Article
Evolutionary Biology
Nicolas Mary, Nathalie Iannuccelli, Geoffrey Petit, Nathalie Bonnet, Alain Pinton, Harmonie Barasc, Amelie Faure, Anne Calgaro, Vladimir Grosbois, Bertrand Servin, Alain Ducos, Juliette Riquet
Summary: The study found that there is hybridization between domestic pigs and French wild boars, and the level of hybridization is influenced by the management of the wild boar populations. The results also suggest that genetic admixture plays a critical role in improving the fitness and population growth of wild boars.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Multidisciplinary Sciences
Kerryn Elliott, Vinod Kumar Singh, Martin Bostrom, Erik Larsson
Summary: Proteins binding to DNA can locally alter DNA damage formation by UV light. Here, Elliott et al. generate high-resolution quantitative UV damage profiles for genomic regions of interest, revealing distinctive damage signatures for specific proteins and elevated UV damage at melanoma mutation hotspots.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Trevor J. Chan, Xingjian Zhang, Michael Mak
Summary: In this study, we propose an analytical method to quantify both single-cell morphologies and cell network topologies of tumor cell populations and predict 3D cell behavior. We utilized a supervised deep learning approach for instance segmentation and identified six distinct morphological subclasses. Differences in tumor growth and invasion dynamics were observed across subclasses in an in vitro 3D spheroid model. Compared to existing methods, our analytical method is more efficient, requires no specialized equipment, and is suitable for high-throughput applications such as drug screening and clinical diagnosis.
Article
Multidisciplinary Sciences
Zhenyu Sun, Bin Fu, Guoli Wang, Lei Zhang, Ruofan Xu, Ying Zhang, Haojie Lu
Summary: The glycoproteome is a key target for biomarker screening due to altered glycosylation in cancer cells. A novel method combining tandem mass tag labeling and chemical labeling-assisted complementary dissociation was developed for quantitative glycoproteomics. Comprehensive site-specific and subclass-specific N-glycosylation profiling of human serum immunoglobulin G (IgG) was performed, revealing IgG1-H3N5F1 and IgG4-H4N3 as potential markers for different stages of liver diseases. The expression changes of glycosylation in liver diseases were successfully validated using targeted parallel reaction monitoring in a separate sample cohort.
NATIONAL SCIENCE REVIEW
(2023)
Review
Agriculture, Dairy & Animal Science
Nerissa Russell
Summary: This article discusses the cognitive distinction between wild and domestic animals among the inhabitants of Neolithic Near East, examining how this affected economic choices and ritual activities through analysis of animal imagery and remains.
Article
Biotechnology & Applied Microbiology
Wellington B. Santos, Gustavo P. Schettini, Amanda M. Maiorano, Fernando O. Bussiman, Julio C. C. Balieiro, Guilherme C. Ferraz, Guilherme L. Pereira, Welder Angelo Baldassini, Otavio R. M. Neto, Henrique N. Oliveira, Rogerio A. Curi
Summary: The study identified genomic regions affected by different selection pressures in the Mangalarga Marchador breed, primarily highlighting recent positive selection. Candidate genes associated with athletic performance, limb development, and energy to muscle activity were found, with the involvement of the HOX family genes. The genome of Mangalarga Marchador showed evidence of recent positive selection with some regions also exhibiting balancing selection.
Article
Multidisciplinary Sciences
Magdalena Niedzialkowska, Ewa Tarnowska, Joanna Ligmanowska, Bogumila Jedrzejewska, Tomasz Podgorski, Anna Radziszewska, Iwona Ratajczyk, Szilvia Kusza, Aleksei N. Bunevich, Gabriel Danila, Maryna Shkvyria, Tomasz Grzybowski, Marcin Wozniak
Summary: The study of genetic diversity and structure of wild boar populations in Central and Eastern Europe revealed five distinct phylogenetic clades with different contributions from various regions.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
David Eyland, Nathalie Luchaire, Llorenc Cabrera-Bosquet, Boris Parent, Steven B. Janssens, Rony Swennen, Claude Welcker, Francois Tardieu, Seabstien C. Carpentier
Summary: This study evaluated genotype-dependent transpiration responses in banana wild relatives and found that they contain useful drought tolerance traits. The research highlights the importance of conserving these wild relatives and their potential for use in breeding programs.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Endocrinology & Metabolism
Yan Kong, Rong Bu, Sandeep Kumar Parvathareddy, Abdul K. Siraj, Nabil Siraj, Saif S. Al-Sobhi, Fouad Al-Dayel, Khawla S. Al-Kuraya
Summary: This study reveals the presence of NTRK fusions in Middle Eastern PTC, particularly enriched in BRAF WT and pediatric age group, and suggests the utility of immunohistochemistry for screening PTC patients with NTRK fusion who may benefit from TRK inhibitors.
