A new allele of the kappa-casein gene in local zebu cattle breeds

2017 ◽  
Vol 85 (1) ◽  
pp. 3-6
Author(s):  
Tauseef Ahmad ◽  
Ashwin Atkulwar ◽  
Sameera Farah ◽  
Vijendra Singh ◽  
Mumtaz Baig
Keyword(s):  
Small Sample Size ◽  
Genetic Erosion ◽  
Agricultural Practices ◽  
Small Sample ◽  
Zebu Cattle ◽  
Full Potential ◽  
Nucleotide Polymorphisms ◽  
Nonsynonymous Mutation ◽  
Cattle Breeds ◽  
Farmer Suicides

Local zebu cattle breeds in Indian villages are crossbred with exotic breeds at an unprecedented rate without utilising the full potential of genomic technologies. In addition to agriculture produce, livestock, particularly cattle, constitute a vital source of livelihood for farmers in India. Age-old agricultural practices, errant monsoon, and frequent crop failures have resulted in Maharashtra having the highest number of farmer suicides in the country. Local cattle breeds are considered low-yield breeds and thus are primarily used as beasts of burden. Information on functional gene variants in Indian cattle breeds is scant and limited to PCR-RFLP study in few breeds. In this study, 32 samples from 8 cattle breeds were obtained from remote villages of Maharashtra state. By using the re-sequencing technology, we sequenced 403 bp of the exon IV CSN3 allele and inferred its haplotypes. From 32 samples, 14 genotypes (G1–G14) defined by 7 single-nucleotide polymorphisms (SNP's) were identified. From these 14 genotypes, we reconstructed 3 haplotypes (H01, H02, and H03) and estimated their frequencies. Of the 3 haplotypes, two (H01 and H03) corresponded to CSN3*B4 and CSN3*B and CSN3*H and CSN3*G alleles, respectively. The third haplotype H02 was identified as a new allele and differed from CSN3*B4 and CSN3*B and CSN3*H and CSN3*G alleles by one nonsynonymous mutation at the position C5306T-Ile100Thr. The neighbour-joining tree reconstruction revealed haplotype sharing or hybridisation between B. t. indicus and B. t. taurus because the 3 haplotypes originated in this study clustered with A1, B2, B4, B, G, and H alleles, which were reported previously in both the subspecies of B. taurus. The occurrence of one new allele in a small sample size highlights the urgency to screen local zebu cattle breeds by using genomic tools for circumventing genetic erosion that is widespread in Indian villages in India.

scholarly journals Genotype and allele frequencies of polymorphisms in ABCG2, PPARGC1A and OLR1 genes in indigenous cattle breeds in Turkey

2014 ◽  
Vol 64 (1) ◽  
pp. 73-80 ◽  
Author(s):  
Atila Ateş ◽  
Gülhan Türkay Hoştürk ◽  
Iraz Akiş ◽  
Feraye Esen Gürsel ◽  
Hasret Yardibi ◽  
...  
Keyword(s):  
Milk Fat ◽  
Autosomal Gene ◽  
Zebu Cattle ◽  
Peroxisome Proliferator ◽  
Nucleotide Polymorphisms ◽  
Fat Percentage ◽  
Indigenous Cattle ◽  
Allele Distribution ◽  
Cattle Breeds ◽  
Abcg2 Gene

Abstract This study was carried out to determine polymorphisms of four genes in South Anatolian Red (SAR) and East Anatolian Red (EAR) indigenous cattle breeds in Turkey. Single nucleotide polymorphisms (SNPs) monitored in this study are Y581S in ATP binding cassette sub family G member 2 (ABCG2) gene, c.1892T>C and c.3359A>C in peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A) gene and g.8232C>A in oxidized low-density lipoprotein receptor 1 (OLR1) gene. The frequency of the ancestral allele A of the ABCG2 gene Y581S polymorphism was found to be very high (SAR: 0.63; EAR: 0.64) in both cattle breeds. The CC genotypes of PPARGC1A gene c.1892T>C (SAR: 0.65; EAR: 0.80) and OLR1 gene g.8232C>A polymorphisms (SAR: 0.82; EAR: 0.86), which are associated with high milk fat percentage, had higher frequencies than those of the other genotypes. In conclusion, we might suggest that the allele distribution of the ABCG2 gene Y581S polymorphism can be the evidence indicating autosomal gene flow from zebu cattle to SAR and EAR cattle breeds.

