Search results for: genotypes

Authors: Manar Makhoul, Buthainah Alsalamah, Salam Lawand, Hassan Azzam

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The major storage proteins in endosperm of 33 cultivated and wild barley genotypes (H.vulgare, H. spontaneum, H. bulbosum, H. murinum, H. marinum) were analyzed to demonstrate the variation in the hordein polypeptides encoded by multigene families in grains. The SDS-PAGE revealed 13 and 17 alleles at the Hor1 and the Hor2 loci respectively, with frequencies from 0.83 to 14 and 0.56 to 13.41% respectively, while seven alleles at the Hor3 locus with frequencies from 3.63 to 30.91% were recognized. The phylogenetic analysis indicated to relevance of the polymorphism in hordein patterns as successful tool in identifying the individual genotypes and discriminating the species according to genome type. We also reported in this research complete nucleotide sequence B-hordein genes of seven wild and cultivated barley genotypes. A 152bp upstream sequence of B-hordein promoter contained a TATA box, CATC box, AAAG motif, N-motif and E-motif. In silico analysis of B-Hordein sequences demonstrated that the coding regions were not interrupted by any intron, and included the complete ORF which varied between 882 and 906 bp, and encoded mature proteins with 293-301 residues characterized by high contents of glutamine (29%), and proline (18%). Comparison of the predicted polypeptide sequences with the published ones suggested that all S-rich prolamins genes are descended from common ancestor. The sequence started at N-terminal with a signal peptide, and then followed directly by two domains; a repetitive one based on the repetition of the repeat unit PQQPFPQQ and C-terminal domain. Also, it was found that positions of the eight cysteine residues were highly conserved in all the B-hordein sequences, but Hordeum bulbosum had additional unpaired one. The phylogenetic tree of B-hordein polypeptide separated the genotypes in distinct seven subgroups. In general, the high homology between B-hordeins and LMW glutenin subunits suggests similar bread-making influences for these B-hordeins.

Keywords: hordeum, phylogenetic tree, sequencing, storage protein

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Authors: Rini Rahul, Manoj Kumar

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Cadmium (Cd) is a poisonous trace metal, which is responsible for excess reactive oxygen species generation (ROS) in plants, thereby adversely affecting their productivity and commercial potential. Ricinus communis (castor) is an industry-efficient non-edible bioenergy crop used for phytoremediation and re-vegetation. We have determined the total Cd content in castor genotypes and established a relationship between the Cd tolerance mechanism and physiological parameters like chlorophyll fluorescence, the total photosynthetic activity, chlorophyll and carotenoid content as well as ROS generation and malondialdehyde content. This study is an effort to comprehend the interrelation between Cd toxicity (control, 250 µM and 500 µM), proline, various ROS scavenging enzymes (anti-oxidative in nature), nicotianamine synthase (NAS) and Natural resistance-associated macrophage protein (NRAMP) gene. The antioxidant enzyme activity increased for WM hence conferring Cd toxicity in this genotype. RcNRAMP genes showed differential expression in GCH2 and WM genotypes; this can also be one of the reasons for Cd toxicity and sensitivity in WM and GCH2, respectively. The cause of pronounced Cd tolerance in WM leaves can be because of enhanced expression of RcNAS1, RcNAS2 and RcNAS3 genes. Our results demonstrate that there is an interrelation between Cd toxicity (control, 250 µM and 500 µM), proline, various ROS scavenging enzymes (anti-oxidative in nature), NAS and NRAMP gene.

Keywords: ricinus communis, cadmium, reactive oxygen species, nicotianamine synthase, NRAMP, malondialdehyde

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Authors: Mehdi Nasr-Esfahani, Leila Mohammad Bagheri, Ava Nasr-Esfahani

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Root and collar rot disease caused by Phytophthora capsici (Leonian) is one of the most serious diseases in pepper, Capsicum annuum L. In this study, a diverse collection of 37 commercial edible and ornamental pepper genotypes infected with P. capsici were investigated for biomass parameters and enzymatic activity of peroxidase or peroxide reductases (EC), superoxide dismutase (SOD), polyphenol oxidase (PPOs), catalase (CAT) and phenylalanine ammonia-lyase (PAL). Seven candidate DEG genes were also evaluated on resistant and susceptible pepper cultivars, through measuring product formation, using spectrophotometry and real-time polymerase chain reaction. All the five enzymes and seven defense-gene candidates were up-regulated in all inoculated pepper accessions to P. capsici. But, the enzymes and DEG genes were highly expressed in resistant cv. 19OrnP-PBI, 37ChillP-Paleo, and “23CherryP-Orsh". The expression level of enzymes were 1.5 to 5.6-fold higher in the resistant peppers, than the control non-inoculated genotypes. Also, the transcriptional levels of related candidate DEG genes were 3.16 to 5.90-fold higher in the resistant genotypes. There was a direct and high correlation coefficient between resistance, bio-mass parameters, enzymatic activity, and resistance gene expression. The related enzymes and candidate genes expressed herein will provide a basis for further gene cloning and functional verification studies, and also will aid in an understanding of the regulatory mechanism of pepper resistance to P. capsici.

Keywords: AP2/ERF, cDNA, enzymes, MIP gene, q-RTPCR, XLOC

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Authors: Fulufhelo Amanda Doboro, Kgomotso Sebeko, Stephen Njiro, Moritz Van Vuuren

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Ovine herpesvirus 2 (OvHV-2) genome obtained from the lymphopblastoid cell line of a BJ1035 cow was recently sequenced in the United States of America (USA). Information on the sequences of OvHV-2 genes obtained from South African strains from bovine or other African countries and molecular characterization of OvHV-2 is not documented. Present investigation provides information on the nucleotide and derived amino acid sequences and genetic diversity of Ov 7, Ov 8 ex2, ORF 27 and ORF 73 genes, of these genes from OvHV-2 strains circulating in South Africa. Gene-specific primers were designed and used for PCR of DNA extracted from 42 bovine blood samples that previously tested positive for OvHV-2. The expected PCR products of 495 bp, 253 bp, 890 bp and 1632 bp respectively for Ov 7, Ov 8 ex2, ORF 27 and ORF 73 genes were sequenced and multiple sequence analysis done on the selected regions of the sequenced PCR products. Two genotypes for ORF 27 and ORF 73 gene sequences, and three genotypes for Ov 7 and Ov 8 ex2 gene sequences were identified, and similar groupings for the derived amino acid sequences were obtained for each gene. Nucleotide and amino acid sequence variations that led to the identification of the different genotypes included SNPs, deletions and insertions. Sequence analysis of Ov 7 and ORF 27 genes revealed variations that distinguished between sequences from SA and reference OvHV-2 strains. The implication of geographic origin among SA sequences was difficult to evaluate because of random distribution of genotypes in the different provinces, for each gene. However, socio-economic factors such as migration of people with animals, or transportation of animals for agricultural or business use from one province to another are most likely to be responsible for this observation. The sequence variations observed in this study have no impact on the antibody binding activities of glycoproteins encoded by Ov 7, Ov 8 ex2 and ORF 27 genes, as determined by prediction of the presence of B cell epitopes using BepiPred 1.0. The findings of this study will be used for selection of gene candidates for the development of diagnostic assays and vaccine development as well.