EUROPEAN JOURNAL OF ENDOCRINOLOGY
(2021)
Article
Genetics & Heredity
Deepali Vasoya, Thomas Tzelos, Lindert Benedictus, Anna Eleonora Karagianni, Scott Pirie, Celia Marr, Charlotta Oddsdottir, Constanze Fintl, Timothy Connelley
Summary: In this study, a MiSeq-based approach was developed and applied to analyze the expressed MHCI and MHCII repertoires in Thoroughbred, Icelandic, and Norwegian Fjord Horses. The results showed limited overlap in MHCI and MHCII haplotypes between different breeds, indicating diverse MHC repertoire among genetically divergent breeds. This study provided novel insights into the structure of the expressed equine MHC repertoire and highlighted unique features of the MHC in horses.
Article
Agriculture, Dairy & Animal Science
Alba Marti-Marco, Samantha Moratal, Irene Torres-Blas, Jesus Cardells, Victor Lizana, Maria Auxiliadora Dea-Ayuela
Summary: This study aimed to evaluate the distribution of Cryptosporidium spp. and Giardia duodenalis in fecal samples from hunted wild boars in eastern Spain. Both parasites were found, indicating a high prevalence, particularly of Cryptosporidium species that affect humans. This suggests a risk of transmission to humans due to close contact with wild boars, especially as their population is increasing and expanding into urban areas.
Article
Agriculture, Dairy & Animal Science
Heqin Cao, Xiongwei Yang, Caichun Peng, Yeying Wang, Qunyi Guo, Haijun Su
Summary: Studying the dietary habits of animals helps us understand their food composition requirements and nutrition strategies, as well as their resource utilization and relationship with prey. In this study, the stomach contents of 14 wild boars in southern China were analyzed using DNA metabarcoding. The results showed that wild boars primarily consumed plant food sources such as Cissus, Dioscorea, Quercus, Actinidia, and Houttuynia, as well as invertebrates and vertebrates. The study revealed the dietary preferences of wild boars in the mountainous area of southwest China and the relationship between their food habits and habitats, providing important scientific evidence for their prevention, control, and resource protection.
Article
Plant Sciences
Rupesh Tayade, Seong-Hoon Kim, Pooja Tripathi, Yi-Dam Choi, Jung-Beom Yoon, Yoon-Ha Kim
Summary: Root system architecture and morphological diversification in wild accessions play an important role in crop improvement and productivity in adzuki beans. This study analyzed the root traits of 61 adzuki bean accessions and identified significant differences in these traits. The results showed that the accessions exhibited a wide range of variation in root traits, and certain accessions had distinct root characteristics compared to others. These findings provide valuable information for the development of new crossing combinations to improve root features in adzuki beans.
Article
Gastroenterology & Hepatology
Yutong Dong, Yuwei Liu, Xu Liu, Heming Ma, Yahui Liu, Guoyue Lv, Junqi Niu
Summary: This study aimed to identify novel hepatic fibrosis genes in human primary hepatic stellate cells (HSCs). Transcriptomic and proteomic approaches were used to analyze the differences in mRNA and protein expression levels between advanced fibrosis group and control group HSCs. A total of 96 upregulated molecules were found to be overlapped in both datasets, indicating their potential role in liver cirrhosis. EH-containing 2 was identified as a potential new marker for advanced liver cirrhosis.
JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Ecology
Omid Jafari, Mehrshad Zeinalabedini, Diego Robledo, Jorge M. O. Fernandes, Ali-Akbar Hedayati, Babak Arefnezhad
Summary: Understanding the population structure and genetic diversity of wild populations is crucial for stock management and conservation. This study investigated the population structure and genetic diversity of common carp in the Southern Caspian basin using genotyping-by-sequencing. The results showed low differentiation between populations and high within population variation. Frequent migration events were observed, but each population still had distinct genetic profiles. However, high inbreeding and low heterozygosity were detected, indicating the need for additional conservation efforts.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
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
Cell Biology
Yasamin Nasri-Hasani, Farid Barati, Shahin Eghbalsaied
BIOPRESERVATION AND BIOBANKING
(2021)
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)
Article
Cell Biology
Mohsen Mesbah, Mohsen Forouzanfar, Shahin Eghbalsaied
Summary: The study found that supplementation of 3 and 5 mu M concentrations of estradiol can improve sperm viability and membrane integrity in goat semen, with the 3 mu M concentration also increasing the highest rate of progressive motility. However, a higher concentration of estradiol (5 mu M) reduced progressive motility. Additionally, there is a considerable interaction between EDTA and estradiol for sperm motility, with EDTA reducing the supportive effects of estradiol on sperm cryopreservation parameters.
