Identification of functional consequence of a novel selection signature in CYP11b1 gene for milk fat content in Bubalus bubalis
Publication date: December 2015 Source:Meta Gene, Volume 6 Author(s): J. Maryam, Masroor Ellahi Babar, Asif Nadeem, Tahir Yaqub, Abu Saeed Hashmi Genomic selection for traits of economic importance is an emerging approach carrying tremendous potentials. Many of polygenic traits as milk fat, protein and yield have been characterize at genomic level and important selection signatures have been identified. Cytochrome P450 enzymes are potential loci for affecting many of dairy capabilities. Present study was conducted for genomic dissection of CYP11b1 gene in riverine buffaloes and seven genetic variations were identifi...
Source: Meta Gene - November 19, 2015 Category: Genetics & Stem Cells Source Type: research

D5S351 and D5S1414 located at the spinal muscular atrophy critical region represent novel informative markers in the Iranian population
Publication date: February 2016 Source:Meta Gene, Volume 7 Author(s): Maryam Sedghi, Sadeq Vallian Spinal muscular atrophy (SMA) is a degenerative neuromuscular disease associated with progressive symmetric weakness and atrophy of the limb muscles. In view of the involvement of numerous point mutations and deletions associated with the disease, the application of polymorphic markers flanking the SMA critical region could be valuable in molecular diagnosis of the disease. In the present study, D5S351 and D5S1414 polymorphic markers located at the SMA critical region in the Iranian populations were characterized. Genotyp...
Source: Meta Gene - November 19, 2015 Category: Genetics & Stem Cells Source Type: research

RAPD and ISSR based evaluation of genetic stability of micropropagated plantlets of Morus alba L. variety S-1
Publication date: February 2016 Source:Meta Gene, Volume 7 Author(s): Soumen Saha, Sinchan Adhikari, Tulsi Dey, Parthadeb Ghosh Plant regeneration through rapid in vitro clonal propagation of nodal explants of Morus alba L. variety S-1 was established along with genetic stability analysis of regenerates. Axillary shoot bud proliferation was achieved on Murashige and Skoog (MS) medium in various culture regimes. Highest number of shoots (5.62±0.01), with average length 4.19±0.01cm, was initially achieved with medium containing 0.5mg/lN6-benzyladenine (BA) and 3% sucrose. Repeated subculturing of newly fo...
Source: Meta Gene - November 19, 2015 Category: Genetics & Stem Cells Source Type: research

FokI polymorphism in vitamin D receptor gene: Differential expression of TNFα in peripheral mononuclear cells of type 2 diabetic subjects
Conclusion Our data suggest that VDR FokI polymorphism is associated with T2D, and the genotypes Ff and ff of this variant show a reduced response or resistance to the anti-inflammatory action of VitD, which could indicate a functional role of FokI polymorphism of VDR. (Source: Meta Gene)
Source: Meta Gene - November 19, 2015 Category: Genetics & Stem Cells Source Type: research

Corrigendum to “Mutation Study of Exon II of Methylmalonyl CoA Mutase Gene in Egyptian Families with Methylmalonic Aciduria and the Diagnostic Approach; Identification of 27 Allelic Variants” [Meta Gene 3C (2015) 71–88]
Publication date: Available online 9 October 2015 Source:Meta Gene Author(s): Dina A. Ghoraba, Magdy M. Mohammed, Osama K. Zaki (Source: Meta Gene)
Source: Meta Gene - October 9, 2015 Category: Genetics & Stem Cells Source Type: research

Methylenetetrahydrofolate reductase gene C677T polymorphism and breast cancer risk: Evidence for genetic susceptibility
In conclusion, results of present meta-analysis showed modest association between MTHFR C677T polymorphism with breast cancer in total studies. However, sub-group analysis results based on ethnicity showed strong significant association between TT genotype and breast cancer (TT vs. CC; OR°=°1.26; 95% CI: 1.06–1.51; p=0.009) in Asian population but in Caucasian population such association was not observed (TT vs. CC; OR°=°1.08; 95% CI: 0.99–1.14; p=0.05). (Source: Meta Gene)
Source: Meta Gene - October 2, 2015 Category: Genetics & Stem Cells Source Type: research