scholarly journals Likelihood of mechanistic roles for dopaminergic, serotonergic and glutamatergic receptors in tardive dyskinesia: A comparison of genetic variants in two independent patient populations

2016 ◽  
Vol 4 ◽  
pp. 205031211664367 ◽  
Author(s):  
Svetlana A Ivanova ◽  
Anton JM Loonen ◽  
P Roberto Bakker ◽  
Maxim B Freidin ◽  
Nienke J ter Woerds ◽  
...  
Keyword(s):  
Tardive Dyskinesia ◽  
Genetic Variants ◽  
Intracellular Signaling ◽  
Multiple Testing ◽  
Small Sample Size ◽  
Small Sample ◽  
Nucleotide Polymorphisms ◽  
Small Effect Size ◽  
Dutch Patient

Objectives: An established theory for the pathogenesis of tardive dyskinesia is disturbed dopaminergic receptor sensitivity and/or dopaminergic intracellular signaling. We examined associations between genetic variants of neurotransmitter receptors and tardive dyskinesia. Methods: We assessed tardive dyskinesia in Caucasian psychiatric inpatients from Siberia (N = 431) and a long-stay population from the Netherlands (N = 168). These patients were genotyped for 43 tag single nucleotide polymorphisms in five neurotransmitter receptor genes, and the results for the two populations were compared. Results: Several significant associations with tardive dyskinesia were identified, but only GRIN2A (rs1345423) was found in both patient populations. This lack of agreement was probably due to the small effect size of the associations, the multiple testing and the small sample size of the Dutch patient population. After reviewing the literature, we propose that the constitutive stimulatory activity of serotonergic type 2 receptors may be relevant. Conclusions: Inactivity of the serotonergic, type 2C receptor or blockade of these receptors by atypical antipsychotic drugs may decrease the vulnerability to develop tardive dyskinesia.

scholarly journals ABCB1 polymorphism in clopidogrel-treated Montenegrin patients

2021 ◽  
Vol 16 (1) ◽  
pp. 142-149
Author(s):  
Snezana Mugosa ◽  
Zoran Todorovic ◽  
Jelena Cukic ◽  
Majda Sahman-Zaimovic ◽  
Natasa Djordjevic
Keyword(s):  
Small Sample Size ◽  
Small Sample ◽  
Antiplatelet Drug ◽  
Nucleotide Polymorphisms ◽  
Efficacy And Safety ◽  
Glycoprotein P ◽  
Single Nucleotide ◽  
P Glycoprotein ◽  
Pcr Method ◽  
Variant Alleles

Abstract Clopidogrel is an antiplatelet drug that displays significant interindividual variability in treatment response. Its bioavailability depends on the function of P-glycoprotein (P-gp), which is coded by a highly polymorphic ABCB1 gene. Thus, the aim of this study was to investigate the effect of ABCB1 genetic polymorphism on clopidogrel efficacy and safety and to determine the frequency distribution of its most common single nucleotide polymorphisms (SNPs) in 106 Montenegrin cardiology patients. Clopidogrel efficacy and safety were followed up during 1 year after hospitalization, with the lack of efficacy and adverse drug reactions observed in 11 (10.4%) and 8 patients (7.5%), respectively. Genotyping for ABCB1 SNPs rs1128503 (1236C > T), rs2032582 (2677G > A/T), and rs1045642 (3435C > T) was performed by the real-time PCR method, and the variant alleles were detected with the frequencies of 42.9, 44.8, and 52.8%, respectively. No significant association was observed between any of the examined genotypes and clopidogrel efficacy (p = 0.253) or safety (p = 0.424). Due to small sample size, co-treatment with other drugs, and other genetic factors not taken into account, we believe the absence of correlation between ABCB1 genotypes and indicators of clopidogrel efficacy and safety in this study should be apprehended conditionally, and that larger and better-controlled studies are warranted.

