作者机构：
湖南农业大学动物科学技术学院,湖南畜禽安全生产协同创新中心,长沙410128;中国科学院亚热带农业生态研究所,中国科学院亚热带农业生态过程重点实验室,畜禽养殖污染控制与资源化技术国家工程实验室,动物营养生理与代谢过程湖南省重点实验室,长沙410125;[蒋线吉; 印遇龙] Hunan Co⁃Innovation Center of Animal Production Safety, Hunan Agricultural University, Changsha, 410128, China, Key Laboratory of Animal Nutritional Physiology and Metabolic Process of Hunan, National Engineering Laboratory for Poultry Breeding Pollution Control and Resource Technology, Key Laboratory of Agro⁃Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China;[李瑞; 冯淦熠] Key Laboratory of Animal Nutritional Physiology and Metabolic Process of Hunan, National Engineering Laboratory for Poultry Breeding Pollution Control and Resource Technology, Key Laboratory of Agro⁃Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
通讯机构：
[Li, R.] K;Key Laboratory of Animal Nutritional Physiology and Metabolic Process of Hunan, China
摘要：
The purpose of this study is to reveal the effects of different particle sizes of rice straw on the rumen protozoa count, nutrient disappearance rate, rumen fermentation, and microbial community in a rumen simulation technique (RUSITEC) system. In this experiment, a single-factor random trial design was adopted. According to the different particle sizes of rice straw, there were three treatments with three replies in each treatment. Three kinds of goat total mixed ration (TMR), with the same nutrients were used to carry out a 10 days in vitro fermentation experiment using the rumen simulation system developed by Hunan Agricultural University, including 6 days the pretrial period and 4 days formal period. This study found that the organic matter disappearance rate, concentrations of total volatile fatty acids (VFAs), acetate, propionate, and iso-butyrate were greatest in the 4 mm group (p < 0.05). There were no significant differences in the alpha diversity, among the three groups (p > 0.05). The relative abundance of Treponema and Ruminococcus of the 2 mm group increased; the relative abundance of Butyrivibrio and Prevotella in samples increased in the 4 mm group. In addition, the results of correlation analysis showed that Prevotella and Ruminococcus was positively correlated with butyrate, ammonia-N, dOM and d ADF (p < 0.05) and negatively correlated with valerate (p < 0.05); Oscillospira was positively correlated with valerate (p < 0.01) and negatively correlated with propionate, butyrate, ammonia-N, dOM and dADF (p < 0.05). The present results imply that compared to the other groups, rice straw particle size of 4 mm may improve the disappearance rate of nutrients and promote the production of volatile fatty acids by regulating ruminal microorganisms.
期刊：
STAR Protocols,2023年4(4):102589 ISSN：2666-1667
通讯作者：
Ren, Ruimin;Wang, Heng
作者机构：
[Ren, Ruimin] College of Animal Science and Technology, Hunan Agricultural University, Changsha, China. Electronic address: ruimin.ren@hunau.edu.cn;[Hua, Yao] College of Animal Science and Technology, Shandong Agricultural University, Taian, China;[Wang, Heng] College of Animal Science and Technology, Shandong Agricultural University, Taian, China. Electronic address: wangheng@sdau.edu.cn
通讯机构：
[Wang, Heng; Ren, Ruimin] C;College of Animal Science and Technology, Hunan Agricultural University, Changsha, China. Electronic address: ruimin.;College of Animal Science and Technology, Shandong Agricultural University, Taian, China. Electronic address:
摘要：
Pioneer transcription factors (TFs) can directly establish higher-order chromatin interactions to instruct gene transcription. Here, we present a protocol for capturing TF-mediated 3D chromatin interactions using affinity tag-based bridge linker (BL)-Hi-chromatin immunoprecipitation (HiChIP). We describe steps for constructing FLAG-tagged TF, performing BL-HiChIP, and preparing the library. We then detail procedures for sequencing, data analysis, and quality control. This protocol has potential applications in 3D chromatin analysis centered on any specific TF in any type of cells without the need of optimal antibodies. For complete details on the use and execution of this protocol, please refer to Ren etal. (2022).(1).
