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Rajawat D, Nayak SS, Jain K, Sharma A, Parida S, Sahoo SP, Bhushan B, Patil DB, Dutt T, Panigrahi M. Genomic patterns of selection in morphometric traits across diverse Indian cattle breeds. Mamm Genome 2024; 35:377-389. [PMID: 39014170 DOI: 10.1007/s00335-024-10047-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 06/09/2024] [Indexed: 07/18/2024]
Abstract
This study seeks a comprehensive exploration of genome-wide selective processes impacting morphometric traits across diverse cattle breeds, utilizing an array of statistical methods. Morphometric traits, encompassing both qualitative and quantitative variables, play a pivotal role in characterizing and selecting livestock breeds based on their external appearance, size, and physical attributes. While qualitative traits, such as color, horn structure, and coat type, contribute to adaptive features and breed identification, quantitative traits like body weight and conformation measurements bear a closer correlation with production characteristics. This study employs advanced genotyping technologies, including the Illumina BovineSNP50 Bead Chip and next-generation sequencing methods like Reduced Representation sequencing, to identify genomic signatures associated with these traits. We applied four intra-population methods to find evidence of selection, such as Tajima's D, CLR, iHS, and ROH. We found a total of 40 genes under the selection signature, that were associated with morphometric traits in five cattle breeds (Kankrej, Tharparkar, Nelore, Sahiwal, and Gir). Crucial genes such as ADIPDQ, DPP6, INSIG1, SLC35D2 in Kankrej, LPL, ATP6V1B2, CDC14B in Tharparkar, HPSE2, PLAG1 in Nelore, PCSK1, PRKD1 in Sahiwal, and GNAQ, HPCAL1 in Gir were identified in our study. This approach provides valuable insights into the genetic basis of variations in body weight and conformation traits, facilitating informed selection processes and offering a deeper understanding of the evolutionary and domestication processes in diverse cattle breeds.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Karan Jain
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Anurodh Sharma
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | | | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
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Stavros S, Panagopoulos P, Machairiotis N, Potiris A, Mavrogianni D, Sfakianakis A, Drakaki E, Christodoulaki C, Panagiotopoulos D, Sioutis D, Karampitsakos T, Antonakopoulos N, Christopoulos P, Drakakis P. Association between cytokine polymorphisms and recurrent pregnancy loss: A review of current evidence. Int J Gynaecol Obstet 2024. [PMID: 38706379 DOI: 10.1002/ijgo.15575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/09/2024] [Accepted: 04/20/2024] [Indexed: 05/07/2024]
Abstract
Cytokines are a type of protein that play an important role in the immune response and can also affect many physiological processes in the body. Cytokine polymorphisms refer to genetic variations or mutations that occur within the genes that code for cytokines, which may affect the level of cytokine production and function. Some cytokine polymorphisms have been associated with an increased risk of developing certain diseases, while others may be protective or have no significant effect on health. In recent years, the role of cytokine polymorphisms in the development of recurrent pregnancy loss (RPL) has been studied. RPL or miscarriage is defined as the occurrence of two or more consecutive pregnancy losses before the 20th week of gestation. There are diverse causes leading to RPL, including genetic, anatomical, hormonal, and immunological factors. With regard to cytokine polymorphisms, a few of them have been found to be associated with an increased risk of RPL, for instance, variations in the genes that code for interleukin-6, tumor necrosis factor-alpha, and interleukin-10. The exact mechanisms by which cytokine polymorphisms affect the risk of recurrent miscarriage are still being studied, and further research is essential to fully understand this complex condition. This brief review aims to summarize the recent literature on the association between cytokine polymorphisms and RPL.
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Affiliation(s)
- Sofoklis Stavros
- Third Department of Obstetrics and Gynecology, University General Hospital "ATTIKON", Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Periklis Panagopoulos
- Third Department of Obstetrics and Gynecology, University General Hospital "ATTIKON", Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolaos Machairiotis
- Third Department of Obstetrics and Gynecology, University General Hospital "ATTIKON", Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastasios Potiris
- Third Department of Obstetrics and Gynecology, University General Hospital "ATTIKON", Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Despoina Mavrogianni
- First Department of Obstetrics and Gynecology, Alexandra Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Eirini Drakaki
- First Department of Obstetrics and Gynecology, Alexandra Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Chrysi Christodoulaki
- Department of Obstetrics and Gynecology, Chania General Hospital "St. George", Chania, Greece
| | - Dimitrios Panagiotopoulos
- Third Department of Obstetrics and Gynecology, University General Hospital "ATTIKON", Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimos Sioutis
- Third Department of Obstetrics and Gynecology, University General Hospital "ATTIKON", Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Theodoros Karampitsakos
- Third Department of Obstetrics and Gynecology, University General Hospital "ATTIKON", Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Panagiotis Christopoulos
- Second Department of Obstetrics and Gynecology, University Hospital Aretaieion, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Peter Drakakis
- Third Department of Obstetrics and Gynecology, University General Hospital "ATTIKON", Medical School, National and Kapodistrian University of Athens, Athens, Greece
- First Department of Obstetrics and Gynecology, Alexandra Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Khazaal NM, Alghetaa HF, Al-Shuhaib MBS, Al-Thuwaini TM, Alkhammas AH. A novel deleterious oxytocin variant is associated with the lower twinning ratio in Awassi ewes. Anim Biotechnol 2023; 34:3404-3415. [PMID: 36449364 DOI: 10.1080/10495398.2022.2152038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
This study aimed to assess the possible association of oxytocin (OXT) gene with reproductive traits in two groups of Awassi ewes that differ in their reproductive potentials. Sheep were genotyped using PCR-single-stranded conformation polymorphism approach. Three genotypes were detected in exon 2, CC, CA, and AA, and a novel SNP was identified with a missense effect on oxytocin (c.188C > A → p.Arg55Leu). A significant (p < 0.01) association of p.Arg55Leu with the twinning rate was found as ewes with AA and CA genotypes exhibited, respectively a lower twinning ratio than those with the wild-type CC genotype. The deleterious impact of p.Arg55Leu was demonstrated by all in silico tools that were utilized to assess the effect of this variant on the structure, function, and stability of oxytocin. Molecular docking showed that p.Arg55Leu caused a dramatic alteration in the binding of oxytocin with its receptor and reduced the number of interacted amino acids between them. Our study suggests that ewes with AA and CA genotypes showed a lower reproductive performance due to the presence of p.Arg55Leu, which caused damaging impacts on oxytocin and is binding with the OXT receptor. The utilization of the p.Arg55Leu could be useful for improving Awassi reproductive potential.
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Affiliation(s)
- Neam M Khazaal
- Department of Physiology, Biochemistry and Pharmacology, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Hasan F Alghetaa
- Department of Physiology, Biochemistry and Pharmacology, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | | | - Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Iraq
| | - Ahmed H Alkhammas
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Iraq
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Özcan Gökçek E, Işık R, Karahan B, Gamsız K. Characterisation of Single Nucleotide Polymorphisms and Haplotypes of MSTN Associated with Growth Traits in European Sea Bass (Dicentrarchus labrax). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:347-357. [PMID: 37162623 DOI: 10.1007/s10126-023-10211-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/24/2023] [Indexed: 05/11/2023]
Abstract
The myostatin (MSTN) gene, known as growth differentiation factor-8 (GDF-8), is a member of the transforming growth factor-β (TGF-β) superfamily and plays a specific inhibitory role during the critical phases of skeletal muscle mass development in vertebrates. This study was conducted to investigate MSTN polymorphisms in harvest size European sea bass reared in Turkey. Nine single nucleotide polymorphisms (SNPs) and two indels were identified in exons 1-3 of MSTN in the European sea bass population The associations between the g.16612A indel located in intron 1 and standard length were significant. The MSTN g.15252 T > A locus in intron 2 was significantly related to the total weight, fillet weight and standard length (P < 0.05). The relationship between the g.14873C > T locus in exon 3 of MSTN and standard height, head length, body length, pre-anal length, abdominal length, post-anal length and head width was significant (P < 0.05). According to the results of the haplotype analysis, two haplogroup and eight haplotype combinations were detected in the population. The haplogroup 2 had significant associations with all measured growth traits (P < 0.05). Thus, SNPs and haplotypes identified in this study could be useful for European sea bass breeding and marker-assisted selection.
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Affiliation(s)
- Emel Özcan Gökçek
- Faculty of Fisheries, Department of Aquaculture, Ege University, İzmir, 35100, Türkiye.
| | - Raziye Işık
- Faculty of Agriculture, Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, Tekirdağ, 59030, Türkiye
| | - Bilge Karahan
- Faculty of Fisheries, Department of Aquaculture, Ege University, İzmir, 35100, Türkiye
| | - Kutsal Gamsız
- Faculty of Fisheries, Department of Aquaculture, Ege University, İzmir, 35100, Türkiye
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Ye M, Fan Z, Xu Y, Luan K, Guo L, Zhang S, Luo Q. Exploring the association between fat-related traits in chickens and the RGS16 gene: insights from polymorphism and functional validation analysis. Front Vet Sci 2023; 10:1180797. [PMID: 37234072 PMCID: PMC10205986 DOI: 10.3389/fvets.2023.1180797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction Excessive fat deposition in chickens can lead to reduced feed utilization and meat quality, resulting in significant economic losses for the broiler industry. Therefore, reducing fat deposition has become an important breeding objective in addition to achieving high broiler weight, growth rate, and feed conversion efficiency. In our previous studies, we observed high expression of Regulators of G Protein Signaling 16 Gene (RGS16) in high-fat individuals. This led us to speculate that RGS16 might be involved in the process of fat deposition in chickens. Methods Thus, we conducted a polymorphism and functional analysis of the RGS16 gene to investigate its association with fat-related phenotypic traits in chickens. Using a mixed linear model (MLM), this study explored the relationship between RGS16 gene polymorphisms and fat-related traits for the first time. We identified 30 SNPs of RGS16 in a population of Wens Sanhuang chickens, among which 8 SNPs were significantly associated with fat-related traits, including sebum thickness (ST), abdominal fat weight (AFW), and abdominal fat weight (AFR). Furthermore, our findings demonstrated that AFW, AFR, and ST showed significant associations with at least two or more out of the eight identified SNPs of RGS16. We also validated the role of RGS16 in ICP-1 cells through various experimental methods, including RT-qPCR, CCK- 8, EdU assays, and oil red O staining. Results Our functional validation experiments showed that RGS16 was highly expressed in the abdominal adipose tissue of high-fat chickens and played a critical role in the regulation of fat deposition by promoting preadipocyte differentiation and inhibiting their proliferation. Taken together, our findings suggest that RGS16 polymorphisms are associated with fat-related traits in chickens. Moreover, the ectopic expression of RGS16 could inhibit preadipocyte proliferation but promote preadipocyte differentiation. Discussion Based on our current findings, we propose that the RGS16 gene could serve as a powerful genetic marker for marker-assisted breeding of chicken fat-related traits.