Nucleotide polymorphisms in the bovine lymphotoxin A gene and their distribution among Bos indicus zebu cattle breeds

Gene ◽  
2016 ◽  
Vol 579 (1) ◽  
pp. 82-94 ◽  
Author(s):  
Jyotsna Dhingra Behl ◽  
Priyanka Mishra ◽  
N.K. Verma ◽  
S.K. Niranjan ◽  
P.S. Dangi ◽  
...  
Keyword(s):  
Bos Indicus ◽  
Zebu Cattle ◽  
Nucleotide Polymorphisms ◽  
Cattle Breeds

scholarly journals Association of NAT2 genetic polymorphism with the efficacy of Neurotropin® for the enhancement of aggrecan gene expression in nucleus pulposus cells: a pilot study

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Tomoko Nakai ◽  
Daisuke Sakai ◽  
Yoshihiko Nakamura ◽  
Natsumi Horikita ◽  
Erika Matsushita ◽  
...  
Keyword(s):  
Intervertebral Disc ◽  
Nucleus Pulposus ◽  
Core Protein ◽  
Small Sample Size ◽  
Small Sample ◽  
Nucleotide Polymorphisms ◽  
Nucleus Pulposus Cells ◽  
Glycosaminoglycan Synthesis ◽  
Rapid Acetylators ◽  
Acetylator Status

Abstract Background Intervertebral disc degeneration, one of the major causes of low-back pain, results from altered biosynthesis/turnover of extracellular matrix in the disc. Previously, we reported that the analgesic drug Neurotropin® (NTP) had an anabolic effect on glycosaminoglycan synthesis in cultured nucleus pulposus (NP) cells via the stimulation of chondroitin sulfate N-acetylgalactosaminyltransferase 1. However, its effect on the aggrecan core protein was not significantly detected, because of the data variance. A microarray analysis suggested that the effect of NTP on aggrecan was correlated with N-acetyltransferase 2 (NAT2), a drug-metabolizing enzyme. Specific NAT2 alleles are known to correlate with rapid, intermediate, and slow acetylation activities and side effects of various drugs. We investigated the association between the efficacy of NTP on aggrecan expression and the NAT2 genotype in cell donors. Methods NP cells were isolated from intervertebral disc tissues donated by 31 Japanese patients (28–68 years) who underwent discectomy. NTP was added to the primary cell cultures and its effect on the aggrecan mRNA was analyzed using real-time quantitative PCR. To assess acetylator status, genotyping was performed based on the inferred NAT2 haplotypes of five common single-nucleotide polymorphisms using allele-specific PCR. Results The phenotype frequencies of NAT2 in the patients were 0%, 42.0%, and 58.0% for slow, intermediate, and rapid acetylators, respectively. The proportions of responders to NTP treatment (aggrecan upregulation, ≥ 1.1-fold) in the intermediate and rapid acetylators were 76.9% and 38.9%, respectively. The odds ratio of the comparison of the intermediate acetylator status between responders and nonresponders was 5.2 (95% CI 1.06–26.0, P = 0.036), and regarding the 19 male patients, this was 14.0 (95% CI 1.54–127.2, P = 0.012). In the 12 females, the effect was not correlated with NAT2 phenotype but seemed to become weaker along with aging. Conclusions An intermediate acetylator status significantly favored the efficacy of NTP treatment to enhance aggrecan production in NP cells. In males, this tendency was detected with higher significance. This study provides suggestive data of the association between NAT2 variants and the efficacy of NTP treatment. Given the small sample size, results should be further confirmed.

CYP17A1 Polymorphisms and Clinical Outcome of Castration-Resistant Prostate Cancer Patients Treated with Abiraterone

2016 ◽  
Vol 31 (3) ◽  
pp. 264-269 ◽  
Author(s):  
Samanta Salvi ◽  
Valentina Casadio ◽  
Salvatore Luca Burgio ◽  
Vincenza Conteduca ◽  
Lorena Rossi ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Clinical Outcome ◽  
Small Sample Size ◽  
Progression Free Survival ◽  
Small Sample ◽  
Nucleotide Polymorphisms ◽  
Castration Resistant Prostate Cancer ◽  
Single Nucleotide ◽  
Castration Resistant

Background We evaluated the role of single nucleotide polymorphisms in the CYP17A1 gene for predicting clinical outcome in castration-resistant prostate cancer (CRPC) patients treated with abiraterone. Methods Sixty-four patients were genotyped for the selected polymorphisms (rs743572, rs10883783, rs17115100 and rs284849) in CYP17A1. We hypothesized that different genotypes could be associated with progression-free survival (PFS) and overall survival (OS). Results Statistical analyses highlighted no significant associations between these polymorphisms and clinical outcome. However, individuals with the most common TT genotype for rs10883783 had a 3 months’ longer PFS than individuals with the TA + AA genotype. Conclusions With the limitation of the retrospective study design and the small sample size, the analyzed polymorphisms do not seem to be correlated with clinical outcome of CRPC patients treated with abiraterone.