Absence of somatic mutations of the mTOR gene in differentiated thyroid cancer
Publication date: December 2015 Source:Meta Gene, Volume 6 Author(s): Avaniyapuram Kannan Murugan, Eman A. Humudh, Ebtesam Qasem, Hindi Al-Hindi, Mai Almohanna, Zeinab Korany Hassan, Ali S. Alzahrani Thyroid cancer is the most common endocrine malignancy with increasing incidence. Mammalian target of rapamycin (mTOR) is an important downstream mediator of phosphatidylinositol 3-kinase (PI3K/Akt) signaling and regulates cell growth, apoptosis and metabolism. The mTOR gene is frequently mutated in human cancers. Although PI3K/Akt pathway and its component genes were extensively studied in thyroid cancer, it is not k...
Source: Meta Gene - September 28, 2015 Category: Genetics & Stem Cells Source Type: research

Variations in the PBEF1 gene are associated with body mass index: A population-based study in northern China
Conclusions These findings indicate that genetic variants in PBEF1 gene may modify individual BMI in the Chinese population. (Source: Meta Gene)
Source: Meta Gene - September 21, 2015 Category: Genetics & Stem Cells Source Type: research

Association between glutathione S-transferase P1 Ile (105) Val gene polymorphism and chronic obstructive pulmonary disease: A meta-analysis based on seventeen case–control studies
Conclusions In conclusion, the current meta-analysis, based on the most updated information, showed no significant association between GSTP1 Ile (105) Val gene polymorphism and COPD risk in any genetic models. The results of subgroup analysis also showed no significant association between GSTP1 Ile (105) Val gene polymorphism and COPD risk in Asian population and Caucasian population. Further studies involving large populations and careful control with age, sex, ethnicity, and cigarette smoking are greatly needed. (Source: Meta Gene)
Source: Meta Gene - September 17, 2015 Category: Genetics & Stem Cells Source Type: research

TGF-β1 gene −509C>T promoter polymorphism modulates TGF-β1 levels in hepatitis E patients
Publication date: December 2015 Source:Meta Gene, Volume 6 Author(s): Sanjay B. Rathod, Anuradha S. Tripathy Elevated levels of transforming growth factor-β1 (TGF-β1) and its positive correlation with Foxp3 expression in hepatitis E patients have indicated involvement of TGF-β1 in hepatitis E pathogenesis. The current study determined polymorphisms in TGF-β1 gene, plasma TGF-β1 levels and T effector (Teff) cell proliferation and explored their association in a case control study. Polymorphisms in three selected sites (−509C>T, +869T>C and +915G>C) of TGF-β1 gene ...
Source: Meta Gene - September 17, 2015 Category: Genetics & Stem Cells Source Type: research

Frequency of rs731236 (Taql), rs2228570 (Fok1) of Vitamin-D Receptor (VDR) gene in Emirati healthy population
In this study 282 (female, 187; male, 95) unrelated healthy UAE nationals were involved. Two hundreds and eight two DNA samples been collected to genotype rs731236 (Taq1) and rs2228570 (Fok1) VDR SNPs. Our results indicate that the distribution of the alleles and genotypes of rs731236 (Taq1) and rs2228570 (Fok1) vary considerably in different populations. In the Emirati population the distribution of rs731236 (Taq1) and rs2228570 (Fok1) were AA 38%, AG 42%, GG 20% and AA 27%, AG 42%, GG 31% respectively. The Emirati population genotype and allele distribution of rs731236 (Taq1) and rs2228570 (Fok1) had no difference with C...
Source: Meta Gene - September 17, 2015 Category: Genetics & Stem Cells Source Type: research

ATM rs189037 (G>A) polymorphism and risk of lung cancer and head and neck cancer: A meta-analysis
Publication date: December 2015 Source:Meta Gene, Volume 6 Author(s): Aditi Bhowmik, Sayantan Nath, Sambuddha Das, Sankar Kumar Ghosh, Yashmin Choudhury A number of different epidemiological studies have measured the association between the risk of different cancers and polymorphism at promoter region of 5′ untranslated region (5′-UTR) of the Ataxia-telangiectasia mutated (ATM) gene. However the results were contentious rather than conclusive. The current study was aimed at evaluating the association between the SNP (rs189037 G>A) and the risk of head and neck cancer and lung cancer by conducting ...
Source: Meta Gene - September 4, 2015 Category: Genetics & Stem Cells Source Type: research