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Affiliation(s)
- Mao Ye
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Zhexia Fan
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Yuhang Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Kang Luan
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Lijin Guo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Siyu Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Qingbin Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
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Molecular Cloning, Screening of Single Nucleotide Polymorphisms, and Analysis of Growth-Associated Traits of igf2 in Spotted Sea Bass (Lateolabrax maculatus). Animals (Basel) 2023; 13:ani13060982. [PMID: 36978523 PMCID: PMC10044540 DOI: 10.3390/ani13060982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/27/2023] [Accepted: 03/05/2023] [Indexed: 03/12/2023] Open
Abstract
The insulin-like growth factor 2 gene (igf2) is thought to be a key factor that could regulate animal growth. In fish, few researchers have reported on the single nucleotide polymorphisms (SNPs) located in igf2 and their association with growth traits. We screened the SNPs of igf2 from the spotted sea bass (Lateolabrax maculatus) by Sanger sequencing and made an association between these SNPs with growth traits. The full-length complementary (c) DNA of igf2 was 1045 bp, including an open reading frame of 648 bp. The amino acid sequence of Igf2 contained a signal peptide, an IGF domain, and an IGF2_C domain. Multiple sequence alignment showed that the IGF domain and IGF2_C domain were conserved in vertebrates. The genome sequence of igf2 had a length of 6227 bp. Fourteen SNPs (13 in the introns and one in one of the exons) were found in the genome sequence of igf2. Four SNPs located in the intron were significantly associated with growth traits (p < 0.05). These results demonstrated that these SNPs could be candidate molecular markers for breeding programs in L. maculatus.
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Montero-Ovalle W, Sanabria-Salas MC, Mesa-López de Mesa J, Varela-Ramírez R, Segura-Moreno YY, Sánchez-Villalobos SA, Nuñez-Lemus M, Serrano ML. Determination of TMPRSS2-ERG, SPOP, FOXA1, and IDH1 prostate cancer molecular subtypes in Colombian patients and their possible implications for prognosis. Cell Biol Int 2023; 47:1017-1030. [PMID: 36740223 DOI: 10.1002/cbin.12000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/30/2022] [Accepted: 01/21/2023] [Indexed: 02/07/2023]
Abstract
Prostate cancer (PCa) is one of cancer with of the highest incidence and mortality worldwide. Current disease prognostic markers do not differentiate aggressive from indolent PCa with sufficient certainty, and characterization by molecular subtypes has been sought to allow a better classification. TMPRSS2-ERG, SPOP, FOXA1, and IDH1 molecular subtypes have been described, but the association of these subtypes with prognosis in PCa is unclear; their frequency in Colombian patients is also unknown. Formalin-fixed and paraffin-embedded samples of radical prostatectomy from 112 patients with PCa were used. The TMPRSS2-ERG subtype was assessed with fluorescent in situ hybridization. The mutations in SPOP, FOXA1, and IDH1 in hot-spot regions were evaluated using Sanger sequencing. Fusion was detected in 71 patients (63.4%). No statistically significant differences were found between the state of fusion and the variables analyzed. In the 41 fusion-negative cases (36.6%), two patients (4.9%) had missense mutations in SPOP (p.F102C and p.F133L), representing a 1.8% of the overall cohort. The low frequency of this subtype in Colombians could be explained by the reported variability in the frequency of these mutations according to the population (5%-20%). No mutations were found in FOXA1 in the cases analyzed. The synonym SNP rs11554137 IDH1105GGT was found in tumor tissue but not in the normal tissue in one case. A larger cohort of Colombian PCa patients is needed for future studies to validate these findings and gain a better understanding of the molecular profile of this cancer in our population and if there are any differences by Colombian regions.
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Affiliation(s)
- Wendy Montero-Ovalle
- Cancer Biology Research Group, Instituto Nacional de Cancerología, Bogotá, Colombia.,Department of Chemistry, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | - Rodolfo Varela-Ramírez
- Department of Oncological Urology, Instituto Nacional de Cancerología, Bogotá, Colombia.,Department of Surgery, Faculty of Medicine Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | - Marcela Nuñez-Lemus
- Research Support and Monitoring Group, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Martha L Serrano
- Cancer Biology Research Group, Instituto Nacional de Cancerología, Bogotá, Colombia.,Department of Chemistry, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá, Colombia
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Shahid K, Khan K, Badshah Y, Mahmood Ashraf N, Hamid A, Trembley JH, Shabbir M, Afsar T, Almajwal A, Abusharha A, Razak S. Pathogenicity of PKCγ Genetic Variants-Possible Function as a Non-Invasive Diagnostic Biomarker in Ovarian Cancer. Genes (Basel) 2023; 14:236. [PMID: 36672978 PMCID: PMC9858858 DOI: 10.3390/genes14010236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Ovarian cancer has the highest mortality rate among gynecologic malignancies, owing to its misdiagnosis or late diagnosis. Identification of its genetic determinants could improve disease outcomes. Conventional Protein Kinase C-γ (PKCγ) dysregulation is reported in several cancers. Similarly, its variant rs1331262028 is also reported to have an association with hepatocellular carcinoma. Therefore, the aim of the present study was to analyze the variant rs1331262028 association with ovarian cancer and to determine its impact on PKCγ's protein interactions. Association of variation was determined through genotyping PCR (cohort size:100). Protein-protein docking and molecular dynamic simulation were carried out to study the variant impact of PKCγ interactions. The study outcome indicated the positive association of variant rs1331262028 with ovarian cancer and its clinicopathological features. Molecular dynamics simulation depicted the potential influence of variation on PKCγ molecular signaling. Hence, this study provided the foundations for assessing variant rs1331262028 as a potential prognostic marker for ovarian cancer. Through further validation, it can be applied at the clinical level.
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Affiliation(s)
- Kanza Shahid
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44010, Pakistan
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44010, Pakistan
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44010, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Pakistan
| | - Arslan Hamid
- LIMES Institute (AG-Netea), University of Bonn, Carl-Troll-Str. 31, 53115 Bonn, Germany
| | - Janeen H. Trembley
- Minneapolis VA Health Care System Research Service, Minneapolis, MN 55417, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44010, Pakistan
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Ali Abusharha
- Department of Optometry, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
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Association between Synonymous SNPs of SOX10 and Plumage Color and Reproductive Traits of Ducks. Animals (Basel) 2022; 12:ani12233345. [PMID: 36496864 PMCID: PMC9736065 DOI: 10.3390/ani12233345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022] Open
Abstract
Mutations in the SOX10 gene affect the plumage color of chickens and pigeons. The mutation also causes abnormal pigmentation of the skin and hair color, as well as postnatal growth retardation and reproduction problems in humans and mice. In this study, we investigated the association between the SOX10 gene and plumage color and reproductive traits of ducks using SNPs. We found six novel SNPs from 11 identified SNP sites using direct sequencing for PCR products from three different mixed DNA pools. We found two coding SNPs to be associated with the plumage color of ducks (ZJU1.0 Chr1. g.54065419C>T and g.54070844C>T), and found three coding SNPs associated with the reproductive traits of ducks (g.54065419C>T, g.54070844C>T, and g.54070904C>T), which were age at sexual maturity, body weight at sexual maturity, and the Haugh unit for egg quality traits and egg production in different productive periods. These results also indicated that the T alleles of the three SNPs of the coding region of SOX10 contribute to lower reproductive traits.
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Artificial Neural Network-Based Identification of Associations between UCP2 and UCP3 Gene Polymorphisms and Meat Quantity Traits. J FOOD QUALITY 2022. [DOI: 10.1155/2022/6017374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In identifying mutations occurring in distinct cow breeds, genetic elements must be taken into consideration. More recently, these hereditary features have gained attention throughout the world. As in many underdeveloped nations, to bridge the deficit in molecular genetics, multiple solutions are required. The inner membrane anion carrier superfamily contains the uncoupling proteins (UCPs), vital to energy regulation. Research on heredity has shown that variations in the UCP2 and UCP3 genes are connected to obesity and metabolic syndrome. This research aimed to investigate if any mutation in the UCP 2 and UCP 3 genes are related to many characteristics in Pakistan’s three indigenous cattle breeds using artificial neural network (ANN). For better analysis, the output of the ANN model is loaded into the Primer Premier 3 software. Using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and sequencing, the results of this study indicated 07 variations in the exon 4 region of the UCP2 gene and 03 variants in the exon 3 area of the UCP3 gene among 215 indigenous cow breeds. The association study revealed that the g.C35G mutation in the UCP3 gene is strongly related to meat quantity characteristics such as carcass weight and drip percentage (P0.05) but not with body height or hip width (
). Sequence analysis showed five distinct diplotypes: AA, BC, AC, CC, and CD. Cattle with the novel heterozygous diplotype BC perform better in carcass trait and drip percentage than animals with other genotypes. The study’s findings suggest that the UCP3 gene may be utilized for marker-assisted selection (MAS) and breed mixing in Pakistan cattle breeds to aid in the country’s economic growth.
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Nair RR, Mohan M, Rudramurthy GR, Vivekanandam R, Satheshkumar PS. Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus. Pathogens 2021; 10:1649. [PMID: 34959603 PMCID: PMC8703355 DOI: 10.3390/pathogens10121649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Trends associated with codon usage in molluscum contagiosum virus (MCV) and factors governing the evolution of codon usage have not been investigated so far. In this study, attempts were made to decipher the codon usage trends and discover the major evolutionary forces that influence the patterns of codon usage in MCV with special reference to sub-types 1 and 2, MCV-1 and MCV-2, respectively. Three hypotheses were tested: (1) codon usage patterns of MCV-1 and MCV-2 are identical; (2) SCUB (synonymous codon usage bias) patterns of MCV-1 and MCV-2 slightly deviate from that of human host to avoid affecting the fitness of host; and (3) translational selection predominantly shapes the SCUB of MCV-1 and MCV-2. Various codon usage indices viz. relative codon usage value, effective number of codons and codon adaptation index were calculated to infer the nature of codon usage. Correspondence analysis and correlation analysis were performed to assess the relative contribution of silent base contents and significance of codon usage indices in defining bias in codon usage. Among the tested hypotheses, only the second and third hypotheses were accepted.
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Affiliation(s)
- Rahul Raveendran Nair
- Centre for Evolutionary Ecology, Aushmath Biosciences, Vadavalli Post, Coimbatore 641041, India
| | - Manikandan Mohan
- College of Pharmacy, University of Georgia, Athens, GA 30605, USA;
| | | | - Reethu Vivekanandam
- Department of Biotechnology, Bharathiyar University, Coimbatore 641046, India;
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12
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Wang S, Cheng Y, Liu S, Xu Y, Gao Y, Wang C, Wang Z, Feng T, Lu G, Song J, Xia P, Hao L. A synonymous mutation in IGF-1 impacts the transcription and translation process of gene expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:1446-1465. [PMID: 34938600 PMCID: PMC8655398 DOI: 10.1016/j.omtn.2021.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/10/2021] [Indexed: 11/18/2022]
Abstract
Insulin-like growth factor 1 (IGF-1) is considered to be a crucial gene in the animal development of bone and body size. In this study, a unique synonymous mutation (c.258 A > G) of the IGF-1 gene was modified with an adenine base editor to observe the growth and developmental situation of mutant mice. Significant expression differences and molecular mechanisms among vectors with different alanine synonymous codons were explored. Although modification of a single synonymous codon rarely interferes with animal phenotypes, we observed that the expression and secretion of IGF-1 were different between 8-week-old homozygous (Ho) and wild-type (WT) mice. In addition, the IGF-1 with optimal codon combinations showed a higher expression content than other codon combination modes at both transcription and translation levels and performed proliferation promotion. The gene stability and translation initiation efficiency also changed significantly. Our findings illustrated that the synonymous mutation altered the IGF-1 gene expression in individual mice and suggested that the synonymous mutation affected the IGF-1 expression and biological function through the transcription and translation processes.
