Article
Biochemical Research Methods
Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity Law, Sean Davis, Vincent Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Summary: Researchers developed a framework for assessing enrichment methods based on defined criteria, evaluated 10 major enrichment methods using a curated compendium of expression datasets, and provided practical recommendations for efficient interpretation of results when applying these methods.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Thira Faruangsaeng, Sermporn Thaweesapphitak, Chompak Khamwachirapitak, Thantrira Porntaveetus, Vorasuk Shotelersuk
Summary: The molecular control of tooth development differs between the maxilla and mandible, with PITX1 gene expression significantly higher in mandibular posterior teeth compared to maxillary posterior teeth. These differences should be considered in molecular studies of dental pulp stem cells and may contribute to more precise treatments in regenerative dentistry.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Sue A. Krause, Gayle Overend, Julian A. T. Dow, David P. Leader
Summary: FlyAtlas 2 is a database and web application for studying gene expression in different tissues of Drosophila melanogaster, with enhancements including a 'Profile' search function and a dedicated feature for exploring gene expression in the larval midgut. The database now includes data from 13 tissues, five sex-specific tissues, and eight larval tissues, with major improvements to the interface.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Mengting Huang, Yixuan Yang, Xingzhao Wen, Weiqiang Xu, Na Lu, Xiao Sun, Jing Tu, Zuhong Lu
Summary: Although single cell RNA sequencing technologies are well developed, acquiring large-scale single cell expression data can still be costly. The study proposes a method of compressing expression profiles from the sample dimension by assigning each cell into multiple pools and demonstrates that expression profiles can be inferred from pool expression data with a overlapping pooling design and compressed sensing strategy. This approach, when combined with plate-based scRNA-seq measurement, maintains superior gene detection sensitivity and individual identity while reducing library costs by half.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Computer Science, Artificial Intelligence
Bruno I. Grisci, Bruno Cesar Feltes, Joice de Faria Poloni, Pedro H. Narloch, Marcio Dorn
Summary: A review of over 1200 publications on feature selection and gene expression between 2010 and 2020 found that 57% of the publications used outdated datasets, 23% used only outdated data, and 32% did not cite data sources. Problems such as referencing unavailable databases, slow adoption of RNA-seq datasets, and bias towards human cancer data were also identified. These issues can result in inaccurate and misleading biological results.
WILEY INTERDISCIPLINARY REVIEWS-DATA MINING AND KNOWLEDGE DISCOVERY
(2023)
Article
Multidisciplinary Sciences
Amichay Afriat, Vanessa Zuzarte-Luis, Keren Bahar Halpern, Lisa Buchauer, Sofia Marques, Angelo Ferreira Chora, Aparajita Lahree, Ido Amit, Maria M. Mota, Shalev Itzkovitz
Summary: This study characterized the temporal expression programs of the rodent malaria parasite Plasmodium berghei ANKA and the host hepatocyte in a zonally controlled manner using single-cell RNA sequencing and single-molecule transcript imaging. The study identified differences in parasite gene expression in distinct zones and identified a subpopulation of hepatocytes with reduced levels of Plasmodium transcripts and parasitophorous vacuole breakdown. These findings provide insights into the liver stage of Plasmodium infection.
Article
Biology
Ana Gutierrez-Franco, Franz Ake, Mohamed N. Hassan, Natalie Chaves Cayuela, Loris Mularoni, Mireya Plass
Summary: The critical step in single-cell transcriptomics is sample preparation. Different preservation methods show varying effects on cell quality and expression biases. In this study, methanol fixation is identified as the preferred method for droplet-based single-cell transcriptomics experiments on neural cell populations derived from induced pluripotent stem cells.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Xiaonan Fu, Li Sun, Runze Dong, Jane Y. Chen, Runglawan Silakit, Logan F. Condon, Yiing Lin, Shin Lin, Richard D. Palmiter, Liangcai Gu
Summary: This study introduces a stamping method for fabricating polony gels, reducing the cost and time of barcode sequencing, and developing a single-cell spatial transcriptomic assay. This method offers high resolution and RNA capture efficiency for mapping and analyzing cell-cell communication in tissues.
