Journal articles on the topic 'Genotype II'
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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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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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Hashim, Amna, Marguerite Clyne, Grace Mulcahy, Donna Akiyoshi, Rachel Chalmers, and Billy Bourke. "Host Cell Tropism Underlies Species Restriction of Human and Bovine Cryptosporidium parvum Genotypes." Infection and Immunity 72, no. 10 (October 2004): 6125–31. http://dx.doi.org/10.1128/iai.72.10.6125-6131.2004.
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ABSTRACT It has been recognized recently that human cryptosporidiosis is usually caused by Cryptosporidium parvum genotype I (“human” C. parvum), which is not found in animals. Compared to C. parvum genotype II, little is known of the biology of invasion of the human-restricted C. parvum genotype I. The aims of the present study were (i) to explore and compare with genotype II the pathogenesis of C. parvum genotype I infection by using an established in vitro model of infection and (ii) to examine the possibility that host-specific cell tropism determines species restriction among C. parvum genotypes by using a novel ex vivo small intestinal primary cell model of infection. Oocysts of C. parvum genotypes I and II were used to infect HCT-8 cells and primary intestinal epithelial cells in vitro. Primary cells were harvested from human endoscopic small-bowel biopsies and from bovine duodenum postmortem. C. parvum genotype I infected HCT-8 cells with lower efficiency than C. parvum genotype II. Actin colocalization at the host parasite interface and reduction in levels of invasion after treatment with microfilament inhibitors (cytochalasin B and cytochalasin D) were observed for both genotypes. C. parvum genotype II invaded primary intestinal epithelial cells, regardless of the species of origin. In contrast, C. parvum genotype I invaded only human small-bowel cells. The pathogenesis of C. parvum genotype I differs from C. parvum genotype II. C parvum genotype I does not enter primary bovine intestinal cells, suggesting that the species restriction of this genotype is due to host tissue tropism of the infecting isolate.
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van der Kleij, Frank G. H., Paul E. de Jong, Rob H. Henning, Dick de Zeeuw, and Gerjan Navis. "Enhanced Responses of Blood Pressure, Renal Function, and Aldosterone to Angiotensin I in the DD Genotype Are Blunted by Low Sodium Intake." Journal of the American Society of Nephrology 13, no. 4 (April 2002): 1025–33. http://dx.doi.org/10.1681/asn.v1341025.
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ABSTRACT. Angiotensin-converting enzyme (ACE) activity is increased in the DD genotype, but the functional significance for renal function is unknown. Blunted responses of BP and proteinuria to ACE inhibition among DD renal patients during periods of high sodium intake were reported. It was therefore hypothesized that sodium status affects the phenotype in the ACE I/D polymorphism. The effects of angiotensin I (AngI) and AngII among 27 healthy subjects, with both low (50 mmol sodium/d) and liberal (200 mmol sodium/d) sodium intakes, were studied. Baseline mean arterial pressure (MAP) values, renal hemodynamic parameters, and renin-angiotensin system parameters were similar for all genotypes with either sodium intake level. With liberal sodium intake, the increases in MAP, renal vascular resistance, and aldosterone levels during AngI infusion (8 ng/kg per min) were significantly higher for the DD genotype, compared with the ID and II genotypes (all parameters presented as percent changes ± 95% confidence intervals), with mean MAP increases of 22 ± 2% (DD genotype), 13 ± 5% (ID genotype), and 12 ± 6% (II genotype) (P < 0.05), mean increases in renal vascular resistance of 100.1 ± 19.7% (DD genotype), 73.0 ± 16.3% (ID genotype), and 63.2 ± 16.9% (II genotype) (P < 0.05), and increases in aldosterone levels of 650 ± 189% (DD genotype), 343 ± 71% (ID genotype), and 254 ± 99% (II genotype) (P < 0.05). Also, the decrease in GFR was more pronounced for the DD genotype, with mean decreases of 17.9 ± 4.7% (DD genotype), 8.8 ± 3.4% (ID genotype), and 6.4 ± 5.9% (II genotype) (P < 0.05). The effective renal plasma flow, plasma AngII concentration, and plasma renin activity values were similar for the genotypes. In contrast, with low sodium intake, the responses to AngI were similar for all genotypes. The responses to AngII were also similar for all genotypes, with either sodium intake level. In conclusion, the responses of MAP, renal hemodynamic parameters, and aldosterone concentrations to AngI are enhanced for the DD genotype with liberal but not low sodium intake. These results support the presence of gene-environment interactions between ACE genotypes and dietary sodium intake.
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Wu, Zhiliang, Isao Nagano, Thidarut Boonmars, Takumi Nakada, and Yuzo Takahashi. "Intraspecies Polymorphism of Cryptosporidium parvum Revealed by PCR-Restriction Fragment Length Polymorphism (RFLP) and RFLP-Single-Strand Conformational Polymorphism Analyses." Applied and Environmental Microbiology 69, no. 8 (August 2003): 4720–26. http://dx.doi.org/10.1128/aem.69.8.4720-4726.2003.
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ABSTRACT A glycoprotein (Cpgp40/15)-encoding gene of Cryptosporidium parvum was analyzed to reveal intraspecies polymorphism within C. parvum isolates. Forty-one isolates were collected from different geographical origins (Japan, Italy, and Nepal) and hosts (humans, calves, and a goat). These isolates were characterized by means of DNA sequencing, PCR-restriction fragment length polymorphism (PCR-RFLP), and RFLP-single-strand conformational polymorphism (RFLP-SSCP) analyses of the gene for Cpgp40/15. The sequence analysis indicated that there was DNA polymorphism between genotype I and II, as well as within genotype I, isolates. The DNA and amino acid sequence identities between genotypes I and II differed, depending on the isolates, ranging from 73.3 to 82.9% and 62.4 to 80.1%, respectively. Those among genotype I isolates differed, depending on the isolates, ranging from 69.0 to 85.4% and 54.8 to 79.2%, respectively. Because of the high resolution generated by PCR-RFLP and RFLP-SSCP, the isolates of genotype I could be subtyped as genotypes Ia1, Ia2, Ib, and Ie. The isolates of genotype II could be subtyped as genotypes IIa, IIb, and IIc. The isolates from calves, a goat, and one Japanese human were identified as genotype II. Within genotype II, the isolates from Japan were identified as genotype IIa, those from calves in Italy were identified as genotype IIb, and the goat isolate was identified as genotype IIc. All of the genotype I isolates were from humans. The Japanese isolate (code no. HJ3) and all of the Nepalese isolates were identified as genotypes Ia1 and Ia2, respectively. The Italian isolates were identified as genotype Ib, and the Japanese isolate (code no. HJ2) was identified as genotype Ie. Thus, the PCR-RFLP-SSCP analysis of this glycoprotein Cpgp40/15 gene generated a high resolution that has not been achieved by previous methods of genotypic differentiation of C. parvum.
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Nevrkla, Pavel, Zdeněk Hadaš, Pavel Horký, and Vendula Kamanová. "Effect of Genotype and Sex of Piglets on Their Losses Before Weaning." Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis 65, no. 3 (2017): 893–97. http://dx.doi.org/10.11118/actaun201765030893.
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The aim of the experiment was to analyze selected reproductive characteristics in sows and losses of piglets according to their age and to evaluate the effect of sex on survivability of piglets before weaning. The experimental observation involved 80 sows with their second litters (40 sows of genotye I and 40 sows of genotype II). The sows were mated with a boar of Danish Duroc. No significant difference was found between the evaluated genotypes of sows in numbers of live‑born piglets and reared piglets, however it is evident that better results were reached by the sows of the genotype II. Also the losses of piglets per litter were lower, by 0.65 piece (P ≤ 0.05). In sows of the genotype I a high correlation (P ≤ 0.01) was confirmed between the number of live‑born piglets and the number of reared piglets per litter (r = 0.750). Another correlation was found between the number of live‑born piglets and their losses before weaning (r = 0.716). Similar trend was observed in the genotype II, however without significant correlation between the number of live‑born piglets and the losses of piglets before weaning. The results also revealed that the piglets died mostly before the 14th day of age, while the losses of male piglets were more frequent than of female piglets. Losses of female piglets of the genotype I before the 14th day of age were 6.82 %, in the genotype II they were 3.01 %. In this period, the losses of male piglets reached 9.56 % in the genotype I and 4.49 % in the genotype II. From the 14th day to weaning the losses of female piglets counted 2.39 % vs. 0.75 %, the losses of male piglets 1.37 % vs. 2.88 %. The total losses from birth to weaning were 9.22 % vs. 3.76 % in female piglets and 10.92 % vs. 7.37 % in male piglets.
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Hernandez, Jonathan R., Shuling Liu, Chris L. Fredregill, and Patricia V. Pietrantonio. "Impact of the V410L kdr mutation and co-occurring genotypes at kdr sites 1016 and 1534 in the VGSC on the probability of survival of the mosquito Aedes aegypti (L.) to Permanone in Harris County, TX, USA." PLOS Neglected Tropical Diseases 17, no. 1 (January 23, 2023): e0011033. http://dx.doi.org/10.1371/journal.pntd.0011033.
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Harris County, TX, is the third most populous county in the USA and upon detection of arboviruses Harris County Public Health applies insecticides (e.g., pyrethroid-based Permanone 31–66) against adults of Culex quinquefasciatus to prevent disease transmission. Populations of Aedes aegypti, while not yet a target of public health control, are likely affected by pyrethroid exposure. As this species is a vector of emerging arboviruses, its resistance status to Permanone and the kdr mutations in the voltage-gated sodium channel (VGSC) associated with pyrethroid resistance were investigated. We examined females of known genotype at the V1016I and F1534C sites (N = 716) for their genotype at the 410 amino acid position in the VGSC, and for the influence of their kdr genotype on survival to Permanone at three different distances from the insecticide source in field tests. Most females (81.8%) had at least one resistant L allele at the 410 position, being the first report of the V410L mutation in Ae. aegypti for Texas. When only genotypes at the 410 position were analyzed, the LL genotype exhibited higher survivorship than VL or VV. Out of 27 possible tri-locus kdr genotypes only 23 were found. Analyses of the probability of survival of tri-locus genotypes and for the V410L genotype using a multivariate logistic regression model including area, distance, and genotype found significant interactions between distance and genotype. When only the most common tri-locus genotypes were analyzed (LL/II/CC, 48.2%; VL/II/CC, 19.1%; and VV/II/CC, 10.1%) genotype had no effect on survival, but significant interactions of distance and genotype were found. This indicated that the V410L kdr allele increased survival probability at certain distances. Genotypes did not differ in survivorship at 7.62-m, but LL/II/CC had higher survivorship than VL/II/CC at 15.24- and 22.86-m. The model also identified differences in survivorship among the operational areas investigated.
