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Šimon M, Mikec Š, Atanur SS, Konc J, Morton NM, Horvat S, Kunej T. Whole genome sequencing of mouse lines divergently selected for fatness (FLI) and leanness (FHI) revealed several genetic variants as candidates for novel obesity genes. Genes Genomics 2024; 46:557-575. [PMID: 38483771 PMCID: PMC11024027 DOI: 10.1007/s13258-024-01507-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 02/25/2024] [Indexed: 04/18/2024]
Abstract
BACKGROUND Analysing genomes of animal model organisms is widely used for understanding the genetic basis of complex traits and diseases, such as obesity, for which only a few mouse models exist, however, without their lean counterparts. OBJECTIVE To analyse genetic differences in the unique mouse models of polygenic obesity (Fat line) and leanness (Lean line) originating from the same base population and established by divergent selection over more than 60 generations. METHODS Genetic variability was analysed using WGS. Variants were identified with GATK and annotated with Ensembl VEP. g.Profiler, WebGestalt, and KEGG were used for GO and pathway enrichment analysis. miRNA seed regions were obtained with miRPathDB 2.0, LncRRIsearch was used to predict targets of identified lncRNAs, and genes influencing adipose tissue amount were searched using the IMPC database. RESULTS WGS analysis revealed 6.3 million SNPs, 1.3 million were new. Thousands of potentially impactful SNPs were identified, including within 24 genes related to adipose tissue amount. SNP density was highest in pseudogenes and regulatory RNAs. The Lean line carries SNP rs248726381 in the seed region of mmu-miR-3086-3p, which may affect fatty acid metabolism. KEGG analysis showed deleterious missense variants in immune response and diabetes genes, with food perception pathways being most enriched. Gene prioritisation considering SNP GERP scores, variant consequences, and allele comparison with other mouse lines identified seven novel obesity candidate genes: 4930441H08Rik, Aff3, Fam237b, Gm36633, Pced1a, Tecrl, and Zfp536. CONCLUSION WGS revealed many genetic differences between the lines that accumulated over the selection period, including variants with potential negative impacts on gene function. Given the increasing availability of mouse strains and genetic polymorphism catalogues, the study is a valuable resource for researchers to study obesity.
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Affiliation(s)
- Martin Šimon
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia.
| | - Špela Mikec
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
| | - Santosh S Atanur
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, SW7 2AZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Janez Konc
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, 1000, Slovenia
| | - Nicholas M Morton
- The Queen's Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Simon Horvat
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
| | - Tanja Kunej
- Chair of Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia.
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Expression of ovine CTNNA3 and CAP2 genes and their association with growth traits. Gene 2022; 807:145949. [PMID: 34481004 DOI: 10.1016/j.gene.2021.145949] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/10/2021] [Accepted: 08/30/2021] [Indexed: 11/22/2022]
Abstract
Growth traits is a critical economic trait for animal husbandry. In this study, the SNPs of CTNNA3 and CAP2 genes were investigated to check whether they are associated with growth traits (body weight, body height, body length and chest circumference) in Hu sheep. The result of the association analysis indicated that the mutation in CTNNA3 (g.2018018 A > G) were associated significantly with body weight, body height, body length and chest circumference (P < 0.05), the mutation in CAP2 (g.8588 T > C) were associated significantly with body height at 140, 160, 180 days (P < 0.05), AA and CC of CTNNA3 and CAP2 were the dominant genotypes associated with growth traits in Hu sheep. Moreover, combined effect analyses indicated that the growth traits with combined genotypes AACTNNA3-CCCAP2 and AACTNNA3-CTCAP2 were higher than those with genotype GGCTNNA3-CTCAP2. RT-qPCR indicated that CTNNA3 expression levels were significantly higher in liver and lung than in other nine tissues (P < 0.05), CAP2 expression levels were significantly higher in bone, heart, liver, lung and duodenum than in other six tissues (P < 0.05). In conclusion, CTNNA3 and CAP2 polymorphisms could be used as genetic markers for improving growth traits in Hu sheep husbandry.
