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Chai, Jun, Qinglu Wang, Bo Qin, Shengkui Wang, Youtao Wang, Muhammad Shahid, Kai Liu, Yifang Zhang, and Weijie Qu. "Association of NOS2A gene polymorphisms with susceptibility to bovine tuberculosis in Chinese Holstein cattle." PLOS ONE 16, no. 6 (June 17, 2021): e0253339. http://dx.doi.org/10.1371/journal.pone.0253339.
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Bovine tuberculosis (bTB) is a global zoonotic disease that has detrimental economic impacts worldwide. The NOS2A gene plays a key role in immunological control of many infectious diseases. However, research on the association between NOS2A polymorphisms and bTB infection in Holstein cattle reared on the Yunnan-Guizhou plateau of China is scarce. This study investigated a possible linkage between NOS2A polymorphisms and risk of developing bTB in Chinese Holstein cattle. The NOS2A gene was genotyped in 144 bTB-infected Holstein cows and 139 healthy controls were genotyped through nucleotide sequencing. Ten single-nucleotide polymorphisms (SNPs) were detected, six of which were associated with susceptibility/resistance patterns of bTB. Furthermore, the C/T genotypes of 671 and 2793, and T/T genotype of E22 (+15) were significantly associated with susceptibility risk; the G/A genotype of 2857, T/T genotype of E9 (+65), and C/C genotype of E9 (+114) probably increased resistance to bTB. In addition, the haplotypes of NOS2A-2 and NOS2A-9 were risk factors for bTB susceptibility, while the NOS2A-5 and NOS2A-8 haplotypes were contributing protective variants against tuberculosis. There is a significant association between variation in SNPs of NOS2A and tuberculosis susceptibility/resistance pattern. These findings suggest that substitution of genetic selection would be helpful for eradicating bTB. However, further investigation is required to study the underlying mechanism through which NOS2A polymorphisms affect bTB infection.
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Aftab Ahmad Khan, Naghmi Asif, Rizwan Uppal, and Gul E Rehan. "HCV GENOTYPES AND ITS ASSOCIATION WITH RESPONSE TO TREATMENT." Journal of University Medical & Dental College 11, no. 2 (July 10, 2020): 27–33. http://dx.doi.org/10.37723/jumdc.v11i2.404.
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BACKGROUND & OBJECTIVE: primary Hepatitis C is a serious public health problem and is the cause of liver cirrhosis, hepatocellular carcinoma (HCC), and numerous end-stage liver disease manifestations. The management of hepatitis C is to preclude liver cirrhosis, lessen the risk of hepatocellular carcinoma or hepatoma, and curing the extra hepatic diseases. Initially, interferon was the cornerstone for treating hepatitis C, but due to its cumbersome complications, route of administration, and limited treatment access, many patients showed noncompliance. New therapies for chronic hepatitis C have been introduced based on direct antiviral effects. Several genotypes of hepatitis C have been discovered and they are responsive to different antiviral therapies. Our objective was to assess the genotypic distribution of HCV in our local setup and their pattern of response to different combination of anti-viral therapies by assessing the sustained viral response (SVR) after 12 weeks post-treatment. To determine the most prevalent genotype of hepatics C virus in our population and pattern of the response of multiple genotypes to different antiviral regimens.
METHODOLOGY: It is a cross-sectional study conducted for duration of six months and recruited those patients whose polymerase chain reaction (PCR) was found positive for hepatitis C virus at Islamabad Diagnostic Center. We analyzed 100 patients, both children and adults. Patients were assessed for different genotypes and then different combinations of antiviral treatments were administered. Their clinical data, hematological parameters and viral load before and after treatment were also analyzed.
RESULTS: In a total of 100 positive hepatitis C virus-infected patients, 55% were females and 45% males. The frequencies of genotypes observed were 91 %, 06%, and 03% of genotype 3, 1a, and 1b respectively. 51 out of 91 patients with type 3 genotype, who were on antiviral therapy of sofosbuvir and ribavirin, all of them achieved SVR. 30 out of 91 patients with type 3 genotype were treated with sofosbuvir alone, the percentage of failure to achieve SVR in them was 6.7%. Treatment failure percentage of 10% was observed when a combination of Interferon (INF) alpha and ribavirin was used in type 3 genotype. Remaining six patients with type 1a and three patients of type 1b genotype achieved SVR with different regimens used.
CONCLUSION: Although the increased load of HCV in our setup is an alarming situation the prevalence of type 3 genotype is a blessing in disguise. The success of sustained viral response after various combinations of direct antiviral therapy and interferon-free treatment is hope for the ultimate cure of the disease and avoidance of debilitating side effects related to interferon.
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CRIȘAN, Ioana, and Andrei STOIE. "Seasonal arbuscular mycorrhiza colonization dynamic displays genotype-specific pattern in Iris sibirica L." Notulae Scientia Biologicae 13, no. 1 (January 19, 2021): 10838. http://dx.doi.org/10.15835/nsb13110838.
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Arbuscular mycorrhiza (AM) is a widespread symbiotic association between plants and Glomeromycota fungi, that brings nutritional-derived benefits for phytobiont. Influence of plant breeding on arbuscular mycorrhiza susceptibility is a topic of current interest that can have many practical implications. Insights into whether new cultivars have a lower mycorrhizal potential, are critical for optimization of AM use. Aim of this research was to conduct a comparative assessment of AM colonization across a phenophase gradient in two Iris sibirica genotypes: one displaying the wild traits versus a modern reblooming cultivar with double flowers. Analysis showed that both Iris sibirica genotypes developed Paris-morphotype. Results indicated that on average the genotype with simple flowers had a higher AM colonization frequency (84.44±2.15) compared to the new cultivar with double flowers (52.22±6.09). Significant influence was exercised both by genotype (p<0.001) as well as by phenophase (p=0.0013), over colonization frequency. The genotypes displayed contrasting colonization dynamics: highest AM frequency level occurred in spring for the genotype with simple flowers, and in autumn for the one with double flowers. Results suggest that host metabolic state has regulating role over functionality of established AM-symbiotic association according to plant nutritional requirements, while fungi might also respond to increased or decreased carbon flux in the plant, associated with geophyte phenology.
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Ayelagbe, Olubunmi G., Oluwakemi O. Daodu, Olusola A. Akanbi, Anaelechi J. Onuegbu, and Olusola Ojurongbe. "Interleukin -10 – 1082A/G single nucleotide polymorphism and risk of Type 2 Diabetes Mellitus in a Southwestern population of Nigeria." Pan African Journal of Life Sciences 1, no. 1 (November 1, 2018): 54–59. http://dx.doi.org/10.36108/pajols/8102/10(0190).
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Introduction: Type 2 diabetes mellitus (T2DM) is a metabolic, multifactorial disease caused by genetic, dietary and environmental interactions with alterations in the pattern of cytokine expression. Association between interleukin (IL)-10 polymorphism and T2DM is not known in Black Af-ricans. This study therefore investigates the relationship between IL-10 -1082A/G polymorphism and risk of T2DM in Southwest Nigeria. Methods: 100 patients with T2DM and 105 healthy controls were enrolled. Anthropomet-ric indices were measured and fasting blood sample was obtained from all subjects. Plasma glucose and lipid profile were estimated by standard laboratory procedures. IL-10 (-1082A/G) gene polymorphism was genotyped using Allele Refractory Mutation detection System-Polymerase Chain Reaction (ARMS-PCR) technique. Odds ratio analysis (95%CI) was used to determine association between genotype and diabetes mellitus in studied subjects. Results: T2DM patients had the highest frequency of IL 10 -1082G/G genotype (58.3%) while -1082AG frequency was highest (63.1%) in non-diabetics. Non- significant associations between IL 10 -1082 gene polymorphism and T2DM risk (for AG genotype: OR=0.95, 95%CI =0.19-4.2, p = 0.95; for GG genotype: OR=0.49, 95%CI = 0.10-2.41, p = 0.38) were recorded. Fasting plasma glucose, 2hours post-prandial, total cholesterol and triglyceride were all significantly elevated in IL 10 -1082G/G than AG and AA genotypes in T2DM subjects (p<0.001). Expression of A allele was higher in controls than DM patients . Conclusion: This case-control study did not find a significant association between IL 10-1082A/G polymorphism and T2DM; however further studies with larger sample size and IL-10 plasma level meas-urement will be recommended to validate this observation.
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PANAYIOTOU, C., J. RICHTER, M. KOLIOU, N. KALOGIROU, E. GEORGIOU, and C. CHRISTODOULOU. "Epidemiology of respiratory syncytial virus in children in Cyprus during three consecutive winter seasons (2010–2013): age distribution, seasonality and association between prevalent genotypes and disease severity." Epidemiology and Infection 142, no. 11 (January 24, 2014): 2406–11. http://dx.doi.org/10.1017/s0950268814000028.
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SUMMARYThis study reports the epidemiology of respiratory syncytial virus (RSV) in hospitalized children in Cyprus over three successive seasons (2010–2013) and the association between prevalent genotypes and disease severity. RSV infections had a circulation pattern from December to March. Most RSV-positive children (83%) were aged <2 years. Genotyping of RSV isolates showed that during the first winter season of the study (2010–2011), the only RSV genotype circulating was GA2 (RSV-A), followed by genotype BA (RSV-B) in the next winter season with only few sporadic cases of GA2. During the last winter season of the study (2012–2013) the newly emerged RSV genotype ON1 (RSV-A) was virtually the only circulating genotype. Children infected with genotype ON1 suffered a significantly milder illness compared to infections with genotypes GA2 and BA with a higher percentage of BA-infected children requiring oxygen. Our findings are in contrast to the majority of published reports that suggest RSV-A causes more severe illness than RSV-B. Therefore, further investigation of the association between RSV genotypes and disease severity is required, as it might affect treatment strategies in the future.
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Balatsky, V. N., L. P. Grishina, A. M. Saenko, V. A. Vovk, and P. A. Vaschenko. "ASSOCIATION OF THE ESR1 GENE WITH REPRODUCTIVE TRAITS OF SOWS OF LARGE WHITE AND MIRGOROD BREEDS." Animal Breeding and Genetics 52 (November 1, 2016): 150–58. http://dx.doi.org/10.31073/abg.52.19.
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The speciality of the modern methodology in breeding is using the molecular information, received during genome analysis. This methodology can significantly accelerate the improvement of productivity traits and it is particularly useful in relation to the traits with low coefficient of inheritance while classic methods are not effective enough. The reproductive traits are one of the most important in pig farming, estrogen receptor 1 gene (ESR1) is involved in their control. Meanwhile, the use of ESR1 locus polymorphism in the marker-assisted selection needs to determine the extent of its association with the reproductive traits of animals in those populations where it is planned to conduct such selection. Implementation of marker-assisted selection in Large White and Mirgorod breeds for improving the reproductive traits is an actual task, but a necessary step in this work is the associative analysis. The purpose of the work is to research the association of polymorphisms of ESR1 locus with some reproductive traits of sows of Large White breed (ULW-1 and ULW-3 lines) and sows of Mirgorod breed. Materials and methods of research. Experimental groups: 1) the sows of Large White breed, ULW-3 line, bred in "Bahmutskiy Agrarian Union" farm, Donetsk region; 2) the sows of Large White breed, ULW-1 line, bred in “Stepne” farm, Poltava region; 3) the sows of Mirgorod breed, bred in «Named after Dekabristy» farm, Poltava region. All the experimental animals were previously genotyped on RYR1 gene and had RYR1CC genotype. The animals were genotyped on estrogen receptor 1 locus with aid of PCR-RFLP analysis on PvuII-polymorphic restriction site in the third intron of the gene – DNA marker for estrogen receptor 1 gene. Associations between genotypes and the studied traits were calculated using ANOVA in Excel 2007. Results. ULW-3 sows with ESR1BB genotype turned out to have 1.36 more piglets in a litter (analysing data from 2nd-4th farrows) comparing to animals with ESR1AA genotype. There is a tendency for bigger amount of newborn piglets in the heterozygotes animals than in sows with homozygous ESR1AA. A similar pattern appears in the 1st farrowing, the sows with ESR1BB and ESR1AB genotypes had the advantage in the total number of piglets at birth. In the experimental group of ULW-1 sows statistically proven patterns were not found, there was only a tendency to slight predominance of sows with ESR1BB and ESR1AB genotypes comparing to individuals with ESR1AA genotype. In the experimental group of Mirgorod sows there was a tendency to have most part of individuals with heterozygous genotype. Analysis of prolificacy of ULW-3 sows due to their genotype for the estrogen receptor 1 gene confirmed the superiority of ESR1BB and ESR1AB genotypes comparing to ESR1AA sows. According to 2nd-4th farrows, sows with ESR1BB and ESR1AB genotypes had the advantage in prolificacy comparing to ESR1AA sows by 1.15 and 0.53 piglets, respectively. According to the 1st farrowing difference between genotypes was absent. ESR1/PvuII-polymorphism do es not influence on prolificacy of ULW-1 sows. According to the 1st farrowing the trend towards a higher level of prolificacy of Mirgorod sows with ESR1AA genotype was found, while difference in 2nd-4th farrows between the groups was absent. It was found that ESR1/PvuII-polymorphism impact on the total number of piglets at birth and prolificacy for ULW-3 sows is characterized by predominance of additive component with a little contribution of the dominant component, the similar trend is observed for ULW-1 sows. There is a complex nature of the impact of ESR1/PvuII-polymorphism on the reproductive traits of Mirgorod sows in the predominance of the dominant component. Conclusions. The impact of polymorphism in estrogen receptor 1 gene on the total number of piglets in the litter after the birth and prolificacy in ULW-3 sows was detected. ULW-3 sows with ESR1BB genotype have 1.36 more piglets in a litter (analysing data from 2nd-4th farrows) and 1.15 more comparing to animals with ESR1AA genotype. ESR1/PvuII-polymorphism was not associated with total number of piglets in a litter and prolificacy in ULW-1 sows and Mirgorod sows. The counted parameters of additive-dominant model indicate that ESR1/PvuII polymorphism impact on the total number of piglets at birth and prolificacy for ULW-3 sows is characterized by predominance of additive component with a little contribution of the dominant component.