Genetic polymorphism of estrogen receptor alpha gene in Egyptian women with type II diabetes mellitus
Publication date: December 2015 Source:Meta Gene, Volume 6 Author(s): Tarek M.K. Motawi, Mahmoud A. El-Rehany, Sherine M. Rizk, Maggie M. Ramzy, Doaa M. el-Roby Estrogen might play an important role in type 2 diabetes mellitus pathogenesis. A number of polymorphisms have been reported in the estrogen receptor alpha gene including the XbaI and PvuII restriction enzyme polymorphisms. The aim of this study was to determine if ESRα gene polymorphisms are associated with type 2 diabetes mellitus and correlated with lipid profile. Ninety diabetic Egyptian patients were compared with forty healthy controls. ESR&alpha...
Source: Meta Gene - September 2, 2015 Category: Genetics & Stem Cells Source Type: research

Mutational analysis of SCN5A gene in long QT syndrome
Publication date: December 2015 Source:Meta Gene, Volume 6 Author(s): Sameera Fatima Qureshi, Altaf Ali, Princy John, Amol P. Jadhav, Ananthapur Venkateshwari, Hygriv Rao, M.P. Jayakrishnan, Calambur Narasimhan, Jayaprakash Shenthar, Kumarasamy Thangaraj, Pratibha Nallari The SCN5A gene encodes for the INa channel implicated in long QT syndrome type-3 (LQTS-type-3). Clinical symptoms of this type are lethal as most patients had a sudden death during sleep. Screening of SCN5A in South Indian cohort by PCR-SSCP analyses revealed five polymorphisms — A29A (exon-2), H558R (exon-12), E1061E and S1074R (exon-1...
Source: Meta Gene - September 2, 2015 Category: Genetics & Stem Cells Source Type: research

Expression profile of six stress-related genes and productive performances of fast and slow growing broiler strains reared under heat stress conditions
Publication date: December 2015 Source:Meta Gene, Volume 6 Author(s): Simona Rimoldi, Emiliano Lasagna, Francesca Maria Sarti, Stefano Paolo Marelli, Maria Cristina Cozzi, Giovanni Bernardini, Genciana Terova High temperature is one of the prominent environmental factors causing economic losses to the poultry industry as it negatively affects growth and production performance in broiler chickens. We used One Step TaqMan real time RT-PCR (reverse transcription polymerase chain reaction) technology to study the effects of chronic heat stress on the expression of genes codifying for the antioxidative enzymes superoxi...
Source: Meta Gene - September 1, 2015 Category: Genetics & Stem Cells Source Type: research

Association between pro-(IL-8) and anti-inflammatory (IL-10) cytokine variants and their serum levels and H. pylori-related gastric carcinogenesis in northern India
Conclusions Pro-(IL-8)-251 T/A and anti-inflammatory (IL-10)-819 C/T gene polymorphisms and their circulating levels may play a role in H. pylori-associated gastric carcinogenesis in northern India. (Source: Meta Gene)
Source: Meta Gene - August 28, 2015 Category: Genetics & Stem Cells Source Type: research

Association of the NAD(P)H oxidase p22 phox gene C242T polymorphism with type 2 diabetes mellitus, diabetic nephropathy, and carotid atherosclerosis with type 2 diabetes mellitus: A meta-analysis
Conclusions Results of this meta-analysis suggest that the NAD(P)H oxidase p22 phox gene 242T allele might be associated with an increased risk of T2DM and DN, but not CA. Graphical abstract (Source: Meta Gene)
Source: Meta Gene - August 26, 2015 Category: Genetics & Stem Cells Source Type: research

Structural modeling and in silico analysis of non-synonymous single nucleotide polymorphisms of human 3β-hydroxysteroid dehydrogenase type 2
In this study sixteen nsSNP of HSD3B2 were subjected to in silico analysis using nine different algorithms: SIFT, PROVEAN, PolyPhen, MutPred, SNPeffect, nsSNP Analyzer, PhD SNP, stSNP, and I Mutant 2.0. The results obtained from the analysis revealed that the prioritization of diseases associated amino acid substitution as evident from possible alteration in structure–function relationship. Structural phylogenetic analysis using ConSurf revealed that the functional residues are highly conserved in human HSD3B2; and most of the disease associated nsSNPs are within these conserved residues. Structural theoritical model...
Source: Meta Gene - August 9, 2015 Category: Genetics & Stem Cells Source Type: research

