Journal articles on the topic 'Genotype'
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Alacam, Sema, Ayfer Bakir, and Aysel Karatas. "Hepatitis C virus genotypes and viremia in a tertiary hospital in Istanbul, Turkey." Journal of Infection in Developing Countries 16, no. 04 (April 30, 2022): 668–74. http://dx.doi.org/10.3855/jidc.15256.
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Introduction: The World Health Organization estimates that 71 million people with chronic HCV infection lived worldwide in 2015. HCV is a globally prevalent pathogen, that genotype1 is the most common. In this study, the prevalence of anti-HCV, distributions of HCV genotype, and viremia rates in patients with chronic hepatitis C were evaluated.
Methodology: In this retrospective single-center study, anti-HCV results of 197,081 patients were evaluated between 2017 and 2020. Quantitative HCV-RNA PCR tests were performed on the Rotor-Gene Q real-time PCR instrument. HCV genotypes determination of 546 samples was carried out with the Gen-C 2.0 Reverse Hybridization strip and HCV Genotype Plus Real-TM kit.
Results: The prevalence of anti-HCV was 0.95% and viremic HCV infection was 0.3% (610/197,081). HCV viremia rate was 33.17%. HCV viremia rate was highest in 2017 (52.36%) and the lowest in 2020 (18.3%) (p < 0.001). Genotype1 (72%) was the most common genotype, followed by genotype3 (14.1%), and genotype4 (8.8%). The most common subtypes were determined as genotype1b (56.2%) and genotype1a (13.2%). The viral load was higher in patients infected with genotype5.
Conclusions: In this study, the rate of viremic HCV infection was found to be 0.3%. This rate was lower than the worldwide rate of HCV viremia. The distribution of HCV genotypes was like the global data. The identification of circulating genotypes and subtypes is essential for epidemiological purposes and remains important in the choice of treatment in patients with chronic HCV.
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Tecle, Tesfaldet, Blenda Böttiger, Claes Örvell, and Bo Johansson. "Characterization of two decades of temporal co-circulation of four mumps virus genotypes in Denmark: identification of a new genotype." Journal of General Virology 82, no. 11 (November 1, 2001): 2675–80. http://dx.doi.org/10.1099/0022-1317-82-11-2675.
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Twenty-nine Danish virus isolates and 14 serum samples from patients with mumps were genotyped by nucleotide sequencing of the small hydrophobic (SH) protein gene and the deduced 57 amino acid sequences were aligned with sequences of mumps virus strains published previously. Four neurovirulent genotypes of the SH protein gene, genotypes C, D, H and a new genotype, designated J, were found. There was a dynamic fluctuation of the different genotypes over the two decade period of time. Genotype J was found from 1981 to 1988; genotypes C and H exhibited a similar distribution in time. Genotype D was found between 1979 and 1982, it then disappeared and reappeared again in 1996. From 1996 onwards, genotype D was found to be the predominant genotype, which is in contrast to the situation seen in the neighbouring country of Sweden, where, since 1985, only genotype A has been found.
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Sami, Hiba, Meher Rizvi, Mohd Azam, Rathindra M. Mukherjee, Indu Shukla, M. R. Ajmal, and Abida Malik. "Emergence of Hepatitis B Virus Genotype F in Aligarh Region of North India." Advances in Virology 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/846849.
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Introduction. HBV genotypes and subtypes are useful clinical and epidemiological markers. In this study prevalent HBV genotypes were assessed in relation to serological profile and clinical status.Material & Methods. 107 cases of HBV were genotyped. Detailed clinical history was elicited from them. HBsAg, HBeAg, anti-HBs, anti-HBe, and anti-HBc-IgM were assessed. HBV genotyping was performed using Kirschberg's type specific primers (TSP-PCR), heminested PCR, and Naito's monoplex PCR. Nucleotide sequencing was performed.Results. A total of 97 (91%) were genotyped following the methods of Kirschberg et al./Naito et al. Genotype D was by far the most prevalent genotype 91 (85.04%) in this region. A surprising finding was the detection of genotype F in 5 (4.67%) of our patients. Genotype A strangely was observed only in one case. In 85.7% genotype D was associated with moderate to severe liver disease, 43.9% HBeAg, and 18.7% anti-HBc-IgM positivity. Majority of genotype F (80%) was seen in mild to moderate liver disease. It was strongly associated with HBeAg 60% and 20% anti-HBc-IgM positivity.Conclusion. Emergence of genotype F in India merits further study regarding its clinical implications and treatment modalities. Knowledge about HBV genotypes can direct a clinician towards more informed management of HBV patients.
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Genç, Serpil, Mediha Uğur, Emel Uzunoğlu Karagöz, and Esin Avcı. "Giresun İli Hepatit C Hastalarında Genotip Dağılımının Araştırılması." Flora the Journal of Infectious Diseases and Clinical Microbiology 25, no. 4 (December 30, 2020): 549–54. http://dx.doi.org/10.5578/flora.69198.
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Introduction: HCV infections are an important public health problem due to their high chronicity, cirrhosis and advanced complications like hepatocellular carcinoma. In HCV infections, it is important and necessary to determine genotypes before treatment because treatment times and protocols vary according to genotypes. The aim of this study was to determine the distribution of HCV genotypes in HCV-RNA positive individuals in Giresun province and to investigate whether there was a statistically significant difference between genotypes and patient ages. Materials and Methods: HCV-RNA level and HCV genotype of 147 patients were included in the study. HCV RNA levels of the samples were studied by QIAsymphony SP (Qiagen) automated device, genotype determination by Rotor Gene Q (Qiagen) automated device by “real-time polymerase chain reaction (PCR)” method. Each sample was tested for HCV genotypes 1a, 1b, 2, 3, 4, 5a and 6. Results: Of the 147 patients genotyped; 128 (87%) genotype 1b, 9 (6%) genotype 1a, 8 (6%) genotype 3, 2 (1%) genotype 2 were detected. Genotypes 4, 5a and 6 were not detected. According to the HCV genotype distribution, median age and range (min.-max.) of the patients weren50 (30-83) for 1a, 70 (22-87) for 1b, 48.5 (36-61) for 2 and 33 (25-52) for 3. HCV RNA levels were between 37 and 12.630.170 IU/mL. Conclusion: The predominant genotype in the world and Turkey is genotype 1b. In our study, the most common genotype was also genotype 1b (87%), consistent with other studies in our country. This study contributed to HCV genotype distribution data in our region and country.
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de Vries, F., H. Hamann, C. Drögemüller, M. Ganter, and O. Distl. "Analysis of associations between the prion protein genotype and reproduction traits in meat sheep breeds." Animal Science 79, no. 3 (December 2004): 397–404. http://dx.doi.org/10.1017/s1357729800090263.
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AbstractThe objective of this study was to analyse the associations between ovine prion protein (PrP) genotypes and reproduction traits in three German meat sheep breeds. Reproduction traits were age at first early lambing, age at first late lambing, first lambing interval, second lambing interval and total number of lambs born. The data set included 595 genotyped German Texel sheep among 5225 recorded sheep, 351 genotyped German Black-Headed Mutton among 10 177 sheep and 282 genotyped Suffolk sheep among 2849 sheep. Linear animal models were employed for the analysis of the PrP-genotype effect. The PrP-genotype effect was analysed by comparing the most frequent PrP genotypes ARR/ARR, ARR/ARQ, and ARQ/ARQ. In a more general analysis three PrP genotype classes of animals with two, one or no copy of the ARR allele were compared.In most cases, no significant associations were found between the PrP genotypes and the reproduction traits investigated. Only for the traits age at first early lambing in German Texel and second lambing interval in German Black-Headed Mutton and Suffolk could a significant association with the PrP genotype be observed.
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Kousar, Khalida, Hayat Ur Rehman, Abida Yasmeen, and Muhammad Fayaz. "HCV Genotypes Distribution among HCV Patients with Biochemical markers in District Mardan." Global Drug Design & Development Review VII, no. III (September 30, 2022): 1–7. http://dx.doi.org/10.31703/gdddr.2022(vii-iii).01.
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Hepatitis C causes chronic liver disease, cirrhosis, and hepatocellular cancer, and its genotypes vary widely among countries. This study aimed to determine HCV patients' genotype distribution and biochemical indicators. Blood samples from enrolled HCV-positive cases were processed and viral RNA was extracted using the "RNA extraction Qiagene kit" to genotype and quantify viral load using Real Time polymerase chain reaction (Rotor Gene Q-PCR equipment).Analysis was performed by SPSS with p-value < 0.05. Results showed that 198 (91.66%) of 216 patients were 3a genotyped and had higher Alanine aminotransferase (ALT; 39-85%). Genotype 3a dominates in Mardan and nearby areas. Infected patients with genotype-3a had a greater pre-treatment HCV viral load than those with genotypes 1a, 1b, and 5a, although other genotypes had higher biochemical markers (P<0.05).
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Schaper, M., A. E. Durán, and J. Jofre. "Comparative Resistance of Phage Isolates of Four Genotypes of F-Specific RNA Bacteriophages to Various Inactivation Processes." Applied and Environmental Microbiology 68, no. 8 (August 2002): 3702–7. http://dx.doi.org/10.1128/aem.68.8.3702-3707.2002.
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ABSTRACT The effect of natural inactivation in freshwater, chlorination, ammonia, extreme pHs, temperature, and salt content on phage inactivation was evaluated on mixtures of F-specific RNA bacteriophage isolates belonging to genotypes I, II, III, and IV. The bacteriophages studied were previously but recently isolated from natural samples, characterized as F-specific RNA bacteriophages and genotyped by plaque hybridization with genotype-specific probes. Natural inactivation in river water was modeled by in situ incubation of bacteriophages inside submerged dialysis tubes. After several days bacteriophages of genotype I showed the highest persistence, which was significantly different from that of bacteriophages of genotype II, IV, or III. The pattern of resistance of phages belonging to the various genotypes to extreme pHs, ammonia, temperature, salt concentration, and chlorination was similar. In all cases, phages of genotype I showed the highest persistence, followed by the phages of genotypes II, III, and IV. The phages of genotypes III and IV were the least resistant to all treatments, and resistance of genotypes III and IV to the treatments was similar. Bacteriophages of genotype II showed intermediate resistance to some of the treatments. The resistance of four phages of genotype I to natural inactivation and chlorination did not differ significantly. These results indicate that genotypes III and IV are much more sensitive to environmental stresses and to treatments than the other genotypes, especially than genotype I. This should be taken into consideration in future studies aimed at using genotypes of F-specific RNA bacteriophages to fingerprint the origin of fecal pollution.
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Rahmiati, Tengku Mia, Yohanes Aris Purwanto, Slamet Budijanto, and Nurul Khumaida. "Sifat Fisikokimia Tepung dari 10 Genotipe Ubi Kayu (Manihot esculenta Crantz) Hasil Pemuliaan (Physicochemical Properties of Cassava Flour (Manihot esculenta Crantz) of 10 Breeding Genotipes)." Agritech 36, no. 4 (February 25, 2017): 459. http://dx.doi.org/10.22146/agritech.16771.