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Zubieta AS, Marín A, Savian JV, Soares Bolzan AM, Rossetto J, Barreto MT, Bindelle J, Bremm C, Quishpe LV, Valle SDF, Decruyenaere V, de F. Carvalho PC. Low-Intensity, High-Frequency Grazing Positively Affects Defoliating Behavior, Nutrient Intake and Blood Indicators of Nutrition and Stress in Sheep. Front Vet Sci 2021; 8:631820. [PMID: 34235194 PMCID: PMC8255917 DOI: 10.3389/fvets.2021.631820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 05/26/2021] [Indexed: 11/13/2022] Open
Abstract
The intensity and frequency of grazing affect the defoliating strategy of ruminants, their daily nutrient intake, thus nutrition and physiological status. Italian ryegrass (Lolium multiflorum Lam.) pastures were grazed by sheep either under a low-intensity/high-frequency grazing strategy (Rotatinuous stocking; RN) with nominal pre- and post-grazing sward heights of 18 and 11 cm, respectively, or under a high-intensity/low-frequency strategy (traditional rotational stocking; RT) with nominal pre- and post-grazing sward heights of 25 and 5 cm, respectively. Treatments were arranged under a complete randomized design and evaluated over two periods, in different years. In 2017, the aim was to depict the type of bites that sheep perform during the grazing-down and associate them to the grazing management strategy according to their relative contribution to the diet ingested. In 2018 we estimated the total nutrient intake and evaluated blood indicators of the nutritional status and immune response to stress of sheep. The bite types accounting the most for the diet ingested by RN sheep were those performed on the "top stratum" of plants with around 20, 15, and 25 cm, whereas the type of bites accounting the most for the diet of RT sheep were those performed on "grazed plants" with around 10, 5, and ≤ 3 cm. In 2018, the RN sheep increased by 18% the total organic matter (OM) intake and by 20-25% the intake of soluble nutrients (i.e., crude protein, total soluble sugars, crude fat), digestible OM and of metabolizable energy, and had 17.5, 18, and 6.1% greater blood concentration of glucose, urea nitrogen (BUN) and albumin, respectively, but 17% lower blood neutrophil-to-lymphocyte (N:L) ratio. Sheep grazing vegetative Italian ryegrass pastures under the low-intensity/high-frequency grazing strategy (RN) ingested a diet of better quality from bites allocated on the top stratum of plants, had greater intake of soluble nutrients and blood parameters positively associated with nutritional status and immune response to stress.
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Affiliation(s)
- Angel S. Zubieta
- Grazing Ecology Research Group, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Alejandra Marín
- Grazing Ecology Research Group, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
- Facultad de Ciencias Agrarias, Departamento de Producción Animal, Universidad Nacional de Colombia, Medellín, Colombia
| | - Jean V. Savian
- Instituto Nacional de Investigación Agropecuaria, Programa Pasturas y Forrajes, Estación Experimental INIA Treinta y Tres, Treinta y Tres, Uruguay
| | | | - Jusiane Rossetto
- Grazing Ecology Research Group, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Mariana T. Barreto
- Animal Production and Ruminant Nutrition Research Group, Federal University of Pampa, Rua Promorar Luiz Joaquim de Sá Brito, Itaquí, Brazil
| | - Jéromê Bindelle
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA, Teaching and Research Centre, University of Liège, Gembloux, Belgium
| | - Carolina Bremm
- Grazing Ecology Research Group, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
- Department of Agricultural Research and Diagnosis, Secretariat of Agriculture, Livestock and Rural Development, Porto Alegre, Brazil
| | - Laura V. Quishpe
- Department of Clinical Veterinary Pathology, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Stella de Faria Valle
- Department of Clinical Veterinary Pathology, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Virginie Decruyenaere
- Productions in Agriculture Department, Animal Production Unit, Walloon Agricultural Research Centre (CRA-W), Gembloux, Belgium
| | - Paulo C. de F. Carvalho
- Grazing Ecology Research Group, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
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Zhang Q, Yang Y, Lu Y, Cao Z. iTRAQ-based quantitative proteomic analyses the cycle chronic heat stress affecting liver proteome in yellow-feather chickens. Poult Sci 2021; 100:101111. [PMID: 33965807 PMCID: PMC8120948 DOI: 10.1016/j.psj.2021.101111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/16/2020] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Heat stress (HS) is one of the main environmental factors affecting the efficiency of poultry production. The yellow-feather chickens (YFC) as an indigenous strain of chicken is a popular poultry breed in China. Our previous study used the RNA-seq to analyze the gene expression profiles of male YFC under HS and showed that the lipid and energy metabolism pathways are activated in livers of YFC exposed to acute HS (38°C, 4 h and 25°C recovery 2 