Association analysis of polymorphism in thyroglobulin gene promoter with milk production traits in riverine buffalo (Bubalus bubalis)
In this study, we investigated the genetic variation within thyroglobulin promoter region of swamp and riverine buffaloes using PCR–SSCP technique and sequencing, and also analyzing association of polymorphism with the milk production traits. The study revealed four conformational patterns, A, B, C, and D among 323 buffaloes of two riverine breeds and different swamp populations. The frequency of SSCP variant ‘A’ was found to be invariably high among all buffalo populations. Variant ‘C’ was found to be absent in pure swamp population and present with higher frequency among riverine dairy breed...
Source: Meta Gene - July 28, 2015 Category: Genetics & Stem Cells Source Type: research

Mutation rate estimation for 15 autosomal STR loci in a large population from Mainland China
In this study, we focused on 15 autosomal STR loci. DNA samples from a total of 42,416 unrelated healthy individuals (19,037 trios) from the population of Mainland China collected between Jan 2012 and May 2014 were successfully investigated. In our study, the allele frequencies, paternal mutation rates, maternal mutation rates and average mutation rates were detected. Furthermore, we also investigated the relationship between paternal ages, maternal ages, area, the time of pregnancy and average mutation rate. We found that the paternal mutation rate was higher than the maternal mutation rate and the paternal, maternal, and...
Source: Meta Gene - July 26, 2015 Category: Genetics & Stem Cells Source Type: research

Genetic basis of cystinosis in Tunisian patients: Identification of novel mutation in CTNS gene
This study was performed to investigate mutations of the CTNS gene in three Tunisian families with NC. Polymerase chain reaction (PCR), ARMS multiplex PCR and direct sequencing were performed for molecular characterization of the CTNS gene in 3 unrelated Tunisian patients and their parents. Based on family history, prenatal diagnosis (PND) was performed in fetal DNA isolated from chorionic villi obtained at 10–12 weeks of gestation. None of the patients showed the most common 57-kb deletion in heterozygous or homozygous status. One patient was homozygous for the previously reported mutation c.1515G>A (p.G308R)...
Source: Meta Gene - July 25, 2015 Category: Genetics & Stem Cells Source Type: research

A SNP (g.358A>T) at intronic region of CD9 molecule of crossbred bulls may associate with spermatozoal motility
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Sushil Kumar, Umesh Singh, Rajib Deb, Shrikant Tyagi, D.K. Mandal, Mahesh Kumar, G. Sengar, Sheetal Sharma, Rani Singh, Rupali Singh The surface expression of CD9 (cluster-of-differentiation antigen-9) in sperms of certain mammalian species has been attributed to its fusion with the egg and thereby dictating the fertility of species. In the present study, we investigated the association of CD9 with crossbred bull sperm quality and quantity trait was analyzed using a total of 96 Frieswal (HF×Sahiwal) crossbred. A single nucleotide polym...
Source: Meta Gene - July 24, 2015 Category: Genetics & Stem Cells Source Type: research

Secondary association of PDLIM5 with paranoid schizophrenia in Emirati patients
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Hamdy Moselhy, Valsamma Eapen, Nadia A. Akawi, Ali Younis, Badr Salih, Aws R. Othman, Said Yousef, Raymond A. Clarke, Bassam R. Ali Schizophrenia is a clinically and genetically heterogeneous disorder of unknown etiology. PDLIM5 variants have been linked to schizophrenia and other related neuropsychiatric disorders and upregulated in the brain of schizophrenia patients suggesting a possible pathogenic role in disease progression. The aim of this study is to examine the potential association of schizophrenia in Emirati patients with previously...
Source: Meta Gene - July 22, 2015 Category: Genetics & Stem Cells Source Type: research

Genotyping and meta-analysis of KIF6 Trp719Arg polymorphism in South Indian Coronary Artery Disease patients: A case–control study
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Durairajpandian Vishnuprabu, Subramanian Geetha, Lakkakula V.K.S. Bhaskar, Nitish R. Mahapatra, Arasambattu K. Munirajan The KIF6 719Arg allele is an interesting genomic variant widely screened in various populations and is reported to be associated with the risk of Coronary Artery Disease (CAD) and statin treatment outcome. Recent population based clinical studies and large-scale meta-analyses pondered over the role of 719Arg variant in CAD risk and treatment response. We screened the KIF6 Trp719Arg polymorphism (rs20455) in south Indian CAD pat...
Source: Meta Gene - July 16, 2015 Category: Genetics & Stem Cells Source Type: research