Keywords: amino acid, genetic diversity, genes, nucleotide

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Authors: Gordana Branković, Vesna Dragičević, Dejan Dodig, Desimir Knežević, Srbislav Denčić, Gordana Šurlan-Momirović

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Phytic acid is a major pool in the flux of phosphorus through agroecosystems and represents a sum equivalent to > 50% of all phosphorus fertilizer used annually. Nutrition rich in phytic acid can substantially decrease micronutrients apsorption as calcium, zink, iron, manganese, copper due to phytate salts excretion by human and non-ruminant animals as poultry, swine and fish, having in common very scarce phytase activity, and consequently the ability to digest and utilize phytic acid, thus phytic acid derived phosphorus in animal waste contributes to water pollution. The tested accessions consisted of 15 genotypes of bread wheat (Triticum aestivum L. ssp. vulgare) and of 15 genotypes of durum wheat (Triticum durum Desf.). The trials were sown at the three test sites in Serbia: Rimski Šančevi (RS) (45º19´51´´N; 19º50´59´´E), Zemun Polje (ZP) (44º52´N; 20º19´E) and Padinska Skela (PS) (44º57´N 20º26´E) during two vegetation seasons 2010-2011 and 2011-2012. The experimental design was randomized complete block design with four replications. The elementary plot consisted of 3 internal rows of 0.6 m2 area (3 × 0.2 m × 1 m). Grains were grinded with Laboratory Mill 120 Perten (“Perten”, Sweden) (particles size < 500 μm) and flour was used for the analysis. Phytic acid grain content was determined spectrophotometrically with the Shimadzu UV-1601 spectrophotometer (Shimadzu Corporation, Japan). Objectives of this study were to determine: i) variability and stability of the phytic acid content among selected genotypes of bread and durum wheat, ii) predominant source of variation regarding genotype (G), environment (E) and genotype × environment interaction (GEI) from the multi-environment trial, iii) influence of climatic variables on the GEI for the phytic acid content. Based on the analysis of variance it had been determined that the variation of phytic acid content was predominantly influenced by environment in durum wheat, while the GEI prevailed for the variation of the phytic acid content in bread wheat. Phytic acid content expressed on the dry mass basis was in the range 14.21-17.86 mg g-1 with the average of 16.05 mg g-1 for bread wheat and 14.63-16.78 mg g-1 with the average of 15.91 mg g-1 for durum wheat. Average-environment coordination view of the genotype by environment (GGE) biplot was used for the selection of the most desirable genotypes for breeding for low phytic acid content in the sense of good stability and lower level of phytic acid content. The most desirable genotypes of bread and durum wheat for breeding for phytic acid were Apache and 37EDUYT /07 No. 7849. Models of climatic factors in the highest percentage (> 91%) were useful in interpreting GEI for phytic acid content, and included relative humidity in June, sunshine hours in April, mean temperature in April and winter moisture reserves for genotypes of bread wheat, as well as precipitation in June and April, maximum temperature in April and mean temperature in June for genotypes of durum wheat.

Keywords: genotype × environment interaction, phytic acid, stability, variability

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Authors: Khabat Barkhordari

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

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Authors: Nahida Sultana

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Globally, an estimated 58 million people have chronic hepatitis C virus infection, with about 1.5 million new infections occurring per year. The hepatitis C virus is a blood-borne virus, and most infections occur through exposure to blood from unsafe injection practices, unsafe health care, unscreened blood transfusion, injection drug use, and sexual practices that lead to exposure to blood. Hepatitis C virus (HCV) causes chronic infections that mainly affect the liver leading to liver diseases. This study aimed to determine whether there is any significant association between HCV transmission risk factors in relation to genotypes in HCV-infected Bangladeshi patients. After quantification of HCV viral load, 36 samples were randomly selected for HCV genotyping and risk factor measurement. A greater proportion of genotype 1 (p > 0.05) patients (40%) underwent blood transfusion compared to patients (22.6%) with genotype 3 infections. More genotype 1 patient underwent surgery and invasive procedures (20%), and rather than those with genotype 3 patients (16.1%). The history of IDUs (25.8%) and sexual exposure (3.2%) are only prevalent in genotype 3 patients and absent in patients with genotype 1 (p >0.05). There was no significant statistical difference found in HCV transmission risk factors (blood transfusion, IDUs, Surgery& interventions, sexual transmission) between patients infected with genotypes 1 and 3. In HCV infection, genotype may have no relation to transmission risk factors among Bangladeshi patients.

Keywords: HCV genotype, alanine aminotransferase (ALT), HCV viral load, IDUs

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Authors: Upasana Bhumbla

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Background: Hepatitis C virus is a major cause of chronic hepatitis, which can further lead to cirrhosis of the liver and hepatocellular carcinoma. Worldwide the burden of Hepatitis C infection has become a serious threat to the human race. Hepatitis C virus (HCV) has population-specific genotypes and provides valuable epidemiological and therapeutic information. Genotyping and assessment of viral load in HCV patients are important for planning the therapeutic strategies. The aim of the study is to study the changing trends of prevalence and genotypic distribution of hepatitis C virus in a tertiary care hospital in Western India. Methods: It is a retrospective study; blood samples were collected and tested for anti HCV antibodies by ELISA in Dept. of Microbiology. In seropositive Hepatitis C patients, quantification of HCV-RNA was done by real-time PCR and in HCV-RNA positive samples, genotyping was conducted. Results: A total of 114 patients who were seropositive for Anti HCV were recruited in the study, out of which 79 (69.29%) were HCV-RNA positive. Out of these positive samples, 54 were further subjected to genotype determination using real-time PCR. Genotype was not detected in 24 samples due to low viral load; 30 samples were positive for genotype. Conclusion: Knowledge of genotype is crucial for the management of HCV infection and prediction of prognosis. Patients infected with HCV genotype 1 and 4 will have to receive Interferon and Ribavirin for 48 weeks. Patients with these genotypes show a poor sustained viral response when tested 24 weeks after completion of therapy. On the contrary, patients infected with HCV genotype 2 and 3 are reported to have a better response to therapy.