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The objectives of this study were to characterize and evaluate the physicochemical properties of 10 cassava breeding genotypes developed by cassava crop improvement of (Institut Pertanian Bogor) IPB research group. The physicochemical characterization was performed by measuring water content, ash, protein, fat, carbohydrate, pasta (pasting properties), starch total, amylose content, and whiteness. The results showed that each genotype has different chemical content and gelatinization properties. The highest water content (11.48 ± 0.12 %) was found in genotype V4D0 (variant genotype Malang 4), ash (1.83 ± 0.02 %) in V5D2 (1) (A variant of genotype Malang 4-1), fat (1.62 ± 0.93 %) and protein (4.73 ± 0.19 %) in V3D1 (1) (variant UJ 5-1). Genotype V1D1-1(1) (A variant of genotype Ratim-1) has the highest amylose (23.33 ± 0.04 %) and the lowest ones (13.13 ± 0.48 %) was found in genotype V2D1-1(3). Genotype V2D0 has the highest total starch (88.67 %) and the lowest (74.3%) was obtained in V5D2 (1). The highest whiteness value was measured in genotype V1D0 i.e. 93.13 %. For pasting properties testing, it was measured that genotype V2D1-1 (3) had the lowest peak viscosity i.e 4,006 cP and the high of end of viscosity occurred 2,592 cP in genotype V4D2-1 (2) (A variant of genotype Adira 4-1), were correlated with high amylose content owned flour is 22.03 ± 0.25%. ABSTRAKPenelitian ini bertujuan untuk mengkarakterisasi dan mengevaluasi sifat fisikokimia 10 genotipe ubi kayu hasil pemuliaan team crop improvement ubi kayu Institut Pertanian Bogor (IPB). Karakterisasi fisikokimia dilakukan dengan cara melakukan analisis kadar air, abu, protein, lemak, karbohidrat, pasta (pasting properties), total pati, kadar amilosa, dan derajat putih. Dari hasil karakterisasi diperoleh bahwa setiap genotipe ubi kayu memiliki kandungan kimia dan sifat gelatinisasi yang berbeda-beda. Kadar air tertinggi dimiliki genotipe V4D0 (Genotipe Malang 4) 11,48 ± 0,12 % , kadar abu dan lemak tertinggi adalah genotipe (V5D2 (1) (Varian dari genotipe Malang 4-1) yaitu 1,83 % ± 0,02 dan 1,62 ± 0,93 % serta kadar protein tertinggi adalah V3D1 (1) (Varian UJ 5-1) 4,73 ± 0,19 %. Genotipe V1D1-1 (1) (Varian dari genotipe Jame-1) memiliki kadar amilosa tertinggi yaitu 23,33 ± 0,04 % sedangkan yang terendah dihasilkan oleh genotipe V2D1-1 (3) (Varian dari genotipe Ratim-1) yaitu 13,13 ± 0,48 %. Genotipe V2D1-1 (3) (Varian genotipe Ratim-1) memiliki viskositas puncak terendah yaitu 4.006 cP berkorelasi positif dengan kandungan amilosa paling rendah yang dimilikinya. Viskositas akhir yang tinggi terjadi pada genotipe V4D2-1(2) (Varian genotipe Adira 4-1) yaitu 2.592 cP yang berkorelasi dengan tingginya kandungan amilosa yang dimiliki tepung tersebut yaitu 22,03 ± 0,25 %.
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Unzhakova, Anastasiia, Nikolai Kochnev, and Galina Goncharenko. "Association of κ-casein, β-lactoglobulin, α-lactalbumin and leptin gene polymorphisms with bovine productivity traits in Western Siberia." E3S Web of Conferences 273 (2021): 02021. http://dx.doi.org/10.1051/e3sconf/202127302021.
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The Simmental breed (n=182) and Siberian breed (n=131) cows were genotyped using the CSN3, BLG, LALBA, and LEP genes. In both populations, the frequency of homozygotes did not exceed 10 %, and the proportion of heterozygotes was at the level of 40-45%. The actual genotype distribution corresponded to the theoretically expected Hardy-Weinberg distribution. In terms of milk yield, cows of the «Sibiryachka» breed with the BLGAA genotype significantly outperformed cows with the BLGBB genotype (p<0.05), and in the Simmental breed, cows with the BLGAA genotype had a higher milk yield than BLGAB (p<0.01). According to the LALBA gene in the Simmental breed, cows with the LALBABB genotype were superior to cows with LALBAAA in fat content (p<0.05), in the «Sibiryachka» breed, higher fat content was observed in cows with the LALBAAB genotype (p<0.05). In both breeds, cows with the LEPCC genotype outperformed cows with the LEPTT genotype in fat content (p<0.05). According to the reproduction indicators, cows with the LALBAAA and LEPCT genotypes had an earlier age of insemination in comparison with cows with the LALBABB and LEPCC genotypes (p<0.05). Cows with the LEPCT genotype had a longer calving interval than cows with the LEPCC genotype (p<0.05).
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Ezward, Chairil, Desta Andriani, A. Haitami, Risdianas Risdianas, Ilham Yaumil Pitra, Delfi Dwi Ningsi, and Tri Nur Utami. "Genotipe Padi Lokal (Oryza sativa L.) Kuantan Singingi Toleran Cekaman Kekeringan." Jurnal AGROSAINS dan TEKNOLOGI 8, no. 2 (December 22, 2023): 54. http://dx.doi.org/10.24853/jat.8.2.54-60.
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Kekeringan memiliki dampak luas terhadap pertanian, seperti penurunan produktivitas dan produksi. Upaya mengatasi permasalahan ini salah satunya yaitu dengan menggunakan bahan tanam (benih) genotipe padi lokal. Genotipe padi lokal telah beradaptasi dengan lingkungan setempat yang spesifik, sehingga memiliki kemampuan beradaptasi pada kondisi cekaman kekeringan. Penelitian ini bertujuan untuk mengetahui genotipe yang toleran terhadap cekaman kekeringan, dengan menggunakan metode eksperimen yaitu dengan sengaja memberikan perlakuan kekeringan pada pot wadah penelitian pada fase pertumbuhan (vegetatif). Cekaman kekeringan diberikan mulai umur tanaman 57 hst sampai 73 hst (selama 16 hari). Selama kondisi cekaman kekeringan muncul gejala daun menggulung dan daun mengering. Hal ini menjadi acuan dalam menentukan tanaman toleran dan peka. Pengamatan fase pertumbuhan tanaman dilakukan pada 4 genotipe padi lokal asal Kabupaten Kuantan Singingi (A = Sironda Putih, B = Saronda Merah, C = Pandan Wangi dan D = Ronda Putiah) ditambah 1 varietas kontrol toleran kekeringan (Inpago 9). Pengamatan dilakukan secara visual pada morfologi daun berdasarkan buku IRRI edisi tahun 1996. Hasil penelitian diperoleh genotipe yang memiliki kriteria toleran cekaman kekeringan yaitu genotipe Sironda Putih, kriteria agak toleran genotipe Saronda Merah, kriteria agak peka yaitu genotipe Pandan Wangi dan kriteria sangat peka genotipe Ronda Putiah. Genotipe Ronda Putiah dapat digunakan sebagai bahan budidaya pada lahan sawah tadah hujan.ABSTRACTDrought has a broad impact on agriculture, such as reducing productivity and production. One way to overcome this problem is by using planting material (seed) of local rice genotypes. Local rice genotypes have adapted to specific local environments, so they have the ability to adapt to drought stress conditions. This research aims to determine genotypes that are tolerant to drought stress, using an experimental method, namely deliberately providing drought treatment to research pots in the growth (vegetative) phase. Drought stress is given from 57 days after planting to 73 days after planting (for 16 days). During drought stress conditions, symptoms of leaf curling and drying of the leaves appear. This becomes a reference in determining tolerant and sensitive plants. Plant growth phase observations were carried out on 4 local rice genotypes from Kuantan Singingi Regency (A = Sironda Putih, B = Saronda Merah, C = Pandan Wangi and D = Ronda Putiah) plus 1 drought tolerant control variety (Inpago 9). Observations were made visually on leaf morphology based on the 1996 edition of the IRRI book. The results of the research obtained genotypes that had drought stress tolerance criteria, namely the White Sironda genotype, moderately tolerant criteria for the Red Saronda genotype, slightly sensitive criteria for the Pandan Wangi genotype and very sensitive criteria for the Ronda Putiah genotype. . The Ronda Putiah genotype can be used as cultivation material in rainfed rice fields.
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Khushman, Moh’d, Girijesh Kumar Patel, Anu Singh Maharjan, Gwendolyn A. McMillin, Cindy Nelson, Peter Hosein, and Ajay P. Singh. "The prevalence and clinical relevance of 2R/2R TYMS genotype in patients with gastrointestinal malignancies treated with fluoropyrimidine-based chemotherapy regimens." Pharmacogenomics Journal 21, no. 3 (February 19, 2021): 308–17. http://dx.doi.org/10.1038/s41397-021-00210-2.
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Abstract Introduction The prevalence of 2R/2R TYMS genotype is variable but estimated to be around 20–30% in Caucasians. The clinical relevance of TYMS 2R/2R genotype in predicting severe fluoropyrimidine-related adverse events (FrAE) is controversial. Here, we explored the prevalence and clinical relevance of 2R/2R TYMS genotype. Methods Between 2011 and 2018, 126 patients were genotyped for TYMS. FrAEs were graded according to CTCAE version 5.0. Fisher’s exact test was used for statistical analysis. Results The prevalence of TYMS 2R/2R genotype was 24.6%. Among patients with TYMS genotypes (N = 71) that predict decreased TS expression, 2R/2R TYMS genotype was the most common TYMS genotype seen in female (57%) and African American (60%) patients. Among patients with genotypes that predict increased TS expression (N = 55), 12 patients had grade 3–4 FrAEs (22%), while among patients with genotypes that predict decreased TS expression (N = 71), 30 patients had grade 3–4 FrAEs (42%) (p = 0.0219). Compared to patients with genotypes predicting increased TS expression, 17 out of 31 patients (55%) with TYMS 2R/2R genotype had grade 3–4 FrAEs (p = 0.0039) and 15 out 40 patients (38%) with TYMS 2R/3RC and TYMS 3RC/3RC genotype had grade 3–4 FrAEs (p = 0.1108). Conclusion The prevalence of TYMS 2R/2R genotype was 24.6%, and it had a unique sex and ethnic distribution. Polymorphism in the promoter region of TYMS gene that predicts decreased TS expression due to 2R/2R variant was associated with grade 3–4 FrAEs. These data suggest that genotyping patients who are not DPD deficient for TYMS might identify patients at risk of severe FrAEs.
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Amorim, Regina M. S., Tainá Raiol, José E. Trevizoli, Francisco A. R. Neves, Cláudia R. F. Martins, and Regina M. B. Martins. "Hepatitis C virus genotypes in hemodialysis patients in the Federal District, Brazil." Revista do Instituto de Medicina Tropical de São Paulo 52, no. 1 (February 2010): 57–60. http://dx.doi.org/10.1590/s0036-46652010000100010.
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Hepatitis C virus (HCV) genotypes and subtypes were determined in hemodialysis patients in the Federal District, Brazil, by sequencing of the 5' noncoding (NC) and nonstructural 5B (NS5B) regions. From 761 patients, 66 anti-HCV-positive samples were tested for HCV RNA. All 51 HCV RNA-positive samples by PCR of the 5' NC region were genotyped as genotypes 1 (90.2%) and 3 (9.8%). Subtype 1a (82.3%) was the most prevalent, followed by subtypes 3a (9.8%), 1b (5.9%) and 1a/1b (2.0%). Forty-two samples could be amplified and genotyped in the NS5B region: 38 (90.5%) as genotype 1, subtypes 1a, and 8 (9.5%) as genotype 3, subtype 3a. For the 42 samples sequenced in both regions, the genotypes and subtypes determined were concordant in 100% and 95.2% of cases, respectively. Two samples presented discrepant results, with the 5' NC region not distinguishing correctly the subtypes 1a and 1b. These findings indicate that the HCV genotype 1, subtype 1a, is the most prevalent among hemodialysis patients in the Federal District, Brazil.
