maslove, Alistair Nichol, Malcolm G. Semple, Julian Knight, Manu Shankar-Hari, Charlotte Summers, Charles Hinds, Peter Horby, Lowell Ling, Danny McAuley, Hugh Montgomery, Peter J. M. Openshaw, Colin Begg, Timothy Walsh, Albert Tenesa, Carlos Flores, Jose A. Riancho, Augusto Rojas-Martinez, Pablo Lapunzina, Jian Yang, Chris P. Ponting, James F. Wilson, Veronique Vitart, Malak Abedalthagafi, Andre D. Luchessi, Esteban J. Parra, Raquel Cruz, Angel Carracedo, Angie Fawkes, Lee Murphy, Kathy Rowan, Alexandre C. Pereira, Andy Law, Benjamin Fairfax, Sara Clohisey Hendry, J. Kenneth Baillie
Summary: This study analyzed genetic data from 24,202 severe COVID-19 cases and identified potentially druggable targets, including inflammatory signaling, monocyte-macrophage activation and endothelial permeability, immunometabolism, and host factors required for viral entry and replication.
Review
Virology
Daniel Sepulveda-Crespo, Ana Trevino-Nakoura, Jose M. Bellon, Amanda Fernandez-Rodriguez, Pablo Ryan, Isidoro Martinez, Maria A. Jimenez-Sousa, Salvador Resino
Summary: This meta-analysis evaluated the diagnostic performance of the Abbott ARCHITECT HCV Ag assay for diagnosing active hepatitis C. The assay showed excellent sensitivity, specificity, and accuracy. However, its diagnostic utility may be limited in low prevalence settings, and further confirmation is recommended.
REVIEWS IN MEDICAL VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hernan D. Laviano, Gerardo Gomez, Maria Munoz, Juan M. Garcia-Casco, Yolanda Nunez, Rosa Escudero, Ana Heras Molina, Antonio Gonzalez-Bulnes, Cristina Ovilo, Clemente Lopez-Bote, Ana I. Rey
Summary: Modifying the composition of a sow's milk, specifically by supplementing with vitamin E and/or hydroxytyrosol, can improve the intestinal health and growth of piglets. The study found that vitamin E supplementation increased the levels of C18:1n-7 in colostrum, while hydroxytyrosol increased the levels of polyunsaturated fatty acids. Vitamin E supplementation also decreased certain fatty acids and increased ?-6-desaturase activity in 7-day milk. The lowest levels of milk lipid oxidation were observed in the vitamin E supplemented group, while hydroxytyrosol supplementation increased oxidation.
Correction
Medicine, Research & Experimental
Sergio Salguero, Oscar Brochado-Kith, Ana Virseda Verdices, Juan Berenguer, Juan Gonzalez-Garcia, Isidoro Martinez, Cristina Diez, Victor Hontanon, Leire Perez-Latorre, Amanda Fernandez-Rodriguez, Maria Angeles Jimenez-Sousa, Salvador Resino
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Medicine, Research & Experimental
Ruben Martin-Escolano, Ana Virseda-Berdices, Juan Berenguer, Juan Gonzalez-Garcia, Oscar Brochado-Kith, Amanda Fernandez-Rodriguez, Cristina Diez, Victor Hontanon, Salvador Resino, Maria Angeles Jimenez-Sousa
Summary: This study aimed to evaluate the association between plasma immune checkpoint proteins at baseline with hepatic steatosis index increase at the end of follow-up in HIV/HCV-coinfected patients. The results showed that higher levels of immune checkpoint proteins BTLA, CD137, CD80, GITR, LAG-3, and PD-L1 before HCV therapy were associated with a long-term increase in hepatic steatosis index after successful HCV therapy, suggesting a potential predictive role for early detection of progression towards steatosis in HIV/HCV-coinfected patients.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Virology
Violeta Lara-Aguilar, Celia Crespo-Bermejo, Manuel Llamas-Adan, Sergio Grande-Garcia, Maria Engracia Cortijo-Alfonso, Luz Martin-Carbonero, Lourdes Dominguez, Pablo Ryan, Ignacio de los Santos, Sofia Bartolome-Sanchez, Daniel Valle-Millares, Maria Angeles Jimenez-Sousa, Veronica Briz, Amanda Fernandez-Rodriguez
Summary: Coinfection with HCV and HIV leads to immune activation, inflammation, oxidative stress, and premature senescence. Chronic HCV infection in PLWHIV is associated with increased nitrate concentration and secretion of senescence-associated factors.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hernan D. Laviano, Gerardo Gomez, Rosa Escudero, Yolanda Nunez, Juan M. Garcia-Casco, Maria Munoz, Ana Heras-Molina, Clemente Lopez-Bote, Antonio Gonzalez-Bulnes, Cristina Ovilo, Ana I. Rey
Summary: This study evaluates the effects of dietary supplementation of vitamin E, hydroxytyrosol, or the combination of the two on gut health and piglet growth. The results suggest that vitamin E supplementation is superior to hydroxytyrosol supplementation in improving intestinal homeostasis and piglet growth.