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Affiliation(s)
- S.Y. Wang
- College of Animal Science, Jilin University, Changchun 130062, China
- Beijing Advanced Innovation Centre for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Y.Y. Cheng
- Ministry of Health Key Laboratory of Radiobiology, College of Public Health, Jilin University, Changchun, Jilin 130021, China
| | - S.C. Liu
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Y.X. Xu
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Y. Gao
- College of Animal Science, Jilin University, Changchun 130062, China
| | - C.L. Wang
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Z.G. Wang
- College of Animal Science, Jilin University, Changchun 130062, China
| | - T.Q. Feng
- College of Animal Science, Jilin University, Changchun 130062, China
| | - G.H. Lu
- College of Animal Science, Jilin University, Changchun 130062, China
| | - J. Song
- College of Animal Science, Jilin University, Changchun 130062, China
| | - P.J. Xia
- College of Animal Science, Jilin University, Changchun 130062, China
| | - L.L. Hao
- College of Animal Science, Jilin University, Changchun 130062, China
- Corresponding author: Linlin Hao, College of Animal Science, Jilin University, Changchun 130062, China.
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13
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Ali A, Javed K, Zahoor I, Anjum KM, Sharif N. Identification of polymorphisms in the MSTN and ADRB3 genes associated with growth and ultrasound carcass traits in Kajli sheep. Anim Biotechnol 2021:1-16. [PMID: 34775903 DOI: 10.1080/10495398.2021.2000428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The aim of this investigation was to find single nucleotide polymorphisms (SNPs) in the myostatin (MSTN) and the beta-3 adrenergic receptor (ADRB3) genes associated with growth and ultrasound carcass traits in Kajli sheep. The five growth traits were birth weight (BWT-EBV), 120-day weight (120DWT-EBV), 180-day weight (180DWT-EBV), 270-day weight (270DWT-EBV), and 365-day weight (365DWT-EBV). The three ultrasound carcass traits were width (WLD) and depth of longissimus dorsi (DLD) and back fat thickness (BFT). The analysis of the MSTN sequence revealed one non-synonymous substitution (c.197T > A) in exon 1, one single nucleotide substitution (c.373 + 18G > T) in intron 1, and one synonymous substitution (c.861T > A) in exon 3. However, there were four single nucleotide synonymous substitutions (c.130C > T, c.294C > G, c.579G > T, and c.654C > G) in exon 1 of the ADRB3 gene. All the SNPs in the MSTN gene, except for c.373 + 18G > T, were in Hardy-Weinberg Equilibrium (HWE). Conversely, none of the SNPs found in ADRB3 were in HWE. Two of the MSTN SNPs (c.197T > A and c.373 + 18G > T) had significant associations with all evaluated growth and ultrasound carcass traits. The SNPs c.130C > T and c.294C > G in ADRB3 were significantly associated with 180DWT-EBV. Collectively, these findings indicate that several SNPs in the studied genes were significantly related to growth and carcass traits in Kajli sheep.
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Affiliation(s)
- Asad Ali
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Khalid Javed
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Imran Zahoor
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Khalid Mahmood Anjum
- Department of Wildlife & Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Numan Sharif
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
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14
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Ali DA, Al-Shuhaib MBS, Farhadi G, Al-Kafajy FR, Al-Thuwaini TM, Esmailizadeh A. Detection of a novel single nucleotide polymorphism in IGF2 gene with a negative impact on egg production and body weight in Japanese quail (Coturnix japonica). J Genet Eng Biotechnol 2021; 19:170. [PMID: 34735645 PMCID: PMC8569122 DOI: 10.1186/s43141-021-00271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/19/2021] [Indexed: 11/10/2022]
Abstract
Background Insulin-like growth factor 2 (IGF2) is one of three hormones that share high structural similarity to insulin. It is involved in several insulin-like growth-regulating and mitogenic activities. This study was conducted to genotype the coding regions of the IGF2 gene in Japanese quail (Coturnix japonica) using PCR-SSCP-sequencing, and to assess the possible association of the polymorphism of these regions with the main egg production traits. A total of 240 female birds with an equal number of three Japanese quail populations (Brown or BR, Black or BL, and White or WT) were included in this study. Results All the genotyped regions exerted no heterogeneity in their sequences with one exception detected in the exon 2. In this locus, a novel single nucleotide polymorphism (SNP) was detected in which “A” was substituted with “G” at 81 position with a silent effect (p.F79=SNP) on IGF2 protein. Association analyses indicated a significant (P < 0.05) relation of this SNP with egg number (EN) and bird weight (BW) in the analyzed populations, in which the birds with AG genotype had lower EN and BW than those with AA genotype. The p.F79=SNP was largely detected in the WT line than the other two lines. Conclusion The detected p.F79=SNP has a highly negative effect on EN and BW in Japanese quail. Thus, the implementation of the variations of the IGF2 gene can be a useful marker in the marker-assisted selection of Japanese quail. This is the first report to describe IGF2 gene variations in Japanese quail, which strongly suggests raising the birds from the BR line with AA genotype when breeders desire to raise Japanese quail for large-scale egg production.
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Affiliation(s)
- Dhafer A Ali
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Golzar Farhadi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran
| | - Fadhil R Al-Kafajy
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran.
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15
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Bagatoli A, de Melo ALP, Gasparino E, Rodrigues MT, Ferreira L, Garcia OSR, Soares MAM. Association between polymorphisms of APOB, SLC27A6, AGPAT6 and PRLR genes and milk production and quality traits in goats. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Komar AA. A Code Within a Code: How Codons Fine-Tune Protein Folding in the Cell. BIOCHEMISTRY (MOSCOW) 2021; 86:976-991. [PMID: 34488574 DOI: 10.1134/s0006297921080083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genetic code sets the correspondence between the sequence of a given nucleotide triplet in an mRNA molecule, called a codon, and the amino acid that is added to the growing polypeptide chain during protein synthesis. With four bases (A, G, U, and C), there are 64 possible triplet codons: 61 sense codons (encoding amino acids) and 3 nonsense codons (so-called, stop codons that define termination of translation). In most organisms, there are 20 common/standard amino acids used in protein synthesis; thus, the genetic code is redundant with most amino acids (with the exception of Met and Trp) are being encoded by more than one (synonymous) codon. Synonymous codons were initially presumed to have entirely equivalent functions, however, the finding that synonymous codons are not present at equal frequencies in mRNA suggested that the specific codon choice might have functional implications beyond coding for amino acid. Observation of nonequivalent use of codons in mRNAs implied a possibility of the existence of auxiliary information in the genetic code. Indeed, it has been found that genetic code contains several layers of such additional information and that synonymous codons are strategically placed within mRNAs to ensure a particular translation kinetics facilitating and fine-tuning co-translational protein folding in the cell via step-wise/sequential structuring of distinct regions of the polypeptide chain emerging from the ribosome at different points in time. This review summarizes key findings in the field that have identified the role of synonymous codons and their usage in protein folding in the cell.
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Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA. .,Department of Biochemistry and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,DAPCEL, Inc., Cleveland, OH 44106, USA
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17
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Yamagishi MEB. Is our immune system a powerful vaccine factory? Genet Mol Biol 2021; 44:e20200468. [PMID: 34410292 PMCID: PMC8358740 DOI: 10.1590/1678-4685-gmb-2020-0468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/05/2021] [Indexed: 11/21/2022] Open
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18
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The Identification of the SARS-CoV-2 Whole Genome: Nine Cases Among Patients in Banten Province, Indonesia. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.2.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain of virus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the current pandemic. Viral genome sequencing has been widely applied during outbreaks to study the relatedness of this virus to other viruses, its transmission mode, pace, evolution and geographical spread, and also its adaptation to human hosts. To date, more than 90,000 SARS-CoV-2 genome sequences have been uploaded to the GISAID database. The availability of sequencing data along with clinical and geographical data may be useful for epidemiological investigations. In this study, we aimed to analyse the genetic background of SARS-CoV-2 from patients in Indonesia by whole genome sequencing. We examined nine samples from COVID-19 patients with RT-PCR cycle threshold (Ct) of less than 25 using ARTIC Network protocols for Oxford Nanopore’s Gridi On sequencer. The analytical methods were based on the ARTIC multiplex PCR sequencing protocol for COVID-19. In this study, we found that several genetic variants within the nine COVID-19 patient samples. We identified a mutation at position 614 P323L mutation in the ORF1ab gene often found in our severe patient samples. The number of SNPs and their location within the SARS-CoV-2 genome seems to vary. This diversity might be responsible for the virulence of the virus and its clinical manifestation.
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19
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Karavidha KK, Burmeister M, Greenwald MK. β-Arrestin 2 (ARRB2) Polymorphism is Associated With Adverse Consequences of Chronic Heroin Use. Am J Addict 2021; 30:351-357. [PMID: 33783060 DOI: 10.1111/ajad.13150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/10/2020] [Accepted: 12/28/2020] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND AND OBJECTIVES β-arrestin 2 is an intracellular protein recruited during the activation of G-protein-coupled receptors. In preclinical studies, β-arrestin 2 has been implicated in µ-opioid receptor desensitization and internalization and the development of opioid tolerance and dependence. The present study investigated relationships between variants in the gene encoding β-arrestin 2 (ARRB2) and clinically relevant phenotypes among individuals with opioid use disorder (OUD). We hypothesized that ARRB2 variants would be associated with the negative effects of long-term heroin use. METHODS Chronic heroin users (N = 201; n = 103 African American; n = 98 Caucasian) were genotyped for ARRB2 r1045280 (synonymous, also affecting binding motif of transcription factor GTF2IRD1), rs2036657 (3'UTR) and rs3786047 (intron) and assessed for the past-month frequency of use, injection use, and lifetime duration of heroin use, number of heroin quit-attempts, and heroin use-related consequences. RESULTS Lifetime heroin-use consequences (especially occupational and health-related) were significantly lower for African American ARRB2 r1045280 C-allele carriers compared with the TT genotype. There was no significant genotype difference in the Caucasian group. ARRB2 rs2036657 was in strong linkage disequilibrium with rs1045280. DISCUSSION AND CONCLUSIONS These results, consistent with extant data, illustrate a role for ancestry-dependent allelic variation in ARRB2 r1045280 on heroin-use consequences. The ARRB2 r1045280 C-allele played a protective role in African-descent participants. SCIENTIFIC SIGNIFICANCE These first-in-human findings, which should be replicated, provide support for mechanistic investigations of ARRB2 and related intracellular signaling molecules in OUD etiology, treatment, and relapse prevention. (Am J Addict 2021;00:00-00).