Effect of genetic polymorphisms on toxicity and survival in advanced non-small cell lung cancer (NSCLC) patients (pts) treated with carboplatin (CBDCA) and pemetrexed disodium regimen

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e19028-e19028
Author(s):  
V. Ludovini ◽  
L. Crinò ◽  
L. Pistola ◽  
I. Floriani ◽  
M. Meacci ◽  
...  
Keyword(s):  
Genetic Polymorphisms ◽  
Advanced Nsclc ◽  
Cox Model ◽  
Small Sample Size ◽  
Progression Free Survival ◽  
Small Sample ◽  
Response To Therapy ◽  
Taqman Probe ◽  
Nucleotide Polymorphisms ◽  
Data Set

e19028 Background: Identification of genetic polymorphisms which influence chemotherapy outcome may help towards individually optimized therapy. We investigated the influence of ten single nucleotide polymorphisms (SNPs) of 7 genes (P53 Arg72Pro (G/C); XRCC3 Thr241Met (C/T); XPD Lys751Gln (A/C); ERCC1 Asn118Asn (C/T); GARFT C/G, GARFT C/T, DHFR C/G, DHFR A/G, TS 5’UTR, TS 3’UTR involved with metabolism of CBDCA and Alimta regimen in pts with advanced NSCLC. Methods: Genomic DNA was extracted from whole blood samples using the QIAamp DNA estraction kit on Biorobot EZ1 (Qiagen). Polymorphisms were detected with TaqMan-probe based assays using the 7300 Real-Time PCR system (Applied Biosystems, Foster City, CA) or PCR followed by RFLP. The results of SNPs were assessed by Cox model for survival/PFS & logistics regression for response/toxicity. Results: We performed a retrospective analysis in 57 advanced pretreated (2nd or 3th line) NSCLC pts treated with CBDCA(AUC=5) + Alimta (500 mg/m2). Median age was 59 years (range 26–79), M/F:63/37%; Adeno/Squa/other Ca:65/20/15%; ECOG PS:0–1/2–3:96/4%. Overall response rate was 38.6%, stable disease 38.6% and disease progression 21.1%. At median follow-up of 7.9 months, 10 pts (17.5%) died, 47 pts (82.5%) are alive. The median progression free survival (PFS) was 7.4 months, the median survival time not reached. P53 Pro72Pro was significantly associated with shorter survival (HR 5.5, 95%CI 1.01–30.5, p=0.04) when compared to P53 Arg72Arg. None of the analyzed polymorphisms was related to response to therapy. No associations were found between the analyzed polymorphisms and toxicity considered either as the maximum observed grade, or as sum of each toxicity pattern grade, probably due to low number of events observed for toxicity within this data set. Conclusions: P53 Pro72Pro may be associated with shorter survival in pts with advanced NSCLC. Further studies are warranted to validate this finding. Genotype-related differences in common toxicities and in response to therapy were not observed. The small sample size limits interpretation of these data. No significant financial relationships to disclose.

DNA sequence and haplotype variation in two candidate genes for dilated cardiomyopathy in the turkey Meleagris gallopavo

Genome ◽  
2007 ◽  
Vol 50 (5) ◽  
pp. 463-469 ◽  
Author(s):  
Kuan-chin Lin ◽  
Jun Xu ◽  
Davida Kamara ◽  
Tuoyu Geng ◽  
Kwaku Gyenai ◽  
...  
Keyword(s):  
Dilated Cardiomyopathy ◽  
Candidate Genes ◽  
Troponin T ◽  
Small Sample Size ◽  
Meleagris Gallopavo ◽  
Small Sample ◽  
Snp Analysis ◽  
Chromosome 2 ◽  
Nucleotide Polymorphisms ◽  
Haplotype Variation

Determining variation in genes is fundamental to understanding their function in the disease state. Cardiac troponin T (cTnT) and phospholamban (PLN) genes have been implicated in dilated cardiomyopathy (DCM) in human and model species. To investigate the role of these 2 candidate genes in DCM in the turkey Meleagris gallopavo, understanding sequence variants and map position distribution is necessary. To this end, a total of 1854 and 1771 bp of cTnT and PLN gene sequences, respectively, were scanned for single nucleotide polymorphisms (SNPs) in a randomly bred population. A total of 15 SNPs was identified in the cTnT and PLN genomic sequences. Nine haplotypes, 5 in cTnT and 4 in PLN, were identified. Observed heterozygosities (0.02–0.39) in the turkey population were low for both genes. Within each gene, 1 SNP corresponding to a restriction enzyme site was identified and used to develop a PCR–restriction fragment length polymorphism (RFLP) genotyping assay. The PLN gene was genetically mapped to turkey chromosome 2, equivalent to Gallus gallus chromosome 3, and cTnT mapped to a turkey microchromosome. Although limited because of the relatively small sample size of 55 birds, the data from this SNP analysis of PLN and cTnT provide a foundation from which to evaluate the function of cTnT and PLN in the turkey. Information about the distribution of the SNPs and haplotypes will facilitate future association and linkage studies.

