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Sample records for icea genotypes status

  1. Helicobacter pylori isolated from Iranian drinking water: vacA, cagA, iceA, oipA and babA2 genotype status and antimicrobial resistance properties.

    PubMed

    Ranjbar, Reza; Khamesipour, Faham; Jonaidi-Jafari, Nematollah; Rahimi, Ebrahim

    2016-05-01

    Despite the clinical importance of Helicobacter pylori in human gastric disorders, its exact route of transmission is still uncertain. Based on the contentious hypothesis and findings of previous investigations, water may play an important role in the transmission of H. pylori to humans. This study was carried out to investigate the vacA, cagA, oipA, iceA and babA2 genotype status and antimicrobial resistance properties of H. pylori strains isolated from the drinking water samples of four major provinces in Iran. A total of 400 drinking water samples were cultured and tested. H. pylori-positive strains were analyzed for the presence of various genotypes and antimicrobial resistance. Twelve of 400 (3%) water samples were positive for H. pylori. Samples from Isfahan province had the highest, while those from Shiraz had the lowest prevalence of H. pylori. The seasonal distribution was also determined, with the highest prevalence of bacteria in the summer season (7.36%). H. pylori strains harbored the highest levels of resistance against ampicillin (100%), erythromycin (75%), clarithromycin (75%), and trimethoprim (58.3%). The most commonly detected genotypes were vacAs1a (83.3%), vacAm1a (66.6%), vacAs2 (50%) and cagA (50%). The presence of similar genotypes in the H. pylori strains of drinking water and those of human clinical samples suggest that contaminated water maybe the sources of bacteria. Spiramycin and furazolidone are suggested for the treatment of cases of H. pylori infection.

  2. Prevalence of Helicobacter pylori vacA, cagA, cagE, oipA, iceA, babA2 and babB genotypes in Iranian dyspeptic patients.

    PubMed

    Dabiri, Hossein; Jafari, Fereshteh; Baghaei, Kaveh; Shokrzadeh, Leila; Abdi, Saeed; Pourhoseingholi, Mohamad Amin; Mohammadzadeh, Alireza

    2017-04-01

    There is diversity in clinical outcome of Helicobacter pylori infection in different regions. Microbial, host and environmental factors seem to be reason of such variation. Considering microbial factors, we studied H. pylori genotypes and their association with clinical feature of the infection. Overall 160 H. pylori-positive patients were enrolled in this study. Clinical information and biopsy were collected from each patient. The presence of the major virulence genes were determined by PCR. Regardless to clinical outcomes, vacA, cagA, cagE, oipA, iceA1, babA2 and babB genes was positive in 100%, 69%, 51%, 55%, 26%,78% and 28% of 160 strains respectively. The s1m2 was more common vacA allels and s1a and m1a were predominant s and m regions. In patient with gastric cancer (GC), the oipA was less frequent while the iceA1 was the most common. The babA2 was common in all patient groups. The babB was significantly observed in strains isolated from patients with GC. There were significant association among cagA status with presence of vacAs1, vacAm2, cagE, oipA, iceA1 and babA2. Presence of the babB and oipA was connected with higher and lower risk for GC respectively. There was no association between the cagA, vacA, cagE or iceA status and clinical outcome in patients in Iran. We showed that presence of the babB and iceA1 were significantly connected with higher risk for gastric cancer development in Iranian dyspeptic patients while H. pylori isolates with positive oipA had little threat for leading patients to cancer.

  3. Genetic characterisation of Helicobacter pylori isolates from an Argentinean adult population based on cag pathogenicity island right-end motifs, lspA-glmM polymorphism and iceA and vacA genotypes.

    PubMed

    Leanza, A G; Matteo, M J; Crespo, O; Antelo, P; Olmos, J; Catalano, M

    2004-09-01

    Isolates of Helicobacter pylori from 88 patients were characterised by cagA status, cagA pathogenicity island (PAI) right-end motifs, iceA, vacA and lspA-glmM genotypes, primarily by PCR-based analysis, to investigate whether Argentinean isolates differed from those recovered in southern Europe or other Latin American countries. PCR-based analysis of vacA alleles was confirmed by reverse hybridisation in 56 cases, while sequence analysis was performed either when iceA and vacA genotypes could not be determined by PCR, or to investigate PCR and reverse hybridisation vacA genotyping discordance. Typing by lspA-glmM restriction fragment length polymorphism was performed with HhaI and AluI. The pattern of cag PAI right-end motifs and the prevalence of type Ia were similar to those in isolates from southern European countries, with cagA(+)/iceA1/vacA-s1 m1 being the commonest genotype. Reverse hybridisation identified a vacA-s1a/s1b recombinant allele, confirmed by sequencing analysis. Analysis of lspA-glmM genotypes identified at least 73 unrelated strains. Few mixed infections were identified, but in one case, isolates from a single biopsy exhibiting two vacA alleles were shown by lspA-glmM fingerprints to be two unrelated strains. No associated effect on ulcer disease risk was demonstrated by analysis of cagA, vacA and iceA status. Overall, the isolates of H. pylori from Argentina were similar to isolates from southern Europe or Latin American countries, and infections were associated mainly with single H. pylori strains.

  4. Relationship between the iceA gene of Helicobacter pylori and clinical outcomes

    PubMed Central

    Huang, Xiaojun; Deng, Zhaomin; Zhang, Qiang; Li, Wanyi; Wang, Baoning; Li, Mingyuan

    2016-01-01

    Background The complex pathogenesis of Helicobacter pylori (H. pylori) and the features of the host influence the diverse clinical outcomes. A mass of studies about virulence genes have accelerated the exploration of pathogenesis of H. pylori infection. Induced by contact with epithelium gene A (iceA) is one of the biggest concerned virulence genes. In this study, we explored the relationship between iceA and the magnitude of the risk for clinical outcomes and the prevalence of iceA-positive H. pylori in People’s Republic of China and other countries. Methods We searched the electronic databases of PubMed, Embase, CNKI, VIP, and Wanfang by literature search strategy. The studies conforming to the inclusion criteria were assessed. With these data, we systematically analyzed the relationship between the iceA gene of H. pylori and clinical outcomes. Results Nineteen articles with 22 studies, a total of 2,657 cases, were involved in the study. The iceA1 gene was significantly associated with peptic ulcer disease (odds ratio =1.28, 95% confidence interval =1.03–1.60; P=0.03), especially in People’s Republic of China (odds ratio =1.40, 95% confidence interval =1.07–1.83; P=0.01). Moreover, the prevalence of iceA1 was significantly higher than iceA2 in People’s Republic of China (P<0.0001). The prevalence of both iceA1 and iceA2 was significantly different (P<0.0001) in People’s Republic of China and in other countries. Conclusion The system analysis showed that infection with the iceA1-positive H. pylori significantly increased the overall risk for peptic ulcer disease, especially in People’s Republic of China. The iceA2 gene status and clinical outcome of H. pylori infection have no significant correlation. H. pylori iceA1 genotype is the major epidemic strain in People’s Republic of China. PMID:27462162

  5. APOE genotype influences functional status among elderly without dementia

    SciTech Connect

    Albert, S.M.; Jacobs, D.M.; Stern, Y.

    1995-12-18

    The presence of apolipoprotein-{epsilon}4 (APOE-{epsilon}4) significantly increases the risk of Alzheimer`s disease (AD). The association between APOE-{epsilon}4 status and functional abilities was explored further in a multicultural sample of community-dwelling, nondemented elders. The sample was limited to cognitively-intact, community-dwelling elders, who were free of stroke or other neurologic disability. In 218 elders who met research criteria, the presence of APOE-{epsilon}4 was associated with poorer functional status, apart from the effects of neuropsychological performance, gender, age, and education (OR = 2.5, 95% CI: 1.3, 4.9). In 158 subjects without an APOE-{epsilon}4 allele, 50% reported no functional limitation; in the 60 subjects with an {epsilon}4 allele, only 28% reported no functional limitation (P < .01). The relationship was not explained by the distribution of co-morbidities. The association between poorer function and the presence of an APOE-{epsilon}4 allele was evident in each ethnic group. In path analyses, the presence of an APOE-{epsilon}4 allele was associated with decreased functional ability in non-demented elders not simply through an association with poorer cognitive status, but also independently. These results suggest that the APOE-{epsilon}4 genotype is associated with functional deficit in people with normal neuropsychological profiles. 29 refs., 1 fig., 3 tabs.

  6. [Genotypes distribution among hepatitis B virus infected patients with different immune statuses in Guangxi north region].

    PubMed

    Yang, Li-Sha; Wu, Lin-Ling; Jiang, Dong-Xiang; Wang, Ji-Ye; Huang, Ya-Qin

    2012-09-01

    In order to find out the distribution of Genotype of those people infected with HBV (hepatitis B virus) from north Guangxi and the relationship between different immune status of HBV infected people and their genotypes, the HBV infected people are classified into three types according to immune tolerance, immune clearance ( response) and immune incompetence (residues). 150 cases from each type, a total of 450 cases are chosen to be tested with real time fluorescence quantitative PCR assay for detection of HBV infection in three kinds of different immune state of the HBV genotype. In the 450 cases, 323 cases belong to type B, 94 cases belong to type B, 23 cases belong to mixed type B+C and 10 cases belong to none B and none C type. Type B are the majority in all the three HBV immune status, made up to 70%, 78%, 67.33% of each type. The different immune state genotype proportion difference don't have statistical significance; immune state and genotypic correlation isn't statistically significant; type B HBV-DNA load is higher than that of type C, groups of persons aged 30 years or older with type C are significantly higher than that of < 30 years of age, the difference was statistically significant; among the genotypes of alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBil) positive rate showed no significant difference between male and female; there was no significant difference in genotype distribution. The results show that, in North Guangxi HBV genotypes B, C accounts for the proportion, a small amount of B+C hybrid, occasionally fails to type HBV infection; among immune tolerance, immune clearance (response) and immune incompetence (residues) type B are in majority in these three kinds of immune state, chronic HBV infection immunity with the HBV genotype correlations were not statistically significant.

  7. Impact of Genotype on EPA and DHA Status and Responsiveness to Increased Intakes.

    PubMed

    Minihane, Anne Marie

    2016-03-02

    At a population level, cardioprotective and cognitive actions of the fish oil (FO) derived long-chain n-3 polyunsaturated fatty acids (LC n-3 PUFAs) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have been extensively demonstrated. In addition to dietary intake, which is limited for many individuals, EPA and DHA status is dependent on the efficiency of their biosynthesis from α-linolenic acid. Gender and common gene variants have been identified as influencing the rate-limiting desaturase and elongase enzymes. Response to a particular intake or status is also highly heterogeneous and likely influenced by genetic variants which impact on EPA and DHA metabolism and tissue partitioning, transcription factor activity, or physiological end-point regulation. Here, available literature relating genotype to tissue LC n-3 PUFA status and response to FO intervention is considered. It is concluded that the available evidence is relatively limited, with much of the variability unexplained, though APOE and FADS genotypes are emerging as being important. Although genotype × LC n-3 PUFA interactions have been described for a number of phenotypes, few have been confirmed in independent studies. A more comprehensive understanding of the genetic, physiological and behavioural modulators of EPA and DHA status and response to intervention is needed to allow refinement of current dietary LC n-3 PUFA recommendations and stratification of advice to "vulnerable" and responsive subgroups.

  8. Hepatitis B virus in Pakistan: A systematic review of prevalence, risk factors, awareness status and genotypes

    PubMed Central

    2011-01-01

    In Pakistan, there are estimated 7-9 million carriers of hepatitis B virus (HBV) with a carrier rate of 3-5%. This article reviews the available literature about the prevalence, risk factors, awareness status and genotypes of the HBV in Pakistan by using key words; HBV prevalence, risk factors, awareness status and genotypes in Pakistani population in PubMed, PakMediNet, Directory of Open Access Journals (DOAJ) and Google Scholar. One hundred and six different studies published from 1998 to 2010 were included in this study. Weighted mean and standard deviation were determined for each population group. The percentage of hepatitis B virus infection in general population was 4.3318% ± 1.644%, healthy blood donors (3.93% ± 1.58%), military recruits (4.276% ± 1.646%), healthcare persons (3.25% ± 1.202%), pregnant women (5.872% ± 4.984), prisoners (5.75% ± 0.212%), surgical patients (7.397% ± 2.012%), patients with cirrhosis (28.87% ± 11.90%), patients with HCC (22% ± 2.645%), patients with hepatitis (15.896% ± 14.824%), patients with liver diseases (27.54% ± 6.385%), multiple transfused patients (6.223% ± 2.121%), opthalmic patients (3.89% ± 1.004%) and users of injectable drugs (14.95% ± 10.536%). Genotype D (63.71%) is the most prevalent genotype in Pakistani population. Mass vaccination and awareness programs should be initiated on urgent basis especially in populations with HBV infection rates of more than 5%. PMID:21375760

  9. The longitudinal and interactive effects of HIV status, stimulant use, and host genotype upon neurocognitive functioning.

    PubMed

    Levine, Andrew J; Reynolds, Sandra; Cox, Christopher; Miller, Eric N; Sinsheimer, Janet S; Becker, James T; Martin, Eileen; Sacktor, Ned

    2014-06-01

    Both human immunodeficiency virus (HIV)-1 infection and illicit stimulant use can adversely impact neurocognitive functioning, and these effects can be additive. However, significant variability exists such that as-of-yet unidentified exogenous and endogenous factors affect one's risk for neurocognitive impairment. Literature on both HIV and stimulant use indicates that host genetic variants in immunologic and dopamine-related genes are one such factor. In this study, the individual and interactive effects of HIV status, stimulant use, and genotype upon neurocognitive functioning were examined longitudinally over a 10-year period. Nine hundred fifty-two Caucasian HIV+ and HIV- cases from the Multicenter AIDS Cohort Study were included. All cases had at least two comprehensive neurocognitive evaluations between 1985 and 1995. Pre-highly active antiretroviral therapy (HAART) data were examined in order to avoid the confounding effect of variable drug regimens. Linear mixed models were used, with neurocognitive domain scores as the outcome variables. No four-way interactions were found, indicating that HIV and stimulant use do not interact over time to affect neurocognitive functioning as a function of genotype. Multiple three-way interactions were found that involved genotype and HIV status. All immunologically related genes found to interact with HIV status affected neurocognitive functioning in the expected direction; however, only C-C chemokine ligand 2 (CCL2) and CCL3 affected HIV+ individuals specifically. Dopamine-related genetic variants generally affected HIV-negative individuals only. Neurocognitive functioning among HIV+ individuals who also used stimulants was not significantly different from those who did not use stimulants. The findings support the role of immunologically related genetic differences in CCL2 and CCL3 in neurocognitive functioning among HIV+ individuals; however, their impact is minor. Being consistent with findings from another cohort

  10. Study of Helicobacter pylori genotype status in saliva, dental plaques, stool and gastric biopsy samples

    PubMed Central

    Momtaz, Hassan; Souod, Negar; Dabiri, Hossein; Sarshar, Meysam

    2012-01-01

    AIM: To compare genotype of Helicobacter pylori (H. pylori) isolated from saliva, dental plaques, gastric biopsy, and stool of each patient in order to evaluate the mode of transmission of H. pylori infection. METHODS: This cross-sectional descriptive study was performed on 300 antral gastric biopsy, saliva, dental plaque and stool samples which were obtained from patients undergoing upper gastrointestinal tract endoscopy referred to endoscopy centre of Hajar hospital of Shahrekord, Iran from March 2010 to February 2011. Initially, H. pylori strains were identified by rapid urease test (RUT) and polymerase chain reaction (PCR) were applied to determine the presence of H. pylori (ureC) and for genotyping of voculating cytotoxin gene A (vacA) and cytotoxin associated gene A (cagA) genes in each specimen. Finally the data were analyzed by using statistical formulas such as Chi-square and Fisher’s exact tests to find any significant relationship between these genes and patient’s diseases. P < 0.05 was considered statistically significant. RESULTS: Of 300 gastric biopsy samples, 77.66% were confirmed to be H. pylori positive by PCR assay while this bacterium were detected in 10.72% of saliva, 71.67% of stool samples. We were not able to find it in dental plaque specimens. The prevalence of H. pylori was 90.47% among patients with peptic ulcer disease (PUD), 80% among patients with gastric cancer, and 74.13% among patients with none ulcer dyspepsia (NUD) by PCR assay. The evaluation of vacA and cagA genes showed 6 differences between gastric biopsy and saliva specimens and 11 differences between gastric and stool specimens. 94.42% of H. pylori positive specimens were cagA positive and all samples had amplified band both for vacA s and m regions. There was significant relationship between vacA s1a/m1a and PUD diseases (P = 0.04), s2/m2 genotype and NUD diseases (P = 0.05). No statically significant relationship was found between cagA status with clinical outcomes and

  11. Riboflavin status, MTHFR genotype and blood pressure: current evidence and implications for personalised nutrition.

    PubMed

    McAuley, E; McNulty, H; Hughes, C; Strain, J J; Ward, M

    2016-08-01

    Clinical deficiency of the B-vitamin riboflavin (vitamin B2) is largely confined to developing countries; however accumulating evidence indicates that suboptimal riboflavin status is a widespread problem across the developed world. Few international data are available on riboflavin status as measured by the functional biomarker, erythrocyte glutathione reductase activation coefficient, considered to be the gold standard index. One important role of riboflavin in the form of flavin dinucleotide is as a co-factor for the folate-metabolising enzyme methylenetetrahydrofolate reductase (MTHFR). Homozygosity for the common C677T polymorphism in MTHFR, affecting over 10 % of the UK and Irish populations and up to 32 % of other populations worldwide, has been associated with an increased risk of CVD, and more recently with hypertension. This review will explore available studies reporting riboflavin status worldwide, the interaction of riboflavin with the MTHFR C677T polymorphism and the potential role of riboflavin in personalised nutrition. Evidence is accumulating for a novel role of riboflavin as an important modulator of blood pressure (BP) specifically in individuals with the MTHFR 677TT genotype, with results from a number of recent randomised controlled trials demonstrating that riboflavin supplementation can significantly reduce systolic BP by 5-13 mmHg in these genetically at risk adults. Studies are however required to investigate the BP-lowering effect of riboflavin in different populations and in response to doses higher than 1·6 mg/d. Furthermore, work focusing on the translation of this research to health professionals and patients is also required.

  12. Genotype, B-vitamin status, and androgens affect spaceflight-induced ophthalmic changes

    PubMed Central

    Zwart, Sara R.; Gregory, Jesse F.; Zeisel, Steven H.; Gibson, Charles R.; Mader, Thomas H.; Kinchen, Jason M.; Ueland, Per M.; Ploutz-Snyder, Robert; Heer, Martina A.; Smith, Scott M.

    2016-01-01

    Ophthalmic changes have occurred in a subset of astronauts on International Space Station missions. Visual deterioration is considered the greatest human health risk of spaceflight. Affected astronauts exhibit higher concentrations of 1-carbon metabolites (e.g., homocysteine) before flight. We hypothesized that genetic variations in 1-carbon metabolism genes contribute to susceptibility to ophthalmic changes in astronauts. We investigated 5 polymorphisms in the methionine synthase reductase (MTRR), methylenetetrahydrofolate reductase (MTHFR), serine hydroxymethyltransferase (SHMT), and cystathionine β-synthase (CBS) genes and their association with ophthalmic changes after flight in 49 astronauts. The number of G alleles of MTRR 66 and C alleles of SHMT1 1420 both contributed to the odds of visual disturbances. Preflight dehydroepiandrosterone was positively associated with cotton wool spots, and serum testosterone response during flight was associated with refractive change. Block regression showed that B-vitamin status and genetics were significant predictors of many of the ophthalmic outcomes that we observed. In one example, genetics trended toward improving (P = 0.10) and B-vitamin status significantly improved (P < 0.001) the predictive model for refractive change after flight. We document an association between MTRR 66 and SHMT1 1420 polymorphisms and spaceflight-induced vision changes. This line of research could lead to therapeutic options for both space travelers and terrestrial patients.—Zwart, S. R., Gregory, J. F., Zeisel, S. H., Gibson, C. R., Mader, T. H., Kinchen, J. M., Ueland, P. M., Ploutz-Snyder, R., Heer, M. A., Smith, S. M. Genotype, B-vitamin status, and androgens affect spaceflight-induced ophthalmic changes. PMID:26316272

  13. Primate genotyping via high resolution melt analysis: rapid and reliable identification of color vision status in wild lemurs.

    PubMed

    Jacobs, Rachel L; Spriggs, Amanda N; MacFie, Tammie S; Baden, Andrea L; Irwin, Mitchell T; Wright, Patricia C; Louis, Edward E; Lawler, Richard R; Mundy, Nicholas I; Bradley, Brenda J

    2016-10-01

    Analyses of genetic polymorphisms can aid our understanding of intra- and interspecific variation in primate sociality, ecology, and behavior. Studies of primate opsin genes are prime examples of this, as single nucleotide variants (SNVs) in the X-linked opsin gene underlie variation in color vision. For primate species with polymorphic trichromacy, genotyping opsin SNVs can generally indicate whether individual primates are red-green color-blind (denoted homozygous M or homozygous L) or have full trichromatic color vision (heterozygous ML). Given the potential influence of color vision on behavior and fitness, characterizing the color vision status of study subjects is becoming commonplace for many primate field projects. Such studies traditionally involve a multi-step sequencing-based method that can be costly and time-consuming. Here we present a new reliable, rapid, and relatively inexpensive method for characterizing color vision in primate populations using high resolution melt analysis (HRMA). Using lemurs as a case study, we characterized variation at exons 3 and/or 5 of the X-linked opsin gene for 87 individuals representing nine species. We scored opsin genotypes and color vision status using both traditional sequencing-based methods as well as our novel melting-curve based HRMA protocol. For each species, the melting curves of varying genotypes (homozygous M, homozygous L, heterozygous ML) differed in melting temperature and/or shape. Melting curves for each sample were consistent across replicates, and genotype-specific melting curves were consistent across DNA sources (blood vs. feces). We show that opsin genotypes can be quickly and reliably scored using HRMA once lab-specific reference curves have been developed based on known genotypes. Although the protocol presented here focuses on genotyping lemur opsin loci, we also consider the larger potential for applying this approach to various types of genetic studies of primate populations.

  14. Relevance of secretor status genotype and microbiota composition in susceptibility to rotavirus and norovirus infections in humans.

    PubMed

    Rodríguez-Díaz, Jesús; García-Mantrana, Izaskun; Vila-Vicent, Susana; Gozalbo-Rovira, Roberto; Buesa, Javier; Monedero, Vicente; Collado, Maria Carmen

    2017-03-30

    Host genetic factors, such as histo-blood group antigens (HBGAs), are associated with susceptibility to norovirus (NoV) and rotavirus (RV) infections. Recent advances point to the gut microbiome as a key player necessary for a viral pathogen to cause infection. In vitro NoV attachment to host cells and resulting infections have been linked to interactions with certain bacterial types in the gut microbiota. We investigated the relationship between host genotype, gut microbiota, and viral infections. Saliva and fecal samples from 35 adult volunteers were analysed for secretor status genotype, the gut microbiota composition by 16S rRNA gene sequencing, and salivary IgA titers to NoV and RV. Higher levels of IgA against NoV and RV were related to secretor-positive status. No significant differences were found between the FUT2 genotype groups, although the multivariate analysis showed a significant impact of host genotype on specific viral susceptibilities in the microbiome composition. A specific link was found between the abundance of certain bacterial groups, such as Faecalibacterium and Ruminococcus spp., and lower IgA titers against NoV and RV. As a conclusion, we can state that there is a link between host genetics, gut microbiota, and susceptibility to viral infections in humans.

  15. Relevance of secretor status genotype and microbiota composition in susceptibility to rotavirus and norovirus infections in humans

    PubMed Central

    Rodríguez-Díaz, Jesús; García-Mantrana, Izaskun; Vila-Vicent, Susana; Gozalbo-Rovira, Roberto; Buesa, Javier; Monedero, Vicente; Collado, Maria Carmen

    2017-01-01

    Host genetic factors, such as histo-blood group antigens (HBGAs), are associated with susceptibility to norovirus (NoV) and rotavirus (RV) infections. Recent advances point to the gut microbiome as a key player necessary for a viral pathogen to cause infection. In vitro NoV attachment to host cells and resulting infections have been linked to interactions with certain bacterial types in the gut microbiota. We investigated the relationship between host genotype, gut microbiota, and viral infections. Saliva and fecal samples from 35 adult volunteers were analysed for secretor status genotype, the gut microbiota composition by 16S rRNA gene sequencing, and salivary IgA titers to NoV and RV. Higher levels of IgA against NoV and RV were related to secretor-positive status. No significant differences were found between the FUT2 genotype groups, although the multivariate analysis showed a significant impact of host genotype on specific viral susceptibilities in the microbiome composition. A specific link was found between the abundance of certain bacterial groups, such as Faecalibacterium and Ruminococcus spp., and lower IgA titers against NoV and RV. As a conclusion, we can state that there is a link between host genetics, gut microbiota, and susceptibility to viral infections in humans. PMID:28358023

  16. Influence of delta virus infection on the virologic status in Egyptian patients with chronic hepatitis B virus genotype D.

    PubMed

    Fouad, Rabab; Abdo, Mahmoud; Eldeen, Hadeel Gamal; Sabry, Dina; Atef, Mira; Ahmed, Rasha; Zayed, Naglaa

    2016-05-01

    Hepatitis delta virus (HDV) usually have an unfavorable clinical outcome in chronic hepatitis B virus (HBV) patients. In Egypt, data about epidemiology, the spectrum of disease, and impact of HDV on HBV infection are rare. To assess the prevalence, clinical and virological characteristics of HDV infection among Egyptian patients with chronic HBV. Adult patients with Hepatitis B surface antigen (HBsAg)-positive were evaluated for the presence of HDV using anti HDV-IgG and HDV RNA by RT-PCR. Routine laboratory investigations, genotypes and subtypes for both HBV and HDV, abdominal sonography, and transient elastography (TE) were done. Liver biopsy was performed only in whenever indicated. One hundred and twenty-one treatment-naïve chronic HBV patients were included. Wild HBV genotype-D2 was found in 98.2% and 81.9% were HBeAg negative. Prevalence of HDV was 8.3% by anti-HDV IgG and 9.9% by RT-PCR. Wild HDV genotype-IIb was reported in 83.3%. HDV infection was more common in males, 90.9% of delta patients were HBeAg negative. Compared to the mono-infected HBV, concomitant HBV/HDV infection was not associated with more derangment in ALT nor advanced stage of fibrosis. 66.7% of HDV patients had significantly lower HBV-DNA level compared to the non-delta patients (P < 0.001). HDV is not uncommon in Egypt. HBV genotype-D was associated with HDV genotype-IIb. Delta infection was associated with negative HBeAg status, reduction of HBV replication, but neither influenced the clinical course nor increased significant liver damage risk.

  17. Supraphysiological hormonal status, anxiety disorders, and COMT Val/Val genotype are associated with reduced sensorimotor gating in women.

    PubMed

    Comasco, Erika; Hellgren, Charlotte; Olivier, Jocelien; Skalkidou, Alkistis; Sundström Poromaa, Inger

    2015-10-01

    Pregnancy is a period characterized by a supraphysiological hormonal status, and greater anxiety proneness, which can lead to peripartum affective symptoms with dramatic consequences not only for the woman but also for the child. Clinical psychiatry is heavily hampered by the paucity of objective and biology-based intermediate phenotypes. Prepulse inhibition (PPI) of the startle response, a neurophysiological measure of sensorimotor gating, has been poorly investigated in relation to anxiety and in pregnant women. In the present study, the PPI of healthy non-pregnant women (n = 82) and late pregnant women (n = 217) was investigated. Age, BMI, depression and anxiety symptoms, tobacco use, and antidepressant medication were considered. We investigated and provided evidence of lower PPI: (i) in healthy pregnant women compared to healthy non-pregnant controls, (ii) in pregnant women with anxiety disorders compared to healthy pregnant women, (iii) in pregnant women with anxiety disorders using SSRI compared to un-medicated pregnant women with anxiety disorders, and (iv) in healthy pregnant women carrying the COMT Val158Met Val/Val genotype compared to Met carriers. Altogether, a reduced sensorimotor gating as an effect of supraphysiological hormonal status, anxiety disorders, SSRIs, and catecholaminergic genotype, implicate the putative relevance of lower PPI as an objective biological correlate of anxiety proneness in pregnant women. These findings call for prospective studies to dissect the multifactorial influences on PPI in relation to mental health of pregnant women.

  18. Assignment of polled status using single nucleotide polymorphism genotypes and predicted gene content

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is growing interest in cattle that are naturally polled, but the polled allele has a very low frequency. The best way to increase its frequency is by index selection, which requires known polled status for all animals. Laboratory tests for polled are used as data, and US and Canadian bulls wit...

  19. Photosynthetic and carbohydrate status of easy and difficult-to-acclimate sea oats (Uniola Paniculata L.) genotypes during in vitro culture and ex vitro acclimation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Photosynthesis and carbohydrate status of an easy-to-acclimatize (EK 16-3) and a difficult-to-acclimatize (EK 11-1) genotype of sea oats (Uniola paniculata), a native dune species of the southeastern U.S., were evaluated during in vitro culture and ex vitro greenhouse acclimatization. During in vitr...

  20. Genotype, B-vitamin status, and androgens affect spaceflight-induced ophthalmic changes.

    PubMed

    Zwart, Sara R; Gregory, Jesse F; Zeisel, Steven H; Gibson, Charles R; Mader, Thomas H; Kinchen, Jason M; Ueland, Per M; Ploutz-Snyder, Robert; Heer, Martina A; Smith, Scott M

    2016-01-01

    Ophthalmic changes have occurred in a subset of astronauts on International Space Station missions. Visual deterioration is considered the greatest human health risk of spaceflight. Affected astronauts exhibit higher concentrations of 1-carbon metabolites (e.g., homocysteine) before flight. We hypothesized that genetic variations in 1-carbon metabolism genes contribute to susceptibility to ophthalmic changes in astronauts. We investigated 5 polymorphisms in the methionine synthase reductase (MTRR), methylenetetrahydrofolate reductase (MTHFR), serine hydroxymethyltransferase (SHMT), and cystathionine β-synthase (CBS) genes and their association with ophthalmic changes after flight in 49 astronauts. The number of G alleles of MTRR 66 and C alleles of SHMT1 1420 both contributed to the odds of visual disturbances. Preflight dehydroepiandrosterone was positively associated with cotton wool spots, and serum testosterone response during flight was associated with refractive change. Block regression showed that B-vitamin status and genetics were significant predictors of many of the ophthalmic outcomes that we observed. In one example, genetics trended toward improving (P = 0.10) and B-vitamin status significantly improved (P < 0.001) the predictive model for refractive change after flight. We document an association between MTRR 66 and SHMT1 1420 polymorphisms and spaceflight-induced vision changes. This line of research could lead to therapeutic options for both space travelers and terrestrial patients.