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Affiliation(s)
- Klevis K Karavidha
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University, Detroit, Michigan
| | - Margit Burmeister
- Department of Computational Medicine & Bioinformatics, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan
| | - Mark K Greenwald
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University, Detroit, Michigan.,Department of Pharmacy Practice, Wayne State University, Detroit, Michigan
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20
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Gonçalves AM, Pereira-Santos AR, Esteves AR, Cardoso SM, Empadinhas N. The Mitochondrial Ribosome: A World of Opportunities for Mitochondrial Dysfunction Toward Parkinson's Disease. Antioxid Redox Signal 2021; 34:694-711. [PMID: 32098485 DOI: 10.1089/ars.2019.7997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Significance: Mitochondrial ribosomes (mitoribosomes) are organelles that translate mitochondrial messenger RNA in the matrix and, in mammals, have evolved to translate 13 polypeptides of the pathway that performs oxidative phosphorylation (OXPHOS). Although a number of devastating diseases result from defects in this mitochondrial translation apparatus, most are associated with genetic mutations and little is known about allelopathic defects caused by antibiotics, toxins, or nonproteinogenic amino acids. Recent Advances: The levels of mitochondrial ribosomal subunits 12S and 16S ribosomal RNA (rRNA) in cells/tissues from patients carrying mutations in these genes have been associated with alterations in mitochondrial translation efficiency and with impaired OXPHOS activities, as well as with the severity of clinical phenotypes. In recent decades, important studies revealed a prominent role of mitochondrial dysfunction in Parkinson's disease (PD); however, the involvement of mitoribosomes remains largely unknown. Critical Issues: Considering that mitoribosomal structure and function can determine the efficiency of OXPHOS and that an impaired mitochondrial respiratory chain is a common finding in PD, we argue that the mitoribosome may be key to disease onset and progression. With this review, we comprehensively integrate the available knowledge on the composition, assembly, and role of the mitoribosome in mitochondrial efficiency, reflecting on its possible involvement in the etiopathogenesis of this epidemic disease as an appealing research avenue. Future Directions: If a direct correlation between mitoribosome failure and PD pathology is demonstrated, these mitochondrial organelles will provide valuable early clinical markers and potentially attractive targets for the development of innovative PD-directed therapeutic agents.
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Affiliation(s)
- Ana Mafalda Gonçalves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Pereira-Santos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Esteves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra M Cardoso
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Nuno Empadinhas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC-Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
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21
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Hodgman MW, Miller JB, Meurs TE, Kauwe JSK. CUBAP: an interactive web portal for analyzing codon usage biases across populations. Nucleic Acids Res 2020; 48:11030-11039. [PMID: 33045750 PMCID: PMC7641757 DOI: 10.1093/nar/gkaa863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/18/2020] [Accepted: 09/22/2020] [Indexed: 12/19/2022] Open
Abstract
Synonymous codon usage significantly impacts translational and transcriptional efficiency, gene expression, the secondary structure of both mRNA and proteins, and has been implicated in various diseases. However, population-specific differences in codon usage biases remain largely unexplored. Here, we present a web server, https://cubap.byu.edu, to facilitate analyses of codon usage biases across populations (CUBAP). Using the 1000 Genomes Project, we calculated and visually depict population-specific differences in codon frequencies, codon aversion, identical codon pairing, co-tRNA codon pairing, ramp sequences, and nucleotide composition in 17,634 genes. We found that codon pairing significantly differs between populations in 35.8% of genes, allowing us to successfully predict the place of origin for African and East Asian individuals with 98.8% and 100% accuracy, respectively. We also used CUBAP to identify a significant bias toward decreased CTG pairing in the immunity related GTPase M (IRGM) gene in East Asian and African populations, which may contribute to the decreased association of rs10065172 with Crohn's disease in those populations. CUBAP facilitates in-depth gene-specific and codon-specific visualization that will aid in analyzing candidate genes identified in genome-wide association studies, identifying functional implications of synonymous variants, predicting population-specific impacts of synonymous variants and categorizing genetic biases unique to certain populations.
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Affiliation(s)
- Matthew W Hodgman
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Justin B Miller
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Taylor E Meurs
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
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22
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Imran FS, Al-Thuwaini TM, Al-Shuhaib MBS, Lepretre F. A Novel Missense Single Nucleotide Polymorphism in the GREM1 Gene is Highly Associated with Higher Reproductive Traits in Awassi Sheep. Biochem Genet 2020; 59:422-436. [PMID: 33048279 DOI: 10.1007/s10528-020-10006-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/29/2020] [Indexed: 11/24/2022]
Abstract
GREM1 (gremlin1) is a known inhibitor for BMP15 (bone morphogenetic protein 15) family, but its genetic diversity in sheep is unknown. The present study was conducted to analyze the polymorphism of GREM1 gene using PCR- single-strand conformation polymorphism (SSCP) and DNA sequencing methods and to assess the possible association of GREM1 gene polymorphism with reproductive traits in Awassi ewes. A total of 224 ewes, 124 producing singles and 100 producing twins, were included in the study. Two SSCP patterns were detected in two amplified loci within the exon 2. Two exonic novel single nucleotide polymorphism (SNP)s were identified, c.74 T > G (the silent SNP p.Met123 =) and c.30 T > A with (the missense SNP p.Ile237Phe). Statistical analyses indicated a non-significant (P > 0.05) association of p.Met123 = with the analyzed reproductive traits of fecundity, prolificacy, litter size, and twinning rate. Meanwhile, p.Ile237Phe SNP exhibited a highly significant (P < 0.01) association with the measured reproductive traits, in which ewes with TA genotype (with p.Ile237Phe SNP) exhibited higher litter size, twinning ratio, fecundity, and prolificacy than those with TT genotype (without p.Ile237Phe SNP). The deleterious impact of p.Ile237Phe SNP was observed by the means of ten different state-of-the-art in silico tools that predicted a highly damaging effect of p.Ile237Phe SNP on the structure, function, and stability of gremlin1. In conclusion, the results of our study suggest that p.Ile237Phe SNP has a remarkable negative impact on the gremlin1 structure, function, and stability. Since gremlin1 is a known inhibitor of reproductive performance, a consequent higher reproductive performance was observed in ewes with damaged gremlin1 (with p.Ile237Phe SNP) than those with non-damaged gremlin1 (without p.Ile237Phe SNP). Therefore, it can be stated that the implementation of the novel p.Ile237Phe SNP in the GREM1 gene could be a useful marker in marker-assisted selection. This manuscript is the first one to describe GREM1 gene variations in sheep.
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Affiliation(s)
- Faris S Imran
- Branch of Physiology, College of Veterinary Medicine, University of Kerbala, Fraiha, Kerbala, 56001, Iraq
| | - Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq.
| | - Frederic Lepretre
- Univ. Lille, Plateau de Genomique Fonctionnelle Et Structurale, CHU Lille, Lille, France
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23
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El-Tarabany MS, Saleh AA, El-Araby IE, El-Magd MA. Association of LEPR polymorphisms with egg production and growth performance in female Japanese quails. Anim Biotechnol 2020; 33:599-611. [PMID: 32865111 DOI: 10.1080/10495398.2020.1812617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This study aimed to screen intron 8 of the leptin receptor (LEPR) gene for polymorphisms in female Japanese quails. Two adjacent novel SNPs (A277G and A304G) were detected using PCR-SSCP and sequencing. These SNPs produced three haplotypes (AA/AA, AG/AG, and GG/GG) that were significantly (p ≤ 0.05) associated with growth and egg production traits. GG/GG haplotype-quails had significantly (p ≤ 0.05) lower egg production, feed intake, growth performance, lipid profile, serum levels of sex hormones (estradiol, progesterone, FSH, LH), and ovarian expressions of survivin, FSHR, and IGF1 than other quails. However, GG/GG quails had significantly (p ≤ 0.05) higher serum levels of LEP and mRNA levels of LEPR, LEP, and caspase 3 in the hypothalamus and ovaries. These higher levels of LEP/LEPR could not only reduce feed intake and body weight gain but also could induce apoptosis of ovarian cells (as indicated by lower survivin and IGF1 and higher caspase3 expression) which could inhibit the development of the follicles and the release of sex hormones with a subsequent decrease in egg production in GG/GG quails. Therefore, with these results, we suggest selecting Japanese quails with AA/AA and AG/AG haplotypes to improve the reproduction and growth performance of this flock.
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Affiliation(s)
- Mahmoud S El-Tarabany
- Department of Animal Wealth Development, Animal Breeding and Production, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Ayman A Saleh
- Department of Animal Wealth Development, Veterinary Genetics & Genetic Engineering, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Iman E El-Araby
- Department of Animal Wealth Development, Veterinary Genetics & Genetic Engineering, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Mohammed A El-Magd
- Department of Anatomy & Embryology, Faculty of Veterinary Medicine, Kafrelsheikh University, Zagazig, Egypt
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24
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Liu CW, Lin CJ, Hu HC, Liu HJ, Chiu YC, Lee SW, Wu LSH. The association of inflammasome and TLR2 gene polymorphisms with susceptibility to tuberculosis in the Han Taiwanese population. Sci Rep 2020; 10:10184. [PMID: 32576967 PMCID: PMC7311452 DOI: 10.1038/s41598-020-67299-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/13/2020] [Indexed: 01/20/2023] Open
Abstract
Pulmonary tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is a global public health concern. Although inflammasome and the toll-like receptor 2 (TLR2) genes play an important role in host defense against Mtb, the associations of polymorphisms in these genes with TB risk are incompletely understood. A total of 230 TB patients and 213 individuals without TB were enrolled in this study. A significant difference in the frequencies of different AIM2 rs2276405 genotypes between the non-TB and TB groups was detected. When the patients were stratified by gender or age, significant differences in genotype frequencies at NLRP3 rs34298354 in men and in non-aged (≤65-year-old) subjects and at IFI16 rs1772408 in women were found. OR analysis showed that the TC rs34298354 genotype in NLRP3 was associated with reduced risk of TB. In women, the AG rs1772408 genotype in IFI16 was associated with decreased TB risk. Haplotype analysis showed that, in comparison with the most common haplotype (T-T) of rs3804099-rs3804100 in the TLR2 gene, the C-T haplotype was associated with an increased risk for TB. Our study indicates that rs34298354 in NLRP3 and rs1772408 in IFI16 protect individuals from TB, and that the less common TLR2 haplotype is associated with increased TB susceptibility.
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Affiliation(s)
- Chi-Wei Liu
- Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Chou-Jui Lin
- Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Hui-Chun Hu
- Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Hsiu-Jung Liu
- Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Yu-Chi Chiu
- Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Shih-Wei Lee
- Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan.
| | - Lawrence Shih-Hsin Wu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
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Wang C, Liu S, Wu Q, Cheng Y, Feng T, Song J, Yang R, Geng H, Lu G, Wang S, Hao L. Porcine IGF-1R synonymous mutations in the intracellular domain affect cell proliferation and alter kinase activity. Int J Biol Macromol 2020; 152:147-153. [PMID: 32109480 DOI: 10.1016/j.ijbiomac.2020.02.281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 01/04/2023]
Abstract
Miniature pigs are regarded as ideal organ donors for xenotransplantation into humans. Elucidating the formation mechanism of miniature pigs is important. The insulin-like growth factor 1 receptor (IGF-1R) is crucial in the regulation of cell proliferation and organismal growth. According to our previous research, the IGF-1R expression levels between large and miniature pigs showed different profiles in liver and muscle tissues. Here, five synonymous mutations of IGF-1R in the coding sequence (CDS) of intracellular domain (ICD) between large and miniature pigs were analysed by constructing expression vectors of two haplotypes and named pcDNA3.1-LP (with the CDS of IGF-1R ICD of Large White pigs, LP group) and pcDNA3.1-BM (with the CDS of IGF-1R ICD of Bama Xiang pigs, BM group). The IGF-1R of the BM group was expressed lower than that of the LP group in transcription, translation and autophosphorylation levels. The IGF-1R of the BM group also down-regulated the protein levels of p-AKT/p-ERK than that of the LP group. PK-15 and C2C12 cell proliferation were detected to further understand the function of the haplotype. Results showed that the proliferation viability of PK-15 and C2C12 cells weakened in the BM group. Moreover, the mRNA and protein stabilities of the BM group were higher than those of the LP group. Our data indicated that two haplotypes of IGF-1R CDS in ICD between large and miniature pigs altered IGF-1R expression and down-regulated AKT and ERK signalling pathways at translation levels, resulting in an inhibitory effect on PK-15 and C2C12 cell proliferation.