h). In this study, we used quantitative proteome analysis based on iTRAQ to study the liver response of YFC to cycle chronic HS (38 ± 1°C, 8 h/d, 7 d, CyCHS). The male YFCs treatment used the CyCHS from 22 to 28 days of age. The liver tissue samples were collected at 28 d old. A total of 39,327 unique peptides matches were detected using iTRAQ analysis and 4,571 proteins exhibited a false discovery rate of 1% or less. Forty-six significant differentially expressed proteins (DEPs) were detected in the CyCHS group compared with the control group for the liver samples, including up- and down-regulated DEPs were 18 and 28, respectively. We found that the enriched biological process terms of the DEPs expressed in the liver were related to DNA metabolic process, oxidation-reduction process, oxidative stress and gluconeogenesis. In KEGG pathway analysis. Most of the hepatic DEPs were annotated to glutathione metabolism and TCA cycle in response to CyCHS. The up-regulation of 5 DEPs (GPX1, GSTT1, GSTT1L, RRM2, and LOC100859645) in the glutathione metabolism pathway likely reflects an attempt to deal with oxidative damage by CyCHS. The down-regulation of 3 DEPs (Isocitrate dehydrogenase [IDH3A], IDH3B, and phosphoenolpyruvate carboxykinase 1) in the TCA cycle pathway contributes to the regulation mechanism of energy metabolism and probably to cope with the balance of heat production and dissipation during CyCHS in order to adapt to high temperature environments. Our results provide insights into the potential molecular mechanism in heat-induced oxidative stress and energy in YFCs and future studies will investigate the functional genes associated with the response to HS.
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Affiliation(s)
- Quan Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China.
| | - YuZe Yang
- Beijing General Station of Animal Husbandry, Beijing, China
| | - YongQiang Lu
- Beijing General Station of Animal Husbandry, Beijing, China
| | - ZiWen Cao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
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Zhang J, Gao Y, Guo H, Ding Y, Ren W. Comparative metabolome analysis of serum changes in sheep under overgrazing or light grazing conditions. BMC Vet Res 2019; 15:469. [PMID: 31878922 PMCID: PMC6933664 DOI: 10.1186/s12917-019-2218-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/19/2019] [Indexed: 12/28/2022] Open
Abstract
Background Overgrazing is a primary contributor to severe reduction in forage quality and production in Inner Mongolia, leading to extensive ecosystem degradation, sheep health impairment and growth performance reduction. Further studies to identify serum biomarkers that reflect changes in sheep health and nutritional status following overgrazing would be beneficial. We hereby hypothesize that reduced sheep growth performance under overgrazing conditions would be associated with metabolic and immune response alterations. This study used an untargeted metabolomics analysis by conducting ultra-high-performance liquid chromatography combined with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF/MS) of sheep serum under overgrazing and light grazing conditions to identify metabolic disruptions in response to overgrazing. Results The sheep body weight gains as well as serum biochemical variables associated with immune responses and nutritional metabolism (immunoglobulin G, albumin, glucose, and nonesterified fatty acids) were significantly decreased with overgrazing compared with light grazing condition. In contrast, other serum parameters such as alanine and aspartate aminotransferase, alkaline phosphatase, total bilirubin, blood urea nitrogen, and interleukin-8 were markedly higher in the overgrazing group. Principal component analysis discriminated the metabolomes of the light grazing from the overgrazing group. Multivariate and univariate analyses revealed changes in the serum concentrations of 15 metabolites (9 metabolites exhibited a marked increase, whereas 6 metabolites showed a significant decrease) in the overgrazing group. Major changes of fatty acid oxidation, bile acid biosynthesis, and purine and protein metabolism were observed. Conclusions These findings offer metabolic evidence for putative biomarkers for overgrazing-induced changes in serum metabolism. Target-identification of these particular metabolites may potentially increase our knowledge of the molecular mechanisms of altered immune responses, nutritional metabolism, and reduced sheep growth performance under overgrazing conditions.
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Affiliation(s)
- Jize Zhang
- Key Laboratory of Forage Grass, Ministry of Agriculture, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, Inner Mongolia, China
| | - Yang Gao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, 130018, China
| | - Huiqin Guo
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010019, Inner Mongolia, China
| | - Yong Ding
- Key Laboratory of Forage Grass, Ministry of Agriculture, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, Inner Mongolia, China
| | - Weibo Ren
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China.