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Persson, Karin, Annette C. E. Säfholm, Rolf G. G. Andersson, and Johan Ahlner. "Glyceryl trinitrate-induced angiotensin-converting enzyme (ACE) inhibition in healthy volunteers is dependent on ACE genotype." Canadian Journal of Physiology and Pharmacology 83, no. 12 (December 2005): 1117–22. http://dx.doi.org/10.1139/y05-118.
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Evidence concerning the importance of angiotensin-converting enzyme (ACE) genotype in cardiovascular diseases is accumulating. The aim of this study was to investigate if nitric oxide (NO), generated from glyceryl trinitrate (GTN), affects human serum ACE activity in vivo, and if so, whether this effect was dependent on ACE genotype and (or) reflected in blood pressure reduction. A tablet containing 5 mg GTN was bucally administered for 5 minutes to 17 healthy volunteers. Blood pressure (BP) was recorded, and serum ACE activity, ACE genotype, and plasma cGMP was analyzed. GTN administration significantly reduced BP only in individuals with the deletion/deletion (DD) genotype. Sixty minutes after GTN administration, serum ACE activity was reduced in individuals with the insertion/insertion (II) and insertion/deletion (ID) genotypes, but not the DD genotype. Comparing the change in ACE activity over time between the genotypes resulted in the following: II vs. DD, p < 0.01; II vs. ID, p < 0.05; and ID vs. DD, p < 0.05. There was no significant difference in plasma cGMP content neither between the ACE genotypes nor before and after GTN administration. In conclusion, GTN inhibits serum ACE in vivo in individuals with the II and ID, but not the DD genotype.
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Reed, Carrie, Gregory D. Sturbaum, Paul J. Hoover, and Charles R. Sterling. "Cryptosporidium parvum Mixed Genotypes Detected by PCR-Restriction Fragment Length Polymorphism Analysis." Applied and Environmental Microbiology 68, no. 1 (January 2002): 427–29. http://dx.doi.org/10.1128/aem.68.1.427-429.2002.
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ABSTRACT Combinations of 10 Cryptosporidium parvum oocysts, with various ratios of genotype I to genotype II, were isolated and subjected to PCR-restriction fragment length polymorphism analysis. Amplification of both genotypes in these samples ranged from 31 to 74% and yielded no information about the genotype proportions. In addition, since both genotypes were not always detected, amplification of a single genotype is not conclusive evidence that the sample contains only a single genotype.
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Kruzliak, Peter, Gabriela Kovacova, Olga Pechanova, and Stefan Balogh. "Association between Angiotensin II Type 1 Receptor Polymorphism and Sudden Cardiac Death in Myocardial Infarction." Disease Markers 35 (2013): 287–93. http://dx.doi.org/10.1155/2013/731609.
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Objective. The renin-angiotensin system is involved in the pathogenesis of coronary artery disease and myocardial infarction (MI). Angiotensin II (Ang II) has many adverse effects such as vasoconstriction and vascular remodeling, and these actions are mediated by the angiotensin II type 1 receptor (AT1R).Patients and Methods. A total of 1376 patients were recruited from January 2010 to April 2012. The study group consisted of 749 patients with ACS (317 females and 432 males) and of 627 healthy controls.Results. The ACS patients demonstrated a lower proportion of AA genotypes and AC genotypes but higher proportions of CC genotypes than the control population. The AT1R CC genotype conferred a 2.76-fold higher risk of MI compared with the genotype AC and AA. In addition, the CC genotype was also associated with a 4.08 times higher risk of left anterior descending artery infarction and a 3.07 times higher risk of anterior wall infarction. We also found that the CC genotype was independently associated with sudden cardiac death.In Summary. This study demonstrated that the AT1R CC genotype is an independent risk factor for ACS incidence, and this genotype is associated with a greater ACS severity and greater risk of sudden cardiac death.
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Ivaniushina, Valeria, Nadjia Radjef, Marfa Alexeeva, Elyanne Gault, Sergei Semenov, Mohammed Salhi, Oleg Kiselev, and Paul Dény. "Hepatitis delta virus genotypes I and II cocirculate in an endemic area of Yakutia, Russia." Journal of General Virology 82, no. 11 (November 1, 2001): 2709–18. http://dx.doi.org/10.1099/0022-1317-82-11-2709.
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Currently, three genotypes of hepatitis delta virus (HDV) are described. The most common, genotype I, has a worldwide distribution; in contrast, genotype II has been found previously only in Japan and Taiwan, while genotype III is found exclusively in South America. Considering the high prevalence of HDV in Northern Siberia (Russia), restriction fragment length polymorphism (RFLP) was used to analyse HDV genotypes from 29 infected patients living in Yakutia. Of these isolates, 11 were characterized by partial nucleotide sequencing and two isolates were completely sequenced. Phylogenetic inference methods included maximum parsimony, maximum likelihood and distance analyses. A restriction pattern consistent with HDV genotype I was found in 14 samples, while the remaining 15 showed a different restriction pattern, inconsistent with any known genotype. Five Yakutian HDV isolates with the type I restriction pattern were sequenced and confirmed to be affiliated with genotype I, although the phylogenetic results indicate that they were heterogeneous and did not cluster together. Sequencing of eight isolates with the new RFLP pattern revealed that these isolates were most closely related to HDV genotype II. In contrast to HDV Yakutian genotype I sequences, all of these type II sequences formed a well-defined clade on phylogenetic trees. Comparison of clinical presentations during hospitalization between patients infected with HDV type I (n=14) and type II (n=15) did not reveal any differences in the severity of infection. These data indicate that the distribution of genotype II is not restricted to Taiwan or Japan, but spreads over Northern Asia, appearing in the native population of Yakutia. Type II Yakutian strains appeared to form a well-defined subclade and could be associated with severe chronic hepatitis in this area.
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Bujdoso, Geza, Benjamin Illes, Virag Varjas, and Klara Cseke. "Is “Esterhazy II”, an Old Walnut Variety in the Hungarian Gene Bank, the Original Genotype?" Plants 10, no. 5 (April 23, 2021): 854. http://dx.doi.org/10.3390/plants10050854.
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The old walnut (Juglans regia L.) genotype called “Esterhazy II” was well-known in the Austro-Hungarian Monarchy before World War II, and it can still be found in the Austrian, German and Swiss backyard gardens today. Unfortunately, nowadays, vegetatively propagated progenies of the original “Esterhazy II” are not available anymore around the world because walnut grafting started later than this genotype had become well-known. Although various accessions with “Esterhazy II”-“blood“ are available, it is difficult to determine which one can be considered true or the most similar to the original one. In this paper, phenological and nut morphological characteristics of an “Esterhazy II” specimen planted in a Hungarian gene bank were compared to the varieties “Milotai 10” and “Chandler”. Examined characteristics were: budbreak, blossom time, type of dichogamy, ripening time, nut and kernel features. An additional SSR fingerprinting was used to identify identical genotypes and to demonstrate the relatedness of the analyzed “Esterhazy II” genotype to the other Hungarian walnut cultivars. It can be concluded that under the name “Esterhazy II”, several different genotypes can be observed. All the checked characteristics except budbreak fitted well with the previous descriptions. Our results confirmed that the examined “Esterhazy II” genotype shows high similarity to the “original“ “Esterhazy II” described in the literature.
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Gull, Dwain D., Peter J. Stoffella, Salvador J. Locascio, Steve M. Olson, Herbert H. Bryan, Paul H. Everett, Teresa K. Howe, and John W. Scott. "Stability Differences among Fresh-market Tomato Genotypes: II. Fruit Quality." Journal of the American Society for Horticultural Science 114, no. 6 (November 1989): 950–54. http://dx.doi.org/10.21273/jashs.114.6.950.
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Abstract Ten fresh-market tomato (Lycopersicon esculentum Mill.) genotypes were evaluated for stability of fruit firmness, citric acid, soluble solids, β-carotene and ascorbic acid concentrations, sugar : acid ratio, color, N content, and dry weight when grown in nine environments. Linear relationships between the genotype means for a given trait and the mean for the trait in each environment were used as an indicator of stability. A stable genotype for a given trait was considered to possess a regression coefficient (b1) ⩽ a coefficient of linear determination (r2) > 0.50, a genotype mean above the grand mean (mean of all genotypes), and a nonsignificant deviation from regression mean square (S2d). Using these criteria, stability in the nine environments was shown by the fruits of the various cultivars as follows: ‘Flora-Dade’, ‘FTE-12’, and D76I27 for firmness; ‘Castlehy 1035’ and ‘Sunny’ for citric acid; ‘Walter’ for soluble solids concentration; ‘FTE-12’ for ascorbic acid concentration; ‘Hayslip’, ‘Walter’, and ‘Burgis’ for sugar : acid ratio; ‘FTE-12’ and ‘Hayslip’ for β-carotene concentration: ‘Flora-Dade’ and 827115-IBK for color a/b; ‘Castlehy 1035’ and ‘Hayslip’ for dry weight; and ‘Walter’ for N content. Stable genotypes are less sensitive to environmental changes and are more adapted to favorable and unfavorable conditions than unstable genotypes. No genotype was found to be stable for every fruit quality trait in the nine environments. Stability of fruit quality characteristics should be considered in tomato breeding programs to develop genotypes adapted to diverse environmental and management conditions.
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Panko, N. "P75 Relation between polymorphism of folic acid cycle genes and effectiveness of methotrexate in children with juvenile idiopathic arthritis." Archives of Disease in Childhood 104, no. 6 (May 17, 2019): e48.1-e48. http://dx.doi.org/10.1136/archdischild-2019-esdppp.113.
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BackgroundMethotrexate (MTX) is the basic treatment of patient with Juvenile Idiopathic Arthritis (JIA), but effectiveness of this therapy is different. We aimed to study effectiveness of MTX in children with JIA with different genotypes of folic acid cycle genes.MethodsThe study included 8 patients with JIA. For determination of MTX effectiveness the American College of Rheumatology pediatric criteria (ACR-pedi) was used. Patients were divided into 2 groups according the effectiveness of MTX treatment. Group I included 4 patients, who were non-responders because ACR-pedi was less than 10%. Second group contained 4 patients, who had ACR-pedi more than 10%. The megerment of genotypes of genes of folate cycle, such as 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR), 5-methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR), 5,10methylenetetrahydrofolate reductase C677T and A1298C variants (MTHFR-677 and MTHFR129) by polymerase chain reaction (PCR) was performed for all patients.ResultsIn II group effectiveness of therapy according ACR-pedi was from 30% to 70% in 75% of children and more then 70% - in 25% of patients. In general, MTR gene indicated AA-genotype in 50% of patients, AG and GG-genotypes - in 25%; MTRR gene was performed with AA-genotype in 25%, AC-genotype in 12.5% and CC-genotype in 62.5%. MTHFR1298 gene was presented in 50% of patients with AA-alleles, in 25% - with AC and CC-genotypes. 50% of children had CC-genotype of MTHFR677 gene and other 50% - AC-genotype of MTHFR677 gene. CC-genotype of MTHFR1298 gene more frequently was determined in II group (p< 0.01). In group of non-responders AA-genotype of MTR gene was found more frequent in comparison with patients from group II (p< 0.01).ConclusionResponse to standard therapy in patients with JIA depends on time of prescription of MTX and genotype of MTHFR1298 and MTR genes.Disclosure(s)Nothing to disclose
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Fathi, Mehrangiz, and Ghorban Elyasi-Zarringhobaie. "Association of polymorphisms in the promoter region of turkey prolactin with egg performance." Genetika 46, no. 2 (2014): 591–99. http://dx.doi.org/10.2298/gensr1402591f.