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Uzelac, Aleksandra, Ivana Klun, Vladimir Ćirković, Neda Bauman, Branko Bobić, Tijana Štajner, Jelena Srbljanović, Olivera Lijeskić, and Olgica Djurković-Djaković. "Toxoplasma gondii Genotypes Circulating in Serbia—Insight into the Population Structure and Diversity of the Species in Southeastern Europe, a Region of Intercontinental Strain Exchange." Microorganisms 9, no. 12 (December 7, 2021): 2526. http://dx.doi.org/10.3390/microorganisms9122526.
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In Europe, Toxoplasma gondii lineage II is dominant, and ToxoDB#1 the most frequently occurring genotype. The abundance of lineage III genotypes varies geographically and lineage I are rare, yet present in several regions of the continent. Data on the T. gondii population structure in southeastern Europe (SEE) are scarce, yet necessary to appreciate the diversity of the species in Europe. To help fill this gap, we genotyped 67 strains from nine species of intermediate hosts in Serbia by MnPCR-RFLP, determined the population structure, and identified the genotypes using ToxoDB. A neighbor-joining tree was also constructed from the isolates genotyped on nine loci. While 42% of the total genotype population consisted of ToxoDB#1 and ToxoDB#2, variant genotypes of both lineages comprised 46% of the population in wildlife and 28% in domestic animals and humans. One genotype of Africa 4 lineage was detected in a human sample. Interestingly, the findings include one lineage III variant and one II/III recombinant isolate with intercontinental distribution, which appear to be moderately related to South American genotypes. Based on these findings, SEE is a region of underappreciated T. gondii genetic diversity and possible strain exchange between Europe and Africa.
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Saleha, Shamim, Anwar Kamal, Farman Ullah, Nasar Khan, Asif Mahmood, and Sanaullah Khan. "Prevalence of Hepatitis C Virus Genotypes in District Bannu, Khyber Pakhtunkhwa, Pakistan." Hepatitis Research and Treatment 2014 (June 30, 2014): 1–5. http://dx.doi.org/10.1155/2014/165826.
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Determination of an individual’s hepatitis C virus (HCV) genotypes prior to antiviral therapy has become increasingly important for the clinical management and prognosis of HCV infection. Therefore, this study was conducted to investigate the prevalence of HCV genotypes in HCV infected patients of district Bannu in Khyber Pakhtunkhwa region of Pakistan. Serum samples of 117 seropositive patients were screened for HCV-RNA by using reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) and then PCR positive samples were subjected to HCV genotyping. Out of 117 seropositive samples, 110 samples were found positive by PCR analysis. Genotype 3a was the most prevalent one detected in 38% of patients, followed by genotype 3b in 21% of patients, and then genotype 2a in 12% of patients. However 21% of HCV-PCR positive samples could not be genotyped by method used in this study. Genotype 3a was the most prevalent genotype in patients of all age groups and its prevalence was found high among patients with increasing age (>34 years). Moreover, genotypes 3a and 3b were found to be the most prevalent genotypes in patients with history of shaving by barbers, receiving multiple injections, and dental procedures. In conclusion there is need of further investigation of genotypes of HCV by using more sensitive assays and considering large sample size in district Bannu.
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Plitt, Sabrina S., Ryan Kichuk, Sheena Geier, Trenton Smith, Felicia Roy, Alberto Severini, and Carmen L. Charlton. "Distribution of HPV genotypes among women with abnormal cytology results in Alberta, Canada." Official Journal of the Association of Medical Microbiology and Infectious Disease Canada 6, no. 2 (July 2021): 94–103. http://dx.doi.org/10.3138/jammi-2020-0048.
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Background: Persistent infection with a subset of human papillomavirus (HPV) genotypes can cause abnormal cytology and invasive cervical cancer. This study examines the circulating HPV genotype strains in a local population of the province of Alberta (a largely unvaccinated population) to establish baseline frequency of vaccine and non-vaccine genotypes causing abnormal cervical cytology. Method: Remnant liquid-based cytology specimens from the Alberta Cervical Cancer Screening Program (March 2014–January 2016) were examined. Only specimens from women who had a cytology grading of atypical squamous cells of undetermined significance or higher were included. HPV genotype was determined for all samples, and results were stratified by demographics and cytology results. Results: Forty-four unique HPV genotypes were identified from 4,794 samples. Of the 4,241 samples with a genotype identified, the most common genotypes were HPV 16, 18, 31, and 51, with 1,599 (37.7%), 441 (12.2%), 329 (7.8%), and 354 (8.4%), respectively. HPV9 vaccine genotypes made up 73.2% of these genotyped samples. Compared with specimens in which HPV9 vaccine genotypes were not detected, those with a genotype covered by the HPV9 vaccine were from younger women (33 [interquartile range {IQR] 28 to 42] y versus 40 [IQR 32 to 51] y; p < 0.00001). Conclusions: The baseline distribution of HPV genotypes in this largely unvaccinated population indicates that the HPV9 vaccine provides good protection from high-risk HPV infections. Determining the frequency of genotypes causing abnormal cytology in this population post–vaccine implementation will be important to assess efficacy of vaccination and monitor for any potential genotype replacement.
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Lee, Eun Jin, Han-Sung Kim, Hyun Soo Kim, Jae-Seok Kim, Wonkeun Song, MiYoung Kim, Young Kyung Lee, and Hee Jung Kang. "Human Bocavirus in Korean Children with Gastroenteritis and Respiratory Tract Infections." BioMed Research International 2016 (2016): 1–5. http://dx.doi.org/10.1155/2016/7507895.
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Human bocaviruses (HBoVs) are suggested to be etiologic agents of childhood respiratory and gastrointestinal infections. There are four main recognized genotypes of HBoVs (HBoV1–4); the HBoV-1 genotype is considered to be the primary etiologic agent in respiratory infections, whereas the HBoV2–4 genotypes have been mainly associated with gastrointestinal infections. The aim of the present study was to determine the distribution of HBoV genotypes in children with respiratory or gastrointestinal infections in a hospital in Korea. A total of 662 nasopharyngeal swabs (NPSs) and 155 fecal specimens were collected from children aged 5 years or less. Polymerase chain reaction (PCR) was conducted to detect theNS1HBoV gene. TheVP1gene of HBoV was further amplified in samples that were positive for theNS1gene. The PCR products ofVP1gene amplification were genotyped by sequence analysis. HBoV was detected in 69 (14.5%) of 662 NPSs and in 10 (6.5%) of 155 fecal specimens. Thirty-three isolates from NPSs and five isolates from fecal specimens were genotyped, and all 38 sequenced isolates were identified as the HBoV-1 genotype. HBoV-1 is the most prevalent genotype in children with respiratory or gastrointestinal HBoV infections in a hospital in Korea.
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Kovács, K., J. Völgyi-Csík, A. Zsolnai, I. Györkös, and L. Fésüs. "Associations between the AluI polymorphism of growth hormone gene and production and reproduction traits in a Hungarian Holstein-Friesian bull dam population." Archives Animal Breeding 49, no. 3 (October 10, 2006): 236–49. http://dx.doi.org/10.5194/aab-49-236-2006.
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Abstract. The aim of this paper was to study the polymorphisms of bovine growth hormone gene. The authors genotyped 363 Hungarian Holstein-Friesian bull dams from 6 farms all over the country. Two variants (L and V) of the bovine growth hormone gene digested with AluI enzyme were identified in the experiment. Genotyping was carried out by PCR-RFLP method. The frequency data of L and V allele was 0.93 and 0.07 respectively. Distribution of the three genotypes were 87.05% (LL), 12.40% (LV) and 0.55% (VV). The studied population was in H-W equilibrium considering the genotype distribution. SPSS 11.0 for Windows was used to reveal the possible correlations between GH genotypes and production and reproduction traits and further statistical analyses. On the basis of statistical analyses it can be found that VV genotype cows had the longest milking period and LL had the shortest dry period. Both differences were significant. Cows with LV genotype had significantly higher test milking data than LL cows. Furthermore, LV genotype seemed to be advantageous for 305 days lactation milk yield. While milk composition traits, as 305 days milk fat and protein percent showed the opposite tendency, since LL genotyped dams produced significantly higher values in these traits.
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Loparev, Vladimir N., Antonio Gonzalez, Marlene Deleon-Carnes, Graham Tipples, Helmut Fickenscher, Einar G. Torfason, and D. Scott Schmid. "Global Identification of Three Major Genotypes of Varicella-Zoster Virus: Longitudinal Clustering and Strategies for Genotyping." Journal of Virology 78, no. 15 (August 1, 2004): 8349–58. http://dx.doi.org/10.1128/jvi.78.15.8349-8358.2004.
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ABSTRACT By analysis of a single, variable, and short DNA sequence of 447 bp located within open reading frame 22 (ORF22), we discriminated three major varicella-zoster virus (VZV) genotypes. VZV isolates from all six inhabited continents that showed nearly complete homology to ORF22 of the European reference strain Dumas were assigned to the European (E) genotype. All Japanese isolates, defined as the Japanese (J) genotype, were identical in the respective genomic region and proved the most divergent from the E strains, carrying four distinct variations. The remaining isolates carried a combination of E- and J-specific variations in the target sequence and thus were collectively termed the mosaic (M) genotype. Three hundred twenty-six isolates collected in 27 countries were genotyped. A distinctive longitudinal distribution of VZV genotypes supports this approach. Among 111 isolates collected from European patients, 96.4% were genotype E. Consistent with this observation, approximately 80% of the VZV strains from the United States were also genotype E. Similarly, genotype E viruses were dominant in the Asian part of Russia and in eastern Australia. M genotype viruses were strongly dominant in tropical regions of Africa, Indochina, and Central America, and they were common in western Australia. However, genotype M viruses were also identified as a minority in several countries worldwide. Two major intertypic variations of genotype M strains were identified, suggesting that the M genotype can be further differentiated into subgenotypes. These data highlight the direction for future VZV genotyping efforts. This approach provides the first simple genotyping method for VZV strains in clinical samples.
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Utami, Puteri Rizki. "SELEKSI GENERASI M2 BERUMUR GENJAH HASIL IRADIASI BEBERAPA KULTIVAR PADI LOKAL SUMATERA BARAT." Jurnal BiBieT 3, no. 1 (November 21, 2018): 10. http://dx.doi.org/10.22216/jbbt.v3i1.1060.
