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Imprinting at the KBTBD6 locus involves species-specific m ternal methylation and monoallelic expression in livestock animals

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Journal of animal Science and Biotechnology 2024年第1期15卷 127-145页

作者： Jinsoo Ahn In-Sul Hwang Mi-Ryung Park Seongsoo Hwang Kichoon Lee Department of animal Sciences The Ohio State UniversityColumbusOH 43210USA animal Biotechnology Division Rural Development AdministrationNational Institute of Animal ScienceJeonbuk 55365Republic of Korea Columbia center for Translational Immunology Columbia University Irving Medical CenterColumbia UniversityNew YorkNY 10032USA animal Welfare Research Team National Institute of Animal ScienceRDA1500Kongjwipatjwi‑roJeollabuk‑do 55365Republic of Korea

Background The primary differentially methylated regions(DMRs) which are maternally hypermethylated serve as imprinting control regions(ICRs) that drive monoallelic gene expression, and these ICRs have been investigated due to their implications in mammalian development. Although a subset of genes has been identified as imprinted, in-depth comparative approach needs to be developed for identification of species-specific imprinted genes. Here, we examined DNA methylation status and allelic expression at the KBTBD6 locus across species and tissues and explored potential mechanisms of *** Using whole-genome bisulfite sequencing and RNA-sequencing on parthenogenetic and normal porcine embryos, we identified a maternally hypermethylated DMR between the embryos at the KBTBD6 promoter Cp G island and paternal monoallelic expression of KBTBD6. Also, in analyzed domesticated mammals but not in humans, non-human primates and mice, the KBTBD6 promoter Cp G islands were methylated in oocytes and/or allelically methyl-ated in tissues, and monoallelic KBTBD6 expression was observed, indicating livestock-specific imprinting. Further analysis revealed that these Cp G islands were embedded within transcripts in porcine and bovine oocytes which coexisted with an active transcription mark and DNA methylation, implying the presence of transcription-dependent *** In this study, our comparative approach revealed an imprinted expression of the KBTBD6 gene in domesticated mammals, but not in humans, non-human primates, and mice which implicates species-specific evolution of genomic imprinting.

关键词： Differentially methylated region Domesticated mammal Imprinting KBTBD6 Parthenogenetic

Investigation on mechanical properties regulation of rock-like specimens based on 3D printing and similarity quantification

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International Journal of Mining Science and Technology 2024年第5期34卷 573-585页

作者： Duanyang Zhuang Zexu Ning Yunmin Chen Jinlong Li Qingdong Li Wenjie Xu center for Hypergravity experiment and Interdisciplinary Research Zhejiang UniversityHangzhou 310058China MOE Key Laboratory of Soft Soils and Geoenvironmental Engineering Zhejiang UniversityHangzhou 310058China

3D printing is widely adopted to quickly produce rock mass models with complex structures in batches,improving the consistency and repeatability of physical *** is necessary to regulate the mechanical properties of 3D-printed specimens to make them proportionally similar to natural *** study investigates mechanical properties of 3D-printed rock analogues prepared by furan resin-bonded silica sand *** mechanical property regulation of 3D-printed specimens is realized through quantifying its similarity to sandstone,so that analogous deformation characteristics and failure mode are *** similarity conversion,uniaxial compressive strength,cohesion and stress–strain relationship curve of 3D-printed specimen are similar to those of *** the study ranges,the strength of 3D-printed specimen is positively correlated with the additive content,negatively correlated with the sand particle size,and first increases then decreases with the increase of curing *** regulation scheme with optimal similarity quantification index,that is the sand type of 70/140,additive content of 2.5‰and curing temperature of 81.6℃,is determined for preparing 3D-printed sandstone analogues and *** effectiveness of mechanical property regulation is proved through uniaxial compression contrast *** study provides a reference for preparing rock-like specimens and engineering models using 3D printing technology.

关键词： 3D printing Mechanical property regulation Similarity quantification Rock analogue Sandstone

Identification of novel genes associated with atherosclerosis in Bama miniature pig

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animal Models and experimental Medicine 2024年第3期7卷 377-387页

作者： Dengfeng Ding Yuqiong Zhao Yunxiao Jia Miaomiao Niu Xuezhuang Li Xinou Zheng Hua Chen Laboratory animal center Chinese PLA General HospitalBeijingChina

Background:Atherosclerosis is a chronic cardiovascular disease of great ***,it is difficult to establish a direct connection between conventional small animal models and clinical *** pig's genome,physiology,and anatomy reflect human biology better than other laboratory animals,which is crucial for studying the pathogenesis of ***:We used whole-genome sequencing data from nine Bama minipigs to perform a genome-wide linkage analysis,and further used bioinformatic tools to filter and identify underlying candidate *** gene function prediction was performed using the online prediction tool STRING *** and immunofluorescence were used to detect the expression of proteins encoded by candidate ***:We mapped differential single nucleotide polymorphisms(SNPs)to genes and obtained a total of 102 differential genes,then we used GO and KEGG pathway enrichment analysis to identify four candidate genes,including SLA-1,SLA-2,SLA-3,and *** cause changes in the primary and tertiary structures of SLA-I and TAP2 proteins,the primary structures of these two proteins have undergone amino acid changes,and the tertiary structures also show slight *** addition,immunohistochemistry and immunofluorescence results showed that the expression changes of TAP2 protein in coronary arteries showed a trend of increasing from the middle layer to the inner ***:We have identified SLA-I and TAP2 as potential susceptibility genes of atherosclerosis,highlighting the importance of antigen processing and immune response in atherogenesis.