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The induction and regulation of broodiness is of the most important role of prolactin in avian species. In this study, the association between prolactin promoter region alleles and reproductive traits in Fars native turkey was investigated. These traits consisted of mean egg weight (MEW), number of egg (EN) and egg mass, during the first laying period. In total, 115 laying turkeys, randomly selected from the flock of the Breeding Center for Fars Native turkey, and DNA was purificated from blood samples, 231 bp of prolactin promoter region was amplified and Genotype of Samples was determinate by PCR-SSCP technique were genotyped. Two alleles D and I were identified. Based on the results obtained, the frequency of D and I alleles were 0.67 and 0.33, respectively. Frequencies of DD, II and ID genotypes were 0.385, 0.044 and 0.571, respectively. The association analysis between the polymorphism PRL gene promoter region and egg performance was carried out. Significant relationship was found between genotypes with egg production (P<0.01). Individuals with II genotype produced higher egg production than DD and ID genotype. The results of current study showed that using information of genes related to egg production could be used to improve the performance of native turkey of East Azerbaijan province.
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Alves, Cléber Rene, Tiago Fernandes, José Ribeiro Lemos, Flávio de Castro Magalhães, Ivani Credidio Trombetta, Guilherme Barreto Alves, Glória de Fátima Alves da Mota, et al. "Aerobic exercise training differentially affects ACE C- and N-domain activities in humans: Interactions with ACE I/D polymorphism and association with vascular reactivity." Journal of the Renin-Angiotensin-Aldosterone System 19, no. 2 (April 9, 2018): 147032031876172. http://dx.doi.org/10.1177/1470320318761725.
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Introduction: Previous studies have linked angiotensin-converting enzyme ( ACE) insertion (I)/deletion (D) polymorphism (II, ID and DD) to physical performance. Moreover, ACE has two catalytic domains: NH2 (N) and COOH (C) with distinct functions, and their activity has been found to be modulated by ACE polymorphism. The aim of the present study is to investigate the effects of the interaction between aerobic exercise training (AET) and ACE I/D polymorphism on ACE N- and C-domain activities and vascular reactivity in humans. Materials and methods: A total of 315 pre-selected healthy males were genotyped for II, ID and DD genotypes. Fifty completed the full AET (II, n = 12; ID, n = 25; and DD, n = 13), performed in three 90-minute sessions weekly, in the four-month exercise protocol. Pre- and post-training resting heart rate (HR), peak O2 consumption (VO2 peak), mean blood pressure (MBP), forearm vascular conduction (FVC), total circulating ACE and C- and N-domain activities were assessed. One-way ANOVA and two -way repeated-measures ANOVA were used. Results: In pre-training, all variables were similar among the three genotypes. In post-training, a similar increase in FVC (35%) was observed in the three genotypes. AET increased VO2 peak similarly in II, ID and DD (49±2 vs. 57±1; 48±1 vs. 56±3; and 48±5 vs. 58±2 ml/kg/min, respectively). Moreover, there were no changes in HR and MBP. The DD genotype was also associated with greater ACE and C-domain activities at pre- and post-training when compared to II. AET decreased similarly the total ACE and C-domain activities in all genotypes, while increasing the N-domain activity in the II and DD genotypes. However, interestingly, the measurements of N-domain activity after training indicate a greater activity than the other genotypes. These results suggest that the vasodilation in response to AET may be associated with the decrease in total ACE and C-domain activities, regardless of genotype, and that the increase in N-domain activity is dependent on the DD genotype. Conclusions: AET differentially affects the ACE C- and N-domain activities, and the N-domain activity is dependent on ACE polymorphism.
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Cutrín, J. M., J. L. Barja, B. L. Nicholson, I. Bandín, S. Blake, and C. P. Dopazo. "Restriction Fragment Length Polymorphisms and Sequence Analysis: an Approach for Genotyping Infectious Pancreatic Necrosis Virus Reference Strains and Other Aquabirnaviruses Isolated from Northwestern Spain." Applied and Environmental Microbiology 70, no. 2 (February 2004): 1059–67. http://dx.doi.org/10.1128/aem.70.2.1059-1067.2004.
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ABSTRACT Reference strains of infectious pancreatic necrosis virus resembling the 10 recognized serotypes and local isolates of aquabirnaviruses isolated in northwestern Spain from reservoirs (mollusks) and from asymptomatic and carrier cultured fish were genotyped by restriction fragment length polymorphism (RFLP) and nucleic acid sequence analyses. The RFLP analysis yielded seven genogroups, each of which was clearly correlated with a serotype. Sequence analysis of the three open reading frames provided quite similar results in terms of genogrouping. Based on the results of this study and in order to unify the two types of assays, we propose placing aquabirnaviruses into six genogroups, four of which can be subdivided into two genotypes based on a two-step restriction analysis. The genotyping corresponds with serotyping as follows: genogroup I includes two genotypes corresponding to serotypes A9 (genotype I.1) and A1 (genotype I.2); genogroup II corresponds to serotype A3; genogroup III includes genotypes III.1 (serotype A2) and III.2 (serotype B1); genogroups IV and V include two genotypes, each corresponding to serotypes A5, A6, A7, and A8 (genotypes IV.1, IV.2, V.1, and V.2, respectively);and genogroup VI corresponds to serotype A4. As expected, most local isolates belonged to genotype III.1 and genogroup II. However, a few local isolates corresponded to the American types of genogroup I. Finally, based on the results of this study and due to its simplicity, the two-step restriction analysis assay is proposed as a method for typing new isolates of aquabirnaviruses, and the results correspond to the results of conventional serotyping.
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Wang, Yuyan, Biao Zhang, Lei Hou, Wei Han, Fang Xue, Yanhong Wang, Yong Tang, et al. "Interaction of ACE genotype and salt intake on hypertension among Chinese Kazakhs: results from a population-based cross-sectional study." BMJ Open 7, no. 5 (May 2017): e014246. http://dx.doi.org/10.1136/bmjopen-2016-014246.
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ObjectivesTo explore the effect of interaction between ACE genotype and salt intake on hypertension among Chinese Kazakhs, and to compare applications of interactions between logistic model and generalised partially linear tree-based regression (GPLTR) model.DesignPopulation-based cross-sectional study.SettingHong Dun, North Xinjiang, China.ParticipantsNon-consanguineous Chinese Kazakh participants (n=916, 342 men and 574 women) aged ≥30 years.Main outcome measuresAssociation between ACE genotype and hypertension, association between salt intake and hypertension, and interaction of ACE genotype and salt intake on hypertension in two models.ResultsAssociations between salt intake and hypertension were different in ACE genotype of II and ID+DD. Under the logistic models, main and interaction effects were not observed for men, but effects were present in opposite directions for women (main effect of ACE: OR=0.20, p=0.003; interaction effect: OR=1.07, p=0.027). Under the GPLTR model, Bayesian information criterion trees included both salt intake and ACE genotype as split variables. Individuals with a salt intake ≥19.5 g/day and ID+DD genotypes had a 3.99-fold (p=0.004) higher risk of hypertension compared with the II genotype for men, whereas salt intake <20.1 g/day and ID+DD genotypes had an OR=0.55 (p=0.014) compared with the II genotype for women.ConclusionsAn interaction of ACE genotype and salt intake on hypertension was observed among Chinese Kazakhs but in different ways according to sex. The GPLTR model appears to be more suitable for an exploration of interactions in complex diseases.
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Varney, V. A., A. Warner, A. Ghosh, A. Nicholas, and N. Sumar. "IgE-Mediated Anaphylaxis to Foods, Venom, and Drugs: Influence of Serum Angiotensin Converting Enzyme Levels and Genotype." Journal of Allergy 2012 (December 19, 2012): 1–9. http://dx.doi.org/10.1155/2012/258145.
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Circulating angiotensin-II protects the circulation against sudden falls in blood pressure and is generated by the enzymatic action of angiotensin converting enzyme (ACE) on angiotensin-I. The ACE genes have 2 allelic forms, “I” and “D.” The “D” genotype has both highest angiotensin-II generation and serum ACE levels compared to “I”. 120 patients with IgE-anaphylaxis, 119 healthy controls, and 49 atopics had serum ACE levels, ACE genotype, and renin levels determined. Plasma renin levels were identical for all groups. Serum ACE levels and genotypes were similar for healthy controls (HC) and atopics, but lower in anaphylaxis (), with ACE genotypes also showing increased “I” genes (). This effect was more pronounced in subjects manifesting airway angioedema and cardiovascular collapse (AACVS) than mild cutaneous and respiratory (CRA) symptoms. AACVS was significantly associated with the presence of “I” genes. For “ID” genotype OR is 5.6, 95% CI 1.8 to 17.4, and for “II” genotype OR is 44, 95% CI 5 to 1891 within the anaphylaxis group = 0.001. The results show a difference in the genotype frequency between control and anaphylaxis, suggesting a role for the renin angiotensin system in anaphylaxis manifesting with airway angioedema and cardiovascular collapse.
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Hsu, Sheng-Chieh, Jaw-Ching Wu, I.-Jane Sheen, and Wan-Jr Syu. "Interaction and Replication Activation of Genotype I and II Hepatitis Delta Antigens." Journal of Virology 78, no. 6 (March 15, 2004): 2693–700. http://dx.doi.org/10.1128/jvi.78.6.2693-2700.2004.
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ABSTRACT The nucleotide sequences of hepatitis D viruses (HDV) vary 5 to 14% among isolates of the same genotype and 23 to 34% among different genotypes. The only viral-genome-encoded antigen, hepatitis delta antigen (HDAg), has two forms that differ in size. The small HDAg (HDAg-S) trans-activates viral replication, while the large form (HDAg-L) is essential for viral assembly. Previously, it has been shown that the packaging efficiency of HDAg-L is higher for genotype I than for genotype II. In this study, the question of whether other functional properties of the HDAgs are affected by genotype differences is addressed. By coexpression of the two antigens in HuH-7 cells followed by specific antibody precipitation, it was found that HDAgs of different origins interacted without genotypic discrimination. Moreover, in the presence of hepatitis B virus surface antigen, HDAg-S was incorporated into virion-like particles through interaction with HDAg-L without genotype restriction. As to the differences in replication activation of genotype I HDV RNA, all HDAg-S clones tested had some trans-activation activity, and this activity varied greatly among isolates. As to the support of HDV genotype II replication, only clones of HDAg-S from genotype II showed trans-activation activity, and this activity also varied among isolates. In conclusion, genotype has no effect on HDAg interaction and genotype per se only partly predicts how much the HDAg-S of an HDV isolate affects the replication of a second HDV isolate.