Keywords: hepatocellular, genotype, ribavarin, seropositive

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Authors: Atsuko Okazaki, Jurg Ott

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Some genetic diseases (‘digenic traits’) are due to the interaction between two DNA variants. For example, certain forms of Retinitis Pigmentosa (a genetic form of blindness) occur in the presence of two mutant variants, one in the ROM1 gene and one in the RDS gene, while the occurrence of only one of these mutant variants leads to a completely normal phenotype. Detecting such digenic traits by genetic methods is difficult. A common approach to finding disease-causing variants is to compare 100,000s of variants between individuals with a trait (cases) and those without the trait (controls). Such genome-wide association studies (GWASs) have been very successful but hinge on genetic effects of single variants, that is, there should be a difference in allele or genotype frequencies between cases and controls at a disease-causing variant. Frequent pattern mining (FPM) methods offer an avenue at detecting digenic traits even in the absence of single-variant effects. The idea is to enumerate pairs of genotypes (genotype patterns) with each of the two genotypes originating from different variants that may be located at very different genomic positions. What is needed is for genotype patterns to be significantly more common in cases than in controls. Let Y = 2 refer to cases and Y = 1 to controls, with X denoting a specific genotype pattern. We are seeking association rules, ‘X → Y’, with high confidence, P(Y = 2|X), significantly higher than the proportion of cases, P(Y = 2) in the study. Clearly, generally available FPM methods are very suitable for detecting disease-associated genotype patterns. We use fpgrowth as the basic FPM algorithm and built a framework around it to enumerate high-frequency digenic genotype patterns and to evaluate their statistical significance by permutation analysis. Application to a published dataset on opioid dependence furnished results that could not be found with classical GWAS methodology. There were 143 cases and 153 healthy controls, each genotyped for 82 variants in eight genes of the opioid system. The aim was to find out whether any of these variants were disease-associated. The single-variant analysis did not lead to significant results. Application of our FPM implementation resulted in one significant (p < 0.01) genotype pattern with both genotypes in the pattern being heterozygous and originating from two variants on different chromosomes. This pattern occurred in 14 cases and none of the controls. Thus, the pattern seems quite specific to this form of substance abuse and is also rather predictive of disease. An algorithm called Multifactor Dimension Reduction (MDR) was developed some 20 years ago and has been in use in human genetics ever since. This and our algorithms share some similar properties, but they are also very different in other respects. The main difference seems to be that our algorithm focuses on patterns of genotypes while the main object of inference in MDR is the 3 × 3 table of genotypes at two variants.

Keywords: digenic traits, DNA variants, epistasis, statistical genetics

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Authors: Hossein Rassi, Marjan Moradi Fard, Masoud Houshmand

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Background: Cervical cancer is multistep disease that is thought to result from an interaction between genetic background and environmental factors. Human papillomavirus (HPV) infection is the leading risk factor for cervical intraepithelial neoplasia(CIN)and cervical cancer. In other hand, some of p53 and miRNA polymorphism may plays an important role in carcinogenesis. This study attempts to clarify the relation of p53 genotypes and miR-146a rs2910164 polymorphism in cervical lesions. Method: Forty two archival samples with cervical lesion retired from Khatam hospital and 40 sample from healthy persons used as control group. A simple and rapid method was used to detect the simultaneous amplification of the HPV consensus L1 region and HPV-16,-18, -11, -31, 33 and -35 along with the b-globin gene as an internal control. We use Multiplex PCR for detection of P53 and miR-146a rs2910164 genotypes in our lab. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Cervix lesions were collected from 42 patients with Squamous metaplasia, cervical intraepithelial neoplasia, and cervical carcinoma. Successful DNA extraction was assessed by PCR amplification of b-actin gene (99bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of cervical lesions in the study population. In this study, we detected 13 HPV 18 from 42 cervical cancer. Conclusion: The connection between several SNP polymorphism and human virus papilloma in rare researches were seen. The reason of these differences in researches' findings can result in different kinds of races and geographic situations and also differences in life grooves in every region. The present study provided preliminary evidence that a p53 GG genotype and miR-146a rs2910164 CC genotype may effect cervical cancer risk in the study population, interacting synergistically with HPV 18 genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with HPV18 can serve as major risk factors in the early identification of cervical cancers. Furthermore, the results indicate the possibility of primary prevention of cervical cancer by vaccination against HPV18 in Iran.

Keywords: cervical cancer, p53, miR-146a, rs2910164, polymorphism

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Authors: Hossein Rassi, Marjan Moradi fard, Masoud Houshmand

Abstract:

Background: Cervical cancer is multistep disease that is thought to result from an interaction between genetic background and environmental factors. Human Papillomavirus (HPV) infection is the leading risk factor for Cervical Intraepithelial Neoplasia (CIN) and cervical cancer. In other hand, some of p53 and miRNA polymorphism may plays an important role in carcinogenesis. This study attempts to clarify the relation of p53 genotypes and miR-146a rs2910164 polymorphism in cervical lesions. Method: Forty two archival samples with cervical lesion retired from Khatam hospital and 40 sample from healthy persons used as control group. A simple and rapid method was used to detect the simultaneous amplification of the HPV consensus L1 region and HPV-16,-18, -11, -31, 33, and -35 along with the b-globin gene as an internal control. We use Multiplex PCR for detection of P53 and miR-146a rs2910164 genotypes in our lab. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Cervix lesions were collected from 42 patients with Squamous metaplasia, cervical intraepithelial neoplasia, and cervical carcinoma. Successful DNA extraction was assessed by PCR amplification of b-actin gene (99 bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of cervical lesions in the study population. In this study, we detected 13 HPV 18 from 42 cervical cancer. Conclusion: The connection between several SNP polymorphism and human virus papilloma in rare researches were seen. The reason of these differences in researches' findings can result in different kinds of races and geographic situations and also differences in life grooves in every region. The present study provided preliminary evidence that a p53 GG genotype and miR-146a rs2910164 CC genotype may effect cervical cancer risk in the study population, interacting synergistically with HPV 18 genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with HPV18 can serve as major risk factors in the early identification of cervical cancers. Furthermore, the results indicate the possibility of primary prevention of cervical cancer by vaccination against HPV18 in Iran.