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<p>Penelitian berjudul Seleksi Generasi M2 Yang Berumur Genjah Hasil Iradiasi Beberapa Kultivar Lokal Sumatera Barat dengan tujuan penelitian ini adalah untuk mendapatkan genotype calon mutan yang berumur genjah. Penelitian ini telah dilakukan di Kabupaten Dharmasraya (SUMBAR). Penelitian ini menggunakan kultivar padi lokal, yaitu; Sijunjuang, Kuriak Kusuik. .Metode yang digunakan dalam penelitian ini adalah metode seleksi silsilah. Kesimpulan akhir bahwa: mutan Calon di M2 generasi iradiasi Sijunjuang kultivar yang terdiri dari: a) 2 genotipe mutan calon yang sangat genjah(104 hss), b) 153 calon genotipe mutan yang genjah (110 hss - 120 hss), c) 18 genotipe mutan calon yang genjah dan memiliki kriteria tinggi untuk ideal, dan d) 2 genotipe potensial mutan yang genjah dan memiliki jumlah ideal anakan, e) memiliki 7 calon genotipe mutan yang memiliki bobot gabah kering panen diatas rata-rata produksi deskripsi kultivar Sijunjuang mutan calon generasi M2 iradisasi hasil Kuriak Kusuik terdiri dari: a) 2 genotipe mutan calon yang sangat genjah (104 hss), b) 76 calon genotipe mutan yang genjah (113 -124 hss), c) 323 kandidat untuk genotipe mutan sedang (126 -140 hss), d) 123 genotipe calon mutan genjah dan memiliki kriteria tinggi untuk ideal</p><p> </p><p><em>The study titled Seleksi Padi Generasi M2 yang Berumur Genjah Hasil Iradiasi Beberapa Kultivar Lokal Sumatera Barat with the aim of the research is to obtain genotypes that old early maturin mutant candidates.The experiment was conducted in Kabupaten Dharmasraya (SUMBAR). This study used</em> t<em>wo local rice cultivars, namely; Sijunjuang, KuriakKusuik, in radiation. The method used in this study was the pedigree selection method. In this study, The final conclusion that: Candidate mutants in M2 generation irradiated Sijunjuang cultivars consisting of: a) 2 genotypes of candidate mutants that are very early maturing (104 hss), b) 153 candidates mutant genotypes that are early maturing (110 hss - 120 hss), c) 18 genotypes of candidate mutants that are early maturing and has high criteria for an ideal, and d) 2 genotype potential mutant that is early maturing and has the ideal total number of tillers, e) has 7 candidates for the mutant genotype which has a weight of dry grain harvest above average production average description of cultivars Sijunjuang candidate mutants in M2 generation iradisasi Kuriak Kusuik resulted consist of: a) 2 genotypes of candidate mutants that are very early maturing (104 hss), b) 76 prospective mutant genotypes that are early maturing (113 -124 hss), c) 325 candidates for the mutant genotypes that are currently (126 – 140 hss), d) 123 genotype of mutant candidates that were very early maturing and has high criteria for an ideal.</em></p>
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Hu, Yu-Wen, Evan Balaskas, Milena Furione, Pei-Hua Yen, Garry Kessler, Vito Scalia, Linda Chui, and Graham Sher. "Comparison and Application of a Novel Genotyping Method, Semiautomated Primer-Specific and Mispair Extension Analysis, and Four Other Genotyping Assays for Detection of Hepatitis C Virus Mixed-Genotype Infections." Journal of Clinical Microbiology 38, no. 8 (2000): 2807–13. http://dx.doi.org/10.1128/jcm.38.8.2807-2813.2000.
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To date the true prevalence of hepatitis C virus (HCV) mixed-genotype infections has not been established mainly because currently available methods are not suitable for the detection of mixed genotypes in a viral population. A novel semiautomated genotyping method, primer-specific and mispair extension analysis (S-PSMEA), which is more reliable than other genotyping assays was developed for detection of HCV mixed-genotype infections. A genotype present at levels as low as 0.8% in a defined mix of HCV genotypes was detected, showing a 20-fold increase in sensitivity over that of direct DNA sequencing. A total of 434 HCV isolates were genotyped and analyzed for a comparative study of the accuracy between S-PSMEA and four current genotyping methods. The results showed that viruses in approximately 40% of the samples from this group determined to be infected with mixed genotypes by S-PSMEA were undetected by direct DNA sequencing due to its low sensitivity. Type-specific PCR, line probe assay, and restriction fragment length polymorphism analysis performed poorly, being able to identify only 38.5, 16.1, and 15.4% of mixed-genotype infections, respectively, that were detected by direct DNA sequencing. The prevalence of mixed-genotype infections detected by S-PSMEA was 7.9% (12 of 152 donors) among HCV-infected blood donors, 14.3% (15 of 105) among patients with chronic hepatitis C, and 17.1% (6 of 36) among thalassemia patients who had received multiple transfusions. The data lead us to conclude that HCV mixed-genotype infections are more common than previously estimated and that S-PSMEA may be the method of choice when detection of genotypes present at low levels in mixed-genotype infections is required due to its higher level of sensitivity.
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Örvell, Claes, Tesfaldet Tecle, Bo Johansson, Hiroyuki Saito, and Agneta Samuelson. "Antigenic relationships between six genotypes of the small hydrophobic protein gene of mumps virus." Journal of General Virology 83, no. 10 (October 1, 2002): 2489–96. http://dx.doi.org/10.1099/0022-1317-83-10-2489.
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Six different genotypes of mumps virus, A, C, D, G, H and I, genotyped on the basis of the small hydrophobic protein gene sequence, were subjected to antigenic comparison. Monoclonal antibodies directed against the haemagglutinin–neuraminidase protein of the SBL-1 strain of genotype A were used in immunofluorescence tests with different mumps virus strains. In addition, the six virus genotypes were compared by cross-neutralization tests with human post-vaccination sera after vaccination with the Jeryl Lynn (JL) strain of mumps virus and with rabbit hyperimmune sera directed against the A or D genotypes of mumps virus. Genotypes C, D, G, H and I could not be antigenically separated. In contrast, three different virus strains of genotype A, SBL-1, JL and Kilham, were distinct and were found to represent three different serotypes within the A genotype of mumps virus. Vaccination of Swedish children with the JL strain of mumps virus resulted in clearly lower neutralization titres against the SBL-1 strain, which is endemic in Sweden, compared to the homologous vaccine titres.
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Nückel, Holger, Ulrich H. Frey, Maja Bau, Ludger Sellmann, Jens Stanelle, Jan Dürig, Karl-Heinz Jöckel, Ulrich Dührsen, and Winfried Siffert. "Association of a novel regulatory polymorphism (−938C>A) in the BCL2 gene promoter with disease progression and survival in chronic lymphocytic leukemia." Blood 109, no. 1 (September 7, 2006): 290–97. http://dx.doi.org/10.1182/blood-2006-03-007567.
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Abstract Bcl-2 plays a key role in the regulation of apoptosis. We investigated the role of a novel regulatory single-nucleotide polymorphism (−938C>A) in the inhibitory P2 BCL2 promoter in B-cell chronic lymphocytic leukemia (B-CLL). The −938C allele displayed significantly increased BCL2 promoter activity and binding of nuclear proteins compared with the A allele. Concomitantly, Bcl-2 protein expression in B cells from CLL patients carrying the −938 AA genotype was significantly increased compared with CC genotypes. Genotype distribution between 123 CLL patients (42 AA, 55 AC, 26 CC) and 120 genotyped healthy controls (36 AA, 63 AC, 21 CC) was not significantly different, suggesting that genotypes of this polymorphism do not increase the susceptibility for B-CLL. However, median time from first diagnosis to initiation of chemotherapy and median overall survival were significantly shorter in patients with −938AA genotype (38 and 199 months, respectively) compared with AC/CC genotypes (120 and 321 months, respectively; P = .008 and P = .003, respectively). Multivariable Cox regression identified the BCL2−938AA genotype as an independent prognostic factor for the time to first treatment (hazard ratio [HR] 1.9; P = .034) together with disease stage at diagnosis (HR 2.5; P = .004) and ZAP-70 status (HR 3.0; P = .001). The BCL2−938AA genotype is associated with increased Bcl-2 expression and a novel unfavorable genetic marker in patients with B-CLL.
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Sayu Putu Yuni Paryati, Dedi Rahmat Dudi. "PENGARUH KERAGAMAN GEN DGAT1 TERHADAP KADAR KOLESTEROL DAN TRIGELISERIDA DARAH DOMBA PADJADJARAN (The Effect of DGAT1 Gene Diversity on Padjadjaran Sheep to Cholesterol and Triglyceride Levels)." JANHUS: Jurnal Ilmu Peternakan Journal of Animal Husbandry Science 2, no. 1 (March 29, 2018): 1. http://dx.doi.org/10.52434/janhus.v2i1.255.
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Abstrak
Penelitian dilakukan untuk mengetahui pengaruh keragaman gen DGAT1 pada domba Padjadjaran terhadap kandungan kolesterol dan trigiserida darah. Ternak domba yang digunakan dalam penelitian ini merupakan domba Padjadjaran umur 1,5 tahun, yang telah diidentifikasi memiliki genotipe tertentu berdasarkan gen DGAT1. Total sampel domba yang digunakan sebanyak 15 ekor. Sampel yang digunakan terdistribusi dalam tiga genotipe (5 CC, 5 CT dan 5 TT). Penilaian komponen lemak meliputi: (1) Kandungan kolesterol total dan Kandungan Trigeliserida. Pemeriksaan kolesterol menggunakan metode: CHOD-PAP (Cholesterol Oxidase-Peroxidase Aminoantipyrine Phenol). Hasil penelitian menunjukkan bahwa kadar kolesterol total darah domba Padjajaran berada pada kisaran normal dan keragaman gen DGAT1 tidak berpengaruh nyata terhadap kadar kolesterol darah. Dari ketiga genotype DGAT, menunjukkan kelompok CC memiliki kadar kolesterol total paling rendah, dibandingkan kelompok lainnya, sedangkan kadar trigliserida terendah didapatkan pada genotype TT, namun tidak berbeda nyata dibandingkan dengan genotype CC dan CT.
Kata-kata kunci: domba Padjadjaran, gen DGAT1, kolesterol
Abstract
The study was conducted to determine the effect of DGAT1 gene diversity on Padjadjaran sheep to cholesterol and triglyceride levels. The sheep used in this study is a 1.5-year-old Padjadjaran sheep, which has a specific genotype based on the DGAT1 gene. Total sample of sheep that used as many as 15 tail. The samples used were distributed in three genotypes (5 CC, 5 CT and 5 TT). Assessment of fat content are total cholesterol and Trigeliserida.,using cholesterol method: CHOD-PAP (Cholesterol Oxidase-Peroxidase Aminoantipyrine Phenol). The results showed that total DGAT1 did not significantly affect to blood cholesterol level. Of the three DGAT genotypes, the CC group had the lowest total cholesterol levels, compared to the other groups, while the triglyceride levels were low in the TT genotype, but not significantly different from the CC and CT genotypes.
Keywords : Padjadjaran sheep, DGAT1, Choleseterol
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Bin Huraib, Ghaleb, Fahad Al Harthi, Misbahul Arfin, Mohammed Al-Sugheyr, Sadaf Rizvi, and Abdulrahaman Al-Asmari. "Cytokine Gene Polymorphisms in Saudi Patients With Atopic Dermatitis: A Case-Control Study." Biomarker Insights 13 (January 1, 2018): 117727191877776. http://dx.doi.org/10.1177/1177271918777760.
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The cause of atopic dermatitis (AD) is multifactorial and a number of genes including cytokines have been involved. We genotyped 315 subjects for polymorphisms in TNF-α and TNF-β and IL-10 genes. Patients had significantly higher frequency of GA genotype of TNF-α (−308 G/A) than healthy controls. Patients with AD and controls had similar distribution of A and G alleles. Genotype AA was found in 7.11% of controls while completely absent in cases. The frequencies of genotypes GG and AA of TNF-β (+252 A/G) polymorphism were higher whereas the frequency of genotype GA was significantly lower in patients than the controls. The frequencies of genotypes GG and AA of IL-10 (1082 G/A) polymorphism were significantly increased whereas genotype GA was decreased in patients than the controls. It is concluded that TNF-α (−308 G/A), TNF-β (+252 A/G), and IL-10 (−1082 G/A) polymorphisms are linked with the susceptibility of AD in Saudis and can be a risk factor.