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Mu'in, Muhammad Affan, and Sintje Lumatauw. "Heritabilitas Produki Telur Ayam Lokal Papua Berbeda Genotip dari Lokus 24- bp Insertion-Deletion dalam Promotor Gen Prolaktin." Jurnal Ilmu Peternakan dan Veteriner Tropis (Journal of Tropical Animal and Veterinary Science) 11, no. 2 (July 30, 2021): 137. http://dx.doi.org/10.46549/jipvet.v11i2.161.
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The heritability (h2) of a trait shows phenotypes variance of the trait caused by additive genetic variance. The h2 value is used to estimate the quantitative trait breeding value of livestock in order to improve these traits through selection. This study aims to estimate the h2 of egg production characteristics in Papua local chickens with different genotypes from the 24-bp InDel (Insertion-Deletion) locus in the prolactin gene promoter region (24-bp InDel/cPRLp locus). A total of 13 pairs of Papua local chickens consisting of 3 pairs of II genotypes (♂II x ♀II) and 11 female offspring, 5 pairs of ID genotypes (♂ID x ♂ID) and 19 female offspring, and 5 pairs of DD genotypes (DD x ♀DD) and 17 female offspring were used in this study. Observations were made on the characteristics of egg production in female offspring of each genotype group. The variance component for h2 estimation is obtained by the one-way analysis of variance method and the separation of the variance components for single pairs. The results showed that the h2 at first laying of eggs in all genotype groups was moderate (0.10 to 0.30); the h2 of the number of eggs produced from the time they first laid eggs until the age of 240 days in II and ID genotype groups was high (> 0.3), while in the DD genotype group was classified as moderate (0.10 to 0.30); and the h2 of egg weight in all genotype groups was moderate (0.10 to 0.30). The high h2 of a trait indicates that the trait is more dominated by additive genes and is more responsive to the selection treatment.
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Aaskov, John, Katie Buzacott, Emma Field, Kym Lowry, Alain Berlioz-Arthaud, and Edward C. Holmes. "Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient." Journal of General Virology 88, no. 12 (December 1, 2007): 3334–40. http://dx.doi.org/10.1099/vir.0.83122-0.
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Between 2000 and 2004, dengue virus type 1 (DENV-1) genotypes I and II from Asia were introduced into the Pacific region and co-circulated in some localities. Envelope protein gene sequences of DENV-1 from 12 patients infected on the island of New Caledonia were obtained, five of which carried genotype I viruses and six, genotype II viruses. One patient harboured a mixed infection, containing viruses assigned to both genotypes I and II, as well as a number of inter-genotypic recombinants. This is the first report of a population of dengue viruses isolated from a patient containing both parental and recombinant viruses.
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Zhou, Ling, Hailu Kassa, Monica L. Tischler, and Lihua Xiao. "Host-Adapted Cryptosporidium spp. in Canada Geese (Branta canadensis)." Applied and Environmental Microbiology 70, no. 7 (July 2004): 4211–15. http://dx.doi.org/10.1128/aem.70.7.4211-4215.2004.
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ABSTRACT The prevalence and distribution of Cryptosporidium spp. in the fecal droppings of the free-living waterfowl Canada geese were examined at 13 sites in Ohio and Illinois. On the basis of the analysis of the small-subunit rRNA gene by PCR, followed by restriction fragment length polymorphism analysis and DNA sequencing, 49 (23.4%) of 209 fecal specimens collected from 10 sites (76.9%) were positive for Cryptosporidium spp. The following five Cryptosporidium species and genotypes were identified: Cryptosporidium goose genotype I (in 36 specimens), Cryptosporidium goose genotype II (in 9 specimens), Cryptosporidium duck genotype (in 1 specimen), Cryptosporidium parvum (in 4 specimens), and C. hominis (in 2 specimens). Cryptosporidium goose genotype I was the most prevalent parasite and was found at all five Cryptosporidium-positive sites in Ohio and at four of five positive sites in Illinois, followed by Cryptosporidium goose genotype II, which was found at two of five positive sites in Ohio and at four of five positive sites in Illinois. Cryptosporidium goose genotype II was detected for the first time, and it is phylogenetically related to goose genotype I and the duck genotype. All three genotypes have not so far been reported in humans, and their pathogenicity in geese has not been determined. Only 10.2% of the Cryptosporidium-positive specimens had C. parvum and C. hominis. The results of this study indicate that Canada geese might only serve as accidental carriers of cryptosporidia infectious to humans and probably play a minor role in the animal-to-human transmission cycle of the pathogen.
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Araújo, Irene Trigueiros, Marcos Bryan Heinemann, Joana D'Arc P. Mascarenhas, Rosane M. Santos Assis, Alexandre Madi Fialho, and José Paulo G. Leite. "Molecular analysis of the NSP4 and VP6 genes of rotavirus strains recovered from hospitalized children in Rio de Janeiro, Brazil." Journal of Medical Microbiology 56, no. 6 (June 1, 2007): 854–59. http://dx.doi.org/10.1099/jmm.0.46787-0.
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Group A rotaviruses are the main cause of acute gastroenteritis in children throughout the world. The two outer capsid proteins, VP4 and VP7, define the P and G genotypes, respectively. Rotaviruses with P[8]G1, P[4]G2, P[8]G3 and P[8]G4 genotypes are predominant in infecting humans and the G9 genotype is emerging in most continents as the fifth most common G type worldwide. The inner capsid protein VP6 is responsible for subgroup (SG) specificities, allowing classification of rotaviruses into SG I, SG II, SG I+II and SG non-I-non-II. The non-structural protein 4 (NSP4) encoded by segment 10 has a role in viral morphogenesis and five genetic groups have been described, NSP4 genotypes A–E. The aim of this investigation was to characterize the NSP4 and VP6 genes of rotavirus strains recovered from hospitalized children. Thirty rotavirus strains were submitted to RT-PCR followed by sequencing and phylogenetic analysis. Among the different G and P genotype combinations, two distinct genetic groups could be recognized for the NSP4 gene. Twenty-eight clustered with NSP4 genotype B. The two P[4]G2 strains fell into NSP4 genotype A and clustered distinctly, with a 100 % bootstrap value. The strains distinguished within a group were closely related to each other at the nucleotide and amino acid levels. A phylogenetic tree was constructed for the VP6 gene including the human strains RMC100, E210, Wa, US1205 and 1076, and the animal strains Gott, NCDV, SA-11, FI-14 and EW. This is the first report on Brazilian rotavirus strains describing NSP4 genotype A strains associated with VP6 SG I, and NSP4 genotype B strains associated with VP6 SG II.
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Ito, Takafumi, Jun Kurita, Motohiko Sano, Helle Frank Skall, Niels Lorenzen, Katja Einer-Jensen, and Niels Jørgen Olesen. "Typing of viral hemorrhagic septicemia virus by monoclonal antibodies." Journal of General Virology 93, no. 12 (December 1, 2012): 2546–57. http://dx.doi.org/10.1099/vir.0.043091-0.
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Seven mAbs with specific reaction patterns against each of the four genotypes and eight subtypes of viral hemorrhagic septicemia virus (VHSV) were produced, aiming to establish an immunoassay for typing VHSV isolates according to their genotype. Among the mAbs, VHS-1.24 reacted with all genotypes except genotype Ie, whilst mAb VHS-9.23 reacted with all genotypes except genotype III. mAb VHS-3.80 reacted with genotypes Ib, Ic, Id and II. mAb VHS-7.57 reacted with genotypes II and IVa, and mAb VHS-5.18 with genotype Ib only. Interestingly, mAb VHS-3.75 reacted with all of the genotype III isolates except a rainbow trout-pathogenic isolate from the west coast of Norway, and reacted in addition with the IVb isolate, CA-NB00-01, from the east coast of the USA. Finally, mAb VHS-1.88 reacted with all genotype IVb isolates from the Great Lakes, but not with CA-NB00-01. In conclusion, we can distinguish between all four genotypes and between five of eight subtypes of VHSV by testing isolates in immunoassay using a panel of nine mAbs. By Western blotting and transfection of cell cultures, it was shown that mAb VHS-1.24 recognized an epitope on the viral phosphoprotein (P), whilst all others recognized antigenic determinants on the nucleoprotein (N). From amino acid alignments of the various genotypes and subtypes of VHSV isolates, it was possible to determine the epitope specificity of mAb VHS-1.24 to be aa 32–34 in the P-protein; the specificities of mAbs VHS-3.80, VHS-7.57 and VHS-3.75 were found to be aa 43 and 45–48, aa 117 and 121, and aa 103, 118 and 121 of the N-protein, respectively.
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Dengel, Donald R., Michael D. Brown, Robert E. Ferrell, Thomas H. Reynolds, and Mark A. Supiano. "Exercise-induced changes in insulin action are associated with ACE gene polymorphisms in older adults." Physiological Genomics 11, no. 2 (October 29, 2002): 73–80. http://dx.doi.org/10.1152/physiolgenomics.00048.2002.
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We evaluated the association between insulin resistance and the angiotensin-converting enzyme (ACE) insertion (I)/deletion (D) gene polymorphism in a group of older hypertensive subjects (63 ± 1 yr, n = 35) before and after a 6-mo aerobic exercise program (AEX). Insulin sensitivity index (SI), assessed by the frequently sampled intravenous glucose tolerance test, was significantly ( P = 0.0001) increased following AEX. In addition, there was a significant ( P = 0.001) interaction between AEX and ACE genotype. SI increased significantly ( P < 0.05) more in those with the II (2.5 ± 0.8 μU × 10−4 · min−1 · ml−1) ACE genotype compared with both the DD and ID (0.7 ± 0.1 and 0.7 ± 0.2 μU × 10−4 · min−1 · ml−1, respectively) ACE genotypes. Similarly, there was a significant ( P = 0.036) decrease in the acute insulin response to glucose (AIRG) and a significant ( P = 0.05) interaction between AEX and ACE genotype. AIRG decreased significantly ( P < 0.05) more in those with the II (−17.6 ± 5.6 mU/ml) ACE genotype compared with both the DD and ID (−1.4 ± 6.2 and −3.6 ± 2.5 mU/ml) ACE genotypes. In conclusion, we demonstrated that those older hypertensives with the ACE II genotype have the greatest improvement in insulin action following AEX.
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LINDSTRÖM, I., N. SUNDAR, J. LINDH, F. KIRONDE, J. D. KABASA, O. C. H. KWOK, J. P. DUBEY, and J. E. SMITH. "Isolation and genotyping ofToxoplasma gondiifrom Ugandan chickens reveals frequent multiple infections." Parasitology 135, no. 1 (September 25, 2007): 39–45. http://dx.doi.org/10.1017/s0031182007003654.