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Levy, Simone Carvalho, Lívia Azeredo Alves Antunes, Julia Guimaraes Barcellos de Abreu, Jullia Assis da Silva Nascimento, Ana Carolina Kuntz, Walter Luis Soares Fialho, Amanda Silva Rodrigues, et al. "Determination of TNF-a Gene Polymorphisms on Skeletal Pattern in Class II Malocclusion." Brazilian Dental Journal 30, no. 2 (March 2019): 152–56. http://dx.doi.org/10.1590/0103-6440201902367.
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Abstract Bone development and growth is a non-going, life-long process, varying greatly among individuals and much of this variation could be modulated by genetic factors. The purpose of this study was to evaluate the association between the polymorphisms in the TNF-a gene and skeletal class II malocclusion. Single nucleotide polymorphisms in TNF-a (rs1799724; rs1800629) gene were studied in 79 skeletal class II malocclusion and 102 skeletal class I malocclusion subjects from Straight Wire Group of Studies on Orthodontics and Functional Orthopedics for Maxillary from Rio de Janeiro, Brazil. The Genotyping of these selected polymorphisms was carried out by TaqMan real-time PCR using genomic DNA extracted from buccal cells. All allele and genotype frequencies were compared between the groups using the PLINK® software in a free, in a dominant and in a recessive model using a chi-square test (p≤0.05). There was no significant association of TNF-a (rs1799724; rs1800629) genotype and allele distribution with skeletal class II malocclusion. Regardless of the dominant or recessive genetic model, the preferential genotype associations for rs1799724 and rs1800629 was insignificant. In conclusion, no evidence of association is apparent between genetic polymorphisms involving TNF-a and skeletal class II malocclusion or the position of the maxilla and mandible in the postero-anterior direction.
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Ogorevc, Jernej, Mojca Simčič, Minja Zorc, Monika Škrjanc, and Peter Dovč. "TLR2 polymorphism (rs650082970) is associated with somatic cell count in goat milk." PeerJ 7 (July 31, 2019): e7340. http://dx.doi.org/10.7717/peerj.7340.
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Pathogens invading the mammary gland are recognized through a range of pattern recognition receptors (PRRs), residing on the plasma membrane of mammary epithelial cells. Toll-like receptor 2 (TLR2) signalling is responsible for recognition of Gram-positive bacteria, which are the most common mastitis-causing pathogens in goats. Somatic cell counts (SCC) in milk are routinely determined in goat dairy flocks and serve as an indicator of milk quality, which is highly correlated to intramammary infections. Recently, a single nucleotide polymorphism of the TLR2 was suggested to be associated with SCC in goat milk. To further test the suggested association, we genotyped 61 Slovenian Alpine goats included in the dataset. The effect of the genotype was analysed using the general linear model (GLM) procedure of SAS/STAT software. We found the TLR2 genotypes significantly (p = 0.0007) associated with milk SCC. Animals with the A/G genotype had significantly (p ≤ 0.05) lower SCC value in milk compared to the G/G genotype. Our data suggest that the A allele is the minor one and is associated with lower milk SCC. In the current study, we provide a validated PCR-RFLP based genotyping assay for the TLR2 SNP (rs650082970) and confirm its association with milk SCC. Further studies to confirm the association on a larger number of animals of different breeds and to explain functional consequences of the polymorphism in relation to SCC are encouraged.
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Gok, Ilhami, and Ozkan Ozden. "Examination of RAD51 gene G135C polymorphism in gastric cancer patients in northeastern Anatolia." Archives of Biological Sciences 71, no. 2 (2019): 209–13. http://dx.doi.org/10.2298/abs181121002g.
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Polymorphisms of DNA repair and genome integrity genes are associated with DNA repair capacity and elevated cancer risk. To establish an association between the pattern of polymorphism and the incidence of any type of cancer, studies across different populations are required. Polymorphic regions have been identified in the RAD51 repair gene in various cancer types; however, the influence of specific genetic variants on gastric cancer prevalence has not been empirically demonstrated. We conducted a case-control study with 76 gastric cancer patients and 78 healthy individuals from northeastern Anatolia to examine the association between polymorphism and gastric cancer. We genotyped the previously identified G135C polymorphism of RAD51 in all individuals and estimated the allele and genotype frequencies in the two groups. Our results indicated that the two groups differed both in allele and genotype frequencies. Additionally, a significant and elevated odd ratio (3.53) of gastric cancer for the C allele of RAD51 was observed. The genotypes GC and CC had also significant and high odd ratios (>3.75). Our results indicate that G135C polymorphism of the RAD51 gene was associated with an increased risk of gastric cancer in the examined population.
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Wardofa, Gadisa A., Hussein Mohammed, Dawit Asnake, and Tesfahun Alemu. "Genotype X Environment Interaction and Yield Stability of Bread Wheat Genotypes in central Ethiopia." Journal of Plant Breeding and Genetics 7, no. 2 (November 3, 2019): 87–94. http://dx.doi.org/10.33687/pbg.007.02.2847.
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The present study was conducted to interpret Genotype main effect and GEI obtained by AMMI analysis and group the genotype having similar response pattern over all environments. Fifteen bread wheat genotypes were evaluated by RCBD using four replications at six locations in Ethiopia. The main effect differences among genotypes, environments, and the interaction effects were highly significant (P ≤ 0.001) for the total variance of grain yield. Results of AMMI analysis of mean grain yield for the six locations showed significant differences (P0.001) among the genotypes, environments and GEI. The environment had the greatest effect with the environmental sum of squares (35.28%) than the genotypes (33.46%) and GEI (31.45%) effect. The AMMI analysis for the IPCA1 captured 46.1% and the IPCA2 explained 28.6%. The two IPC cumulatively captured 74.7% of the sum of square the GEI of bread wheat genotypes, when the IPCA1 was plotted against IPCA2. The genotype ETBW8075, ETBW8070 and ETBW9470 were unstable as they are located far apart from the other genotypes in the biplot when plotted on the IPCA1 and IPCA2 scores. The ETBW8078, ETBW8459, Hidase and ETBW8311 were genotype located near to the origin of the biplot which implying that it was stable bread wheat genotypes across environments. There is closer association between Lemu and ETBW8065 which indicate similar response of the genotypes to the environment. The best genotype with respect to location Kulumsa was ETBW9470, ETBW8075 was the best genotype for Dhera, ETBW8070 was the best genotype for Holeta while ETBW9466 was the best genotype for Arsi Robe. Arsi Robe and Kulumsa is the most favorable environment for all genotypes with nearly similar yield response for grain yield.
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Noor, Roudhotul Ismaillya, Aryati Aryati, and Pudjo Hartono. "GENOTIPE HPV DAN POLA INFEKSINYA TERKAIT JENIS HISTOPATOLOGI KANKER LEHER RAHIM (HPV Genotype and HPV Infection Pattern Related to the Histopathological Type of Cervical Cancer)." INDONESIAN JOURNAL OF CLINICAL PATHOLOGY AND MEDICAL LABORATORY 21, no. 1 (April 15, 2018): 67. http://dx.doi.org/10.24293/ijcpml.v21i1.1262.
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Uterine cervical cancer is the number one cause of female cancer in Indonesia. The most common cause is a persistent infection with ahigh risk of HPV (Human Papilloma Virus). A multiple genotype HPV infection with high risk HPV increases the poor prognosis of cervicalcancer. Non-squamous type of cervical cancer has a poorer prognosis than the squamous type. The aim of this study was to know theassociation between HPV genotype and HPV infection pattern with histopathological type of cervical cancer in patients of the Dr. SoetomoHospital, Surabaya. This study was an analytical observational-cross sectional research. The samples consisted of 44 uterine cervicalswabs from the Oncology Out-Patient Clinic, proven and diagnosed as the related cervical cancer in October-November 2012. PCR resultsshowed 33 HPV positive, seven (7) HPV negative and 4 invalid. The Fisher’s exact test was only done for the 33 positive HPV samples.The positive HPV samples consisted of 24 squamouse and nine (9) non-squamous types of uterine cervical cancer. A 90.9% (30/33) highrisk HPV genotypes was found in 72.7% (24/30) squamous and 18.2% (6/30) non-squamous types. Multiple genotype HPV infection9.1% (3/33) occurred in 3% (1/3) squamous and 6.1% (2/3) non-squamous types. There was a significant association between HPVgenotype and histopathological type of the uterine cervical cancer (p=0.015). There was no association between HPV infection patternand histopathological type of uterine cervical cancer (p=0.174). Negative HPV and low risk HPV genotypes can be found in uterine cervicalcancer patients of the Dr. Soetomo Hospital, Surabaya. Multiple genotype HPV infections have a 2.86 times greater risk in developingnonsquamous type with a poor prognosis.
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Perez-Diaz-del-Campo, Nuria, Itziar Abete, Irene Cantero, Bertha Araceli Marin-Alejandre, J. Ignacio Monreal, Mariana Elorz, José Ignacio Herrero, et al. "Association of the SH2B1 rs7359397 Gene Polymorphism with Steatosis Severity in Subjects with Obesity and Non-Alcoholic Fatty Liver Disease." Nutrients 12, no. 5 (April 29, 2020): 1260. http://dx.doi.org/10.3390/nu12051260.
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Non-alcoholic fatty liver disease (NAFLD) is a major cause of liver disease worldwide. Some genetic variants might be involved in the progression of this disease. The study hypothesized that individuals with the rs7359397 T allele have a higher risk of developing severe stages of NAFLD compared with non-carriers where dietary intake according to genotypes could have a key role on the pathogenesis of the disease. SH2B1 genetic variant was genotyped in 110 overweight/obese subjects with NAFLD. Imaging techniques, lipidomic analysis and blood liver biomarkers were performed. Body composition, general biochemical and dietary variables were also determined. The SH2B1 risk genotype was associated with higher HOMA-IR p = 0.001; and Fatty Liver Index (FLI) p = 0.032. Higher protein consumption (p = 0.028), less mono-unsaturated fatty acid and fiber intake (p = 0.045 and p = 0.049, respectively), was also referred to in risk allele genotype. Lipidomic analysis showed that T allele carriers presented a higher frequency of non-alcoholic steatohepatitis (NASH) (69.1% vs. 44.4%; p = 0.006). In the genotype risk group, adjusted logistic regression models indicated a higher risk of developing an advanced stage of NAFLD measured by FLI (OR 2.91) and ultrasonography (OR 4.15). Multinomial logistic regression models showed that risk allele carriers had higher liver fat accumulation risk (RRR 3.93) and an increased risk of NASH (RRR 7.88). Consequently, subjects carrying the T allele were associated with a higher risk of developing a severe stage of NAFLD. These results support the importance of considering genetic predisposition in combination with a healthy dietary pattern in the personalized evaluation and management of NAFLD.