Article
Biochemistry & Molecular Biology
Gerardo Gomez, Hernan D. Laviano, Juan M. Garcia-Casco, Rosa Escudero, Maria Munoz, Ana Heras-Molina, Antonio Gonzalez-Bulnes, Cristina Ovilo, Clemente Lopez-Bote, Ana I. Rey
Summary: Different feeding strategies are being applied to sows in order to obtain homogeneous piglets' weights and improved health status. This study evaluated the effects of dietary supplementation of vitamin E (VE), hydroxytyrosol (HXT), or their combination on the growth pattern and oxidative status of piglets, as well as the factors contributing to these effects. The results showed that both VE and HXT improved the oxidative status of sows and piglets, and modified the growth pattern of the piglets depending on the growing period. The study also found that colostrum composition played a significant role in the growth patterns of the piglets.
Article
Agriculture, Dairy & Animal Science
Patricia Palma-Granados, Juan Maria Garcia-Casco, Carmen Caraballo, Pedro Vazquez-Ortego, Fernando Gomez-Carballar, Fernando Sanchez-Esquiliche, Cristina Ovilo, Maria Munoz
Summary: We investigated the transcriptome of Iberian pigs to identify candidate genes and long non-coding RNA associated with intramuscular fat and fatty acids. Based on this information, we designed a low-density panel of 50 single-nucleotide polymorphisms (SNP) and evaluated their effects on intramuscular fat content and backfat fatty acid profile in a commercial population of Iberian pigs. We found significant associations between three SNP (ADIPOQ:g.124646194T>G, ELOVL6:g.112186423A>G, and FASN_rs331694510G>A) and intramuscular fat and fatty acid composition.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Microbiology
Cristina Sebastia, Josep M. Folch, Maria Ballester, Jordi Estelle, Magi Passols, Maria Munoz, Juan M. Garcia-Casco, Ana I. Fernandez, Anna Castello, Armand Sanchez, Daniel Crespo-Piazuelo
Summary: The gut microbiota is closely related to the composition of short-chain fatty acids in the host, with Prevotella spp. and Akkermansia spp. potentially serving as biomarkers for acetic and n-butyric acid levels, and Rikenellaceae RC9 gut group potentially influencing the fatty acid composition in backfat and muscle of the pig.
Article
Agriculture, Dairy & Animal Science
Klavdija Poklukar, Camille Mestre, Martin Skrlep, Marjeta Candek-Potokar, Cristina Ovilo, Luca Fontanesi, Juliette Riquet, Samuele Bovo, Giuseppina Schiavo, Anisa Ribani, Maria Munoz, Maurizio Gallo, Ricardo Bozzi, Rui Charneca, Raquel Quintanilla, Goran Kusec, Marie-Jose Mercat, Christoph Zimmer, Violeta Razmaite, Jose P. Araujo, Cedomir Radovic, Radomir Savic, Danijel Karolyi, Bertrand Servin
Summary: Based on genetic and phenotypic analysis of European local pig breeds, this study identified significant genetic variations associated with stature, fatness, growth, and reproductive performance traits. These findings suggest the presence of candidate genes that may have adapted to different living environments and production systems.
GENETICS SELECTION EVOLUTION
(2023)
Article
Food Science & Technology
Patricia Palma-Granados, Maria Munoz, Miguel A. Delgado-Gutierrez, Cristina Ovilo, Yolanda Nunez, Miguel A. Fernandez-Barrosso, Fernando Sanchez-Esquiliche, Luisa Ramirez, Juan M. Garcia-Casco
Summary: This study evaluated the effects of a set of 26 polymorphisms on premium cuts weights and meat quality in a larger population. The results suggest that these polymorphisms are associated with meat quality traits but may not have undesirable effects on carcass composition. Further research is needed to validate these findings.