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SUMMARYThe genetic make-up of an infectingToxoplasma gondiistrain may be important for the outcome of infection and the risk of reactivation of chronic disease. In order to survey the distribution of different genotypes within an area, free-range chickens act as a good model species. In this study 85 chickens were used to investigate the prevalence, genotype and mouse virulence ofT. gondiiin Kampala, Uganda. Antibodies were detected in 40 chickens, of which 20 had MAT-titres of 1:20 or higher and were also positive by PCR. Genotyping of 5 loci (SAG1, SAG2, SAG3, BTUB and GRA6) showed that 6 strains belonged to genotype I, 8 to Type II and 1 to Type III. Five chickens had multiple infections; 3 individuals with Type I plus Type II and a further 2 harbouring Types I, II and III. Isolates were obtained from 9 chickens via bioassay in mice, 6 were Type II strains and 3 were from animals with mixed infection. This is the first set of AfricanT. gondiistrains to be genotyped at multiple loci and in addition to the 3 predominant lineages we found a small number of new polymorphisms and a high frequency of multiple infections.
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Zhou, Qin, Yu-feng Gao, Xiao-miao Zhao, Fa-ming Pan, and Xu Li. "Single Nucleotide Polymorphisms rs2227284, rs2243283 and rs2243288 in the IL-4 Gene Show no Association with Susceptibility to Chronic Hepatitis B in a Chinese Han Population." Infection International 3, no. 1 (March 1, 2014): 16–21. http://dx.doi.org/10.1515/ii-2017-0068.
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Abstract Objective To investigate the relationship between single nucleotide polymorphisms (SNPs) of the interleukin-4 (IL-4) gene and outcome of hepatitis B virus (HBV) infection in a Chinese Han population. Methods Total of 501 patients with chronic hepatitis B virus (HBV) infection and 301 controls with selflimiting HBV infection were studied. Three tag SNPs in the IL-4 gene (rs2227284G/T, rs2243283C/G and rs2243288A/G) were genotyped by the Multiplex snapshot technique. The genotype and allele frequencies were calculated and analyzed. Results The three SNPs showed no significant genotype/allele associations with chronic HBV infection. Overall allele P values were: rs2227284, P = 0.655, odds ratio (OR) [95% confidence interval (CI)] = 1.070 (0.793-1.445); rs2243283, P = 0.849, OR (95% CI) = 0.976 (0.758-1.257); rs2243288, P = 0.659, OR (95% CI) = 1.060 (0.818-1.375). Overall genotype P values were: rs2227284, P = 0.771; rs2243283, P = 0.571; rs2243288, P = 0.902. There were no statistically significant differences between patients with chronic HBV infection and controls. Haplotypes generated by these three SNPs also had no significant differences between the two groups. Conclusions The three tag SNPs of IL-4 were not associated with the outcome of HBV infection in the Han Chinese population.
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Wang, Huan Yu, Tomohiko Takasaki, Shi Hong Fu, Xiao Hong Sun, Hai Lin Zhang, Zhao Xiao Wang, Zong Yu Hao, et al. "Molecular epidemiological analysis of Japanese encephalitis virus in China." Journal of General Virology 88, no. 3 (March 1, 2007): 885–94. http://dx.doi.org/10.1099/vir.0.82185-0.
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Sixty-two new Japanese encephalitis virus (JEV) isolates were obtained from mosquitoes, biting midges, human cerebrospinal fluid and human blood samples in China during 2002–2005. The E and prM genes were sequenced and phylogenetic analyses were performed with 38 JEV other isolates from China and 36 JEV strains from other countries. Phylogenetic trees based on the E and prM gene sequences were similar. The results indicate that: (i) recent JEV isolates from China are divided into two genotypes, genotype 1 and genotype 3; (ii) recent JEV isolates from China are grouped into the same clusters within genotypes 1 and 3; and (iii) genotype 1 JEV strains have been isolated in China since 1979, whilst genotype 3 JEV strains were isolated before the 1970s. The results suggest that genotype 1 JEV was introduced to China around 1979 and that JEV strains belonging to genotypes 1 and 3 circulate in China.
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Akhter, Asma, Mahwish Javed, and Muhammad Imran. "Comparative Analysis of PCR and LIPA Method for HCV Genotypes Screening." BioScientific Review 01, no. 04 (December 2019): 29–38. http://dx.doi.org/10.32350/bsr.0104.04.
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Background: Hepatitis C virus (HCV) is a major health problem worldwide. About 6% of the population of Pakistan is suffering from HCV infection. HCV has a high mutation rate and consists of seven genotypes and sixty-seven subtypes. Genotype information of patients infected with HCV is significant for its treatment. Methods: In this study, 416 HCV serum samples were collected and HCV prevalence rate was studied in different districts of Punjab, Pakistan. Nested PCR and INNO LIPA HCV-II were used for HCV genotyping and their respective performance was evaluated. This study was conducted by the approval of Lahore Clinical Laboratory and Research Centre situated at Shadman, Lahore. Results: The highest prevalence of HCV was found in Shekhupura district followed by Bhakkar, Narowal and Okara districts, respectively. In Punjab, the most prevalent genotype was 3a (70.29%), followed by genotype 1 (5.47%), untypable genotypes (5.44%) and genotype 3a/3b (4.64%). Nested PCR was found to be more reliable than INNO LIPA-II. Nested PCR results were more accurate and only 5 samples remained untypable whereas 33 samples could not be typed by LIPA method. Conclusion: This study was focused on the comparative analysis of Nested PCR and LIPA method for screening HCV genotypes and their prevalence in different districts of Punjab, Pakistan. HCV genotyping is important since different genotypes require different therapeutic treatments. In Punjab, 3a is the most prevalent genotype followed by non-typable genotypes. LIPA is the most commonly used HCV genotype assay but this study found Nested PCR to be a highly sensitive and cost-effective method in this regard. This study can lead to the better selection of genotyping methods and treatment.
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Cheng, Saipeng, Huiguang Wu, and Zhenhai Chen. "Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective." International Journal of Molecular Sciences 21, no. 21 (October 24, 2020): 7898. http://dx.doi.org/10.3390/ijms21217898.
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Transmissible gastroenteritis virus (TGEV) is a coronavirus associated with diarrhea and high mortality in piglets. To gain insight into the evolution and adaptation of TGEV, a comprehensive analysis of phylogeny and codon usage bias was performed. The phylogenetic analyses of maximum likelihood and Bayesian inference displayed two distinct genotypes: genotypes I and II, and genotype I was classified into subtypes Ia and Ib. The compositional properties revealed that the coding sequence contained a higher number of A/U nucleotides than G/C nucleotides, and that the synonymous codon third position was A/U-enriched. The principal component analysis based on the values of relative synonymous codon usage (RSCU) showed the genotype-specific codon usage patterns. The effective number of codons (ENC) indicated moderate codon usage bias in the TGEV genome. Dinucleotide analysis showed that CpA and UpG were over-represented and CpG was under-represented in the coding sequence of the TGEV genome. The analyses of Parity Rule 2 plot, ENC-plot, and neutrality plot displayed that natural selection was the dominant evolutionary driving force in shaping codon usage preference in genotypes Ia and II. In addition, natural selection played a major role, while mutation pressure had a minor role in driving the codon usage bias in genotype Ib. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses suggested that genotype I might be more adaptive to pigs than genotype II. Current findings contribute to understanding the evolution and adaptation of TGEV.
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Koskinen, Maarit K., Johanna Lempainen, Eliisa Löyttyniemi, Olli Helminen, Anne Hekkala, Taina Härkönen, Minna Kiviniemi, et al. "Class II HLA Genotype Association With First-Phase Insulin Response Is Explained by Islet Autoantibodies." Journal of Clinical Endocrinology & Metabolism 103, no. 8 (December 28, 2017): 2870–78. http://dx.doi.org/10.1210/jc.2017-02040.
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Abstract Context A declining first-phase insulin response (FPIR) is characteristic of the disease process leading to clinical type 1 diabetes. It is not known whether reduced FPIR depends on class II human leukocyte antigen (HLA) genotype, islet autoimmunity, or both. Objective To dissect the role of class II HLA DR-DQ genotypes and biochemical islet autoantibodies in the compromised FPIR. Design, Setting, Participants A total of 438 children with defined HLA DR-DQ genotype in the prospective Finnish Type 1 Diabetes Prediction and Prevention Study were analyzed for FPIR in a total of 1149 intravenous glucose tolerance tests and were categorized by their HLA DR-DQ genotype and the number of biochemical islet autoantibodies at the time of the first FPIR. Age-adjusted hierarchical linear mixed models were used to analyze repeated measurements of FPIR. Main Outcome Measure The associations between class II HLA DR-DQ genotype, islet autoantibody status, and FPIR. Results A strong association between the degree of risk conferred by HLA DR-DQ genotype and positivity for islet autoantibodies existed (P < 0.0001). FPIR was inversely associated with the number of biochemical autoantibodies (P < 0.0001) irrespective of HLA DR-DQ risk group. FPIR decreased over time in children with multiple autoantibodies and increased in children with no biochemical autoantibodies (P < 0.0001 and P = 0.0013, respectively). Conclusions The class II HLA DR-DQ genotype association with FPIR was secondary to the association between HLA and islet autoimmunity. Declining FPIR was associated with positivity for multiple islet autoantibodies irrespective of class II HLA DR-DQ genotype.
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Jackson, R. E., J. R. Bradley, and J. W. Van Duyn. "Performance of Feral and Cry1Ac-Selected Helicoverpa zea (Lepidoptera: Noctuidae) Strains on Transgenic Cottons Expressing One or Two Bacillus thuringiensis ssp. kurstaki Proteins Under Greenhouse Conditions." Journal of Entomological Science 39, no. 1 (January 1, 2004): 46–55. http://dx.doi.org/10.18474/0749-8004-39.1.46.
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Efficacy of Bollgard (DP50B) and Bollgard II (DP50BX) cottons that express either one or two Bacillus thuringiensis Berliner proteins, respectively, along with the conventional sister genotype (DP50), was determined for a feral strain of bollworm, Helicoverpa zea (Boddie), and a Cry1Ac-selected bollworm strain in 1999. In 2000, a greenhouse study was designed to compare the efficacy of three transgenic cottons expressing either the Cry1Ac endotoxin alone (DP50B), the Cry2Ab endotoxin alone (DP50X), or both the CrylAc and Cry2Ab endotoxins (DP50BX) against a feral and a Cry1Ac-selected bollworm strain. Results from the 1999 greenhouse study evaluating both a feral and a Cry1Ac-selected bollworm strain demonstrated that when averaged across bollworm strains, the Bollgard II genotype significantly reduced larval survival and fruit penetration by bollworm compared to the Bollgard variety. Also, the Cry1Ac-selected bollworm strain displayed increased larval survival, superficial fruit damage, and fruit penetration compared to the feral strain when averaged across genotypes. In the 2000 study, the Bollgard II genotype significantly reduced fruit penetration by bollworm below that of the Bollgard variety when averaged across strains; however, the single Cry2Ab-producing genotype performed similarly to both Bollgard and Bollgard II with respect to fruit penetration. The Cry1Ac-selected bollworm strain exhibited significantly greater larval survival and superficial fruit damage on the Bollgard variety compared to the feral strain, but no differences among larval strains were evident for other genotypes. Also, when averaged across genotypes, the Cry1Ac-selected bollworm strain penetrated a higher proportion of cotton fruit compared to the feral strain. These results suggest that commercialization of Bollgard II cottons would significantly reduce bollworm survival and damage compared to that experienced by current Bollgard varieties. Bollgard II plantings also should have a positive impact on Bt resistance management of bollworm.