Article
Food Science & Technology
Alicja Wierzbicka, Malgorzata Swiatkiewicz, Miroslaw Tyra, Tomasz Szmatola, Maria Oczkowicz
Summary: This study compared the effects of cholecalciferol and calcidiol on meat quality and muscle tissue transcriptome. The results suggest that increasing the dose of cholecalciferol and using calcidiol in the diet of finishers may improve meat texture parameters, but have no significant effect on muscle tissue transcriptome.
Article
Multidisciplinary Sciences
Asia Mendelevich, Svetlana Vinogradova, Saumya Gupta, Andrey A. Mironov, Shamil R. Sunyaev, Alexander A. Gimelbrant
Summary: The study demonstrates that relying on a single RNA-seq library for allele-specific analysis can lead to variable error rates. Therefore, the development of a computational tool like Qllelic, which accurately accounts for technical noise by utilizing replicate RNA-seq libraries, greatly decreases false positive rates and improves reproducibility of AI estimates.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Peijie Zhou, Shuxiong Wang, Tiejun Li, Qing Nie
Summary: MuTrans is a method based on multiscale reduction technique that can identify the underlying stochastic dynamics governing cell-fate transitions, construct cell-fate dynamical manifold, distinguish stable and transition cells, and quantify transition probabilities between cell states. The method is consistent with Langevin equation and transition rate theory, and has been shown to robustly unravel complex cell fate dynamics induced by transition cells in various systems. It bridges data-driven and model-based approaches for single-cell resolution analysis of cell-fate transitions.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Renying Wang, Peijing Zhang, Jingjing Wang, Lifeng Ma, E. Weigao, Shengbao Suo, Mengmeng Jiang, Jiaqi Li, Haide Chen, Huiyu Sun, Lijiang Fei, Ziming Zhou, Yincong Zhou, Yao Chen, Weiqi Zhang, Xinru Wang, Yuqing Mei, Zhongyi Sun, Chengxuan Yu, Jikai Shao, Yuting Fu, Yanyu Xiao, Fang Ye, Xing Fang, Hanyu Wu, Qile Guo, Xiunan Fang, Xia Li, Xianzhi Gao, Dan Wang, Peng-Fei Xu, Rui Zeng, Gang Xu, Lijun Zhu, Lie Wang, Jing Qu, Dan Zhang, Hongwei Ouyang, He Huang, Ming Chen, Shyh-Chang Ng, Guang-Hui Liu, Guo-Cheng Yuan, Guoji Guo, Xiaoping Han
Summary: By using single-cell RNA sequencing, researchers mapped organism-level cell landscapes for mice, zebrafish, and Drosophila. They identified structural inflammation and mitochondrial dysfunction as common hallmarks of organism aging.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Luis V. Herrera-Marcos, Roberto Martinez-Beamonte, Manuel Macias-Herranz, Carmen Arnal, Cristina Barranquero, Juan J. Puente-Lanzarote, Sonia Gascon, Tania Herrero-Continente, Gonzalo Gonzalo-Romeo, Victor Alastrue-Vera, Dolores Gutierrez-Blazquez, Jose M. Lou-Bonafonte, Joaquin C. Surra, Maria J. Rodriguez-Yoldi, Agustin Garcia-Gil, Antonio Guemes, Jesus Osada
Summary: This study describes a new experimental swine model for initial and reversible non-alcoholic fatty liver disease (NAFLD). Gene expression analysis revealed several genes associated with steatosis and steatohepatitis. The results suggest that LGALS3 may play an important role in the transition from NAFLD to non-alcoholic steatohepatitis (NASH).
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Wancen Mu, Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, Michael Love
Summary: The study introduces a statistical method called airpart for identifying differential cell-type-specific allelic imbalance from single-cell RNA-sequencing data, or dynamics allelic imbalance from other spatially or time-resolved datasets. The method accurately detects common mechanisms of cis-genetic regulation and shows lower error rates in single-cell data.
Article
Biochemical Research Methods
Pontus Eriksson, Nour-al-dain Marzouka, Gottfrid Sjodahl, Carina Bernardo, Fredrik Liedberg, Mattias Hoglund
Summary: In this study, we evaluated the behavior of gene-pair-based single sample predictors (SSPs) in gene expression-based multiclass prediction tasks. We found that these methods showed excellent performance, with high accuracy and informative prediction scores, in many expression-based classification tasks. However, the compatibility of gene-pair-based predictors with new datasets still needs to be verified.