通讯机构：
[Zhipeng Gao; Jiajing Guo] H;Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, Hunan Province, China<&wdkj&>Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China
关键词：
Citrus aurantium L. var. amara Engl.;E. coli;Linalool;Lipopolysaccharide;Proteome;Ribosomal assembly;Substrate transportation;Transcriptome
期刊：
International Journal of Biological Macromolecules,2023年240:124384 ISSN：0141-8130
通讯作者：
Xiang Zhao
作者机构：
[Ying, Yan-Rong; Xiao, Tiao-Yi; Long, Zhe; Xiong, Shu-Ting; Zhao, Xiang; Li, Jun-Hua] Hunan Agr Univ, Coll Fisheries, Changsha 410128, Peoples R China.;[Xiao, Tiao-Yi; Long, Zhe; Xiong, Shu-Ting; Li, Jun-Hua] Hunan Agr Univ, Hunan Engn Technol Res Ctr Featured Aquat Resource, Changsha 410128, Peoples R China.;[Zhang, Yi-Bing; Zhao, Xiang] Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China.
通讯机构：
[Xiang Zhao] C;College of Fisheries, Hunan Agricultural University, Changsha 410128, China<&wdkj&>State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
摘要：
Membrane-associated RING-CH-type finger (MARCH) proteins have been reported to regulate type I IFN production during host antiviral innate immunity. The present study reported the zebrafish MARCH family member, MARCH7, as a negative regulator in virus-triggered type I IFN induction via targeting TANK-binding kinase 1 (TBK1) for degradation. As an IFN-stimulated gene (ISG), we discovered that MARCH7 was significantly induced by spring viremia of carp virus (SVCV) or poly(I:C) stimulation. Ectopic expression of MARCH7 reduced the activity of IFN promoter and dampened the cellular antiviral responses triggered by SVCV and grass carp reovirus (GCRV), which concomitantly accelerated the viral replication. Accordingly, the knockdown of MARCH7 by siRNA transfection significantly promoted the transcription of ISG genes and inhibited SVCV replication. Mechanistically, we found that MARCH7 interacted with TBK1 and degraded it via K48-linked ubiquitination. Further characterization of truncated mutants of MARCH7 and TBK1 confirmed that the C-terminal RING of MARCH7 is essential in the MARCH7-mediated degradation of TBK1 and the negative regulation of IFN antiviral response. This study reveals a molecular mechanism by which zebrafish MARCH7 negatively regulates the IFN response by targeting TBK1 for protein degradation, providing new insights into the essential role of MARCH7 in antiviral innate immunity.
作者：
Pu, Xuan Xuan;Zhang, Xiu Min;Li, Qiu Shuang;Wang, Rong;Zhang, Min;...
期刊：
Frontiers in Microbiology,2023年13:1079056 ISSN：1664-302X
通讯作者：
Tan, Z.L.;Wang, M.
作者机构：
[Tan, Zhi Liang; Tan, Bie; Pu, Xuan Xuan] Univ Hunan Agr Univ, Dept Anim Sci & Technol, Changsha, Hunan, Peoples R China.;[Tan, Zhi Liang; Zhang, Xiu Min; Wang, Rong; Pu, Xuan Xuan; Zhang, Shi Zhe; Li, Qiu Shuang; Wang, Min] Chinese Acad Sci, Inst Subtrop Agr, CAS Key Lab Agroecol Proc Subtrop Reg, Natl Engn Lab Pollut Control & Waste Utilizat Live, Changsha, Hunan, Peoples R China.;[Lin, Bo; Zhang, Min] Univ Guangxi, Dept Anim Sci & Technol, Nanning, Guangxi, Peoples R China.
通讯机构：
[Tan, Z.L.] D;[Wang, M.] C;CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, Hunan, China;Department of Animal Science and Technology, Hunan, China
通讯机构：
[Wenbing Zhang] T;The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs), The Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China<&wdkj&>Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China<&wdkj&>Author to whom correspondence should be addressed.
期刊：
FRONTIERS IN ENDOCRINOLOGY,2023年14:1070692 ISSN：1664-2392
通讯作者：
Hussain, T.;Tan, B.