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Han, Mi-Soon, Yongjung Park, and Hyon-Suk Kim. "Comparison of Abbott RealTime genotype II, GeneMatrix restriction fragment mass polymorphism and Sysmex HISCL HCV Gr assays for hepatitis C virus genotyping." Clinical Chemistry and Laboratory Medicine (CCLM) 55, no. 8 (July 26, 2017): 1122–28. http://dx.doi.org/10.1515/cclm-2016-0130.
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AbstractBackground:Hepatitis C virus (HCV) genotype is a predictive marker for treatment response. We sequentially evaluated the performances of two nucleic acid amplification tests (NAATs) and one serology assay for HCV genotype: Abbott RealTimegenotype II (RealTimeII), GeneMatrix restriction fragment mass polymorphism (RFMP), and Sysmex HISCL HCV Gr (HISCL Gr).Methods:We examined 281 clinical samples with three assays. The accuracy was assessed using the HCV Genotype Performance Panel PHW204 (SeraCare Life Sciences) for two NAATs. Discrepant cases were re-genotyped by the Versant HCV v.2.0 (line probe 2.0) assay.Results:With the RealTimeII assay, clinic samples were analyzed as follows: genotypes 1b (43.1%), 2 (40.2%), 1 subtypes other than 1a and 1b (12.5%), 3 (1.8%), 4 (1.4%), 1a (0.7%), 6 (0.4%), and mixed (1.1%). The RealTimeII and RFMP assays showed a type concordance rate of 97.5% (274/281) (κ=0.80) and no significant discordance (p=0.25). Both assays accurately genotyped all samples in the Performance Panel by the subtype level. The HISCL Gr assay showed concordance rates of about 91% (κ<0.40) and statistically significant discordances with two NAATs (p<0.05). In confirmation tests, the results of RFMP assay were the most consistent with those of Versant 2.0 assay.Conclusions:The three HCV assays provided genotyping and serotyping results with good concordance rates. The two NAATs (RealTimeII and RFMP) showed comparable performance and good agreement. However, the results of the HISCL Gr assay showed statistically significant differences with those of the NAATs.
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Stene-Johansen, Kathrine, Tom Øystein Jonassen, and Kjell Skaug. "Characterization and genetic variability of Hepatitis A virus genotype IIIA." Journal of General Virology 86, no. 10 (October 1, 2005): 2739–45. http://dx.doi.org/10.1099/vir.0.81155-0.
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Molecular epidemiological studies of hepatitis A outbreaks in Norway showed the emergence of Hepatitis A virus (HAV) genotype IIIA in association with parenteral transmission among haemophiliacs and intravenous drug users. The complete genomic sequence of one of these outbreak isolates, NOR-21, was determined. This is the first complete genomic sequence of HAV genotype IIIA. Phylogenetic analysis showed that genotype IIIA/NOR-21 was genetically distinct from the other human and simian genotypes. Phylogenetic analysis of the nucleotide sequences clearly distinguished the different HAV genotypes, regardless of the genomic region used for analysis, whereas the amino acid sequences showed a more vague distinction between human HAV genotypes I and II. In particular, the inferred phylogeny based on the capsid proteins showed that the human HAV strains were related more closely to each other than to the simian strains. The greatest variability and clearest distinction between genotypes were observed for the polymerase gene. The outbreak isolates of HAV genotype IIIA in this study showed greater nucleotide variability than is generally seen in outbreaks of genotype I. This high nucleotide variability, which may be characteristic of this HAV genotype, the mode of transmission in this outbreak or parallel introductions, is discussed.
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Zhou, Wen-Sheng, Ai-Lun Yang, Chiao-Nan Chen, Nai-Wen Kan, Joanna Ting-Hui Kuo, Lee-Hwa Chen, and Kuei-Yu Chien. "Effects of Acute Aquatic High-Intensity Intermittent Exercise on Blood Pressure and Arterial Stiffness in Postmenopausal Women with Different ACE Genotypes." International Journal of Environmental Research and Public Health 19, no. 15 (July 23, 2022): 8985. http://dx.doi.org/10.3390/ijerph19158985.
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The present study investigated the effects of acute aquatic high-intensity intermittent jumping (HIIJ) on blood pressure (BP) and arterial stiffness in postmenopausal women with different angiotensin-converting enzyme genotypes (ACE). We recruited 12 postmenopausal women carrying the ACE deletion/deletion (DD) genotype and 61 carrying the insertion/insertion or insertion/deletion (II/ID) genotype. The participants performed 12 trials of 30 s, 75% heart rate reserve (HRR) jumping, and 60 s, 50% HRR recovery, and 3 trials of 40 s upper limb resistance exercises were performed as fast as possible. The heart rate (HR) and BP were measured before exercise, immediately, 10 min, and 45 min after exercise. The brachial-ankle pulse wave velocity (baPWV) was measured before and after exercise. The systolic blood pressure (SBP) of the DD genotype increased more significantly than those with the II/ID genotype post-exercise (30.8 ± 4.48 vs. 20.4 ± 2.00 mmHg, p = 0.038). The left and right sides of baPWV increased significantly after exercise (1444.8 ± 29.54 vs. 1473.4 ± 32.36 cm/s, p = 0.020; 1442.1 ± 30.34 vs. 1472.0 ± 33.09, p = 0.011), and there was no significant difference between the two groups. The HIIJ increased baPWV. The postmenopausal women with the DD genotype have a higher SBP increased post-exercise than those with II/ID genotype. These findings suggest that the aquatic exercise program has better effects in decreasing blood pressure in postmenopausal women with the II/ID genotype. Those with the DD genotype should pay attention to the risk of increasing blood pressure after aquatic HIIJ exercise.
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Chen, Han-chun, Yan-fei Cao, Wei-xin Hu, Xin-fa Liu, Qing-xia Liu, Ji Zhang, and Jia Liu. "Genetic Polymorphisms of Phase II Metabolic Enzymes and Lung Cancer Susceptibility in a Population of Central South China." Disease Markers 22, no. 3 (2006): 141–52. http://dx.doi.org/10.1155/2006/436497.
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A case-control study was conducted for analyzing the genetic polymorphisms of phase II metabolic enzymes in 97 patients with lung cancer and 197 healthy subjects from Han ethnic group of Hunan Province located in Central South China. The results showed that the frequencies of glutathione S-transferase (GST) M1-null (GSTM1-) or GSTT1-null (GSTT1-) genotype alone, or combined form of both in lung cancer patients were significantly higher than those of the controls. Genotypes of combining GSTP1 mutant/GSTM1(-) or GSTP1 mutant/GSTT1(-) led to high risk of lung cancer. Individuals carrying any two or all three of GSTM1(-), GSTT1(-) and GSTP1 mutant genotypes have a distinctly increased risk of lung cancer when compared to those with GSTM1 present (GSTM1+: GSTM1+/+ or GSTM1+/−), GSTT1 present (GSTT1+: GSTT1+/+ or GSTT1+/−) and GSTP1 wild genotypes. Furthermore, individuals possessing combined genotypes of N-acetyltransferase 2 (NAT2) rapid acetylator, GSTP1 mutant and both GSTT1(-) and GSTM1(-) have a remarkably higher lung cancer risk than those carrying combined NAT2 slow acetylator genotype, GSTP1 wild genotype and both GSTT1(+) and GSTM1(+) genotypes. All these findings suggest that the genetic polymorphisms of phase II metabolic enzymes affect the susceptibility of lung cancer in the Han ethnic group of Central South China.
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Szalai, Klaudia, Károly Tempfli, Erika Lencsés-Varga, and Ágnes Bali Papp. "Single nucleotide polymorphism analysis in meat-production related genes in broiler chickens." Acta Agraria Debreceniensis, no. 75 (December 28, 2018): 79–82. http://dx.doi.org/10.34101/actaagrar/75/1650.
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In broiler chickens, the intensive selection for growth rate, feed efficiency, body composition (breast muscle weight) traits in the last decades was successful. To improve economically important characteristics, it is possible to use molecular markers associated with meat production traits. The aim of this study was to examine genotype polymorphisms in ROSS 308 broilers for thyroid hormone responsive Spot14α, insulinlike growth factor 1 (IGF1), IGF-binding protein 2 (IGFBP2), somatostatin (SST) and prolactin (PRL) genes. A further goal of this investigation was to study the relationship between the polymorphisms and phenotypic characteristics.
In the investigated broiler population, the frequency for CC homozygous genotype was 0.77 in Spot14α (AY568628), AA homozygous genotype was 0.80 in IGF1 (M74176), GG homozygous genotype was 0.85 in IGFBP2 (U15086), DD homozygous genotype was 0.60 in PRL (FJ663023 or FJ434669). Only the AA homozygous genotype was found in SST (X60191). Chickens with AC genotype in Spot14α, and with GG genotype in IGFBP2 had higher body weight (BW) and carcass weight (CW), compared to CC and GT genotypes. However, the differences were not significant (P>0.05). There was significant association (P<0.05) between PRL genotypes and body and carcass weight, where chicken with homozygous DD surpassed individuals with homozygous II genotypes.
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Benton, Michael J., and Sheldon I. Guttman. "Allozyme Genotype and Differential Resistance to Mercury Pollution in the Caddisfly, Nectopsyche albida. II. Multilocus Genotypes." Canadian Journal of Fisheries and Aquatic Sciences 49, no. 1 (January 1, 1992): 147–49. http://dx.doi.org/10.1139/f92-017.
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While a number of papers document that sensitivity to pollution is correlated with single-locus genotype, only one has addressed associations with multilocus complexes. We exposed larval caddisflies, Nectopsyche albida, to inorganic mercury and recorded individual times to death, genetically characterized each individual at six polymorphic loci by starch gel electrophoresis, and tested the effects of multilocus genotype on time to death. Two two-locus complexes and two three-locus complexes were significantly correlated with survival time. This supports earlier studies that monitoring multilocus and single-locus genotype frequencies may be useful in detecting and measuring environmental impacts; however, we disagree that variation in survival time among genotypes per se supports selectionist theory, because no heritability of resistance has been demonstrated. We also disagree that enzyme systems not exhibiting such variation are nonadaptive and discuss how the elimination of sensitive multilocus genotypes may hinder population persistence.