  1. ACTN3 Genotype, Athletic Status, and Life Course Physical Capability: Meta-Analysis of the Published Literature and Findings from Nine Studies

    PubMed Central

    Alfred, Tamuno; Ben-Shlomo, Yoav; Cooper, Rachel; Hardy, Rebecca; Cooper, Cyrus; Deary, Ian J; Gunnell, David; Harris, Sarah E; Kumari, Meena; Martin, Richard M; Moran, Colin N; Pitsiladis, Yannis P; Ring, Susan M; Sayer, Avan Aihie; Smith, George Davey; Starr, John M; Kuh, Diana; Day, Ian NM

    2011-01-01

    The ACTN3 R577X (rs1815739) genotype has been associated with athletic status and muscle phenotypes, although not consistently. Our objective was to conduct a meta-analysis of the published literature on athletic status and investigate its associations with physical capability in several new population-based studies. Relevant data were extracted from studies in the literature, comparing genotype frequencies between controls and sprint/power and endurance athletes. For life course physical capability, data were used from two studies of adolescents and seven studies in the Healthy Ageing across the Life Course (HALCyon) collaborative research program, involving individuals aged between 53 and 90+ years. We found evidence from the published literature to support the hypothesis that in Europeans the RR genotype is more common among sprint/power athletes compared with their controls. There is currently no evidence that the X allele is advantageous to endurance athleticism. We found no association between R577X and grip strength (P = 0.09, n = 7,672 in males; P = 0.90, n = 7,839 in females), standing balance, timed get up and go, or chair rises in our studies of physical capability. The ACTN3 R577X genotype is associated with sprint/power athletic status in Europeans, but does not appear to be associated with objective measures of physical capability in the general population. Hum Mutat 32:1–11, 2011. © 2011 Wiley-Liss, Inc. PMID:21542061

  2. Biomass partitioning, morphology and water status of four alfalfa genotypes submitted to progressive drought and subsequent recovery.

    PubMed

    Erice, Gorka; Louahlia, Saïd; Irigoyen, Juan José; Sanchez-Diaz, Manuel; Avice, Jean-Christophe

    2010-01-15

    The predicted worldwide increase of arid areas and water stress episodes will strongly affect crop production. Numerous plants have developed specific morphological and physiological mechanisms as a means to increase their tolerance to drought. Water stress modifies dry matter partitioning and morphological components such as leaf area ratio (LAR), specific leaf area (SLA) and leaf weight ratio (LWR). Alfalfa has a wide-ranging distribution and is thus expected to show differing levels of drought tolerance. The aim of our study was to determine the effect of progressive drought and subsequent recovery in four alfalfa genotypes differing in drought sensitivity: three cultivars adapted to a Mediterranean climate, Tafilalet (TA), Tierra de Campos (TC) and Moapa (MO), and another representative of an oceanic climate, Europe (EU). Mild drought did not affect biomass production or water status in the studied varieties. Under moderate drought conditions, TA and MO showed decreased leaf production, which may help them to maintain relative water content (RWC). Despite observations that water stress did not affect root growth, after the recovery period, TA increased its root biomass, making higher water soil prospecting possible. Mediterranean cultivars modified LAR and SLA depending on water availability, whereas EU alters LWR. At the end of the experiment, TC was the most productive cultivar, but severe drought did not predict differences among cultivars. Severe water stress increased the root/shoot ratio in order to diminish water consumption and increase absorption of water. In spite of all cultivars showing a decreased LWR, TA also decreased SLA, which may suggest higher drought resistance. Morphological traits from Mediterranean cultivars, including the ability to alter SLA or LAR may be used for drought-tolerant cultivar improvement.

  3. Optimization of Clonazepam Therapy Adjusted to Patient’s CYP3A Status and NAT2 Genotype

    PubMed Central

    Tóth, Katalin; Csukly, Gábor; Sirok, Dávid; Belic, Ales; Kiss, Ádám; Háfra, Edit; Déri, Máté; Menus, Ádám; Bitter, István

    2016-01-01

    Background: The shortcomings of clonazepam therapy include tolerance, withdrawal symptoms, and adverse effects such as drowsiness, dizziness, and confusion leading to increased risk of falls. Inter-individual variability in the incidence of adverse events in patients partly originates from the differences in clonazepam metabolism due to genetic and nongenetic factors. Methods: Since the prominent role in clonazepam nitro-reduction and acetylation of 7-amino-clonazepam is assigned to CYP3A and N-acetyl transferase 2 enzymes, respectively, the association between the patients’ CYP3A status (CYP3A5 genotype, CYP3A4 expression) or N-acetyl transferase 2 acetylator phenotype and clonazepam metabolism (plasma concentrations of clonazepam and 7-amino-clonazepam) was evaluated in 98 psychiatric patients suffering from schizophrenia or bipolar disorders. Results: The patients’ CYP3A4 expression was found to be the major determinant of clonazepam plasma concentrations normalized by the dose and bodyweight (1263.5±482.9 and 558.5±202.4ng/mL per mg/kg bodyweight in low and normal expressers, respectively, P<.0001). Consequently, the dose requirement for the therapeutic concentration of clonazepam was substantially lower in low-CYP3A4 expresser patients than in normal expressers (0.029±0.011 vs 0.058±0.024mg/kg bodyweight, P<.0001). Furthermore, significantly higher (about 2-fold) plasma concentration ratio of 7-amino-clonazepam and clonazepam was observed in the patients displaying normal CYP3A4 expression and slower N-acetylation than all the others. Conclusion: Prospective assaying of CYP3A4 expression and N-acetyl transferase 2 acetylator phenotype can better identify the patients with higher risk of adverse reactions and can facilitate the improvement of personalized clonazepam therapy and withdrawal regimen. PMID:27639091

  4. Impact of COX2 genotype, ER status and body constitution on risk of early events in different treatment groups of breast cancer patients.

    PubMed

    Markkula, Andrea; Simonsson, Maria; Rosendahl, Ann H; Gaber, Alexander; Ingvar, Christian; Rose, Carsten; Jernström, Helena

    2014-10-15

    The COX2 rs5277 (306G>C) polymorphism has been associated with inflammation-associated cancers. In breast cancer, tumor COX-2 expression has been associated with increased estrogen levels in estrogen receptor (ER)-positive and activated Akt-pathway in ER-negative tumors. Our study investigated the impact of COX2 genotypes on early breast cancer events and treatment response in relation to tumor ER status and body constitution. In Sweden, between 2002 and 2008, 634 primary breast cancer patients, aged 25-99 years, were included. Disease-free survival was assessed for 570 rs5277-genotyped patients. Body measurements and questionnaires were obtained preoperatively. Clinical data, patient- and tumor-characteristics were obtained from questionnaires, patients' charts, population registries and pathology reports. Minor allele(C) frequency was 16.1%. Genotype was not linked to COX-2 tumor expression. Median follow-up was 5.1 years. G/G genotype was not associated with early events in patients with ER-positive tumors, adjusted HR 0.77 (0.46-1.29), but conferred an over 4-fold increased risk in patients with ER-negative tumors, adjusted HR 4.41 (1.21-16.02)(p(interaction) = 0.015). Chemotherapy-treated G/G-carriers with a breast volume ≥ 850 ml had an increased risk of early events irrespective of ER status, adjusted HR 8.99 (1.14-70.89). Endocrine-treated C-allele carriers with ER-positive tumors and a breast volume ≥ 850 ml had increased risk of early events, adjusted HR 2.30 (1.12-4.75). COX2 genotype, body constitution and ER status had a combined effect on the risk of early events and treatment response. The high risk for early events in certain subgroups of patients suggests that COX2 genotype in combination with body measurements may identify patients in need of more personalized treatment.

  5. Anal human papillomavirus genotype distribution in HIV-infected men who have sex with men by geographical origin, age, and cytological status in a Spanish cohort.

    PubMed

    Torres, Montserrat; González, Cristina; del Romero, Jorge; Viciana, Pompeyo; Ocampo, Antonio; Rodríguez-Fortúnez, Patricia; Masiá, Mar; Blanco, José Ramón; Portilla, Joaquín; Rodríguez, Carmen; Hernández-Novoa, Beatriz; del Amo, Julia; Ortiz, Marta

    2013-11-01

    Knowledge of human papillomavirus (HPV) type distribution in populations at risk for anal cancer is needed. Here, we describe the anal HPV genotype distribution in a large Spanish cohort (Cohort of the Spanish HIV Research Network HPV [CoRIS-HPV]) of HIV-positive men who have sex with men (MSM) according to geographical origin, age, and cytological status. A cross-sectional analysis of baseline data from 1,439 HIV-infected MSM (2007 to 2012) was performed. Anal HPV genotyping was performed using the Linear Array HPV genotyping test. Descriptive analyses of subject characteristics, prevalences, and 95% confidence intervals (CI) were performed. The global prevalences of HPV, high-risk HPV (HR-HPV), and low-risk HPV (LR-HPV) types were 95.8%, 83.0%, and 72.7%, respectively. Among the HR-HPV types, HPV16 was the most common, followed by HPV59, -39, -51, -18, and -52. The prevalence of multiple HR-HPV infections was 58.5%. There were no differences in the crude analyses between Spanish and Latin-American MSM for most HPV types, and a peak in prevalence for most HPV types was seen in patients in their late thirties. Globally and by specific HPV groups, men with abnormal anal cytologies had a higher prevalence of infection than those with normal cytologies. This study has the largest number of HIV-positive MSM with HPV genotype data analyzed according to cytological status as far as we know. The information gained from this study can help with the design of anal cancer prevention strategies in HIV-positive patients.

  6. Anal Human Papillomavirus Genotype Distribution in HIV-Infected Men Who Have Sex with Men by Geographical Origin, Age, and Cytological Status in a Spanish Cohort

    PubMed Central

    Torres, Montserrat; González, Cristina; del Romero, Jorge; Viciana, Pompeyo; Ocampo, Antonio; Rodríguez-Fortúnez, Patricia; Masiá, Mar; Blanco, José Ramón; Portilla, Joaquín; Rodríguez, Carmen; Hernández-Novoa, Beatriz; del Amo, Julia

    2013-01-01

    Knowledge of human papillomavirus (HPV) type distribution in populations at risk for anal cancer is needed. Here, we describe the anal HPV genotype distribution in a large Spanish cohort (Cohort of the Spanish HIV Research Network HPV [CoRIS-HPV]) of HIV-positive men who have sex with men (MSM) according to geographical origin, age, and cytological status. A cross-sectional analysis of baseline data from 1,439 HIV-infected MSM (2007 to 2012) was performed. Anal HPV genotyping was performed using the Linear Array HPV genotyping test. Descriptive analyses of subject characteristics, prevalences, and 95% confidence intervals (CI) were performed. The global prevalences of HPV, high-risk HPV (HR-HPV), and low-risk HPV (LR-HPV) types were 95.8%, 83.0%, and 72.7%, respectively. Among the HR-HPV types, HPV16 was the most common, followed by HPV59, -39, -51, -18, and -52. The prevalence of multiple HR-HPV infections was 58.5%. There were no differences in the crude analyses between Spanish and Latin-American MSM for most HPV types, and a peak in prevalence for most HPV types was seen in patients in their late thirties. Globally and by specific HPV groups, men with abnormal anal cytologies had a higher prevalence of infection than those with normal cytologies. This study has the largest number of HIV-positive MSM with HPV genotype data analyzed according to cytological status as far as we know. The information gained from this study can help with the design of anal cancer prevention strategies in HIV-positive patients. PMID:23966501

  7. Genotype status of the dopamine-related catechol-O-methyltransferase (COMT) gene corresponds with desirability of “unhealthy” foods

    PubMed Central

    Wallace, Deanna L.; Aarts, Esther; Uquillas, Federico d’Oleire; Dang, Linh C.; Greer, Stephanie M.; Jagust, William J.; D’Esposito, Mark

    2015-01-01

    The role of dopamine is extensively documented in weight regulation and food intake in both animal models and humans. Yet the role of dopamine has not been well studied in individual differences for food desirability. Genotype status of the dopamine-related catechol-O-methyltransferase (COMT) gene has been shown to influence dopamine levels, with greater COMT enzymatic activity in val/val individuals corresponding to greater degradation of dopamine. Decreased dopamine has been associated with poorer cognitive control and diminished goal-directed behavior in various behavioral paradigms. Additionally, dopaminergic-rich regions such as the frontal cortex and dorsal striatum have been shown to be important for supporting food-related decision-making. However, the role of dopamine, as assessed by COMT genotype status, in food desirability has not been fully explored. Therefore, we utilized an individual’s COMT genotype status (n=61) and investigated food desirability based on self-rated “healthy” and “unhealthy” food perceptions. Here we found val/val individuals (n=19) have greater desirability for self-rated “unhealthy” food items, but not self-rated “healthy” food items, as compared to val/met (n=24) and met/met (n=18) individuals (p<0.005). Utilizing an objective health measure for the food items, we also found val/val and val/met individuals have greater desirability for objectively defined “unhealthy” food items, as compared to met/met individuals (p<0.01). This work further substantiates a role of dopamine in food-related behaviors and more specifically in relationship to food desirability for “unhealthy” food items. PMID:25963102

  8. Vitamin D Status and VDR Genotype in NF1 Patients: A Case-Control Study from Southern Brazil

    PubMed Central

    Souza Mario Bueno, Larissa; Rosset, Clévia; Aguiar, Ernestina; Pereira, Fernando de Souza; Izetti Ribeiro, Patrícia; Scalco, Rosana; Matzenbacher Bittar, Camila; Brinckmann Oliveira Netto, Cristina; Gischkow Rucatti, Guilherme; Chies, José Artur; Camey, Suzi Alves; Ashton-Prolla, Patricia

    2015-01-01

    Neurofibromatosis type 1 (NF1) patients are more likely to have vitamin D deficiency when compared to the general population. This study aimed to determine the levels of 25-OH-vitamin D [25(OH)D] in individuals with NF1 and disease-unaffected controls and analyze FokI and BsmI VDR gene polymorphisms in a case and in a control group. Vitamin D levels were compared between a group of 45 NF1 patients from Southern Brazil and 45 healthy controls matched by sex, skin type, and age. Genotypic and allelic frequencies of VDR gene polymorphisms were obtained from the same NF1 patients and 150 healthy controls. 25(OH)D deficiency or insufficiency was not more frequent in NF1 patients than in controls (p = 0.074). We also did not observe an association between FokI and BsmI VDR gene polymorphisms and vitamin D levels in NF1 patients, suggesting that their deficient or insufficient biochemical phenotypes are not associated with these genetic variants. The differences between the groups in genotypic and allelic frequencies for FokI and BsmI VDR gene polymorphisms were small and did not reach statistical significance. These polymorphisms are in partial linkage disequilibrium and the haplotype frequencies also did not differ in a significant way between the two groups (p = 0.613). PMID:26161090

  9. The Study of HFE Genotypes and Its Expression Effect on Iron Status of Iranian Haemochromatosis, Iron Deficiency Anemia Patients, Iron-Taker and Non Iron-Taker Controls.

    PubMed

    Beiranvand, Elham; Abediankenari, Saeid; Rostamian, Mosayeb; Beiranvand, Behnoush; Naazeri, Saeed

    2015-01-01

    The role of HFE gene mutations or its expression in regulation of iron metabolism of hereditary haemochromatosis (HH) patients is remained controversial. Therefore here the correlation between two common HFE genotype (p.C282Y, p.H63D) and HFE gene expression with iron status in HH, iron deficiency anemia (IDA) and healthy Iranian participants was studied. For this purpose genotype determination was done by polymerase chain reaction--restriction fragment length polymorphism (PCR-RFLP). Real-Time PCR was applied for evaluation of HFE gene expression. Biochemical parameters and iron consumption were also assessed. Homozygote p.H63D mutation was seen in all HH patients and p.C282Y was not observed in any member of the population. A significant correlation was observed between serum ferritin (SF) level and gender or age of HH patients. p.H63D homozygote was seen to be able to significantly increase SF and transferrin saturation (TS) level without affecting on liver function. Our results also showed that iron consumption affects on TS level increasing. HFE gene expression level of IDA patients was significantly higher than other groups. Also the HFE gene expression was negatively correlated with TS. Finally, the main result of our study showed that loss of HFE function in HH is not derived from its gene expression inhibition and much higher HFE gene expression might lead to IDA. However we propose repeating of the study for more approval of our finding.

  10. Capsaicin consumption, Helicobacter pylori CagA status and IL1B-31C>T genotypes: a host and environment interaction in gastric cancer.

    PubMed

    López-Carrillo, Lizbeth; Camargo, M Constanza; Schneider, Barbara G; Sicinschi, Liviu A; Hernández-Ramírez, Raúl U; Correa, Pelayo; Cebrian, Mariano E

    2012-06-01

    Gastric cancer (GC) has been associated with a complex combination of genetic and environmental factors. In contrast to most countries, available information on GC mortality trends showed a gradual increase in Mexico. Our aim was to explore potential interactions among dietary (chili pepper consumption), infectious (Helicobacter pylori) and genetic factors (IL1B-31 genotypes) on GC risk. The study was performed in three areas of Mexico, with different GC mortality rates. We included 158 GC patients and 317 clinical controls. Consumption of capsaicin (Cap), the pungent active substance of chili peppers, was estimated by food frequency questionnaire. H. pylori CagA status was assessed by ELISA, and IL1B-31 genotypes were determined by TaqMan assays and Pyrosequencing in DNA samples. Multivariate unconditional logistic regression was used to estimate potential interactions. Moderate to high Cap consumption synergistically increased GC risk in genetically susceptible individuals (IL1B-31C allele carriers) infected with the more virulent H. pylori (CagA+) strains. The combined presence of these factors might explain the absence of a decreasing trend for GC in Mexico. However, further research on gene-environment interactions is required to fully understand the factors determining GC patterns in susceptible populations, with the aim of recommending preventive measures for high risk individuals.

  11. Apolipoprotein E ε4 genotype status is not associated with neuroimaging outcomes in a large cohort of HIV+ individuals.

    PubMed

    Cooley, Sarah A; Paul, Robert H; Fennema-Notestine, Christine; Morgan, Erin E; Vaida, Florin; Deng, Qianqian; Chen, Jie Ashley; Letendre, Scott; Ellis, Ronald; Clifford, David B; Marra, Christina M; Collier, Ann C; Gelman, Benjamin B; McArthur, Justin C; McCutchan, J Allen; Simpson, David M; Morgello, Susan; Grant, Igor; Ances, Beau M

    2016-10-01

    Previous neuroimaging studies suggest a negative relationship between the apolipoprotein (ApoE) ε4 allele and brain integrity in human immunodeficiency virus (HIV)-infected (HIV+) individuals, although the presence of this relationship across adulthood remains unclear. The purpose of this study is to clarify the discrepancies using a large, diverse group of HIV+ individuals and multiple imaging modalities sensitive to HIV. The association of ApoE ε4 with structural neuroimaging and magnetic resonance spectroscopy (MRS) was examined in 237 HIV+ individuals in the CNS HIV Anti-Retroviral Therapy Effects Research (CHARTER) study. Cortical and subcortical gray matter, abnormal and total white matter, ventricles, sulcal cerebrospinal fluid (CSF), and cerebellar gray matter, white matter, and CSF volumes, and MRS concentrations of myo-inositol, creatine, N-acetyl-aspartate, and choline in the frontal white matter (FWM), frontal gray matter (FGM), and basal ganglia were examined. Secondary analyses explored this relationship separately in individuals ≥50 years old (n = 173) and <50 years old (n = 63). No significant differences were observed between ApoE ε4+ (ApoE ε3/ε4 and ApoE ε4/ε4) individuals (n = 69) and ApoE ε4- (ApoE ε2/ε3 and ApoE ε3/ε3) individuals (n = 167). When individuals were further divided by age, no significant genotype group differences were identified in individuals <50 or ≥50 years of age on any neuroimaging outcome. The ApoE ε4 allele did not affect brain integrity in this large, diverse sample of HIV+ individuals. The effects of ApoE ε4 may not be apparent until more advanced ages and may be more prominent when present along with other risk factors for neuronal damage.

  12. Genotype and fetal size affect maternal-fetal amino acid status and fetal endocrinology in Large White × Landrace and Meishan pigs.

    PubMed

    Ashworth, Cheryl J; Nwagwu, Margaret O; McArdle, Harry J

    2013-01-01

    This study compared maternal plasma amino acid concentrations, placental protein secretion in vitro and fetal body composition and plasma amino acid and hormone concentrations in feto-placental units from the smallest and a normally-sized fetus carried by Large White × Landrace or Meishan gilts on Day 100 of pregnancy. Compared with Large White × Landrace, Meishan placental tissue secreted more protein and Meishan fetuses contained relatively more fat and protein, but less moisture. Fetal plasma concentrations of insulin, triiodothryonine, thyroxine and insulin-like growth factor (IGF)-II were higher in Meishan than Large White × Landrace fetuses. In both breeds, fetal cortisol concentrations were inversely related to fetal size, whereas concentrations of IGF-I were higher in average-sized fetuses. Concentrations of 10 amino acids were higher in Large White × Landrace than Meishan gilts, while glutamine concentrations were higher in Meishan gilts. Concentrations of alanine, aspartic acid, glutamic acid and threonine were higher in Meishan than Large White × Landrace fetuses. Average-sized fetuses had higher concentrations of asparagine, leucine, lysine, phenylalanine, threonine, tyrosine and valine than the smallest fetus. This study revealed novel genotype and fetal size differences in porcine maternal-fetal amino acid status and fetal hormone and metabolite concentrations.

  13. Genetic and epigenetic transgenerational implications related to omega-3 fatty acids. Part I: maternal FADS2 genotype and DNA methylation correlate with polyunsaturated fatty acid status in toddlers: an exploratory analysis.

    PubMed

    Lupu, Daniel S; Cheatham, Carol L; Corbin, Karen D; Niculescu, Mihai D

    2015-11-01

    Polyunsaturated fatty acid metabolism in toddlers is regulated by a complex network of interacting factors. The contribution of maternal genetic and epigenetic makeup to this milieu is not well understood. In a cohort of mothers and toddlers 16 months of age (n = 65 mother-child pairs), we investigated the association between maternal genetic and epigenetic fatty acid desaturase 2 (FADS2) profiles and toddlers' n-6 and n-3 fatty acid metabolism. FADS2 rs174575 variation and DNA methylation status were interrogated in mothers and toddlers, as well as food intake and plasma fatty acid concentrations in toddlers. A multivariate fit model indicated that maternal rs174575 genotype, combined with DNA methylation, can predict α-linolenic acid plasma concentration in all toddlers and arachidonic acid concentrations in boys. Arachidonic acid intake was predictive for its plasma concentration in girls, whereas intake of 3 major n-3 species (eicosapentaenoic, docosapentaenoic, and docosahexaenoic acids) were predictive for their plasma concentrations in boys. FADS2 genotype and DNA methylation in toddlers were not related to plasma concentrations or food intakes, except for CpG8 methylation. Maternal FADS2 methylation was a predictor for the boys' α-linolenic acid intakes. This exploratory study suggests that maternal FADS2 genetic and epigenetic status could be related to toddlers' polyunsaturated fatty acid metabolism.

  14. Venom Alkaloid and Cuticular Hydrocarbon Profiles Are Associated with Social Organization, Queen Fertility Status, and Queen Genotype in the Fire Ant Solenopsis invicta

    PubMed Central

    Eliyahu, Dorit; Ross, Kenneth G.; Haight, Kevin L.; Keller, Laurent

    2013-01-01

    Queens in social insect colonies advertise their presence in the colony to: a) attract workers’ attention and care; b) gain acceptance by workers as replacement or supplemental reproductives; c) prevent reproductive development in nestmates. We analyzed the chemical content of whole body surface extracts of adult queens of different developmental and reproductive stages, and of adult workers from monogyne (single colony queen) and polygyne (multiple colony queens) forms of the fire ant Solenopsis invicta. We found that the composition of the most abundant components, venom alkaloids, differed between queens and workers, as well as between reproductive and non-reproductive queens. Additionally, workers of the two forms could be distinguished by alkaloid composition. Finally, sexually mature, non-reproductive queens from polygyne colonies differed in their proportions of cis-piperidine alkaloids, depending on their Gp-9 genotype, although the difference disappeared once they became functional reproductives. Among the unsaturated cuticular hydrocarbons characteristic of queens, there were differences in amounts of alkenes/alkadienes between non-reproductive polygyne queens of different Gp-9 genotypes, between non-reproductive and reproductive queens, and between polygyne and monogyne reproductive queens, with the amounts increasing at a relatively higher rate through reproductive ontogeny in queens bearing the Gp-9 b allele. Given that the genotype-specific piperidine differences reflect differences in rates of reproductive maturation between queens, we speculate that these abundant and unique compounds have been co-opted to serve in fertility signaling, while the cuticular hydrocarbons now play a complementary role in regulation of social organization by signaling queen Gp-9 genotype. PMID:22095515

  15. Novel drug metabolism indices for pharmacogenetic functional status based on combinatory genotyping of CYP2C9, CYP2C19 and CYP2D6 genes

    PubMed Central

    Villagra, David; Goethe, John; Schwartz, Harold I; Szarek, Bonnie; Kocherla, Mohan; Gorowski, Krystyna; Windemuth, Andreas; Ruaño, Gualberto

    2011-01-01

    Aims We aim to demonstrate clinical relevance and utility of four novel drug-metabolism indices derived from a combinatory (multigene) approach to CYP2C9, CYP2C19 and CYP2D6 allele scoring. Each index considers all three genes as complementary components of a liver enzyme drug metabolism system and uniquely benchmarks innate hepatic drug metabolism reserve or alteration through CYP450 combinatory genotype scores. Methods A total of 1199 psychiatric referrals were genotyped for polymorphisms in the CYP2C9, CYP2C19 and CYP2D6 gene loci and were scored on each of the four indices. The data were used to create distributions and rankings of innate drug metabolism capacity to which individuals can be compared. Drug-specific indices are a combination of the drug metabolism indices with substrate-specific coefficients. Results The combinatory drug metabolism indices proved useful in positioning individuals relative to a population with regard to innate drug metabolism capacity prior to pharmacotherapy. Drug-specific indices generate pharmacogenetic guidance of immediate clinical relevance, and can be further modified to incorporate covariates in particular clinical cases. Conclusions We believe that this combinatory approach represents an improvement over the current gene-by-gene reporting by providing greater scope while still allowing for the resolution of a single-gene index when needed. This method will result in novel clinical and research applications, facilitating the translation from pharmacogenomics to personalized medicine, particularly in psychiatry where many drugs are metabolized or activated by multiple CYP450 isoenzymes. PMID:21861665

  16. Abnormalities in apolipoprotein and lipid levels in an HIV-infected Brazilian population under different treatment profiles: the relevance of apolipoprotein E genotypes and immunological status.

    PubMed

    Malavazi, Iran; Abrão, Emiliana P; Mikawa, Angela Y; Landgraf, Viviane O; da Costa, Paulo I

    2004-05-01

    HIV infection is associated with disturbances in lipid metabolism due to a host's response mechanism and the current antiretroviral therapy. The pathological appearance and progression of atherosclerosis is dependent on the presence of injurious agents in the vascular endothelium and variations in different subsets of candidate genes. Therefore, the Hha I polymorphism in the apolipoprotein E gene was evaluated in addition to triglycerides, total cholesterol, very low-density lipoprotein (VLDL), LDL, high-density lipoprotein (HDL), and apolipoprotein (apo) Al, B and E levels in 86 Brazilian HIV-infected patients and 29 healthy controls. The allele frequency for apoE in the HIV-infected group and controls was in agreement with data on the Brazilian population. Dyslipidemia was observed in the HIV group and verified by increased levels of triglycerides, VLDL and apoE, and decreased levels of HDL and apoAl. The greatest abnormalities in these biochemical variables were shown in the HIV-infected individuals whose immune function was more compromised. The effect of the genetic variation at the APOE gene on biochemical variables was more pronounced in the HIV-infected individuals who carried the apoE2/3 genotype. The highly active anti-retroviral therapy (HAART)-receiving group presented increased levels of total cholesterol and apoE. Dyslipidemia was a predictable consequence of HIV infection and the protease inhibitors intensified the increase in apoE values.

  17. The relation of developmental changes in brain serotonin transporter (5HTT) and 5HT1A receptor binding to emotional behavior in female rhesus monkeys: effects of social status and 5HTT genotype.

    PubMed

    Embree, M; Michopoulos, V; Votaw, J R; Voll, R J; Mun, J; Stehouwer, J S; Goodman, M M; Wilson, M E; Sánchez, M M

    2013-01-03

    The goal of the present study was to examine how social subordination stress and 5HTT polymorphisms affect the development of brain serotonin (5HT) systems during the pubertal transition in female rhesus monkeys. We also examined associations with developmental changes in emotional reactivity in response to a standardized behavioral test, the Human Intruder (HI). Our findings provide the first longitudinal evidence of developmental increases in 5HT1A receptor and 5HTT binding in the brain of female primates from pre- to peripuberty. The increase in 5HT1A BP(ND) in these socially housed female rhesus monkeys is a robust finding, occurring across all groups, regardless of social status or 5HTT genotype, and occurring in the left and right hemispheres of all prefrontal regions studied, as well as the amygdala, hippocampus, hypothalamus, and raphe nuclei. 5HTT BP(ND) also showed an increase with age in raphe, anterior cingulate cortex, and dorsolateral prefrontal cortex. These changes in brain 5HT systems take place as females establish more adult-like patterns of social behavior, as well as during the HI paradigm. Indeed, the main developmental changes in behavior during the HI (increase in freezing and decrease in submission/appeasement) were related to neurodevelopmental increases in 5HT1A receptors and 5HTT, because the associations between these behaviors and 5HT endpoints emerge at peripuberty. We detected an effect of social status on 5HT1A BP(ND) in the hypothalamus and on 5HTT BP(ND) in the orbitofrontal cortex, with subordinates showing higher BP(ND) than dominants in both cases during the pubertal transition. No main effects of 5HTT genotype were observed for 5HT1A or 5HTT BP(ND). Our findings indicate that adolescence in female rhesus monkeys is a period of central 5HT reorganization, partly influenced by exposure to the social stress of subordination, that likely functions to integrate adrenal and gonadal systems and shape the behavioral response to

  18. Genotypic and phenotypic evaluation of Rutilus spp. from Skadar, Ohrid and Prespa Lakes supports revision of endemic as well as taxonomic status of several taxa.