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Hua R, Zhou L, Zhang H, Yang H, Peng W, Wu K. Studying the variations in differently expressed serum proteins of Hainan black goat during the breeding cycle using isobaric tags for relative and absolute quantitation (iTRAQ) technology. J Reprod Dev 2019; 65:413-421. [PMID: 31308307 PMCID: PMC6815738 DOI: 10.1262/jrd.2018-105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Hainan black goat is a high-quality local goat breed in Hainan Province of China. It is resistant to high temperatures, humidity, and disease. Although the meat of this breed is tender
and delicious, its reproductive performance and milk yield are low. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) technology was used to analyze the
differentially expressed proteins in the serum of female Hainan black goats during the reproductive cycle (empty pregnant, estrus, gestation, and lactation). The pathway enrichment analysis
results showed that most of the differentially expressed proteins between each period belonged to the complement and coagulation cascades. Analysis of the differential protein expression and
function revealed seven proteins that were directly associated with reproduction, namely pre-SAA21, ANTXR2, vWF, SFRP3, β4GalT1, pre-IGFBP2 and Ran. This study revealed the changing patterns
of differentially expressed proteins in the reproductive cycle of the Hainan black goat. pre-SAA21, ANTXR2, vWF, SFRP3, β4GalT1, pre-IGFBP2, and Ran were identified as candidate proteins for
mediating the physiological state of Hainan black goats and regulating their fertility. This study elucidated the changes in expression levels of differentially expressed proteins during the
reproductive cycle of Hainan black goats and also provides details about its breeding pattern.
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Affiliation(s)
- Rui Hua
- Key Laboratory of Tropical Animal Breeding and Epidemic Disease Research of Hainan Province, Hainan University, Hainan 570228, People's Republic of China
| | - Lu Zhou
- Key Laboratory of Tropical Animal Breeding and Epidemic Disease Research of Hainan Province, Hainan University, Hainan 570228, People's Republic of China
| | - Haiwen Zhang
- Key Laboratory of Tropical Animal Breeding and Epidemic Disease Research of Hainan Province, Hainan University, Hainan 570228, People's Republic of China.,Laboratory of Tropical Animal Breeding, Reproduction and Nutrition, Hainan University, Hainan 570228, People's Republic of China
| | - Hui Yang
- Key Laboratory of Tropical Animal Breeding and Epidemic Disease Research of Hainan Province, Hainan University, Hainan 570228, People's Republic of China
| | - Wenchuan Peng
- Key Laboratory of Tropical Animal Breeding and Epidemic Disease Research of Hainan Province, Hainan University, Hainan 570228, People's Republic of China
| | - Kebang Wu
- Key Laboratory of Tropical Animal Breeding and Epidemic Disease Research of Hainan Province, Hainan University, Hainan 570228, People's Republic of China.,Laboratory of Tropical Animal Breeding, Reproduction and Nutrition, Hainan University, Hainan 570228, People's Republic of China
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Ren W, Badgery W, Ding Y, Guo H, Gao Y, Zhang J. Hepatic transcriptome profile of sheep (Ovis aries) in response to overgrazing: novel genes and pathways revealed. BMC Genet 2019; 20:54. [PMID: 31272371 PMCID: PMC6610972 DOI: 10.1186/s12863-019-0760-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/26/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Overgrazing is a major factor that causes steppe degradation in Inner Mongolian, resulting in extensive ecosystem damage. Scarcity of grass means sheep are smaller and therefore mutton and cashmere production is greatly reduced, which has resulted in massive annual economic losses. Liver is the primary metabolic organ in mammals. It is also the key source of energy supply and detoxification of metabolites in animals, has a close relationship with animal growth. However, investigations on the responses of sheep induced by consequence of overgrazing, particularly those relating to liver-related molecular mechanisms and related metabolic pathways, remain elusive. RESULTS The body weight daily gain of sheep, immune organ indices (liver and spleen), and serum parameters related to immune response, protein synthesis and energy supply (IgG, albumin, glucose and non-esterified fatty acid) were significantly lower in the overgrazing group. Other serum parameters including alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, total bilirubin, blood urea nitrogen and interleukin-6 were significantly higher in the overgrazing group. For the RNA-Seq results, we identified approximately 50 differentially expressed genes, of which half of were up-regulated and the other half were down-regulated (overgrazing group versus light grazing group). Bioinformatics analysis identified two enriched KEGG pathways including peroxisome proliferator-activated receptor (PPAR) signaling pathway (related to lipolysis) and ECM-receptor interaction (related to liver injury and apoptosis). Additionally, several of the down-regulated genes were related to detoxification and immune response. CONCLUSIONS Overall, based on the high-throughput RNA sequencing profile integrated with the results of serum biochemical analyses, consequences of lower forage availability and quality under overgrazing condition induced altered expression levels of genes participating in energy metabolism (particularly lipid metabolism) and detoxification and immune responses, causing lipolysis and impaired health status, which might be key reasons for the reduced growth performance of sheep. This investigation provides a novel foundation for the development of sheep hepatic gene interactive networks that are a response to the degraded forage availability under overgrazing condition.