Keywords: cervical cancer, miR-146a rs2910164 polymorphism, p53 polymorphism, intraepithelial, neoplasia, HPV

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Authors: Hossein Rassi, Marjan Moradi Fard, Masoud Houshmand

Abstract:

Background: Cervical cancer is multistep disease that is thought to result from an interaction between genetic background and environmental factors. Human papillomavirus (HPV) infection is the leading risk factor for cervical intraepithelial neoplasia (CIN) and cervical cancer. In other hand, some of p53 and miRNA polymorphism may plays an important role in carcinogenesis. This study attempts to clarify the relation of p53 genotypes and miR-146a rs2910164 polymorphism in cervical lesions. Method: Forty two archival samples with cervical lesion retired from Khatam hospital and 40 sample from healthy persons used as control group. A simple and rapid method was used to detect the simultaneous amplification of the HPV consensus L1 region and HPV-16,-18, -11, -31, 33 and -35 along with the b-globin gene as an internal control. We use Multiplex PCR for detection of P53 and miR-146a rs2910164 genotypes in our lab. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Cervix lesions were collected from 42 patients with Squamous metaplasia, cervical intraepithelial neoplasia, and cervical carcinoma. Successful DNA extraction was assessed by PCR amplification of b-actin gene (99bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of cervical lesions in the study population. In this study, we detected 13 HPV 18 from 42 cervical cancer. Conclusion: The connection between several SNP polymorphism and human virus papilloma in rare researches were seen. The reason of these differences in researches' findings can result in different kinds of races and geographic situations and also differences in life grooves in every region. The present study provided preliminary evidence that a p53 GG genotype and miR-146a rs2910164 CC genotype may effect cervical cancer risk in the study population, interacting synergistically with HPV 18 genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with HPV18 can serve as major risk factors in the early identification of cervical cancers. Furthermore, the results indicate the possibility of primary prevention of cervical cancer by vaccination against HPV18 in Iran.

Keywords: cervical cancer, HPV18, p53 codon 72 polymorphism, miR-146a rs2910164 polymorphism

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Authors: Yun-Hsuan Chang, Chih-Chun Huang, Ru-Band Lu

Abstract:

Dopamine, metabolized to 3,4-dihydroxyphenylacetic acid (DOPAC) by aldehyde dehydrogenase 2 (ALDH2), ALDH2*1/*1, and ALDH2*1/*2+ALDH*2/*2 equally carried in Han Chinese. The relationship between dopamine metabolic enzyme and cognitive performance in bipolar II disorder comorbid with anxiety disorder (AD) remains unclear. This study proposed to explore the association between ALDH2 polymorphisms, anxiety comorbidity in bipolar II disorder. One hundred and ninety-seven BPII with or without AD comorbidity were recruited and compared with 130 Health controls (HC). A polymerase chain reaction and restriction fragment length polymorphism analysis was used to determine genotypes for ALDH2, and neuropsychological battery was performed. Two factor analyses with AD comorbidity and ALDH2 showed a significant main effect of ALDH2 on attention and marginally significant interaction between AD and ALDH2 memory performance. The ALDH2 polymorphisms may play a different role in the neuropsychological performance on varied neuropsychological performance in BPII comorbid with and without AD.

Keywords: anxiety disorder, bipolar II disorder, comorbidity, genetic

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Authors: Carlo Stephen O. Moneva, Sharon Rose M. Tabugo

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The present study aims to assess polymorphism in the prolactin (C576A) gene and determine the influence of different prolactin (PRL) genotypes to milk yield performance in crossbred Anglo-Nubian dairy goats raised from Awang, Opol, Misamis Oriental and Talay, Dumaguete City, Negros Oriental. Genomic DNA was extracted from hair follicles and Polymerase Chain Reaction – Restriction Fragment Length Polymorphism (PCR-RFLP) was performed for the genotyping of the C576A polymorphism located in exon 5 of goats’ prolactin gene using Eco241 restriction enzyme. Genotypic and allelic frequencies of 0.56 for AA, 0.44 for AB, 0.78 for A, and 0.22 for B were recorded. Observed heterozygosity values were higher than the expected heterozygosity. All populations followed the Hardy–Weinberg principle at p>0.05, except for dairy goats from Farm A located in Opol, Misamis Oriental. A two-way factorial (2 x 4) in a Randomized Complete Block Design was used to be able to evaluate the relationship between genotypes and milk yield performance. PRL genotypes and parity were used as main factors and farm as the blocking factor. AB genotype goats produced significantly higher average daily milk yield and total milk production than AA genotype (p<0.05), an indication that the polymorphism in the caprine PRL (C576A) gene influenced milk yield performance in the population of crossbred Anglo-Nubian goats from Opol, Misamis Oriental and Dumaguete City, Negros Oriental. However, these results have to be validated in other dairy goat breeds.

Keywords: polymorphism, prolactin, milk yield, Anglo-Nubian, PCR-RFLP

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Authors: Rahim Ada, Mustafa Harmankaya, Sadiye Ayse Celik

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The safflower seed contains about 25-40% solvent extract and 20-33% fiber. It is well known that dietary phospholipids lower serum cholesterol levels effectively. The nutrient composition of safflower seed changes depending on region, soil and genotypes. This research was made by using of six natural selected (A22, A29, A30, C12, E1, F4, G8, G12, J27) and three commercial (Remzibey, Dincer, Black Sun1) varieties of safflower genotypes. The research was conducted on field conditions for two years (2009 and 2010) in randomized complete block design with three replications in Konya-Turkey ecological conditions. Oil contents, mineral contents and their correlations were determined in the research. According to the results, oil content was ranged from 22.38% to 34.26%, while the minerals were in between the following values: 1469, 04-2068.07 mg kg^-1 for Ca, 7.24-11.71 mg kg^-1 for B, 13.29-17.41 mg kg^-1 for Cu, 51.00-79.35 mg kg^-1 for Fe, 3988-6638.34 mg kg^-1 for K, 1418.61-2306.06 mg kg^-1 for Mg, 11.37-17.76 mg kg^-1 for Mn, 4172.33-7059.58 mg kg^-1 for P and 32.60-59.00 mg kg^-1 for Zn. Correlation analysis that was made separately for the commercial varieties and wild lines showed that high level of oil content was negatively affected by all the investigated minerals except for K and Zn in the commercial varieties.