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Niemi, Suvi, Eija Hiltunen-Back, and Mirja Puolakkainen. "Chlamydia trachomatisGenotypes and the Swedish New Variant among UrogenitalChlamydia trachomatisStrains in Finland." Infectious Diseases in Obstetrics and Gynecology 2011 (2011): 1–6. http://dx.doi.org/10.1155/2011/481890.
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Our aims were to genotypeChlamydia trachomatisstrains present in urogenital samples and to investigate the occurrence of the Swedish new variant ofC. trachomatisin Finland. We genotyped 160C. trachomatispositive samples withompAreal-time PCR and analyzed 495 samples for the new variant. The three most prevalent genotypes were E (40%), F (28%), and G (13%). Only two specimens containing bacteria with the variant plasmid were detected. It seems that in Finland the percentage of infections due to genotypes F and G has slightly increased during the last 20 years. Genotypes E and G appear to be more common, and genotypes J/Ja and I/Ia appear to be less common in Europe than in the USA. Although the genotype E was the most common genotype amongC. trachomatisstrains, the new variant was rarely found in Finland.
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Grundy, B., and R. M. Lewis. "Gene frequency estimation from a biased sample of individuals." Proceedings of the British Society of Animal Science 2001 (2001): 44. http://dx.doi.org/10.1017/s1752756200004269.
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With individual genes being identified that have an important effect on performance and fitness in livestock it is likely that such genes will be included in selection programmes. However, in order to devise sensible strategies to achieve this, knowledge of the frequency of the gene of interest is required. In practice, it is possible that estimates for gene frequency are based on genotype testing of only a subset of the population. The question then arises as to what conclusions can be drawn about the population gene frequency particularly in the likely scenario where the sample genotyped is not chosen at random. A procedure was developed by Van Arendonk et al. (1989) to have genotype information on as many individuals as possible given financial limits in the numbers genotyped. In this procedure the genotypes of individuals are predicted using pedigree information and the rules of Mendelian inheritance. What is less clear is the value of the additional information in predicting the population gene frequency. The objective of this study was to assess to consequence of sampling procedures on estimates of gene frequency when additional genotype information is or is not obtained by predicting genotypes on individuals themselves not tested.
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Herman, Mariana, Amanda Manara Caceres, Ana Luísa H. Albuquerque, Raíssa O. Leite, César Erineudo T. Araújo, Diego José Z. Delfiol, Rogério A. Curi, Alexandre S. Borges, and José P. Oliveira-Filho. "DMRT3 Allele Frequencies in Batida- and Picada-Gaited Donkeys and Mules in Brazil." Animals 13, no. 24 (December 12, 2023): 3829. http://dx.doi.org/10.3390/ani13243829.
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In Brazil, the production of mules with a comfortable gait involves primarily the breeding of marching saddle mules. This is achieved by crossing gaited Pêga donkeys with horses from the Mangalarga Marchador and Campolina breeds. The DMRT3:g.22999655C>A SNP is implicated in regulating gait phenotypes observed in various horse breeds, including the batida (CC) and picada (CA) gaits found in these horse breeds. We aimed to determine if genotypes influenced gait type in 159 mules and 203 donkeys genotyped for the DMRT3 SNP using PCR-RFLP analysis. About 47% of mules had the CC-genotype, while 53% had the CA-genotype. Donkeys predominantly had the CC-genotype (97%), with no AA-genotype detected. Both CC- and CA-genotypes were evenly distributed among mules with batida or picada gaits. In donkeys, the CC-genotype frequencies were consistent regardless of gait type. However, the CA-genotype was more common in picada-gaited donkeys compared to batida-gaited ones. The prevalence of CA mules and the rare presence of the non-reference allele in donkeys align with previous findings in Mangalarga Marchador and Campolina horses. This suggests the non-reference allele likely originated from the mares involved in donkey crosses. Additionally, our results imply that factors beyond this variant, such as other genes and polymorphisms, influence gait traits in equids.
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Roslini, Nur, Bakhtiar Bakhtiar, and Siti Hafsah. "Uji Daya Hasil S5 Jagung (Zea mays L.) Hibrida." Jurnal Ilmiah Mahasiswa Pertanian 5, no. 2 (May 1, 2020): 31–40. http://dx.doi.org/10.17969/jimfp.v5i2.14868.
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Abstrak. Penelitian ini bertujuan untuk menyeleksi tanaman jagung berdaya hasil tinggi. Penelitian ini dilaksanakan di PT Syngenta Seed Indonesia Kediri Field Station dusun Sukodono desa Kedungmalang kecamatan Papar kabupaten Kediri, Jawa Timur yang berlangsung pada Mei sampai Oktober 2019. Rancangan yang digunakan dalam penelitian ini adalah Rancangan Acak Kelompok (RAK) non faktorial dengan 24 genotipe uji, 4 genotipe pembanding (untuk uji daya hasil) dengan 2 ulangan. Pada uji daya hasil diperoleh 7 genotipe yaitu 18ID010144, 18ID010123, 18ID006020, 18ID010135, 18ID010125, 18ID007419 dan 18ID010148 yang memiliki daya hasil tinggi diatas genotipe pembanding daya hasil tertinggi. 24 genotipe uji yaitu 18ID010125 memiliki daya hasil 14,12 ton ha-1 genotipe 18ID010123 memiliki daya hasil tertinggi 15,28 ton ha-1 dan genotipe 18ID010148 memiliki daya hasil 13,91 ton ha-1. Yield Trial Screening on S5 Hybrid Maize (Zea mays L.)Abstract. This research aims to select maize are high yield. This research was conducted at PT Syngenta Seed Indonesia Kediri Field Station Sukodono in Sukodono sub-village, Kedungmalang village, Papar district, Kediri district, East Java, which took place from May to October 2019. The design used in this research was Non Factorial Randomized Block Design (RBD) with 24 test genotypes, 4 comparative genotypes (for yield trial) with 2 replications. The results showed that In yield trial was obtained 7 genotypes (18ID010144, 18ID010123, 18ID006020, 18ID010135, 18ID010125, 18ID007419 dan 18ID010148) which have high yields above the highest comparative yield genotypes. There were 3 genotypes selected from 24 test genotypes consist 18ID010125 has yield 14,12 tons ha-1,genotype 18ID010123 has the highest yield 15,28 tons ha-1 and genotype 18ID010148 has yield 13,91 tons ha-1.
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Kim, Dong Hwan, Hee Kyung Ahn, Wei Xu, Suzanne Kamel-Reid, Xiangdong Liu, Katherine Siminovitch, and Jeffrey H. Lipton. "Clinical Relevance of Vascular Endothelial Growth Factor (VEGFA) and VEGF Receptor (VEGFR2) Gene Single Nucleotide Polymorphism on the Treatment Outcomes Following Imatinib Mesylate Therapy." Blood 112, no. 11 (November 16, 2008): 1110. http://dx.doi.org/10.1182/blood.v112.11.1110.1110.
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Abstract Imatinib mesylate (IM) could reverse marrow angiogenesis and decrease the plasma level of vascular endothelial growth factor (VEGF) in chronic myeloid leukemia (CML) patients. The current study investigated the impact of 4 VEGF (VEGFA) and 3 VEGF receptor (VEGFR2) gene polymorphisms on the outcomes of 228 CML patients following IM therapy (male:female 96:132; median age at start of IM, 55 years-old; chronic phase: accelerated phase: blastic crisis, 205/17/2). The DNAs from blood samples were genotyped using MALDI-TOF-based method. VEGFA genotypes such as -2578C>A (rs699947), -460T>C (rs833061), +405G>C (rs2010963) and +936 C>T (rs3025039) loci, and VEGFR2 genotypes including rs1531289, rs1870377 and rs2305948 were analyzed. In single marker analyses, strong correlations were noted between complete cytogenetic response (CCyR) and VEGFR2 genotypes (rs1531289 and rs1870377), treatment failure and VEGFR2 genotype (rs1870377), dose escalation and VEGFR2 genotype (rs1870377), complete molecular response (CMoR) and VEGFA genotype (rs3025039), progression to advanced disease stage and VEGFA genotypes (rs699947 and rs833061). Three haplotypes of VEGFR2 gene were generated as follows: GT (46.1%), AT (27.9%) and GA (25.7%). Haplotype analyses showed good correlations between VEGFR2 haplotype and CCyR, treatment failure, and dose escalation of IM. Multivariate analyses confirmed strong correlations of VEGFR2 polymorphisms (especially rs1531289, rs1870377 or VEGFR2 haplotype) with CCyR, treatment failure, dose escalation and of VEGFA genotype (rs699947) with progression to advanced disease stage. The VEGFR2 genotypes and haplotype correlate well with cytogenetic response, treatment failure and dose escalation of IM therapy in CML patients, while VEGFA genotype correlates with progression to advanced disease stage.
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Beni, Behrouz Taheri, Hossein Motamedi, and Mohammad Roayaei Ardakani. "Genotyping of the prevalent Chlamydia trachomatis strains involved in cervical infections in women in Ahvaz, Iran." Journal of Medical Microbiology 59, no. 9 (September 1, 2010): 1023–28. http://dx.doi.org/10.1099/jmm.0.016717-0.
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To determine the prevalence of cervical Chlamydia trachomatis genotypes in Iran for the first time and their association with three clinical symptoms/signs, i.e. abnormal vaginal discharge, lower abdominal pain (LAP) and swab-induced bleeding, and patient age, 620 cervical specimens were obtained from women with symptomatic genital infection referred to gynaecological clinics and 108 C. trachomatis-positive specimens were genotyped by direct omp1 gene PCR-RFLP analysis. Eight genotypes were identified. The most prevalent genotype was E (31.5 %), followed by F (23.1 %), D/Da (13 %), K (9.2 %), I (8.3 %), G (7.5 %), H (5.5 %) and J (1.9 %). For analysing the association of C. trachomatis genotypes with symptoms/signs and age, P-values were separately evaluated for genogroups and genotypes. The analysis of genogroups showed that women infected with genogroup F/G manifested the symptom of LAP significantly more often than those infected with the other genogroups (P=0.02), while the analysis of genotypes revealed that women infected with genotype F reported LAP slightly more often than women infected with the other genotypes (P=0.08). No significant correlation between genogroups and age was found; however, genotype E was somewhat less prevalent among women aged 25–34 years than among other age groups (P=0.08).
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Waqar, Muhammad, Habib Ur Rehman, Muhammad Wasim, Asad Ullah Khan, Tauseef Ahmad, Noor Ul Akbar, Mubarak Zeb, et al. "Molecular detection of the Hepatitis C virus genotypes circulating among both sexes of Khyber Pakhtunkhwa, Pakistan." Asian Journal of Medical Sciences 5, no. 3 (February 26, 2014): 72–76. http://dx.doi.org/10.3126/ajms.v5i3.9449.