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Sinha, Rebeka, Nihar Ranjan Sahoo, Kush Shrivastava, Pushpendra Kumar, Salauddin Qureshi, Amit Kumar, Gandham Venkata Papa Pydi Siva Ravi Kumar, and Bharat Bhushan. "Effect of Mucin13 gene polymorphism on diarrhoeagenic <i>E. coli</i> adhesion pattern and its expression analysis in native Indian pigs." Archives Animal Breeding 61, no. 3 (July 30, 2018): 321–28. http://dx.doi.org/10.5194/aab-61-321-2018.
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Abstract. We identified genetic polymorphism in Mucin13 gene affecting E. coli adhesion patterns using (local isolate) diarrhoeagenic E. coli in Indian desi pigs. Five SNPs and one indel previously reported to be associated with enterotoxigenic E. coli (ETEC) F4ab/ac adhesion pattern were examined by designing PCR-RFLP protocol. The genotypic frequencies of only one SNP (g.22304A > G) differed significantly (at P≤0.05) in adhesive, non-adhesive and weakly adhesive population. The AA (306 sbp, 231 bp), AG (306, 231, 108, 198 bp) and GG (231, 198 bp, 108 b) genotypes of g.22304A > G locus were observed with frequencies 50.0 %, 21.25 % and 28.75 %, respectively and AG genotype was significantly (P≤0.05) associated with a non-adhesive pattern. The polymorphism information content of SNPs ranged from 17.67 (g.22124T > C) to 37.36 % (g.21471C > T) loci. Three loci (g.21471C > T, g.22124T > C and g.22304A > G) were significantly departed from Hardy–Weinberg equilibrium. The linkage disequilibrium analysis revealed locus g.22124T > C and g.22304A > G were significantly (P≤0.05) associated with each other. Expression profiling of target gene in jejuna of animals having AA, AG and GG genotypes revealed differences in various genotypes with the highest in the AA, moderate in the GG and low levels in the AG genotype, although they were statistically non-significant (at P≤0.05). The absence of significant effect of genotypes on MUC13 mRNA expression indicates no direct functional role, although the structural role can not be ignored as the putative receptor gene is located within targeted genomic region. Further, reports of same SNP association with an ETEC F4ab/ac adhesion pattern indicate the target gene's role in diarrhoea even caused by other strains of E. coli which is not ETEC.
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Khan, Mosin S., Abid Shoukat, Syed Mudassar, Zaffar Kawoosa, Altaf H. Shah, and Showkat Ali Zargar. "Impact of IL28B genetic variant's and viral genotype on treatment outcome of hepatitis C infected patients." Journal of Infection in Developing Countries 12, no. 09 (September 30, 2018): 762–70. http://dx.doi.org/10.3855/jidc.10175.
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Introduction: Viral genotype and variation in host genes involved in the immune response may predict the treatment response in patients infected with HCV. The present study was designed to determine the distribution pattern of HCV and host genotypes in Chronic Hepatitis C (CHC) patients and their association with virological response and other risk factors.
Methodology: Two hundred and fifty (n = 250) HCV positive patients were included in the study. HCV and Interleukin 28B (IL28B) genotyping was carried out by PCR-RFLP.
Results: Viral genotype 3 was the predominant genotype seen in 187 (74.8%) patients. Wild genotype predominated in rs12979860, rs12980275 and rs8099917 SNP of IL28B gene. A significant difference was found in end stage virological response (EVR) between HCV genotype 1 infected patients with wild and variant genotype for rs12980275 and rs8099917 SNPs respectively (P < 0.05). On multivariate analysis all the SNPs were found to be associated with each other (P < 0.05) with rs12980275 SNP associated with history of Jaundice (P < 0.05). Viral genotype 3 was significantly associated with age (< 50 years) and rapid virological response (RVR) while as viral genotype 1 was significantly associated with history of surgery on multivariate analysis (P < 0.05).
Conclusions: The viral genotype and IL28B polymorphisms are important factors to personalize antiviral therapy of patients with CHC.
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Heath, Andrew C., Lindon J. Eaves, Katherine M. Kirk, and Nicholas G. Martin. "Effects of lifestyle, personality, symptoms of anxiety and depression, and genetic predisposition on subjective sleep disturbance and sleep pattern." Twin Research 1, no. 4 (August 1, 1998): 176–88. http://dx.doi.org/10.1375/twin.1.4.176.
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AbstractThe effects on sleep pattern (‘short-sleep’ versus ‘long-sleep’) and subjective sleep disturbance of genotype, personality, symptoms of anxiety and depression, and lifestyle, were examined using survey data on a clinically unselected sample of adult Australian twin pairs, aged 17–88 years. When the effects of genotype, personality and symptoms were ignored, lifestyle variables appeared to account for roughly 4% of the variance in sleep disturbance, and 9% of the variance in sleep pattern. Significant genetic effects on sleep disturbance and sleep pattern were found, which were only partly explained by the effects of personality and symptoms of anxiety and depression. Much of the association between sleep disturbance and lifestyle appeared to be explained by separate effects of personality and symptoms of anxiety and depression on sleep and lifestyle (‘genotype – risk-factor correlation’). There was little evidence for genetically determined differences in sensitivity to the lifestyle variables (‘genotype × risk-factor interaction’).
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VERMA, S. K., D. AJZENBERG, A. RIVERA-SANCHEZ, C. SU, and J. P. DUBEY. "Genetic characterization ofToxoplasma gondiiisolates from Portugal, Austria and Israel reveals higher genetic variability within the type II lineage." Parasitology 142, no. 7 (February 13, 2015): 948–57. http://dx.doi.org/10.1017/s0031182015000050.
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SUMMARYThis study compared genetic diversity ofToxoplasma gondiiisolates from Portugal, Austria and Israel. For this, we genotyped 90T. gondiiisolates (16 from Portugal, 67 from Austria and 7 from Israel) using 10 nested PCR-restriction length polymorphism (RFLP) genetic markers and 15 microsatellite (MS) markers. By PCR-RFLP typing, 7 isolates from Portugal chickens were identified as type II (ToxoDB #1 or #3), 4 were type III (ToxoDB #2) and the remaining 4 isolates have unique genotype pattern were designated as ToxoDB #254. One mouse virulent isolate from a bovine fetus (Bos taurus) in Portugal was type I (ToxoDB #10) at all loci and designated as TgCowPr1. All 67 isolates from Austria and 7 from Israel were type II (ToxoDB #1 or #3). By MS typing, many additional genetic variations were revealed among the type II and type III isolates. Phylogenetic analysis showed that isolates from the same geographical locations tend to cluster together, and there is little overlapping of genotypes among different locations. This study demonstrated that the MS markers can provide higher discriminatory power to reveal association of genotypes with geographical locations. Future studies of the type II strains in Europe by these MS markers will be useful to reveal transmission patterns of the parasite.
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Bragonzi, Alessandra, Lutz Wiehlmann, Jens Klockgether, Nina Cramer, Dieter Worlitzsch, Gerd Döring, and Burkhard Tümmler. "Sequence diversity of the mucABD locus in Pseudomonas aeruginosa isolates from patients with cystic fibrosis." Microbiology 152, no. 11 (November 1, 2006): 3261–69. http://dx.doi.org/10.1099/mic.0.29175-0.
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The mucA gene of the muc operon, which is instrumental in the control of the biosynthesis of the exopolysaccharide alginate, is a hotspot of mutation in Pseudomonas aeruginosa, a micro-organism that chronically colonizes the airways of individuals with cystic fibrosis (CF). The mucA, mucB and mucD genes were sequenced in nine environmental isolates from aquatic habitats, and in 37 P. aeruginosa strains isolated from 10 patients with CF, at onset or at a late stage of chronic airway colonization, in order to elucidate whether there was any association between mutation and background genotype. The 61 identified single nucleotide polymorphisms (SNPs) segregated into 18 mucABD genotypes. Acquired and de novo stop mucA mutations were present in 14 isolates (38 %) of five mucABD genotypes. ΔG430 was the most frequent and recurrent mucA mutation detected in four genotypes. The classification of strains by mucABD genotype was generally concordant with that by genome-wide SpeI fragment pattern or multilocus SNP genotypes. The exceptions point to intragenic mosaicism and interclonal recombination as major forces for intraclonal evolution at the mucABD locus.
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SAWALHA, R. M., L. BELL, S. BROTHERSTONE, I. WHITE, A. J. WILSON, and B. VILLANUEVA. "Scrapie-resistant sheep show certain coat colour characteristics." Genetics Research 91, no. 1 (February 2009): 39–46. http://dx.doi.org/10.1017/s0016672308009968.
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SummarySusceptibility to scrapie is known to be associated with polymorphisms at the prion protein (PrP) gene, and this association is the basis of current selective programmes implemented to control scrapie in many countries. However, these programmes might have unintended consequences for other traits that might be associated withPrPgenotype. The objective of this study was to investigate the relationship betweenPrPgenotype and coat colour characteristics in two UK native sheep breeds valued for their distinctive coat colour patterns. Coat colour pattern, darkness and spotting andPrPgenotype records were available for 11 674 Badgerfaced Welsh Mountain and 2338 Shetland sheep. The data were analysed with a log–linear model using maximum likelihood. Results showed a strong significant association ofPrPgenotype with coat colour pattern in Badgerfaced Welsh Mountain and Shetland sheep and with the presence of white spotting in Shetland sheep. Animals with the ARR/ARR genotype (the most scrapie resistant) had higher odds of having a light dorsum and a dark abdomen than the reverse pattern. The implication of these associations is that selection to increase resistance to scrapie based only onPrPgenotype could result in change in morphological diversity and affect other associated traits such as fitness.
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Yu, Yun, Henk Bovenhuis, Zhou Wu, Kimberley Laport, Martien A. M. Groenen, and Richard P. M. A. Crooijmans. "Deleterious Mutations in the TPO Gene Associated with Familial Thyroid Follicular Cell Carcinoma in Dutch German Longhaired Pointers." Genes 12, no. 7 (June 29, 2021): 997. http://dx.doi.org/10.3390/genes12070997.
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Familial thyroid cancer originating from follicular cells accounts for 5–15% of all the thyroid carcinoma cases in humans. Previously, we described thyroid follicular cell carcinomas in a large number of the Dutch German longhaired pointers (GLPs) with a likely autosomal recessive inheritance pattern. Here, we investigated the genetic causes of the disease using a combined approach of genome-wide association study and runs of homozygosity (ROH) analysis based on 170k SNP array genotype data and whole-genome sequences. A region 0–5 Mb on chromosome 17 was identified to be associated with the disease. Whole-genome sequencing revealed many mutations fitting the recessive inheritance pattern in this region including two deleterious mutations in the TPO gene, chr17:800788G>A (686F>V) and chr17:805276C>T (845T>M). These two SNP were subsequently genotyped in 186 GLPs (59 affected and 127 unaffected) and confirmed to be highly associated with the disease. The recessive genotypes had higher relative risks of 16.94 and 16.64 compared to homozygous genotypes for the reference alleles, respectively. This study provides novel insight into the genetic causes leading to the familial thyroid follicular cell carcinoma, and we were able to develop a genetic test to screen susceptible dogs.
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Chaston, John M., Adam J. Dobson, Peter D. Newell, and Angela E. Douglas. "Host Genetic Control of the Microbiota Mediates the Drosophila Nutritional Phenotype." Applied and Environmental Microbiology 82, no. 2 (November 13, 2015): 671–79. http://dx.doi.org/10.1128/aem.03301-15.
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ABSTRACTA wealth of studies has demonstrated that resident microorganisms (microbiota) influence the pattern of nutrient allocation to animal protein and energy stores, but it is unclear how the effects of the microbiota interact with other determinants of animal nutrition, including animal genetic factors and diet. Here, we demonstrate that members of the gut microbiota inDrosophila melanogastermediate the effect of certain animal genetic determinants on an important nutritional trait, triglyceride (lipid) content. Parallel analysis of the taxonomic composition of the associated bacterial community and host nutritional indices (glucose, glycogen, triglyceride, and protein contents) in multipleDrosophilagenotypes revealed significant associations between the abundance of certain microbial taxa, especiallyAcetobacteraceaeandXanthamonadaceae, and host nutritional phenotype. By a genome-wide association study ofDrosophilalines colonized with a defined microbiota, multiple host genes were statistically associated with the abundance of one bacterium,Acetobacter tropicalis. Experiments using mutantDrosophilavalidated the genetic association evidence and reveal that host genetic control of microbiota abundance affects the nutritional status of the flies. These data indicate that the abundance of the resident microbiota is influenced by host genotype, with consequent effects on nutrient allocation patterns, demonstrating that host genetic control of the microbiome contributes to the genotype-phenotype relationship of the animal host.