scholarly journals The −839(A/C) Polymorphism in the ECE1 Isoform b Promoter Associates With Osteoporosis and Fractures

2019 ◽  
Vol 3 (11) ◽  
pp. 2041-2050 ◽  
Author(s):  
Karen E Hansen ◽  
Michael G Johnson ◽  
Tonia C Carter ◽  
John Mayer ◽  
Nicholas S Keuler ◽  
...  
Keyword(s):  
Postmenopausal Women ◽  
Small Sample Size ◽  
Medical Center ◽  
Small Sample ◽  
Bone Biomechanics ◽  
Mouse Strains ◽  
Nucleotide Polymorphisms ◽  
Mineral Density ◽  
Clinical Fractures ◽  
Isoform B

Abstract Context We previously found that variation in a quantitative trait locus, including the gene-encoding endothelin-converting enzyme 1 (Ece1), accounted for 40% of the variance in bone biomechanics and bone mineral density (BMD) in an intercross of recombinant congenic mouse strains. Objective We hypothesized that single nucleotide polymorphisms (SNPs) within the human ECE1 isoform b promoters, at ECE1 b −338(G/T) and ECE1 b −839(A/C), would associate with osteoporosis in postmenopausal women. Design We genotyped DNA for the ECE1 −338(G/T) and −839(A/C) SNPs. Setting A community medical center. Participants Postmenopausal women (3564) with ≥1 dual-energy X-ray absorptiometry scan ≥60 years of age. Main Outcome Measures BMD, osteoporosis, and clinical fractures. Results In multivariate models controlling for age, weight, healthcare duration, and tobacco, the CC genotype reduced the odds of lifetime fracture (OR 0.33, 95% CI 0.12, 0.87) and fracture ≥50 years of age (OR 0.31, 95% CI 0.11, 0.87), whereas the AC genotype increased odds of osteoporosis (OR 1.34, 95% CI 1.02 1.78) relative to the AA genotype. However, when controlling the false-discovery rate, findings were no longer significant. We found no consistent relationship between the ECE1 b −338(G/T) and study outcomes. Conclusions The CC genotype was associated with fewer fractures, whereas the AC genotype was associated with osteoporosis. Our small sample size and few minorities are study limitations. Findings should be tested in another cohort to confirm a link between the ECE1 −839(A/C) SNPs and osteoporosis.

Probing the ultrastructure of the mitotic and meiotic spindle in eggs: An expeditious approach based on semi-thin (0.25 μm) serial sections

1983 ◽  
Vol 41 ◽  
pp. 552-555
Author(s):  
Conly L. Rieder ◽  
S. Bowser ◽  
R. Nowogrodzki ◽  
K. Ross ◽  
G. Sluder
Keyword(s):  
Small Sample Size ◽  
Small Sample ◽  
Meiotic Spindle ◽  
Serial Sections ◽  
Mitotic Apparatus ◽  
Thin Sections ◽  
Cell Cycles ◽  
Ultrastructural Studies

Eggs have long been a favorite material for studying the mechanism of karyokinesis in-vivo and in-vitro. They can be obtained in great numbers and, when fertilized, divide synchronously over many cell cycles. However, they are not considered to be a practical system for ultrastructural studies on the mitotic apparatus (MA) for several reasons, the most obvious of which is that sectioning them is a formidable task: over 1000 ultra-thin sections need to be cut from a single 80-100 μm diameter egg and of these sections only a small percentage will contain the area or structure of interest. Thus it is difficult and time consuming to obtain reliable ultrastructural data concerning the MA of eggs; and when it is obtained it is necessarily based on a small sample size.We have recently developed a procedure which will facilitate many studies concerned with the ultrastructure of the MA in eggs. It is based on the availability of biological HVEM's and on the observation that 0.25 μm thick serial sections can be screened at high resolution for content (after mounting on slot grids and staining with uranyl and lead) by phase contrast light microscopy (LM; Figs 1-2).

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