    PubMed

    Milošević, D; Winkler, K A; Marić, D; Weiss, S

    2011-11-01

    One mtDNA gene (cytochrome b), one nuclear DNA fragment, five microsatellites and a suite of morphological characters were evaluated in samples of Rutilus spp. from Skadar, Ohrid and Prespa Lakes. Both genetic and phenotypic data supported two sympatric taxa in Lake Skadar, whereby Prespa and Ohrid Lakes revealed only a single taxon each. One of the taxa from Lake Skadar was similar to samples from Lake Prespa, whereas the second taxon was the most divergent in the data set. The estimated time to the most recent common ancestor of these two sympatric taxa in Lake Skadar was between 125 000 and 500 000 years. The data did not support existing taxonomic schemes for Rutilus in these lakes. This study poses the following working hypothesis: (1) Rutilus prespensis lives both in Lake Prespa and Lake Skadar and therefore is not endemic to Lake Prespa, (2) Rutilus ohridanus lives in Lake Ohrid only and therefore could be considered an endemic if its species status is retained and (3) a third recently described taxon (Rutilus albus) sympatric to R. prespensis lives in Lake Skadar.

  19. A pilot study of Helicobacter pylori genotypes and cytokine gene polymorphisms in reflux oesophagitis and peptic ulcer disease.

    PubMed

    Akdogan, R A; Ozgur, O; Gucuyeter, S; Kaklikkaya, N; Cobanoglu, U; Aydin, F

    2014-01-01

    Helicobacter pylori causes various diseases such as chronic gastritis, peptic ulcer and gastric cancer. While majority of the people infected with H. pylori is asymptomatic, 15-20 % of them develop such diseases. The main factors, which determine the development of H. pylori related diseases might be bacterial virulence, host genetic and environmental factors.The aim of this study was to reveal the factors that play a role in the disease development in patients with reflux esophagitis and peptic ulcer, infected with Helicobacter pylori. Environmental factors such as medical agents, smoking and body mass index were evaluated. The factors specific to bacteria such as vacA, CagA, babA and iceA virulence genotypes and the host factors such as IL-1, IL-2, IL-4, IL-6, IL-10, IL-12, interferon-γ, TNF-α, ve TGF-β1 gene polymorphisms were compared between the two groups.H. pylori infected twenty five patients with reflux esophagitis and peptic ulcer were enrolled in the study. There was no statistical difference between the two groups regarding environmental factors. IL-2 -330T +166T (p=0.037) and IL10 -1082A; -819C (p=0.049) gene polymorphisms were significantly more common in the group of patients with peptic ulcer compared to the group with reflux esophagitis. In both groups of patients, either with reflux esophagitis or peptic ulcer, multiple H. pylori virulence genotypes (cagA, vacA, babA) (mean values 74 %, 78 %, 54 % respectively) were observed.In this study, we revealed that cytokine gene polymorphisms may play a role in the development peptic ulcer while H. pylori virulence genotypes seem to be crucial for the development of associated diseases (Tab. 4, Ref. 51).

  20. APOE Genotyping, Cardiovascular Disease

    MedlinePlus

    ... high level of triglycerides in the blood, and atherosclerosis that develops at an early age. APOE genotyping ... and is associated with an increased risk of atherosclerosis . People with these genotypes could be predisposed to ...

  1. Transforming Microbial Genotyping: A Robotic Pipeline for Genotyping Bacterial Strains

    PubMed Central

    Velayudhan, Vimalkumar; Murphy, Ronan A.; Achtman, Mark

    2012-01-01

    Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost. PMID:23144721

  2. Axiom turkey genotyping array

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Axiom®Turkey Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turk...

  3. Emergence of Hepatitis B Virus Genotype F in Aligarh Region of North India

    PubMed Central

    Sami, Hiba; Rizvi, Meher; Azam, Mohd; Mukherjee, Rathindra M.; Shukla, Indu; Ajmal, M. R.; Malik, Abida

    2013-01-01

    Introduction. HBV genotypes and subtypes are useful clinical and epidemiological markers. In this study prevalent HBV genotypes were assessed in relation to serological profile and clinical status. Material & Methods. 107 cases of HBV were genotyped. Detailed clinical history was elicited from them. HBsAg, HBeAg, anti-HBs, anti-HBe, and anti-HBc-IgM were assessed. HBV genotyping was performed using Kirschberg's type specific primers (TSP-PCR), heminested PCR, and Naito's monoplex PCR. Nucleotide sequencing was performed. Results. A total of 97 (91%) were genotyped following the methods of Kirschberg et al./Naito et al. Genotype D was by far the most prevalent genotype 91 (85.04%) in this region. A surprising finding was the detection of genotype F in 5 (4.67%) of our patients. Genotype A strangely was observed only in one case. In 85.7% genotype D was associated with moderate to severe liver disease, 43.9% HBeAg, and 18.7% anti-HBc-IgM positivity. Majority of genotype F (80%) was seen in mild to moderate liver disease. It was strongly associated with HBeAg 60% and 20% anti-HBc-IgM positivity. Conclusion. Emergence of genotype F in India merits further study regarding its clinical implications and treatment modalities. Knowledge about HBV genotypes can direct a clinician towards more informed management of HBV patients. PMID:24381592

  4. Antarctic Sea Ice-a Habitat for Extremophiles

    NASA Astrophysics Data System (ADS)

    Thomas, D. N.; Dieckmann, G. S.

    2002-01-01

    The pack ice of Earth's polar oceans appears to be frozen white desert, devoid of life. However, beneath the snow lies a unique habitat for a group of bacteria and microscopic plants and animals that are encased in an ice matrix at low temperatures and light levels, with the only liquid being pockets of concentrated brines. Survival in these conditions requires a complex suite of physiological and metabolic adaptations, but sea-ice organisms thrive in the ice, and their prolific growth ensures they play a fundamental role in polar ecosystems. Apart from their ecological importance, the bacterial and algae species found in sea ice have become the focus for novel biotechnology, as well as being considered proxies for possible life forms on ice-covered extraterrestrial bodies.

  5. HBV Genotypic Variability in Cuba

    PubMed Central

    Loureiro, Carmen L.; Aguilar, Julio C.; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H.

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions. PMID:25742179

  6. AN EVALUATION OF CRYPTOSPORIDIUM PARVUM GENOTYPING

    EPA Science Inventory

    We evaluated the specificity and sensitivity of 11 previously described species differentiation and genotyping PCR protocols for detection of Cryptosporidium parasites. Genomic DNA from three species of Crytosporidium parasites (genotype 1 and genotype 2 of C. parvum, C. muris, a...

  7. Genotype Specification Language.

    PubMed

    Wilson, Erin H; Sagawa, Shiori; Weis, James W; Schubert, Max G; Bissell, Michael; Hawthorne, Brian; Reeves, Christopher D; Dean, Jed; Platt, Darren

    2016-06-17

    We describe here the Genotype Specification Language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language based on traditional genetic notation, as well as a set of low-level DNA manipulation primitives. The language allows facile incorporation of parts from a library of cloned DNA constructs and from the "natural" library of parts in fully sequenced and annotated genomes. GSL was designed to engage genetic engineers in their native language while providing a framework for higher level abstract tooling. To this end we define four language levels, Level 0 (literal DNA sequence) through Level 3, with increasing abstraction of part selection and construction paths. GSL targets an intermediate language based on DNA slices that translates efficiently into a wide range of final output formats, such as FASTA and GenBank, and includes formats that specify instructions and materials such as oligonucleotide primers to allow the physical construction of the GSL designs by individual strain engineers or an automated DNA assembly core facility.

  8. Hepatitis B virus in Buenos Aires, Argentina: genotypes, virological characteristics and clinical outcomes.

    PubMed

    Pezzano, S C; Torres, C; Fainboim, H A; Bouzas, M B; Schroder, T; Giuliano, S F; Paz, S; Alvarez, E; Campos, R H; Mbayed, V A

    2011-02-01

    Hepatitis B virus (HBV) is classified into eight major genotypes, A-H, which are geographically distributed worldwide. The aim of this work was to describe the clinical characteristics associated with the HBV genotypes circulating in Buenos Aires city. The study included 139 patients infected with HBV, whose clinical courses were classified as acute symptomatic self-limiting hepatitis, inactive carrier state and chronic active hepatitis (HBV e-antigen (HBeAg)-positive and HBeAg-negative). The HBV genotypes were determined in 128 patients by PCR-restriction fragment length polymorphism and phylogenetic analysis. Biochemical, virological, clinical and histological features were analysed. A differential distribution of genotypes between acute symptomatic and chronic infections was found. Among the acute cases, genotype F was predominant (65.2%, 30/46) and genotype D was rare (4.3%, 2/46), whereas among the chronic infections, a homogeneous distribution of genotypes A (26.8%, 22/82), D (31.7%, 26/82) and F (36.6%, 30/82), with an unusual presence of genotypes B (1.2%, 1/82) and C (3.7%, 3/82), was observed. Regarding the liver histology of chronically infected patients, genotype F tended to display higher histological activity indexes. Mutations related to HBV surface antigen immunoreactivity, antiviral resistance and HBeAg-negative status were studied. This work constitutes, to our knowledge, the first description of the clinical characteristics related to HBV genotypes in Argentina, where the distribution of genotypes in patients with acute infection has not been reported previously. Finally, it was established that genotype F is the prevalent genotype among the acute symptomatic infections in Buenos Aires city, and that it shows a tendency to cause an adverse disease outcome among the chronic cases.

  9. Hepatitis B virus infection and genotype in asymptomatic people from 10 ethnic groups in Yunnan, China

    PubMed Central

    Shen, Yuan-Ying; Hou, Wei; Yang, Zhan-Qiu; Xiao, Wen

    2015-01-01

    AIM: To evaluate the infection and genotype distribution of hepatitis B virus (HBV) in ethnic groups in Yunnan, China. METHODS: Two thousand five hundred and eighty-four asymptomatic local people from 10 ethnic groups were investigated in Yunnan, China. Infection and genotype distribution were evaluated by serological and genetic methods. Genotyping was verified by sequencing. Ethnic genotype distribution was compared by proportion test. RESULTS: Four types of infection model based on HBV serum markers were identified, and the average HBV infection rate was 5.7% in those asymptomatic local people. The genotype prevalence was 59.6% for B, 21.1% for C and 19.3% BC; subgenotypes Ba, Cs and Ce were identified in this study. Hepatitis B surface antigen-positive rate and the proportion of genotype B were significantly lower in ethnic groups with a northern origin compared to those with a southern origin (50% vs 73.9%, P = 0.037; 4.2% vs 10.5%, P = 0.000). CONCLUSION: Genotype B is dominant and genotype BC has high occurrence in asymptomatic local ethnic groups in Yunnan. HBV infection status and genotype distribution may associate with ethnic origin. PMID:26640334

  10. Clinical and Serological Variation between Patients Infected with Different Hepatitis B Virus Genotypes

    PubMed Central

    Kidd-Ljunggren, Karin; Myhre, Erling; Bläckberg, Jonas

    2004-01-01

    Hepatitis B virus (HBV) has eight genotypes which have distinct geographical distributions. Studies comparing differences in the clinical outcomes of infections caused by strains with genotype-related variations in the HBV genome have largely compared genotypes B and C and genotypes A and D but not all four genotypes. The present study included 196 HBV-infected patients attending an infectious diseases outpatient clinic in Sweden. The age and geographic origin, liver function, HBeAg and anti-HBe status, and the presence or absence of HBV DNA were analyzed for each patient. HBV DNA was detected in 144 patients, and the HBV genotype and the core promoter and precore sequences were determined for the isolates from 101 of these patients. Among the patients who might be considered most likely to be nonviremic, namely, anti-HBe-positive HBV carriers with normal alanine aminotransferase (ALT) levels, 65% had detectable HBV DNA and were thus viremic. Among the viremic patients, HBeAg-positive patients were more likely to have elevated ALT levels than anti-HBe-positive patients. HBV genotypes A to F were represented in the study, and their distributions coincided accurately with the origin of the patient. A significantly higher number of genotype D-infected patients were anti-HBe positive and had elevated ALT levels (42% of genotype D-infected patients but 0% of patients infected with genotypes B and C). Genotype D strains with mutations in the core promoter and precore regions were significantly correlated with elevated ALT levels in the patients. The differences were not age related. Therefore, in this large-scale cross-sectional study, genotype D appears to be associated with more active disease. PMID:15583320

  11. HBV genotypes prevalence, precore and basal core mutants in Morocco.

    PubMed

    Baha, Warda; Ennaji, My Mustapha; Lazar, Fatiha; Melloul, Marouane; El Fahime, Elmostafa; El Malki, Abdelouahad; Bennani, Abdelouaheb

    2012-08-01

    The study of hepatitis B virus (HBV) genomic heterogeneity has become a major issue in investigations aimed at understanding the relationship between HBV mutants and the wide spectrum of clinical and pathological conditions associated with HBV infection. The objective of the current study was to find out the pattern of HBV genotypes circulating in Morocco and to investigate the precore (PC) and basal core promoter (BCP) mutants' status in Moroccan chronic hepatitis B patients. Viral genotypes were determined in 221 chronic carriers using INNO-LiPA HBV assay and hemi-nested PCR. Phylogenetic analysis was performed in 70 samples, and multiplex PCR method was used to confirm some genotyping results. PC and CP mutants were determined using Inno-Lipa. All isolates were successfully genotyped. The genotype distribution was D in 90.45% of cases, A (5.9%), E (1 case), and mixed genotypes (5 A/D and 2 D/F) in 3.17% patients. HBV carried in the HBV/D samples could be assigned to D7 (63.3%), D1 (32.7%) and 2% of strains to each D4 and D5, all HBV/A belonged to A2 subgenotype and HBV/E strain could not be sub-genotyped. In 70 studied strains, HBV mutants were detected in 88.6% of cases; PC mutants were detected in (40%) of patients and 21.5% present a mixture of wild type and G1896A mutation. BCP mutants were observed in 65.7% of cases, 22.9% were found to have the T1762/1764A double mutation, 18.6% had A1762/1764T mutation and 22.9% of patients showed the A1762T/G1764A double mutation with either A1762T/G1764T mutation. Co-infection by PC and BCP mutants was detected in 52.9% of cases. Movement from place to place most likely shapes the observed genotype distribution and consequent prevalence of genotypes other than A2 or D7 in this population. High circulation of PC and BCP mutants is common in chronic hepatitis B infection in Morocco.

  12. Population samples and genotyping technology.

    PubMed

    Mack, S J; Sanchez-Mazas, A; Single, R M; Meyer, D; Hill, J; Dron, H A; Jani, A J; Thomson, G; Erlich, H A

    2007-04-01

    The 14th International HLA (human leukocyte antigen) Immunogenetics Workshop (14th-IHIWS) Biostatistics and Anthropology/Human Genetic Diversity project continues the population sampling, genotype data generation, and biostatistic analyses of the 13th International Histocompatibility Workshop Anthropology/Human Genetic Diversity Component, with the overall goal of further characterizing global HLA allele and haplotype diversity and better describing the relationships between major histocompatibility complex diversity, geography, linguistics, and population history. Since the 13th Workshop, new investigators have and continue to be recruited to the project and new high-resolution class I and class II genotype data are being generated for 112 population samples from around the world.

  13. Genotype imputation via matrix completion

    PubMed Central

    Chi, Eric C.; Zhou, Hua; Chen, Gary K.; Del Vecchyo, Diego Ortega; Lange, Kenneth

    2013-01-01

    Most current genotype imputation methods are model-based and computationally intensive, taking days to impute one chromosome pair on 1000 people. We describe an efficient genotype imputation method based on matrix completion. Our matrix completion method is implemented in MATLAB and tested on real data from HapMap 3, simulated pedigree data, and simulated low-coverage sequencing data derived from the 1000 Genomes Project. Compared with leading imputation programs, the matrix completion algorithm embodied in our program MENDEL-IMPUTE achieves comparable imputation accuracy while reducing run times significantly. Implementation in a lower-level language such as Fortran or C is apt to further improve computational efficiency. PMID:23233546

  14. Genotype networks in metabolic reaction spaces

    PubMed Central

    2010-01-01

    Background A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism needs to survive and reproduce. Previous work has focused on the properties of individual genotypes while little is known about how genome-scale metabolic networks with a given function can vary in their reaction content. Results We here characterize spaces of such genotypes. Specifically, we study metabolic genotypes whose phenotype is viability in minimal chemical environments that differ in their sole carbon sources. We show that regardless of the number of reactions in a metabolic genotype, the genotypes of a given phenotype typically form vast, connected, and unstructured sets -- genotype networks -- that nearly span the whole of genotype space. The robustness of metabolic phenotypes to random reaction removal in such spaces has a narrow distribution with a high mean. Different carbon sources differ in the number of metabolic genotypes in their genotype network; this number decreases as a genotype is required to be viable on increasing numbers of carbon sources, but much less than if metabolic reactions were used independently across different chemical environments. Conclusions Our work shows that phenotype-preserving genotype networks have generic organizational properties and that these properties are insensitive to the number of reactions in metabolic genotypes. PMID:20302636

  15. Genotyping with TaqMAMA.

    PubMed

    Li, Baohui; Kadura, Ibrahim; Fu, Dong-Jing; Watson, David E

    2004-02-01

    TaqMAMA combines the quantitative strengths of TaqMan with the allele-specific PCR of MAMA. In this article we develop TaqMAMA as a technique for screening human DNA samples for known genetic polymorphisms. In the first set of experiments, plasmids that model all types of genetic polymorphisms were used to understand the relationship between TaqMAMA primer/template mismatches and their strength of allelic discrimination. These data can be used to improve allelic discrimination of other primer extension genotyping methodologies through directed use of nucleotide mismatches. We used the data to derive a guide for TaqMAMA primer design and DNA strand selection for TaqMAMA genotyping assays. The guide was then used to develop assays for 11 known and novel human genetic polymorphisms. Genotypes were assigned quickly and accurately in all cases. TaqMAMA genotyping assays require minimal development time, have a high probability of success, produce reliable data that are straightforward to analyze, and are very cost-competitive.

  16. Genotype × genotype interactions between the toxic cyanobacterium Microcystis and its grazer, the waterflea Daphnia

    PubMed Central

    Lemaire, Veerle; Brusciotti, Silvia; van Gremberghe, Ineke; Vyverman, Wim; Vanoverbeke, Joost; De Meester, Luc

    2012-01-01

    Toxic algal blooms are an important problem worldwide. The literature on toxic cyanobacteria blooms in inland waters reports widely divergent results on whether zooplankton can control cyanobacteria blooms or cyanobacteria suppress zooplankton by their toxins. Here we test whether this may be due to genotype × genotype interactions, in which interactions between the large-bodied and efficient grazer Daphnia and the widespread cyanobacterium Microcystis are not only dependent on Microcystis strain or Daphnia genotype but are specific to genotype × genotype combinations. We show that genotype × genotype interactions are important in explaining mortality in short-time exposures of Daphnia to Microcystis. These genotype × genotype interactions may result in local coadaptation and a geographic mosaic of coevolution. Genotype × genotype interactions can explain why the literature on zooplankton–cyanobacteria interactions is seemingly inconsistent, and provide hope that zooplankton can contribute to the suppression of cyanobacteria blooms in restoration projects. PMID:25568039

  17. Invasive genotypes are opportunistic specialists not general purpose genotypes

    PubMed Central

    Drown, Devin M; Levri, Edward P; Dybdahl, Mark F

    2011-01-01

    It is not clear which forms of plasticity in fitness-related traits are associated with invasive species. On one hand, it may be better to have a robust performance across environments. On the other, it may be beneficial to take advantage of limited favorable conditions. We chose to study a worldwide invasive species, Potamopyrgus antipodarum, and compare the plasticity of life-history traits of a sample of invasive genotypes to a sample of ancestral-range genotypes. We examined the responses to salinity in this freshwater snail because it varies spatially and temporally in the introduced range and contributes to variation in fitness in our system. We used a recently developed statistical method that quantifies aspects of differences in the shape among reaction norms. We found that the invasive lineages survived and reproduced with an increased probability at the higher salinities, and were superior to ancestral-range lineages in only two traits related to reproduction. Moreover, we found that in terms of traits related to growth, the invasive lineages have a performance optimum that is shifted to higher salinities than the ancestral-range lineages as well as having a narrower niche breadth. Contrary to the prediction of the general purpose genotype hypothesis, we found that invasive lineages tended to be opportunistic specialists. PMID:25567958

  18. Selection of common bean (Phaseolus vulgaris L.) genotypes using a genotype plus genotype x environment interaction biplot.

    PubMed

    Corrêa, A M; Teodoro, P E; Gonçalves, M C; Santos, A; Torres, F E

    2016-08-05

    Recently, the genotype plus genotype x environment interaction (GGE) biplot methodology has been used to investigate genotype x environment interactions in several crop species, but has not been applied to the common bean (Phaseolus vulgaris L.) crop in Brazil. The aim of this study was to identify common bean genotypes that exhibit high grain yield and stability in the State of Mato Grosso do Sul, Brazil. We conducted 12 trials from 2000 to 2006 in the municipalities of Aquidauana and Dourados, and evaluated 13 genotypes in a randomized block design with three replications. Grain yield data were subjected to individual and joint analyses of variance. After analyzing the GE interaction, the adaptability and phenotypic stability of the common bean genotypes were analyzed using GGE biplot methodology. The genotypes EMGOPA-201, Xamego, and Aporé are recommended for growing in Mato Grosso do Sul, because they exhibited high grain yield and phenotypic stability.

  19. Plant genotype, microbial recruitment and nutritional security

    PubMed Central

    Patel, Jai S.; Singh, Akanksha; Singh, Harikesh B.; Sarma, Birinchi K.

    2015-01-01

    Agricultural food products with high nutritional value should always be preferred over food products with low nutritional value. Efforts are being made to increase nutritional value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritional value of food is increased under natural environmental conditions especially in agricultural farms. Fragmented researches have demonstrated possibilities in achieving the same. The rhizosphere is vital in this regard for not only health and nutritional status of plants but also for the microorganisms colonizing the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of a plant host in discriminating its colonizers (Zancarini et al., 2012). A large number of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome (Berendsen et al., 2012; Marques et al., 2014). PMID:26300905

  20. Distribution of human papillomavirus genotypes in cervical lesions

    PubMed Central

    Ma, Li; Cong, Xiao; Shi, Mai; Wang, Xiu-Hong; Liu, Hai-Yan; Bian, Mei-Lu

    2017-01-01

    The aims of the present study were to investigate the distribution of human papillomavirus (HPV) genotypes in cervical lesions, and the association between different HPV genotypes and cervical lesions. Between January 2013 and June 2014, the HPV type determinations of nucleic acid by use of fluorescence polymerase chain reaction (PCR) method of 15,192 outpatients in China-Japan Friendship Hospital were performed and the infection status was analyzed. The results showed that: i) 2,366 Cases were HPV positive and 12,826 cases were HPV negative, the overall infection rate was 15.57% (2,366/15,192), in which a single genotype of HPV infection rate was 11.63% (1,767/15,192), and multiple genotypes of HPV infection rate was 3.94% (599/15,192); ii) HPV16, HPV52 and HPV58 infections were the most common HPV genotypes, the infection rates were 3.95% (600/15,192), 2.86% (435/15,192) and 2.67% (406/15,192), respectively; and iii) According to the gold standard of histopathological analysis via hematoxylin-eosin staining, HPV16, HPV52 and HPV58 accounted for 58.80% (154/267) of all CIN2 or above squamous epithelial lesions. Furthermore, three cases with pathological changes of the cervical severe glandular epithelium were all HPV18 infection. The difference was statistically significant (χ2=60.74, P<0.001). Single HPV subtype infection was primarily associated with HPV16, HPV52 and HPV58. In conclusion, HPV type detection had a may be important in screening of cervical lesions as a difference in pathogenic ability was noted among different HPV genotypes. As cervical cancer is an infectious disease, HPV testing may help detect more precancerous lesions, thus reducing the morbidity and mortality of cervical cancer. HPV16, HPV52 and HPV58 were associated with severe cervical squamous epithelial lesions; HPV18 was associated with cervical severe glandular cell pathological changes, although it was not the most common HPV genotype in China. When positive, a clinical cervical

  1. eCOMPAGT – efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology

    PubMed Central

    Schönherr, Sebastian; Weißensteiner, Hansi; Coassin, Stefan; Specht, Günther; Kronenberg, Florian; Brandstätter, Anita

    2009-01-01

    Background High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-related personal information, which needs to be handled with care by following data privacy protection guidelines. In addition, genotyping core facilities handling cooperative projects require a straightforward solution to monitor the status and financial resources of the different projects. Description We developed a database system for an efficient combination and management of phenotypes and genotypes (eCOMPAGT) deriving from genetic epidemiological studies. eCOMPAGT securely stores and manages genotype and phenotype data and enables different user modes with different rights. Special attention was drawn on the import of data deriving from TaqMan and SNPlex genotyping assays. However, the database solution is adjustable to other genotyping systems by programming additional interfaces. Further important features are the scalability of the database and an export interface to statistical software. Conclusion eCOMPAGT can store, administer and connect phenotype data with all kinds of genotype data and is available as a downloadable version at . PMID:19432954

  2. The ACTN3 R577X genotype is associated with muscle function in a Japanese population.

    PubMed

    Kikuchi, Naoki; Yoshida, Shou; Min, Seok-ki; Lee, Kihyuk; Sakamaki-Sunaga, Mikako; Okamoto, Takanobu; Nakazato, Koichi

    2015-04-01

    Homozygosity for the common nonsense polymorphism R577X in the α-actinin-3 gene (ACTN3) causes complete α-actinin-3 deficiency in fast-twitch skeletal muscle fibers. This study investigated whether the ACTN3 R577X polymorphism affects fitness status using a battery of tests in a large Japanese cohort. In the present study, 1227 subjects (age: 25-85 years) were genotyped for the ACTN3 R577X polymorphism (rs1815739) using a TaqMan SNP genotyping assay (Applied Biosystems). All subjects were divided into 2 groups based on their age (<55 years and ≥55 years). All subjects completed a questionnaire about exercise habits and were subjected to a battery of tests to assess their fitness status (including grip strength test, chair stand test, and 8-foot walking test). A significant association between the ACTN3 R577X genotype and chair stand test performance was observed in the group of men ≥55 using ANCOVA adjusted for age and exercise habits (p = 0.036). The ACTN3 R577X genotype accounted for 2.5% of the variability in the results of the chair stand test among men in the ≥55 age group. Moreover, for the ≥55 age group, performance in the chair stand test was lower among those with the XX genotype than among those with the RR genotype (p = 0.024) or RX genotype (p = 0.005), unlike results for the <55 age group. No significant difference was noted for hand grip strength or 8-foot walking time. Thus, our results suggest that the ACTN3 R577X genotype is associated with lower-extremity muscle function in the Japanese population.

  3. HBV genotype F: natural history and treatment.

    PubMed

    Marciano, Sebastián; Galdame, Omar A; Gadano, Adrián C

    2013-01-01

    The analysis of the HBV genome revealed the existence of 10 genotypes, named A-J. Evidence of the influence of the different genotypes in the natural history and treatment response to nucleoside/nucleotide analogues or interferon-based regimens is scant. HBV genotype F is one of the most prevalent circulating genotypes in South America and the Arctic Circle. Since most of the available information on HBV is from Asia, the US and Europe, it reflects their predominant genotypes: A, B, C and D. To date, the evidence is not fully confirmed, but it appears that genotype F chronic hepatitis B is associated with a more aggressive course of liver disease, reflected by higher histological indexes, a higher risk of development of hepatocellular carcinoma and a higher rate of liver-related mortality. In terms of treatment response, the available data is, unfortunately, even more limited; however, what data is available suggests acceptable and similar response rates to pegylated interferon-α2a in genotype F compared to genotype A. Response rates to nucleoside/nucleotide analogues is not influenced by genotype. The review of this limited data sheds light on the necessity to conduct further studies in South America and the Arctic Circle in order to better understand the different aspects of HBV genotype F, especially in relation to treatment response.

  4. HIV Infection Affects Streptococcus mutans Levels, but Not Genotypes

    PubMed Central

    Liu, G.; Saxena, D.; Chen, Z.; Norman, R.G.; Phelan, J.A.; Laverty, M.; Fisch, G.S.; Corby, P.M.; Abrams, W.; Malamud, D.; Li, Y.

    2012-01-01

    We report a clinical study that examines whether HIV infection affects Streptococcus mutans colonization in the oral cavity. Whole stimulated saliva samples were collected from 46 HIV-seropositive individuals and 69 HIV-seronegative control individuals. The level of S. mutans colonization was determined by conventional culture methods. The genotype of S. mutans was compared between 10 HIV-positive individuals before and after highly active antiretroviral therapy (HAART) and 10 non-HIV-infected control individuals. The results were analyzed against viral load, CD4+ and CD8+ T-cell counts, salivary flow rate, and caries status. We observed that S. mutans levels were higher in HIV-infected individuals than in the non-HIV-infected control individuals (p = 0.013). No significant differences in S. mutans genotypes were found between the two groups over the six-month study period, even after HAART. There was a bivariate linear relationship between S. mutans levels and CD8+ counts (r = 0.412; p = 0.007), but not between S. mutans levels and either CD4+ counts or viral load. Furthermore, compared with non-HIV-infected control individuals, HIV-infected individuals experienced lower salivary secretion (p = 0.009) and a positive trend toward more decayed tooth surfaces (p = 0.027). These findings suggest that HIV infection can have a significant effect on the level of S. mutans, but not genotypes. PMID:22821240

  5. Detection of Rotavirus Genotypes in Korea 5 Years after the Introduction of Rotavirus Vaccines.

    PubMed

    Chung, Ju-Young; Kim, Min-Sung; Jung, Tae Woong; Kim, Seong Joon; Kang, Jin-Han; Han, Seung Beom; Kim, Sang Yong; Rhim, Jung Woo; Kim, Hwang-Min; Park, Jae Hong; Jo, Dae Sun; Ma, Sang Hyuk; Jeong, Hye-Sook; Cheon, Doo-Sung; Kim, Jong-Hyun

    2015-10-01

    Rotavirus (RV) is one of the most important viral etiologic agents of acute gastroenteritis (AGE) in children. Although effective RV vaccines (RVVs) are now used worldwide, novel genotypes and outbreaks resulting from rare genotype combinations have emerged. This study documented RV genotypes in a Korean population of children with AGE 5 yr after the introduction of RVV and assessed potential genotype differences based on vaccination status or vaccine type. Children less than 5-yr-old diagnosed with AGE between October 2012 and September 2013 admitted to 9 medical institutions from 8 provinces in Korea were prospectively enrolled. Stool samples were tested for RV by enzyme immunoassay and genotyped by multiplex reverse-transcription polymerase chain reaction. In 346 patients, 114 (32.9%) were RV-positive. Among them, 87 (76.3%) patients were infected with RV alone. Eighty-six of 114 RV-positive stool samples were successfully genotyped, and their combinations of genotypes were G1P[8] (36, 41.9%), G2P[4] (12, 14.0%), and G3P[8] (6, 7.0%). RV was detected in 27.8% of patients in the vaccinated group and 39.8% in the unvaccinated group (P=0.035). Vaccination history was available for 67 of 86 cases with successfully genotyped RV-positive stool samples; RotaTeq (20, 29.9%), Rotarix (7, 10.4%), unvaccinated (40, 59.7%). The incidence of RV AGE is lower in the RV-vaccinated group compared to the unvaccinated group with no evidence of substitution with unusual genotype combinations.