Article
Agriculture, Dairy & Animal Science
V. A. Balteanu, T. F. Cardoso, M. Amills, M. G. Luigi-Sierra, I. Egerszegi, I. Anton, A. Zsolnai
Summary: The Mangalitza lard-type pig breed, known for its fat appearance and curly hair, was created with four main lines through artificial selection in the nineteenth century. The study identified a region on chromosome 16 potentially influencing hair pigmentation in Mangalitza pigs, with the SLC45A2 gene as a candidate gene. The results suggest a strong association between specific genetic polymorphisms in SLC45A2 and the red and blond coat colors of Mangalitza pigs, indicating the impact of divergent directional selection on coat color in domestic species.
Article
Biochemistry & Molecular Biology
Yosra Ressaissi, Marcel Amills, Antonia Noce, Mohamed Ben Hamouda
Summary: The Arbi goat breed in Tunisia is an important economic resource with high mitochondrial diversity, possibly linked to the maritime diffusion during the Neolithic period. Analysis showed that the Arbi goats do not cluster with other goat breeds genetically, indicating potential historical crossbreeding practices.
BIOCHEMICAL GENETICS
(2021)
Editorial Material
Agriculture, Dairy & Animal Science
Maria Gracia Luigi-Sierra, Joaquim Casellas, Amparo Martinez, Juan Vicente Delgado, Javier Fernandez Alvarez, Francesc Xavier Such, Jordi Jordana, Marcel Amills
Article
Biotechnology & Applied Microbiology
Emma Sole, Rayner Gonzalez-Prendes, Yelyzaveta Oliinychenko, Marc Tor, Roger Ros-Freixedes, Joan Estany, Ramona N. Pena
Summary: Restricting dietary vitamin A during the fattening period did not improve intramuscular fat content, but there was an interaction between vitamin A and SCD genotype on the desaturation of fatty acids in muscle.
Article
Multidisciplinary Sciences
Christos Dadousis, Maria Munoz, Cristina Ovilo, Maria Chiara Fabbri, Jose Pedro Araujo, Samuele Bovo, Marjeta Candek Potokar, Rui Charneca, Alessandro Crovetti, Maurizio Gallo, Juan Maria Garcia-Casco, Danijel Karolyi, Goran Kusec, Jose Manuel Martins, Marie-Jose Mercat, Carolina Pugliese, Raquel Quintanilla, Cedomir Radovic, Violeta Razmaite, Anisa Ribani, Juliet Riquet, Radomir Savic, Giuseppina Schiavo, Martin Skrlep, Silvia Tinarelli, Graziano Usai, Christoph Zimmer, Luca Fontanesi, Riccardo Bozzi
Summary: This study revealed the ancestral information and evolutionary relationships of several local pig breeds in Europe through genetic analysis and discriminant analysis on principal components. It also validated the reliability of SNP data in traceability of breed-specific pig products.
SCIENTIFIC REPORTS
(2022)
Article
Agriculture, Dairy & Animal Science
Emilio Marmol-Sanchez, Susanna Cirera, Laura M. Zingaretti, Mette Juul Jacobsen, Yuliaxis Ramayo-Caldas, Claus B. Jorgensen, Merete Fredholm, Taina Figueiredo Cardoso, Raquel Quintanilla, Marcel Amills
Summary: This study investigated the role of miRNAs in mRNA post-transcriptional regulation in porcine tissues. The results suggest that miRNAs play a more prominent role in the regulation of gene expression in the skeletal muscle system. Several genes related to energy homeostasis were also identified.
Article
Agriculture, Dairy & Animal Science
Laura Sarri, Joaquim Balcells, Ahmad Reza Seradj, Ramona N. Pena, Gustavo A. Ramirez, Marc Tor, Gabriel de la Fuente
Summary: Fat metabolism is an important process in meat production companies, which affects the quality of meat. The source and incorporation rate of fat differ in different growth phases. The liver plays a critical role in fat metabolism during the fattening phase. Leaner pigs rely more on dietary fatty acids for fat deposition compared to fatter pigs. The activity of stearoyl-CoA desaturase is higher in the fattening phase.