作者机构：
[Tan, Bie; Hussain, Tarique] Hunan Agr Univ, Coll Anim Sci & Technol, Changsha, Hunan, Peoples R China.;[Yaseen, Anjaleena; Chughtai, Muhammad Ismail; Hussain, Tarique] Nucl Inst Agr & Biol, Pakistan Inst Engn & Appl Sci PIEAS, Coll NIAB C, Anim Sci Div, Faisalabad, Pakistan.;[Kandeel, Mahmoud] King Faisal Univ, Coll Vet Med, Dept Biomed Sci, Al Hufuf, Al Ahsa, Saudi Arabia.;[Kandeel, Mahmoud] Kafrelshikh Univ, Fac Vet Med, Dept Pharmacol, Kafrelshikh, Egypt.;[Metwally, Elsayed] Suez Canal Univ, Fac Vet Med, Dept Cytol & Histol, Ismailia, Egypt.
通讯机构：
[Hussain, T.; Tan, B.] C;College of Animal Science and Technology, Hunan, China
关键词：
male infertility;ROS;Oxidative Stress;Semen quality;Steriodogenesis
摘要：
Male infertility is a widely debated issue that affects males globally. There are several mechanisms involved. Oxidative stress is accepted to be the main contributing factor, with sperm quality and quantity affected by the overproduction of free radicals. Excess reactive oxygen species (ROS) cannot be controlled by the antioxidant system and, thus, potentially impact male fertility and hamper sperm quality parameters. Mitochondria are the driving force of sperm motility; irregularities in their function may lead to apoptosis, alterations to signaling pathway function, and, ultimately, compromised fertility. Moreover, it has been observed that the prevalence of inflammation may arrest sperm function and the production of cytokines triggered by the overproduction of ROS. Further, oxidative stress interacts with seminal plasma proteomes that influence male fertility. Enhanced ROS production disturbs the cellular constituents, particularly DNA, and sperms are unable to impregnate the ovum. Here, we review the latest information to better understand the relationship between oxidative stress and male infertility, the role of mitochondria, the cellular response, inflammation and fertility, and the interaction of seminal plasma proteomes with oxidative stress, as well as highlight the influence of oxidative stress on hormones; collectively, all of these factors are assumed to be important for the regulation of male infertility. This article may help improve our understanding of male infertility and the strategies to prevent it.
摘要：
Simple Summary: With the increase of protease types and products, it is time-consuming and laborious to evaluate the effect of protease on feed protein utilization with animal experiments, and it is not conducive to evaluate a large number of samples in a short time. The purpose of this study was to quickly evaluate the effects of four proteases (acidic, neutral, alkaline and keratinase) on feed ingredients (corn gluten meal, corn and soybean meal) using an in vitro method to determine the optimal dosage of each protease for corn gluten meal and corn and soybean meal, and to explore the factors affecting the effect of proteases. In addition, this research also carried out animal experiments to verify the effect of protease on the corn-soybean meal diet of 31-day-old broilers. Abstract: This study was conducted to investigate the effects of different proteases alone or in combination on protein digestibility of broilers. In vitro, the properties of four proteases in broilers, including acidic protease (AcP), alkaline protease (AlP), neutral protease (NeP) and keratinase (Ker), on endogenous protease activity and their effects on protein digestibility of common ingredients in broiler diets were investigated using a gut-mimicking model. In vivo, 640 1-day-old male broilers were randomly divided into 8 groups of 10 with 8 replicates of 10 birds per replicate cage. Eight dietary treatments included a corn-soybean meal basal diet (control), and the basal diet with 1.6 U AcP/g, 0.8 U NeP/g, 0.8 U AlP/g, 0.4 U Ker/g, 1.6 U AcP/g + 0.8 U NeP/g, 1.6 U AcP/g + 0.8 U AlP/g, or 1.6 U AcP/g + 0.4 U Ker/g added. The experiment lasted for 31 days. The results showed that the optimum pH values of AcP, NeP, AlP and Ker were 3.0, 9.0, 11.0 and 11.0 in vitro, respectively. Ker recovery proportion was 37.68% at pH 3.3-6.2. AcP alone or in combination with NeP, AlP or Ker increased in vitro crude protein digestibility (IVCPD) and decreased ileal apparent digestibility of crude protein in 31-day-old broilers (p < 0.05). All protease supplementation reduced the ileal apparent digestibility of amino acids compared to the control (p < 0.05). Acidic protease had a positive effect on trypsin and chymotrypsin activities, while AlP and Ker showed a negative effect. In vivo, average daily gain and average daily feed intake were significantly (p < 0.05) increased in broiler diets supplemented with AcP compared to the control group. When adding exogenous proteases to broiler diets, their sensitivity to digestive pH and their negative effects on endogenous protease activity, dosage and combination effects should be taken into account. In addition, the properties and dosage of proteases and the protein level in the feed should be considered.