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AGIK, SANDRA, BEVERLY S. FRANEK, AKAASH A. KUMAR, MARISSA KUMABE, TAMMY O. UTSET, RACHEL A. MIKOLAITIS, MEENAKSHI JOLLY, and TIMOTHY B. NIEWOLD. "The Autoimmune Disease Risk Allele of UBE2L3 in African American Patients with Systemic Lupus Erythematosus: A Recessive Effect Upon Subphenotypes." Journal of Rheumatology 39, no. 1 (November 1, 2011): 73–78. http://dx.doi.org/10.3899/jrheum.110590.
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Objective.UBE2L3 is associated with susceptibility to systemic lupus erythematosus (SLE) and rheumatoid arthritis in European ancestry populations, and this locus has not been investigated fully in non-European populations. We studied the UBE2L3 risk allele for association with SLE, interferon-α (IFN-α), and autoantibodies in a predominantly African American SLE cohort.MethodsWe studied 395 patients with SLE and 344 controls. The UBE2L3 rs5754217 polymorphism was genotyped using Taqman primer-probe sets, and IFN-α was measured using a reporter cell assay.Results.The UBE2L3 rs5754217 T allele was strongly enriched in African American patients with anti-La antibodies as compared to controls, and a recessive model was the best fit for this association (OR 2.55, p = 0.0061). Serum IFN-α also demonstrated a recessive association with the rs5754217 genotype in African American patients, and the TT/anti-La-positive patients formed a significantly high IFN-α subgroup (p = 0.0040). Similar nonstatistically significant patterns of association were observed in the European American patients with SLE. Case-control analysis did not show large allele frequency differences, supporting the idea that this allele is most strongly associated with anti-La-positive patients.Conclusion.This pattern of recessive influence within a subgroup of patients may explain why this allele does not produce a strong signal in standard case-control studies, and subphenotypes should be included in future studies of UBE2L3. The interaction we observed between UBE2L3 genotype and autoantibodies upon serum IFN-α suggests a biological role for this locus in patients with SLE in vivo.
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Jiménez-Sousa, Gómez-Moreno, Pineda-Tenor, Sánchez-Ruano, Artaza-Varasa, Martin-Vicente, Fernández-Rodríguez, Martínez, and Resino. "Impact of DARC rs12075 Variants on Liver Fibrosis Progression in Patients with Chronic Hepatitis C: A Retrospective Study." Biomolecules 9, no. 4 (April 9, 2019): 143. http://dx.doi.org/10.3390/biom9040143.
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: The Duffy antigen receptor for chemokines (DARC) rs12075 polymorphism regulates leukocyte trafficking and proinflammatory chemokine homeostasis. Hepatitis C virus (HCV)-mediated liver fibrosis is associated with an uncontrolled inflammatory response. In this study, we evaluate the association between the DARC rs12075 polymorphism and liver stiffness progression in HCV-infected patients. We carried out a retrospective cohort study (repeated measures design) in 208 noncirrhotic patients with chronic hepatitis C (CHC) who had at least two liver stiffness measurements (LSM) with a separation of at least 12 months. We used generalized linear models to analyze the association between DARC rs12075 polymorphism and outcome variables. During a follow-up of 46.6 months, the percentage of patients with stages of fibrosis F0/F1 decreased (p < 0.001), while LSM values and the percentage of patients with cirrhosis increased (p < 0.001). This pattern of changes was maintained in each of the groups of patients analyzed according to their rs12075 genotypes (AA or AG/GG). However, the variations in liver stiffness characteristics were lower in patients with the rs12075 AG/GG genotype (AG/GG versus AA). Thereby, in the adjusted analysis, patients with the rs12075 AG/GG genotype had a lower risk of an increased value of LSM2/LSM1 arithmetic mean ratio (AMR = 0.83; p = 0.001) and of an increase in LSM ≥ 5 kPa (odds ratio (OR) = 0.28; p = 0.009). Besides, patients with rs12075 AG/GG had a lower risk of cirrhosis progression (OR = 0.24; p = 0.009). No significant associations were found for an increase in LSM ≥ 10 kPa. We found an association between the DARC rs12075 single nucleotide polymorphism (SNP) and CHC progression. Specifically, patients with the DARC rs12075 AG/GG genotype had a lower risk of liver fibrosis progression and development of cirrhosis.
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Schürks, M., RYL Zee, JE Buring, and T. Kurth. "MTHFR 677C→T and ACE D/I polymorphisms and migraine attack frequency in women." Cephalalgia 30, no. 4 (September 1, 2009): 447–56. http://dx.doi.org/10.1111/j.1468-2982.2009.01980.x.
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Data on the association of the MTHFR 677C→T and ACE D/I polymorphisms with migraine severity, measured by attack frequency, are scarce. We performed an association study among 24 961 women participating in the Women's Health Study. Migraine, aura status and attack frequency were self-reported. Multinomial logistic regression was used to investigate the genotype–migraine association. Among the 3186 migraineurs with complete genotype and attack frequency data, 1270 reported migraine with aura (MA) (attack frequency 76 ≥ weekly; 219 monthly; 123 every other month; 852 fewer than six times/year) and 1916 migraine without aura (MoA) (attack frequency: 85 ≥ weekly; 414 monthly; 208 every other month; 1209 fewer than six times/year). The MTHFR 677TT genotype was associated with a reduced risk for MA, which only appeared for attacks fewer than six times/year (age-adjusted odds ratio 0.78; 95% confidence interval 0.61, 0.99). We did not find a specific pattern of association of the ACE D/I polymorphism with attack frequency for MA or MoA.
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Nikitina, L. O., M. I. Balabolkin, Y. Yu Kondratiev, G. G. Mamaev, L. M. Demurov, D. A. Chistyakov, V. V. Nosikov, and I. I. Dedov. "Angiotensin I-converting enzyme gene polymorphism in myocardial infarction in patients with type 2 diabetes." Problems of Endocrinology 44, no. 6 (December 1, 1998): 13–16. http://dx.doi.org/10.14341/probl11661.
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Insertion/deletion (I/D) polymorphism of angiotensin I-converting enzyme gene (ACE) as a potential marker of genetic susceptibility to myocardial infarction (MI) was studied in 76 patients with non-insulin-dependent diabetes (NIDDM) surviving after MI, 115 NIDDM patients without history of MI, and 165 subjects without diabetes from the general Moscow population. Case-control association study failed to reveal significant differences in distribution of ACE gene alleles and genotypes between patients with and without MI. However, we observed a tendency of I allele frequency to decrease and of D allele frequency to increase in infarction. Moreover, patients with MI had almost the same pattern of I and D allele and DD genotype distribution as normal subjects from general population (34.9, 65.1, and 46.1% vs. 35.8, 64.2, and 48.5%, respectively). On the other hand, diabetics without infarction had a slightly higher prevalence of I allele and I allele-containing genotypes (ID and II) than patients with documented MI (40.4, 46.1, and 17.4% vs. 34.9, 38.2, and 15.7%, respectively) and lower DD genotype frequency (36.5 vs. 46.1%), respectively). Therefore, we suppose that in Moscow a higher incidence of D allele in comparison with I allele and of its genotypes ID and II may be regarded as a genetic protective factor, whereas D allele and DD genotype as a factor of genetic susceptibility to MI in NIDDM patients.
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Cussenot, Olivier, Abdel Rhamene Azzouzi, Nathalie Nicolaiew, Gaelle Fromont, Philippe Mangin, Luc Cormier, Georges Fournier, et al. "Combination of Polymorphisms From Genes Related to Estrogen Metabolism and Risk of Prostate Cancers: The Hidden Face of Estrogens." Journal of Clinical Oncology 25, no. 24 (August 20, 2007): 3596–602. http://dx.doi.org/10.1200/jco.2007.11.0908.
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Purpose The association between common functional polymorphisms from the CYP17, CYP19, CYP1B1, and COMT genes involved in the estrogen metabolism and the risk of prostate carcinoma was evaluated. Patients and Methods The study investigated 1,983 white French men (1,101 patients with prostate cancer and 882 healthy controls) aged between 40 and 98 years. The different alleles and genotypes were analyzed according to case-control status, aggressiveness pattern of the tumors, age at onset, and family history of cancers. Results The VV (high activity) genotype of the V432L polymorphism from CYP1B1 (odds ratio [OR] = 1.36; 95% CI, 1.03 to 1.79; P = .031), and the long allele (> 175 bp) of the TTTA repeat from CYP19 (OR, 1.26; 95% CI, 1.08 to 1.47; P = .003) were significantly associated with the risk of prostate cancer. An additive effect was observed when we combined the two at-risk alleles (OR = 1.63; 95% CI, 1.24 to 2.13; P < .001). The association was stronger for the CYP1B1 VV genotype (OR = 1.55; 95% CI, 1.13 to 2.13; P = .007) among the group of patients with highly aggressive disease. Stratification by age at onset showed that the associations of CYP1B1 and CYP19 variants were largely confined to the younger prostate cancer patients. Conclusion This association between polymorphisms from genes related to estrogen metabolism and prostate cancer risk suggest new clinical considerations in the management of prostate cancer: the development of new prevention trials based on genetic profiling and the evaluation of specific inhibitors involving the estrogen pathways.
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Lahiri, Apeksha, Nasifa Hasan, Soma Chowdhury, Saheli Podder, Sudip Roy, and Arpita Ghosh. "Distribution Pattern of HCV Genotype and Its Association with Liver Functioning Enzymes and Viral Load." IOSR Journal of Pharmacy and Biological Sciences 9, no. 4 (2014): 74–79. http://dx.doi.org/10.9790/3008-09447479.
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Prieto-Peña, D., F. Genre, S. Remuzgo Martinez, V. Pulito-Cueto, B. Atienza-Mateo, B. Sevilla, J. Llorca, et al. "AB0096 IGA VASCULITIS AND IGA NEPHROPATHY SHARE A SIMILAR IL17A ASSOCIATION PATTERN." Annals of the Rheumatic Diseases 80, Suppl 1 (May 19, 2021): 1076.3–1077. http://dx.doi.org/10.1136/annrheumdis-2021-eular.766.