Association of SOCS1−820 (rs33977706) gene polymorphism with chronic periodontitis: A case–control study in Brazilians
In conclusion, our study found that SOCS1−820 polymorphism is associated with chronic periodontitis. (Source: Meta Gene)
Source: Meta Gene - July 9, 2015 Category: Genetics & Stem Cells Source Type: research

Androgen receptor gene polymorphism in zebra species
We examined the loci AR glutamine repeat (ARQ) in 44 Grevy's zebras, 23 plains zebras, and three mountain zebras, and compared them with those of domesticated horses. We observed polymorphism among zebra species and between zebra and horse. As androgens such as testosterone influence aggressiveness, AR polymorphism among equid species may be associated with differences in levels of aggression and tameness. Our findings indicate that it would be useful to conduct further studies focusing on the potential association between AR and personality traits, and to understand domestication of equid species. (Source: Meta Gene)
Source: Meta Gene - July 7, 2015 Category: Genetics & Stem Cells Source Type: research

Role of glutathione S-transferase M1, T1 and P1 gene polymorphisms in childhood acute lymphoblastic leukemia susceptibility in a Turkish population
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Mehmet Guven , Selin Unal , Duygu Erhan , Nihal Ozdemir , Safa Baris , Tiraje Celkan , Merve Bostancı , Bahadir Batar The variations between different individuals in the xenobiotic metabolizing enzymes' activity were shown to modify susceptibility to childhood acute lymphoblastic leukemia (ALL). Polymorphisms associated with genes coding for the glutathione S-transferase (GST) enzyme were known to affect the metabolism of different carcinogens. The aim of this study was to evaluate the influence of the GSTM1 and GSTT1 deletion polymorphisms, and the ...
Source: Meta Gene - June 17, 2015 Category: Genetics & Stem Cells Source Type: research

Assembly and variation analyses of Clarias batrachus mitogenome retrieved from WGS data and its phylogenetic relationship with other catfishes
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Basdeo Kushwaha , Ravindra Kumar , Suyash Agarwal , Manmohan Pandey , N.S. Nagpure , Mahender Singh , Shreya Srivastava , C.G. Joshi , P. Das , L. Sahoo , P. Jayasankar , P.K. Meher , T.M. Shah , A.B. Patel , Namrata Patel , P. Koringa , Sofia Priyadarsani Das , Siddhi Patnaik , Amrita Bit , Sarika , M.A. Iquebal , Dinesh Kumar , J.K. Jena Whole genome sequencing (WGS) using next generation sequencing technologies paves the way to sequence the mitochondrial genomes with greater ease and lesser time. Here, we used the WGS data of Clarias batrachus, gen...
Source: Meta Gene - June 17, 2015 Category: Genetics & Stem Cells Source Type: research

ADIPOQ single nucleotide polymorphism: Association with adiponectin and lipoproteins levels restricted to men
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Luciane Viater Tureck , Neiva Leite , Ricardo Lehtonen Rodrigues Souza , Luciana da Silva Timossi , Ana Claudia Vecchi Osiecki , Raul Osiecki , Lupe Furtado Alle Adiponectin is an adipokine inversely correlated with obesity, which has beneficial effect on insulin resistance and lipid metabolism. Considering its potential as a therapeutic target in the metabolic disorder contexts, and in order to add knowledge in the area, our study evaluated the ADIPOQ 276G>T polymorphism effect on adiponectin levels, and on lipoproteins of clinical interest in...
Source: Meta Gene - June 17, 2015 Category: Genetics & Stem Cells Source Type: research

Genetic diversity analysis among male and female Jojoba genotypes employing gene targeted molecular markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) markers
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Monika Heikrujam , Jatin Kumar , Veena Agrawal To detect genetic variations among different Simmondsia chinensis genotypes, two gene targeted markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) were employed in terms of their informativeness and efficiency in analyzing genetic relationships among different genotypes. A total of 15 SCoT and 17 CBDP primers detected genetic polymorphism among 39 Jojoba genotypes (22 females and 17 males). Comparatively, CBDP markers proved to be more effective than SCoT markers in ...
Source: Meta Gene - June 16, 2015 Category: Genetics & Stem Cells Source Type: research

Metagenomics: A new horizon in cancer research
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Joyita Banerjee , Neetu Mishra , Yogita Dhas Metagenomics has broadened the scope of targeting microbes responsible for inducing various types of cancers. About 16.1% of cancers are associated with microbial infection. Metagenomics is an equitable way of identifying and studying micro-organisms within their habitat. In cancer research, this approach has revolutionized the way of identifying, analyzing and targeting the microbial diversity present in the tissue specimens of cancer patients. The genomic analyses of these micro-organisms through next gen...
Source: Meta Gene - June 14, 2015 Category: Genetics & Stem Cells Source Type: research