关键词： atherosclerosis candidate genes genome-wide linkage analysis major histocompatibility complex whole genome sequencing

Molybdenum and cadmium co-induce necroptosis through Th1/Th2 imbalance-mediated endoplasmic reticulum stress in duck ovaries

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Journal of Environmental Sciences 2024年第8期142卷 92-102页

作者： Ting Cui Xueyan Dai Huiling Guo Dianyun Wang Bingyan Huang Wenjing Pu Xuesheng Chu Caiying Zhang Jiangxi Provincial Key Laboratory for animal Health Institute of Animal Population HealthCollege of Animal Science and TechnologyJiangxi Agricultural UniversityNanchang 330045China

Cadmium(Cd)and excess molybdenum(Mo)pose serious threats to animal *** previous study has determined that Cd and/or Mo exposure can cause ovarian damage of ducks,while the specific mechanism is still *** further investigate the toxic mechanism of Cd and Mo co-exposure in the ovary,forty 8-day-old female ducks were randomly allocated into four groups for 16 weeks,and the doses of Cd and Mo in basic diet per kg were as follows:control group,Mo group(100 mg Mo),Cd group(4 mg Cd),and Mo+Cd group(100 mg Mo+4 mg Cd).Cadmium sulfate 8/3-hydrate(CdSO_(4)·8/3H_(2)O)and hexaammonium molybdate((NH_(4))_(6)Mo_(7)O_(24)·4H_(2)O)were the origins of Cd and Mo,*** the 16th week of the experiment,all ovary tissues were collected for the detection of related *** data indicated that Mo and/or Cd induced trace element disorders and Th1/Th2 balance to divert toward Th1 in the ovary,which activated endoplasmic reticulum(ER)stress and then provoked necroptosis through triggering RIPK1/RIPK3/MLKL signaling pathway,and eventually caused ovarian pathological injuries and necroptosis *** alterations of above indicators were most apparent in the joint *** all,this research illustrates that Mo and/or Cd exposure can initiate necroptosis through Th1/Th2 imbalance-modulated ER stress in duck ovaries,and Mo and Cd combined exposure aggravates ovarian *** research explores the molecular mechanism of necroptosis caused by Mo and/or Cd,which reveals that ER stress attenuation may be a therapeutic target to alleviate necroptosis.

关键词： Molybdenum Cadmium Th1/Th2 imbalance Endoplasmic reticulum stress Necroptosis Ovary

Extraction,chemical components,bioactive functions and adulteration identification of walnut oils:A review

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Grain & Oil Science and Technology 2024年第1期7卷 30-41页

作者： Yuan Gao Jia Hu Xia Su Qi Li Caihong Su Yongling Li Gaiqin Ma Siyu Zhang Xiuzhu Yu Engineering Research center of Grain and Oil Functionalized Processing College of Food Science and EngineeringNorthwest A&F UniversityShaanxi 712100China animal Products and animal Medicine Feed Quality Inspection center Hebei 050041China

Walnut oil is a functional wood oil known to researchers that may potentially be a large source of Chinese edible *** are various extraction methods for walnut oil,including traditional(pressing,solvent-and enzymeassisted extraction)and novel methods(microwave,ultrasound,supercritical CO_(2),subcritical and other extraction technologies).Walnut oil is rich in nutrients,including phytosterols,tocopherols,polyphenols,squalene and *** provides many health benefits,such as antioxidant,antitumor,anti-inflammatory,antidiabetic and lipid metabolism-related *** addition,the authentication of walnut oil has received much research *** present review provides detailed research on walnut oil extraction,composition,health benefits and adulteration identification *** path toward further walnut oil improvement in the context of the market value of walnut oil is also discussed.