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Background:IgA vasculitis (IgAV) and IgA nephropathy (IgAN) are inflammatory conditions that share pathogenic and molecular mechanisms [1] and may represent different outcomes of a continuous spectrum of disease [2]. Interleukin (IL)17A has been identified as a common genetic risk locus for several immune-mediated diseases [3, 4].Objectives:To determine whether IgAV and IgAN exhibit a different IL17A association pattern.Methods:Five IL17A tag polymorphisms (rs4711998, rs8193036, rs3819024, rs2275913 and rs7747909) were genotyped in 388 Caucasian patients with IgAV, 99 patients with IgAN and 1,003 sex and ethnically matched healthy controls.Results:No statistically significant differences between patients with IgAV and healthy controls and between patients with IgAN and healthy controls were observed when each IL17A genetic variant was analyzed independently (Table 1). Similarly, IgAV patients exhibited similar genotype and allele IL17A frequencies than those with IgAN (Table 1). Moreover, no genotype or allele differences between IgAV patients who developed nephritis and patients with IgAN were detected. Furthermore, haplotype frequencies were similar in patients with IgAV, IgAV and nephritis and those with IgAN.Table 1.Genotype and allele frequencies of IL17A gene in patients with IgA vasculitis, patients with IgA nephropathy and healthy controls.PolymorphismChangeData set1/11/22/212rs4711998G/AIgAV53.4 (207)38.9 (151)7.7 (30)72.8 (565)27.2 (211)IgAN49.0 (48)42.9 (42)8.2 (8)70.4 (138)29.6 (58)Controls52.7 (529)41.2 (413)6.1 (61)73.3 (1471)26.7 (535)rs8193036T/CIgAV57.0 (221)38.4 (149)4.6 (18)76.2 (591)23.8 (185)IgAN64.3 (63)31.6 (31)4.1 (4)80.1 (157)19.9 (39)Controls60.3 (605)35.2 (353)4.5 (45)77.9 (1563)22.1 (443)rs3819024A/GIgAV44.1 (171)43.3 (168)12.6 (49)65.7 (510)34.3 (266)IgAN39.4 (39)54.5 (54)6.1 (6)66.7 (132)33.3 (66)Controls45.6 (457)44.6 (447)9.9 (99)67.8 (1361)32.2 (645)rs2275913G/AIgAV44.6 (172)43.3 (167)12.2 (47)66.2 (511)33.8 (261)IgAN39.8 (39)53.1 (52)7.1 (7)66.3 (130)33.7 (66)Controls44.8 (449)44.2 (443)11.1 (111)66.8 (1341)33.2 (665)rs7747909G/AIgAV53.9 (209)39.4 (153)6.7 (26)73.6 (571)26.4 (205)IgAN41.1 (39)54.7 (52)4.2 (4)68.4 (130)31.6 (60)Controls53.0 (532)39.4 (395)7.6 (76)72.7 (1459)27.3 (547)Conclusion:Our results revealed that IgAV and IgAN share a similar IL17A association pattern.References:[1]N Engl J Med 2013;368:2402-14.[2]Am J Kidney Dis 1988;12:373-7.[3]Ann Rheum Dis 2014;73:1742-5.[4]Mediators Inflamm 2018;2018:1395823.Acknowledgements:This study was supported by European Union FEDER funds and “Fondo de Investigaciones Sanitarias” (grant PI18/00042) from ‘Instituto de Salud Carlos III’ (ISCIII, Health Ministry, Spain). DP-P is a recipient of a Río Hortega programme fellowship from the ISCIII, co-funded by the European Social Fund (ESF, `Investing in your future´) [grant number CM20/00006]; SR-M is supported by funds of the RETICS Program co-funded by the European Regional Development Fund (ERDF) [grant number RD16/0012/0009]; VP-C is supported by a pre-doctoral grant from IDIVAL [grant number PREVAL 18/01]; BA-M is a recipient of a `López Albo´ Post-Residency Programme funded by Servicio Cántabro de Salud; LL-G is supported by funds of IDIVAL [grant number INNVAL20/06]; RL-M is a recipient of a Miguel Servet type I programme fellowship from the ISCIII, co-funded by the European Social Fund (ESF, `Investing in your future´) [grant number CP16/00033].Disclosure of Interests:Diana Prieto-Peña: None declared, Fernanda Genre: None declared, Sara Remuzgo Martinez: None declared, Verónica Pulito-Cueto: None declared, Belén Atienza-Mateo: None declared, Belén Sevilla: None declared, Javier Llorca: None declared, Norberto Ortego: None declared, Leticia Lera-Gómez: None declared, Maite Leonardo: None declared, Ana Peñalba: None declared, Luis Martín-Penagos: None declared, Jose Alberto Miranda-Filloy: None declared, J. Narváez: None declared, LUIS CAMINAL MONTERO: None declared, PAZ COLLADO: None declared, Antonio Fernandez-Nebro: None declared, Gisela Díaz-Cordoves: None declared, Secundino Cigarrán: None declared, Jesús Calviño: None declared, Carmen Cobelo: None declared, Javier Sanchez Perez: None declared, Diego de Argila: None declared, Esteban Rubio-Romero: None declared, MANUEL LEON LUQUE: None declared, Juan María Blanco-Madrigal: None declared, E. Galindez: None declared, Javier Martin Ibanez: None declared, Santos Castañeda: None declared, Ricardo Blanco Speakers bureau: Abbvie, Pfizer, Roche, Bristol-Myers, Janssen and MSD, Consultant of: Abbvie, Pfizer, Roche, Bristol-Myers, Janssen and MSD, Grant/research support from: Abbvie, MSD and Roche, Miguel A González-Gay Speakers bureau: Pfizer, Abbvie, MSD, Grant/research support from: Pfizer, Abbvie, MSD, Raquel López-Mejías: None declared
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Oliveira, Carlos Eduardo Coral de, Marla Karine Amarante, Aparecida de Lourdes Perim, Patricia Midori Murobushi Ozawa, Carlos Hiroki, Glauco Akelinghton Freire Vitiello, Roberta Losi Guembarovski, and Maria Angelica Ehara Watanabe. "Absence of Association betweenCCR5rs333 Polymorphism and Childhood Acute Lymphoblastic Leukemia." Advances in Hematology 2014 (2014): 1–5. http://dx.doi.org/10.1155/2014/924030.
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Acute lymphoblastic leukemia (ALL) is a malignant disorder that originates from one single hematopoietic precursor committed to B- or T-cell lineage. Ordinarily, these cells express CCR5 chemokine receptor, which directs the immune response to a cellular pattern and is involved in cancer pathobiology. The genetic rs333 polymorphism of CCR5 (Δ32), results in a diminished receptor expression, thus leading to impaired cell trafficking. The objective of the present study was to investigate the effect ofCCR5chemokine receptor rs333 polymorphism in the pathogenesis of ALL. The genotype distribution was studied in 79 patients and compared with 80 control subjects, in a childhood population of Southern Brazil. Genotyping was performed using DNA samples amplified by polymerase chain reaction with sequence-specific primers (PCR-SSP). The homozygous (Δ32/Δ32) deletion was not observed in any subject involved in the study. Heterozygous genotype was not associated with ALL risk (OR 0.7%; 95% CI 0.21–2.32;P>0.05), nor recurrence status of ALL (OR 0.86; 95% CI 0.13–5.48;P>0.05). This work demonstrated, for the first time, no significant differences in the frequency of the CCR5/Δ32 genotype between ALL and control groups, indicating no effect of this genetic variant on the ALL susceptibility and recurrence risk.
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Rong, Yu, Mingfei Zeng, Xiwen Guan, Kaixing Qu, Jianyong Liu, Jicai Zhang, Hong Chen, Bizhi Huang, and Chuzhao Lei. "Association of HSF1 Genetic Variation with Heat Tolerance in Chinese Cattle." Animals 9, no. 12 (November 25, 2019): 1027. http://dx.doi.org/10.3390/ani9121027.
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The heat shock factor 1 (HSF1) gene is a regulator of the heat stress response, maximizing HSP protein expression survival. In this research, we explored the frequency distribution of a missense mutation (NC_037341.1 g.616087A > G, rs135258919) in the HSF1 gene in Chinese cattle with amino acid substitution, valine to alanine. This mutation could be related to the heat tolerance in Bos indicus. A total of 941 individuals representing 35 Chinese native cattle breeds, combining pure taurine (Angus) and indicine cattle, were used to determine the genotypes of the mutation through PCR and partial DNA sequencing. The results showed significant differences in allele frequencies and their genotypes amongst Chinese cattle from different regions. Allele G or indicine-specific allele frequency diminished from south to north China, while allele A (genotype AA) or the taurine-specific allele had a contrary pattern, which agreed with the distribution of taurine and indicine cattle. According to the association analysis, the NC_037341.1 g.616087A > G (rs135258919) of the bovine HSF1 gene, annual temperature (T), relative humidity (RH), and the temperature humidity index (THI) (p < 0.01) were interrelated closely, which indicated that the NC_037341.1 g.616087A > G of the HSF1 gene is associated with heat tolerance in indicine cattle.
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Bae, Kyongtae T., Wen Zhou, Chengli Shen, Douglas P. Landsittel, Zhiyuan Wu, Cheng Tao, Arlene B. Chapman, et al. "Growth Pattern of Kidney Cyst Number and Volume in Autosomal Dominant Polycystic Kidney Disease." Clinical Journal of the American Society of Nephrology 14, no. 6 (May 14, 2019): 823–33. http://dx.doi.org/10.2215/cjn.10360818.
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Background and objectivesTo evaluate the growth pattern of kidney cyst number and cyst volume in association with kidney size, demographics, and genotypes in autosomal dominant polycystic kidney disease.Design, setting, participants, & measurementsKidney cyst number and cyst volume were measured from serial magnetic resonance images, giving a maximum follow-up of 14.23 years, from 241 patients with autosomal dominant polycystic kidney disease (15–46 years old at baseline). The growth pattern was analyzed, in association with sex, age, height-adjusted total kidney volume, and genotype, using linear mixed models of repeated measurements and tests of interactions with age (as a time-dependent covariate) to assess rates of change over time. Models were also fit using Irazabal class. Genotypic groups were characterized as either (1) PKD1 truncating, PKD1 nontruncating, and PKD2 plus patients with no mutation detected; or (2) in combination with PKD1 mutation strength groups.ResultsImaging and genetic data were collected (at least one visit) for 236 participants. The mean height-adjusted total cyst number increased exponentially over time from a baseline value of 762 to 1715 at the last clinic visit, while the mean height-adjusted total cyst volume increased exponentially from 305 to 770 ml. Height-adjusted total kidney volume, height-adjusted total cyst number, and height-adjusted total cyst volume were all highly correlated over time. Female participants and participants with larger height-adjusted total kidney volume at baseline showed smaller rates of change in the log of height-adjusted total cyst number and cyst volume. PKD1 was associated with significant increases in both cyst number and volume at a given age, but genotype did not significantly affect the rate of growth.ConclusionsBoth height-adjusted total cyst number and height-adjusted total cyst volume increased exponentially and more than doubled over 14.23 years of follow-up. Compared with PKD2 plus no mutation detected, PKD1 was associated with a greater cyst number and volume at a given age, but no significant difference in the rate of growth.
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Holtmann, Gerald, Elisabeth Grote, Winfried Siffert, Sebastian Haag, Birgit Adam, Ute Braun-Lang, Mathias Langkafel, and Wolfgang Senf. "Symptom pattern in patients with functional dyspepsia: Association with anxiety, depression and G-protein (GNB3) genotype." Gastroenterology 124, no. 4 (April 2003): A391. http://dx.doi.org/10.1016/s0016-5085(03)81978-9.
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Albalawi, Ibrahim A., Rashid Mir, and Fasel M. Abu-Duhier. "Molecular Evaluation of PROGINS Mutation in Progesterone Receptor Gene and Determination of its Frequency, Distribution Pattern and Association with Breast Cancer Susceptibility in Saudi Arabia." Endocrine, Metabolic & Immune Disorders - Drug Targets 20, no. 5 (May 31, 2020): 760–70. http://dx.doi.org/10.2174/1871530319666191125153050.
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Aims: Experimental and clinical evidence demonstrate that progesterone hormone and its nuclear receptor, the Progesterone Receptor (PR), play critical role in controlling mammary gland tumorigenesis and breast cancer development. Hormonal therapy (Tomaxifen) is the frontline treatment for hormone-dependent breast cancers. Progesterone hormone induces its action on the target cells by binding with its Progesterone receptor (PgR) therefore any genetic variations, which might induce alienation in the progesterone receptor, can result in an increased susceptibility of gynecological cancers. Alu insertion (PROGINS) mutation in PgR gene is reported to be associated with an increased risk of ovarian cancer and a decreased risk of breast cancer. However, its association with breast cancer risk remains inconclusive. Therefore, we investigated the association of PROGINS allele and its link with breast cancer risk. Methods: This case control study was performed on 200 subjects in which 100 were breast cancer cases and 100 gender matched healthy controls.The mutation was detected by using mutation specific PCR and results were confirmed by direct Sanger sequencing. Results: A clinically significant difference was reported in genotype distribution of PROGINs allele among the cases and gender-matched healthy controls (P<0. 032). Genotype frequencies of A1/A1, A1/A2, A2/A2 reported in cases was 81%, 19% (18% & 1%) and in matched healthy controls were 93%, 7% (6% & 1%). The higher frequency of PROGINs allele (19%) was observed in cases than the healthy controls (7%). The findings indicated that PgR variants (CC vs CT) increased the risk of Breast cancer in codominant inheritance model with OR= 3.44, 95% CI =1. 30-9.09, P<0.021) whereas nonsignificant association was found for CC vs TT genotypes with OR=1.14, 95% CI=0.07-18.658, P=0. 92. However, subgroup analysis revealed that CT + TT vs CC genotype increased the risk of breast cancer in dominant inheritance model tested OR = 3. 11, 95% CI = (1.24-7.79), P = 0.015). A nonsignificant association for PgR (CC+CT) vs TT) genotypes were reported in breast cancer OR = 1. 0, 95% CI= (0. 061-16.21), P=1) in recessive inheritance model tested. However, analysis with clinicalpathological variables revealed that the PROGINs allele is significantly associated with the distant metastasis and advanced stage of the disease. Conclusion: The mutation specific PCR was successfully developed as an alternative to Sanger sequencing for the cost-effective detection for PROGINS allele of progesterone receptor gene. A clinically significant correlation of PROGINs allele was reported with the distant metastasis and advanced stage of the disease. Taken together, these results demonstrated that PROGINS variant is associated with an increased susceptibility to Breast cancer, providing novel insights into the genetic etiology and underlying biology of Breast carcinogenesis. Further studies with large sample sizes are required to validate our findings.