Keywords: safflower, oil, quality, mineral content

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Authors: Sumeeta Khurana, Kirti Megha, Amit Gupta, Rakesh Sehgal

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Background: Amoebic keratitis is a painful vision threatening infection caused by a free living pathogenic amoeba Acanthamoeba. It can be misdiagnosed and very difficult to treat if not suspected early. The epidemiology of Acanthamoeba genotypes causing infection in our geographical area is not yet known to the best of our knowledge. Objective: To characterize Acanthamoeba isolates from amoebic keratitis patients. Methods: A total of 19 isolates obtained from patients with amoebic keratitis presenting to the Advanced Eye Centre at Postgraduate Institute of Medical Education and Research, a tertiary care centre of North India over a period of last 10 years were included. Their corneal scrapings, lens solution and lens case (in case of lens wearer) were collected for microscopic examination, culture and molecular diagnosis. All the isolates were maintained in the Non Nutrient agar culture medium overlaid with E.coli and 13 strains were axenised and maintained in modified Peptone Yeast Dextrose Agar. Identification of Acanthamoeba genotypes was based on amplification of diagnostic fragment 3 (DF3) region of the 18srRNA gene followed by sequencing. Nucleotide similarity search was performed by BLAST search of sequenced amplicons in GenBank database (http//www.ncbi.nlm.nih.gov/blast). Multiple Sequence alignments were determined by using CLUSTAL X. Results: Nine out of 19 Acanthamoeba isolates were found to belong to Genotype T4 followed by 6 isolates of genotype T11, 3 T5 and 1 T3 genotype. Conclusion: T4 is the predominant Acanthamoeba genotype in our geographical area. Further studies should focus on differences in pathogenicity of these genotypes and their clinical significance.

Keywords: Acanthamoeba, free living amoeba, keratitis, genotype, ocular

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Authors: Faith Eweluegim Enahoro-Ofagbe, Alika Eke Joseph

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Information on genetic variation within a population is crucial for utilizing heterozygosity for breeding programs that aim to improve crop species. The study was conducted to ascertain the genotypic similarities among twelve sugarcane (Saccharum officinarum) varieties to group them for purposes of hybridizations for cane yield improvement. The experiment was conducted at the University of Benin, Faculty of Agriculture Teaching and Research Farm, Benin City. Twelve sugarcane varieties obtained from National Cereals Research Institute, Badeggi, Niger State, Nigeria, were planted in three replications in a randomized complete block design. Each variety was planted on a five-row plot of 5.0 m in length. Data were collected on 12 agronomic traits, including; the number of millable cane, cane girth, internode length, number of male and female flowers (fuss), days to flag leaf, days to flowering, brix%, cane yield, and others. There were significant differences, according to the findings among the twelve genotypes for the number of days to flag leaf, number of male and female flowers (fuss), and cane yield. The relationship between the twelve sugarcane varieties was expressed using hierarchical cluster analysis. The twelve genotypes were grouped into three major clusters based on hierarchical classification. Cluster I had five genotypes, cluster II had four, and cluster III had three. Cluster III was dominated by varieties characterized by higher cane yield, number of leaves, internode length, brix%, number of millable stalks, stalk/stool, cane girth, and cane length. Cluster II contained genotypes with early maturity characteristics, such as early flowering, early flag leaf development, growth rate, and the number of female and male flowers (fuss). The maximum inter-cluster distance between clusters III and I indicated higher genetic diversity between the two groups. Hybridization between the two groups could result in transgressive recombinants for agronomically important traits.

Keywords: sugarcane, Saccharum officinarum, genotype, cluster analysis, principal components analysis

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Authors: H. Boulahyaoui, S. Alaoui Amine, C. Loutfi, H. El Annaz, N. Touil, El M. El Fahim, S. Mrani

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Three Moroccan children fully vaccinated with Rotarix™ have been hospitalized for Rotavirus Gastroenteritis (RVGE) in the pediatric division of the Farabi Hospital, Oujda. Rotavirus G/P genotypes could not be typed because of their delayed crossing threshold (Ct) resolute with a group A rotavirus (RVA) real time RT-PCR. These strains were adapted to cell culture. All viruses replicated and caused extensive cytopathic effects after four or five passages in MA104 cell lines. Significant improvements have been obtained in the amount of viral particles. Each virus multiplied to a high titer (7.5 TCID50/ml). VP7 and VP4 partial gene sequencing revealed distinct genotypes compared to the Rotarix(®) vaccine strain. Two strains were of G2P[4] genotype whereas the third was G9P[8] genotype. Virus isolation while labor intensive, is recommended as a second test, especially when higher sensitivity for conventional RVA genotyping RT-PCR is needed. VP7 antigenic similarities between these strains and Rotarix were determined.