  6. Rotavirus genotypes in Belarus, 2008-2012.

    PubMed

    Semeiko, Galina V; Yermalovich, Marina A; Poliakova, Nadezhda; Mijatovic-Rustempasic, Slavica; Kerin, Tara K; Wasley, Annemarie; Videbaek, Dovile; Gentsch, Jon R; Bowen, Michael D; Samoilovich, Elena O

    2014-12-01

    This study describes group A rotavirus (RVA) genotype prevalence in Belarus from 2008 to 2012. In 2008, data from 3 sites in Belarus (Brest, Mogilev, Minsk) indicated that G4P[8] was the predominant genotype. Data from Minsk (2008-2012) showed that G4P[8] was the predominant RVA genotype in all years except in 2011 when G3P[8] was most frequently detected. Other RVA genotypes common in Europe (G1P[8], G2P[4]) were detected each year of the study. This study reveals the dominance of genotype G4P[8] in Belarus and helps to establish the baseline genotype prevalence prior to RVA vaccine introduction in the country.

  7. The joint effect of smoking and hOGG1 genotype on oral cancer in Taiwan.

    PubMed

    Tsai, Chia-Wen; Tsai, Ming-Hsui; Tsou, Yung-An; Shih, Liang-Chun; Tseng, Hsien-Chang; Chang, Wen-Shin; Ho, Chien-Yi; Lee, Hong-Zin; Bau, Da-Tian

    2012-09-01

    This study aimed at evaluating the association and interaction among human 8-oxoguanine DNA N-glycosylase 1 (hOGG1) genotypic polymorphism, smoking status and oral cancer risk in Taiwan. For this purpose, the well-known polymorphic variants of hOGG1, codon 326, was analyzed for its association with oral cancer susceptibility, and its joint effect with individual smoking habits on oral cancer susceptibility. In total, 620 patients with oral cancer and 620 healthy controls were recruited from the China Medical Hospital and genotyped. The results showed that the hOGG1 codon 326 genotypes were differently distributed between the oral cancer and control groups (p=0.0266), with the C allele of hOGG1 codon 326 being significantly (p=0.0046) more frequently found in cancer patients than in controls. We further analyzed the genetic-smoking joint effects on oral cancer risk and found an interaction between hOGG1 codon 326 genotypes and smoking status. The hOGG1 codon 326 CC genotype was associated with oral cancer risk only in the smoker group (p=0.0198), but not in the non-chewer group (p=0.8357). Our results provide evidence that the C allele of hOGG1 codon 326 may have a joint effect with smoking on the development of oral cancer.

  8. Hepatitis C virus genotypes in Myanmar

    PubMed Central

    Win, Nan Nwe; Kanda, Tatsuo; Nakamoto, Shingo; Yokosuka, Osamu; Shirasawa, Hiroshi

    2016-01-01

    Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined. PMID:27468202

  9. Coxiella burnetii Genotypes in Iberian Wildlife.

    PubMed

    González-Barrio, David; Hagen, Ferry; Tilburg, Jeroen J H C; Ruiz-Fons, Francisco

    2016-11-01

    To investigate if Coxiella burnetii, the causative agent of Q fever, genotypes circulating in wildlife are associated with those infecting livestock and humans, multiple-locus variable number tandem-repeat analysis (MLVA-6-marker) was carried out over C. burnetii obtained from red deer (Cervus elaphus), Eurasian wild boar (Sus scrofa), European wild rabbit (Oryctolagus cuniculus), black rat (Rattus rattus), and wood mouse (Apodemus sylvaticus). MLVA typing was performed by using six variable loci in C. burnetii: Ms23, Ms24, Ms27, Ms28, Ms33, and Ms34. The C. burnetii cooperative database from MLVABank 5.0 was employed to compare genotypes found in this study with 344 isolates of diverse origin. Twenty-two genotypes from wildlife and two genotypes from domestic goats were identified. Some MLVA genotypes identified in wildlife or in farmed game clustered with genotypes of human Q fever clinical cases, supporting the idea that humans and wildlife share C. burnetii genotypes. The major part of genotypes identified in coexisting red deer and rabbits clustered according to their host of origin, suggesting host specificity for particular C. burnetii genotypes. These findings provide important insights to understand the epidemiology of C. burnetii at the wildlife-livestock-human interface.

  10. SNP genotyping by heteroduplex analysis.

    PubMed

    Paniego, Norma; Fusari, Corina; Lia, Verónica; Puebla, Andrea

    2015-01-01

    Heteroduplex-based genotyping methods have proven to be technologically effective and economically efficient for low- to medium-range throughput single-nucleotide polymorphism (SNP) determination. In this chapter we describe two protocols that were successfully applied for SNP detection and haplotype analysis of candidate genes in association studies. The protocols involve (1) enzymatic mismatch cleavage with endonuclease CEL1 from celery, associated with fragment separation using capillary electrophoresis (CEL1 cleavage), and (2) differential retention of the homo/heteroduplex DNA molecules under partial denaturing conditions on ion pair reversed-phase liquid chromatography (dHPLC). Both methods are complementary since dHPLC is more versatile than CEL1 cleavage for identifying multiple SNP per target region, and the latter is easily optimized for sequences with fewer SNPs or small insertion/deletion polymorphisms. Besides, CEL1 cleavage is a powerful method to localize the position of the mutation when fragment resolution is done using capillary electrophoresis.

  11. Association between susceptible genotypes to periodontitis and clinical outcomes of periodontal regenerative therapy: A systematic review

    PubMed Central

    Koidou, Vasiliki-Petros

    2016-01-01

    Background The aim of this review is to systematically investigate the effect of a susceptible genotype to periodontitis with the clinical outcomes of periodontal regeneration. Material and Methods Based on a focused question, an electronic search identified 155 unique citations. Three journals (Journal of Periodontology, Journal of Clinical Periodontology and Journal of Periodontal Research), references of relevant studies and review articles were hand-searched. Two independent reviewers implementing eligibility inclusion criteria selected the studies. Results Of the 155, four studies fulfilled the inclusion criteria. All studies were published between 2000 and 2004 and the samples’ size was 40 to 86 patients. Polymorphisms of Interleukin-1 (IL-1) gene were included in all. Three out of four studies failed to identify an association between susceptible genotypes to periodontitis and clinical outcomes of periodontal regeneration, while one found an association. The heterogeneity and small number of studies included prevented the conduct of a meta-analysis. No studies were identified evaluating the effect of other genotypes and as a result only IL-1 genotype studies were included. Conclusions Within the limits of the present review, no direct conclusion for the effect of a susceptible IL-1 genotype status to the clinical outcome after periodontal regeneration could be drawn. The need of more qualitative studies to explore a possible association emerges. Key words:Periodontitis, genotype, periodontal therapy, regeneration, susceptibility, systematic review. PMID:26946210

  12. Genetic diversity of standard leaf nutrients in Coffea canephora genotypes during phenological phases.

    PubMed

    Gomes, W R; Rodrigues, W P; Vieira, H D; Oliveira, M G; Dias, J R M; Partelli, F L

    2016-10-06

    Diagnosing foliar nutritional status is essential for fertilizer recommendations and for the identification of nutrient imbalances. This study aimed to verify genetic diversity and establish mean standards (leaf nutrient contents; LNCs) and relationships among leaf nutrients (LNC relationships; LNCRs) in seven conilon coffee genotypes during both pre-flowering and bean-filling stages. Twenty crops from several cities in the northern region of Espírito Santo State, Brazil, with crop yield either equal to or greater than 100 bags per hectare (during two harvests) were assessed. A total of 140 samples were collected during each evaluation period for quantification of leaf nutrient contents (N, P, K, Ca, Mg, S, Fe, Zn, Cu, Mn, and B). The Ward procedure, a hierarchical genetic clustering method, was used to quantify the genetic diversity among genotypes. To examine differences between the LNCs and LNCRs, F-and Scott-Knott tests were used. LNCs and LNCRs showed significant differences among the conilon coffee genotypes during the evaluation periods. Additionally, the 8V, 10V,and 12V genotypes exhibited the highest values for most of the nutrients, especially for N, P, and Cu. Therefore, the clustering method revealed genetic diversity among genotypes for standard leaf nutrient levels, implying that leaf diagnosis could be specific to each genotype and phenological stage.

  13. Using genotypic information to reduce disease

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this presentation is to provide a cursory overview of how genotypic data may be utilized by veterinarians in the future. Genotypic information is accumulating at a rapid pace. This information may reveal deleterious genes, quantitative trait loci, and genetic predisposition for a ...

  14. Estimating Genotype- and Environment-Specific Heritabilities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The advantages of computing genotype- and environment-specific heritabilities are discussed. A statistical approach is used in which logvariances of both genotype by environment interaction and error are modeled as random variables. Resulting estimators of variances are weighted averages of a pool...

  15. Genotype imputation efficiency in Nelore Cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genotype imputation efficiency in Nelore cattle was evaluated in different scenarios of lower density (LD) chips, imputation methods and sets of animals to have their genotypes imputed. Twelve commercial and virtual custom LD chips with densities varying from 7K to 75K SNPs were tested. Customized L...

  16. Toward fully automated genotyping: genotyping microsatellite markers by deconvolution.

    PubMed Central

    Perlin, M W; Lancia, G; Ng, S K

    1995-01-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA)n repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. PMID:7485172

  17. Ascaris: development of selected genotypes in mice.

    PubMed

    Peng, Weidong; Yuan, Keng; Peng, Guohua; Qiu, Lin; Dai, Zhifang; Yuan, Fang; Hu, Yinying; Hu, Ningyan

    2012-05-01

    Using nucleotide variation in the first internal transcribed spacer of nuclear ribosomal DNA, five different genotypes (designated G1-G5) have been identified and the preponderance of genotype G1 in humans and of genotype G3 in pigs led to the proposal that parasites bearing the two genotypes have an affinity for a particular host species. A subsequent study using eggs of genotype G1 from humans and G3 from pigs to infect pigs and mice indicated that there is a significant difference in the ability to infect and establish as larvae in mice and as adults in pigs between the two genotypes. Extending previous investigations, the present study investigated whether there are differences in development as designated by egg hatching, larvae migration and distribution in the mice between the Ascaris strains with known genotypes. Ascaris eggs of genotypes G1 (predominating in human-derived worms) and G3 (predominating in pig-derived worms) were used to infect C57BL/6 mice orally. Eggs/larvae were examined from the small and large intestines, thoracic and abdominal cavities, peripheral blood, livers and lungs at intervals of 2h until 12h post-infection, then periodically until 34 days of infection. Results showed distinct differences in egg hatching (the timing and location of hatching, and the numbers hatched), and in larvae migration and distribution (the means and constituent ratios, the time of peak recovery, and larvae reappearing in intestines) between the two strains. The results can explain the findings of significantly higher larval recovery of genotype G1 than G3 in the mice, and may shed some enlightenment to understand the difference in host affiliation of Ascaris of different genotypes.

  18. High-Throughput Genotyping with TaqMan Allelic Discrimination and Allele-Specific Genotyping Assays.

    PubMed

    Heissl, Angelika; Arbeithuber, Barbara; Tiemann-Boege, Irene

    2017-01-01

    Real-time PCR-based genotyping methods, such as TaqMan allelic discrimination assays and allele-specific genotyping, are particularly useful when screening a handful of single nucleotide polymorphisms in hundreds of samples; either derived from different individuals, tissues, or pre-amplified DNA. Although real-time PCR-based methods such as TaqMan are well-established, alternative methods, like allele-specific genotyping, are powerful alternatives, especially for genotyping short tandem repeat (STR) length polymorphisms. Here, we describe all relevant aspects when developing an assay for a new SNP or STR using either TaqMan or allele-specific genotyping, respectively, such as primer and probe design, optimization of reaction conditions, the experimental procedure for typing hundreds of samples, and finally the data evaluation. Our goal is to provide a guideline for developing genotyping assays using these two approaches that render reliable and reproducible genotype calls involving minimal optimization.

  19. Effect of reference population size and available ancestor genotypes on imputation of Mexican Holstein genotypes.

    PubMed

    García-Ruiz, A; Ruiz-Lopez, F J; Wiggans, G R; Van Tassell, C P; Montaldo, H H

    2015-05-01

    The effects of reference population size and the availability of information from genotyped ancestors on the accuracy of imputation of single nucleotide polymorphisms (SNP) were investigated for Mexican Holstein cattle. Three scenarios for reference population size were examined: (1) a local population of 2,011 genotyped Mexican Holsteins, (2) animals in scenario 1 plus 866 Holsteins in the US genotype database (GDB) with genotyped Mexican daughters, and (3) animals in scenario 1 and all US GDB Holsteins (338,073). Genotypes from 4 chip densities (2 low density, 1 mid density, and 1 high density) were imputed using findhap (version 3) to the 45,195 markers on the mid-density chip. Imputation success was determined by comparing the numbers of SNP with 1 or 2 alleles missing and the numbers of differently predicted SNP (conflicts) among the 3 scenarios. Imputation accuracy improved as chip density and numbers of genotyped ancestors increased, and the percentage of SNP with 1 missing allele was greater than that for 2 missing alleles for all scenarios. The largest numbers of conflicts were found between scenarios 1 and 3. The inclusion of information from direct ancestors (dam or sire) with US GDB genotypes in the imputation of Mexican Holstein genotypes increased imputation accuracy by 1 percentage point for low-density genotypes and by 0.5 percentage points for high-density genotypes, which was about half the gain found with information from all US GDB Holsteins. A larger reference population and the availability of genotyped ancestors improved imputation; animals with genotyped parents in a large reference population had higher imputation accuracy than those with no or few genotyped relatives in a small reference population. For small local populations, including genotypes from other related populations can aid in improving imputation accuracy.

  20. Compliance status

    SciTech Connect

    Black, D.G.

    1995-06-01

    This section of the 1994 Hanford Site Environmental Report summarizes the activities conducted to ensure that the Hanford Site is in compliance with federal environmental protection statutes and related Washington State and local environmental protection regulations and the status of Hanford`s compliance with these requirements. Environmental permits required under the environmental protection regulations are discussed under the applicable statute.

  1. Flavonoid profile of green asparagus genotypes.

    PubMed

    Fuentes-Alventosa, J M; Jaramillo, S; Rodríguez-Gutiérrez, G; Cermeño, P; Espejo, J A; Jiménez-Araujo, A; Guillén-Bejarano, R; Fernández-Bolaños, J; Rodríguez-Arcos, R

    2008-08-27

    The determination of flavonoid profiles from different genotypes of triguero asparagus and their comparison to those from green asparagus commercial hybrids was the main goal of this study. The samples consisted of 32 commercial hybrids and 65 genotypes from the Huetor-Tajar population variety (triguero). The analysis of individual flavonoids by HPLC-DAD-MS has allowed the determination of eight naturally occurring flavonol derivatives in several genotypes of triguero asparagus. Those compounds included mono-, di-, and triglycosides of three flavonols, that is, quercetin, isorhamnetin, and kaempferol. The detailed analysis of the flavonoid profiles revealed significant differences among the distinct genotypes. These have been classified in three distinct groups as the result of a k-means clustering analysis, two of them containing both commercial hybrids and triguero asparagus and another cluster constituted by 21 genotypes of triguero asparagus, which contain several key flavonol derivatives able to differentiate them. Hence, the triglycosides tentatively identified as quercetin-3-rhamnosyl-rutinoside, isorhamnetin-3-rhamnosyl-rutinoside, and isorhamnetin-3-O-glucoside have been detected only in the genotypes grouped in the above-mentioned cluster. On the other hand, the compound tentatively identified as isorhamnetin-3-glucosyl-rutinoside was present in most genotypes of triguero asparagus, whereas it has not been detected in any of the commercial hybrids.

  2. ALG: automated genotype calling of Luminex assays.

    PubMed

    Bourgey, Mathieu; Lariviere, Mathieu; Richer, Chantal; Sinnett, Daniel

    2011-05-06

    Single nucleotide polymorphisms (SNPs) are the most commonly used polymorphic markers in genetics studies. Among the different platforms for SNP genotyping, Luminex is one of the less exploited mainly due to the lack of a robust (semi-automated and replicable) freely available genotype calling software. Here we describe a clustering algorithm that provides automated SNP calls for Luminex genotyping assays. We genotyped 3 SNPs in a cohort of 330 childhood leukemia patients, 200 parents of patient and 325 healthy individuals and used the Automated Luminex Genotyping (ALG) algorithm for SNP calling. ALG genotypes were called twice to test for reproducibility and were compared to sequencing data to test for accuracy. Globally, this analysis demonstrates the accuracy (99.6%) of the method, its reproducibility (99.8%) and the low level of no genotyping calls (3.4%). The high efficiency of the method proves that ALG is a suitable alternative to the current commercial software. ALG is semi-automated, and provides numerical measures of confidence for each SNP called, as well as an effective graphical plot. Moreover ALG can be used either through a graphical user interface, requiring no specific informatics knowledge, or through command line with access to the open source code. The ALG software has been implemented in R and is freely available for non-commercial use either at http://alg.sourceforge.net or by request to mathieu.bourgey@umontreal.ca.

  3. Bovine viral diarrhea virus: global status.

    PubMed

    Ridpath, Julia F

    2010-03-01

    Despite the success of regional bovine viral diarrhea viruses (BVDV) eradication programs, infections remain a source of economic loss for producers. The wide variation among BVDV results in differences in genotype, biotype, virulence, and types of infections. BVDV infect a range of domestic and wild ruminants. Clinical presentation varies depending on strain of virus, species of host, immune status of host, reproductive status of host, age of host, and concurrent infections. Recent advances in BVDV research and diagnostics have led to the development of regional eradication/control programs, the most efficacious of which focus on biosecurity, surveillance, and control.

  4. Mixed-genotype white spot syndrome virus infections of shrimp are inversely correlated with disease outbreaks in ponds.

    PubMed

    Hoa, Tran Thi Tuyet; Zwart, Mark P; Phuong, Nguyen T; Oanh, Dang T H; de Jong, Mart C M; Vlak, Just M

    2011-03-01

    Outbreaks of white spot syndrome virus (WSSV) in shrimp culture and the relationship between the virus and virulence are not well understood. Here, we provide evidence showing that WSSV mixed-genotype infections correlate with lower outbreak incidence and that disease outbreaks correlate with single-genotype infections. We tested 573 shrimp samples from 81 shrimp ponds in the Mekong delta with outbreak or non-outbreak status. The variable number tandem repeat (VNTR) loci of WSSV were used as molecular markers for the characterization of single- and mixed-genotype infections. The overall prevalence of mixed-genotype WSSV infections was 25.7 %. Non-outbreak ponds had a significantly higher frequency of mixed-genotype infections than outbreak ponds for all VNTR loci, both at the individual shrimp as well as at the pond level. The genetic composition of WSSV populations appears to correlate with the health status of shrimp culture in ponds. The causal relationship between genotypic diversity and disease outbreaks can now be experimentally approached.

  5. Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis

    PubMed Central

    Kim, Byoung-Jun; Kim, Bo-Ram; Lee, So-Young; Kim, Ga-Na; Kook, Yoon-Hoh; Kim, Bum-Joon

    2016-01-01

    Recently, we introduced a distinct Mycobacterium intracellulare INT-5 genotype, distantly related to other genotypes of M. intracellulare (INT-1 to -4). The aim of this study is to determine the exact taxonomic status of the M. intracellulare INT-5 genotype via genome-based phylogenetic analysis. To this end, genome sequences of the two INT-5 strains, MOTT-H4Y and MOTT-36Y were compared with M. intracellulare ATCC 13950T and Mycobacterium yongonense DSM 45126T. Our phylogenetic analysis based on complete genome sequences, multi-locus sequence typing (MLST) of 35 target genes, and single nucleotide polymorphism (SNP) analysis indicated that the two INT-5 strains were more closely related to M. yongonense DSM 45126T than the M. intracellulare strains. These results suggest their taxonomic transfer from M. intracellulare into M. yongonense. Finally, we selected 5 target genes (argH, dnaA, deaD, hsp65, and recF) and used SNPs for the identification of M. yongonese strains from other M. avium complex (MAC) strains. The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs. In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense. Our results also suggest that M. yongonense could be divided into 2 distinct genotypes (the Type I genotype with the M. parascrofulaceum rpoB gene and the Type II genotype with the M. intracellulare rpoB gene) depending on the presence of the lateral gene transfer of rpoB from M. parascrofulaceum. PMID:27031100

  6. Strict blood pressure control associates with decreased mortality risk by APOL1 genotype.

    PubMed

    Ku, Elaine; Lipkowitz, Michael S; Appel, Lawrence J; Parsa, Afshin; Gassman, Jennifer; Glidden, David V; Smogorzewski, Miroslaw; Hsu, Chi-Yuan

    2017-02-01

    Although APOL1 high-risk genotype partially accounts for the increased susceptibility of blacks to chronic kidney disease (CKD), whether APOL1 associates differentially with mortality risk remains controversial. Here we evaluate the association between APOL1 genotype and risk of death and determine whether APOL1 status modifies the association between strict versus usual blood pressure control and mortality risk. We performed a retrospective analysis of the African American Study of Kidney Disease and Hypertension trial that randomized black participants with CKD to strict versus usual blood pressure control from 1995 to 2001. This included 682 participants with known APOL1 genotype (157 with high-risk genotype) previously assigned to either strict (mean arterial pressure [MAP] 92 mm Hg or less) versus usual blood pressure control (MAP 102-107 mm Hg) during the trial. During a median follow-up of 14.5 years, risk of death did not differ between individuals with high- versus low-risk APOL1 genotypes (unadjusted hazard ratio 1.00 [95% confidence interval 0.76-1.33]). However, a significant interaction was detected between the APOL1 risk group and blood pressure control strategy. In the APOL1 high-risk group, the risk of death was 42% lower comparing strict versus usual blood pressure control (0.58 [0.35-0.97]). In the APOL1 low-risk group, the risk of death comparing strict versus usual blood pressure control was not significantly different (1.09 [0.84-1.43]). Thus, strict blood pressure control during CKD associates with a lower risk of death in blacks with the high-risk CKD APOL1 genotype. Knowledge of APOL1 status could inform selection of blood pressure treatment targets in black CKD patients.

  7. HPV genotypes concordance between sex partners.

    PubMed

    Benevolo, M; Mottolese, M; Marandino, F; Carosi, M; Diodoro, M G; Sentinelli, S; Visca, P; Rollo, F; Mariani, L; Vocaturo, G; Sindico, R; Di Giannuario, D; Perrone Donnorso, R; Pellicciotta, M; Vocaturo, A

    2007-12-01

    The HPV genotype concordance in the sexual couples could support the sexual viral transmission of HPV infection. The present study contains a case-report of a stable Italian sex couple harbouring the same five HPV genotypes in their genital samples. The female partner, affected by vulvar condilomatosis, evidenced positivity in her cervicovaginal scraping with high risk HPV DNA Hybrid Capture 2 test and was negative at liquid-based performed Pap Test and at colposcopic examination. The male partner was clinically healthy regarding his external genitalia. In both male and female genital scrapings, the following HPV genotypes were detected by means of a PCR-based assay: 6, 16, 53, 73 and 84. This considerably high genotype concordance does not appear to be casual and supports, in our opinion, the hypothesis that genital HPV types are sexually transmitted agents

  8. Genotypes and phenotypes of 162 families with a glomulin mutation.

    PubMed

    Brouillard, P; Boon, L M; Revencu, N; Berg, J; Dompmartin, A; Dubois, J; Garzon, M; Holden, S; Kangesu, L; Labrèze, C; Lynch, S A; McKeown, C; Meskauskas, R; Quere, I; Syed, S; Vabres, P; Wassef, M; Mulliken, J B; Vikkula, M

    2013-04-01

    A decade ago, we identified a novel gene, glomulin (GLMN) in which mutations cause glomuvenous malformations (GVMs). GVMs are bluish-purple cutaneous vascular lesions with characteristic glomus cells in the walls of distended venous channels. The discovery of the genetic basis for GVMs allowed the definition of clinical features to distinguish GVMs from other venous anomalies. The variation in phenotype was also highlighted: from a single punctate blue dot to a large plaque-like lesion. In this study, we screened GLMN in a large cohort of patients to broaden the spectrum of mutations, define their frequency and search for possible genotype-phenotype correlations. Taking into account 6 families published by others, a mutation in GLMN has been found in 162 families. This represents 40 different mutations; the most frequent one being present in almost 45% of them. Expressivity varies largely, without a genotype/phenotype relationship. Among 381 individuals with a mutation, we discovered 37 unaffected carriers, implying a penetrance of 90%. As nonpenetrant individuals may transmit the disease to their descendants, knowledge on the mutational status is needed for appropriate genetic counseling.

  9. Genotypes and Phenotypes of 162 Families with a Glomulin Mutation

    PubMed Central

    Brouillard, P.; Boon, L.M.; Revencu, N.; Berg, J.; Dompmartin, A.; Dubois, J.; Garzon, M.; Holden, S.; Kangesu, L.; Labrèze, C.; Lynch, S.A.; McKeown, C.; Meskauskas, R.; Quere, I.; Syed, S.; Vabres, P.; Wassef, M.; Mulliken, J.B.; Vikkula, M.

    2013-01-01

    A decade ago, we identified a novel gene, glomulin (GLMN) in which mutations cause glomuvenous malformations (GVMs). GVMs are bluish-purple cutaneous vascular lesions with characteristic glomus cells in the walls of distended venous channels. The discovery of the genetic basis for GVMs allowed the definition of clinical features to distinguish GVMs from other venous anomalies. The variation in phenotype was also highlighted: from a single punctate blue dot to a large plaque-like lesion. In this study, we screened GLMN in a large cohort of patients to broaden the spectrum of mutations, define their frequency and search for possible genotype-phenotype correlations. Taking into account 6 families published by others, a mutation in GLMN has been found in 162 families. This represents 40 different mutations; the most frequent one being present in almost 45% of them. Expressivity varies largely, without a genotype/phenotype relationship. Among 381 individuals with a mutation, we discovered 37 unaffected carriers, implying a penetrance of 90%. As nonpenetrant individuals may transmit the disease to their descendants, knowledge on the mutational status is needed for appropriate genetic counseling. PMID:23801931

  10. Genotyping approach for non-invasive foetal RHD detection in an admixed population

    PubMed Central

    Boggione, Carolina Trucco; Luján Brajovich, Melina E.; Mattaloni, Stella M.; Di Mónaco, René A.; García Borrás, Silvia E.; Biondi, Claudia S.; Cotorruelo, Carlos M.

    2017-01-01

    Background Non-invasive foetal RHD genotyping can predict haemolytic disease of the foetus and the newborn in pregnancies with anti-D alloantibodies and also avoid antenatal anti-D prophylaxis in pregnant women carrying an RHD negative foetus. Considering that the Argentine genetic background is the result of generations of intermixing between several ethnic groups, we evaluated the diagnostic performance of a non-invasive foetal RHD determination strategy to guide targeted antenatal RhD immunoprophylaxis. This algorithm is based on the analysis of four regions of the RHD gene in cell-free foetal DNA in maternal plasma and maternal and paternal RHD genotyping. Materials and methods DNA from 298 serologically D negative pregnant women between 19–28 weeks gestation were RHD genotyped. Foetal RHD status was determined by real-time PCR in 296 maternal plasma samples. In particular cases, RHDΨ and RHD-CE-Ds alleles were investigated in paternal DNA. Umbilical cord blood was collected at birth, and serological and molecular studies were performed. Results Of the 298 maternal samples, 288 were D−/RHD− and 10 D−/RHD+ (2 RHD*DAR; 5 RHD-CE-Ds; 3 RHDΨ). Plasma from RHD*DAR carriers was not analysed. Real-time PCR showed 210 RHD+ and 78 RHD− foetuses and 8 inconclusive results. In this latter group, paternal molecular studies were useful to report a RHD negative status in 5 foetuses while only 3 remained inconclusive. All the results, except one false positive due to a silent allele (RHD[581insG]), agreed with the neonatal typing performed in cord blood. Discussion The protocol used for non-invasive prenatal RHD genotyping proved to be suitable to determine foetal RHD status in our admixed population. The knowledge of the genetic background of the population under study and maternal and paternal molecular analysis can reduce the number of inconclusive results when investigating foetal RHD status. PMID:27136427

  11. Rapid Genotyping of Swine Influenza Viruses

    PubMed Central

    Mak, Polly W.Y.; Wong, Chloe K.S.; Li, Olive T.W.; Chan, Kwok Hung; Cheung, Chung Lam; Ma, Edward S.; Webby, Richard J.; Guan, Yi; Peiris, Joseph S. Malik

    2011-01-01

    The emergence of pandemic (H1N1) 2009 virus highlighted the need for enhanced surveillance of swine influenza viruses. We used real-time reverse–transcription PCR–based genotyping and found that this rapid and simple genotyping method may identify reassortants derived from viruses of Eurasian avian-like, triple reassortant-like, and pandemic (H1N1) 2009 virus lineages. PMID:21470462

  12. Mitochondrial phylogeny of the genus Echinococcus (Cestoda: Taeniidae) with emphasis on relationships among Echinococcus canadensis genotypes.