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Hernandez, Jonathan R., Michael Longnecker, Chris L. Fredregill, Mustapha Debboun, and Patricia V. Pietrantonio. "Kdr genotyping (V1016I, F1534C) of the Nav channel of Aedes aegypti (L.) mosquito populations in Harris County (Houston), Texas, USA, after Permanone 31–66 field tests and its influence on probability of survival." PLOS Neglected Tropical Diseases 15, no. 11 (November 4, 2021): e0009833. http://dx.doi.org/10.1371/journal.pntd.0009833.
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Aedes aegypti (L.) is an important mosquito vector of emerging arboviruses such as Zika, dengue, yellow fever, and chikungunya. To quell potential disease outbreaks, its populations are controlled by applying pyrethroid insecticides, which selection pressure may lead to the development of insecticide resistance. Target site insensitivity to pyrethroids caused by non-synonymous knockdown resistance (kdr) mutations in the voltage-gated sodium (NaV) channel is a predominant mechanism of resistance in mosquitoes. To evaluate the potential impact of pyrethroid resistance on vector control, Ae. aegypti eggs were collected from eight mosquito control operational areas in Harris County, Texas, and emerged females were treated in field tests at four different distances from the pyrethroid Permanone 31–66 source. The females were genotyped by melting curve analyses to detect two kdr mutations (V1016I and F1534C) in the NaV channel. Harris County females had higher survivorship rates at each distance than the pyrethroid-susceptible Orlando strain females. Survivorship increased with distance from the pyrethroid source, with 39% of field-collected mosquitoes surviving at 7.62 m and 82.3% at 22.86 m from the treatment source. Both the V1016I and F1534C pyrethroid resistant genotypes were widely distributed and at high frequency, with 77% of the females being double homozygous resistant (II/CC), this being the first report of kdr mutations in Ae. aegypti in Harris County. Analysis of the probability of survival for each mutation site independently indicated that the CC genotype had similar probability of survival as the FC heterozygous, while the II genotype had higher survival than both the VI and VV, that did not differ. The double homozygous resistant genotype (II/CC) had the highest probability of survival. A linear model estimated probability of survival for areas and genotypes. The high frequency and widespread distribution of double-homozygote pyrethroid-resistant Ae. aegypti may jeopardize disease vector control efforts in Harris County.
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Aydin-Yüce, Tünay, Gina Kurscheid, Hagen Sjard Bachmann, Thorsten Gehrke, Marcel Dudda, Markus Jäger, Christian Wedemeyer, and Max Daniel Kauther. "No Association of CALCA Polymorphisms and Aseptic Loosening after Primary Total Hip Arthroplasty." BioMed Research International 2018 (June 5, 2018): 1–7. http://dx.doi.org/10.1155/2018/3687415.
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Studies of aseptic loosening showed an influence of calcitonin andα-CGRP, both encoded from the calcitonin/α-CGRP (CALCA) gene by alternative splicing. The aim of this study was to detect a possible association of the CALCA polymorphisms P1(rs1553005), P2(rs35815751), P3(rs5240), and P4(rs2956) with the time to aseptic loosening after THA. 320 patients suffering from aseptic loosening after primary total hip arthroplasty were genotyped for CALCA-P1 polymorphism and 161 patients for CALCA-P2 and CALCA-P3 polymorphisms and 160 patients for CALCA-P4 polymorphism. CALCA genotypes were determined by polymerase chain reaction and restriction-fragment length polymorphism. The genotype distribution of CALCA-P1 was CC 10%, CT 43%, and 46% TT. CALCA-P2 showed a distribution of 90.7%II, 8.7% ID, and 0.6% DD. The CALCA-P3 genotype distribution was 97.5% TT and 2.5% TC. The CALCA-P4 genotype distribution was 48.1% AA, 40% AT, and 11.9% TT. Significant differences between the CALCA genotypes were not found concerning age at implantation and replantation, BMI, gender, and cementation technique. No associations of the time for aseptic loosening were found. In conclusion, we did not find a significant association of CALCA polymorphisms and the time to aseptic loosening after primary THA in a Western European group.
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Martínez-Laso, Jorge, Angela Román, Miriam Rodriguez, Isabel Cervera, Jacqueline Head, Iciar Rodríguez-Avial, and Juan J. Picazo. "Diversity of the G3 genes of human rotaviruses in isolates from Spain from 2004 to 2006: cross-species transmission and inter-genotype recombination generates alleles." Journal of General Virology 90, no. 4 (April 1, 2009): 935–43. http://dx.doi.org/10.1099/vir.0.007807-0.
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Rotavirus evolves by using multiple genetic mechanisms which are an accumulation of spontaneous point mutations and reassortment events. Other mechanisms, such as cross-species transmission and inter-genotype recombination, may be also involved. One of the most interesting genotypes in the accumulation of these events is the G3 genotype. In this work, six new Spanish G3 sequences belonging to 0–2-year-old patients from Madrid were analysed and compared with 160 others of the same genotype obtained from humans and other host species to establish the evolutionary pathways of the G3 genotype. The following results were obtained: (i) there are four different lineages of the G3 genotype which have evolved in different species; (ii) Spanish G3 rotavirus sequences are most similar to the described sequences that belong to lineage I; (iii) several G3 genotype alleles were reassigned as other G genotypes; and (iv) inter-genotype recombination events in G3 viruses involving G1 and G2 were described. These findings strongly suggest multiple inter-species transmission events between different non-human mammalian species and humans.
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Nusifera, Sosiawan, and Agung Kurniawan. "Analisis Stabilitas Hasil Ubi 27 Genotipe Bengkuang (Pachyrhizus erosus L. Urban) di Jatinangor Jawa Barat Berdasarkan Model AMMI." Buletin Plasma Nutfah 14, no. 1 (October 7, 2016): 19. http://dx.doi.org/10.21082/blpn.v14n1.2008.p19-25.
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<p>Research aimed at estimating yield stability of 27 yam bean (Pachyrhizus erosus L. Urban) genotypes in Jatinangor was conducted at dry and rain seasons at the experimental station of Faculty of Agriculture Unpad, Jatinangor. Field trials at dry season was started from February to August 2006 and at rain season started from November 2006 to May 2007. Field plot consisted of four sets arranged in Randomized Block Design with 27 genotypes collected from various Indonesia regions and its ancestor from Central and South America as treatment and replicated twice. The four field trial sets were differed based on season and reproductive pruning treatment and considered as four different environment. Character observed was tuber weight per plant (g). Data was analysed with AMMI (additive main effect and multiplicative interaction). Result indicated that B-23/EC040 was highest yielding genotype, but less stable. In contrast, B-33/J, B-26/NS, B-10/EC550, and B-94/ENT were moderate yielded but had higher level of stability. Environment IV (rain season; pruning) was good environment where genotypic variation seemed more consistent with B-23/EC040 as best genotype. Best genotype in discriminating environment (I) was B-55/CJ, and in environment II was B-80/ENT. Whereas in Less discriminating environment III, B-15/EC104 was the best genotype</p><p><strong>Abstrak</strong></p><p>Penelitian yang bertujuan untuk mengetahui stabilitas hasil dari 27 genotipe bengkuang (Pachyrhizus erosus L. Urban) telah dilakukan pada musim kemarau dan musim hujan di Kebun Percobaan Fakultas Pertanian Unpad, Jatinangor. Percobaan pada musim kemarau berlangsung sejak Februari-Agustus 2006 dan percobaan pada musim hujan berlangsung sejak November 2006-Mei 2007. Percobaan terdiri atas empat set, masing-masing disusun dalam rancangan acak kelompok dengan 27 genotipe bengkuang yang dikoleksi dari berbagai wilayah Indonesia dan genotipe leluhurnya dari Amerika Tengah dan Selatan sebagai perlakuan dan diulang dua kali. Empat set percobaan tersebut dibedakan berdasarkan kombinasi musim dan perlakuan pemangkasan sink reproduktif, atau representasi dari empat lingkungan yang berbeda. Karakter yang diamati adalah bobot ubi per tanaman. Data dianalisis dengan model AMMI (additive main effect and multiplicative interaction). Hasil penelitian menunjukkan B-23/EC040 adalah genotipe berdaya hasil tertinggi, namun kurang stabil. Sebaliknya, B-33/J, B-26/NS, B-10/EC550, dan B-94/ENT adalah genotipe dengan hasil di atas rata-rata namun memiliki stabilitas yang lebih tinggi. Lingkungan IV (musim hujan dengan pemangkasan) adalah lingkungan baik di mana variasi genotipe terlihat lebih konsisten dengan B-23/EC040 sebagai genotipe terbaik. Genotipe terbaik pada lingkungan I adalah B-55/CJ, pada lingkungan II B-80/ENT, dan pada lingkungan III B-15/EC104.</p>
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Ziebell, Kim, Marina Steele, Yongxiang Zhang, Andrew Benson, Eduardo N. Taboada, Chad Laing, Scott McEwen, Bruce Ciebin, Roger Johnson, and Victor Gannon. "Genotypic Characterization and Prevalence of Virulence Factors among Canadian Escherichia coli O157:H7 Strains." Applied and Environmental Microbiology 74, no. 14 (May 16, 2008): 4314–23. http://dx.doi.org/10.1128/aem.02821-07.
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ABSTRACT In this study, the association between genotypic and selected phenotypic characteristics was examined in a collection of Canadian Escherichia coli O157:H7 strains isolated from humans and cattle in the provinces of Alberta, Ontario, Saskatchewan, and Quebec. In a subset of 69 strains selected on the basis of specific phage types (PTs), a strong correlation between the lineage-specific polymorphism assay (LSPA6) genotype and PT was observed with all strains of PTs 4, 14, 21, 31, 33, and 87 belonging to the LSPA6 lineage I (LSPA6-LI) genotype, while those of PTs 23, 45, 67, and 74 belonged to LSPA6 lineage II (LSPA6-LII) genotypes. This correlation was maintained when additional strains of each PT were tested. E. coli O157:H7 strains with the LSPA6-LI genotype were much more common in the collection than were the LSPA6-LII or lineage I/II (LSPA6-LI/II)-related genotypes (82.6, 11.2, and 5.8%, respectively). Of the strains tested, proportionately more LSPA6-LI than LSPA6-LII genotype strains were isolated from humans (52.7% versus 19.7%) than from cattle (47.8% versus 80.2%). In addition, 96.7% of the LSPA6-LII strains carried the stx 2c variant gene, while only 50.0% of LSPA6-LI/II and 2.7% of LSPA6-LI strains carried this gene. LSPA6-LII strains were also significantly more likely to possess the colicin D gene, cda (50.8% versus 23.2%), and have combined resistance to streptomycin, sulfisoxazole, and tetracycline (72.1% versus 0.9%) than were LSPA6-LI strains. The LSPA6 genotype- and PT-related characteristics identified may be important markers of specific ecotypes of E. coli O157:H7 that have unique epidemiological and virulence characteristics.