Keywords: esacpe-vaccine, Morocco, Rotarix, G2P[4], G9P[8]

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Authors: Tabassum Yasmin, Hamid Pahlevan

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HIV/Hepatitis C co-infection treatments have evolved substantially and they have similar sustained virologic response rates as those of Hepatitis C monoinfected population. There are a few studies on therapy of patients with dual genotypes, especially in HIV/Hepatic C coinfected group. Most studies portrayed case reports of dual genotype chronic Hepatitis C coinfection treatment with Sofosbuvir/Ledipasvir and Ribavirin. A 79-year-old male with a history of HIV on Truvada and Isentress had chronic Hepatitis C with 1a and 2 genotypes. The patient has a history of alcohol intake for 40 years but recently stopped drinking alcohol. He has a history of intravenous drug use in the past and currently is not using any recreational drugs. Patient has Fibro score of 0.7 with Metavir score F2 to F4. AFP is 3.2. The HCV RNA is 493,034 IU/ML. The HBV viral DNA is < 1.30 (not detected). The CD4 is 687CU/MM. The FIB 4 is 3.34 with APRI index 0.717. The HIV viral load is 101 copies/ML. MRI abdomen did not show any liver abnormality. Fixed dose Sofosbuvir/Ledipasvir was used for therapy without Ribavirin. He tolerated medication except for some minor gastrointestinal side effects like abdominal bloating. He demonstrated 100% adherence rate. Patient completed 12 weeks of therapy. HCV RNA was undetectable at 4 and 12 weeks. He achieved SVR at week 12 and subsequently had undetectable RNA for 2 years. Dual genotype prevalence in chronic hepatitis C population is rare, especially in HIV/hepatic coinfection. Our case demonstrates that dual genotypic cases can still be successfully treated with Direct Acting Antiviral agents. The newer agents for therapy for pan genotypes were not available at the time the patient was being treated. We demonstrated that dual agent therapy was still able to maintain SVR in our patient.

Keywords: HIV/Hepatitis C, SVR (sustained virologic response), DAA (direct active antiviral agents, dual genotype

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Authors: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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Authors: Huseyi̇n Das, Bülent Tarim, Sunay Demi̇r, Nurçi̇n Küçükkent, Sevi̇l Cengi̇z, Engi̇n Tülek, Veci̇hi̇ Aksakal

Abstract:

Atak-S laying hens are a high-performance strain obtained by crossing of the Rhode Island Red (RIR) X the Barred Plymouth Rock (BR) and are being produced in the Ankara Poultry Research Institute since 1997. Phenotypic and genetic improving studies are continued for this strain. In this study, 2 from IGF and 1 from IGFBP2, totally 3 different SNP polymorphisms were examined in 200 Atak-S chickens. Genotypes of SNPs were compared using ANOVA to body weight and egg number thorough 32 weeks of age, body weight at sexual maturity, age at sexual maturity and also egg quality traits such as egg shell breaking strength, shell thickness, Haugh unit, albumen index, yolk index, shape index. Only IGF(a) locus was in agreement with Hardy-Weinberg equilibrium, while, the other loci were not. As a result of the performance comparisons to the 3 SNP loci, it was determined that there has a significant association (P<0.05) between only TC genotypes of the IGF(b) locus and body weight at 32 weeks of age, but there was not any association to the other traits.

Keywords: Atak-S, Igf, Igfbp2, single nucleotide polymorphism

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Authors: Faheema Khan

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We have investigated the effects of salt stress on the stability of plant growth, water relations, photosynthetic variables, lipid peroxidation and antioxidant system in salt-tolerant (PK-327) and salt-sensitive (PK-471) soybean genotypes. Ten-day-old salt-tolerant and salt-sensitive soybean plants were subjected to 0-150 mM NaCl for 15 days. While the growth of genotype PK-327 was not affected significantly up to 75 mM NaCl treatment, the growth of the PK-471 was reduced significantly beyond 25 mM NaCl treatments. Salt stress caused severe impairments in photosynthetic variables like photosynthetic rate, chlorophyll fluorescence and chlorophyll content, being more pronounced in salt-sensitive genotype than in salt-tolerant.The activities of antioxidant enzymes (superoxide dismutase, catalase, ascorbate peroxidase and glutathione reductase) were higher in PK-327 than in PK-471 at various levels of salt treatments.It is concluded that tolerance capacity of PK-327 against salinity can be associated with the ability of this genotype in keeping an active photosynthetic system and strong antioxidant defence system.

Keywords: salt stress, soybean, antioxidant, photosynthesis

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Authors: Dorcas Ropo Abejide, Olamide Ahmed Falusi, Oladipupo Abdulazeez Yusuf Daudu, Bolaji Zuluqurineen Salihu, Muhammad Liman Muhammad

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This study evaluated the morpho-agronomic response of twenty-four (24) Nigerian Bambara groundnut landraces to water stress and genetic diversity of some selected accessions using SSR markers. The studies were carried out in the botanical garden of the Department of Plant Biology, Federal University of Technology, Minna, Niger State, Nigeria in a randomized complete block design using three replicates. Molecular analysis using SSR primers was carried out at the International Institute of Tropical Agriculture (IITA) Ibadan in order to characterize ten selected accessions comprising the seven most drought tolerant and three most susceptible accessions from the 24 accessions evaluated. Results revealed that water stress decreased morpho-agronomic traits such as plant height, leaf area, number of leaves per plant, seed yield, etc. A total of 22 alleles were detected by the SSR markers used with a mean number of 4 allelles. SSR markers MBamCO₃₃, Primer 65, and G358B2-D15 each detected 4 allelles, while Primer 3FR and 4FR detected 5 allelles each. The study revealed significantly high polymorphisms in 10 Loci. The mean value of polymorpic information content was 0.6997, implying the usefulness of the primers used in identifying genetic similarities and differences among the Bambara groundnut genotypes. The SSR analysis revealed a comparable pattern between genetic diversity and drought tolerance of the genotypes. The UPGMA dendrogram showed that at a genetic distance of 0.1, the accessions were grouped into three groups according to their level of tolerance to drought. The two most drought-tolerant accessions were grouped together, and the 5th and 6th most drought-tolerant accessions were also grouped together. This suggests that the genotypes grouped together may be genetically close, may possess similar genes, or have a common origin. The degree of genetic variants obtained from this profiling could be useful in Bambara groundnut breeding for drought tolerance. The identified drought tolerant Bambara groundnut landraces are important genetic resources for drought stress tolerance breeding programme of Bambara groundnut. The genotypes are also useful for germplasm conservation and global implications.