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Affiliation(s)
- Chunli Wang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Songcai Liu
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China; Five-Star Animal Health Pharmaceutical Factory of Jilin Province, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Qingyan Wu
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Yunyun Cheng
- Guangdong Provincial Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Tianqi Feng
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Jie Song
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Rui Yang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Hongwei Geng
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Guanhong Lu
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Siyao Wang
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China
| | - Linlin Hao
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, China.
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Thumser-Henner P, Nytko KJ, Rohrer Bley C. Mutations of BRCA2 in canine mammary tumors and their targeting potential in clinical therapy. BMC Vet Res 2020; 16:30. [PMID: 32005245 PMCID: PMC6995156 DOI: 10.1186/s12917-020-2247-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/17/2020] [Indexed: 02/08/2023] Open
Abstract
Dogs develop cancer spontaneously with age, with breed-specific risk underlying differences in genetics. Mammary tumors are reported as the most frequent neoplasia in intact female dogs. Their high prevalence in certain breeds suggests a genetic component, as it is the case in human familial breast cancer, distinctly in BRCA2-associated cancers. However, the molecular genetics of BRCA2 in the pathogenesis of canine cancer are still under investigation.Genetic variations of canine BRCA2 comprised single nucleotide polymorphisms, insertions and deletions. The BRCA2 level has been shown to be reduced in tumor gland samples, suggesting that low expression of BRCA2 is contributing to mammary tumor development in dogs. Additionally, specific variations of the BRCA2 gene affect RAD51 binding strength, critically damage the BRCA2-RAD51 binding and further provoke a defective repair. In humans, preclinical and clinical data revealed a synthetic lethality interaction between BRCA2 mutations and PARP inhibition. PARP inhibitors are successfully used to increase chemo- and radiotherapy sensitivity, although they are also associated with numerous side effects and acquired resistance. Cancer treatment of canine patients could benefit from increased chemo- and radiosensitivity, as their cancer therapy protocols usually include only low doses of drugs or radiation. Early investigations show tolerability of iniparib in dogs. PARP inhibitors also imply higher therapy costs and consequently are less likely to be accepted by pet owners.We summarized the current evidence of canine BRCA2 gene alterations and their association with mammary tumors. Mutations in the canine BRCA2 gene have the potential to be exploited in clinical therapy through the usage of PARP inhibitors. However, further investigations are needed before introducing PARP inhibitors in veterinary clinical practice.
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Affiliation(s)
- Pauline Thumser-Henner
- Division of Radiation Oncology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
| | - Katarzyna J Nytko
- Division of Radiation Oncology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Carla Rohrer Bley
- Division of Radiation Oncology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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28
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AbdElMaksoud SS, ElGamal RAE, Pessar SA, Salem DDE, Abdelsamee HF, Agamy HS. Prognostic implications of IDH1rs11554137 and IDH2R140Q SNPs mutations in cytogenetically normal acute myeloid leukemia. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2019. [DOI: 10.1186/s43042-019-0012-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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29
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Challenges to assess substrate-dependent allelic effects in CYP450 enzymes and the potential clinical implications. THE PHARMACOGENOMICS JOURNAL 2019; 19:501-515. [DOI: 10.1038/s41397-019-0105-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 09/09/2019] [Accepted: 10/02/2019] [Indexed: 12/12/2022]
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30
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Yin B, Lu P, Liang J, Zhang W, Xin M, Pei K, Li Y. The ABCB1 3435C > T polymorphism influences docetaxel transportation in ovarian cancer. J Int Med Res 2019; 47:5256-5269. [PMID: 31638462 PMCID: PMC6997784 DOI: 10.1177/0300060519870354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/26/2019] [Indexed: 11/15/2022] Open
Abstract
Objective To investigate the effect of the ATP-binding cassette transporter superfamily B member 1 gene (ABCB1 ) 3435C > T single nucleotide polymorphism (SNP) on docetaxel transportation in ovarian cancer cells. Methods ES-2 and SKOV3 cells were transfected with an ABCB1 3435C > T recombinant plasmid, and mRNA expression was detected by real-time PCR. The MTT assay was used to detect the toxicity of docetaxel. High-performance liquid chromatography determined the drug concentration in different cell models to evaluate intracellular accumulation, and a transmembrane resistance experiment was used to assess permeability and evaluate the effect of P-gp activity on drug transportation. A tumor-bearing mouse model was established to evaluate the effect of ABCB1 3435C > T on docetaxel resistance. Results P-gp was overexpressed in cells transfected with the ABCB1 3435C > T plasmid, leading to a significant increase in drug resistance to docetaxel. ABCB1 3435C/wild-type transfection significantly promoted the transport of docetaxel mediated by P-gp compared with ABCB1 3435T/mutant transfection. Conclusion P-gp encoded by the ABCB1 variant allele appears to be more efficient at transporting docetaxel compared with the wild-type allele. The ABCB1 3435C > T SNP dramatically affected the efflux ability of P-gp against docetaxel, and may influence P-gp expression and activity.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B/genetics
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism
- Animals
- Biological Transport/drug effects
- Cell Death/drug effects
- Cell Line, Tumor
- Cell Membrane/drug effects
- Cell Membrane/metabolism
- Docetaxel/pharmacology
- Docetaxel/therapeutic use
- Drug Resistance, Neoplasm/drug effects
- Female
- Humans
- Mice, Inbred BALB C
- Mice, Nude
- Ovarian Neoplasms/drug therapy
- Ovarian Neoplasms/genetics
- Polymorphism, Single Nucleotide/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Beibei Yin
- Department of Oncology, Shandong Provincial Qianfoshan
Hospital, Shandong University, Jinan, Shandong, China
| | - Ping Lu
- Department of Cardiac Surgery, Shandong Provincial
Qianfoshan Hospital, Shandong University, Jinan, Shandong, China
| | - Jing Liang
- Department of Oncology, Shandong Provincial Qianfoshan
Hospital, Shandong University, Jinan, Shandong, China
| | - Wei Zhang
- Department of Ultrasound, Shandong Provincial
Qianfoshan Hospital, Shandong University, Jinan, Shandong, China
| | - Meng Xin
- Department of Oncology, Shandong Provincial Qianfoshan
Hospital, Shandong University, Jinan, Shandong, China
| | - Ke Pei
- College of Traditional Chinese Medicine, Shandong
University of Traditional Chinese Medicine, Jinan, Shandong,
China
| | - Yan Li
- Department of Oncology, Shandong Provincial Qianfoshan
Hospital, Shandong University, Jinan, Shandong, China
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31
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Wu MF, Shu CC, Wang JY, Yan BS, Lai HC, Chiang BL, Wu LSH, Yu CJ. NLRP3 inflammasome is attenuated in patients with Mycobacterium avium complex lung disease and correlated with decreased interleukin-1β response and host susceptibility. Sci Rep 2019; 9:12534. [PMID: 31467293 PMCID: PMC6715708 DOI: 10.1038/s41598-019-47609-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/28/2019] [Indexed: 01/30/2023] Open
Abstract
The incidence of nontuberculous mycobacteria lung disease (NTM-LD) is increasing in patients without human immunodeficiency virus. Mycobacterium avium complex (MAC) is one of the most common pathogenic species. The presence of MAC has a clinical relevance of around 35~42%, indicating the possibility of host susceptibility. Previous studies have shown that interleukin (IL)-1β and IL-1-receptor knock-out mice are susceptible to mycobacterial infections; however, the role of inflammasome-driven interleukin (IL)-1β has not been studied in MAC-LD. We enrolled patients with MAC-LD and healthy controls. Peripheral blood mononuclear cells (PBMCs), monocytes, and monocyte-derived macrophages were stimulated by MAC bacilli. The responses of interleukin(IL)-1β and the expression of inflammasome and toll-like receptors (TLRs) were measured. Single nucleotide polymorphisms (SNPs) were also examined for NLRP3 and TLR2 genes. In the patients with MAC-LD, the IL-1β responses decreased in PBMCs, monocytes, and macrophages assayed by MAC bacilli in comparison to the healthy controls. In addition, the level of caspase-1 after stimulation was lower in the MAC-LD group, although the mRNA level of IL-1β was not significantly lower. In surveying the activation of IL-1β, the MAC-LD group had an attenuated mRNA level of NLRP3 but similar levels of AIM2 and ASC compared with the controls. The SNPs rs3806268 and rs34298354 in NLRP3 for females and rs3804100 in TLR2 for males were associated with MAC-LD. In conclusion, our patients with MAC-LD had attenuated IL-1β production, which may have been due to lower activation of the NLRP3-caspase-1 axis. Two SNPs of NLRP3 and one of TLR2 were correlated with MAC-LD, possibly indicating host susceptibility.
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Affiliation(s)
- Ming-Fang Wu
- Institute of Statistical Sciences, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chin-Chung Shu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jann-Yuan Wang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Bo-Shiun Yan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-Chih Lai
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, and Research Center for Chinese Herbal Medicine and Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Tao-Yuan, Taiwan
| | - Bor-Luen Chiang
- College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Lawrence Shih-Hsin Wu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan. .,College of Medicine, National Taiwan University, Taipei, Taiwan.
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Luo H, Qin G, Yao C. Correlation between adverse events after drug treatment and the MDR1 C3435T polymorphism in advanced non-small cell lung cancer patients in an Asian population: a meta-analysis. J Int Med Res 2019; 47:3522-3533. [PMID: 31315482 PMCID: PMC6726823 DOI: 10.1177/0300060519858012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Objective To determine the association between the multidrug resistance 1 gene ( MDR1) C3435T polymorphism and adverse drug reactions in advanced non-small cell lung cancer (NSCLC) patients in Asia. Methods Literature about the relationship between the MDR1 C3435T polymorphism and adverse drug reactions in advanced NSCLC patients were collected from three English language databases (PubMed, Cochrane, and Embase) as well as three Chinese databases (Wanfang, China Knowledge Network, and the Chinese Biomedical Literature Database), and summarized by a meta-analysis. Results NSCLC patients with the T allele or TT genotype were significantly more likely to experience diarrhea than those with other genotypes under the allele model (odds ratio [OR] = 1.64, 95% confidence interval [CI]: 1.04–2.61), homozygous model (OR = 3.87, 95% CI: 1.49–10.07), and recessive model (OR = 4.48, 95% CI: 1.88–10.68). Similarly, these patients were significantly more likely to experience skin rash under the allele model (OR = 2.41, 95% CI: 1.24–4.66), homozygous model (OR = 4.77, 95% CI: 1.13–20.15), and dominant model (OR = 1.77, 95% CI: 1.03–3.05). Conclusions Asian NSCLC patients with the MDR1 C3435T T allele or TT genotype are significantly more likely to develop diarrhea and rash after drug treatment.