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Affiliation(s)
- Weibo Ren
- Key Laboratory of Forage Grass, Ministry of Agriculture, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, Inner Mongolia, China
| | - Warwick Badgery
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, 2800, Australia
| | - Yong Ding
- Key Laboratory of Forage Grass, Ministry of Agriculture, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, Inner Mongolia, China
| | - Huiqin Guo
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010019, Inner Mongolia, China
| | - Yang Gao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130018, Jilin, China
| | - Jize Zhang
- Key Laboratory of Forage Grass, Ministry of Agriculture, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, Inner Mongolia, China.
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Yin RH, Huang C, Yuan J, Li W, Yin RL, Li HS, Dong Q, Li XT, Bai WL. iTRAQ-based proteomics analysis reveals the deregulated proteins related to liver toxicity induced by melamine with or without cyanuric acid in mice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 174:618-629. [PMID: 30875555 DOI: 10.1016/j.ecoenv.2019.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
The administration of melamine alone or its combination with cyanuric acid was shown to have certain liver toxicity. However, the injury mechanism of melamine-related toxicity to liver remains poorly understood. In the present study, we investigated the deregulated proteins related to liver toxicity induced by melamine with or without cyanuric acid in mice using iTRAQ quantitative proteomics technique. A total of 166 proteins were significantly changed by the melamine treatment, of which, 36 proteins were up-regulated and 130 proteins were down-regulated. Whereas, 242 proteins were significantly changed by the combined treatment of melamine and cyanuric acid, of which 81 proteins were up-regulated and 161 proteins were down-regulated. The enriched analysis of GO terms and KEGG pathway on the altered proteins showed that both enriched main GO terms and KEGG pathways appear to be different between the two kinds of treatments: melamine and mixture of melamine and cyanuric acid. Based on western blotting technique, it was confirmed that the expression of three proteins: heat shock protein 70 (HSP70), protein disulphide isomerase 6 (PDIA6) and heat shock 70 kDa protein 4-like (HSPA4L) were agreement with the findings in iTRAQ-Based quantitative analysis. These identified proteins might participate in the regulation of a wide range of biological processes, such as immune and inflammatory function, unfolded proteins response in endoplasmic reticulum, DNA damage, and the apoptosis of liver cells. These results from this study provide a new way to gain insight into the mechanisms of melamine-related toxicity to liver in animals.
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Affiliation(s)
- Rong H Yin
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Chen Huang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Jing Yuan
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Wen Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Rong L Yin
- Research Academy of Animal Husbandry and Veterinary Medicine Sciences of Jilin Province, Changchun 130062, PR China
| | - Hua S Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Qiao Dong
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Xi T Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Wen L Bai
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China.
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Zhang J, Shi H, Li S, Cao Z, Yang H, Wang Y. Integrative hepatic metabolomics and proteomics reveal insights into the mechanism of different feed efficiency with high or low dietary forage levels in Holstein heifers. J Proteomics 2019; 194:1-13. [DOI: 10.1016/j.jprot.2018.12.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 01/18/2023]
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De novo transcriptomic profiling of the clonal Leymus chinensis response to long-term overgrazing-induced memory. Sci Rep 2018; 8:17912. [PMID: 30559460 PMCID: PMC6297159 DOI: 10.1038/s41598-018-35605-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/07/2018] [Indexed: 01/26/2023] Open
Abstract
Sheepgrass (Leymus chinensis) is one of the dominant grass species present on typical steppes of the Inner Mongolia Plateau. However, L. chinensis has developed a dwarfing phenotype in response to the stressful habitat in grasslands that are severely degraded due to heavy grazing. The lack of transcriptomic and genomic information has prohibited the understanding of the transgenerational effect on physiological alterations in clonal L. chinensis at the molecular level in response to livestock grazing. To solve this problem, transcriptomic information from the leaves of clonal L. chinensis obtained from overgrazed (GR) and non-grazed (NG) grasslands was studied using a paired-end Illumina HiSeq 2500 sequencing platform. First, despite the influence of grazing being absent during the growth of clonal offspring in our hydroponic experiment, compared with those from the NG group, clonal L. chinensis from the GR group exhibited significant dwarf-type morphological traits. A total of 116,356 unigenes were subsequently generated and assembled de novo, of which 55,541 could be annotated to homologous matches in the NCBI non-redundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), gene ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The expression of 3,341 unigenes significantly differed between the GR group and the NG group with an absolute value of Log2 ratio ≥ 1. The altered expression of genes involved in defence and immune responses, pathogenic resistance and cell development indicates that livestock grazing induces a transgenerational effect on the growth inhibition of clonal L. chinensis. The results of the present study will provide important large-scale transcriptomic information on L. chinensis. Furthermore, the results facilitated our investigation of grazing-induced transgenerational effects on both the morphological and physiological characteristics of L. chinensis at the molecular levels.