关键词： Extraction technology Chemical composition Bioactive Authentication

Hi-Tag:a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers

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Science China(Life Sciences) 2024年第5期67卷 1027-1034页

作者： Xiaolong Qi Lu Zhang Qiulin Zhao Peng Zhou Sai Xian Zhang Jingjin Li Zhuqing Zheng Yue Xiang Xueting Dai Zhe Jin Yaobang Jian Xinyun Li Liangliang Fu Shuhong Zhao Key Lab of Agricultural animal Genetics Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of AgricultureCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China The Cooperative Innovation center for Sustainable Pig Production Wuhan 430070China Hubei Hongshan Laboratory Frontiers Science Center for Animal Breeding and Sustainable ProductionWuhan 430070China

Protein-mediated chromatin interactions can be revealed by coupling proximity-based ligation with chromatin ***,these techniques require complex experimental procedures and millions of cells per experiment,which limits their widespread application in life science ***,we develop a novel method,Hi-Tag,that identifies high-resolution,long-range chromatin interactions through transposase tagmentation and chromatin proximity ligation(with a phosphorothioate-modified linker).Hi-Tag can be implemented using as few as 100,000 cells,involving simple experimental procedures that can be completed within 1.5 ***,Hi-Tag is capable of using its own data to identify the binding sites of specific proteins,based on which,it can acquire accurate interaction *** results suggest that Hi-Tag has great potential for advancing chromatin interaction studies,particularly in the context of limited cell availability.

关键词： Hi-Tag chromatin interactions transposase tagmentation chromatin proximity ligation low cell numbers

A computational model to identify fertility-related proteins using sequence information

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Frontiers of Computer Science 2024年第1期18卷 229-237页

作者： Yan LIN Jiashu WANG Xiaowei LIU Xueqin XIE De WU Junjie ZHANG Hui DING Key Laboratory for animal Disease-Resistance Nutrition of the Ministry of Agriculture Animal Nutrition InstituteSichuan Agricultural UniversityChengdu 611130China School of Life Science and Technology and center for Informational Biology University of Electronic Science and Technology of ChinaChengdu 610054China

Fertility is the most crucial step in the development process,which is controlled by many fertility-related proteins,including spermatogenesis-,oogenesis-and embryogenesis-related *** identification of fertility-related proteins can provide important clues for studying the role of these proteins in ***,in this study,we constructed a two-layer classifier to identify fertility-related *** this classifier,we first used the composition of amino acids(AA)and their physical and chemical properties to code these three fertility-related ***,the feature set is optimized by analysis of variance(ANOVA)and incremental feature selection(IFS)to obtain the optimal feature *** five-fold cross-validation(CV)and independent data tests,the performance of models constructed by different machine learning(ML)methods is evaluated and ***,based on support vector machine(SVM),we obtained a two-layer model to classify three fertility-related *** the independent test data set,the accuracy(ACC)and the area under the receiver operating characteristic curve(AUC)of the first layer classifier are 81.95%and 0.89,respectively,and them of the second layer classifier are 84.74%and 0.90,*** results show that the proposed model has stable performance and satisfactory prediction accuracy,and can become a powerful model to identify more fertility related proteins.

关键词： sfertility-related proteins machine1 learning sequence information feature selection

Strong invariance principle for a counterbalanced random walk

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Applied Mathematics(A Journal of Chinese Universities) 2024年第2期39卷 370-380页

作者： TAN Hui-qun HU Zhi-shui DONG Liang International Institute of Finance School of ManagementUniversity of Science and Technology of ChinaHefei 230026China center for Basic Teaching and experiment Nanjing University of Science and TechnologyJiangyin 214443China

We study a counterbalanced random walkS_(n)=X_(1)+…+X_(n),which is a discrete time non-Markovian process andX_(n) are given recursively as *** n≥2,X_(n) is a new independent sample from some fixed law̸=0 with a fixed probability p,andX_(n)=−X_(v(n))with probability 1−p,where v(n)is a uniform random variable on{1;…;n−1}.We apply martingale method to obtain a strong invariance principle forS_(n).

关键词： random walk martingale invariance principle

Characteristics of genetic basis copy number variation in production and adaptation traits of Chinese indigenous sheep

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Journal of Genetics and Genomics 2024年第5期51卷 566-569页

作者： Meilin Jin Gang Liu Jian Lu Zhiqiang Chen Huihua Wang Taotao Li Caihong Wei State Key Laboratory of animal Biotech Breeding Institute of Animal SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100193China College of animal Science and Technology China Agricultural UniversityBeijing100193China National animal Husbandry Service National Center of Preservation&Utilization of Animal Genetic ResourcesBeijing 100125China Glbizzia Biosciences Beijing 102629China

Copy number variations(CNVs)range in size from 50 base pairs(bp)to several megabases(Mb)and encompass various types of structural variations,such as insertions,deletions,duplications,and complex multiallelic events(MacDonald et al.,2014).These genomic alterations modulate phenotype by altering gene dosage and transcriptional regulation,and are key drivers of biological evolution and determinants of genetic diversity and phenotypic *** recent years,CNVs have been detected in the genomes of various livestock species(Yuan et al.,2021;Chen et al.,2022).Upadhyay et al.(2017)conducted a comprehensive analysis of CNV distribution in the European cattle genome and determined that the Kit gene is associated with color-sidedness in English longhorn *** study presented extensive genome-wide information on CNVs in wild,commercial,and local chicken breeds to gain an integrated understanding of the domestication process and exclusively identified the genes involved(Chen et al.,2022).

关键词： sided number dosage