Article
Agriculture, Dairy & Animal Science
Eduard Molinero, Ramona N. Pena, Joan Estany, Roger Ros-Freixedes
Summary: In this study, a missense polymorphism in the AGPAT5 gene was found to be significantly associated with fat content and composition traits in pigs. The variant showed positive effects on intramuscular fat content and fatty acid composition. The impact of the variant on fat content was more pronounced in fatter pigs and it interacts with other genes that affect overall fatness.
Article
Agriculture, Dairy & Animal Science
Martina Macri, Maria Gracia Luigi-Sierra, Dailu Guan, Juan Vicente Delgado, Javier Fernandez Alvarez, Marcel Amills, Amparo Martinez Martinez
Summary: Hematological traits are important indicators of health status. In humans, the genomic architecture of blood traits has been extensively studied, but the association between marker genotypes and hematological traits in goats has not been investigated yet.
Article
Agriculture, Dairy & Animal Science
Rafael Suarez-Mesa, Roger Ros-Freixedes, Houda Laghouaouta, Ramona N. Pena, Byron Hernandez-Ortiz, Iang Rondon-Barragan, Joan Estany
Summary: Dissecting genetic variation is important for conservation success. This study investigated the genomic variation of Colombian Creole pigs and identified breed-specific variants in genes related to adaptive and economic traits. The findings suggest that Colombian Creole pigs are not exempt from selective introgression of other breeds and provide insights for effective breeding and conservation.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2023)
Article
Agriculture, Dairy & Animal Science
Adriana Siurana, Angela Canovas, Joaquim Casellas, Sergio Calsamiglia
Summary: In the past 20 years, there has been interest in modifying the fatty acid profile to increase polyunsaturated fatty acids, which are healthier for human health. However, this modification causes milk fat depression. This study identified 15 genes as key regulators that may be involved in the resistance or sensitivity of dairy cows to milk fat depression when fed a linseed-rich diet.
Article
Agriculture, Dairy & Animal Science
Houssemeddine Srihi, David Lopez-Carbonell, Noelia Ibanez-Escriche, Joaquim Casellas, Pilar Hernandez, Sara Negro, Luis Varona
Summary: INGA FOOD, S.A. conducted a crossbreeding program to produce hybrid pigs, and studies revealed differences in litter size between reciprocal crosses, suggesting the presence of genomic imprinting effects. A multivariate gametic model was introduced to estimate the gametic correlations between paternal and maternal effects from different genetic backgrounds. The results showed distinct differences in the posterior distribution of gametic correlations between the two populations, which may explain the performance outcomes in the reciprocal crosses.
Article
Biochemistry & Molecular Biology
Haonan Zeng, Wenjing Zhang, Qing Lin, Yahui Gao, Jinyan Teng, Zhiting Xu, Xiaodian Cai, Zhanming Zhong, Jun Wu, Yuqiang Liu, Shuqi Diao, Chen Wei, Wentao Gong, Xiangchun Pan, Zedong Li, Xiaoyu Huang, Xifan Chen, Jinshi Du, Fuping PigGTEx Consortium, Fuping Zhao, Yunxiang Zhao, Maria Ballester, Daniel Crespo-Piazuelo, Marcel Amills, Alex Clop, Peter Karlskov-Mortensen, Merete Fredholm, Pinghua Li, Ruihua Huang, Guoqing Tang, Mingzhou Li, Xiaohong Liu, Yaosheng Chen, Qin Zhang, Jiaqi Li, Xiaolong Yuan, Xiangdong Ding, Lingzhao Fang, Zhe Zhang
Summary: To unlock the potential of pigs in agriculture and biomedical research, the PigBiobank was created to investigate the molecular and cellular mechanisms underlying complex traits in pigs and translate the findings to other species.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Agriculture, Dairy & Animal Science
Houda Laghouaouta, Lorenzo Fraile, Rafael Suarez-Mesa, Roger Ros-Freixedes, Joan Estany, Ramona Natacha Pena
Summary: This study provides new insights into the genetic make-up of resilience in growing pigs by identifying genomic regions and candidate genes associated with resilience indicators. The findings suggest that there are novel genomic regions associated with two resilience indicators (increment BW and increment HP) in pigs, which harbour potential candidate genes involved in immune response and growth pathways, highlighting the strong relationship between resilience and immune response.
GENETICS SELECTION EVOLUTION
(2022)