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Affiliation(s)
- Hua Luo
- Department of Respiratory Medicine, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Guangmei Qin
- Department of Respiratory Medicine, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Caoyuan Yao
- Department of Respiratory Medicine, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
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Zhang T, Sun X, Han J, Han M. Genetic variants of TSPAN12 gene in patients with retinopathy of prematurity. J Cell Biochem 2019; 120:14544-14551. [PMID: 31009104 DOI: 10.1002/jcb.28715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/19/2019] [Accepted: 02/28/2019] [Indexed: 11/10/2022]
Abstract
Genetic susceptibility to retinopathy of prematurity (ROP) has been reported. However, no virulence genes are currently known for ROP. This study aimed to assess FZD4, LRP5, TSPAN12, and NDP, which are known virulence genes involved in familial exudative vitreoretinopathy, an ailment that shares some symptoms with ROP. After approval from the parents of diseased infants, blood samples from 29 Han patients with ROP were collected for genomic DNA extraction. Direct sequencing was used to assess the four candidate genes, namely FZD4, LRP5, TSPAN12, and NDP. Finally, genetic mutations were screened. Changes of three nucleotide sequences were found in the four candidate genes; notably, a c.954G>A hybrid mutation in the TSPAN12 gene was predicted to cause protein structure and function alterations. The molecular pathogenesis of ROP is complex, and likely involves the c.954G>A mutation in TSPAN12.
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Affiliation(s)
- Tongmei Zhang
- Clinical College of Ophthalmology, Tianjin Eye Hospital, Tianjin Medical University, TianJin, PR China
| | - Xiaoli Sun
- Clinical College of Ophthalmology, Tianjin Eye Hospital, Tianjin Medical University, TianJin, PR China
| | - Junlin Han
- Clinical College of Ophthalmology, Tianjin Eye Hospital, Tianjin Medical University, TianJin, PR China
| | - Mei Han
- Clinical College of Ophthalmology, Tianjin Eye Hospital, Tianjin Medical University, TianJin, PR China
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Yang SZ, He H, Zhang ZJ, Niu H, Chen FY, Wen YF, Xu JW, Dang RH, Lan XY, Lei CZ, Chen H, Huang BZ, Huang YZ. Determination of genetic effects of SERPINA3 on important growth traits in beef cattle. Anim Biotechnol 2019; 31:164-173. [PMID: 30929567 DOI: 10.1080/10495398.2018.1560306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Serine protease inhibitor protein 3 (serpin peptidase inhibitor, clade A, member 3, SERPINA3) is a member of the serpin superfamily, probably related to the yield and quality of muscle. This study focuses on the relationship between SERPINA3 gene polymorphism and growth traits in beef cattle. The study first uses sequencing pooled DNA samples (Pool-Seq), PCR-RFLP and Tetra-primer ARMS-PCR techniques to determine the genetic polymorphisms of SERPINA3 in 765 beef cattle. Then, the polymorphic loci were correlated with the growth characters of cattle. Five SNPs (SNP1:A-648G, SNP2:T6496A, SNP3:G2495A, SNP4:T2595A, SNP5:A2615G) were found, located in the promoter, introns 5 and SNP 3, 4, 5 were in exons 2, respectively. The observed He was from 0.44 to 0.5, Ne were approaching 2 (1.78 to 2.00). The maximum and minimum PIC (polymorphism information content) values were 0.37 and 0.34, respectively. The association analysis results showed that the SNPs had a significant height in the chest girth and body length. (p < 0.05 or p < 0.01). This will provide important information for the rapid breeding of Chinese yellow cattle and the establishment of a molecular genetic marker database.
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Affiliation(s)
- Shi-Zhen Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hua He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.,College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Zi-Jing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Hui Niu
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, People's Republic of China
| | - Fu-Ying Chen
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Yi-Fan Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jia-Wei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Rui-Hua Dang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Bi-Zhi Huang
- Yunnan Academy of Grassland Animal Science, Xiaoshao, Kunming, People's Republic of China
| | - Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Liu Y, Fang X, Zhao Z, Li J, Albrecht E, Schering L, Maak S, Yang R. Polymorphisms of the ASIP gene and the haplotype are associated with fat deposition traits and fatty acid composition in Chinese Simmental steers. Arch Anim Breed 2019; 62:135-142. [PMID: 31807623 PMCID: PMC6852852 DOI: 10.5194/aab-62-135-2019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/25/2019] [Indexed: 11/11/2022] Open
Abstract
Unlike specific expression in the skin of wild mice, the agouti signaling protein (ASIP) is expressed widely in the tissue of cattle, including adipose and muscle tissue. Hence, it has been suggested that ASIP plays a role in bovine fat metabolism. An inserted L1-BT element was recently identified upstream of the ASIP locus which led to an ectopic expression of ASIP mRNA in cattle. In this study, we detected the indel of the L1-BT element at g. - 14 643 nt and three SNPs in introns of the ASIP gene (g. - 568 A > G, g. - 554 A > T, and g. 4805A > T) in a Chinese Simmental steer population. The association analysis between variants of ASIP and economic traits showed that the homozygous genotype of L1-BT element insertion, AA genotype of g. - 568 A > G, and AT genotype of g. 4805A > T were significantly correlated with carcass and fat-related traits, such as live weight and back fat thickness. Moreover, three haplotypes (H1: AT; H2: AA; H3: GT) were identified by linkage disequilibrium analysis and formed six combined genotypes. Results indicated that Chinese Simmental steers with an H1H2 combined genotype had a higher measured value of fat-deposition-related traits ( p < 0.05 ), including thickness of back fat and percentage of carcass fat coverage, but a lower content of linoleic acid and α -linolenic acid ( p < 0.05 ). Individuals of an H3H3 combination had a lower marbling score, perirenal fat weight, and carcass weight ( p < 0.05 ). This suggests that these three SNPs and two combined haplotypes might be molecular markers for beef cattle breeding selection.
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Affiliation(s)
- Yinuo Liu
- College of Animal Science, Jilin University, Changchun, 130062, P. R. China
| | - Xibi Fang
- College of Animal Science, Jilin University, Changchun, 130062, P. R. China
| | - Zhihui Zhao
- College of Animal Science, Jilin University, Changchun, 130062, P. R. China.,College of Agriculture, Guangdong Ocean University, Zhanjiang, 523088, P. R. China
| | - Junya Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Elke Albrecht
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, 18196, Germany
| | - Lisa Schering
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, 18196, Germany
| | - Steffen Maak
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, 18196, Germany
| | - Runjun Yang
- College of Animal Science, Jilin University, Changchun, 130062, P. R. China
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36
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Won SY, Kim YC, Kim K, Kim AD, Jeong BH. The First Report of Polymorphisms and Genetic Features of the prion-like Protein Gene ( PRND) in a Prion Disease-Resistant Animal, Dog. Int J Mol Sci 2019; 20:ijms20061404. [PMID: 30897750 PMCID: PMC6470729 DOI: 10.3390/ijms20061404] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 12/21/2022] Open
Abstract
Prion disease has displayed large infection host ranges among several species; however, dogs have not been reported to be infected and are considered prion disease-resistant animals. Case-controlled studies in several species, including humans and cattle, indicated a potent association of prion protein gene (PRNP) polymorphisms in the progression of prion disease. Thus, because of the proximal location and similar structure of the PRNP gene among the prion gene family, the prion-like protein gene (PRND) was noted as a novel candidate gene that contributes to prion disease susceptibility. Several case-controlled studies have confirmed the relationship of the PRND gene with prion disease vulnerability, and strong genetic linkage disequilibrium blocks were identified in prion-susceptible species between the PRNP and PRND genes. However, to date, polymorphisms of the dog PRND gene have not been reported, and the genetic linkage between the PRNP and PRND genes has not been examined thus far. Here, we first investigated dog PRND polymorphisms in 207 dog DNA samples using direct DNA sequencing. A total of four novel single nucleotide polymorphisms (SNPs), including one nonsynonymous SNP (c.149G>A, R50H), were identified in this study. We also found two major haplotypes among the four novel SNPs. In addition, we compared the genotype and allele frequencies of the c.149G>A (R50H) SNP and found significantly different distributions among eight dog breeds. Furthermore, we annotated the c.149G>A (R50H) SNP of the dog PRND gene using in silico tools, PolyPhen-2, PROVEAN, and PANTHER. Finally, we examined linkage disequilibrium between the PRNP and PRND genes in dogs. Interestingly, we did not find a strong genetic linkage between these two genes. To the best of our knowledge, this was the first genetic study of the PRND gene in a prion disease-resistant animal, a dog.
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Affiliation(s)
- Sae-Young Won
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan, Jeonbuk 54531, Korea.
- Department of Bioactive Material Sciences, Chonbuk National University, Jeonju, Jeonbuk 54896, Korea.
| | - Yong-Chan Kim
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan, Jeonbuk 54531, Korea.
- Department of Bioactive Material Sciences, Chonbuk National University, Jeonju, Jeonbuk 54896, Korea.
| | - Kiwon Kim
- Haemalken Animal Hospital, Yangju, Gyeonggi 11492, Korea.
| | - An-Dang Kim
- Cool-Pet Animal Hospital, Anyang, Gyeonggi 14066, Korea.
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan, Jeonbuk 54531, Korea.
- Department of Bioactive Material Sciences, Chonbuk National University, Jeonju, Jeonbuk 54896, Korea.
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Uh ST, Park JS, Koo SM, Kim YK, Kim KU, Kim MA, Shin SW, Son JH, Park HW, Shin HD, Park CS, Chang HS. Association of Genetic Variants of NLRP4 with Exacerbation of Asthma: The Effect of Smoking. DNA Cell Biol 2018; 38:76-84. [PMID: 30526007 DOI: 10.1089/dna.2018.4433] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Asthma exacerbation is induced by the interaction of genes and environmental factors such as cigarette smoke. NLRP4 counteracts the activity of the inflammasome, which is responsible for asthma exacerbation. In this study, we analyzed the association of single-nucleotide polymorphisms of NLRP4 with the annual rate of exacerbation and evaluated the additive effect of smoking in 1454 asthmatics. Asthmatics possessing the minor allele of rs1696718G > A had more frequent exacerbation episodes than those homozygous for the common allele (0.59 vs. 0.36/year) and the association was present only in current and ex-smokers. There was a significant interaction between the amount smoked and rs16986718 genotypes (p = 0.014) and a positive correlation between the number of annual exacerbation episodes and amount smoked only in rs16986718G > A AA homozygotes. The prevalence of frequent exacerbators (≥2 exacerbation episodes/year) was 2.5 times higher in rs16986718G > A minor allele homozygotes than in common allele homozygotes (12.0% vs. 5.9%). Furthermore, the prevalence was 6 times higher in rs16986718G > A minor allele homozygotes who were current and ex-smokers than in nonsmokers (25.6% vs. 4.1%). The minor allele of rs16986718G > A in NLRP4 may be a genetic marker that predicts asthma exacerbation in adult asthmatics who smoke.