BIOPRESERVATION AND BIOBANKING
(2022)
Article
Anatomy & Morphology
Shahin Eghbalsaied, Wilfried A. Kues
Summary: In this study, a protocol for electrotransfection of sheep embryonic fibroblast cells was developed. Optimal pulsing conditions and the addition of 3% dimethyl sulfoxide (DMSO) resulted in high transfection efficiency (>98%) and cell survival rate (>97%). CRISPR/Cas9-mediated gene editing of BMP15 and GDF9 genes in sheep EF cells was successfully achieved using the electroporation method.
CELLS TISSUES ORGANS
(2023)
Article
Reproductive Biology
Mehras Mazandarani, Farid Barati, Khosro Farahmand, Farzaneh Hoseini, Shahin Eghbalsaied
Summary: The study evaluated the implementation of ultrasound for monitoring gestation in mini-lop rabbits, demonstrating the effectiveness of ultrasound biometrics in accurately tracking pregnancy and detecting abnormal fetuses.
Correction
Multidisciplinary Sciences
Anna Puig-Oliveras, Manuel Revilla, Anna Castello, Ana I. Fernandez, Josep M. Folch, Maria Ballester
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
Multidisciplinary Sciences
Jesus Valdes-Hernandez, Yuliaxis Ramayo-Caldas, Magi Passols, Cristina Sebastia, Lourdes Criado-Mesas, Daniel Crespo-Piazuelo, Anna Esteve-Codina, Anna Castello, Armand Sanchez, Josep M. Folch
Summary: This study identified a list of candidate genes associated with fatty acid traits in pig muscle, including both well-known and novel genes. Additionally, it revealed the involvement of biological processes and pathways related to energy, lipid, and carbohydrate metabolism in the modulation of fatty acid compositions.
SCIENTIFIC REPORTS
(2023)
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
Multidisciplinary Sciences
Yron Joseph Yabut Manaig, Lourdes Criado-Mesas, Anna Esteve-Codina, Emilio Marmol-Sanchez, Anna Castello, Armand Sanchez, Josep M. M. Folch
Summary: The n-6/n-3 PUFA ratio in pig skeletal muscle affects the transcriptome expression related to muscle growth and immune pathways, as well as adipogenesis and immune response. Predicted miRNA-to-mRNA regulatory networks are involved in lipid metabolism, obesity, muscle growth, and protein degradation. The n-6/n-3 PUFA ratio differences revealed genes, miRNAs, and enriched pathways involved in lipid metabolism, cell proliferation, and inflammation.
Article
Multidisciplinary Sciences
Shahin Eghbalsaied, Wilfried A. Kues
Summary: In this study, large plasmids containing the CRISPR/Cas9 system and a puromycin transgene were used to evaluate the efficiency of targeted integration. The inclusion of nocodazole and RNase HII during electroporation significantly improved the rate of high-fidelity repair events.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Yuliaxis Ramayo-Caldas, Daniel Crespo-Piazuelo, Jordi Morata, Olga Gonzalez-Rodriguez, Cristina Sebastia, Anna Castello, Antoni Dalmau, Sebastian Ramos-Onsins, Konstantinos G. Alexiou, Josep M. Folch, Raquel Quintanilla, Maria Ballester
Summary: This study found that structural variants in the pig genome are associated with the diversity and composition of the pig gut microbiota. By analyzing whole-genome sequencing data, a CNV named DUP was found to be associated with richness and Shannon alpha-diversity of the fecal bacterial diversity. This association was validated using real-time quantitative PCR and confirmed in an independent crossbreed population. These results highlight the importance of considering host-genome structural variants as potential modulators of microbial ecosystems and identify ABCC2-DNMBP CNV as a host-genetic factor for the modulation of the pig fecal microbiota.
MICROBIOLOGY SPECTRUM
(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
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)