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Xu X, Mishra B, Qin N, Sun X, Zhang S, Yang J, Xu R. Differential Transcriptome Analysis of Early Postnatal Developing Longissimus Dorsi Muscle from Two Pig Breeds Characterized in Divergent Myofiber Traits and Fatness. Anim Biotechnol 2018; 30:63-74. [PMID: 29471750 DOI: 10.1080/10495398.2018.1437045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Meat quality traits (MQTs) are very important in the porcine industry, which are mainly determined by skeletal muscle fiber composition, extra-muscular and/or intramuscular fat content. To identify the differentially expressed candidate genes affecting the meat quality traits, first we compared the MQTs and skeletal muscle fiber characteristics in the longissimus dorsi muscle (LDM) of the Northeast Min pig (NM) and the Changbaishan wild boar (CW) with their body weight approaching 90 kg. The significant divergences in the skeletal muscle fiber phenotypes and fatness traits between the two porcine breeds established an ideal model system for further identifying potential key functional genes that dominated MQTs. Further, a transcriptome profile analysis was performed using the Illumina sequencing method in early postnatal developing LDM from the two breeds at the ages of 42 days. Comparative analysis between these two cDNA libraries showed that there were 17,653 and 22,049 unambiguous tag-mapped sense transcripts detected from NM and CW, respectively. 4522 differentially expressed genes (DEGs) were revealed between the two tissue samples, of them, 4176 genes were found as having been upregulated and 346 genes were identified as having been downregulated in the NM library. By pathway enrichment analysis, a set of significantly enriched pathways were identified for the DEGs, which are potentially involved in myofiber development, differentiation and growth, lipogenesis and lipolysis in porcine skeletal muscle. The expression levels of 30 out of the DEGs were validated by real-time quantitative reverse transcriptase PCR (qRT-PCR) and the observed result was consistent noticeably with the Illumina transcriptome profiles. The findings from this study can contribute to future investigations of skeletal muscle growth and development mechanism and to establishing molecular approaches to improve meat quality traits in pig breeding.
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Affiliation(s)
- Xiaoxing Xu
- a Department of Human Nutrition, Food, and Animal Sciences , University of Hawaii at Manoa , Honolulu , HI , USA
| | - Birendra Mishra
- a Department of Human Nutrition, Food, and Animal Sciences , University of Hawaii at Manoa , Honolulu , HI , USA
| | - Ning Qin
- b College of Animal Science and Technology , Jilin Agricultural University , Changchun , China
| | - Xue Sun
- b College of Animal Science and Technology , Jilin Agricultural University , Changchun , China
| | - Shumin Zhang
- c Institute of Pig Science , Academy of Agricultural Sciences of Jilin Province , Gongzhuling , China
| | - Jinzeng Yang
- a Department of Human Nutrition, Food, and Animal Sciences , University of Hawaii at Manoa , Honolulu , HI , USA
| | - Rifu Xu
- b College of Animal Science and Technology , Jilin Agricultural University , Changchun , China
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Petit EI, Michalak Z, Cox R, O'Tuathaigh CMP, Clarke N, Tighe O, Talbot K, Blake D, Joel J, Shaw A, Sheardown SA, Morrison AD, Wilson S, Shapland EM, Henshall DC, Kew JN, Kirby BP, Waddington JL. Dysregulation of Specialized Delay/Interference-Dependent Working Memory Following Loss of Dysbindin-1A in Schizophrenia-Related Phenotypes. Neuropsychopharmacology 2017; 42:1349-1360. [PMID: 27986973 PMCID: PMC5437891 DOI: 10.1038/npp.2016.282] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 11/28/2016] [Accepted: 12/11/2016] [Indexed: 01/12/2023]
Abstract
Dysbindin-1, a protein that regulates aspects of early and late brain development, has been implicated in the pathobiology of schizophrenia. As the functional roles of the three major isoforms of dysbindin-1, (A, B, and C) remain unknown, we generated a novel mutant mouse, dys-1A-/-, with selective loss of dysbindin-1A and investigated schizophrenia-related phenotypes in both males and females. Loss of dysbindin-1A resulted in heightened initial exploration and disruption in subsequent habituation to a novel environment, together with heightened anxiety-related behavior in a stressful environment. Loss of dysbindin-1A was not associated with disruption of either long-term (olfactory) memory or spontaneous alternation behavior. However, dys-1A-/- showed enhancement in delay-dependent working memory under high levels of interference relative to controls, ie, impairment in sensitivity to the disruptive effect of such interference. These findings in dys-1A-/- provide the first evidence for differential functional roles for dysbindin-1A vs dysbindin-1C isoforms among phenotypes relevant to the pathobiology of schizophrenia. Future studies should investigate putative sex differences in these phenotypic effects.