    PubMed

    Nakao, Minoru; Yanagida, Tetsuya; Konyaev, Sergey; Lavikainen, Antti; Odnokurtsev, Valeriy A; Zaikov, Vladimir A; Ito, Akira

    2013-11-01

    The mitochondrial genomes of the genus Echinococcus have already been sequenced for most species and genotypes to reconstruct their phylogeny. However, two important taxa, E. felidis and E. canadensis G10 genotype (Fennoscandian cervid strain), were lacking in the published phylogeny. In this study, the phylogeny based on mitochondrial genome sequences was completed with these taxa. The present phylogeny highly supports the previous one, with an additional topology showing sister relationships between E. felidis and E. granulosus sensu stricto and between E. canadensis G10 and E. canadensis G6/G7 (closely related genotypes referred to as camel and pig strains, respectively). The latter relationship has a crucial implication for the species status of E. canadensis. The cervid strain is composed of two genotypes (G8 and G10), but the present phylogeny clearly suggests that they are paraphyletic. The paraphyly was also demonstrated by analysing the complete nucleotide sequences of mitochondrial cytochrome c oxidase subunit 1 (cox1) of E. canadensis genotypes from various localities. A haplotype network analysis using the short cox1 sequences from worldwide isolates clearly showed a close relatedness of G10 to G6/G7. Domestic and sylvatic life cycles based on the host specificity of E. canadensis strains have been important for epidemiological considerations. However, the taxonomic treatment of the strains as separate species or subspecies is invalid from a molecular cladistic viewpoint.

  13. Complexity of the alpha-globin genotypes identified with thalassemia screening in Sardinia.

    PubMed

    Origa, Raffaella; Paglietti, Maria E; Sollaino, Maria C; Desogus, Maria F; Barella, Susanna; Loi, Daniela; Galanello, Renzo

    2014-01-01

    α-Thalassemia commonly results from deletions or point mutations in one or both α-globin genes located on chromosome 16p13.3 giving rise to complex and variable genotypes and phenotypes. Rarely, unusual non-deletion defects or atypical deletions down-regulate the expression of the α-globin gene. In the last decade of the program for β-thalassemia carrier screening and genetic counseling in Sardinia, the association of new techniques of molecular biology such as gene sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA) to conventional methods has allowed to better define several thalassemic genotypes and the complex variability of the α-cluster with its flanking regions, with a high frequency of different genotypes and compound heterozygosity for two α mutations even in the same family. The exact molecular definition of the genotypes resulting from the interactions among the large number of α-thalassemia determinants and with β-thalassemia, is important for a correct correlation of genotype-phenotype and to prevent underdiagnosis of carrier status which could hamper the effectiveness of a screening program particularly in those regions where a high frequency of hemoglobinopathies is present.

  14. Gas film retention and underwater photosynthesis during field submergence of four contrasting rice genotypes.

    PubMed

    Winkel, Anders; Pedersen, Ole; Ella, Evangelina; Ismail, Abdelbagi M; Colmer, Timothy D

    2014-07-01

    Floods can completely submerge some rice (Oryza sativa L.) fields. Leaves of rice have gas films that aid O2 and CO2 exchange under water. The present study explored the relationship between gas film persistence and underwater net photosynthesis (PN) as influenced by genotype and submergence duration. Four contrasting genotypes (FR13A, IR42, Swarna, and Swarna-Sub1) were submerged for 13 days in the field and leaf gas films, chlorophyll, and the capacity for underwater PN at near ambient and high CO2 were assessed with time of submergence. At high CO2 during the PN assay, all genotypes initially showed high rates of underwater PN, and this rate was not affected by time of submergence in FR13A. This superior photosynthetic performance of FR13A was not evident in Swarna-Sub1 (carrying the SUB1 QTL) and the declines in underwater PN in both Swarna-Sub1 and Swarna were equal to that in IR42. At near ambient CO2 concentration, underwater PN declined in all four genotypes and this corresponded with loss of leaf gas films with time of submergence. FR13A retained leaf gas films moderately longer than the other genotypes, but gas film retention was not linked to SUB1. Diverse rice germplasm should be screened for gas film persistence during submergence, as this trait could potentially increase carbohydrate status and internal aeration owing to increased underwater PN, which contributes to submergence tolerance in rice.

  15. ACTN3 R577X genotype is associated with sprinting in elite Japanese athletes.

    PubMed

    Mikami, E; Fuku, N; Murakami, H; Tsuchie, H; Takahashi, H; Ohiwa, N; Tanaka, H; Pitsiladis, Y P; Higuchi, M; Miyachi, M; Kawahara, T; Tanaka, M

    2014-02-01

    The ACTN3 R577X genotype has been found to associate with sprint/power phenotypes in all elite athlete cohorts investigated. This association has not been extensively studied in elite Asian athletes. The present study was undertaken to investigate the association between the ACTN3 R577X genotype and elite Japanese track and field athlete status. 299 elite Japanese track and field athletes (134 sprint/power athletes; 165 endurance/middle-power athletes) and 649 Japanese controls were genotyped for the ACTN3 R577X polymorphism. All athletes were of national or international level. Sprint/power athletes showed a higher frequency of RR + RX genotype than controls (111/134 [82.8%] vs. 478/649 [73.7%], P = 0.025 under the R-dominant model), while there was no significant difference between endurance/middle-power athletes and controls (126/165 [76.4%] vs. 478/649 [73.7%], P = 0.48 under the R-dominant model). Sprinters with the RR + RX genotype had significantly faster personal best times for the 100 m than those with XX genotype (10.42 ± 0.05 s vs. 10.64 ± 0.09 s, P = 0.042); no such association was found in the 400 m sprinters (47.02 ± 0.36 s vs. 47.56 ± 0.99 s, P = 0.62). ACTN3 R577X genotype is associated with sprint/power performance in elite Japanese track and field athletes, especially short sprint performance.

  16. Monitoring coyote population dynamics by genotyping faeces.

    PubMed

    Prugh, L R; Ritland, C E; Arthur, S M; Krebs, C J

    2005-04-01

    Reliable population estimates are necessary for effective conservation and management, and faecal genotyping has been used successfully to estimate the population size of several elusive mammalian species. Information such as changes in population size over time and survival rates, however, are often more useful for conservation biology than single population estimates. We evaluated the use of faecal genotyping as a tool for monitoring long-term population dynamics, using coyotes (Canis latrans) in the Alaska Range as a case study. We obtained 544 genotypes from 56 coyotes over 3 years (2000-2002). Tissue samples from all 15 radio-collared coyotes in our study area had > or = 1 matching faecal genotypes. We used flexible maximum-likelihood models to study coyote population dynamics, and we tested model performance against radio telemetry data. The staple prey of coyotes, snowshoe hares (Lepus americanus), dramatically declined during this study, and the coyote population declined nearly two-fold with a 1(1/2)-year time lag. Survival rates declined the year after hares crashed but recovered the following year. We conclude that long-term monitoring of elusive species using faecal genotyping is feasible and can provide data that are useful for wildlife conservation and management. We highlight some drawbacks of standard open-population models, such as low precision and the requirement of discrete sampling intervals, and we suggest that the development of open models designed for continuously collected data would enhance the utility of faecal genotyping as a monitoring tool.

  17. Prediction of CYP2D6 phenotype from genotype across world populations

    PubMed Central

    Gaedigk, Andrea; Sangkuhl, Katrin; Whirl-Carrillo, Michelle; Klein, Teri; Leeder, J. Steven

    2017-01-01

    Purpose: Owing to its highly polymorphic nature and major contribution to the metabolism and bioactivation of numerous clinically used drugs, CYP2D6 is one of the most extensively studied drug-metabolizing enzymes and pharmacogenes. CYP2D6 alleles confer no, decreased, normal, or increased activity and cause a wide range of activity among individuals and between populations. However, there is no standard approach to translate diplotypes into predicted phenotype. Methods: We exploited CYP2D6 allele-frequency data that have been compiled for Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines (>60,000 subjects, 173 reports) in order to estimate genotype-predicted phenotype status across major world populations based on activity score (AS) assignments. Results: Allele frequencies vary considerably across the major ethnic groups predicting poor metabolizer status (AS = 0) between 0.4 and 5.4% across world populations. The prevalence of genotypic intermediate (AS = 0.5) and normal (AS = 1, 1.5, or 2) metabolizers ranges between 0.4 and 11% and between 67 and 90%, respectively. Finally, 1 to 21% of subjects (AS >2) are predicted to have ultrarapid metabolizer status. Conclusions: This comprehensive study summarizes allele frequencies, diplotypes, and predicted phenotype across major populations, providing a rich data resource for clinicians and researchers. Challenges of phenotype prediction from genotype data are highlighted and discussed. Genet Med 19 1, 69–76. PMID:27388693

  18. RHIC Status

    NASA Astrophysics Data System (ADS)

    Peggs, Steve

    1997-05-01

    The design and construction status of the Relativistic Heavy Ion Collider, RHIC, is discussed. Those novel performance features of a heavy ion collider that are distinct from hadron colliders in general are noted. These features are derived from the experimental requirements of operation with a variety of ion species over a wide energy range, including collisions between protons and ions, and between ions of unequal energies. The project is in the fifth year of a seven year construction cycle. A brief review of the recent Sextant Test is given, together with progress to date on machine construction.

  19. Tevatron status

    SciTech Connect

    Dugan, G.

    1989-03-01

    The Fermilab Tevatron is both the world's highest energy accelerator system and first large-scale superconducting synchrotron. Since Tevatron commissioning in July 1983, the accelerator has operated in 1984, 1985 and 1987 with extracted beams of 800 GeV for three runs of fixed target physics, and in 1987, and 1988, with proton-antiproton colliding beams at 900 /times/ 900 GeV. This paper will focus on the collider operation of the Tevatron: its present status and the outlook for its longer-term future evolution. 18 refs., 3 figs., 2 tabs.

  20. Choline Intake, Plasma Riboflavin, and the Phosphatidylethanolamine N-Methyltransferase G5465A Genotype Predict Plasma Homocysteine in Folate-Deplete Mexican-American Men with the Methylenetetrahydrofolate Reductase 677TT Genotype12

    PubMed Central

    Caudill, Marie A.; Dellschaft, Neele; Solis, Claudia; Hinkis, Sabrina; Ivanov, Alexandre A.; Nash-Barboza, Susan; Randall, Katharine E.; Jackson, Brandi; Solomita, Gina N.; Vermeylen, Francoise

    2009-01-01

    We previously showed that provision of the folate recommended dietary allowance and either 300, 550, 1100, or 2200 mg/d choline for 12 wk resulted in diminished folate status and a tripling of plasma total homocysteine (tHcy) in men with the methylenetetrahydrofolate reductase (MTHFR) 677TT genotype. However, the substantial variation in tHcy within the 677TT genotype at wk 12 implied that several factors were interacting with this genotype to affect homocysteine. As an extension of this work, the present study sought to identify the main predictors of wk-12 plasma tHcy, alone and together with the MTHFR C677T genotype (29 TT, 31 CC), using linear regression analysis. A basic model explaining 82.5% of the variation (i.e. adjusted R2 = 0.825) was constructed. However, the effects of the variables within this model were dependent upon the MTHFR C677T genotype (P for interaction ≤ 0.021). Within the 677TT genotype, serum folate (P = 0.005) and plasma riboflavin (P = 0.002) were strong negative predictors (inversely related) explaining 12 and 15%, respectively, of the variation in tHcy, whereas choline intake (P = 0.003) and serum creatinine (P < 0.001) were strong positive predictors, explaining 19 and 25% of the variation. None of these variables, except creatinine (P = 0.021), correlated with tHcy within the 677CC genotype. Of the 8 additional polymorphisms tested, none appeared to influence tHcy. However, when creatinine was not in the model, the phosphatidylethanolamine N-methyltransferase 5465G→A variant predicted lower tHcy (P < 0.001); an effect confined to the MTHFR 677TT genotype. Thus, in folate-deplete men, several factors with roles in 1-carbon metabolism interact with the MTHFR C677T genotype to affect plasma tHcy. PMID:19211833

  1. Regulation of tillering in sorghum: genotypic effects

    PubMed Central

    Kim, Hae Koo; Luquet, Delphine; van Oosterom, Erik; Dingkuhn, Michael; Hammer, Graeme

    2010-01-01

    Background and Aims Genotypic variation in tillering can be caused by differences in the carbon supply–demand balance within a plant. The aim of this study was to understand and quantify the effects of genotype on tillering as a consequence of the underlying internal competition for carbohydrates. Methods Five sorghum hybrids, derived from inbred lines with a common genetic background and with similar phenology and plant height but contrasting tillering, were grown in five experiments. The experiments covered a wide range in radiation and temperature conditions, so that number of tillers produced varied significantly. Data on leaf area, tiller number, and biomass accumulation and partitioning were collected at regular intervals. To quantify internal plant competition for carbohydrates, a carbohydrate supply–demand index (S/Dindex) was developed and related to variation in tillering. Key Results The appearance of main shoot leaves and tillers was highly co-ordinated across genotypes. High-tillering hybrids had a greater appearance frequency of early tiller ranks than low-tillering hybrids, and this was associated with narrower and hence smaller main shoot leaves. A generalized S/Dindex of internal plant competition accounted for most of the observed variation in maximum tiller number (Ntiller,max) across genotypes. However, genotypic differences in the relationship between the S/Dindex and Ntiller,max suggested that high-tillering hybrids also had a lower S/D threshold at which tillers appeared, possibly associated with hormonal effects. Conclusions The results support the hypothesis that genotypic differences in tillering were associated with differences in plant carbon S/D balance, associated with differences in leaf size and in the threshold at which tillers grow out. The results provide avenues for phenotyping of mapping populations to identify genomic regions regulating tillering. Incorporating the results in crop growth simulation models could provide

  2. High-throughput RAD-SNP genotyping for characterization of sugar beet genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High-throughput SNP genotyping provides a rapid way of developing resourceful set of markers for delineating the genetic architecture and for effective species discrimination. In the presented research, we demonstrate a set of 192 SNPs for effective genotyping in sugar beet using high-throughput mar...

  3. Accuracy of genotype imputation in sheep breeds.

    PubMed

    Hayes, B J; Bowman, P J; Daetwyler, H D; Kijas, J W; van der Werf, J H J

    2012-02-01

    Although genomic selection offers the prospect of improving the rate of genetic gain in meat, wool and dairy sheep breeding programs, the key constraint is likely to be the cost of genotyping. Potentially, this constraint can be overcome by genotyping selection candidates for a low density (low cost) panel of SNPs with sparse genotype coverage, imputing a much higher density of SNP genotypes using a densely genotyped reference population. These imputed genotypes would then be used with a prediction equation to produce genomic estimated breeding values. In the future, it may also be desirable to impute very dense marker genotypes or even whole genome re-sequence data from moderate density SNP panels. Such a strategy could lead to an accurate prediction of genomic estimated breeding values across breeds, for example. We used genotypes from 48 640 (50K) SNPs genotyped in four sheep breeds to investigate both the accuracy of imputation of the 50K SNPs from low density SNP panels, as well as prospects for imputing very dense or whole genome re-sequence data from the 50K SNPs (by leaving out a small number of the 50K SNPs at random). Accuracy of imputation was low if the sparse panel had less than 5000 (5K) markers. Across breeds, it was clear that the accuracy of imputing from sparse marker panels to 50K was higher if the genetic diversity within a breed was lower, such that relationships among animals in that breed were higher. The accuracy of imputation from sparse genotypes to 50K genotypes was higher when the imputation was performed within breed rather than when pooling all the data, despite the fact that the pooled reference set was much larger. For Border Leicesters, Poll Dorsets and White Suffolks, 5K sparse genotypes were sufficient to impute 50K with 80% accuracy. For Merinos, the accuracy of imputing 50K from 5K was lower at 71%, despite a large number of animals with full genotypes (2215) being used as a reference. For all breeds, the relationship of

  4. Automated SNP genotype clustering algorithm to improve data completeness in high-throughput SNP genotyping datasets from custom arrays.

    PubMed

    Smith, Edward M; Littrell, Jack; Olivier, Michael

    2007-12-01

    High-throughput SNP genotyping platforms use automated genotype calling algorithms to assign genotypes. While these algorithms work efficiently for individual platforms, they are not compatible with other platforms, and have individual biases that result in missed genotype calls. Here we present data on the use of a second complementary SNP genotype clustering algorithm. The algorithm was originally designed for individual fluorescent SNP genotyping assays, and has been optimized to permit the clustering of large datasets generated from custom-designed Affymetrix SNP panels. In an analysis of data from a 3K array genotyped on 1,560 samples, the additional analysis increased the overall number of genotypes by over 45,000, significantly improving the completeness of the experimental data. This analysis suggests that the use of multiple genotype calling algorithms may be advisable in high-throughput SNP genotyping experiments. The software is written in Perl and is available from the corresponding author.

  5. RHIC status

    SciTech Connect

    Peggs, S.

    1997-08-01

    The design and construction status of the Relativistic Heavy Ion Collider, RHIC, which is in the seventh year of a nine year construction cycle, is discussed. Those novel performance features of a heavy ion collider that are distinct from hadron colliders in general are noted. These features are derived from the experimental requirements of operation with a variety of ion species over a wide energy range, including collisions between protons and ions, and between ions of unequal energies. Section 1 gives a brief introduction to the major parameters and overall layout of RHIC. A review of the superconducting magnet program is given in Section 2. Activities during the recent Sextant Test are briefly reviewed in Section 3. Finally, Section 4 presents the plans for RHIC commissioning in 1999.

  6. Interleukin-28b CC genotype predicts early treatment response and CT/TT genotypes predicts non-response in patients infected with HCV genotype 3.

    PubMed

    Gupta, Abhishak Chander; Trehanpati, Nirupma; Sukriti, Sukriti; Hissar, Syed; Midha, Vandana; Sood, Ajit; Sarin, Shiv K

    2014-04-01

    Response to antiviral therapy for hepatitis C virus (HCV) depends upon the genotype and host immune response. IL28b gene mutations have been shown to modulate host antiviral immune response against genotype 1. However, the predictive value of IL28b polymorphism in genotype 3 HCV patients is largely unknown. The association of IL28b polymorphism with virological response was studied in 356 patients with genotype 3 chronic HCV undergoing treatment with peg-interferon and ribavirin and was compared with matched controls. IL28b genotyping followed by DNA sequencing was performed to identify the CC, CT, or TT genotypes. Two log reduction of HCV RNA at Day 7 (Quick Viral Response, QVR) and HCV RNA negativity at Day 28 (Rapid Viral Response, RVR) were analyzed with CC and non-CC genotypes in addition to other predictors of response. The associations of alleles with the response patterns were predicted. Sustained viral response was seen in 250 (70.2%) patients and the IL28b genotype CC/CT/TT distribution was 61.1%; 30.5%; and 8.4%, respectively. The non-CC genotypes were significantly higher in non-responders when compared to responders (67.6% vs. 38.9%, P < 0.001). Interestingly, the rapid viral response in responders was observed in 72.7% with the CC genotype and in 27.2% with the non-CC genotype (P < 0.001). Multivariate analysis showed CC genotype as an independent factor predicting the sustained viral response in patients infected with HCV genotype 3. In conclusion, the IL28b CT/TT genotype strongly correlates with treatment non-response in patients infected with HCV genotype 3 and CC genotype of IL28b is associated with higher quick viral response.

  7. Saponin profile of green asparagus genotypes.

    PubMed

    Vázquez-Castilla, Sara; Jaramillo-Carmona, Sara; Fuentes-Alventosa, Jose María; Jiménez-Araujo, Ana; Rodríguez-Arcos, Rocío; Cermeño-Sacristán, Pedro; Espejo-Calvo, Juan Antonio; Guillén-Bejarano, Rafael

    2013-11-20

    The main goal of this study was to determine the saponin profiles of different "triguero" asparagus genotypes and to compare them to green asparagus commercial hybrids. The samples consisted of 31 commercial hybrids and 58 genotypes from the Huétor-Tájar (HT) population variety ("triguero"). The saponin analysis by high-performance liquid chromatography-mass spectrometry allowed for the determination of 12 saponins derived from a furostan-type steroidal genin, 4 of which had never been described in the edible part of asparagus. The saponin profile of "triguero" asparagus was a combination of these new saponins and protodioscin. Although protodioscin was the major saponin found in commercial hybrids, some of these 12 saponins were detected as major components in some of the commercial hybrids. The total contents of saponins described in some of these HT genotypes reach values as high as 10-100 times higher than those found in commercial hybrids.

  8. Estimating population size by genotyping faeces.

    PubMed

    Kohn, M H; York, E C; Kamradt, D A; Haught, G; Sauvajot, R M; Wayne, R K

    1999-04-07

    Population size is a fundamental biological parameter that is difficult to estimate. By genotyping coyote (Canis latrans) faeces systematically collected in the Santa Monica Mountains near Los Angeles, California, we exemplify a general, non-invasive method to census large mammals. Four steps are involved in the estimation. First, presumed coyote faeces are collected along paths or roadways where coyotes, like most carnivores, often defaecate and mark territorial boundaries. Second, DNA is extracted from the faeces and species identity and sex is determined by mitochondrial DNA and Y-chromosome typing. Third, hypervariable microsatellite loci are typed from the faeces. Lastly, rarefaction analysis is used to estimate population size from faecal genotypes. This method readily provides a point count estimate of population size and sex ratio. Additionally, we show that home range use paternity and kinship can be inferred from the distribution and relatedness patterns of faecal genotypes.

  9. Efavirenz and Metabolites in Cerebrospinal Fluid: Relationship with CYP2B6 c.516G→T Genotype and Perturbed Blood-Brain Barrier Due to Tuberculous Meningitis

    PubMed Central

    Chau, Tran Thi Hong; Fisher, Martin; Nelson, Mark; Winston, Alan; Else, Laura; Carr, Daniel F.; Taylor, Steven; Ustianowski, Andrew; Back, David; Pirmohamed, Munir; Solomon, Tom; Farrar, Jeremy; Törok, M. Estée; Khoo, Saye

    2016-01-01

    Efavirenz (EFZ) has been associated with neuropsychiatric side effects. Recently, the 8-hydroxy-EFZ (8OH-EFZ) metabolite has been shown to be a potent neurotoxin in vitro, inducing neuronal damage at concentrations of 3.3 ng/ml. EFZ induced similar neuronal damage at concentrations of 31.6 ng/ml. We investigated the effect of genotype and blood-brain barrier integrity on EFZ metabolite concentrations in cerebrospinal fluid (CSF). We measured CSF drug concentrations in subjects from two separate study populations: 47 subjects with tuberculous meningitis (TBM) coinfection in Vietnam receiving 800 mg EFZ with standard antituberculous treatment and 25 subjects from the PARTITION study in the United Kingdom without central nervous system infection receiving 600 mg EFZ. EFZ and metabolite concentrations in CSF and plasma were measured and compared with estimates of effectiveness and neurotoxicity from available published in vitro and in vivo data. The effect of the CYP2B6 c.516G→T genotype (GG genotype, fast EFV metabolizer status; GT genotype, intermediate EFV metabolizer status; TT genotype, slow EFV metabolizer status) was examined. The mean CSF concentrations of EFZ and 8OH-EFZ in the TBM group were 60.3 and 39.3 ng/ml, respectively, and those in the no-TBM group were 15.0 and 5.9 ng/ml, respectively. Plasma EFZ and 8OH-EFZ concentrations were similar between the two groups. CSF EFZ concentrations were above the in vitro toxic concentration in 76% of samples (GG genotype, 61%; GT genotype, 90%; TT genotype, 100%) in the TBM group and 13% of samples (GG genotype, 0%; GT genotype, 18%; TT genotype, 50%) in the no-TBM group. CSF 8OH-EFZ concentrations were above the in vitro toxic concentration in 98% of the TBM group and 87% of the no-TBM group; levels were independent of genotype but correlated with the CSF/plasma albumin ratio. Potentially neurotoxic concentrations of 8OH-EFZ are frequently observed in CSF independently of the CYP2B6 genotype, particularly in those

  10. Association between GSTP1 genotypes and hormone receptor phenotype in invasive ductal carcinomas of breast.

    PubMed

    Khabaz, Mohamad Nidal; Gari, Mamdooh Abdullah; Al-Maghrabi, Jaudah Ahmed; Nedjadi, Taoufik; Bakarman, Marwan

    2015-01-01

    Eighty six cases of invasive ductal breast carcinomas were utilized to investigate GSTP1 polymorphisms in certain immunohistochemistry (IHC) subtypes of breast cancer with respect to ER, PR and HER2 expression. The frequency of wild allele homozygote, heterozygote and variant allele homozygote genotypes were 46.5%, 52.3% and 1.16% respectively; Whereas 54.3% of the control subjects were GSTP1 wild type allele homozygous, 40.0% were heterozygous and 5.71% mutant allele homozygous. There was dramatic inverted relation between positive IHC ER staining and increasing grade of tumors in general (100%, 88.6%, 40.4%) and especially among tumors with heterozygote genotype of GSTP1 (70%, 35.4%, 22.7). There was increase in positive IHC HER2 staining consistent with higher grades in general (20%, 29.6%, 50.0%), especially among tumors with GSTP1 wild allele homozygote genotype (5.0%, 9.1%, 31.8%). A remarkable reverse relation was also observed between the fraction of IHC hormone receptor phenotype ER+/PR+/ HER2- and increased grade of tumors (60.0%, 45.5%, and 27.3%) especially among tumors with GSTP1 heterozygote genotype, and a similar link was noted regarding ER+/PR-/ HER2- and tumor grade. There was increase in frequency of ER-/PR-/ HER2- (0.0%, 6.8%, and 18.2%) and ER-/PR-/ HER2+ (0.0%, 4.54%, and 40.9%) consistent with the higher grades of tumors in general and especially GSTP1 heterozygote genotype tumors. As a conclusion, there is no correlation between GSTP1 polymorphism and increased risk of breast cancer i.e. the mutant allele is randomly distributed in cancer and control cases. However, there is a link between GSTP1 genotypes and hormone receptor expression status and certain phenotypes of breast cancer, which may have clinical importance.

  11. Prevalence and genotyping ofToxoplasma gondii among Saudi pregnant women in Saudi Arabia.

    PubMed

    Alghamdi, Jawahir; Elamin, Maha Hussein; Alhabib, Samia

    2016-11-01

    Introduction: Toxoplasma gondii (T. gondii) is an intracellular protozoan that can infect all mammals, who serve as intermediate host. It causes congenital, neurological, eyes complications and mild or asymptomatic infections in humans. Purpose of this study: To investigate not only the prevalence of T. gondii, but also to find out its genotyping using multiple sequential molecular methods to predict exactly the precise genotyping of T. gondii among Saudi pregnant women. Methods: A cross-sectional study was conducted using multi-stage methods. Initial stage involved enrolment of 250 Saudi pregnant women from multi-centre healthcare and community based settings in the capital of Saudi Arabia Riyadh. The second stage was embracement of the laboratory investigation that included Enzyme immunoassay (ELISA), DNA extraction, PCR, nested-PCR assay, and genotyping of the seropositive cases. Results: 203 women agreed to take part in our study with a response rate of 81.2% (203/250). Using ELISA, we found that the prevalence of Toxoplasma gondii IgG and IgM antibodies was 32.5% and 6.4%, respectively. We found that 29 samples (80.6%) were of genotype II; however 7 samples (19.4%) were of genotype III. Conclusion: Defining the population structure of T. gondii from Saudi Arabia has important implications for transmission, immunogenicity, pathogenesis, and in planning preventive strategies. Relationship between such variation in structure and disease manifestation in pregnant women is still difficult to assess due to the role of host immune status and genetic background on the control of infection, and of other parasitic features such as the infecting dose or parasite stage. Our finding of the genotyping of T. gondii might facilitate and inform future studies on comparative genomics and identification of genes that control important biological phenotypes including pathogenesis and transmission among Saudi women.

  12. Echinococcus granulosus genotypes in livestock of Iran indicating high frequency of G1 genotype in camels.

    PubMed

    Sharbatkhori, Mitra; Mirhendi, Hossein; Harandi, Majid Fasihi; Rezaeian, Mostafa; Mohebali, Mehdi; Eshraghian, Mohammadreza; Rahimi, Hamidreza; Kia, Eshrat Beigom

    2010-04-01

    In this study, 112 Echinococcus granulosus isolates from different livestock of Iran were genotyped by PCR amplification of ribosomal DNA-internal transcribed spacer 1 (rDNA-ITS1) region followed by restriction fragment length polymorphism (RFLP) with the enzyme RsaI. The possibility of intra-genotype variation was also investigated using randomly amplified polymorphic DNA (RAPD) analysis. Isolates from sheep, goats, cattle and the majority of camels (12 of 18; 66.7%) were identified as the G1 genotype and a few camel isolates (6 of 18; 33.3%) belonged to the G6 genotype. Overall G1 and G6 genotypes were identified in 94.6% (106 of 112) and 5.3% (6 of 112) of all isolates, respectively. RAPD analysis based on 15 separate primers showed 7-14 bands of 200-3000bp for strain G1. Considering each individual primer, no differences observed among isolates from different hosts and between livers and lungs. This study confirmed the existence of G1 and G6 genotypes in Iran. Moreover, G1 is much more prevalent even in camels, indicating the importance of sheep-dog cycle in public health. Studying intra-genotypic variation of E. granulosus warrants more research using other primers and methods.

  13. Hepatitis C Genotype Influences Post-Liver Transplant Outcomes

    PubMed Central

    Campos-Varela, Isabel; Lai, Jennifer C.; Verna, Elizabeth C.; O'Leary, Jacqueline G.; Stravitz, R. Todd; Forman, Lisa M.; Trotter, James F.; Brown, Robert S.; Terrault, Norah A.