The complete mitochondrial genome of Papilio glaucus and its phylogenetic implications
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Jinhui Shen , Qian Cong , Nick V. Grishin Due to the intriguing morphology, lifecycle, and diversity of butterflies and moths, Lepidoptera are emerging as model organisms for the study of genetics, evolution and speciation. The progress of these studies relies on decoding Lepidoptera genomes, both nuclear and mitochondrial. Here we describe a protocol to obtain mitogenomes from Next Generation Sequencing reads performed for whole-genome sequencing and report the complete mitogenome of Papilio (Pterourus) glaucus. The circular mitogenome is 15,306bp in...
Source: Meta Gene - June 14, 2015 Category: Genetics & Stem Cells Source Type: research

Proteomic analysis of differentially expressed protein in hemocytes of wild giant freshwater prawn Macrobrachium rosenbergii infected with infectious hypodermal and hematopoietic necrosis virus (IHHNV)
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): T. Alinejad , Kwong Q. Bin , J. Vejayan , R.Y. Othman , S. Bhassu Epizootic diseases cause huge mortality and economical loses at post larvae stages in freshwater prawn aquaculture industry. These prawns seem less susceptible to viral diseases except for infectious hypodermal and hematopoietic necrosis virus (IHHNV). During viral infection in prawns, hemocytes are the primary organ that shows immunological response within the early stages of infection. We applied proteomic approaches to understand differential expression of the proteins in hemocytes d...
Source: Meta Gene - June 6, 2015 Category: Genetics & Stem Cells Source Type: research

Impact of polymorphisms of the GGCX gene on maintenance warfarin dose in Chinese populations: Systematic review and meta-analysis
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Lihong Tian , Jinhua Zhang , Shiji Xiao , Jinlong Huang , Yuanyuan Zhang , Jianzhen Shen The meta-analysis was conducted to investigate the impact of gamma-glutamyl carboxylase (GGCX) on maintenance warfarin dose. 8 studies were included, focusing on the impact of GGCX single nucleotide polymorphisms (SNPs) on mean daily warfarin dose (MDWD). GGCX (rs699664; AA versus GG, GA versus GG, A versus GG) and GGCX (rs12714145; GA versus GG, AA versus GG, A versus GG) showed no significant differences on mean daily warfarin dose (MDWD). This meta-analysis was...
Source: Meta Gene - June 5, 2015 Category: Genetics & Stem Cells Source Type: research

Splicing variants of porcine synphilin-1
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Knud Larsen , Lone Bruhn Madsen , Leila Farajzadeh , Christian Bendixen Parkinson's disease (PD), idiopathic and familial, is characterized by degradation of dopaminergic neurons and the presence of Lewy bodies (LB) in the substantia nigra. LBs contain aggregated proteins of which α-synuclein is the major component. The protein synphilin-1 interacts and colocalizes with α-synuclein in LBs. The aim of this study was to isolate and characterize porcine synphilin-1 and isoforms hereof with the future perspective to use the pig as a model for ...
Source: Meta Gene - June 3, 2015 Category: Genetics & Stem Cells Source Type: research

Association between interleukin-18 gene promoter (−607C/A and −137G/C) polymorphisms and chronic hepatitis C virus infections: A meta-analysis
Conclusions The present meta-analysis suggested that IL-18 −137G/C polymorphism in promoter region was associated with chronic hepatitis C virus infections, but no evidence indicate association between −607C/A polymorphism and chronic hepatitis C virus infections. High-quality studies with larger sample size and larger number are warranted. (Source: Meta Gene)
Source: Meta Gene - May 22, 2015 Category: Genetics & Stem Cells Source Type: research

Gene–gene and gene–environment interactions in the etiology of type 2 diabetes mellitus in the population of Hyderabad, India
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Kommoju Uma Jyothi , Battini Mohan Reddy Fifteen SNPs from nine different genes were genotyped on 1379 individuals, 758 T2DM patients and 621 controls, from the city of Hyderabad, India, using Sequenom Massarray platform. These data were analyzed to examine the role of gene–gene and gene–environment interactions in the manifestation of T2DM. The multivariate analysis suggests that TCF7L2, CDKAL1, IGF2BP2, HHEX and PPARG genes are significantly associated with T2DM, albeit only the first two of the above 5 were associated in the univariate ...
Source: Meta Gene - May 22, 2015 Category: Genetics & Stem Cells Source Type: research