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Affiliation(s)
- Emilie I Petit
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zuzanna Michalak
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Clinical and Experimental Epilepsy, University College London Institute of Neurology, London, UK
| | - Rachel Cox
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Colm M P O'Tuathaigh
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Medicine, University College Cork, Cork, Ireland
| | - Niamh Clarke
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Office of Research and Innovation, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Orna Tighe
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Konrad Talbot
- Department of Neurology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Derek Blake
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Josephine Joel
- Neurology Centre of Excellence for Drug Discovery, GlaxoSmithKline, Harlow, UK
- Horizon Discovery, Cambridge, UK
| | - Alexander Shaw
- Neurology Centre of Excellence for Drug Discovery, GlaxoSmithKline, Harlow, UK
| | - Steven A Sheardown
- Neurology Centre of Excellence for Drug Discovery, GlaxoSmithKline, Harlow, UK
- Takeda Cambridge, Cambridge, UK
| | - Alastair D Morrison
- Neurology Centre of Excellence for Drug Discovery, GlaxoSmithKline, Harlow, UK
- Worldwide Business Development, GlaxoSmithKline, Stevenage, UK
| | - Stephen Wilson
- Neurology Centre of Excellence for Drug Discovery, GlaxoSmithKline, Harlow, UK
- Laboratory Animal Sciences, GlaxoSmithKline, Stevenage, UK
| | - Ellen M Shapland
- Neurology Centre of Excellence for Drug Discovery, GlaxoSmithKline, Harlow, UK
| | - David C Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - James N Kew
- Neurology Centre of Excellence for Drug Discovery, GlaxoSmithKline, Harlow, UK
| | - Brian P Kirby
- School of Pharmacy, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - John L Waddington
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Jiangsu Key Laboratory of Translational Research & Therapy for Neuro-Psychiatric-Disorders and Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
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Dissecting bipolar disorder complexity through epigenomic approach. Mol Psychiatry 2016; 21:1490-1498. [PMID: 27480490 PMCID: PMC5071130 DOI: 10.1038/mp.2016.123] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 01/16/2023]
Abstract
In recent years, numerous studies of gene regulation mechanisms have emerged in neuroscience. Epigenetic modifications, described as heritable but reversible changes, include DNA methylation, DNA hydroxymethylation, histone modifications and noncoding RNAs. The pathogenesis of psychiatric disorders, such as bipolar disorder, may be ascribed to a complex gene-environment interaction (G × E) model, linking the genome, environmental factors and epigenetic marks. Both the high complexity and the high heritability of bipolar disorder make it a compelling candidate for neurobiological analyses beyond DNA sequencing. Questions that are being raised in this review are the precise phenotype of the disorder in question, and also the trait versus state debate and how these concepts are being implemented in a variety of study designs.
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Mei T, Shen CM, Liu YS, Meng HT, Zhang YD, Guo YX, Dong Q, Wang XX, Yan JW, Zhu BF, Zhang LP. Population genetic structure analysis and forensic evaluation of Xinjiang Uigur ethnic group on genomic deletion and insertion polymorphisms. SPRINGERPLUS 2016; 5:1087. [PMID: 27468387 PMCID: PMC4947079 DOI: 10.1186/s40064-016-2730-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/30/2016] [Indexed: 02/07/2023]
Abstract
Background The Uigur ethnic minority is the largest ethnic group in the Xinjiang Uygur Autonomous Region of China, and valuable resource for the study of ethnogeny. The objective of this study was to estimate the genetic diversities and forensic parameters of 30 insertion-deletion loci in Uigur ethnic group from Xinjiang Uigur Autonomous Region of China and to analyze the genetic relationships between Xinjiang Uigur group and other previously published groups based on population data of these loci. Results All the tested loci were conformed to Hardy–Weinberg equilibrium after Bonferroni correction. The observed and expected heterozygosity ranged from 0.3750 to 0.5515; and 0.4057 to 0.5037, respectively. The combined power of discrimination and probability of exclusion in the group were 0.99999999999940 and 0.9963, respectively. We analyzed the DA distance, interpopulation differentiations and population structure, conducted principal component analysis and neighbor-joining tree based on our studied group and 21 reference groups. The present results indicated that the studied Xinjiang Uigur group (represented our samples from the whole territory of Xinjiang Uigur Autonomous Region) had a close relationships with Urumchi Uigur (represented previously reported samples from Urumchi of Xinjiang) and Kazak groups. Conclusions The present study may provide novel biological information for the study of population genetics, and can also increase our understanding of the genetic relationships between Xinjiang Uigur group and other groups. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2730-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ting Mei
- Department of Biochemistry and Molecular Biology, Basic Medicine College, Xinjiang Medical University, Urumqi, 830011 People's Republic of China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Chun-Mei Shen
- Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710062 China.,Blood Center of Shaanxi Province, Xi'an, 710061 People's Republic of China
| | - Yao-Shun Liu
- Department of Biochemistry and Molecular Biology, Basic Medicine College, Xinjiang Medical University, Urumqi, 830011 People's Republic of China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Hao-Tian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Yu-Dang Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Yu-Xin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Qian Dong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Xin-Xin Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Jiang-Wei Yan
- Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 People's Republic of China
| | - Bo-Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Li-Ping Zhang
- Department of Biochemistry and Molecular Biology, Basic Medicine College, Xinjiang Medical University, Urumqi, 830011 People's Republic of China
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