Keywords: Bambara groundnut, genetic diversity, germplasm, SSR markers, water stress

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Authors: Maria Toader, Gheorghe Valentin Roman, Alina Maria Ionescu

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Crops diversity and maintaining and enhancing the fertility of agricultural lands are basic principles of organic farming. With a wider range of crops in agroecosystem can improve the ability to control weeds, pests and diseases, and the performance of crops rotation and food safety. In this sense, the main objective of the research was to study the productivity and chemical composition of some alternative crops and their adaptability to soil and climatic conditions of the agricultural area in Southern Romania and to cultivation in the organic farming system. The alternative crops were: lentil (7 genotypes); five species of grain legumes (5 genotypes); four species of oil crops (5 genotypes). The seed production was, on average: 1343 kg/ha of lentil; 2500 kg/ha of field beans; 2400 kg/ha of chick peas and blackeyed peas; more than 2000 kg/ha of atzuki beans, over 1250 kg/ha of fenugreek; 2200 kg/ha of safflower; 570 kg/ha of oil pumpkin; 2150 kg/ha of oil flax; 1518 kg/ha of camelina. Regarding chemical composition, lentil seeds contained: 22.18% proteins, 3.03% lipids, 33.29% glucides, 4.00% minerals, and 259.97 kcal energy values. For field beans: 21.50% proteins, 4.40% lipids, 63.90% glucides, 5.85% minerals, 395.36 kcal energetic value. For chick peas: 21.23% proteins, 4.55% lipids, 53.00% glucides, 3.67% minerals, 348.22 kcal energetic value. For blackeyed peas: 23.30% proteins, 2.10% lipids, 68.10% glucides, 3.93% minerals, 350.14 kcal energetic value. For adzuki beans: 21.90% proteins, 2.60% lipids, 69.30% glucides, 4.10% minerals, 402.48 kcal energetic value. For fenugreek: 21.30% proteins, 4.65% lipids, 63.83% glucides, 5.69% minerals, 396.54 kcal energetic value. For safflower: 12.60% proteins, 28.37% lipids, 46.41% glucides, 3.60% minerals, 505.78 kcal energetic value. For camelina: 20.29% proteins, 31.68% lipids, 36.28% glucides, 4.29% minerals, 526.63 kcal energetic value. For oil pumpkin: 29.50% proteins, 36.92% lipids, 18.50% glucides, 5.41% minerals, 540.15 kcal energetic value. For oil flax: 22.56% proteins, 34.10% lipids, 27.73% glucides, 5.25% minerals, 558.45 kcal energetic value.

Keywords: adaptability, alternative crops, chemical composition, organic farming productivity

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Authors: I. Boroňová, J.Bernasovská, J. Kľoc, Z. Tomková, E. Petrejčíková, D. Gabriková, S. Mačeková

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Osteoporosis is a complex health disease characterized by low bone mineral density, which is determined by an interaction of genetics with metabolic and environmental factors. Current research in genetics of osteoporosis is focused on identification of responsible genes and polymorphisms. TNFRSF11B gene plays a key role in bone remodeling. The aim of this study was to investigate the genotype and allele distribution of A163G (rs3102735) osteoprotegerin gene promoter and G1181C (rs2073618) osteoprotegerin first exon polymorphisms in the group of 180 unrelated postmenopausal women with diagnosed osteoporosis and 180 normal controls. Genomic DNA was isolated from peripheral blood leukocytes using standard methodology. Genotyping for presence of different polymorphisms was performed using the Custom Taqman®SNP Genotyping assays. Hardy-Weinberg equilibrium was tested for each SNP in the groups of participants using the chi-square (χ2) test. The distribution of investigated genotypes in the group of patients with osteoporosis were as follows: AA (66.7%), AG (32.2%), GG (1.1%) for A163G polymorphism; GG (19.4%), CG (44.4%), CC (36.1%) for G1181C polymorphism. The distribution of genotypes in normal controls were follows: AA (71.1%), AG (26.1%), GG (2.8%) for A163G polymorphism; GG (22.2%), CG (48.9%), CC (28.9%) for G1181C polymorphism. In A163G polymorphism the variant G allele was more common among patients with osteoporosis: 17.2% versus 15.8% in normal controls. Also, in G1181C polymorphism the phenomenon of more frequent occurrence of C allele in the group of patients with osteoporosis was observed (58.3% versus 53.3%). Genotype and allele distributions showed no significant differences (A163G: χ2=0.270, p=0.605; χ2=0.250, p=0.616; G1181C: χ2= 1.730, p=0.188; χ2=1.820, p=0.177). Our results represents an initial study, further studies of more numerous file and associations studies will be carried out. Knowing the distribution of genotypes is important for assessing the impact of these polymorphisms on various parameters associated with osteoporosis. Screening for identification of “at-risk” women likely to develop osteoporosis and initiating subsequent early intervention appears to be most effective strategy to substantially reduce the risks of osteoporosis.

Keywords: osteoporosis, real-time PCR method, SNP polymorphisms

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Authors: Sima Parvizi Omran, Rezvan Tavakoli, Mahnaz Safari, Mohammadreza Aghasadeghi, Abolfazl Fateh, Pooneh Rahimi

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Background: SARS-CoV-2, a single-stranded RNA betacoronavirus causes the global outbreak of coronavirus disease 2019 (COVID-19). Several clinical and scientific concerns are raised by this pandemic. Genetic factors can contribute to pathogenesis and disease susceptibility. There are single nucleotide polymorphisms (SNPs) in many of the genes in the immune system that affect the expression of specific genes or functions of some proteins related to immune responses against viral infections. In this study, we analyzed the impact of polymorphism in the interferon alpha and beta receptor subunit 2 (IFNAR2) and dipeptidyl peptidase 9 (Dpp9) genes and clinical parameters on the susceptibility and resistance to Coronavirus disease (COVID-19). Methods: A total of 330- SARS-CoV-2 positive patients (188 survivors and 142 nonsurvivors) were included in this study. All single-nucleotide polymorphisms (SNPs) on IFNAR2 (rs2236757) and Dpp9 (rs2109069) were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Results: In survivor patients, the frequency of the favourable genotypes of IFNAR2 SNP (rs2236757 GC) was significantly higher than in nonsurvivor patients, and also Dpp9 (rs2109069 AT) genotypes were associated with the severity of COVID-19 infection. Conclusions: This study demonstrated that the severity of COVID- 19 patients was strongly associated with clinical parameters and unfavourable IFNAR2, Dpp9 SNP genotypes. In order to establish the relationship between host genetic factors and the severity of COVID-19 infection, further studies are needed in multiple parts of the world.