Genetic model selection for a case–control study and a meta-analysis
Publication date: September 2015 Source:Meta Gene, Volume 5 Author(s): Nobuyuki Horita , Takeshi Kaneko A case–control study often compares the prevalence of a specific disease among persons with normal alleles and persons with variant alleles, which generates an odds ratio (OR). The most common type of allele variation, single-nucleotide polymorphism, consists of a major allele (M) and a minor allele (m). Thus, the genotype can be a major allele homozygote (MM), a heterozygote (Mm) or a minor allele homozygote (mm). Odds are given for each genotype, and a pair of odds generates an OR. Summarizing data using two-by...
Source: Meta Gene - May 22, 2015 Category: Genetics & Stem Cells Source Type: research

Association of interleukin-6 genetic polymorphisms with risk of OSCC in Indian population
Conclusion The genotype GC and allele C of IL-6 (−174) G/C gene polymorphism play a significant role in OSCC susceptibility. (Source: Meta Gene)
Source: Meta Gene - May 16, 2015 Category: Genetics & Stem Cells Source Type: research

Enriched transcription factor signatures in triple negative breast cancer indicates possible targeted therapies with existing drugs
Conclusion With the increasing number of large sample size breast cancer cohorts, an exploratory analysis of genes that are consistently enriched in TN sharing common promoter motifs allows for the identification of possible therapeutic targets with extensive validation in patient derived data sets. (Source: Meta Gene)
Source: Meta Gene - May 16, 2015 Category: Genetics & Stem Cells Source Type: research

Initial description of primate-specific cystine-knot Prometheus genes and differential gene expansions of D-dopachrome tautomerase genes
Publication date: June 2015 Source:Meta Gene, Volume 4 Author(s): Marko Premzl Using eutherian comparative genomic analysis protocol and public genomic sequence data sets, the present work attempted to update and revise two gene data sets. The most comprehensive third party annotation gene data sets of eutherian adenohypophysis cystine-knot genes (128 complete coding sequences), and d-dopachrome tautomerases and macrophage migration inhibitory factor genes (30 complete coding sequences) were annotated. For example, the present study first described primate-specific cystine-knot Prometheus genes, as well as differential g...
Source: Meta Gene - April 26, 2015 Category: Genetics & Stem Cells Source Type: research

Analysis of consequences of non-synonymous SNP in feed conversion ratio associated TGF-β receptor type 3 gene in chicken
Publication date: June 2015 Source:Meta Gene, Volume 4 Author(s): Kiran D. Rasal , Tejas M. Shah , Megha Vaidya , Subhash J. Jakhesara , Chaitanya G. Joshi The recent advances in high throughput sequencing technology accelerate possible ways for the study of genome wide variation in several organisms and associated consequences. In the present study, mutations in TGFBR3 showing significant association with FCR trait in chicken during exome sequencing were further analyzed. Out of four SNPs, one nsSNP p.Val451Leu was found in the coding region of TGFBR3. In silico tools such as SnpSift and PANTHER predicted it as deleteri...
Source: Meta Gene - April 26, 2015 Category: Genetics & Stem Cells Source Type: research

Structural and functional analyses of Barth syndrome-causing mutations and alternative splicing in the tafazzin acyltransferase domain
Publication date: June 2015 Source:Meta Gene, Volume 4 Author(s): Atsushi Hijikata , Kei Yura , Osamu Ohara , Mitiko Go Tafazzin is a mitochondrial phospholipid transacylase, and its mutations cause Barth syndrome (BTHS). Human tafazzin gene produces four distinct alternatively spliced transcripts. To understand the molecular mechanisms of tafazzin deficiency, we performed an atomic resolution analysis of the influence of the BTHS mutations and of alternative splicing on the structure and function of tafazzin. From the three-dimensional (3D) homology modeling of tafazzin, we identified candidate amino acid residues that ...
Source: Meta Gene - April 24, 2015 Category: Genetics & Stem Cells Source Type: research