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Biriukova, O. D., T. M. Suprovych, M. P. Suprovych, S. V. Laiter-Moskaliuk, and I. O. Chornyi. "FEATURES OF DIAGNOSIS OF NECROBACTERIOSIS OF COWS BY PCR-RFLP." Podilian Bulletin: Agriculture, Engineering, Economics, no. 32 (June 29, 2020): 26–37. http://dx.doi.org/10.37406/2706-9052-2020-1-3.
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Molecular genetic markers can detect polymorphism at the DNA level. This feature determines the possibility of their widespread use in genetics and breeding. Alleles of the BoLA-DRB3 gene (exon 2) can act as such markers if a statically significant association between the disease and the allele is established. The presence of such DNA markers in the genotype of animals makes it possible to judge the likelihood of disease in postnatal ontogenesis immediately after the birth of a heifer, based on which we can conclude about the conditions of further use of the animal in the main herd. According to the results of studying the polymorphism of the BoLA-DRB3 gene in cows of the Ukrainian black and white dairy breed resistant and susceptible to necrobacteriosis, four "informative" alleles were revealed. Two of them *03 and *22 are associated with resistance, and the other two - *16 and *23 with susceptibility to necrobacteriosis. The presence of these alleles in the genotype of the animal is determined by testing performed by PCR-RFLP. The method is time consuming, labor intensive and costly. To simplify it, the following technique is proposed. Restriction fragments of alleles *03, *16, *22 and *23 for endocluases RsaI, XhoII and HaeIII have the following DNA patterns: bbb, jbd, mba and nba. Due to the peculiarity of the restriction fragments, which is that endonuclease XhoII reveals in these alleles only one pattern b with length of 284 bp, the process of determining informative alleles can be simplified. Isolation of DNA from blood samples and amplification of a fragment of the BoLA-DRB3.2 gene with a size of 284 bp is carried out according to the established technique. Next, the restriction of the fragment by endonuclease XhoII and sampling having a pattern b. Selected samples are treated with RsaI endonuclease and only those with patterns b, j, m and n remain. The next step is to restrict the selected samples with HaeIII endonuclease and select heifers with bbb (*03) and nba (*23) genotypes. After the first restriction, blood samples without pattern b are eliminated from the experimental sample; after the second – two alleles with patterns RsaI + XhoII jb (*16) and mb (*22) are unambiguously determined, after the third – genotypes bbb and nba, which correspond to alleles *03 and *23. In total, only 75% of blood samples are typed, which reduces the material consumption, time and cost of work to identify heifers genetically susceptible (resistant) to necrobacteriosis.
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Bozokalfa, Kadri, Bülent Yağmur, Dursun Eşiyok, and Aşçioğul Kaygisiz. "Genetic variability and association pattern among quantitative nutritional traits in Swiss chard (Beta vulgaris subsp. L. var. cicla) accessions and its implication for breeding." Genetika 46, no. 2 (2014): 505–14. http://dx.doi.org/10.2298/gensr1402505b.
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In addition to improving agronomic traits, enriched cultivar such as nutritional elements and health promoting compounds are new demands for today's and the future's perspectives of crop breeding. In this respect, among leafy vegetables Swiss chard is a good source of nutritional elements and supplies large amounts of health promoting compounds. The existing knowledge of genetic variability for mineral composition both at the phenotype and genotype level, heritability of characters and also relationships among investigated minerals is fundamental for variety selection in Swiss chard. This also applies for the assurance of desirable agronomic traits with optimum mineral concentrations. This research analysis of variance indicated highly significant differences among Swiss chard accessions for all investigated mineral concentrations and the accessions display higher phenotype coefficient variation than genotype coefficient variation for all traits. The results revealed that phosphorus, magnesium, sodium, iron, copper, zinc, manganese, nitrate and nitrite exhibited high genetic advance accompanied with high heritability (>60%). The remaining mineral content demonstrated high heritability with moderate genetic advance. Genotype correlations were higher than the phenotype correlation for significant mineral concentrations. Genotype and phenotype correlations followed similar trends in all significant cases indicating the high heritable nature of the characters and the results showed that Swiss chard accessions should allow for the selection of individuals for enriched mineral concentration in edible parts of the plant.
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Ramachandran, V., J. D. McArthur, C. E. Behm, C. Gutzeit, M. Dowton, P. K. Fagan, R. Towers, B. Currie, K. S. Sriprakash, and M. J. Walker. "Two Distinct Genotypes of prtF2, Encoding a Fibronectin Binding Protein, and Evolution of the Gene Family in Streptococcus pyogenes." Journal of Bacteriology 186, no. 22 (November 15, 2004): 7601–9. http://dx.doi.org/10.1128/jb.186.22.7601-7609.2004.
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ABSTRACT The group A Streptococcus (GAS) is an important pathogen that is responsible for a wide range of human diseases. Fibronectin binding proteins (FBPs) play an important role in promoting GAS adherence and invasion of host cells. The prtF2 gene encodes an FBP and is present in approximately 60% of GAS strains. In the present study we examined 51 prtF2-positive GAS strains isolated from the Northern Territory of Australia, and here we describe two genotypes of prtF2 which are mutually exclusive. The two genotypes have been identified previously as pfbp and fbaB. We show that these genotypes map to the same chromosomal location within the highly recombinatorial fibronectin-collagen-T antigen (FCT) locus, indicating that they arose from a common ancestor, and in this study these genotypes were designated the pfbp type and the fbaB type. Phylogenetic analysis of seven pfbp types, 14 fbaB types, and 11 prtF2-negative GAS strains by pulsed-field gel electrophoresis (PFGE) produced 32 distinct PFGE patterns. Interpretation of evolution based on the PFGE dendrogram by parsimony suggested that the pfbp type had a recent origin compared to the fbaB type. A comparison of multiple DNA sequences of the pfbp and fbaB types revealed a mosaic pattern for the amino-terminal region of the pfbp types. The fbaB type is generally conserved at the amino terminus but varies in the number of fibronectin binding repeats in the carboxy terminus. Our data also suggest that there is a possible association of the pfbp genotype with sof (84.2%), while the fbaB genotype was found in a majority of the GAS strains negative for sof (90.6%), indicating that these two prtF2 subtypes may be under different selective pressures.
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Santos, Roseane M. "Preliminary Studies on Genetic Profiling of Coffee and Caffeine Consumption." Beverages 5, no. 3 (July 1, 2019): 41. http://dx.doi.org/10.3390/beverages5030041.
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Regular coffee intake has been associated with reduced risk of developing serious chronic diseases. The hypothesis of this study is that coffee consumers present a particular pattern/trend of genotypes that ultimately will shed light on new gene targets to treat the diseases, from which regular coffee intake has preventive effects. Sixteen SNPs identified at genome-wide association studies (GWAS) on coffee and caffeine consumption were genotyped using real-time restriction-fragment length polymorphism-polymerase chain reaction (RT-PCR). The DNA samples were the same from a previous pilot study where 15 healthy volunteers donated two blood samples collected before and after drinking a standard cup of coffee and had caffeine plasma levels and CYP 1A2 genotype (rs762551) determined. The cross-examination of the data showed that six of the sixteen SNPs exhibited a negative allelic effect direction and nine of them showed a positive effect direction of which three of them had results confirmed by a recent GWAS. There is a need of a more in-depth study to understand the effects of the presence or absence of specific variant alleles as players to benefit the health of coffee consumers.
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Liu, Haipei, Amanda J. Able, and Jason A. Able. "Genotypic water-deficit stress responses in durum wheat: association between physiological traits, microRNA regulatory modules and yield components." Functional Plant Biology 44, no. 5 (2017): 538. http://dx.doi.org/10.1071/fp16294.
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In Mediterranean environments, water-deficit stress that occurs before anthesis significantly limits durum wheat (Triticum turgidum L. ssp. durum) production. Stress tolerant and stress sensitive durum varieties exhibit genotypic differences in their response to pre-anthesis water-deficit stress as reflected by yield performance, but our knowledge of the mechanisms underlying tolerance is limited. We have previously identified stress responsive durum microRNAs (miRNAs) that could contribute to water-deficit stress tolerance by mediating post-transcriptional silencing of genes that lead to stress adaptation (e.g. miR160 and its targets ARF8 (auxin response factor 8) and ARF18). However, the temporal regulation pattern of miR160-ARFs after induction of pre-anthesis water-deficit stress in sensitive and tolerant varieties remains unknown. Here, the physiological responses of four durum genotypes are described by chlorophyll content, leaf relative water content, and stomatal conductance at seven time-points during water-deficit stress from booting to anthesis. qPCR examination of miR160, ARF8 and ARF18 at these time-points revealed a complex stress responsive regulatory pattern, in the flag leaf and the head, subject to genotype. Harvest components and morphological traits measured at maturity confirmed the stress tolerance level of these four varieties for agronomic performance, and their potential association with the physiological responses. In general, the distinct regulatory pattern of miR160-ARFs among stress tolerant and sensitive durum varieties suggests that miRNA-mediated molecular pathways may contribute to the genotypic differences in the physiological traits, ultimately affecting yield components (e.g. the maintenance of harvest index and grain number).
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Strehlow, Becke, Friederike de Mol, and Christine Struck. "History of Oilseed Rape Cropping and Geographic Origin Affect the Genetic Structure of Plasmodiophora brassicae Populations." Phytopathology® 104, no. 5 (May 2014): 532–38. http://dx.doi.org/10.1094/phyto-07-13-0210-r.
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The soilborne pathogen Plasmodiophora brassicae causes clubroot on Brassica crops, a common disease in many oilseed rape growing regions. Here, we investigate genetic diversity and geographic differentiation of P. brassicae populations from different regions in Germany. We compared three regions that differ in oilseed rape cropping history, oilseed rape acreage, and incidence of clubroot. These regions were either spatially separated or separated by the former inner German border. Plasmodiophora isolates were collected from 59 fields (29, 17, and 13 fields per region, respectively) and 174 amplified fragment length polymorphism (AFLP) markers were analyzed. Every field isolate showed a unique genotype pattern; that is, no genotype was shared among the regions and different fields. The mean gene diversity was 0.27, suggesting that P. brassicae is a genetically diverse species. The comparison of indexes (gene diversity, genotypic diversity, and linkage disequilibrium) between the regions does not support our hypotheses that cropping history, oilseed rape acreage, and incidence of clubroot affect these estimates. Principal component analysis (PCA), fixation index (FST), and generalized linear model (GLM) were suitable to specify regional differences. PCA revealed two clusters of isolates based on the geographic origin of the isolates and FST showed that these clusters were highly differentiated. Hypotheses about association of genotypes with different spatial scales were tested with GLM: the region, reflecting the cropping history, and the individual field had a significant effect on the AFLP pattern. We propose that individual field isolates represent a discrete population and that geographic differentiation results from low levels of gene flow due to the limited dispersal of this soilborne pathogen and from localized selection pressure as unifying force on the genotypes.
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Riddle, Nicole C. "Variation in the response to exercise stimulation in Drosophila: marathon runner versus sprinter genotypes." Journal of Experimental Biology 223, no. 18 (July 31, 2020): jeb229997. http://dx.doi.org/10.1242/jeb.229997.
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ABSTRACTAnimals' behaviors vary in response to their environment, both biotic and abiotic. These behavioral responses have significant impacts on animal survival and fitness, and thus, many behavioral responses are at least partially under genetic control. In Drosophila, for example, genes impacting aggression, courtship behavior, circadian rhythms and sleep have been identified. Animal activity also is influenced strongly by genetics. My lab previously has used the Drosophila melanogaster Genetics Reference Panel (DGRP) to investigate activity levels and identified over 100 genes linked to activity. Here, I re-examined these data to determine whether Drosophila strains differ in their response to rotational exercise stimulation, not simply in the amount of activity, but in activity patterns and timing of activity. Specifically, I asked whether there are fly strains exhibiting either a ‘marathoner’ pattern of activity, i.e. remaining active throughout the 2 h exercise period, or a ‘sprinter’ pattern, i.e. carrying out most of the activity early in the exercise period. The DGRP strains examined differ significantly in how much activity is carried out at the beginning of the exercise period, and this pattern is influenced by both sex and genotype. Interestingly, there was no clear link between the activity response pattern and lifespan of the animals. Using genome-wide association studies (GWAS), I identified 10 high confidence candidate genes that control the degree to which Drosophila exercise behaviors fit a marathoner or sprinter activity pattern. This finding suggests that, similar to other aspects of locomotor behavior, the timing of activity patterns in response to exercise stimulation is under genetic control.