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Affiliation(s)
- Soo-Taek Uh
- 1 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Seoul Hospital , Seoul, Korea
| | - Jong-Sook Park
- 2 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital , Bucheon, Korea
| | - So-My Koo
- 1 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Seoul Hospital , Seoul, Korea
| | - Yang-Ki Kim
- 1 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Seoul Hospital , Seoul, Korea
| | - Ki Up Kim
- 1 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Seoul Hospital , Seoul, Korea
| | - Mi-Ae Kim
- 3 Department of Pulmonology, Allergy and Critical Care Medicine, CHA Bundang Medical Center, CHA University , Seongnam, Korea
| | - Seung-Woo Shin
- 4 Genome Research Center for Allergy and Respiratory Diseases, Soonchunhyang University Bucheon Hospital , Bucheon, Korea
| | - Ji-Hye Son
- 5 Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University , Bucheon, Korea
| | - Heung-Woo Park
- 6 Department of Internal Medicine, Seoul National University College of Medicine , Seoul, Korea
| | - Hyoung Doo Shin
- 7 Department of Life Sciences, Sogang University , Seoul, Korea
| | - Choon-Sik Park
- 2 Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital , Bucheon, Korea.,4 Genome Research Center for Allergy and Respiratory Diseases, Soonchunhyang University Bucheon Hospital , Bucheon, Korea
| | - Hun Soo Chang
- 5 Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University , Bucheon, Korea
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Polymorphism of melatonin receptor (MTNR1A) gene and its association with seasonal reproduction in water buffalo (Bubalus bubalis). Anim Reprod Sci 2018; 199:51-59. [DOI: 10.1016/j.anireprosci.2018.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/18/2018] [Accepted: 10/22/2018] [Indexed: 12/15/2022]
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Wang X, Chen X, Yang Z, Dou H, Lu L, Bi J, Zou L, Yu J, Bao L. Correlation of TET2 SNP rs2454206 with improved survival in children with acute myeloid leukemia featuring intermediate-risk cytogenetics. Genes Chromosomes Cancer 2018; 57:379-386. [PMID: 29664232 DOI: 10.1002/gcc.22540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 12/19/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) may influence the disease course and outcome of hematologic neoplasms. SNP rs2454206 is common in the TET2 gene, which plays a role in epigenetic regulation of myelopoiesis. Few investigations examined the role of TET2 SNP rs2454206 in acute myeloid leukemia (AML) and none of those studies was performed in Chinese populations. Here, we report the prevalence and clinical relevance of TET2 SNP rs2454206 in 254 Chinese patients with childhood AML. Our data demonstrate that TET2 SNP rs2454206AG/GG is associated with improved overall survival and event-free survival in AML patients with intermediate-risk cytogenetics features. The prognostic impact of TET2 SNP rs2454206AG/GG was independent of other common AML risk factors, such as age, white blood cell count, and FLT3-ITD. No difference in TET2 expression levels in AML with TET2 SNP rs2454206AA and TET2 SNP rs2454206AG/GG was detected, indicating that TET2 SNP rs2454206 status does not affect TET2 expression in pediatric AML.
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Affiliation(s)
- Xingjuan Wang
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xi Chen
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zhenzhen Yang
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Hu Dou
- Department of Clinical Laboratory, Key Laboratory of Pediatrics in Chongqing, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Ling Lu
- Department of Rheumatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Junqin Bi
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Lin Zou
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Yu
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Liming Bao
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire
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40
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Accounting for Programmed Ribosomal Frameshifting in the Computation of Codon Usage Bias Indices. G3-GENES GENOMES GENETICS 2018; 8:3173-3183. [PMID: 30111621 PMCID: PMC6169388 DOI: 10.1534/g3.118.200185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Experimental evidence shows that synonymous mutations can have important consequences on genetic fitness. Many organisms display codon usage bias (CUB), where synonymous codons that are translated into the same amino acid appear with distinct frequency. Within genomes, CUB is thought to arise from selection for translational efficiency and accuracy, termed the translational efficiency hypothesis (TEH). Indeed, CUB indices correlate with protein expression levels, which is widely interpreted as evidence for translational selection. However, these tests neglect -1 programmed ribosomal frameshifting (-1 PRF), an important translational disruption effect found across all organisms of the tree of life. Genes that contain -1 PRF signals should cost more to express than genes without. Thus, CUB indices that do not consider -1 PRF may overestimate genes’ true adaptation to translational efficiency and accuracy constraints. Here, we first investigate whether -1 PRF signals do indeed carry such translational cost. We then propose two corrections for CUB indices for genes containing -1 PRF signals. We retest the TEH in Saccharomyces cerevisiae under these corrections. We find that the correlation between corrected CUB index and protein expression remains intact for most levels of uniform -1 PRF efficiencies, and tends to increase when these efficiencies decline with protein expression. We conclude that the TEH is strengthened and that -1 PRF events constitute a promising and useful tool to examine the relationships between CUB and selection for translation efficiency and accuracy.
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41
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Cheng Y, Liu S, Wang G, Wei W, Huang S, Yang R, Geng H, Li H, Song J, Sun L, Yu H, Hao L. Porcine IGF1 synonymous mutation alter gene expression and protein binding affinity with IGF1R. Int J Biol Macromol 2018; 116:23-30. [DOI: 10.1016/j.ijbiomac.2018.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 12/15/2022]
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42
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Chiddarwar AS, D'Silva SZ, Colah RB, Ghosh K, Mukherjee MB. Genetic lesions in the UGT1A1 genes among Gilbert's syndrome patients from India. Mol Biol Rep 2018; 45:2733-2739. [PMID: 30105552 DOI: 10.1007/s11033-018-4305-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/09/2018] [Indexed: 11/26/2022]
Abstract
The present study was undertaken to investigate genetic variations present in the coding regions of the UGT1A1 gene among the Gilbert's syndrome patients. Analysis of genetic variations was performed by direct DNA sequencing among the patients that do not have any polymorphic variations in the promoter regions of the UGT1A1 gene. We identified seven different sequence variations among Gilbert's Syndrome patients, of which four were novel. Out of seven variants, six missense and one silent single nucleotide substitutions were present in the UGT1A1 gene. In addition, molecular modeling of UGT1A1 (H55R, P152S and N212H) variants suggested a reduced activity of the enzyme. This study demonstrates that different variations present in the UGT1A1 gene and specifically, the H55R variation had a significant effect on bilirubin levels and could be genetic risk factors for hyperbilirubinemia.
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Affiliation(s)
- Ashish S Chiddarwar
- National Institute of Immunohaematology (ICMR), 13th Floor, NMS Building, K.E.M Hospital Campus, Parel, Mumbai, 400012, India
| | - Selma Z D'Silva
- National Institute of Immunohaematology (ICMR), 13th Floor, NMS Building, K.E.M Hospital Campus, Parel, Mumbai, 400012, India
| | - Roshan B Colah
- National Institute of Immunohaematology (ICMR), 13th Floor, NMS Building, K.E.M Hospital Campus, Parel, Mumbai, 400012, India
| | - Kanjaksha Ghosh
- National Institute of Immunohaematology (ICMR), 13th Floor, NMS Building, K.E.M Hospital Campus, Parel, Mumbai, 400012, India
| | - Malay B Mukherjee
- Department of Haematogenetics, National Institute of Immunohaematology (ICMR), 13th Floor, NMS Building, K.E.M Hospital Campus, Parel, Mumbai, 400012, India.
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El-Magd MA, Saleh AA, Nafeaa AA, El-Komy SM, Afifi MA. Polymorphisms of the IGF1 gene and their association with growth traits, serum concentration and expression rate of IGF1 and IGF1R in buffalo. J Zhejiang Univ Sci B 2018; 18:1064-1074. [PMID: 29204986 DOI: 10.1631/jzus.b1600573] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The insulin-like growth factor 1 (IGF1) gene is a member of the group of somatotropin axis genes that play a significant role in cell proliferation and growth of muscles. Here, we searched for polymorphisms in buffalo IGF1 and found two novel single nucleotide polymorphisms (SNPs), G64A and G280A, in the noncoding sequences of exon 1 and exon 4, respectively. Statistical analysis of different genotypes showed that the individuals with GG genotypes had significantly (P<0.05) higher body weight (BW) and average daily gain (ADG) than those with other genotypes at ages of 3-6 months in G64A SNP and 6-9 months in G280A SNP. The combined genotypes of these two SNPs produced three haplotypes, GG/GG, AG/AG, and AA/AA, which were significantly associated (P<0.0001) with BW and ADG at an age from 3 to 12 months. Buffaloes with the homozygous GG/GG haplotype showed higher growth performance than other buffaloes. The two SNPs were correlated with mRNA levels of IGF1 and IGF1 receptor (IGF1R) in semitendinosus muscle as well as with the serum concentration level of IGF1. Also, buffaloes with GG/GG haplotype showed higher mRNA and serum concentration levels. The data revealed that these two SNPs could be valuable genetic markers for selection of Egyptian buffaloes for better performance in the population.
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Affiliation(s)
- Mohammed A El-Magd
- Department of Anatomy & Embryology, Faculty of Veterinary Medicine, Kafrelsheikh University, El-Geish Street, Kafrelsheikh, Egypt
| | - Ayman A Saleh
- Department of Animal Wealth Development, Veterinary Genetics & Genetic Engineering, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Abeer A Nafeaa
- Department of Physiology, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
| | - Shymaa M El-Komy
- Department of Animal Production, Faculty of Agriculture, Tanta University, Tanta, Egypt
| | - Mohamed A Afifi
- Department of Animal Wealth Development, Biostatistics, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt.,Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
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Fu W, Chen N, Han S, Huang J, Li F, Hao R, Chen H, Lei C, Ma Y. Tissue expression and variation analysis of three bovine adipokine genes revealed their effect on growth traits in native Chinese cattle. Reprod Domest Anim 2018; 53:1227-1234. [PMID: 30011090 DOI: 10.1111/rda.13244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/12/2018] [Accepted: 05/17/2018] [Indexed: 11/28/2022]
Abstract
Adipokines play a crucial role in the regulation of energy homeostasis; however, little is known about genetic alterations in this family that may contribute to economic traits in cattle. Therefore, this study conducts transcript profiles, variations and association studies of three major adipokines, leptin (LEP), tumour necrosis factor (TNF) and angiopoietin-like protein 8 (ANGPTL8), to evaluate their effects on native Chinese cattle. Using quantitative real-time PCR, the study revealed that the bovine LEP was expressed primarily in the back and visceral fat, while TNF was predominantly expressed in spleen and ANGPTL8 was mainly expressed in back fat and liver. Five single nucleotide polymorphisms (SNPs) including two missense SNPs (SNP1: g.12254T>C and SNP2: g.14177C>T) in LEP, a synonymous SNP (SNP3: g.2130A>G) in TNF and two SNPs (SNP4: g.629G>A and SNP5: g.884T>C) in the 5'UTR of ANGPTL8 were identified and genotyped in 537 individuals from six Chinese cattle breeds. Bioinformatics analysis revealed that SNP1 might disrupt the efficient binding of LEP to its receptor, SNP3 might affect translation efficiency of TNF, and SNP4 and SNP5 were likely to affect stability, splicing and nuclear export of ANGPTL8 mRNA. Consistently, association studies indicated that three SNPs (SNP1, SNP3 and SNP5) were significantly associated with body weight, heart girth, average daily gain, hip width and body length in 100 Nanyang cattle (p < 0.05). Overall, our results support the view that LEP, TNF and ANGPTL8 could be used as biomarkers to improve the growth performance in Chinese cattle selection programmes.