    2015-01-01

    Background In non-transplant patients with chronic hepatitis C virus (HCV), HCV genotype has been linked with a differential response to antiviral therapy, risk of steatosis and fibrosis, as well as all-cause mortality, but the role of HCV genotypes in post-transplant disease progression is less clear. Methods Using the multicenter CRUSH-C cohort, genotype-specific rates of advanced fibrosis, HCV-specific graft loss and, response of antiviral therapy were examined. Results Among 745 recipients [605 (81%) genotype 1, 53 (7%) genotype 2, and 87 (12%) genotype 3] followed for a median of 3.1 years (range 2.0-8.0) the unadjusted cumulative rate of advanced fibrosis at 3 years was 31%, 19% and 19% for genotypes 1, 2 and 3 (p=0.008). After multivariable adjustment, genotype remained a significant predictor, with genotype 2 having a 66% lower risk (p=0.02) and genotype 3 having a 41% lower risk (p=0.07) of advanced fibrosis compared to genotype 1 patients. The cumulative 5-year rates of HCV-specific graft survival were 84%, 90% and 94% for genotypes 1, 2 and 3, p=0.10. A total of 37% received antiviral therapy, with higher rates of sustained virologic response in patients with genotype 2 (HR=5.10; p=0.003) and genotype 3 (HR=3.27; p=0.006) compared to patients with genotype 1. Conclusion Risk of advanced fibrosis and response to therapy are strongly influenced by genotype. LT recipients with HCV genotype 1 have the highest risk of advanced fibrosis and lowest SVR rate. These findings highlight the need for genotype-specific management strategies. PMID:25211520

  14. Transformation of QTL genotypic effects to allelic effects

    PubMed Central

    Nagamine, Yoshitaka

    2005-01-01

    The genotypic and allelic effect models are equivalent in terms of QTL detection in a simple additive model, but the QTL allelic model has the advantage of providing direct information for marker-assisted selection. However, the allelic matrix is four times as large as the genotypic IBD matrix, causing computational problems, especially in genome scans examining multiple positions. Transformation from genotypic to allelic effects, after estimating the genotypic effects with a smaller IBD matrix, can solve this problem. Although the validity of transformation from genotypic to allelic effects has been disputed, this work proves that transformation can successfully yield unique allelic effects when genotypic and allelic IBD matrixes exist. PMID:16093016

  15. Selection of Shade Tolerant Tall Fescue Genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tall fescue (Schedonorus arundinaceus) is genetically variable for many agronomic traits, so it might be possible to increase its persistence and productivity in shaded agroforestry applications. The objective of this research was to identify high yielding, shade-tolerant genotypes. Seed was obtai...

  16. The Relativity of Genotypes and Phenotypes.

    ERIC Educational Resources Information Center

    Willie, Charles Vert

    1995-01-01

    Asserts that Herrnstein and Murray's "The Bell Curve" (1994) is an attempt to influence and control public discourse about public policy and inequality. It examines four of the book's flaws in classification, analyses, research, and its failure to recognize intelligence as having both genotypic and phenotypic manifestations. (GR)

  17. Camelina: Adaptation and performance of genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Camelina (Camelina sativa L. Crantz) has shown potential as an alternative and biofuel crop in cereal-based cropping systems. Our study investigated the adaption, performance, and yield stability among camelina genotypes across diverse US Pacific Northwest (PNW) environments. Seven named camelina ge...

  18. Phenotyping peanut genotypes for drought tolerance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Drought and heat stress can result in aflatoxin contamination of peanuts especially when this occurs during the last three to six weeks of the growing season. Identifying drought-tolerant genotypes may aid in development of peanuts that are less susceptible to aflatoxin contamination. This study w...

  19. Non-destructive Analysis Chlorophyll Content of Different Genotypes of Poplars Based on Hyperspectral Reflectance Data

    NASA Astrophysics Data System (ADS)

    Jin, S.; Dian, Y.; Wang, R.; Peng, L.; Liu, X.; Zhou, Z.; Zhong, S.; Wang, Y.

    2016-11-01

    Leaf Chlorophyll content (Ct) indicates plant physiological status and can be detected by hyperspectral measurements. However, it is difficult to conclude that different genotypes of same species have the same relationship with the hyperspectral data. The aim of this paper was to test that whether the different genotypes of same species have the similar relationship with hyperspectral reflectance. First of all, spectral reflectance of populus simonii (Populus simonii Carr) and I-72 poplar (Populus euramericana cv. ‘San Martino I-72/58’) were collected by spectrometric meter, and then extract chlorophyll index (CI) and other 11 types of vegetation indices from the hyperspectral reflectance data. At last, relationships between different vegetation indices and Ct of the two genotypes of poplar were compared. Results show that (1) the relationships between SPAD value and Ct are different in the low and high Ct level, we can choose proper vegetation index, REPIG, mSR705 and SDr/SDb et al to predict the Ct value. (2) Meanwhile, we can use PSSRb and PRI to distinguish fine difference between different genotypes.

  20. 6 HCV Genotyping 9G Test and its Comparison with VERSANT HCV Genotype 2.0 Assay (LiPA) for the Hepatitis C Virus Genotyping.

    PubMed

    Chantratita, Wasun; Song, Keum-Soo; GunHo, Choi; Pongthanapisith, Viroj; Thongbaiphet, Nipa; Wongtabtim, Garanyuta; Pasomsub, Ekawat; Angkanavin, Kanokwan; Nimse, Satish Balasaheb; Sonawane, Mukesh Digambar; Warkad, Shrikant Dasharath; Kim, Taisun

    2016-10-25

    In this article, we describe the 6 HCV Genotyping 9G test and its evaluation by using clinical samples and plasmid DNA standards. In tests with 981 plasmid DNA standards, the 6 HCV Genotyping 9G test showed higher than 92.5% sensitivity and 99.4% specificity. The 6 HCV Genotyping 9G test was compared with the VERSANT HCV Genotype 2.0 assay (LiPA 2.0) for detection and discrimination of HCV genotypes in clinical samples. The results of both tests were verified by genomic sequencing. The 6 HCV Genotyping 9G test demonstrated a 100% agreement with the sequencing results, which was higher than LiPA 2.0. These results indicate that the 6 HCV Genotyping 9G test can be a reliable, sensitive, and accurate diagnostic tool for the correct identification of HCV genotypes in clinical specimens. 6 HCV Genotyping 9G test can genotype six HCV types in 1 PCR in 30min after PCR amplification. The 6 HCV Genotyping 9G test, thus provide critical information to physicians and assist them to apply accurate drug regimen for the effective hepatitis C treatment.

  1. 6 HCV genotyping 9G test and its comparison with VERSANT HCV genotype 2.0 assay (LiPA) for the hepatitis C virus genotyping.

    PubMed

    Chantratita, Wasun; Song, Keum-Soo; GunHo, Choi; Pongthanapisith, Viroj; Thongbaiphet, Nipa; Wongtabtim, Garanyuta; Pasomsub, Ekawat; Angkanavin, Kanokwan; Nimse, Satish Balasaheb; Sonawane, Mukesh Digambar; Warkad, Shrikant Dasharath; Kim, Taisun

    2017-01-01

    In this article, we describe the 6 HCV Genotyping 9G test and its evaluation by using clinical samples and plasmid DNA standards. In tests with 981 plasmid DNA standards, the 6 HCV Genotyping 9G test showed higher than 92.5% sensitivity and 99.4% specificity. The 6 HCV Genotyping 9G test was compared with the VERSANT HCV Genotype 2.0 assay (LiPA 2.0) for detection and discrimination of HCV genotypes in clinical samples. The results of both tests were verified by genomic sequencing. The 6 HCV Genotyping 9G test demonstrated a 100% agreement with the sequencing results, which was higher than LiPA 2.0. These results indicate that the 6 HCV Genotyping 9G test can be a reliable, sensitive, and accurate diagnostic tool for the correct identification of HCV genotypes in clinical specimens. 6 HCV Genotyping 9G test can genotype six HCV types in 1 PCR in 30min after PCR amplification. The 6 HCV Genotyping 9G test, thus provide critical information to physicians and assist them to apply accurate drug regimen for the effective hepatitis C treatment.

  2. Haptoglobin 2-2 Genotype Is Associated with TNF-α and IL-6 Levels in Subjects with Obesity

    PubMed Central

    Huerta-Guerrero, Héctor M.; Rodríguez-Morán, Martha; Guerrero-Romero, Fernando

    2014-01-01

    Objective. To evaluate the association between Haptoglobin (HP) gene polymorphisms with inflammatory status in obese subjects. Materials and Methods. A cross-sectional study was carried out. A total of 276 apparently healthy men and nonpregnant obese women were enrolled and allocated according to the HP genotype into the HP1/HP1, HP2/HP1, and HP2/HP2 groups. Distribution of HP genotypes was 49, 87, and 140 for the HP1/HP1, HP2/HP1, and HP2/HP2, respectively. The HP genotype was determined using the polymerase chain reaction method. A multiple linear regression analysis adjusted by age, sex, waist circumference, and total body fat was used to determine the association between HP genotypes with TNF-α, IL-6, and high-sensitivity C-reactive protein (hsCRP) levels. Results. A multiple linear regression analysis adjusted by sex, waist circumference, and total body fat was performed showing a significant association between the HP2/HP2 genotype and TNF-α (β = 0.180; 95% CI 14.41–159.64, P = 0.01) and IL-6 (β = 0.188; 95% CI 1.53–12.72, P = 0.01) levels, but not with hsCRP (β = −0.008; 95% CI −1.64–1.47, P = 0.914) levels, whereas the HP2/HP1 genotype showed no association compared with the HP1/HP1 genotype (control group). Conclusion. Results of our study show that the HP2/HP2 genotype is associated with elevated TNF-α and IL-6, but not with hsCRP, levels in obese subjects. PMID:24868113

  3. In Vitro Conservation of Sweet Potato Genotypes

    PubMed Central

    Arrigoni-Blank, Maria de Fátima; Tavares, Fernanda Ferreira; dos Santos, Maria Clézia; Menezes, Thays Saynara Alves; de Santana, Aléa Dayane Dantas

    2014-01-01

    The aim of this study was to develop a protocol for the in vitro conservation of sweet potato genotypes using the slow growth technique. The first experiment was conducted in a 4 × 5 × 2 factorial scheme, testing four genotypes (IPB-007, IPB-052, IPB-072, and IPB-137), five concentrations of abscisic acid (ABA) (0.0, 1.0, 2.0, 4.0, and 8.0 mg·L−1), and two temperatures (18 and 25°C). The second experiment was conducted in a 4 × 3 × 3 factorial scheme at 18°C, testing four genotypes (IPB-007, IPB-052, IPB-072, and IPB-137), three variations of MS salts (50, 75, and 100%), and three concentrations of sucrose (10, 20, and 30 g·L−1). Every three months, we evaluated the survival (%), shoot height, and shoot viability. In vitro conservation of the sweet potato genotypes IPB-052 and IPB-007 was obtained over three and six months, respectively, using MS medium plus 2.0 mg·L−1 of ABA at either 18 or 25°C. Genotypes IPB-072 and IPB-137 can be kept for three and six months, respectively, in MS medium without ABA at 18°C. It is possible to store IPB-052 and IPB-072 for six months and IPB-007 and IPB-137 for nine months using 30 g·L−1 of sucrose and 50% MS salts. PMID:24563627

  4. Multivariate Analysis of Genotype-Phenotype Association.

    PubMed

    Mitteroecker, Philipp; Cheverud, James M; Pavlicev, Mihaela

    2016-04-01

    With the advent of modern imaging and measurement technology, complex phenotypes are increasingly represented by large numbers of measurements, which may not bear biological meaning one by one. For such multivariate phenotypes, studying the pairwise associations between all measurements and all alleles is highly inefficient and prevents insight into the genetic pattern underlying the observed phenotypes. We present a new method for identifying patterns of allelic variation (genetic latent variables) that are maximally associated-in terms of effect size-with patterns of phenotypic variation (phenotypic latent variables). This multivariate genotype-phenotype mapping (MGP) separates phenotypic features under strong genetic control from less genetically determined features and thus permits an analysis of the multivariate structure of genotype-phenotype association, including its dimensionality and the clustering of genetic and phenotypic variables within this association. Different variants of MGP maximize different measures of genotype-phenotype association: genetic effect, genetic variance, or heritability. In an application to a mouse sample, scored for 353 SNPs and 11 phenotypic traits, the first dimension of genetic and phenotypic latent variables accounted for >70% of genetic variation present in all 11 measurements; 43% of variation in this phenotypic pattern was explained by the corresponding genetic latent variable. The first three dimensions together sufficed to account for almost 90% of genetic variation in the measurements and for all the interpretable genotype-phenotype association. Each dimension can be tested as a whole against the hypothesis of no association, thereby reducing the number of statistical tests from 7766 to 3-the maximal number of meaningful independent tests. Important alleles can be selected based on their effect size (additive or nonadditive effect on the phenotypic latent variable). This low dimensionality of the genotype-phenotype map

  5. Hepatitis C genotype 4: The past, present, and future

    PubMed Central

    Abdel-Ghaffar, Tawhida Y; Sira, Mostafa M; El Naghi, Suzan

    2015-01-01

    Hepatitis C virus (HCV) genotype (GT) 4 represents 12%-15% (15-18 million) of total global HCV infection. It is prevalent in Northern and Equatorial Africa and the Middle East, and is also present in some countries in Europe. GT-4 (and subtype 4a in particular) dominates the HCV epidemic in Egypt. In underdeveloped countries, risk factors associated with HCV infection may be due to unsafe medical practices or other factors such as familial transmission, mother’s HCV status, or illiteracy. HCV prevention and control programs should include health education, increased community awareness towards the disease, controlling infection distribution in health-care centers, proper sterilization of medical and dental instruments, and ensuring safe supply of blood and blood-products. Response rates to a 48-wk combined pegylated-interferon (PEG-IFN) and ribavirin (RBV) treatment range from 40%-69%, and HCV-GT-4 has been considered better than GT-1 but worse than GT-2 and GT-3 in treatment with PEG-IFN/RBV. However, with the introduction of the HCV-GT-1 effective protease inhibitors boceprevir and telaprevir in 2011, HCV-GT-4 became the “most difficult (GT) to treat”. Recently, the direct-acting antivirals (DAAs) with pan- genotypic activities simeprevir, sofosbuvir, and daclatasvir have been recommended in triple regimens with PEG-IFN/RBV for the treatment of HCV-GT-4. An IFN-free regimen will be available for treatment of all genotypes of HCV in the near future. To date, several DAAs have been developed and are currently being evaluated in various combinations in clinical trials. As new regimens and new agents are being approved by the Food and Drug Administration, we can expect the guidelines for HCV treatment to be changed. The availability of shorter, simpler, and more tolerable treatment regimens can reduce the morbidity and mortality associated with HCV infection. With such a large number of therapeutic agents available, we can end up with a range of choices that we

  6. Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

    PubMed Central

    Jayashree, B; Reddy, Praveen T; Leeladevi, Y; Crouch, Jonathan H; Mahalakshmi, V; Buhariwalla, Hutokshi K; Eshwar, KE; Mace, Emma; Folksterma, Rolf; Senthilvel, S; Varshney, Rajeev K; Seetha, K; Rajalakshmi, R; Prasanth, VP; Chandra, Subhash; Swarupa, L; SriKalyani, P; Hoisington, David A

    2006-01-01

    Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application

  7. Apolipoprotein E4 Genotype Does Not Increase Risk of HIV-associated Neurocognitive Disorders

    PubMed Central

    Morgan, E.E.; Woods, S.P.; Letendre, S.L.; Franklin, D.R.; Bloss, C.; Goate, A.; Heaton, R.K.; Collier, A.C.; Marra, C.M.; Gelman, B.B.; McArthur, J.C.; Morgello, S.; Simpson, D.M.; McCutchan, J.A.; Ellis, R.J.; Abramson, I.; Gamst, A.; Fennema-Notestine, C.; Smith, D.M.; Grant, I.; Vaida, F.; Clifford, D.B.

    2013-01-01

    This is a cross-sectional, observational study to evaluate the hypothesis that HIV-seropositive (HIV+) apolipoprotein E4 (APOE4) carriers are at increased risk for HIV-associated Neurocognitive Disorders (HAND) compared to APOE4 noncarriers with HIV in the CNS HIV Antiretroviral Therapy Effects Research (CHARTER) Group sample. APOE genotype was determined in 466 CHARTER participants with varying disease stages and histories of antiretroviral treatment who did not have severe psychiatric or medical comorbid conditions that preclude diagnosis of HAND. HAND diagnoses were based on results of comprehensive neurobehavioral evaluation and use of current neuroAIDS diagnostic criteria. HAND status consisting of two levels: neuropsychologically normal status (i.e., no HAND) and any HAND diagnosis (i.e., asymptomatic neurocognitive impairment, minor neurocognitive disorder, HIV-associated dementia). Logistic regression analyses revealed no association between APOE4 carrier status and HAND, and there were no interactions between APOE4 carrier status and ethnicity, age, substance use disorders, duration of infection, or nadir CD4. Results did not differ when analysis was restricted to symptomatic HAND, and no APOE4 gene dose-dependent relationship to HAND emerged. APOE4 status was not associated with concurrent HAND in this large, well-characterized sample. This does not preclude emergence of an association between APOE4 status and HAND as this population ages. Prospective, longitudinal studies are needed to examine APOE4 as a risk factor for neurocognitive decline, incident HAND at older ages, and potential associations with CSF amyloid. PMID:23408335

  8. A genotype probability index for multiple alleles and haplotypes.

    PubMed

    Percy, A; Kinghorn, B P

    2005-12-01

    We use linear algebra to calculate an index of information content in genotype probabilities which has previously been calculated using trigonometry. The new method can be generalized allowing the index to be calculated for loci with more than two alleles. Applications of this index include its use in genotyping strategies, strategies to manage genetic disorders and in estimation of genotype effects.

  9. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid...

  10. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid...

  11. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid...

  12. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid...

  13. New description of Toxoplasma gondii genotypes from French Polynesia.

    PubMed

    Yera, Hélène; Ajzenberg, Daniel; Lesle, Florence; Eyrolle-Guignot, Dominique; Besnard, Marianne; Baud, Alain; Georges, Amandine; Dupouy-Camet, Jean; Dardé, Marie Laure

    2014-06-01

    We report here the first isolation and genotyping of two human Toxoplasma gondii strains from French Polynesia. The parasites had new and atypical genotypes, and were responsible for asymptomatic congenital toxoplasmosis. Both genotypes were divergent from the common strains isolated in Europe, North America, South America, Africa and China.

  14. megasat: automated inference of microsatellite genotypes from sequence data.

    PubMed

    Zhan, Luyao; Paterson, Ian G; Fraser, Bonnie A; Watson, Beth; Bradbury, Ian R; Nadukkalam Ravindran, Praveen; Reznick, David; Beiko, Robert G; Bentzen, Paul

    2017-03-01

    megasat is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important feature of megasat is the generation of histograms of the length-frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. megasat is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demonstrate megasat using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0-1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs.

  15. Pathogenicity island cag, vacA and IS605 genotypes in Mexican strains of Helicobacter pylori associated with peptic ulcers

    PubMed Central

    2011-01-01

    Background Helicobacter pylori is associated with chronic gastritis, peptic ulcers, and gastric cancer. Two major virulence factors of H. pylori have been described: the pathogenicity island cag (cag PAI) and the vacuolating cytotoxin gene (vacA). Virtually all strains have a copy of vacA, but its genotype varies. The cag PAI is a region of 32 genes in which the insertion of IS605 elements in its middle region has been associated with partial or total deletions of it that have generated strains with varying virulence. Accordingly, the aim of this work was to determine the cag PAI integrity, vacA genotype and IS605 status in groups of isolates from Mexican patients with non-peptic ulcers (NPU), non-bleeding peptic ulcers (NBPU), and bleeding peptic ulcers (BPU). Methods The cag PAI integrity was performed by detection of eleven targeted genes along this locus using dot blot hybridization and PCR assays. The vacA allelic, cag PAI genotype 1 and IS605 status were determined by PCR analysis. Results Groups of 16-17 isolates (n = 50) from two patients with NPU, NBPU, and BPU, respectively, were studied. 90% (45/50) of the isolates harbored a complete cag PAI. Three BPU isolates lacked the cag PAI, and two of the NBPU had an incomplete cag PAI: the first isolate was negative for three of its genes, including deletion of the cagA gene, whereas the second did not have the cagM gene. Most of the strains (76%) had the vacA s1b/m1 genotype; meanwhile the IS605 was not present within the cag PAI of any strain but was detected elsewhere in the genome of 8% (4/50). Conclusion The patients had highly virulent strains since the most of them possessed a complete cag PAI and had a vacA s1b/m1 genotype. All the isolates presented the cag PAI without any IS605 insertion (genotype 1). Combined vacA genotypes showed that 1 NPU, 2 NBPU, and 1 BPU patients (66.6%) had a mixed infection; coexistence of H. pylori strains with different cag PAI status was observed in 1 NBPU and 2 BPU (50

  16. Association of Anxiety Symptoms in Offspring of Bipolar Parents with Serotonin Transporter-Linked Polymorphic Region (5-HTTLPR) Genotype

    PubMed Central

    Park, Min-Hyeon; Sanders, Erica; Howe, Meghan; Singh, Manpreet; Hallmayer, Joachim; Kim, Eunjoo

    2015-01-01

    Abstract Objective: Offspring of parents with bipolar disorder (BD) have been shown to be at high risk for BD. Anxiety symptoms, even at subclinical levels, have been associated with increased risk for BD in these youth. The s-allele of the serotonin transporter-linked polymorphic region (5-HTTLPR) has been implicated in the pathophysiology of both BD and anxiety disorders and has been associated with pharmacological treatment response and increased risk for antidepressant side effects. Therefore, we aimed to explore 1) whether anxiety symptoms in offspring of BD parents were associated with presence of the 5-HTTLPR s-allele and 2) whether anxiety symptoms in the offspring of BD parents according to the 5-HTTLPR genotypes are related to antianxiety medication status. Methods: A total of 64 offspring of BD parents (mean age: 13.7 years) and 51 healthy controls (HC) (mean age: 13.7 years) were compared genetically and on the Multidimensional Anxiety Scale for Children (MASC). Results: Offspring of BD parents showed higher levels of overall anxiety than did the HC group. Only antianxiety medication naïve offspring of BD parents were found to have an association between 5-HTTLPR genotypes and anxiety symptoms. The antianxiety medication naïve offspring of BD parents with the s-allele showed higher level of overall anxiety than offspring of BD parents with the l/l genotype. No significant differences in anxiety symptoms or their association with the 5-HTTLPR genotype were found in the HC group. Conclusions: This study indicated that there may be an association between 5-HTTLPR genotypes and anxiety symptoms in offspring of BD parents, and that antianxiety medication status may affect anxiety symptoms in the offspring of BD patients according to genotype. PMID:26218602

  17. Association between serotonin transporter genotype and extraversion.

    PubMed

    Gillihan, Seth J; Farah, Martha J; Sankoorikal, Geena Mary V; Breland, Jessica; Brodkin, Edward S

    2007-12-01

    Despite the long-standing recognition that extraversion is partially heritable, few specific genes have been found to be associated significantly with this personality trait. The purpose of this study was to examine the association between a functional genetic polymorphism of the serotonin transporter promoter region (5-HTTLPR) and extraversion. Caucasian participants (N=183) were genotyped for the 5-HTTLPR; extraversion scores for participants homozygous for the short allele (s/s) were compared with those participants carrying at least one long allele (s/l and l/l). An s/s genotype at 5-HTTLPR was significantly associated with self ratings of reduced extraversion (P=0.012); presence versus absence of the long allele explained 3.4% of the variance in extraversion. These findings provide support for the effect of the 5-HTTLPR, and for the serotonergic system more broadly, on behaviors related to extraversion.

  18. Implementing genotype-guided antithrombotic therapy.

    PubMed

    Seip, Richard L; Duconge, Jorge; Ruaño, Gualberto

    2010-05-01

    Genotyping has the potential to improve the efficacy and safety of major antithrombotic drugs. For warfarin, the stable maintenance dose varies from 1-10 mg/day. The VKORC1 -1639G>A allele and the CYP2C9*2 and *3 alleles (cumulative frequency: 90% in Asians, 65% in Europeans and 20% in Africans), explain 45% of response variability in European and 30% in African populations. The large clinical trials COAG and EU-PACT will define the extent to which pharmacogenetic dosing affects the safety and efficacy of warfarin and coumarin derivatives. The platelet inhibitor clopidogrel requires activation by the CYP2C19 enzyme. CYP2C19*2 and *3 alleles (cumulative frequency: 20-50%) produce null enzyme activity, and their presence attenuates platelet inhibition and increases cardiovascular events. The US FDA-mandated drug labeling recognizes the relevance of genotyping in the selection and dosing of both warfarin and clopidogrel.

  19. An agent based model of genotype editing

    SciTech Connect

    Rocha, L. M.; Huang, C. F.

    2004-01-01

    This paper presents our investigation on an agent-based model of Genotype Editing. This model is based on several characteristics that are gleaned from the RNA editing system as observed in several organisms. The incorporation of editing mechanisms in an evolutionary agent-based model provides a means for evolving agents with heterogenous post-transcriptional processes. The study of this agent-based genotype-editing model has shed some light into the evolutionary implications of RNA editing as well as established an advantageous evolutionary computation algorithm for machine learning. We expect that our proposed model may both facilitate determining the evolutionary role of RNA editing in biology, and advance the current state of research in agent-based optimization.

  20. Drosophila Genotype Influences Commensal Bacterial Levels

    PubMed Central

    Shanmugarajah, Niroshan; Buchon, Nicolas; Clark, Andrew G.

    2017-01-01

    Host genotype can influence the composition of the commensal bacterial community in some organisms. Composition, however, is only one parameter describing a microbial community. Here, we test whether a second parameter—abundance of bacteria—is a heritable trait by quantifying the presence of four commensal bacterial strains within 36 gnotobiotic inbred lines of Drosophila melanogaster. We find that D. melanogaster genotype exerts a significant effect on microbial levels within the fly. When introduced as monocultures into axenic flies, three of the four bacterial strains were reliably detected within the fly. The amounts of these different strains are strongly correlated, suggesting that the host regulates commensal bacteria through general, not bacteria-specific, means. While the correlation does not appear to be driven by simple variation in overall gut dimensions, a genetic association study suggests that variation in commensal bacterial load may largely be attributed to physical aspects of host cell growth and development. PMID:28095502

  1. Simulation of pedigree genotypes by random walks.

    PubMed Central

    Lange, K; Matthysse, S

    1989-01-01

    A random walk method, based on the Metropolis algorithm, is developed for simulating the distribution of trait and linkage marker genotypes in pedigrees where trait phenotypes are already known. The method complements techniques suggested by Ploughman and Boehnke and by Ott that are based on sequential sampling of genotypes within a pedigree. These methods are useful for estimating the power of linkage analysis before complete study of a pedigree is undertaken. We apply the random walk technique to a partially penetrant disease, schizophrenia, and to a recessive disease, ataxia-telangiectasia. In the first case we show that accessory phenotypes with higher penetrance than that of schizophrenia itself may be crucial for effective linkage analysis, and in the second case we show that impressionistic selection of informative pedigrees may be misleading. PMID:2589323

  2. Human papillomaviruses genotyping in plantar warts.

    PubMed

    de Planell-Mas, Elena; Martínez-Garriga, Blanca; Zalacain, Antonio Jesús; Vinuesa, Teresa; Viñas, Miguel

    2017-05-01

    Plantar warts are caused by human papillomaviruses (HPVs) and have been associated with several HPV genotypes. However, there are few studies focused exclusively on plantar warts. In this work, we aim to identify the HPV genotypes of plantar warts and explore their relation to demographic and clinical characteristics of patients. A total of 72 patients diagnosed with plantar warts were recruited at the Laser unit at Podiatric Hospital, University of Barcelona, Spain. Inner hyperkeratosis laminar sections of warts were collected and DNA of samples were extracted. Amplification of a conserved region of the HPV L1 gene was performed with the SK-Polymerase chain reaction method. DNA amplicons were sequenced and HPV types identified. The most prevalent genotypes detected among the 105 analyzed plantar warts were HPV-57 (37.1%), HPV-27 (23.8%), HPV-1a (20.9%), HPV-2 (15.2%), and HPV-65 (2.8%). The majority of patients (78%) presented one single plantar wart, whereas multiple warts were detected in 22.2% of patients. One patient with multiple warts presented HPV types from two different genera, suggesting the spread of warts by self-inoculation as well as by de novo infection. No significant differences between the number of warts in toes, midfoot and heel were found. The most prevalent HPV types detected in all areas belonged to the alpha genus. This work provides new insight on plantar warts and their associated HPV genotypes, and evidences the usefulness and reliability of both the sample collection procedure and the PCR method used for HPV detection and typing. J. Med. Virol. 89:902-907, 2017. © 2016 Wiley Periodicals, Inc.

  3. Genotypic richness and phenotypic dissimilarity enhance population performance.

    PubMed

    Ellers, Jacintha; Rog, Stefanie; Braam, Ciska; Berg, Matty P

    2011-08-01

    Increases in biodiversity can result from an increase in species richness, as well as from a higher genetic diversity within species. Intraspecific genetic diversity, measured as the number of genotypes, can enhance plant primary productivity and have cascading effects at higher trophic levels, such as an increase in herbivore and predator richness. The positive effects of genotypic mixtures are not only determined by additive effects, but also by interactions among genotypes, such as facilitation or inhibition. However, so far there has been no effort to predict the extent of such effects. In this study, we address the question of whether the magnitude of the effect of genotype number on population performance can be explained by the extent of dissimilarity in key traits among genotypes in a mixture. We examine the relative contribution of genotype number and phenotypic dissimilarity among genotypes to population performance of the soil arthropod, Orchesella cincta. Nearly homogeneous genotypes were created from inbred isofemale lines. Phenotypic dissimilarity among genotypes was assessed in terms of three life-history traits that are associated with population growth rate, i.e., egg size, egg development time, and juvenile growth rate. A microcosm experiment with genotype mixtures consisting of one, two, four, and eight genotypes, showed that genotypic richness strongly increased population size and biomass production and was associated with greater net diversity effects. Most importantly, there was a positive log-linear relationship between phenotypic dissimilarity in a mixture and the net diversity effects for juvenile population size and total biomass. In other words, the degree of phenotypic dissimilarity among genotypes determined the magnitude of the genotypic richness effect, although this relationship leveled off at higher values of phenotypic dissimilarity. Although the exact mechanisms responsible for these effects are currently unknown, similar

  4. Identifying nineteenth century genealogical links from genotypes.

    PubMed

    Stankovich, Jim; Bahlo, Melanie; Rubio, Justin P; Wilkinson, Christopher R; Thomson, Russell; Banks, Annette; Ring, Maree; Foote, Simon J; Speed, Terence P

    2005-07-01

    We have developed a likelihood method to identify moderately distant genealogical relationships from genomewide scan data. The aim is to compare the genotypes of many pairs of people and identify those pairs most likely to be related to one another. We have tested the algorithm using the genotypes of 170 Tasmanians with multiple sclerosis recruited into a haplotype association study. It is estimated from genealogical records that approximately 65% of Tasmania's current population of 470,000 are direct descendants of the 13,000 female founders living in this island state of Australia in the mid-nineteenth century. All cases and four to five relatives of each case have been genotyped with microsatellite markers at a genomewide average density of 4 cM. Previous genealogical research has identified 51 pairwise relationships linking 56 of the 170 cases. Testing the likelihood calculation on these known relative pairs, we have good power to identify relationships up to degree eight (e.g. third cousins once removed). Applying the algorithm to all other pairs of cases, we have identified a further 61 putative relative pairs, with an estimated false discovery rate of 10%. The power to identify genealogical links should increase when the new, denser sets of SNP markers are used. Except in populations where there is a searchable electronic database containing virtually all genealogical links in the past six generations, the algorithm should be a useful aid for genealogists working on gene-mapping projects, both linkage studies and association studies.