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Chowbay, B., S. Lal, X. Shu, S. Jada, L. Ooi, Y. Liu, and Y. Ong. "Hepatic expression of UGT enzymes and implications in pharmacokinetic variations in Asians during chemotherapy." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 14089. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.14089.
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14089 Background: The objective of this study was to screen the promoter and relevant coding regions in the UGT1A1 and UGT1A9 genes and genotypically quantitate expression of these genes in hepatic tissues obtained from Asian cancer patients undergoing hepatectomy. Methods: Non-cancerous Asian hepatic tissues (Chinese: N=36; Malay: N=1; Indian: N=3) were obtained from the institution’s central tissue repository bank. Messenger RNA was isolated from each tissue sample and reverse transcribed to cDNA followed by real time PCR experiments. Results from these gene expression experiments were normalized against GAPDH transcripts. DNA was also extracted from the hepatocytes, screened for variations in the promoter regions (UGT1A1*60, g.3140G>A and UGT1A1*28) and exon 1 (UGT1A1*6) of the UGT1A1 and UGT1A9 (UGT1A9*22, I399C>T) genes. Results: Large interindividual variations were observed in the hepatic expression pattern of UGT1A1 and UGT1A9 mRNA with respect to the different polymorphic variants. There was no significant association between hepatic expression of UGT1A1 mRNA and UGT1A1*60, g-3140G>A and *6 genotypes (P>0.05 in each case). The median expression level of UGT1A1 mRNA was approximately 2-fold higher in liver tissues harboring UGT1A1 6/6 (reference) genotype (N=27, median = 0.478; range: 0.065 to 3.125) compared to the heterozygous 6/7 genotype (N=9, median = 0.254; range: 0.042 to 1.894; P=0.77). The median expression levels of UGT1A9 mRNA were approximately 3-fold higher in liver tissues harboring I399CC genotype (N=3, median = 2.735; range: 0.702 to 3.375) when compared with the homozygous variant TT genotype (N=8, median = 0.973; range: 0.652 to 4.155; P=0.88). Conclusions: The results showed that polymorphisms in the UGT1A genes may influence the expression pattern of the respective proteins and could contribute to the high degree of interpatient variability in the glucuronidation dependent metabolism and elimination of chemotherapeutic agents in Asian cancer patients. No significant financial relationships to disclose.
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Cui, Xiaohui, Yan Sun, Xiuge Wang, Chunhong Yang, Zhihua Ju, Qiang Jiang, Yan Zhang, et al. "A g.-1256 A>C in the promoter region of CAPN1 is associated with semen quality traits in Chinese Holstein bulls." Reproduction 152, no. 1 (July 2016): 101–9. http://dx.doi.org/10.1530/rep-15-0535.
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The micromolar calcium-activated neutral protease gene (CAPN1) is a physiological candidate gene for sperm motility. However, the molecular mechanisms involved in regulating the expression of the CAPN1 gene in bulls remain unknown. In this study, we investigated the expression pattern of CAPN1 in testis, epididymis, and sperm at the RNA and protein levels by qRT-PCR, western blot, immunohistochemistry, and immunofluorescence assay. Results revealed that the expression of CAPN1 levels was higher in the sperm head compared with that in other tissues. Moreover, we identified a novel single-nucleotide polymorphism (g.-1256 A>C, ss 1917715340) in the noncanonical core promoter of the CAPN1 gene between base g.-1306 and g.-1012. Additionally, we observed greater sperm motility in bulls with the genotype CC than in those with the genotype AA (P<0.01), indicating that different genotypes were associated with the bovine semen trait. Furthermore, a higher fluorescence intensity of the C allele than that of the A allele at g. -1256 A>C was revealed by transient transfection in MLTC-1 cells and luciferase report assay. Finally, CAPN1 was highly expressed in the spermatozoa with the CC genotype compared with that with the AA genotype by qRT-PCR. This study is the first report on genetic variant g.-1256 A>C in the promoter region of CAPN1 gene association with the semen quality of Chinese Holstein bulls by influencing its expression. g.-1256 A>C can be a functional molecular marker in cattle breeding.
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Ko, Mi Mi, Tae-Yong Park, Ji Hye Lim, Min Ho Cha, and Myeong Soo Lee. "WNT10B Polymorphism in Korean Stroke Patients with Yin Deficiency Pattern." Evidence-Based Complementary and Alternative Medicine 2012 (2012): 1–6. http://dx.doi.org/10.1155/2012/798131.
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WNT10B has been indicated as a potential regulator of adipogenesisin vivoandin vitromodels of obesity. In this study, we analyzed the distribution of WNT10B polymorphism in elderly Korean subjects with cerebral infarction (CI) and Yin Deficiency pattern and Non-Yin Deficiency pattern. A total of 630 CI patients, including 75 with Yin Deficiency pattern and 555 with Non-Yin Deficiency pattern, participated in this study. SNP (G-607C) genotyping was conducted by primer extension using TaqMan probe; five percent of subjects were regenotyped by direct sequencing to confirm the accuracy of the genotyping. The results were analyzed using a multiple logistic regression model to evaluate the genetic association between the G-607C variant and Yin Deficiency pattern. The frequency of the CC genotype of G-607C in the Yin Deficiency pattern group (29.33%) was significantly higher than that in the Non-Yin Deficiency pattern group (23.96%) (P=0.0339,OR=2.005(1.054–3.814)) in a recessive model. This is the first study to demonstrate an association between a WNT10B polymorphism and the Yin Deficiency pattern of traditional Korean medicine (TKM) in a CI patient population. These results suggest that G-607C might be used as a diagnostic genetic marker for Yin Deficiency pattern in stroke patients and in the development of personalized medical care.
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Tsang, Becky L., Owen J. Devine, Amy M. Cordero, Claire M. Marchetta, Joseph Mulinare, Patricia Mersereau, Jing Guo, et al. "Assessing the association between the methylenetetrahydrofolate reductase (MTHFR) 677C>T polymorphism and blood folate concentrations: a systematic review and meta-analysis of trials and observational studies." American Journal of Clinical Nutrition 101, no. 6 (March 18, 2015): 1286–94. http://dx.doi.org/10.3945/ajcn.114.099994.
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ABSTRACTBackground: The methylenetetrahydrofolate reductase (MTHFR) 677C>T polymorphism is a risk factor for neural tube defects. The T allele produces an enzyme with reduced folate-processing capacity, which has been associated with lower blood folate concentrations.Objective: We assessed the association between MTHFR C677T genotypes and blood folate concentrations among healthy women aged 12–49 y.Design: We conducted a systematic review of the literature published from January 1992 to March 2014 to identify trials and observational studies that reported serum, plasma, or red blood cell (RBC) folate concentrations and MTHFR C677T genotype. We conducted a meta-analysis for estimates of percentage differences in blood folate concentrations between genotypes.Results: Forty studies met the inclusion criteria. Of the 6 studies that used the microbiologic assay (MA) to measure serum or plasma (S/P) and RBC folate concentrations, the percentage difference between genotypes showed a clear pattern of CC > CT > TT. The percentage difference was greatest for CC > TT [S/P: 13%; 95% credible interval (CrI): 7%, 18%; RBC: 16%; 95% CrI: 12%, 20%] followed by CC > CT (S/P: 7%; 95% CrI: 1%, 12%; RBC: 8%; 95% CrI: 4%, 12%) and CT > TT (S/P: 6%; 95% CrI: 1%, 11%; RBC: 9%; 95% CrI: 5%, 13%). S/P folate concentrations measured by using protein-binding assays (PBAs) also showed this pattern but to a greater extent (e.g., CC > TT: 20%; 95% CrI: 17%, 22%). In contrast, RBC folate concentrations measured by using PBAs did not show the same pattern and are presented in the Supplemental Material only.Conclusions: Meta-analysis results (limited to the MA, the recommended population assessment method) indicated a consistent percentage difference in S/P and RBC folate concentrations across MTHFR C677T genotypes. Lower blood folate concentrations associated with this polymorphism could have implications for a population-level risk of neural tube defects.
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Jones, Christopher T., Noor Youssef, Edward Susko, and Joseph P. Bielawski. "A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution." Systematic Biology 69, no. 4 (December 17, 2019): 722–38. http://dx.doi.org/10.1093/sysbio/syz075.
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Abstract A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here, we present a novel approach called the phenotype–genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio $\omega$ to a value $\omega > 1$. As it is becoming increasingly clear that $\omega > 1$ can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include 1) a persistent increase/decrease in $\omega$ at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and 2) a transient increase in $\omega$ at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site’s optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-cause. [Adaptive evolution; branch-site model; confounding; mutation-selection; phenotype–genotype.]
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Gray, Victoria, Sarah Briggs, Claire Palles, Emma Jaeger, Timothy Iveson, Rachel Kerr, Mark P. Saunders, et al. "Pattern Recognition Receptor Polymorphisms as Predictors of Oxaliplatin Benefit in Colorectal Cancer." JNCI: Journal of the National Cancer Institute 111, no. 8 (January 14, 2019): 828–36. http://dx.doi.org/10.1093/jnci/djy215.
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Abstract Background Constitutional loss of function (LOF) single nucleotide polymorphisms (SNPs) in pattern recognition receptors FPR1, TLR3, and TLR4 have previously been reported to predict oxaliplatin benefit in colorectal cancer. Confirmation of this association could substantially improve patient stratification. Methods We performed a retrospective biomarker analysis of the Short Course in Oncology Therapy (SCOT) and COIN/COIN-B trials. Participant status for LOF variants in FPR1 (rs867228), TLR3 (rs3775291), and TLR4 (rs4986790/rs4986791) was determined by genotyping array or genotype imputation. Associations between LOF variants and disease-free survival (DFS) and overall survival (OS) were analyzed by Cox regression, adjusted for confounders, using additive, dominant, and recessive genetic models. All statistical tests were two-sided. Results Our validation study populations included 2929 and 1948 patients in the SCOT and COIN/COIN-B cohorts, respectively, of whom 2728 and 1672 patients had functional status of all three SNPs determined. We found no evidence of an association between any SNP and DFS in the SCOT cohort, or with OS in either cohort, irrespective of the type of model used. This included models for which an association was previously reported for rs867228 (recessive model, multivariable-adjusted hazard ratio [HR] for DFS in SCOT = 1.19, 95% confidence interval [CI] = 0.99 to 1.45, P = .07; HR for OS in COIN/COIN-B = 0.92, 95% CI = 0.63 to 1.34, P = .66), and rs4986790 (dominant model, multivariable-adjusted HR for DFS in SCOT = 0.86, 95% CI = 0.65 to 1.13, P = .27; HR for OS in COIN/COIN-B = 1.08, 95% CI = 0.90 to 1.31, P = .40). Conclusion In this prespecified analysis of two large clinical trials, we found no evidence that constitutional LOF SNPs in FPR1, TLR3, or TLR4 are associated with differential benefit from oxaliplatin. Our results suggest these SNPs are unlikely to be clinically useful biomarkers.
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Koika, Vasiliki, Neoklis A. Georgopoulos, Athanasia Piouka, Nikolaos D. Roupas, Anastasia Karela, Anastasia K. Armeni, Eleni Katsantoni, and Dimitrios Panidis. "Increased frequency of the DI genotype of the angiotensin-I converting enzyme and association of the II genotype with insulin resistance in polycystic ovary syndrome." European Journal of Endocrinology 166, no. 4 (April 2012): 695–702. http://dx.doi.org/10.1530/eje-11-0894.
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ObjectiveThe polycystic ovary syndrome (PCOS) is a common and complex disease with unclear pattern of inheritance, characterized by an androgen excess, while hyperinsulinemia and insulin resistance (IR) are common features of the syndrome. The angiotensin I converting enzyme (ACE) insertion (I)/deletion (D) gene polymorphism was proved to be involved in many pathophysiological conditions, including hypertension and IR.DesignThe purpose of this study was to evaluate the involvement of the ACE gene polymorphism in the pathogenesis of PCOS.MethodsIn a case–control association study involving 801 PCOS women and 266 healthy controls, hormonal determinations and ACE polymorphism genotyping were performed. The PCOS women were classified into three groups: Group A presented biochemical hyperandrogenism, combined with anovulation and polycystic ovarian morphology; Group B, clinical hyperandrogenism combined with anovulation and polycystic ovarian morphology; and Group C, chronic anovulation and polycystic ovarian morphology.ResultsA significant increase in the frequency of the DI genotype of the ACE polymorphism was detected in PCOS women as a whole (P=0.035), in PCOS Group A (P=0.039) and Group B (P=0.010), while there was no difference in Group C (P=0.939). Significant difference was also observed in hyperandrogenic PCOS women as a whole (Group A+B) (P=0.017). The II genotype was positively correlated with HOMA-IR and QUICKI and with fasting insulin and glucose/insulin ratio in these groups.ConclusionsThe association study of the ACE I/D polymorphism in PCOS women demonstrates an increase in the DI genotype incidence and an association of the II genotype with IR.