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Background: Hepatitis C Virus (HCV) is the major cause of viral hepatitis. A few studies revealed that HCV genotypes; 3a, 3b, 1a and 1b are the most common genotypes found in the general population of Khyber Pakhtunkhwa. Aims and Objective: The current is designed to find out the prevalence of HCV genotypes among both sexes of Khyber Pakhtunkhwa. Study Methods: The present study was carried out in various area of Khyber Pakhtunkhwa during the period of July, 2012 to July, 2013. All the HCV positive samples were genotyped. The statistical analysis of the data was done by using Statistix 9.0 software. Result: The results showed that the male, 53.1% (n=340) were more infected as to female, 46.8% (n=300). The overall result shows that in male patients; the high number of cases (216) was reported of 3a whereas the lowest cases (8) were reported of 1b. The mixed genotype is recorded in 8 patients. In female patients; the 3a is detected in 170 patients whereas the lowest cases of genotype (3b) are reported in 5 patients. In female patients; the mixed genotype is reported in 11 patients. Conclusion: From the present study, it was concluded that the male were more infected as compare to female and the genotype 3a was the most common genotype in both sexes. Asian Journal of Medical Science, Volume-5(3) 2014: 72-76 http://dx.doi.org/10.3126/ajms.v5i3.9449
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Yuan, Hongyu, Man Fu, Xianzhang Yang, Kun Huang, and Xiaoyan Ren. "Single nucleotide polymorphism of MTHFR rs1801133 associated with elevated Hcy levels affects susceptibility to cerebral small vessel disease." PeerJ 8 (February 20, 2020): e8627. http://dx.doi.org/10.7717/peerj.8627.
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Background Methylenetetrahydrofolate reductase (MTHFR) is indispensable for the conversion of homocysteine (Hcy) to methionine. The single nucleotide polymorphism (SNP) of MTHFR gene (rs1801133, C667T) is correlated with decreased enzyme activity that eventually results in elevated plasma Hcy levels. Hyperhomocysteinemia has been confirmed to be involved in the pathogenesis of stroke, cerebral small vessel disease (CSVD), various metabolic disorders and so on. However, the relationship between the MTHFR gene polymorphisms, Hcy, and CSVD has not been investigated. In this study, the relationship between SNPs of MTHFR gene and CSVD was determined after adjusting for cardiovascular risk factors, and the potential mechanism based on Hcy levels was explored. Methods A total of 163 consecutive CSVD patients were collected as the case group. In the corresponding period, 326 healthy people were selected as the control group, who were matched to these cases according to age (±2 years) and gender at a ratio of 2:1. SNPs of MTHFR rs1801133, rs1801131, rs2274976, rs4846048, rs4846049, rs13306561 and rs3737964, were genotyped with TaqMan Pre-Designed SNP Genotyping Assays. Plasma Hcy levels were detected using Hcy reagent through enzymatic cycling assay. Multivariate analysis was used to identify the SNPs associated with CSVD susceptibility. Plasma Hcy levels were compared between different genotypes. Results The MTHFR rs1801133 TT and CT genotype had increased risk for CSVD, and the OR was higher in the TT genotype than in the CT genotype (2.307 vs 1.473). The plasma Hcy levels of different genotypes showed the tendency of the TT genotype > CT genotype > CC genotype (19.91 ± 8.73 pg/ml vs 17.04 ± 5.68 pg/ml vs 14.96 ± 4.85 pg/ml). Conclusions The SNP of MTHFR rs1801133 was correlated with CSVD, and the TT and CT genotypes had increased risk for CSVD compared to the CC genotype. The potential mechanism was associated with elevated Hcy levels.
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Zotova, I. V., A. G. Nikitin, E. N. Fattakhova, A. N. Brovkin, D. S. Khodyrev, E. Y. Lavrikova, M. Y. Isaeva, A. S. Kosukhina, V. V. Nosikov, and D. A. Zateyshchikov. "THE AFFECT OF INFLUENCE OF GENES' POLYMORPHISMS CYP2C9 AND VKORC1ON THE SAFETY OF THE THERAPY BY WARFARIN." Journal of Clinical Practice 4, no. 4 (December 15, 2013): 3–10. http://dx.doi.org/10.17816/clinpract443-10.
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To study the distribution of alleles and genotypes of polymorphic markers of genes CYP2C9 and VKORC1 of Russian patients who live in Moscow, and in order to assess the influence of genetic factors on warfarin therapy 400 patients have been genotyped. The dosage of warfarin which is required for achievement of INR target values has been different among owners of different geno- types of polymorphic markers of genes CYP2C9 . Meanwhile the highest average dose has been required for genotype *1/*1 and the lowest – for owners of alleles *2 and *3 . For polymorphism G(- 1639)A of the gene VKORC1 the dosage of warfarin which is required for achievement of the INR target values, has been different among owners of different genotypes. The highest average dose has been required for genotype GG, and the lowest – for genotype AA. The results will allow to work out more accurate algorithm of choosing of the initial dose of warfarin depending on the genotypes of polymorphic markers of genes CYP2C9 and VKORC1.
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Stosic, Ivana, Darko Grujicic, Slobodan Arsenijevic, and Olivera Milosevic-Djordjevic. "Influence of glutathione-s-transferase (GSTT1 and GSTM1) polymorphism on baseline micronuclei frequency in peripheral blood lymphocytes." Genetika 46, no. 3 (2014): 649–59. http://dx.doi.org/10.2298/gensr1403649s.
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We have analyzed impact of polymorphism in GSTT1 and GSTM1 genes on the micronuclei (MN) frequency in peripheral blood lymphocytes (PBLs). A total 134 women from central Serbia were enrolled in the study. Polymorphisms of GST genes were genotyped by performing a multiplex polymerase chain reaction (PCR) and cytokinesis block micronucleus (CBMN) test was used to assess MN frequency. GSTT1 null and GSTM1 null genotype carriers had higher MN frequencies as compared to positive counterparts but without statistical significance. Carriers of dual GSTT1/GSTM1 null genotypes had significantly higher MN frequency than positive/positive, positive/null and null/positive. Smokers and women >45 years old with GSTT1 null genotype and GSTT1null/GSTM1null genotypes have statistically higher MN frequency than positive counterparts. Results suggest possible influence of dual null genotypes of GSTT1/GSTM1 on the baseline MN frequency, as well influence on the level of MN in smokers and in women age >45 years. GSTT1 null genotype may have the potential to influence the baseline MN frequency in PBLs of smokers, as well as in women age >45 years.
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Wodebo, Kibreab Yosefe, Taye Tolemariam, Solomon Demeke, Weyessa Garedew, Tessema Tesfaye, Muluken Zeleke, Deribe Gemiyu, Worku Bedeke, Jane Wamatu, and Mamta Sharma. "AMMI and GGE Biplot Analyses for Mega-Environment Identification and Selection of Some High-Yielding Oat (Avena sativa L.) Genotypes for Multiple Environments." Plants 12, no. 17 (August 25, 2023): 3064. http://dx.doi.org/10.3390/plants12173064.
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This paper reports an evaluation of eleven oat genotypes in four environments for two consecutive years to identify high-biomass-yielding, stable, and broadly adapted genotypes in selected parts of Ethiopia. Genotypes were planted and evaluated with a randomized complete block design, which was repeated three times. The additive main effect and multiplicative interaction analysis of variances revealed that the environment, genotype, and genotype–environment interaction had a significant (p ≤ 0.001) influence on the biomass yield in the dry matter base (t ha−1). The interaction of the first and second principal component analysis accounted for 73.43% and 14.97% of the genotype according to the environment interaction sum of squares, respectively. G6 and G5 were the most stable and widely adapted genotypes and were selected as superior genotypes. The genotype-by-environment interaction showed a 49.46% contribution to the total treatment of sum-of-squares variation, while genotype and environment effects explained 34.94% and 15.60%, respectively. The highest mean yield was obtained from G6 (12.52 kg/ha), and the lowest mean yield was obtained from G7 (8.65 kg/ha). According to the additive main effect and multiplicative interaction biplot, G6 and G5 were high-yielding genotypes, whereas G7 was a low-yielding genotype. Furthermore, according to the genotype and genotype–environment interaction biplot, G6 was the winning genotype in all environments. However, G7 was a low-yielding genotype in all environments. Finally, G6 was an ideal genotype with a higher mean yield and relatively good stability. However, G7 was a poor-yielding and unstable genotype. The genotype, environment, and genotype x environment interaction had extremely important effects on the biomass yield of oats. The findings of the graphic stability methods (additive main effect and multiplicative interaction and the genotype and genotype–environment interaction) for identifying high-yielding and stable oat genotypes were very similar.
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Bei, Chunhua, Shun Liu, Xiangyuan Yu, Moqin Qiu, Bo Tang, Weijia Liao, Songqing He, and Hongping Yu. "Single Nucleotide Polymorphisms inmiR-122Are Associated with the Risk of Hepatocellular Carcinoma in a Southern Chinese Population." BioMed Research International 2018 (December 19, 2018): 1–6. http://dx.doi.org/10.1155/2018/1540201.
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Single nucleotide polymorphisms (SNPs) in microRNA may affect its expression and regulation of target genes, which may consequently alter individual susceptibility to cancer. In this study we aimed to investigate associations betweenmiR-122polymorphisms and hepatocellular carcinoma (HCC) in a southern Chinese population. Three selected SNPs inmiR-122(rs9966765, rs1135519, and rs17669) were genotyped in 1050 HCC patients and 1079 cancer-free controls using Sequenom MassARRAY platform and the associations of the three SNPs and HCC risk were evaluated. We found that individuals with the rs1135519 CC genotypes had a significant increased risk of HCC than those with TT genotypes (adjusted OR=2.71, 95% CI=1.15-6.36, andP=0.022), while the rs9966765 CC genotypes showed a borderline significant association with increased risk of HCC when compared with the GG genotypes (adjusted OR=2.38, 95% CI=0.99-5.75, andP=0.052). There was also a significant increased risk of HCC when combining risk genotypes of these loci, i.e., rs1135519 CC and rs9966765 CC. Compared with the low-risk group (0 risk genotype), the high risk group (1-2 risk genotypes) had significantly increased risk of HCC (OR=1.61, 95% CI=1.05-2.44, andP=0.028). Further genotype-expression analysis revealed that cases carrying the CC genotype of rs1135519 had lower levels ofmiR-122expression than those with the TT genotype. Our results suggest that SNP of rs1135519 modulatesmiR-122expression and contributes to the genetic susceptibility of HCC, either independently or together with rs9966765 inmiR-122.Further well-designed studies with lager sample sizes are needed to confirm our findings.
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Toyé, Rayana Maryse, Carmen Luisa Loureiro, Rossana Celeste Jaspe, Fabien Zoulim, Flor Helene Pujol, and Isabelle Chemin. "The Hepatitis B Virus Genotypes E to J: The Overlooked Genotypes." Microorganisms 11, no. 8 (July 27, 2023): 1908. http://dx.doi.org/10.3390/microorganisms11081908.
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Hepatitis B virus (HBV) genotypes E to J are understudied genotypes. Genotype E is found almost exclusively in West Africa. Genotypes F and H are found in America and are rare in other parts of the world. The distribution of genotype G is not completely known. Genotypes I and J are found in Asia and probably result from recombination events with other genotypes. The number of reported sequences for HBV genotypes E to J is small compared to other genotypes, which could impact phylogenetic and pairwise distance analyses. Genotype F is the most divergent of the HBV genotypes and is subdivided into six subgenotypes F1 to F6. Genotype E may be a recent genotype circulating almost exclusively in sub-Saharan Africa. Genotype J is a putative genotype originating from a single Japanese patient. The paucity of data from sub-Saharan Africa and Latin America is due to the under-representation of these regions in clinical and research cohorts. The purpose of this review is to highlight the need for further research on HBV genotypes E to J, which appear to be overlooked genotypes.