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Affiliation(s)
- Weiwei Fu
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuang Han
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Jieping Huang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Fen Li
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Ruijie Hao
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan, China.,Agricultural College, Ningxia University, Yinchuan, Ningxia, China
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Orlandi A, Paolino MC, Striano P, Parisi P. Clinical reappraisal of the influence of drug-transporter polymorphisms in epilepsy. Expert Opin Drug Metab Toxicol 2018; 14:505-512. [PMID: 29804481 DOI: 10.1080/17425255.2018.1473377] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
INTRODUCTION Although novel antiepileptic drugs (AEDs) have been recently released, the issue of drug resistance in epileptic patients remains unsolved and largely unpredictable. Areas covered: We aim to assess the clinical impact of genetic variations that may influence the efficacy of medical treatment in epilepsy patients. Indeed, many genes, including genes encoding drug transporters (ABCB1), drug targets (SCN1A), drug-metabolizing enzymes (CYP2C9, CYP2C19), and human leucocyte antigen (HLA) proteins, may regulate the mechanisms of drug resistance in epilepsy. This review specifically focuses on the ABC genes, which encode multidrug resistance-associated proteins (MRPs) and may reduce the blood-brain barrier penetration of anticonvulsant AEDs. Expert opinion: Drug resistance remains a crucial problem in epilepsy patients. Pharmacogenomic studies may improve our understanding of drug responses and drug resistance by exploring the impact of gene variants and predicting drug responses and tolerability.
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Affiliation(s)
- Azzurra Orlandi
- a Child Neurology, Chair of Pediatrics, NESMOS Department, Faculty of Medicine and Psychology , Sapienza University, c/o Sant'Andrea Hospital , Rome , Italy
| | - Maria Chiara Paolino
- a Child Neurology, Chair of Pediatrics, NESMOS Department, Faculty of Medicine and Psychology , Sapienza University, c/o Sant'Andrea Hospital , Rome , Italy
| | - Pasquale Striano
- b Pediatric Neurology and Muscular Diseases Unit, Departments of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, "G. Gaslini" Institute , University of Genoa , Genova , Italy
| | - Pasquale Parisi
- a Child Neurology, Chair of Pediatrics, NESMOS Department, Faculty of Medicine and Psychology , Sapienza University, c/o Sant'Andrea Hospital , Rome , Italy
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Effect of complement component 5 polymorphisms on mastitis resistance in Egyptian buffalo and cattle. Res Vet Sci 2018; 119:45-51. [PMID: 29857245 DOI: 10.1016/j.rvsc.2018.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 11/20/2022]
Abstract
Mastitis is one of the costliest diseases affecting the world's dairy industry. The important contribution of complement Component 5 (C5) to phagocytosis, which plays a major role in the defence of the bovine mammary gland against infection, makes this component of innate immunity a potential contributor in defending udder against mastitis. The objectives of this study were to sequence and analyse the whole coding region of the C5 gene in Egyptian buffalo and cattle, to detect any nucleotide variations (polymorphisms) and to investigate their associations with milk somatic cell score (SCS) as an indicator of mastitis in dairy animals. We sequenced a buffalo C5 cDNA fragment of 5336 bp (KP221293) and a cattle C5 cDNA fragment of 5303 bp (KP221294), which included the whole coding region and 3-UTR. Buffalo and cattle C5 cDNA shared sequence identity of 99%. The predicted complement C5 proteins consist of 1677 amino acid residues in both animals, one amino acid less than in humans and three amino acids more than in mouse C5 protein. Comparing cDNA sequences of different animals revealed nine novel SNPs in buffalo and seven SNPs in cattle, with two of them being novel. The association analysis revealed that five SNPs in buffalo are highly associated with SCS; indicating the contribution of complement C5 variants in buffalo mastitis resistance. No significant associations were detected between C5 variants and SCS in cattle. This is the first report about C5 variants in buffalo and its association with SCS.
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Campos-Verdes LM, Costa-Silva DR, da Silva-Sampaio JP, Barros-Oliveira MDC, Escórcio-Dourado CS, Martins LM, Sampaio FA, Revoredo C, Alves-Ribeiro FA, da Silva BB. Review of Polymorphism of the Calcium-Sensing Receptor Gene and Breast Cancer Risk. Cancer Invest 2018; 36:1-7. [PMID: 29504802 DOI: 10.1080/07357907.2018.1430817] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Polymorphism of the calcium-sensing receptor gene (CaSR or CaR) has been associated with an increased risk for breast cancer. This receptor plays an important role in calcium homeostasis, and has also been detected in several tissues that are unrelated to calcium metabolism, such as the skin, brain, and breast. The calcium-sensing receptor on cellular level, it regulates cell differentiation, proliferation, cell death, and gene expression. In breast cancer cells, CaSR seems to stimulate secretion of the parathyroid hormone-related protein (PTHrP), which stimulates cellular proliferation. Likewise, some studies have supported not only an association between calcium receptor gene polymorphism and breast cancer risk, but also a higher aggressiveness and unfavorable outcomes in breast cancer, which led us to make a survey in Pubmed on the subject in the last 10 years. Thus, in the literature there is a paucity of studies on the subject and the aim of this review was to show the role of calcium-sensing receptor and its association with breast cancer risk.
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Affiliation(s)
- Larysse Maira Campos-Verdes
- a Postgraduate Program of Health in Sciences , Federal University of Piauí , 2280 Frei Serafim Avenue, Teresina , Piauí , Brazil
| | - Danylo Rafhael Costa-Silva
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - João Paulo da Silva-Sampaio
- a Postgraduate Program of Health in Sciences , Federal University of Piauí , 2280 Frei Serafim Avenue, Teresina , Piauí , Brazil
| | | | - Carla Solange Escórcio-Dourado
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - Luana Mota Martins
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - Fabiane Araújo Sampaio
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - Camila Revoredo
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - Francisco Adelton Alves-Ribeiro
- b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
| | - Benedito Borges da Silva
- a Postgraduate Program of Health in Sciences , Federal University of Piauí , 2280 Frei Serafim Avenue, Teresina , Piauí , Brazil.,b Postgraduate Program of the Northeast Network of Biotechnology (RENORBIO) , Federal University of Piauí , Teresina , Brazil
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Zhang L, Zhang M, Wang H, Wang Y, Zhou J, Hao Z, Zhang L, Liang C. Comprehensive Review of Genetic Association Studies and Meta-Analysis on polymorphisms in microRNAs and Urological Neoplasms Risk. Sci Rep 2018; 8:3776. [PMID: 29491365 PMCID: PMC5830532 DOI: 10.1038/s41598-018-21749-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/09/2018] [Indexed: 12/20/2022] Open
Abstract
Gene expression is negatively regulated by microRNAs (miRNAs), which commonly act as tumor oncogenes or suppressors. Previous results were inconsistent concerning the relationship between polymorphisms in miRNAs and risk of urological neoplasms. Here, we conducted a comprehensive literature research on diverse databases aiming at enrolling all eligible studies up to August 31, 2016. A total of 13 publications comprising 29 case-control studies were enrolled for three polymorphisms in three miRNAs. Overall analyses suggested significant associations between miR-146a rs2910164 polymorphism and urological neoplasms risk in allelic, homozygote and recessive models. In the stratified analysis by ethnicity, we uncovered a significant association between rs2910164 polymorphism and risk of urological neoplasms in Asian populations in allelic, homozygote and recessive models. Highlighted, when stratified analysis was conducted by cancer type, rs2910164 polymorphism was also significantly associated with an increased risk of bladder cancer in allelic, homozygote and recessive models. Although for rs11614913 and rs3746444 polymorphisms, overall analyses suggested negative results, for rs11614913 polymorphism, when subgroup analysis was conducted by cancer type, a significantly decreased risk of renal cell cancer was identified in recessive model. In brief, current work indicated that miR-146a rs2910164 polymorphism is a risk factor for urological neoplasms, particularly for bladder cancer.
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Affiliation(s)
- Ligang Zhang
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.,Institute of Urology, Anhui Medical University, Hefei, 230022, China
| | - Meng Zhang
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.,Institute of Urology, Anhui Medical University, Hefei, 230022, China
| | - Hao Wang
- Graduate School of Anhui Medical University, Hefei, 230022, China
| | - Yangyang Wang
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.,Institute of Urology, Anhui Medical University, Hefei, 230022, China
| | - Jun Zhou
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.,Institute of Urology, Anhui Medical University, Hefei, 230022, China
| | - Zongyao Hao
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.,Institute of Urology, Anhui Medical University, Hefei, 230022, China
| | - Li Zhang
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China. .,Institute of Urology, Anhui Medical University, Hefei, 230022, China.
| | - Chaozhao Liang
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China. .,Institute of Urology, Anhui Medical University, Hefei, 230022, China.
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Sultana H, Seo D, Choi NR, Bhuiyan MSA, Lee SH, Heo KN, Lee JH. Identification of polymorphisms in MITF and DCT genes and their associations with plumage colors in Asian duck breeds. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:180-188. [PMID: 28823136 PMCID: PMC5767499 DOI: 10.5713/ajas.17.0298] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 05/30/2017] [Accepted: 07/28/2017] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the effect of single nucleotide polymorphisms (SNPs) of the melanogenesis associated transcription factor (MITF) and dopachrome tautomerase (DCT) genes on plumage coloration in Asian native duck breeds. MITF encodes a protein for microphthalmia-associated transcription factor, which regulates the development and function of melanocytes for pigmentation of skin, hair, and eyes. Among the tyrosinase-related family genes, DCT is a pigment cell-specific gene that plays important roles in the melanin synthesis pathway and the expression of skin, feather, and retina color. METHODS Five Asian duck varieties (black Korean native, white Korean native, commercial Peking, Nageswari, and Bangladeshi Deshi white ducks) were investigated to examine the polymorphisms associated with plumage colors. Among previously identified SNPs, three synonymous SNPs and one indel of MITF and nine SNPs in exon regions of DCT were genotyped. The allele frequencies for SNPs of the black and white plumage color populations were estimated and Fisher's exact test was conducted to assess the association between the allele frequencies of these two populations. RESULTS Two synonymous SNPs (c.114T>G and c.147T>C) and a 14-bp indel (GCTGCAAAC AGATG) in intron 7 of MITF were significantly associated with the black- and white-colored breeds (p<0.001). One non-synonymous SNP [c.938A>G (p.His313Arg)] in DCT, was highly significantly associated (p<0.001) and a synonymous SNP (c.753A>G) was significantly associated (p<0.05) with black and white color plumage in the studied duck populations. CONCLUSION The results of this study provide a basis for further investigations of the associations between polymorphisms and plumage color phenotypes in Asian duck breeds.
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Affiliation(s)
- Hasina Sultana
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Dongwon Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Nu-Ri Choi
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Md. Shamsul Alam Bhuiyan
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Kang-Nyeong Heo
- Poultry Science Division, National Institute of Animal Science, RDA, Cheonan 31000, Korea
| | - Jun-Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
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Nikbin S, Panandam JM, Yaakub H, Murugaiyah M. Association of novel SNPs in gonadotropin genes with sperm quality traits of Boer goats and Boer crosses. JOURNAL OF APPLIED ANIMAL RESEARCH 2018. [DOI: 10.1080/09712119.2017.1336441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Saeid Nikbin
- Department of Animal Science, Faculty of Agriculture, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Jothi Malar Panandam
- Department of Animal Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
| | - Halimatun Yaakub
- Department of Animal Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
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