摘要：
Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed horse SVs using a multi-assembly approach. Our findings suggest that SVs with the accumulation of mammalian-wide interspersed repeats related to long interspersed nuclear elements might be a horse-specific mechanism to modulate genome-wide gene regulatory networks. We found that olfactory receptors were commonly loss and accumulated deleterious mutations, but no purge of deleterious mutations occurred during horse domestication. We examined the potential effects of SVs on the spatial structure of chromatin via topologically associating domains (TADs). Breed-specific TADs were significantly enriched by breed-specific SVs. We identified 4199 unique breakpoint-resolved novel insertions across all chromosomes that account for 2.84 Mb sequences missing from the reference genome. Several novel insertions might have potential functional consequences, as 519 appeared to reside within 449 gene bodies. These genes are primarily involved in pathogen recognition, innate immune responses and drug metabolism. Moreover, 37 diverse horses were resequenced. Combining this with public data, we analysed 97 horses through a comparative population genomics approach to identify the genetic basis underlying breed characteristics using Thoroughbreds as a case study. We provide new scientific evidence for horse domestication, an understanding of the genetic mechanism underlying the phenotypic evolution of horses, and a comprehensive genetic variation resource for further genetic studies of horses.
关键词：
WGCNA;weighted gene co-expression network analysis;RNA-Seq;RNA-sequencing;DEGs;differentially expressed genes;qPCR;quantitative real-time polymerase chain reaction;FPKM;fragments per kilobase of transcript per million;GO;Ningxiang pig;backfat tissue;different developmental stage;WGCNA;hub gene;lipid metabolism
摘要：
Fat deposition is an economically important trait in pigs. Ningxiang pig, one of the four famous indigenous breeds in China, is characterized by high fat content. The underlying gene expression pattern in different developmental periods of backfat tissue remains unclear, and the purpose of this investigation is to explore the potential molecular regulators of backfat tissue development in Ningxiang pigs. Backfat tissue (three samples for each stage) was initially collected from different developmental stages (60, 120, 180, 240, 300, and 360 days after birth), and histological analysis and RNA sequencing (RNA-seq) were then conducted. Fragments per kilobase of transcript per million (FPKM) method was used to qualify gene expressions, and differentially expressed genes (DEGs) were identified. Furthermore, strongly co-expressed genes in modules, which were named by color, were clustered by Weighted gene co-expression network analysis (WGCNA) based on dynamic tree cutting algorithm. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment were subsequently implemented, and hub genes were described in each module. Finally, QPCR analysis was employed to validate RNA-seq data. The results showed that adipocyte area increased and adipocyte number decreased with development of backfat tissue. A total of 1,024 DEGs were identified in five comparison groups (120 days vs. 60 days, 180 days vs. 120 days, 240 days vs. 180 days, 300 days vs. 240 days, and 360 days vs. 300 days). The turquoise, red, pink, paleturquoise, darkorange, and darkgreen module had the highest correlation coefficient with 60, 120, 180, 240, 300, and 360 days developmental stage, while the tan, black and turquoise module had strong relationship with backfat thickness, adipocyte area, and adipocyte number, respectively. Thirteen hub genes (ACSL1, ACOX1, FN1, DCN, CHST13, COL1A1, COL1A2, COL6A3, COL5A1, COL14A1, OAZ3, DNM1, and SELP) were recognized. ACSL1 and ACOX1 might perform function in the early developmental stage of backfat tissue (60 days), and FN1, DCN, COL1A1, COL1A2, COL5A1, COL6A3, and COL14A1 have unignorable position in backfat tissue around 120 days developmental stage. Besides, hub genes SELP and DNM1 in modules significantly associated with backfat thickness and adipocyte area might be involved in the process of backfat tissue development. These findings contribute to understand the integrated mechanism underlying backfat tissue development and promote the progress of genetic improvement in Ningxiang pigs.