  5. Indel arrays: an affordable alternative for genotyping.

    PubMed

    Salathia, Neeraj; Lee, Hana N; Sangster, Todd A; Morneau, Keith; Landry, Christian R; Schellenberg, Kurt; Behere, Aditi S; Gunderson, Kevin L; Cavalieri, Duccio; Jander, Georg; Queitsch, Christine

    2007-08-01

    Natural variation and induced mutations are important resources for gene discovery and the elucidation of genetic circuits. Mapping such polymorphisms requires rapid and cost-efficient methods for genome-wide genotyping. Here we report the development of a microarray-based method that assesses 240 unique markers in a single hybridization experiment at a cost of less than US$50 in materials per line. Our genotyping array is built with 70-mer oligonucleotide elements representing insertion/deletion (indel) polymorphisms between the Arabidopsis thaliana accessions Columbia-0 (Col) and Landsberg erecta (Ler). These indel polymorphisms are recognized with great precision by comparative genomic hybridization, eliminating the need for array replicates and complex statistical analysis. Markers are present genome-wide, with an average spacing of approximately 500 kb. PCR primer information is provided for all array indels, allowing rapid single-locus inquiries. Multi-well chips allow groups of 16 lines to be genotyped in a single experiment. We demonstrate the utility of the array for accurately mapping recessive mutations, RIL populations and mixed genetic backgrounds from accessions other than Col and Ler. Given the ease of use of shotgun sequencing to generate partial genomic sequences of unsequenced species, this approach is readily transferable to non-model organisms.

  6. Rapid changes in rotaviral genotypes in Ecuador.

    PubMed

    Hasing, Maria Eloisa; Trueba, Gabriel; Baquero, Maria Ines; Ponce, Karina; Cevallos, William; Solberg, Owen D; Eisenberg, Joseph N S

    2009-12-01

    Previous studies suggest that the emerging G9P[8] genotype was the most prevalent rotavirus genotype in Ecuador during 2005. This present study provides a temporal analysis of the distribution of rotavirus genotypes in two locations within Ecuador by adding additional years (2006 - early 2008) to the originally reported 2005 data. Data were collected in a rural (northern coastal Ecuador) and urban (Quito) area. In the rural area, a community sample of cases (those presenting diarrhea) and controls (those not presenting diarrhea) were collected between August 2003 and March 2008 resulting in a total of 3,300 stool samples (876 cases and 2,424 controls). Of these samples, 260 were positive for rotavirus by an immunochromatographic test (196 cases and 64 controls). In Quito, 59 fecal samples were collected from children presenting diarrhea and diagnosed with rotavirus. An RT-PCR analysis of samples collected between 2005 and 2007 suggested that G9 was replaced by G1 and G2 in the rural and urban settings. During this period G9 decreased from 79% to 9% while G2 increased from 0% to 43% in the rural communities, and G9 decreased from 79% to 37% while G2 increased from 3% to 57% in the urban area of Quito. This rapid replacement of G9 by G1 and G2 reinforces the necessity of surveillance to inform vaccination programs.

  7. Genotype Imputation with Millions of Reference Samples.

    PubMed

    Browning, Brian L; Browning, Sharon R

    2016-01-07

    We present a genotype imputation method that scales to millions of reference samples. The imputation method, based on the Li and Stephens model and implemented in Beagle v.4.1, is parallelized and memory efficient, making it well suited to multi-core computer processors. It achieves fast, accurate, and memory-efficient genotype imputation by restricting the probability model to markers that are genotyped in the target samples and by performing linear interpolation to impute ungenotyped variants. We compare Beagle v.4.1 with Impute2 and Minimac3 by using 1000 Genomes Project data, UK10K Project data, and simulated data. All three methods have similar accuracy but different memory requirements and different computation times. When imputing 10 Mb of sequence data from 50,000 reference samples, Beagle's throughput was more than 100× greater than Impute2's throughput on our computer servers. When imputing 10 Mb of sequence data from 200,000 reference samples in VCF format, Minimac3 consumed 26× more memory per computational thread and 15× more CPU time than Beagle. We demonstrate that Beagle v.4.1 scales to much larger reference panels by performing imputation from a simulated reference panel having 5 million samples and a mean marker density of one marker per four base pairs.

  8. Rapid Changes in Rotaviral Genotypes in Ecuador

    PubMed Central

    Hasing, Maria Eloisa; Trueba, Gabriel; Baquero, Maria Ines; Ponce, Karina; Cevallos, William; Solberg, Owen D.; Eisenberg, Joseph N.S.

    2010-01-01

    Previous studies suggest that the emerging G9P[8] genotype was the most prevalent rotavirus genotype in Ecuador during 2005. This present study provides a temporal analysis of the distribution of rotavirus genotypes in two locations within Ecuador by adding additional years (2006 – early 2008) to the originally reported 2005 data. Data were collected in a rural (northern coastal Ecuador) and urban (Quito) area. In the rural area, a community sample of cases (those presenting diarrhea) and controls (those not presenting diarrhea) were collected between August 2003 and March 2008 resulting in a total of 3,300 stool samples (876 cases and 2,424 controls). Of these samples, 260 were positive for rotavirus by an immunochromatographic test (196 cases and 64 controls). In Quito, 59 fecal samples were collected from children presenting diarrhea and diagnosed with rotavirus. An RT-PCR analysis of samples collected between 2005 and 2007 suggested that G9 was replaced by G1 and G2 in the rural and urban settings. During this period G9 decreased from 79% to 9% while G2 increased from 0% to 43% in the rural communities, and G9 decreased from 79% to 37% while G2 increased from 3% to 57% in the urban area of Quito. This rapid replacement of G9 by G1 and G2 reinforces the necessity of surveillance to inform vaccination programs. PMID:19856474

  9. SNP marker detection and genotyping in tilapia.

    PubMed

    Van Bers, N E M; Crooijmans, R P M A; Groenen, M A M; Dibbits, B W; Komen, J

    2012-09-01

    We have generated a unique resource consisting of nearly 175 000 short contig sequences and 3569 SNP markers from the widely cultured GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 384 SNPs were selected to monitor the wider applicability of the SNPs by genotyping tilapia individuals from different strains and different geographical locations. In all strains and species tested (O. niloticus, O. aureus and O. mossambicus), the genotyping assay was working for a similar number of SNPs (288-305 SNPs). The actual number of polymorphic SNPs was, as expected, highest for individuals from the GIFT population (255 SNPs). In the individuals from an Egyptian strain and in individuals caught in the wild in the basin of the river Volta, 197 and 163 SNPs were polymorphic, respectively. A pairwise calculation of Nei's genetic distance allowed the discrimination of the individual strains and species based on the genotypes determined with the SNP set. We expect that this set will be widely applicable for use in tilapia aquaculture, e.g. for pedigree reconstruction. In addition, this set is currently used for assaying the genetic diversity of native Nile tilapia in areas where tilapia is, or will be, introduced in aquaculture projects. This allows the tracing of escapees from aquaculture and the monitoring of effects of introgression and hybridization.

  10. Genotypic variability and genotype by environment interactions in oil and fatty acids in high, intermediate, and low oleic acid peanut genotypes.

    PubMed

    Singkham, Nattawut; Jogloy, Sanun; Kesmala, Thawan; Swatsitang, Prasan; Jaisil, Prasit; Puppala, Naveen

    2010-05-26

    Variability of genotype and genotype x environment (G x E) interactions for fatty acids are important to develop high-oleic types in peanut varietal improvement programs. The objective of this study was to determine the variation in fatty acid composition among peanut genotypes and G x E interactions of fatty acids in three groups of genotypes with high, intermediate, and low-oleic acid. Twenty-one genotypes were tested in three environments consisting of two rainy seasons and one dry season. The results indicated that G x E interactions were significant for biomass, pod yield, and harvest index and also for oleic, linoleic acids, and O/L ratio. G x E interactions were less important than genotypic main effect. For oleic acid, significant interactions were found in the intermediate and low-oleic groups only. Therefore, selection for high-oleic trait in peanut breeding programs should be effective.

  11. New Highly Divergent rRNA Sequence among Biodiverse Genotypes of Enterocytozoon bieneusi Strains Isolated from Humans in Gabon and Cameroon▿

    PubMed Central

    Breton, Jacques; Bart-Delabesse, Emmanuelle; Biligui, Sylvestre; Carbone, Alessandra; Seiller, Xavier; Okome-Nkoumou, Madeleine; Nzamba, Chantal; Kombila, Maryvonne; Accoceberry, Isabelle; Thellier, Marc

    2007-01-01

    Intestinal microsporidiosis due to Enterocytozoon bieneusi is a leading cause of chronic diarrhea in severely immunocompromised human immunodeficiency virus (HIV)-positive patients. It may be a public health problem in Africa due to the magnitude of the HIV pandemic and to poor sanitary conditions. We designed two prevalence studies of E. bieneusi in Central Africa, the first with HIV-positive patients from an urban setting in Gabon and the second with a nonselected rural population in Cameroon. Stool samples were analyzed by an immunofluorescence antibody test and PCR. Twenty-five out of 822 HIV-positive patients from Gabon and 22 out of 758 villagers from Cameroon were found to be positive for E. bieneusi. The prevalence rates of the two studies were surprisingly similar (3.0% and 2.9%). Genotypic analysis of the internal transcribed spacer region of the rRNA gene showed a high degree of diversity in samples from both countries. In Gabon, 15 isolates showed seven different genotypes: the previously reported genotypes A, D, and K along with four new genotypes, referred to as CAF1, CAF2, CAF3, and CAF4. In Cameroon, five genotypes were found in 20 isolates: the known genotypes A, B, D, and K and the new genotype CAF4. Genotypes A and CAF4 predominated in Cameroon, whereas K, CAF4, and CAF1 were more frequent in Gabon, suggesting that different genotypes present differing risks of infection associated with immune status and living conditions. Phylogenetic analysis of the new genotype CAF4, identified in both HIV-negative and HIV-positive subjects, indicates that it represents a highly divergent strain. PMID:17537939

  12. Hepatitis B virus taxonomy and hepatitis B virus genotypes.

    PubMed

    Schaefer, Stephan

    2007-01-07

    Hepatitis B virus (HBV) is a member of the hepadnavirus family. Hepadnaviruses can be found in both mammals (orthohepadnaviruses) and birds (avihepadnaviruses). The genetic variability of HBV is very high. There are eight genotypes of HBV and three clades of HBV isolates from apes that appear to be additional genotypes of HBV. Most genotypes are now divided into subgenotypes with distinct virological and epidemiological properties. In addition, recombination among HBV genotypes increases the variability of HBV. This review summarises current knowledge of the epidemiology of genetic variability in hepadnaviruses and, due to rapid progress in the field, updates several recent reviews on HBV genotypes and subgenotypes.

  13. Identification of Zoonotic Genotypes of Giardia duodenalis

    PubMed Central

    Sprong, Hein; Cacciò, Simone M.; van der Giessen, Joke W. B.

    2009-01-01

    Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G) which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset). The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG) of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the zoonotic

  14. Avian nephritis virus (ANV) on Brazilian chickens farms: circulating genotypes and intra-genotypic diversity.

    PubMed

    Espinoza, Luis Luna; Beserra, Laila A R; Soares, Rodrigo M; Gregori, Fabio

    2016-12-01

    Avian nephritis virus (ANV), which belongs to the family Astroviridae, is associated with different clinical manifestations (including enteric disorders). Despite being frequently found in the avian industry worldwide, information regarding genetic features of these viruses in Brazil is scarce. Therefore, sixty fecal sample pools (5-6 birds of the same flock), representing 60 poultry farms from six Brazilian States, were screened using an astrovirus-specific hemi-nested-PCR assay targeting the conserved ORF1b gene, followed by nucleotide sequencing of amplified products. PCR and phylogenetic analysis confirmed the detection of 21 positive samples to ANV (35 %). In order to investigate the genetic diversity represented by these viruses, amplification, cloning and phylogenetic analysis of the deduced amino acid sequence of ORF2 gene were attempted. Eight samples were successfully cloned (generating 32 clones in total) and sequenced. Based on phylogenetic analysis of ORF2, sequences defined in this study were classified into three genotypes: genotype 5, which has already been described in birds, and two other novel genotypes, tentatively named genotype 8 and 9, all of which occurred in single or mixed infections. Moreover, high intra-genotypic diversity and co-circulation of distinct strains in a same host population were observed. This study revealed the presence of new strains of ANV in Brazilian poultry and their circulation in commercial chicken flocks.

  15. Changing prevalence of hepatitis B virus genotypes in Iceland.

    PubMed

    Björnsdottir, Thora B; Stanzeit, Barbara; Sällberg, Matti; Löve, Arthur; Hultgren, Catharina

    2005-12-01

    At present eight hepatitis B virus (HBV) genotypes have been characterized: A to H. The most common genotype in Northern Europe is genotype A. So far there is no record of the specific HBV genotype distribution in Iceland. Iceland has a small population whose homogeneity has changed due to increasing migration during the past decades. The distribution of HBV genotypes in Iceland was analyzed using sera from 170 Icelandic patients. The samples were obtained before 1989, during an HBV epidemic among intravenous drug users in 1989 to 1992 and after 1994. A fragment of the HBV S-gene was amplified, sequenced and subjected to phylogenetic analysis. Among samples derived before 1989 genotypes A, C, and D were found. Most of the samples diagnosed during the epidemic belonged to genotype D and a smaller portion to genotype A. This suggests that the epidemic was most likely caused either by an endogenous HBV strain or by a strain imported from Europe or the USA. Among samples obtained after 1994, genotypes A to E and G were found, but the majority were of genotypes A, C, and D. This is consistent with an increase in migration and immigration from regions in Asia and Africa during the past 10 years. Thus, the changing prevalence of HBV genotypes in a small isolated community such as Iceland reflects the influence of migration and increasing contacts with regions outside the Western World.

  16. Changes in hepatitis C virus genotype distribution in Japan.

    PubMed

    Toyoda, H; Kumada, T; Takaguchi, K; Shimada, N; Tanaka, J

    2014-12-01

    Genotypes are associated with the natural course of hepatitis C virus (HCV) infection and response to antiviral therapy for HCV. HCV genotype 1b has been the dominant genotype in Japan, where the prevention of HCV transmission through blood transfusion or nosocomial infection has been established since 1990. The distribution of HCV genotype was investigated based on patient's birth year in 5515 HCV-infected Japanese individuals at three institutions from different areas of Japan. At all three institutions, the proportion of HCV genotype 1b decreased and was <50% in individuals born after 1970. By contrast, the percentage of HCV genotype 2b increased in subsequent birth cohorts after 1920-1929. Significant changes in HCV genotype distribution were observed across Japan regardless of area.

  17. Genotyping by Genome Reducing and Sequencing for Outbred Animals

    PubMed Central

    Yang, Yumei; Chen, Zhenliang; Liao, Rongrong; Xie, Xiaoxian; Wang, Zhen; He, Pengfei; Tu, Yingying; Zhang, Xiangzhe; Yang, Changsuo; Yang, Hongjie; Yu, Fuqing; Zheng, Youmin; Zhang, Zhiwu; Wang, Qishan; Pan, Yuchun

    2013-01-01

    Next-generation sequencing (NGS) approaches are widely used in genome-wide genetic marker discovery and genotyping. However, current NGS approaches are not easy to apply to general outbred populations (human and some major farm animals) for SNP identification because of the high level of heterogeneity and phase ambiguity in the haplotype. Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS) to genotype outbred species. Through an improved procedure for library preparation and a marker discovery and genotyping pipeline, the GGRS approach can genotype outbred species cost-effectively and high-reproducibly. We also evaluated the efficiency and accuracy of our approach for high-density SNP discovery and genotyping in a large genome pig species (2.8 Gb), for which more than 70,000 single nucleotide polymorphisms (SNPs) can be identified for an expenditure of only $80 (USD)/sample. PMID:23874423

  18. Genotype-Phenotype Correlations in Multiple Sclerosis: "HLA" Genes Influence Disease Severity Inferred by [superscript 1]HMR Spectroscopy and MRI Measures

    ERIC Educational Resources Information Center

    Okuda, D. T.; Srinivasan, R.; Oksenberg, J. R.; Goodin, D. S.; Baranzini, S. E.; Beheshtian, A.; Waubant, E.; Zamvil, S. S.; Leppert, D.; Qualley, P.; Lincoln, R.; Gomez, R.; Caillier, S.; George, M.; Wang, J.; Nelson, S. J.; Cree, B. A. C.; Hauser, S. L.; Pelletier, D.

    2009-01-01

    Genetic susceptibility to multiple sclerosis (MS) is associated with the human leukocyte antigen (HLA) "DRB1*1501" allele. Here we show a clear association between DRB1*1501 carrier status and four domains of disease severity in an investigation of genotype-phenotype associations in 505 robust, clinically well characterized MS patients evaluated…

  19. Emergence of Cryptosporidium hominis Monkey Genotype II and Novel Subtype Family Ik in the Squirrel Monkey (Saimiri sciureus) in China.

    PubMed

    Liu, Xuehan; Xie, Na; Li, Wei; Zhou, Ziyao; Zhong, Zhijun; Shen, Liuhong; Cao, Suizhong; Yu, Xingming; Hu, Yanchuan; Chen, Weigang; Peng, Gangneng

    2015-01-01

    A single Cryptosporidium isolate from a squirrel monkey with no clinical symptoms was obtained from a zoo in Ya'an city, China, and was genotyped by PCR amplification and DNA sequencing of the small-subunit ribosomal RNA (SSU rRNA), 70-kDa heat shock protein (HSP70), Cryptosporidium oocyst wall protein, and actin genes. This multilocus genetic characterization determined that the isolate was Cryptosporidium hominis, but carried 2, 10, and 6 nucleotide differences in the SSU rRNA, HSP70, and actin loci, respectively, which is comparable to the variations at these loci between C. hominis and the previously reported monkey genotype (2, 3, and 3 nucleotide differences). Phylogenetic studies, based on neighbor-joining and maximum likelihood methods, showed that the isolate identified in the current study had a distinctly discordant taxonomic status, distinct from known C. hominis and also from the monkey genotype, with respect to the three loci. Restriction fragment length polymorphisms of the SSU rRNA gene obtained from this study were similar to those of known C. hominis but clearly differentiated from the monkey genotype. Further subtyping was performed by sequence analysis of the gene encoding the 60-kDa glycoprotein (gp60). Maximum homology of only 88.3% to C. hominis subtype IdA10G4 was observed for the current isolate, and phylogenetic analysis demonstrated that this particular isolate belonged to a novel C. hominis subtype family, IkA7G4. This study is the first to report C. hominis infection in the squirrel monkey and, based on the observed genetic characteristics, confirms a new C. hominis genotype, monkey genotype II. Thus, these results provide novel insights into genotypic variation in C. hominis.

  20. Emergence of Cryptosporidium hominis Monkey Genotype II and Novel Subtype Family Ik in the Squirrel Monkey (Saimiri sciureus) in China

    PubMed Central

    Zhou, Ziyao; Zhong, Zhijun; Shen, Liuhong; Cao, Suizhong; Yu, Xingming; Hu, Yanchuan; Chen, Weigang; Peng, Gangneng

    2015-01-01

    A single Cryptosporidium isolate from a squirrel monkey with no clinical symptoms was obtained from a zoo in Ya’an city, China, and was genotyped by PCR amplification and DNA sequencing of the small-subunit ribosomal RNA (SSU rRNA), 70-kDa heat shock protein (HSP70), Cryptosporidium oocyst wall protein, and actin genes. This multilocus genetic characterization determined that the isolate was Cryptosporidium hominis, but carried 2, 10, and 6 nucleotide differences in the SSU rRNA, HSP70, and actin loci, respectively, which is comparable to the variations at these loci between C. hominis and the previously reported monkey genotype (2, 3, and 3 nucleotide differences). Phylogenetic studies, based on neighbor-joining and maximum likelihood methods, showed that the isolate identified in the current study had a distinctly discordant taxonomic status, distinct from known C. hominis and also from the monkey genotype, with respect to the three loci. Restriction fragment length polymorphisms of the SSU rRNA gene obtained from this study were similar to those of known C. hominis but clearly differentiated from the monkey genotype. Further subtyping was performed by sequence analysis of the gene encoding the 60-kDa glycoprotein (gp60). Maximum homology of only 88.3% to C. hominis subtype IdA10G4 was observed for the current isolate, and phylogenetic analysis demonstrated that this particular isolate belonged to a novel C. hominis subtype family, IkA7G4. This study is the first to report C. hominis infection in the squirrel monkey and, based on the observed genetic characteristics, confirms a new C. hominis genotype, monkey genotype II. Thus, these results provide novel insights into genotypic variation in C. hominis. PMID:26509708

  1. Concentrations, viability, and distribution of Cryptosporidium genotypes in lagoons of swine facilities in the Southern Piedmont and in coastal plain watersheds of Georgia.

    PubMed

    Jenkins, Michael B; Liotta, Janice L; Lucio-Forster, Araceli; Bowman, Dwight D

    2010-09-01

    Waste lagoons of swine operations are a source of Cryptosporidium oocysts. Few studies, however, have reported on oocyst concentrations in swine waste lagoons; none have reported on oocyst viability status, nor has there been a systematic assessment of species/genotype distributions across different types of swine facilities. Ten swine waste lagoons associated with farrowing, nursery, finishing, and gestation operations were each sampled once a month for a year. Oocysts were extracted from triplicate 900-ml effluent samples, enumerated by microscopy, and assessed for viability by dye exclusion/vital stain assay. DNA was extracted from processed samples, and 18S ribosomal DNA (rDNA) genes were amplified by PCR and sequenced for species and genotype identification. Oocysts were observed at each sampling time at each lagoon. Annual mean concentrations of total oocysts and viable oocysts ranged between 24 and 51 and between 0.6 and 12 oocysts ml(-1) effluent, respectively. The species and genotype distributions were dominated (95 to 100%) by Cryptosporidium suis and Cryptosporidium pig genotype II, the latter of which was found at eight of the lagoons. The lagoon at the gestation facility was dominated by Cryptosporidium muris (90%), and one farrowing facility showed a mix of pig genotypes, Cryptosporidium muris, and various genotypes of C. parvum. The zoonotic C. parvum bovine genotype was observed five times out of 407 18S rDNA sequences analyzed. Our results indicate that pigs can have mixed Cryptosporidium infections, but infection with C. suis is likely to be dominant.

  2. Assessment of genetic variation in Bulgarian tomato (Solanum lycopersicum L.) genotypes, using fluorescent SSR genotyping platform

    PubMed Central

    Todorovska, Elena; Ivanova, Albena; Ganeva, Daniela; Pevicharova, Galina; Molle, Emil; Bojinov, Bojin; Radkova, Mariana; Danailov, Zhivko

    2014-01-01

    Genetic variability in modern crops is limited due to domestication and selection processes. Genetic variation in eight Bulgarian tomato varieties and breeding lines (variety Plovdivska karotina, variety IZK Alya, L21β, L53β, L1140, L1116, L975, L984) differing in their morphological and biochemical composition was assessed using a highly efficient and low-cost fluorescent simple sequence repeat (SSR) genotyping platform. Genotyping was conducted with 165 publicly available microsatellite markers developed from different research groups under a number of projects in tomato (SOL Genomics SSRs, Kazusa TGS and TES, SLM, TMS and LEMDDNa) among which only five (3.03%) failed to amplify the expected PCR fragments. Of the remaining markers, 81 (50.62%) were polymorphic in the whole collection of eight genotypes. Among the marker groups used, SLM markers were most polymorphic, followed by TMS and SOL Genomics SSR markers. The total number of amplified alleles was 299, with a mean of 1.869; and the average polymorphic information content (PIC) was 0.196. The genetic diversity within the collection was relatively low (0.2222). Nei's genetic distance varied from 0.0953 to 0.3992. Cluster analysis using the un-weighted pair group method with arithmetic mean (UPGMA) method indicated that the studied tomato genotypes are grouped in four main clusters, which is to some extent consistent with the morpho- and hemo-types of the studied tomatoes. Variety IZK Alya (cherry type) and two of the breeding lines (L1140, L1116) formed three separate and more distant clusters. The fourth cluster includes the other five genotypes. The observed grouping of these genotypes in two sub-clusters reflects their similar morphological and biochemical composition. The genetic distance information from this study might be useful for further implementation of breeding strategies and crosses among these inbred lines. PMID:26019490

  3. Genotyping of Coxiella burnetii from domestic ruminants in northern Spain

    PubMed Central

    2012-01-01

    Background Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA) panel and Multispacer Sequence Typing (MST). Results A total of 45 samples from 4 goat herds (placentas, N = 4), 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20) and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21) were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM) samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several European countries, but

  4. SBE primer : multiplexing minisequencing-based genotyping

    SciTech Connect

    Kaderali, L.; Deshpande, A.; Uribe-Romeo, F. J.; Schliep, A.; Torney, D. C.

    2002-01-01

    Single-nucleotide polymorphism (SNP) analysis is a powerful tool for mapping and diagnosing disease-related alleles. Most of the known genetic diseases are caused by point mutations, and a growing number of SNPs will be routinely analyzed to diagnose genetic disorders. Mutation analysis by polymerase mediated single-base primer extension (minisequencing) can be massively parallelized using for example DNA microchips or flow cytometry with microspheres as solid support. By adding a unique oligonucleotide tag to the 5-inch end of the minisequencing primer and attaching the complementary anti-tag to the array or bead surface, the assay can be 'demultiplexed'. However, such high-throughput scoring of SNPs requires a high level of primer multiplexing in order to analyze multiple loci in one assay, thus enabling inexpensive and fast polymorphism scoring. Primers can be chosen from either the plus or the minus strand, and primers used in the same experiment must not bind to one another. To genotype a given number of polymorphic sites, the question is which primer to use for each SNP, and which primers to group into the same experiment. Furthermore, a crosshybridization-free tag/anti-tag code is required in order to sort the extended primers to the corresponding microspheres or chip spots. These problems pose challenging algorithmic questions. We present a computer program lo automate the design process for the assay. Oligonucleotide primers for the reaction are automatically selected by the software, a unique DNA tag/anti-tag system is generated, and the pairing of primers and DNA-Tags is automatically done in a way to avoid any crossreactivity. We report first results on a 45-plex genotyping assay, indicating that minisequencing can be adapted to be a powerful tool for high-throughput, massively parallel genotyping.

  5. G Allele of the IGF2 ApaI Polymorphism Is Associated With Judo Status.

    PubMed

    Itaka, Toshio; Agemizu, Kenichiro; Aruga, Seiji; Machida, Shuichi

    2016-07-01

    Itaka, T, Agemizu, K, Aruga, S, and Machida, S. G allele of the IGF2 ApaI polymorphism is associated with judo status. J Strength Cond Res 30(7): 2043-2048, 2016-Previous studies have reported that the insulin-like growth factor 2 (IGF2) ApaI polymorphism is associated with body mass index, fat mass, and grip strength. Competitive judo requires high levels of strength and power. The purpose of this study was to investigate the association between the IGF2 ApaI and ACTN3 R577X polymorphisms and judo status. The subjects were 156 male judo athletes from a top-level university in Japan. They were divided into 3 groups based on their competitive history: international-level athletes, national-level athletes, and others. Genomic DNA was extracted from the saliva of each athlete, and the maximal isometric strength of the trunk muscles and handgrip strength were measured. Genotyping by polymerase chain reaction-restriction fragment length polymorphism was used to detect IGF2 (rs680) and α-actinin-3 (ACTN3) (rs1815739) gene polymorphisms. The genotype frequencies of the 2 gene polymorphisms were compared among the 3 groups of judo athletes and controls. International-level judo athletes showed a higher frequency of the GG + GA genotype of the IGF2 gene than that of the national-level athletes and others. There was an inverse linear correlation between the frequency of the IGF2 AA genotype and level of judo performance (p = 0.041). Back muscle strength relative to height and weight was higher in subjects with the GG + GA genotype than in those with the AA genotype. Conversely, the ACTN3 R577X polymorphism was not associated with judo status. Additionally, no differences were found in back muscle or handgrip strength among the ACTN3 genotypes. In conclusion, the results indicate that the IGF2 gene polymorphism may be associated with judo status.

  6. The distribution of hepatitis B virus genotypes in Thailand.

    PubMed

    Louisirirotchanakul, Suda; Olinger, Christophe M; Arunkaewchaemsri, Panida; Poovorawan, Yong; Kanoksinsombat, Chinda; Thongme, Chittima; Sa-Nguanmoo, Pattaratida; Krasae, Sasithorn; Theamboonlert, Apiradee; Oota, Sineenart; Fongsatitkul, Ladda; Puapairoj, Chintana; Promwong, Charuporn; Weber, Bernard

    2012-10-01

    Phylogenetic analysis was performed on hepatitis B virus (HBV) strains obtained from 86 hepatitis B surface antigen (HBsAg) positive donors from Thailand originating throughout the country. Based on the S gene, 87.5% of strains were of genotype C while 10.5% were of genotype B, with all genotype B strains obtained from patients originating from the central or the south Thailand. No genotype B strains were found in the north of Thailand. Surprisingly, one patient was infected with a genotype H strain while another patient was infected with a genotype G strain. Complete genome sequencing and recombination analysis identified the latter as being a genotype G and C2 recombinant with the breakpoint around nucleotide position 700. The origin of the genotype G fragment was not identifiable while the genotype C2 fragment most likely came from strains circulating in Laos or Malaysia. The performance of different HBsAg diagnostic kits and HBV nucleic acid amplification technology (NAT) was evaluated. The genotype H and G/C2 recombination did not interfere with HBV detection.

  7. Current Status of Acanthamoeba in Iran: A Narrative Review Article

    PubMed Central

    NIYYATI, Maryam; REZAEIAN, Mostafa

    2015-01-01

    Background: Free-living amoebae belonging to the genus Acanthamoeba have an environmental distribution. Amoebic keratitis due to these protozoan parasites continue to rise in Iran and worldwide. In Iran, there are various researches regarding both morphological and molecular identification of Acanthamoeba spp. in environmental and clinical samples. However, there is no thorough review about Acanthamoeba genotypes and their distribution in environmental sources such as water, dust and biofilm in Iran. Besides, according to increasing cases of Amoebic keratitis in the region awareness regarding the pathogenic potential of these sight-threatening amoebae is of utmost importance. Methods: We conducted a thorough review based on the database sources such as MEDLINE, PubMed and Google scholar. No restrictions were placed on study date, study design or language of publication. We searched all valuable and relevant information considering the occurrence of the Acanthamoeba in both environmental and clinical samples. Results: According to our thorough review Acanthamoeba belonging to T4 genotype is the most prevalent type strain in environmental and clinical samples in several regions in Iran and worldwide, however, there are reports regarding Acanthamoeba belonging to other genotypes such as T2, T3, T5, T6 and T11 and the mentioned point could leads us to more researches with the goal of presenting the real genotype dominance of Acanthamoeba and related disease in the country. Conclusion: Overall, the present review will focus on present status of genotypes of Acanthamoeba in Iran during recent years. PMID:26246812

  8. Microsatellite markers in avocado (Persea americana Mill.): genealogical relationships among cultivated avocado genotypes.