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CZEGLÉDI, A., J. HERCZEG, G. HADJIEV, L. DOUMANOVA, E. WEHMANN, and B. LOMNICZI. "The occurrence of five major Newcastle disease virus genotypes (II, IV, V, VI and VIIb) in Bulgaria between 1959 and 1996." Epidemiology and Infection 129, no. 3 (December 2002): 679–88. http://dx.doi.org/10.1017/s0950268802007732.
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Partial sequence and restriction enzyme cleavage site analyses of the fusion protein gene were used to genotype 47 Newcastle disease virus strains isolated between 1959 and 1996 in Bulgaria. Viruses belonged to five major genotypes that appeared to be associated with epizootics characterized by temporal and/or geographical restrictions. Genotype IV viruses (responsible for the European branch of the first panzootic) dominated the scene up to the early 1980s, interspersed with sporadic outbreaks caused by genotype II (US strains causing pneumoencephalitis) viruses. Genotype V viruses (transmitted by psittacines from South America) were first shown in 1973 and persisted until the late 1980s. Genotype VI (earliest members from the Middle-East 1968/70 outbreaks) was represented by scattered isolations between 1974 and 1996. A genotype VIIb (recent Middle East epizootic) virus was isolated as early as in 1984. Newcastle disease epizootics in Bulgaria were highlighted by multiple infection with more than one genotype at any one time.
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Mutebi, John-Paul, Heiman Wang, Li Li, Juliet E. Bryant, and Alan D. T. Barrett. "Phylogenetic and Evolutionary Relationships among Yellow Fever Virus Isolates in Africa." Journal of Virology 75, no. 15 (August 1, 2001): 6999–7008. http://dx.doi.org/10.1128/jvi.75.15.6999-7008.2001.
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ABSTRACT Previous studies with a limited number of strains have indicated that there are two genotypes of yellow fever (YF) virus in Africa, one in west Africa and the other in east and central Africa. We have examined the prM/M and a portion of the E protein for a panel of 38 wild strains of YF virus from Africa representing different countries and times of isolation. Examination of the strains revealed a more complex genetic relationship than previously reported. Overall, nucleotide substitutions varied from 0 to 25.8% and amino acid substitutions varied from 0 to 9.1%. Phylogenetic analysis using parsimony and neighbor-joining algorithms identified five distinct genotypes: central/east Africa, east Africa, Angola, west Africa I, and west Africa II. Extensive variation within genotypes was observed. Members of west African genotype II and central/east African genotype differed by 2.8% or less, while west Africa genotype I varied up to 6.8% at the nucleotide level. We speculate that the former two genotypes exist in enzootic transmission cycles, while the latter is genetically more heterogeneous due to regular human epidemics. The nucleotide sequence of the Angola genotype diverged from the others by 15.7 to 23.0% but only 0.4 to 5.6% at the amino acid level, suggesting that this genotype most likely diverged from a progenitor YF virus in east/central Africa many years ago, prior to the separation of the other east/central African strains analyzed in this study, and has evolved independently. These data demonstrate that there are multiple genotypes of YF virus in Africa and suggest independent evolution of YF virus in different areas of Africa.
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Nakano, Tatsunori, Craig N. Shapiro, Stephan C. Hadler, John L. Casey, Masashi Mizokami, Etsuro Orito, and Betty H. Robertson. "Characterization of hepatitis D virus genotype III among Yucpa Indians in Venezuela." Journal of General Virology 82, no. 9 (September 1, 2001): 2183–89. http://dx.doi.org/10.1099/0022-1317-82-9-2183.
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The complete genome sequences of hepatitis D virus (HDV) strains isolated from three Yucpa Amerindians in Venezuela were determined and found to be genotype III. Comparison of these three genotype III sequences demonstrated the presence of a hypervariable region containing numerous substitutions, insertions/deletions and a highly conserved region containing the self-cleavage domains, which have been reported previously for genotypes I and II. Amino acid changes within the first 90 amino acids of the hepatitis D antigen (HDAg) were found in the genotype III sequences, while the remainder of the HDAg-coding sequence was conserved. The secondary structure for the RNA-editing site differed between genotypes I and III. It was concluded that the serious delta hepatitis outbreaks characterized epidemiologically in the Yucpa Amerindians were caused by HDV genotype III isolates that were related to HDV genotype III isolates from other regions of South America.
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Huang, Ying-Chou, Chung-Feng Huang, Shu-Fen Liu, Hung-Yin Liu, Ming-Lun Yeh, Ching-I. Huang, Meng-Hsuan Hsieh, et al. "The performance of HCV GT plus RUO reagent in determining Hepatitis C virus genotypes in Taiwan." PLOS ONE 16, no. 1 (January 29, 2021): e0246376. http://dx.doi.org/10.1371/journal.pone.0246376.
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Background and aims Hepatitis C virus (HCV) genotyping is a pivotal tool for epidemiological investigation, guiding management and antiviral treatment. Challenge existed in identifying subtypes of genotype-1 (G-1) and genotype (GT) of indeterminate. Recently, the Abbott HCV RealTime Genotype Plus RUO assay (HCV GT Plus) has been developed aiming to overcome the limitations. We aimed to evaluate the performance of the assay compared with 5’ UTR sequencing in clinical samples. Materials and methods Eligible individuals were treatment chronic hepatitis C patients that were enrolled consecutively in a medical center and two core regional hospitals in southern Taiwan from Oct 2017 through Aug 2018. The patient with genotype 1 without subtype and indeterminate previously genotyped by Abbott RealTime HCV GT II will further determinate by Abbott HCV RealTime HCV GT Plus. All of the genotype results were validated by 5' UTR sequencing as a reference standard. Results A total of 100 viremic CHC patients were recruited, including 63 G-1 patients (male: 28), and 37 patients (male: 15) of indeterminate genotyped by Abbott RealTime HCV GT II assay (HCV GT II), respectively. The detection rate of 63 GT1 samples without subtype were 93.7% (59/63), 37 indeterminate samples without genotype were 62.2 (23/37) by HCV GT Plus. 5' UTR sequencing confirmed HCV GT Plus characterized results for 84.7% (50/59) of type1, with 100% (4/4), 82.8 (24/29) and 84.6% (22/26) for 1a, 1b and type6; 65.2% (15/23) of indeterminate with 100% (3/3) and 60% (12/20) for 1b and type 6 samples, respectively. Conclusions The Abbott RealTime HCV GT Plus RUO assay provides additional performance in GT detection.
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MACKNESS, Bharti, Paul N. DURRINGTON, Bashir ABUASHIA, Andrew J. M. BOULTON, and Michael I. MACKNESS. "Low paraoxonase activity in type II diabetes mellitus complicated by retinopathy." Clinical Science 98, no. 3 (February 10, 2000): 355–63. http://dx.doi.org/10.1042/cs0980355.
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Human serum paraoxonase 1 (PON1) is located on high-density lipoprotein and has been implicated in the detoxification of organophosphates, and possibly in the prevention of lipid peroxidation of low-density lipoprotein. PON1 has two genetic polymorphisms, both due to amino acid substitutions: one involving glutamine (Q genotype) and arginine (R genotype) at position 192, and the other involving leucine (L genotype) and methionine (M genotype) at position 55. We investigated the effects of these polymorphisms, and of a polymorphism of the PON2 gene at position 310 (Cys/Ser; C and S genotypes respectively), on serum PON1 activity and concentration, plasma lipids and lipoproteins and glycaemic control in 93 individuals with type II diabetes with no complications and in 101 individuals with type II diabetes with retinopathy. Serum PON1 activity in the group with no complications [median 164.1 nmol·min-1·ml-1 (range 8.0–467.8)] was significantly higher than in the group with retinopathy [113.4 nmol·min-1·ml-1 (3.0–414.6)] (P< 0.001), but the serum PON1 concentration was not different between the groups. The gene frequencies of the PON1-55 and PON1-192 polymorphisms and of the PON2-310 polymorphism were not different between the study populations. The PON1-55 and PON1-192 polymorphisms affected PON1 activity in the way described in a previous study of a control group and subjects with type II diabetes. The PON2-310 polymorphism also significantly affected serum PON1. PON1 activity was significantly higher in individuals with the PON2-310 CC genotype in both groups with type II diabetes, and the PON1 concentration was significantly higher in PON2-310 CC homozygotes with no complications than in the group with retinopathy. Neither the PON1-55 nor the PON1-192 polymorphism was correlated with the serum lipid or lipoprotein concentration in either group. In the group with retinopathy (but not the group with no complications), all three PON polymorphisms were correlated with glycaemic control, which was worse for the PON1-55 genotypes in the order MM > LM > LL (P = 0.0032), for the PON1-192 genotypes in the order RR > QR > QQ (P = 0.011) and for the PON2-310 genotypes in the order CC > CS > SS (P = 0.010). Low serum PON1 activity in retinopathy may be related to an increased tendency for lipid peroxidation. Our findings thus raise the possibility that, in retinopathy, the PON2 gene may influence PON1, and that an inter-relationship between the PON1 and PON2 genes may influence glycaemic control in subjects with type II diabetes complicated by retinopathy.
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Oghan, Hassan Amiri, Naser Sabaghnia, Valiollah Rameeh, Hamid Reza Fanaee, and Ebrahim Hezarjeribi. "Univariate Stability Analysis of Genotype×Environment Interaction of Oilseed Rape Seed Yield." Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis 64, no. 5 (2016): 1625–34. http://dx.doi.org/10.11118/actaun201664051625.
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Thirteen stability statistics were used to analyze genotype × environment (GE) interaction of 36 canola genotypes. Combined analysis of variance indicated that GE interaction significantly influenced seed yield performance. According to Type I stability concept (environmental variance, coefficient of variation and stability variance) genotypes G7, G9 and G13 were the most stable genotypes, while based on the Type II concept (coefficients of three linear regression models), genotypes G33, G27 and G29 could be selected as the most favorable genotypes. Also, genotype G7 was the most favorable genotype according to Type III stability concept (deviation from linear regression method). Genotypes clustering based on stability properties and mean yield grouped them into three distinct classes. Coefficient of determination for the canola genotypes indicated that genotypes G27 and G33 were the most stable genotypes but the genotypes G1, G10 and G25 had the highest desirability index and were the most stable ones. The plot of principal component analysis was used for graphic display of the relationships among statistics and the first axis distinguished the Type II of stability concept from other types and mean yield groups near this stability type. However, based on most statistics and mean yield performance, genotypes G9 or Fanaei‑6 (2592.47 kg ha‑1), G11 or Fanaei‑14 (2592.47 kg ha−1), G12 Fanaei‑15 or (2592.47 kg ha‑1) and G19 or Dez‑7169 (2592.47 kg ha‑1) were the most stable and favorable genotypes and are recommended for national release Iran.