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Zhang Y, Wang Y, Li S, Zhang X, Li W, Luo S, Sun Z, Nie R. ITRAQ-based quantitative proteomic analysis of processed Euphorbia lathyris L. for reducing the intestinal toxicity. Proteome Sci 2018; 16:8. [PMID: 29692685 PMCID: PMC5905050 DOI: 10.1186/s12953-018-0136-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/26/2018] [Indexed: 11/10/2022] Open
Abstract
Background Euphorbia lathyris L., a Traditional Chinese medicine (TCM), is commonly used for the treatment of hydropsy, ascites, constipation, amenorrhea, and scabies. Semen Euphorbiae Pulveratum, which is another type of Euphorbia lathyris that is commonly used in TCM practice and is obtained by removing the oil from the seed that is called paozhi, has been known to ease diarrhea. Whereas, the mechanisms of reducing intestinal toxicity have not been clearly investigated yet. Methods In this study, the isobaric tags for relative and absolute quantitation (iTRAQ) in combination with the liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic method was applied to investigate the effects of Euphorbia lathyris L. on the protein expression involved in intestinal metabolism, in order to illustrate the potential attenuated mechanism of Euphorbia lathyris L. processing. Differentially expressed proteins (DEPs) in the intestine after treated with Semen Euphorbiae (SE), Semen Euphorbiae Pulveratum (SEP) and Euphorbiae Factor 1 (EFL1) were identified. The bioinformatics analysis including GO analysis, pathway analysis, and network analysis were done to analyze the key metabolic pathways underlying the attenuation mechanism through protein network in diarrhea. Western blot were performed to validate selected protein and the related pathways. Results A number of differentially expressed proteins that may be associated with intestinal inflammation were identified. They mainly constituted by part of the cell. The expression sites of them located within cells and organelles. G protein and Eph/Ephrin signal pathway were controlled jointly by SEP and SE. After processing, the extraction of SEP were mainly reflected in the process of cytoskeleton, glycolysis and gluconeogenesis. Conclusions These findings suggest that SE induced an inflammatory response, and activated the Interleukin signaling pathway, such as the Ang/Tie 2 and JAK2/ STAT signaling pathways, which may eventually contribute to injury result from intestinal inflammatory, while SEP could alleviate this injury by down-regulating STAT1 and activating Ang-4 that might reduce the inflammatory response. Our results demonstrated the importance of Ang-4 and STAT1 expression, which are the target proteins in the attenuated of SE after processing based on proteomic investigation. Thus iTRAQ might be a novel candidate method to study scientific connotation of hypothesis that the attenuated of SE after processing expressed lower toxicity from cellular levels.
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Affiliation(s)
- Yu Zhang
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Yingzi Wang
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Shaojing Li
- 2Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dong cheng District, Dongzhimen Neixiang Street on the 16th, Beijing, 100700 People's Republic of China
| | - Xiuting Zhang
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Wenhua Li
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Shengxiu Luo
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Zhenyang Sun
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
| | - Ruijie Nie
- 1College of Traditional Chinese Pharmacy, Beijing University of Chinese Medicine, North Third Ring Road, Number 11, Chaoyang District, Beijing, 100029 People's Republic of China
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Osorio JS, Vailati-Riboni M, Palladino A, Luo J, Loor JJ. Application of nutrigenomics in small ruminants: Lactation, growth, and beyond. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.06.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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