Comparative screening of single nucleotide polymorphisms in β-casein and κ-casein gene in different livestock breeds of India
Publication date: June 2015 Source:Meta Gene, Volume 4 Author(s): Lakshya Veer Singh , S. Jayakumar , Anurodh Sharma , Shishir Kumar Gupta , S.P. Dixit , Neelam Gupta , S.C. Gupta The most polymorphic milk protein gene is β-casein; 13 protein variants are known in cattle. Milk protein genetic polymorphism has received considerable research interest in recent years because of possible associations between milk protein and economically important traits in livestock. The present study was undertaken to explore the genetic polymorphisms in exon 7 of β-casein and exon 4 of κ-casein genes in Arunachali yaks (Bo...
Source: Meta Gene - April 15, 2015 Category: Genetics & Stem Cells Source Type: research

Thrombin-activatable fibrinolysis inhibitor Thr325Ile polymorphism and plasma level in breast cancer: A pilot study
In conclusion, this study showed for the first time that TAFI Thr325Ile polymorphism could have a contribution to BC susceptibility in our population. Furthermore, high TAFI plasma levels may serve as a predictor of poor prognosis in patients with BC. (Source: Meta Gene)
Source: Meta Gene - April 11, 2015 Category: Genetics & Stem Cells Source Type: research

Selecting vaccine strains for H3N2 human influenza A virus
Publication date: June 2015 Source:Meta Gene, Volume 4 Author(s): Yoshiyuki Suzuki H3N2 human influenza A virus causes epidemics of influenza mainly in the winter season in temperate regions. Since the antigenicity of this virus evolves rapidly, several attempts have been made to predict the major amino acid sequence of hemagglutinin 1 (HA1) in the target season of vaccination. However, the usefulness of predicted sequence was unclear because its relationship to the antigenicity was unknown. Here the antigenic model for estimating the degree of antigenic difference (antigenic distance) between amino acid sequences of HA1...
Source: Meta Gene - April 8, 2015 Category: Genetics & Stem Cells Source Type: research

KIR genotype distribution among Lebanese patients with Hodgkin's lymphoma
Conclusion In this first study from the Mediterranean region, KIR genotype does not seem to be associated with Hodgkin's lymphoma. Further clinical and translational research is needed to rule out the protective or predisposing role of KIR genes in this important clinical entity. (Source: Meta Gene)
Source: Meta Gene - March 25, 2015 Category: Genetics & Stem Cells Source Type: research

Association of novel SNPs in the candidate genes affecting caprine milk fatty acids related to human health
Publication date: June 2015 Source:Meta Gene, Volume 4 Author(s): S.P. Dixit , Jayakumar Sivalingam , A.K. Tyagi , V. Saroha , A. Sharma , R.K. Nagda In the present investigation, 618 milk samples of Sirohi breed of goat were collected, and analyzed for conjugated linoleic acid (CLA, C18:2) and other fatty acids. The CLA in studied goat milk samples was 4.87mg/g of milk fat and C18:2 cis-9, trans-11 contributes 2.9mg/g of milk fat and trans10 cis12 contributes 0.82mg/g of milk fat. The saturated fatty acids in the milk accounted for 69.55% and unsaturated fatty acid accounted for 28.50%. The unsaturated fatty acid was co...
Source: Meta Gene - March 21, 2015 Category: Genetics & Stem Cells Source Type: research

Characterization of KfrA proteins encoded by a plasmid of Paenibacillus popilliae ATCC 14706T
Publication date: June 2015 Source:Meta Gene, Volume 4 Author(s): Kazuhiro Iiyama , Hiroaki Mon , Kazuki Mori , Takumi Mitsudome , Jae Man Lee , Takahiro Kusakabe , Kousuke Tashiro , Shin-ichiro Asano , Chisa Yasunaga-Aoki A scaffold obtained from whole-genome shotgun sequencing of Paenibacillus popilliae ATCC 14706T shares partial homology with plasmids found in other strains of P. popilliae. PCR and sequencing for gap enclosure indicated that the scaffold originated from a 15,929-bp circular DNA. The restriction patterns of a plasmid isolated from P. popilliae ATCC 14706T were identical to those expected from the seque...
Source: Meta Gene - March 21, 2015 Category: Genetics & Stem Cells Source Type: research

Mitochondrial COI and nuclear RAG1 DNA sequences and analyses of specimens of the three morphologically established species in the genus Trichopsis (Perciformes: Osphronemidae) reveal new/cryptic species
This study should generate further research to find new/cryptic species of the genus Trichopsis in all countries harboring the fish. (Source: Meta Gene)
Source: Meta Gene - March 12, 2015 Category: Genetics & Stem Cells Source Type: research