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Moraes, Marcia Terezinha Baroni de, Gabriel Azevedo Alves Leitão, Alberto Ignácio Olivares Olivares, Maria da Penha Trindade Pinheiro Xavier, Romanul de Souza Bispo, Sumit Sharma, José Paulo Gagliardi Leite, Lennart Svensson, and Johan Nordgren. "Molecular Epidemiology of Sapovirus in Children Living in the Northwest Amazon Region." Pathogens 10, no. 8 (July 30, 2021): 965. http://dx.doi.org/10.3390/pathogens10080965.
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Sapovirus is an important etiological agent of acute gastroenteritis (AGE), mainly in children under 5 years old living in lower-income communities. Eighteen identified sapovirus genotypes have been observed to infect humans. The aim of this study was to identify sapovirus genotypes circulating in the Amazon region. Twenty-eight samples were successfully genotyped using partial sequencing of the capsid gene. The genotypes identified were GI.1 (n = 3), GI.2 (n = 7), GII.1 (n = 1), GII.2 (n = 1), GII.3 (n = 5), GII.5 (n = 1), and GIV.1 (n = 10). The GIV genotype was the most detected genotype (35.7%, 10/28). The phylogenetic analysis identified sapovirus genotypes that had no similarity with other strains reported from Brazil, indicating that these genotypes may have entered the Amazon region via intense tourism in the Amazon rainforest. No association between histo-blood group antigen expression and sapovirus infection was observed.
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UNICOMB, L. E., L. C. O'REILLY, M. D. KIRK, R. J. STAFFORD, H. V. SMITH, N. G. BECKER, M. S. PATEL, and G. L. GILBERT. "Risk factors for infection withCampylobacter jejuni flaAgenotypes." Epidemiology and Infection 136, no. 11 (January 21, 2008): 1480–91. http://dx.doi.org/10.1017/s0950268807000246.
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SUMMARYWe aimed to exploreCampylobactergenotype-specific risk factors in Australia. Isolates collected prospectively from cases recruited into a case-control study were genotyped usingflaArestriction fragment-length polymorphism typing (flaAgenotyping). Exposure information for cases and controls was collected by telephone interview. Risk factors were examined for majorflaAgenotypes using logistic and multinomial regression. FiveflaAgenotypes accounted for 325 of 590 (55%) cases – flaA-6b (n=129),flaA-6 (n=70),flaA-10 (n=48),flaA-2 (n=43),flaA-131 (n=35). In Australia, infections due toflaA-10 andflaA-2 were found to be significantly associated with eating non-poultry meat (beef and ham, respectively) in both case-control and inter-genotype comparisons. All major genotypes apart fromflaA-10 were associated with chicken consumption in the case-control comparisons. Based on several clinical criteria, infections due toflaA-2 were more severe than those due to other genotypes. Thus genotype analysis may reveal genotype-specific niches and differences in virulence and transmission routes.
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Dakhil Raysan, Adbul-Kadhum, and Ali A. Abdul-Kareem. "Effect of genetic testing for CAPN1 gene polymorphisms on some productive and meat quality traits in broilers." Sumer 2 8, CSS 2 (September 15, 2023): 1–9. http://dx.doi.org/10.21931/rb/css/2023.08.02.88.
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One day, 100 birds of commercial broiler Ross308 were used. The results showed the success of the amplification process for the studied segment of the CAPN1 gene through electrophoresis assay. Three genotypes, CC, CT and TT, were identified, whose frequency was 0.52, 0.34 and 0.14, respectively. C allele frequency was 0.69, and the T allele was 0.31. There are no significant differences in body weight and weight gain among CC, CT and TT genotypes. The results showed that there were highly significant differences (P<0.01) in the Water Holding Capacity (WHC) among the genotypes. The CC genotype was superior to the CT and TT genotypes. Also, there were significant differences in the pH values (P<0.01) among the genotypes. CC genotype was superior to the CT and TT genotypes. There were significant differences in flavor between the genotypes; the CC genotype was superior to the CT genotype, and the CT genotype was superior to the TT genotype. There are significant differences (P<0.01) in tenderness. CC genotype was superior to the TT genotype. CT genotypes did not differ significantly from the CC and TT genotypes. There was a highly significant difference (P<0.01) among the genotypes on the juiciness. The CC genotype was superior to the CT and TT genotypes—no significant differences in color and generally acceptable. Keywords: genetic analysis, polymorphisms, CAPN1 gene, productive, meat qualitative, broiler.
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Vanspauwen, Marijke J., Vera E. J. Knops, Cathrien A. Bruggeman, Walther N. K. A. van Mook, and Catharina F. M. Linssen. "Molecular epidemiology of Pneumocystis jiroveci in human immunodeficiency virus-positive and -negative immunocompromised patients in The Netherlands." Journal of Medical Microbiology 63, no. 10 (October 1, 2014): 1294–302. http://dx.doi.org/10.1099/jmm.0.076257-0.
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Pneumocystis jiroveci infections can cause pneumocystis pneumonia (PCP) or lead to colonization without signs of PCP. Over the years, different genotypes of P. jiroveci have been discovered. Genomic typing of P. jiroveci in different subpopulations can contribute to unravelling the pathogenesis, transmission and spread of the different genotypes. In this study, we wanted to determine the distribution of P. jiroveci genotypes in immunocompetent and immunocompromised patients in The Netherlands and determine the clinical relevance of these detected mutations. A real-time PCR targeting the major surface glycoprotein gene (MSG) was used as a screening test for the presence of P. jiroveci DNA. Samples positive for MSG were genotyped based on the internal transcribed spacer (ITS) and dihydropteroate synthase (DHPS) genes. Of the 595 included bronchoalveolar lavage fluid samples, 116 revealed the presence of P. jiroveci DNA. A total of 52 of the 116 samples were ITS genotyped and 58 DHPS genotyped. The ITS genotyping revealed 17 ITS types, including two types that have not been described previously. There was no correlation between ITS genotype and underlying disease. All ITS- and DHPS-genotyped samples were found in immunocompromised patients. Of the 58 DHPS-genotyped samples, 50 were found to be WT. The other eight samples revealed a mixed genotype consisting of WT and type 1. The majority of the latter recovered on trimethoprim–sulfamethoxazole suggesting no clinical relevance for this mutation.
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Ali Ahmed Abdul-Kareem and Abdul-Kadhum Dakhil Raysan. "Effect of CAPN1 gene polymorphism on some physical and sensory traits in broiler meat." University of Thi-Qar Journal of agricultural research 11, no. 2 (November 3, 2022): 102–11. http://dx.doi.org/10.54174/utjagr.v11i2.188.
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This study was conducted in the poultry field, Animal Production Department, College of Agriculture and Marshes, University of Thi-Qar, from 10/11/2021 to 3/2/2022, the period included field and laboratory stud. A total of 100, one day broilers Ross 308 were used. Laboratory analyzes were carried out in the laboratories of the Marshes Research Center, University of Thi-Qar and the laboratories of the College of Agriculture and Marshes, University of Thi-Qar. Three genotypes CC, CT and TT were identified whose frequency was 0.52, 0.34 and 0.14 respectively and the frequency of the C allele was 0.69 and the frequency of the T allele was 0.31. There were significant differences on Water Holding Capacity (WHC) among the genotypes, the CC genotype was superior to the CT and TT genotypes. As for the thawing and cooking loss, there were no significant differences between the genotypes. A significant differences on pH values among the genotypes, the CC genotype was superior to the CT and TT genotypes. Significant differences in flavor between genotypes, the CC genotype was superior to the CT genotype, and the CT genotype was superior to the TT genotype. Highly significant differences in tenderness, the CC genotype was superior to the TT genotype, while the CT genotype did not differ significantly from the CC and TT genotypes. Highly significant differences between the genotypes in juiciness, the CC genotype was superior to the CT and TT genotypes. No significant differences in color and general acceptable.
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Rodrigues, Fabíola Brasil Barbosa, Rosilene da Silva, Erika Ferreira dos Santos, Mioni Thieli Figueiredo Magalhães de Brito, Andréa Luciana Soares da Silva, Mauro de Meira Leite, Flávia Póvoa da Costa, et al. "Association of Polymorphisms of IL-6 Pathway Genes (IL6, IL6R and IL6ST) with COVID-19 Severity in an Amazonian Population." Viruses 15, no. 5 (May 19, 2023): 1197. http://dx.doi.org/10.3390/v15051197.
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Interleukin-6 has been recognized as a major role player in COVID-19 severity, being an important regulator of the cytokine storm. Hence, the evaluation of the influence of polymorphisms in key genes of the IL-6 pathway, namely IL6, IL6R, and IL6ST, may provide valuable prognostic/predictive markers for COVID-19. The present cross-sectional study genotyped three SNPs (rs1800795, rs2228145, and rs7730934) at IL6. IL6R and IL6ST genes, respectively, in 227 COVID-19 patients (132 hospitalized and 95 non-hospitalized). Genotype frequencies were compared between these groups. As a control group, published data on gene and genotype frequencies were gathered from published studies before the pandemic started. Our major results point to an association of the IL6 C allele with COVID-19 severity. Moreover, IL-6 plasmatic levels were higher among IL6 CC genotype carriers. Additionally, the frequency of symptoms was higher at IL6 CC and IL6R CC genotypes. In conclusion, the data suggest an important role of IL6 C allele and IL6R CC genotype on COVID-19 severity, in agreement with indirect evidence from the literature about the association of these genotypes with mortality rates, pneumonia, and heightening of protein plasmatic levels pro-inflammatory driven effects.
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Saadawy, Sara F., Nermin Raafat, Walaa M. Samy, Ahmed Raafat, and Aliaa Talaat. "Role of Circ-ITCH Gene Polymorphisms and Its Expression in Breast Cancer Susceptibility and Prognosis." Diagnostics 13, no. 12 (June 12, 2023): 2033. http://dx.doi.org/10.3390/diagnostics13122033.
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Introduction/Objective: Breast cancer (BC) is the first leading cause of cancer-related mortality in females worldwide. We have investigated the correlation between circ-ITCH gene polymorphisms, circ-ITCH expression, and their effect on β-catenin levels and BC development. Methods: Participants included 62 BC and 62 controls matched in terms of age. The circ-ITCH polymorphisms rs10485505 and rs4911154 were genotyped using whole blood samples. In addition, mRNA expression analysis of circ-ITCH was performed on BC tissues. The β-catenin levels in serum samples were measured using ELISA. Results: The qRT-PCR results demonstrated that circ-ITCH was significantly downregulated in BC compared to normal healthy tissues. The genotype distribution of rs10485505 and rs4911154 were significantly associated with BC risk. For rs10485505, genotype CT and TT were significantly associated with an increased BC risk. In contrast, there was a significant association between rs4911154, genotypes GA and AA, and an increased BC risk. Regarding the rs10485505 genotype, carriers of the T allele frequently have a poor prognosis compared to carriers of the CC genotype. Serum β-catenin in the BC patients’ group was significantly higher than in the control group. The relative expression levels of circ-ITCH were remarkably decreased in the BC samples of patients carrying the A allele at rs4911154 compared to patients with a GG genotype. Conversely, β-catenin protein levels were increased in patients carrying the A allele, while rs10485505 genotype carriers of the CT and TT genotypes showed downregulation of circ-ITCH expression fold compared to the CC genotype. Contrarily, β-catenin levels markedly increased in TT and CT genotypes compared with the CC genotype. Conclusions: Our research showed that the rs10485505 polymorphism (T allele) and the rs4911154 polymorphism (A allele) are associated with the risk and prognosis of BC. This finding may be due to the effect on the level of circ-ITCH mRNA expression in BC tissues as well as the level of β-catenin in BC patients.