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Beksac, Meral, Merih Kizil, Ender A. Soydan, Esin Serbest, and Klara Dalva. "Interleukin-10(IL-10)1082-A and Tumor Necrosis Factor(TNF)-Alpha 238/308A Genotypes Are Associated with Earlier (Younger Than 55) Onset of Multiple Myeloma." Blood 104, no. 11 (November 16, 2004): 4869. http://dx.doi.org/10.1182/blood.v104.11.4869.4869.
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Abstract The individual differences among the polymorphic regions of the cytokine genes involved in the pathogenesis of myeloma have been investigated by various groups: Neben et al have found the TNF238 A allel to be associated with a higher serum level of TNF-alpha and with better response to Thalidomide. The IL 10-1082 G promoter gene genotype have been found to be associated with high secretory pattern and in increased frequency among myeloma patients compared to normal controls by Zheng et al. Van Ness et al have reported the IL-10-G genotype to be associated with shorter survival compared to IL-10-A allele carriers None of these groups have analyzed the impact of these genotypes on age of onset. With an aim to analyze the association between the frequencies of the cytokines known to be important in the pathogenesis of Myeloma, TNF-alpha, IL-6, IL-10 and the age of diagnosis, we have isolated DNA from peripheral blood of 59 patients. Patients with a median age of 56(28–83)M/F:35/24 diagnosed and treated in our center between 2002–2004 were analyzed. To determine the TNF 238 and 308(G/A), IL-6 174(G/C), IL-10 1082(G/A),819(T/C) and 592(A/C) bp polymorphic allele frequencies Cytokine Genotyping Kit (Pel-Freeze) and/or Cytgen (OneLambda) Genotyping Trays have been used. Evaluation of results were done as described in the worksheets. Interpretation and definition of phenotypes(low and high secretory patterns) were based on the previously published reports. 30 patients(50,8%) were younger than 56 (median=the cutoff:56). TNF-A homozygous alelle couldnot be observed among all patients. The frequencies of all alleles were: TNF-alfa308A, TNF-alfa238A, IL-10 1082 G 20%, 20%, 12% respectively. IL-6 -GG/GC alleles which have been linked with high secretory pattern constituted the majority of the patients(58/59). When TNFalfa-A were detected based on the 238 bp reactivity the association of low phenotype with elder age was remarkable(p=0.019). This finding wasnot valid for the 308 bp location. IL-10 phenotypes were more complicated with an accumulation in the intermediate level of secretion. The impact of TNF was varified with the separate evaluation of this group, based on their TNF-238/308 genotype, p=0.031). Conclusion: There is a trend towards younger age of onset in Myeloma. Genetic factors for susceptibility have not been defined yet. The new tools for detection of single nucleotide polymorphisms have a promising role in this field. In our prospective study we have found a predominance of low IL-10 secretory A genotype and the high secretory TNF-A genotype among patients younger than 56. To our knowledge this is the first report on such an association. Investigation of other genes in linkeage with TNF on the neighboring MHC region may be necessary for understanding myeloma pathogenesis. Age TNF 238 H/L TNF 308 H/L TNF 238,308 H/L IL-10 H/I/L IL-10 I,TNF H(238 or 308)/ IL-10 I,TNF L(238 or308) L:Low, H: High,I:Intermediate secretory, TNF238A:H, TNF238G:L, TNF308A:H, TNF308G:L, IL-10G: H ≤55 5 / 7 6 / 24 7 / 5 1 /16 / 13 5 / 2 >55 1 / 16 6 / 23 4 / 13 6 /13 / 8 1 / 6 N=29, p=0.019 N=59, p=0.948 N=29, p=0.057 N=57, p=0.085 N=14, p=0.031
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Rossi, Davide, Silvia Rasi, Claudio Tripodo, Francesco Forconi, Luca Laurenti, Alessio Bruscaggin, Marco Fangazio, et al. "Host Genetic Background and Risk of Richter Syndrome: The Genotype of LRP4 Is An Independent Predictor of Chronic Lymphocytic Leukemia Transformation to Aggressive Lymphoma." Blood 114, no. 22 (November 20, 2009): 2340. http://dx.doi.org/10.1182/blood.v114.22.2340.2340.
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Abstract Abstract 2340 Poster Board II-317 Richter syndrome (RS) represents the transformation of chronic lymphocytic leukemia (CLL) to aggressive lymphoma, most commonly diffuse large B-cell lymphoma (DLBCL). Mechanisms and risk factors of CLL transformation to RS are known only in part. This study aimed at exploring the role of the host genetic background in RS transformation and was based on a consecutive series of 331 CLL, of which 21 had transformed to RS (all clonally related to the CLL clone). Twenty eight additional cases of clonally related RS were also collected for validation purposes. Using an educated guess approach, SNPs were selected according to the following criteria: i) reported association with CLL prognosis; ii) minor allele frequency >5% in Caucasians. Accordingly, 45 SNPs from 45 genes (APOE, BARD1, BRCA2, CD5, CPA4, CPT2, CYP2C9, CD38, DUSP13, ENPP5, ERBB2IP, ERCC5, ERCC6 ESPL1, FHL5, FOXN1, GALNACT2, GTF2E1, HIPK4, IL16, IL19, INHBC, KLRC4, KRT1, LAMA2, LILRA4, LRP2, LRP4, MDM2, MGMT, MMP10, MYBPC3, PMS2, POLB, SEC23B, SEMA3C, THBS1, TOPBP1, TYR, USP47, XRCC2, ZNF169, ZNF527, ZNF573, IRF4) were genotyped by SNP-minisequencing. The primary endpoint of the study was cumulative probability of transformation measured from CLL diagnosis to RS transformation, death or last follow-up. Univariate Cox analysis controlled for multiple comparisons by FDR testing identified LRP4 rs2306029, a SNP affecting the low density lipoprotein receptor protein 4 gene, as the sole SNP associated with RS transformation. CLL who carried LRP4 rs2306029 TT variant genotype displayed a higher risk of transformation (Events/N: 12/79; 5-year risk: 14.1%) compared to patients carrying the LRP4 rs2306029 CT/CC genotypes that contained the wild type allele (Events/N: 9/252; 5-year risk: 4.7%) (HR:4.08; p<.001; q=.040) (Fig. 1). Other variables at CLL diagnosis associated with an increased risk of RS were advanced Binet stage (p<.001), lymph node size >3 cm, LDH elevation (p<.001), CD38 expression (p=.010), ZAP70 expression (p=.017), unfavorable FISH karyotype (p<.001), IGHV homology >98% (p<.001), and stereotyped HCDR3 (p<.001). None of the patient subgroups carrying the above risk factors was enriched with the LRP4 rs2306029 TT variant genotype (p>.050 in all instances), suggesting that LRP4 rs2306029 TT is not a surrogate of other RS risk factors. Multivariate Cox analysis selected LRP4 rs2306029 TT as an independent predictor of RS (HR:5.66; p<.001), along with stereotyped HCDR3 (HR:5.02; p=.001), and CD38 expression (HR:3.47; p=.011). LRP4 rs2306029 genotyping in an independent RS series (n=28) collected for validation purposes confirmed the enrichment of TT genotype and T alleles observed in the original RS series (TT genotype: 11/28 39.2% vs 12/21, 57.1%; p=.139; T allele: 60.7% vs 64.3%; p=.811). To date, the sole other host genetic factor associated with RS transformation is the CD38 rs6449182 SNP (Aydin et al, Blood 2008; 111: 5646). LRP4 rs2306029 and CD38 rs6449182 genotypes displayed statistical interaction and identified CLL subgroups at different risk of transformation (p=.043). LRP4 rs2306029 is a non-synonymous SNP mapping to exon 31 of LRP4 and leading to Ser1554Gly amino acid substitution. In silico analysis with PupaSuite, PolyPhen, and SNPeffect algorithms predicted LRP4 rs2306029 T variant allele to have functional effect on LRP4 protein. In silico elaboration of public data sets revealed that LRP4 gene expression levels did not differ among LRP4 rs2306029 genotypes (p=.743). LRP protein expression in CLL is unknown and was analyzed in 26 cases. By flow cytometry, LRP4 was expressed in all cases with a median percentage of expression of 92.0% and a MFI of 78.0 that did not vary among genotypes (p=.527 and p=.964, respectively). By immunohistochemistry on bone marrow biopsies, LRP4 showed an expression pattern that varied according to genotype of the rs2306029 SNP, being cytoplasmic in CLL carrying the T allele and nuclear in CLL carrying the CC genotype. The conclusion of our study are threefold: i) LRP4 rs2306029 TT genotype is an independent predictor of CLL transformation to RS; ii) LRP4 protein is expressed in CLL cells; iii) LRP4 rs2306029 genotype may affect the expression pattern of LRP4 in CLL cells. Since LRP4 is involved in suppressing Wnt signalling, the LRP4 rs2306029 T variant may have pathogenetic relevance for RS development. Disclosures: No relevant conflicts of interest to declare.
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Schreiner, Felix, Sonja Stutte, Peter Bartmann, Bettina Gohlke, and Joachim Woelfle. "Association of the Growth Hormone Receptor d3-Variant and Catch-up Growth of Preterm Infants with Birth Weight of Less Than 1500 Grams." Journal of Clinical Endocrinology & Metabolism 92, no. 11 (November 1, 2007): 4489–93. http://dx.doi.org/10.1210/jc.2007-0956.
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Abstract Background: Preterm infants with very low birth weight frequently exhibit impaired longitudinal growth during the first years of life. Recently, the d3-isoform (genomic deletion of exon 3) of the GH receptor (GHR) has been linked to an increased responsiveness to GH. Objective: Our objective was to test whether the GHRd3 isoform is associated with postnatal catch-up growth in very low birth weight preterm infants. Design and Patients: We compared the postnatal growth pattern of 77 otherwise healthy preterm infants (mean gestational age, 28.5 wk; range, 23–35 wk) with a birth weight below 1500 g (mean birth weight, 941 g) to their GHR exon 3 genotype, which was analyzed by multiplex PCR. On examination, mean age of the children was 6.0 yr (range, 4.2–8.0 yr). Results: Children homozygous or heterozygous for the GHRd3 allele showed a significantly higher rate of postnatal catch-up, compared with those homozygous for the full-length allele. Conclusions: Our results define the GHR exon 3 genotype as a predictor for the postnatal growth pattern of very low birth weight preterm infants. Those who carry at least one GHRd3 allele are more likely to catch-up.
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SERRA-PLADEVALL, J., M. J. BARBERÁ, A. E. CALLARISA, R. BARTOLOMÉ-COMAS, and A. ANDREU. "Differences in Neisseria gonorrhoeae population structure and antimicrobial resistance pattern between men who have sex with men and heterosexuals." Epidemiology and Infection 145, no. 2 (October 19, 2016): 379–85. http://dx.doi.org/10.1017/s095026881600234x.
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SUMMARYThis study compared the antimicrobial susceptibility and genotypes of strains of Neisseria gonorrhoeae isolated from men who have sex with men (MSM) and from heterosexuals. One hundred and eleven strains were characterized from 107 patients, comprising 57 strains from 54 heterosexuals and 54 strains from 53 MSM. Antimicrobial resistance rates were higher in strains from heterosexual patients, with resistance to cefixime (P = 0·0159) and ciprofloxacin (P = 0·002) being significantly higher. Typing by N. gonorrhoeae multi-antigen sequence typing (NG-MAST) showed that the most prevalent sequence types (ST) and genogroups (G) respectively were ST2400, ST2992, and ST5793, and G1407, G2992, and G2400. A statistically significant association was observed for MSM and genogroups G2400 (P = 0·0005) and G2992 (P = 0·0488), and G1407 with heterosexuals (P = 0·0002). We conclude that in our region distinct populations of gonococci are circulating among subjects with different sexual practices, with their corresponding transmission patterns. Furthermore, the high prevalence of genotype G2400 in MSM, has not to our knowledge been previously described.