Keywords: SARS-CoV-2, COVID-19, interferon alpha and beta receptor subunit 2, dipeptidyl peptidase 9, single-nucleotide polymorphisms

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Authors: Benjamin Bonsu Bruce, Marian Dorcas Quain David Appiah-Kubi, Gertrude Osei-Diko, Harrison Kwame Dapaah

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Taro [Colocasia esculenta (L.) Schott] is a major staple food and remains a significant crop to many cultural and agricultural customs worldwide. In Ghana, taro is mostly propagated using vegetative material, which is conserved in field collection and recycled from their farms to establish new fields. However, this practice promotes the accumulation of systemic pathogens. Prior exposure to pests and subsequent expression of disease symptoms can also be a huge constraint to sustainable conservation and utilization of taro genetic resources. In vitro, slow growth is one of the most promising techniques to be utilized for conservation. The objective of this study was to find a medium-term in vitro conservation protocol for local and exotic taro genotypes. The medium-term conservation study was conducted using actively growing shoots obtained from in vitro cultures. Explants were cultured to full strength in complete Murashige and Skoog medium supplemented with Mannitol at different concentrations (0g/l, 20g/l, 25g/l, and 30g/l). Another medium that was tested as an additional treatment is the White’s medium. The highest number of shoots (6.33) and leaves (22.67) occurred on medium containing 20 and 25g/l mannitol in genotype SAO 006 as compared to other genotypes, whereas 30g/l mannitol was the best to restrict growth for the entire 6 months period in terms of shoot height (22.50cm). The study reveals that mannitol supplemented culture media could reduce the growth of Colocasia plantlets, especially in stem height. Culture growth following 6 months of conservation, showed that healthy shoot cultures of Taro were obtained after 6 months of storage in a medium containing 20gl⁻¹ and 25gl⁻¹ mannitol.

Keywords: complete murashige, skoog medium, culture conditions, mannitol, slow growth conservation

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Authors: Adrienn Novák

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The field research was carried out at the Látókép AGTC KIT research area of the University of Debrecen in Eastern-Hungary, on the area of the aeolain loess of the Hajdúság. We examined the effects of the sowing time on the phytopathogenic characteristics and yield production by applying various fertilizer treatments on two different sunflower genotypes (NK Ferti, PR64H42) in 2012 and 2013. We applied three different sowing times (early, optimal, late) and two different treatment levels of fungicides (control = no fungicides applied, double fungicide protection). During our investigations, the studied cropyears were of different sowing time optimum in terms of yield amount (2012: early, 2013: average). By Pearson’s correlation analysis, we have found that delaying the sowing time pronouncedly decreased the extent of infection in both crop years (Diaporthe: r=0.663**, r=0.681**, Sclerotinia: r=0.465**, r=0.622**). The fungicide treatment not only decreased the extent of infection, but had yield increasing effect too (2012: r=0.498**, 2013: r=0.603**). In 2012, delaying of the sowing time increased (r=0.600**), but in 2013, it decreased (r= 0.356*) the yield amount.

Keywords: fungicide treatment, genotypes, sowing time, yield, sunflower

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Authors: Zinhle Cindi, Collet Dandara, Mpiko Ntsekhe, Edson Makambwa, Miguel Larceda

Abstract:

Background: Warfarin is the most commonly used drug in the management of thromboembolic disease. However, there is a huge variability in the time, number of doses or starting doses for patients to achieve the required international normalised ratio (INR) which is compounded by a narrow therapeutic index. Many genetic-association studies have reported on European and Asian populations which have led to the designing of specific algorithms that are now being used to assist in warfarin dosing. However, very few or no studies have looked at the pharmacogenetics of warfarin in African populations, yet, huge differences in dosage requirements to reach the same INR have been observed. Objective: We set out to investigate the distribution of 3 SNPs CYP4F2 c.1347C > T, VKORC1 g.-1639G > A and VKORC1 c.1173C > T among South African Mixed Ancestry (MA) and Black African patients. Methods: DNA was extracted from 383 participants and subsequently genotyped using PCR/RFLP for the CYP4F2 c.1347 (V433M) (rs2108622), VKORC1 g.-1639 (rs9923231) and VKORC1 c.1173 (rs9934438) SNPs. Results: Comparing the Black and MA groups, significant differences were observed in the distribution of the following genotypes; CYP4F2 c.1347C/T (23% vs. 39% p=0.03). All VKORC1 g.-1639G > A genotypes (p < 0.006) and all VKORC1 c.1173C > T genotypes (p < 0.007). Conclusion: CYP4F2 c.1347T (V433M) reduces CYP4F2 protein levels and therefore expected to affect the amount of warfarin needed to block vitamin k recycling. The VKORC1 g-1639A variant alters transcriptional regulation therefore affecting the function of vitamin k epoxide reductase in vitamin k production. The VKORC1 c.1173T variant reduces the enzyme activity of VKORC1 consequently enhancing the effectiveness of warfarin. These are preliminary results; more genetic characterization is required to understand all the genetic determinants affecting how patients respond to warfarin.

Keywords: algorithms, pharmacogenetics, thromboembolic disease, warfarin

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Authors: M. Ipek, A. Cansev, A. Ipek, Y. Sahan

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Allium tuncelianum is a close relative of cultivated garlic (A. sativum L.) and naturally grows only in eastern part of Turkey. This species has mild garlic odor and therefore, it is locally consumed as garlic by collecting from its natural flora. This over collection threatens the species to extinction. Although it has morphological resemblance to cultivated garlic, the nutritional value of the species has not been characterized very well. Alliin and allicin are two predominant organosulfur compounds found in cultivated garlic. Allicin derived from alliin precursor gives garlic characteristic odor and most of the garlic health benefits are attributed to this compound. The aims of this work were to determine alliin and allicin contents of A. tuncelianum and to compare them with those of cultivated garlic, onion (A. cepa L.) and leek (A. porrum L.). Alliin and allicin were extracted from 400 mg lyophilized samples and 10 µl extracts were measured with high-performance liquid chromatography attached with diode array detector. The alliin contents of A. tuncelianum genotypes ranged from 2.5 to 7.0 mg/g and the allicin contents changed from 0.5 to 1.5 mg/g, whereas alliin and allicin contents of garlic genotypes ranged from 20.0 to 30.0 mg/g and 3.0 to 6.0 mg/g, respectively. On the other hand, we did not detect any measurable alliin and allicin in onion or leek tissues. In conclusion, alliin and allicin contents of A. tuncelianum were characterized first time in this study, which are about 20% of alliin and allicin contents of cultivated garlic.

Keywords: allicin, alliin, Allium tuncelianum, garlic

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