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Tripathi, Gaurav, Satya Narayan Sankhwar, Raj Kumar Sharma, Vinod Pandirikkal Baburaj, and Suraksha Agrawal. "Role of Thrombotic Risk Factors in End-Stage Renal Disease." Clinical and Applied Thrombosis/Hemostasis 16, no. 2 (June 10, 2009): 132–40. http://dx.doi.org/10.1177/1076029609335911.
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Introduction: Genetic polymorphisms that are found among factors of the coagulation cascade are factor V leiden mutation (FVL), prothrombin (PT), and methylenetetrahydrofolate reductase (MTHFR), reported for thrombotic complications. We have investigated the associations of these gene polymorphisms in patients with end-stage renal disease (ESRD). Methods: We genotyped 258 patients for FV G1691A, PT G20210A, and MTHFR (C677T, A1298C) gene by using polymerase chain reaction—restriction fragment length polymorphism (PCR-RFLP) analysis and were compared with 569 healthy controls. Serum folate, total homocysteine (tHcys), and vitamin B12 were measured in both patients with ESRD and controls. Results: No homozygous individuals for the mutant AA genotype of FVL G1691A were observed in this study. The frequency of the heterozygous genotypes was (11.2%), which was nearly 3 times higher than that observed in controls (3.2%), with a odds ratio of 3.87 (P = .0001, 95% CI = 2.11-7.11). PT G20210A mutation was missing in both patients and the controls. At MTHFR locus, TT genotype of C677T was present in 9.6% among ESRD, while CC genotype of A1298C was present in 11.7% of the ESRD. In control group, it was significantly low that is, 4.2% and 3.2%, respectively (P = .0034; OR = 2.44, 95% CI = 1.36-4.36 and P < .0001; OR = 4.03; 95% CI = 2.2-7.37). The combined analysis of the 2 genotypes showed further increased risk in ESRD ~15 folds. Further, the carrier of TT and CC genotypes of C677T and A1298C had significantly higher total homocysteine (tHcys) level than those with CC and AA genotypes (P < .001). Conclusion: The carrier of FVL, TT genotype of C677T, and CC genotype of A1298C polymorphisms may act as risk factors for ESRD.
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Akalin, Halis, Cüneyt Özakin, and Suna Gedikoğlu. "Epidemiology ofAcinetobacter baumanniiin a University Hospital in Turkey." Infection Control & Hospital Epidemiology 27, no. 4 (April 2006): 404–8. http://dx.doi.org/10.1086/503349.
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Objective.Molecular epidemiologic surveillance ofAcinetobacter baumanniiby polymerase chain reaction-randomly amplified polymorphic DNA analysis in a university hospital for 3 consecutive study periods.Results.Twelve differentAcinetobacter baumanniigenotypes (A-L) were detected. Although only 2 genotypes were detected during the first period and genotype A appeared to be the most common genotype, genotype D was included in these genotypes during the second study period. Genotype A completely disappeared during the third period. Although the presence of genotype C and the genotype D continued during the third period, 9 new genotypes were detected during this period. Genotype A appeared to be the most common genotype in the hospital (detected in 19 different clinics). The distribution of genotypes in clinical samples correlated with patient traffic between them. Some genotypes were found in both clinical and environmental samples. Seventeen different antibiotypes were detected, according to antibiotic susceptibility profiles.Conclusions.Environmental contamination, airborne transmission, patient transfer, and cross-contamination play important roles in epidemics caused byA. baumanniiin our hospital. The distribution of genotypes can change over time, so antibiotyping is not appropriate for the epidemiological analysis ofA. baumaniiinfection.
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YARYSHKIN, A. A., O. S. SHATALINA, and O. I. LESHONOK. "ASSOCIATIONS OF POLYMORPHIC VARIANTS OF THE SOMATOTROPINE GENE WITH ECONOMICALLY VALUABLE INDICATORS OF COWS." Izvestiâ Timirâzevskoj selʹskohozâjstvennoj akademii, no. 2 (2021): 60–70. http://dx.doi.org/10.26897/0021-342x-2021-2-60-70.
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Currently, marker genes are often used in dairy cattle breeding. Scientists are studying the relationship of gene polymorphism with such economically useful traits as milk productivity, productive longevity, growth, development, etc. The short period of the economic use of cows and the late intake of live weight necessary for insemination cause economic losses to agricultural organizations. The goal of the research was to study the relationship of the polymorphism of the somatotropin gene with live weight during the first insemination and productive longevity of cows. The study was conducted in the Sverdlovsk region on cattle of Holstein Black-Motley breed in 2018–2019. Two samples were formed: heifers and retired cows genotyped by the somatotropin gene. In animals, LV-somatotropin gene polymorphism was determined. The determination of polymorphism included the following steps: DNA isolation, polymerase chain reaction (PCR), restriction enzyme production, restriction products run on an agarose gel, visualization using a transilluminator. The research results were processed using IBM SPSS Statistics 23 software,and the reliability criterion was analyzed. LV-polymorphism is represented by three genotypes: LL,LV and VV. The authors studied the frequency of genotypes in the population of holsteinized cattle. It was revealed that the LL genotype is widely represented in the population – 77.2%, animals with the LV genotype are found more rarely – 22.2%. The VV genotype is extremely rare in the population – 0.6%. It was also revealed that the L allele is a common population allele – 88.3%. In the course of studying the relationship of LV polymorphism with live weight during the first insemination, it was found that animals with the LL genotype grow faster and reach the live weight necessary for fruitful insemination earlier. At the same age, heifers with the LV genotype had a mass of 400 kg, with those with the LL genotype – 9 kg more at p ≤ 0.01. When studying the effect of somatotropin gene genotypes on productive longevity, it was found that cows with the LV genotype have a longer economic use. The difference with peers with the LL genotype was 0.5 lactations at p ≤ 0.05. As a result of the studies, it can be concluded that the LL and LV genotypes are the desired option for the holsteinized cattle population. The LL genotype is associated with growth and development, and LV – with productive longevity.
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Al-Mathidy, Aamer Muhsen, Noor Nabeel Al-Talab, Muna Omar Shehab, and Kamal Benyamin Esho. "Identification study of Vicia faba genotypes based on seed properties and mineral content." Kufa Journal for Agricultural Sciences 16, no. 2 (June 11, 2024): 30–40. http://dx.doi.org/10.36077/kjas/2024/v16i2.10913.
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Abstract The presented research was conducted at Vegetable Research Farm, Horticulture and Landscape Design, Agriculture and Forestry College, Univ. of Mosul. The research examines the mineral concentration and protein in fifteen genotypes of faba bean, which were sowing under Mosul condition,using RCBD design with three replicates for each genotype. The result showed that the mineral element concentration was considerable variation amongst the genotypes; genotype (S 2009, 140) gave a high value in the number of seeds in each pod, while genotype (S 2008, 096) was supervised in seed diameter, genotype gave a high value in seed length. At the same time, the genotype (S 2009, 175) was supervise compared with the other genotypes under the study, in the other hand the genotype (S 2008, 034) gave the high value in the seed weight per plant, The genotype (S 2009, 140 ) supervised in Fepercentagewhich was given a high value (5.275%) comparative with the other genotypes, while the genotype (Aguadulce) gave high value in K percentage (4.1%), the genotype (S2009,40) supervised in Ca percentage (1.75%) comparative with the other genotypes under the study, in the other hand the genotypes (S 2009, 116, S 2009, 81,S 2008, 034) gave the zero (0.0%) percentage in Mn., while the genotype (S 2008, 096) gave the high value in Pb percentage (8.710%).The genotype (ILB 1814) was supervised in N percentage and protein, which were (4.9 and 30.625%) respectively. Key words:Faba bean, seed properties, Mineral element,protein
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Tabor, G. M., G. L. Tylka, and C. R. Bronson. "Genotypes A and B of Cadophora gregata Differ in Ability to Colonize Susceptible Soybean." Plant Disease 91, no. 5 (May 2007): 574–80. http://dx.doi.org/10.1094/pdis-91-5-0574.
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Growth chamber experiments were conducted to determine if extent of colonization of soybean stems by genotypes A and B of Cadophora gregata (Phialophora gregata), the causal agent of brown stem rot (BSR) of soybean, is similar in soybean plants resistant or susceptible to genotype A. Upon introduction of the two genotypes separately into the base of stems of 2-week-old seedlings, genotype A advanced with the growing tips of susceptible but not resistant genotypes. In contrast, genotype B did not advance with the growing tips of either resistant or susceptible soybean. In similar experiments, 5 weeks after introduction of genotype A, both mean percent stem length colonized by C. gregata and mean percentage of symptomatic trifoliate leaflets were significantly less for resistant than for susceptible genotypes. For genotype B, there was no or a slight difference between resistant and susceptible soybean genotypes in mean percent stem length colonized and no difference in mean percentage of symptomatic trifoliate leaflets 5 weeks after introduction of the pathogen. These results indicate that genotype A and genotype B differ not only in the severity of foliar symptoms they cause on genotype A-susceptible soybean plants, but also in how severely they colonize the stems of these soybean plants. In our experiments, genotype A and genotype B did not differ consistently in their ability to cause internal stem discoloration. The two genotypes of C. gregata can be distinguished based on how severely they colonize stems of genotype A-susceptible soybean. Thus, a BSR resistance screening method, which relies on assessment of stem colonization by C. gregata, works only for screening soybean lines resistance to genotype A. In light of these results, it is important to distinguish soybean resistance to genotype A versus genotype B of C. gregata. Whether genotype B causes yield loss and whether soybean plants can be distinguished as resistant or susceptible to genotype B needs to be investigated.
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Iwaszko, Milena, Jerzy Świerkot, Marta Dratwa, Barbara Wysoczańska, Lucyna Korman, Bartosz Bugaj, Katarzyna Kolossa, Sławomir Jeka, Piotr Wiland, and Katarzyna Bogunia-Kubik. "Association of MICA-129Met/Val polymorphism with clinical outcome of anti-TNF therapy and MICA serum levels in patients with rheumatoid arthritis." Pharmacogenomics Journal 20, no. 6 (March 3, 2020): 760–69. http://dx.doi.org/10.1038/s41397-020-0164-3.
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AbstractMHC class I polypeptide-related sequence A (MICA) is a stress-induced protein involved in activation of NK and T cells through interaction with NKG2D receptor. These molecules are atypically expressed in synovium of patients diagnosed with rheumatoid arthritis (RA). A total of 279 patients with RA, qualified to TNF-blockade therapy, were genotyped for MICA rs1051792 SNP. The effectiveness of anti-TNF agents was assessed with European League Against Rheumatism criteria. Significant relationship between MICA rs1051792 and outcome of TNF-blockade therapy has been found. The MICA rs1051792 GG genotype was overrepresented in patients non-responsive to anti-TNF drugs in comparison with other genotypes (p = 0.010). On the other hand, beneficial therapeutic response was more frequently detected among RA subjects possessing heterozygous genotype than those with homozygous genotypes (p = 0.003). Furthermore, increased MICA concentrations in serum were observed in patients possessing MICA rs1051792 GG genotype as compared with those with GA or AA genotypes (p = 1.8 × 10−5). The results from this study indicate the potential influence of MICA rs1051792 polymorphism on modulation of therapeutic response to TNF-blockade treatment in RA.