作者机构：
[Yin, Jie; Li, Yunxia; Tian, Yu; Zhou, Feng; Ma, Jie; Xia, Siting; Yang, Tong; Liu, Gang; Huang, Xingguo] College of Animal Science and Technology, Hunan Agriculture University, Changsha 410128, China;[Ma, Libao] College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China;Hunan Chuweixiang Agriculture and Animal Husbandry Co., Ltd., Ningxiang 410600, China;Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China;[Zeng, Qinghua] College of Animal Science and Technology, Hunan Agriculture University, Changsha 410128, China<&wdkj&>Hunan Chuweixiang Agriculture and Animal Husbandry Co., Ltd., Ningxiang 410600, China
通讯机构：
[Yulong Yin; Xingguo Huang] C;College of Animal Science and Technology, Hunan Agriculture University, Changsha 410128, China<&wdkj&>College of Animal Science and Technology, Hunan Agriculture University, Changsha 410128, China<&wdkj&>Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
摘要：
The gut microbiota consistently shows strong correlations with lipid metabolism in humans and animals, and whether the gut microbiota contributes to muscle fatty acid (FA) deposition and meat traits in farm animals has not been fully resolved. In this study, we aimed to unveil the microbial mechanisms underlying muscle FA deposition in pigs. First, we systematically revealed the correlation between the gut microbiome and muscle FA levels in 43 obese Ningxiang pigs and 50 lean Duroc Landrace Yorkshire (DLY) pigs. Mutual fecal microbial transplantation showed that the obese Ningxiang pig-derived microbiota increased the muscle FA content and improved meat quality by reshaping the gut microbial composition in lean DLY pigs. Lactobacillus reuteri has been identified as a potential microbial biomarker in obese Ningxiang pig-derived microbiota-challenged DLY pigs. A gavage experiment using lean DLY pigs confirmed that L. reuteri XL0930 isolated from obese Ningxiang pigs was the causal species that increased the muscle FA content. Mechanistically, SLC22A5, a carnitine transporter, was downregulated in L. reuteri XL0930-fed DLY pigs, resulting in reduced muscle carnitine levels. Muscle and intestinal L-carnitine levels, which correlated with the muscle FA content, impeded fat synthesis and FA accumulation in invitro and invivo models. In conclusion, we uncovered an unexpected and important role of the obese Ningxiang pig-derived microbiota in regulating muscle FA metabolism via the SLC22A5-mediated carnitine system.
通讯机构：
[Duan, YH ] C;Chinese Acad Sci, CAS Key Lab Agroecol Proc Subtrop Reg, Hunan Prov Key Lab Anim Nutr Physiol & Metab Proc, Inst Subtrop Agr,Natl Engn Lab Pollut Control & Wa, Changsha 410125, Peoples R China.;Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
关键词：
weaned piglets;liver injury and restoration;lipopolysaccharide
摘要：
This study aimed to explore the effects of the incremental injection of lipopolysaccharide (LPS) on liver histopathology, inflammation, oxidative status, and mitochondrial function in piglets. Forty healthy Duroc x Landrace x Yorkshire castrated boars (21 +/- 2 days old, weight 6.84 +/- 0.11 kg) were randomly assigned to five groups (n = 8) and then slaughtered on days 0 (group 0, without LPS injection), 1 (group 1), 5 (group 5), 9 (group 9), and 15 (group 15) of LPS injection, respectively. The results showed that, compared to the piglets without LPS injection, LPS injection caused liver injury in the early phase, as manifested by the increased activities of serum liver injury-related parameters (aspartate amino transferase, alanine aminotransferase, alkaline phosphatase, cholinesterase, and total bile acid) on day 1, and impaired liver morphology (disordered hepatic cell cord arrangement, dissolved and vacuolized hepatocytes, karyopycnosis, and inflammatory cell infiltration and congestion) on days 1 and 5. Meanwhile, LPS injection caused liver inflammation, oxidative stress, and mitochondrial dysfunction on days 1 and 5, as reflected by the upregulated mRNA expression of TNF-alpha, IL-6, IL-1 beta, TLR4, MyD88, and NF-kappa B; increased MPO and MDA content; and impaired mitochondrial morphology. However, these parameters were ameliorated in the later phase (days 9 similar to 15). Taken together, our data indicate that the incremental injection of the LPS-induced liver injury of piglets could be self-repaired.