    PubMed

    Ashworth, V E T M; Clegg, M T

    2003-01-01

    Twenty-five microsatellite markers uniquely differentiated 35 avocado cultivars and two wild relatives. Average heterozygosity was high (60.7%), ranging from 32% in P. steyermarkii to 84% in Fuerte and Bacon. In a subset of 15 cultivars, heterozygosity averaged 63.5% for microsatellites, compared to 41.8% for restriction fragment length polymorphisms (RFLPs). A neighbor-joining tree, according to average shared allele distances, consisted of three clusters likely corresponding to the botanical races of avocado and intermediate clusters uniting genotypes of presumably racially hybrid origin. Several results were at odds with existing botanical assignments that are sometimes rendered difficult by incomplete pedigree information, the complexity of the hybrid status (multiple backcrossing), or both. For example, cv. Harvest clustered with the Guatemalan race cultivars, yet it is derived from the Guatemalan x Mexican hybrid cv. Gwen. Persea schiedeana grouped with cv. Bacon. The rootstock G875 emerged as the most divergent genotype in our data set. Considerable diversity was found particularly among accessions from Guatemala, including G810 (West Indian race), G6 (Mexican race), G755A (hybrid Guatemalan x P. schiedeana), and G875 (probably not P. americana). Low bootstrap support, even upon exclusion of (known) hybrid genotypes from the data matrix, suggests the existence of ancient hybridization or that the botanical races originated more recently than previously thought.

  9. The CYP1B1_1358_GG genotype is associated with estrogen receptor-negative breast cancer.

    PubMed

    Justenhoven, Christina; Pierl, Christiane B; Haas, Susanne; Fischer, Hans-Peter; Baisch, Christian; Hamann, Ute; Harth, Volker; Pesch, Beate; Brüning, Thomas; Vollmert, Caren; Illig, Thomas; Dippon, Jürgen; Ko, Yon-Dschun; Brauch, Hiltrud

    2008-09-01

    Cytochrome P450 1B1 (CYP1B1) is a major enzyme in the initial catabolic step of estradiol (E2) metabolism and belongs to the multitude of genes regulated by the estrogen receptor alpha (ERalpha). The common non-synonymous polymorphisms CYP1B1_1358_A>G and CYP1B1_1294_C>G increase CYP1B1 enzymatic activity. Given a relationship between CYP1B1 and breast tumor E2 level as well as E2 level and breast tumor ERalpha expression it is of interest to know whether CYP1B1 polymorphisms have an impact on the ERalpha status of breast cancer. We genotyped the GENICA population-based breast cancer case-control collection (1,021 cases, 1,015 controls) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and investigated in cases the association between genotypes and tumor ERalpha status (739 ERalpha positive cases; 212 ERalpha negative cases) by logistic regression. We observed a significant association between the homozygous variant CYP1B1_1358_GG genotype and negative ERalpha status (P = 0.005; OR 2.82, 95% CI: 1.37-5.82) with a highly significant Ptrend for CYP1B1_1358_A>G and negative ERalpha status (P = 0.003). We also observed an association of CYP1B1_1358_GG and negative PR status (P = 0.015; OR 2.36, 95% CI: 1.18-4.70) and a Ptrend of 0.111 for CYP1B1_1358_A>G and negative progesterone receptor (PR) status. We conclude that the CYP1B1_1358_A>G polymorphism has an impact on ERalpha status in breast cancer in that the CYP1B1_1358_GG genotype known to encode higher CYP1B1 activity is associated with ERalpha negativity.

  10. Neppiness in an Introgressed Population of Cotton: Genotypic Variation and Genotypic Correlation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Neps and seed coat fragments are two types of impurities in ginned fibers causing severe problems in textile processing during spinning and dyeing. The study was designed to investigate the genotypic variation for neps and seed coat fragments remaining in ginned fibers in an introgressed population ...

  11. Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria.

    PubMed

    Wettstein, Sarah; Underhaug, Jarl; Perez, Belen; Marsden, Brian D; Yue, Wyatt W; Martinez, Aurora; Blau, Nenad

    2015-03-01

    The wide range of metabolic phenotypes in phenylketonuria is due to a large number of variants causing variable impairment in phenylalanine hydroxylase function. A total of 834 phenylalanine hydroxylase gene variants from the locus-specific database PAHvdb and genotypes of 4181 phenylketonuria patients from the BIOPKU database were characterized using FoldX, SIFT Blink, Polyphen-2 and SNPs3D algorithms. Obtained data was correlated with residual enzyme activity, patients' phenotype and tetrahydrobiopterin responsiveness. A descriptive analysis of both databases was compiled and an interactive viewer in PAHvdb database was implemented for structure visualization of missense variants. We found a quantitative relationship between phenylalanine hydroxylase protein stability and enzyme activity (r(s) = 0.479), between protein stability and allelic phenotype (r(s) = -0.458), as well as between enzyme activity and allelic phenotype (r(s) = 0.799). Enzyme stability algorithms (FoldX and SNPs3D), allelic phenotype and enzyme activity were most powerful to predict patients' phenotype and tetrahydrobiopterin response. Phenotype prediction was most accurate in deleterious genotypes (≈ 100%), followed by homozygous (92.9%), hemizygous (94.8%), and compound heterozygous genotypes (77.9%), while tetrahydrobiopterin response was correctly predicted in 71.0% of all cases. To our knowledge this is the largest study using algorithms for the prediction of patients' phenotype and tetrahydrobiopterin responsiveness in phenylketonuria patients, using data from the locus-specific and genotypes database.

  12. Effect of reference population size and available ancestor genotypes on imputation of Mexican Holstein genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effects of reference population size and the availability of information from genotyped ancestors on the accuracy of imputation of single nucleotide polymorphisms (SNPs) were investigated for Mexican Holstein cattle. Three scenarios for reference population size were examined: (1) a local popula...

  13. NPDES Permit Status Reports

    EPA Pesticide Factsheets

    These reports show the backlog status nationwide, based on EPA databases and input from EPA regions and states. The reports show a snapshot in time, keep in mind that the status of facilities and the universe of permits change.

  14. Status of Women Microbiologists

    ERIC Educational Resources Information Center

    Kashket, Eva Ruth; And Others

    1974-01-01

    Presents evidence that the status of women microbiologists is lower than that of men and that the lower status of women results, to a large degree, from inequality of opportunity throughout their careers. (Author/JR)

  15. The "thermolabile" variant of methylenetetrahydrofolate reductase and neural tube defects: An evaluation of genetic risk and the relative importance of the genotypes of the embryo and the mother.

    PubMed Central

    Shields, D C; Kirke, P N; Mills, J L; Ramsbottom, D; Molloy, A M; Burke, H; Weir, D G; Scott, J M; Whitehead, A S

    1999-01-01

    Recent reports have implicated the "thermolabile" (T) variant of methylenetetrahydrofolate reductase (MTHFR) in the causation of folate-dependent neural tube defects (NTDs). We report herein the largest genetic study of NTD cases (n=271) and families (n=218) to date, establishing that, in Ireland, the "TT" genotype is found in 18.8% of cases versus 8.3% of controls (odds ratio 2.57; confidence interval [CI] 1.48-4.45; P=.0005). The maternal and paternal TT genotypes have intermediate frequencies of 13.8% and 11.9%, respectively, indicating that the predominant MTHFR-related genetic effect acts via the TT genotype of the developing embryo. Analysis of the 218 family triads of mother, father, and affected child with log-linear models supports this interpretation, providing significant evidence that the case TT genotype is associated with NTDs (P=.02) but no evidence of a maternal TT genotypic effect (P=. 83). The log-linear model predicted that the risk of NTDs conferred by the case TT genotype is 1.61 (CI 1.06-2.46), consistent with the paramount importance of the case TT genotype in determining risk. There is no compelling evidence for more than a modest additional risk conferred by a maternal TT genotype. These results favor a biological model of MTHFR-related NTD pathogenesis in which suboptimal maternal folate status imposes biochemical stress on the developing embryo, a stress it is ill-equipped to tolerate if it has a TT genotype. PMID:10090889

  16. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    NASA Astrophysics Data System (ADS)

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-11-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

  17. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    PubMed Central

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest. PMID:27857198

  18. Adaptability and genotypic stability of Coffea arabica genotypes based on REML/BLUP analysis in Rio de Janeiro State, Brazil.

    PubMed

    Rodrigues, W P; Vieira, H D; Barbosa, D H S G; Souza Filho, G R; Candido, L S

    2013-07-15

    Biannuality in coffee culture causes temporal variability in plant productivity. Consequently, it is essential to evaluate genotypes during various crop years to ensure selection of productive and stable genotypes. We evaluated the effectiveness of simultaneous selection of coffee genotypes along harvests, based on productivity, stability, and adaptability, via mixed models, for indication of varieties suitable for Rio de Janeiro State. We evaluated 25 genotypes during 4 crop seasons (2009-2012), in a randomized block design with 5 replications. The ranking of genotypes was obtained on the basis of the adaptability and temporal stability methods (harmonic average of genetic values, relative performance of genetic values, and harmonic mean of the relative performance of the genetic values), obtained via restricted maximum likelihood/best linear unbiased procedure analysis. The selection accuracy (0.8717), associated with the high magnitude of mean heritability, indicate good reliability and prospects for success in the indication of agronomically superior genotypes. There was little variation in the ordering of genotypes among the environments, indicating low influence of harvests in the performance of the genotypes. Five of the 25 genotypes were superior and could be recommended for planting in the northwestern region of Rio de Janeiro State, due to high predicted productivity and stability. We recommend that these methodologies for evaluation of productivity, stability, and adaptability be included in the selection criteria for recommendation of genotypes for commercial plantings.

  19. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest.

    PubMed

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-11-18

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

  20. Implementing genotype-guided antithrombotic therapy

    PubMed Central

    Seip, Richard L; Duconge, Jorge; Ruaño, Gualberto

    2010-01-01

    Genotyping has the potential to improve the efficacy and safety of major antithrombotic drugs. For warfarin, the stable maintenance dose varies from 1–10 mg/day. The VKORC1 −1639G>A allele and the CYP2C9*2 and *3 alleles (cumulative frequency: 90% in Asians, 65% in Europeans and 20% in Africans), explain 45% of response variability in European and 30% in African populations. The large clinical trials COAG and EU-PACT will define the extent to which pharmacogenetic dosing affects the safety and efficacy of warfarin and coumarin derivatives. The platelet inhibitor clopidogrel requires activation by the CYP2C19 enzyme. CYP2C19*2 and *3 alleles (cumulative frequency: 20–50%) produce null enzyme activity, and their presence attenuates platelet inhibition and increases cardiovascular events. The US FDA-mandated drug labeling recognizes the relevance of genotyping in the selection and dosing of both warfarin and clopidogrel. PMID:20462345

  1. Primer-design for multiplexed genotyping.

    PubMed

    Kaderali, Lars; Deshpande, Alina; Nolan, John P; White, P Scott

    2003-03-15

    Single-nucleotide polymorphism (SNP) analysis is a powerful tool for mapping and diagnosing disease-related alleles. Mutation analysis by polymerase-mediated single-base primer extension (minisequencing) can be massively parallelized using DNA microchips or flow cytometry with microspheres as solid support. By adding a unique oligonucleotide tag to the 5' end of the minisequencing primer and attaching the complementary antitag to the array or bead surface, the assay can be 'demultiplexed'. Such high-throughput scoring of SNPs requires a high level of primer multiplexing in order to analyze multiple loci in one assay, thus enabling inexpensive and fast polymorphism scoring. We present a computer program to automate the design process for the assay. Oligonucleotide primers for the reaction are automatically selected by the software, a unique DNA tag/antitag system is generated, and the pairing of primers and DNA tags is automatically done in a way to avoid any crossreactivity. We report results on a 45-plex genotyping assay, indicating that minisequencing can be adapted to be a powerful tool for high-throughput, massively parallel genotyping. The software is available to academic users on request.

  2. Cryptococcus neoformans shows a remarkable genotypic diversity in Brazil.

    PubMed

    Barreto de Oliveira, M T; Boekhout, T; Theelen, B; Hagen, F; Baroni, F A; Lazera, M S; Lengeler, K B; Heitman, J; Rivera, I N G; Paula, C R

    2004-03-01

    The genotypic diversity of Brazilian Cryptococcus neoformans strains was analyzed. The majority of the samples were alphaA (65%), followed by alphaB (17.5%), alphaD (9%), alphaAaD hybrids (5%), and alphaC (3.5%). A considerable genotypic diversity occurred within C. neoformans var. grubii, and a new amplified fragment length polymorphism genotype, 1B, was recognized.

  3. Genotypic richness predicts phenotypic variation in an endangered clonal plant.

    PubMed

    Evans, Suzanna M; Sinclair, Elizabeth A; Poore, Alistair G B; Bain, Keryn F; Vergés, Adriana

    2016-01-01

    Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen) was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of the species

  4. Genotypic richness predicts phenotypic variation in an endangered clonal plant

    PubMed Central

    Sinclair, Elizabeth A.; Poore, Alistair G.B.; Bain, Keryn F.; Vergés, Adriana

    2016-01-01

    Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen) was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of the species

  5. Molecular genotyping of HCV infection in seropositive blood donor

    NASA Astrophysics Data System (ADS)

    Zarin, Siti Noraziah Abu; Ibrahim, Nazlina

    2013-11-01

    This study is to investigate the prevalence of hepatitis C virus infection in seropositive blood donor. RNA was extracted from 32 positive samples in National Blood Centre and Melaka Hospital. The core and NS5B sequences were obtained from 23 samples. Genotype 3a is most prevalent in this study followed by genotype 1a. Evidence of mixed-genotypes (3a and 1b) infections was found in 5 subjects.

  6. Interferon Lambda 4 Genotype Is Not Associated with Recurrence of Oral or Genital Herpes

    PubMed Central

    Lang Kuhs, Krystle A.; Kuniholm, Mark H.; Pfeiffer, Ruth M.; Chen, Sabrina; Desai, Seema; Edlin, Brian R.; Peters, Marion G.; Plankey, Michael; Sharp, Gerald B.; Strickler, Howard D.; Villacres, Maria C.; Quinn, Thomas C.; Gange, Stephen J.; Prokunina-Olsson, Ludmila; Greenblatt, Ruth M.; O’Brien, Thomas R.

    2015-01-01

    IFNL4-ΔG/TT (rs368234815) genotype is associated with hepatitis C virus clearance and may play a role in other infections. IFN-λ4 protein is generated only in individuals who carry the IFNL4-ΔG allele. The IFNL4 rs12979860-T allele, which is in strong linkage disequilibrium with IFNL4-ΔG, was recently reported to be associated with more frequent and severe oral herpes episodes. We investigated the association of IFNL4-ΔG/TT with herpes simplex virus (HSV)-related outcomes among 2,192 African American and European American participants in the Women’s Interagency HIV Study (WIHS). WIHS is a prospective cohort study of human immunodeficiency virus (HIV)–infected and at-risk women that began in 1994. This report includes follow-up through 2013. Available data included: HSV–1 and HSV–2 antibodies at study entry; bi-annually ascertained episodes of (self-reported) oral herpes, (self-reported) genital sores and (clinician-observed) genital ulcers; HSV–2 DNA in cervicovaginal lavage (CVL) specimens. IFNL4-ΔG/TT genotyping was determined by TaqMan. We compared women with IFNL4-ΔG/ΔG or IFNL4-TT/ΔG genotypes (i.e., IFNL4-ΔG carriers) to those with the IFNL4-TT/TT genotype, adjusting for age, race and HIV status. For outcomes with repeated measurements, the adjusted odds ratio (aOR), 95% confidence interval [CI] and p-value were determined using a generalized estimating equations approach. Median participant age at enrollment was 36 years; 81% were African American, 74% were HIV-infected. Among 1,431 participants tested for antibodies, 72.8% were positive for HSV–1 and 79.0% were positive for HSV–2. We observed no association between IFNL4-ΔG/TT genotype and any outcome: HSV–1 or HSV–2 antibody prevalence (p>0.1, all comparisons); oral herpes (aOR, 1.2; p = 0.35); genital sores (aOR, 1.0; p = 0.71); genital ulcers (aOR, 1.1; p = 0.53); detectable HSV–2 DNA in CVL (N = 322; aOR, 0.71; p = 0.49); HSV–2 DNA level (p = 0.68). In this large

  7. Interferon Lambda 4 Genotype Is Not Associated with Recurrence of Oral or Genital Herpes.

    PubMed

    Lang Kuhs, Krystle A; Kuniholm, Mark H; Pfeiffer, Ruth M; Chen, Sabrina; Desai, Seema; Edlin, Brian R; Peters, Marion G; Plankey, Michael; Sharp, Gerald B; Strickler, Howard D; Villacres, Maria C; Quinn, Thomas C; Gange, Stephen J; Prokunina-Olsson, Ludmila; Greenblatt, Ruth M; O'Brien, Thomas R

    2015-01-01

    IFNL4-ΔG/TT (rs368234815) genotype is associated with hepatitis C virus clearance and may play a role in other infections. IFN-λ4 protein is generated only in individuals who carry the IFNL4-ΔG allele. The IFNL4 rs12979860-T allele, which is in strong linkage disequilibrium with IFNL4-ΔG, was recently reported to be associated with more frequent and severe oral herpes episodes. We investigated the association of IFNL4-ΔG/TT with herpes simplex virus (HSV)-related outcomes among 2,192 African American and European American participants in the Women's Interagency HIV Study (WIHS). WIHS is a prospective cohort study of human immunodeficiency virus (HIV)-infected and at-risk women that began in 1994. This report includes follow-up through 2013. Available data included: HSV-1 and HSV-2 antibodies at study entry; bi-annually ascertained episodes of (self-reported) oral herpes, (self-reported) genital sores and (clinician-observed) genital ulcers; HSV-2 DNA in cervicovaginal lavage (CVL) specimens. IFNL4-ΔG/TT genotyping was determined by TaqMan. We compared women with IFNL4-ΔG/ΔG or IFNL4-TT/ΔG genotypes (i.e., IFNL4-ΔG carriers) to those with the IFNL4-TT/TT genotype, adjusting for age, race and HIV status. For outcomes with repeated measurements, the adjusted odds ratio (aOR), 95% confidence interval [CI] and p-value were determined using a generalized estimating equations approach. Median participant age at enrollment was 36 years; 81% were African American, 74% were HIV-infected. Among 1,431 participants tested for antibodies, 72.8% were positive for HSV-1 and 79.0% were positive for HSV-2. We observed no association between IFNL4-ΔG/TT genotype and any outcome: HSV-1 or HSV-2 antibody prevalence (p>0.1, all comparisons); oral herpes (aOR, 1.2; p = 0.35); genital sores (aOR, 1.0; p = 0.71); genital ulcers (aOR, 1.1; p = 0.53); detectable HSV-2 DNA in CVL (N = 322; aOR, 0.71; p = 0.49); HSV-2 DNA level (p = 0.68). In this large prospective study, IFNL4-

  8. Differential response of kabuli and desi chickpea genotypes toward inoculation with PGPR in different soils

    PubMed Central

    Imran, Asma; Mirza, Muhammad S.; Shah, Tariq M.; Malik, Kauser A.; Hafeez, Fauzia Y.

    2015-01-01

    Pakistan is among top three chickpea producing countries but the crop is usually grown on marginal lands without irrigation and fertilizer application which significantly hampers its yield. Soil fertility and inoculation with beneficial rhizobacteria play a key role in nodulation and yield of legumes. Four kabuli and six desi chickpea genotypes were, therefore, evaluated for inoculation response with IAA-producing Ochrobactrum ciceri Ca-34T and nitrogen fixing Mesorhizobium ciceri TAL-1148 in single and co-inoculation in two soils. The soil type 1 was previously unplanted marginal soil having low organic matter, P and N contents compared to soil type 2 which was a fertile routinely legume-cultivated soil. The effect of soil fertility status was pronounced and fertile soil on average, produced 31% more nodules, 62% more biomass and 111% grain yield than marginal soil. Inoculation either with O. ciceri alone or its co-inoculation with M. ciceri produced on average higher nodules (42%), biomass (31%), grains yield (64%) and harvest index (72%) in both chickpea genotypes over non-inoculated controls in both soils. Soil 1 showed maximum relative effectiveness of Ca-34T inoculation for kabuli genotypes while soil 2 showed for desi genotypes except B8/02. Desi genotype B8/02 in soil type 1 and Pb-2008 in soil type 2 showed significant yield increase as compared to respective un-inoculated controls. Across bacterial inoculation treatments, grain yield was positively correlated to growth and yield contributing parameters (r = 0.294* to 0.838*** for desi and r = 0.388* to 0.857** for kabuli). PCA and CAT-PCA analyses clearly showed a site-specific response of genotype x bacterial inoculation. Furthermore, the inoculated bacterial strains were able to persist in the rhizosphere showing colonization on root and within nodules. Present study shows that plant growth promoting rhizobacteria (PGPR) inoculation should be integrated with national chickpea breading program in

  9. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle

    PubMed Central

    da Silva, Joaquim Manoel; Giachetto, Poliana Fernanda; da Silva, Luiz Otávio Campos; Cintra, Leandro Carrijo; Paiva, Samuel Rezende; Caetano, Alexandre Rodrigues; Yamagishi, Michel Eduardo Beleza

    2015-01-01

    High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production. PMID:26305794

  10. Trichothecene genotypes of Fusarium graminearum from wheat in Uruguay.

    PubMed

    Pan, Dinorah; Calero, Natalia; Mionetto, Ana; Bettucci, Lina

    2013-03-01

    Gibberella zeae (Schwein.) Petch (anamorph F. graminearum Schwabe) is the primary causal agent of FHB of wheat in Uruguay. In the last decade, F. graminearum has produced destructive epidemics on wheat in Uruguay, causing yield losses and price discounts due to reduced seed quality. Strains of F. graminearum clade usually express one of three strain-specific profiles of trichothecene metabolites: nivalenol and its acetylated derivatives (NIV chemotype), deoxynivalenol and 3-acetyldeoxynivalenol (3-AcDON chemotype), or deoxynivalenol and 15-acetyldeoxynivalenol (15-AcDON chemotype). A multiplex PCR assay of Tri3, Tri5, and Tri7 was used to determine the trichothecene genotype of 111 strains of F. graminearum collected during 2003 and 2009 growing seasons from fields located in the major wheat production area of Uruguay. The result showed that all except one of the isolates were of DON genotype, with the remainder of NIV genotype in years 2003 and 2009. All strains with the DON genotype were also of the 15-AcDON genotype in 2003 and nearly all (45/50) in 2009. No DON/3-AcDON genotypes were found in either growing season. No potential shifts in the populations were found in the trichothecene genotypes between 2003 and the 2009 epidemic FHB harvest seasons. This study provides the first data on trichothecene genotypes of F. graminearum strains isolated from wheat in Uruguay and add to the current regional knowledge of trichothecene genotypes.

  11. Genotype X environment interactions. II. Some genetical considerations.

    PubMed

    Mather, K

    1975-08-01

    An algebraic formulation, alternative to that of Mather and Jones (1958) and hierarchial rather than factorial in nauture, is presented for describing the differences among the phenotypes produced by a number of genotypes each grown in each of a number of environments. This formuationdoes not include terms representing statistical interactions between genotypes and environments: it depends instead on comparisons between the different genotypes in their variation over the relevant ranges of environemnts. The two-line case is considered ant eht condition established for linearity of the regress ion of genotype X enviroment interaction (g in Mather and Jones' formulation) on overall effect of the envirronment (e in Mather and Jones' formulation)...

  12. Phenotype-genotype analysis of CYP2C19 in Colombian mestizo individuals

    PubMed Central

    Isaza, Carlos; Henao, Julieta; Martínez, José H Isaza; Arias, Juan C Sepúlveda; Beltrán, Leonardo

    2007-01-01

    Background Omeprazole is metabolized by the hepatic cytochrome P450 (CYP) 2C19 enzyme to 5-hydroxyomeprazole. CYP2C19 exhibits genetic polymorphisms responsible for the presence of poor metabolizers (PMs), intermediate metabolizers (IMs) and extensive metabolizers (EMs). The defective mutations of the enzyme and their frequencies change between different ethnic groups; however, the polymorphism of the CYP2C19 gene has not been studied in Colombian mestizos. The aim of this study was to evaluate the genotype and phenotype status of CYP2C19 in Colombian mestizos, in order to contribute to the use of appropriate strategies of drug therapy for this population. Methods 189 subjects were genotyped using the multiplex SNaPshot technique and a subgroup of 44 individuals received 20 mg of omeprazole followed by blood collection at 3 hours to determine the omeprazole hydroxylation index by HPLC. Results 83.6%, 15.3% and 1.1% of the subjects were genotyped as EMs, IMs and PMs, respectively. The frequencies of the CYP2C29*1 and CYP2C19*2 alleles were 91.3% and 8.7% respectively whereas the *3, *4, *5, *6 and *8 alleles were not found. No discrepancies were found between the genotype and phenotype of CYP2C19. Conclusion The frequency of poor metabolizers (1.1%) in the Colombian mestizos included in this study is similar to that in Bolivian mestizos (1%) but lower than in Mexican-Americans (3.2%), West Mexicans (6%), Caucasians (5%) and African Americans (5.4%). The results of this study will be useful for drug dosage recommendations in Colombian mestizos. PMID:17623107

  13. Hepatitis C virus genotype 4 responds better to pegylated interferon with ribavirin than genotype 1 in HIV-infected patients.

    PubMed

    Mira, José A; Rivero, Antonio; de Los Santos-Gil, Ignacio; López-Cortés, Luis F; Girón-González, José A; Márquez, Manuel; Merino, Dolores; del Mar Viloria, María; Téllez, Francisco; Ríos-Villegas, María J; Omar, Mohamed; Rivero-Juárez, Antonio; Macías, Juan; Pineda, Juan A

    2012-08-24

    We assess the efficacy of pegylated interferon (peg-IFN) with ribavirin (RBV) and the predictors of sustained virological response (SVR) among HIV/hepatitis C virus genotype 4 (HCV-4)-coinfected patients. Thirty-nine (31.5%) of 124 individuals with HCV-4 achieved SVR compared with 103 (22.7%) of 453 individuals with HCV genotype 1 (P=0.046). Only interleukin-28B (IL28B) genotype CC was independently associated with SVR in HIV/HCV-4-coinfected patients. The efficacy of peg-IFN with RBV in coinfected individuals with genotype 4 is significantly higher than in those with genotype 1. IL28B CC genotype is the main predictor of response in this population.

  14. Heuristic status polling

    DOEpatents

    Archer, Charles J.; Blocksome, Michael A.; Heidelberger, Philip; Kumar, Sameer; Parker, Jeffrey J.; Ratterman, Joseph D.

    2011-06-07

    Methods, compute nodes, and computer program products are provided for heuristic status polling of a component in a computing system. Embodiments include receiving, by a polling module from a requesting application, a status request requesting status of a component; determining, by the polling module, whether an activity history for the component satisfies heuristic polling criteria; polling, by the polling module, the component for status if the activity history for the component satisfies the heuristic polling criteria; and not polling, by the polling module, the component for status if the activity history for the component does not satisfy the heuristic criteria.

  15. CYP2D6 genotype and adjuvant tamoxifen: meta-analysis of heterogeneous study populations.

    PubMed

    Province, M A; Goetz, M P; Brauch, H; Flockhart, D A; Hebert, J M; Whaley, R; Suman, V J; Schroth, W; Winter, S; Zembutsu, H; Mushiroda, T; Newman, W G; Lee, M-T M; Ambrosone, C B; Beckmann, M W; Choi, J-Y; Dieudonné, A-S; Fasching, P A; Ferraldeschi, R; Gong, L; Haschke-Becher, E; Howell, A; Jordan, L B; Hamann, U; Kiyotani, K; Krippl, P; Lambrechts, D; Latif, A; Langsenlehner, U; Lorizio, W; Neven, P; Nguyen, A T; Park, B-W; Purdie, C A; Quinlan, P; Renner, W; Schmidt, M; Schwab, M; Shin, J-G; Stingl, J C; Wegman, P; Wingren, S; Wu, A H B; Ziv, E; Zirpoli, G; Thompson, A M; Jordan, V C; Nakamura, Y; Altman, R B; Ames, M M; Weinshilboum, R M; Eichelbaum, M; Ingle, J N; Klein, T E

    2014-02-01

    The International Tamoxifen Pharmacogenomics Consortium was established to address the controversy regarding cytochrome P450 2D6 (CYP2D6) status and clinical outcomes in tamoxifen therapy. We performed a meta-analysis on data from 4,973 tamoxifen-treated patients (12 globally distributed sites). Using strict eligibility requirements (postmenopausal women with estrogen receptor-positive breast cancer, receiving 20 mg/day tamoxifen for 5 years, criterion 1); CYP2D6 poor metabolizer status was associated with poorer invasive disease-free survival (IDFS: hazard ratio = 1.25; 95% confidence interval = 1.06, 1.47; P = 0.009). However, CYP2D6 status was not statistically significant when tamoxifen duration, menopausal status, and annual follow-up were not specified (criterion 2, n = 2,443; P = 0.25) or when no exclusions were applied (criterion 3, n = 4,935; P = 0.38). Although CYP2D6 is a strong predictor of IDFS using strict inclusion criteria, because the results are not robust to inclusion criteria (these were not defined a priori), prospective studies are necessary to fully establish the value of CYP2D6 genotyping in tamoxifen therapy.

  16. Molecular Genetics External Quality Assessment Pilot Scheme for Irinotecan-Related UGT1A1 Genotyping in China

    PubMed Central

    Zhang, Kuo; Wang, Lunan; Zhang, Rui; Xie, Jiehong; Li, Jinming

    2016-01-01

    Irinotecan is widely used in the treatment of solid tumors, especially in colorectal cancer and lung cancer. Molecular testing for UGT1A1 genotyping is increasingly required in China for optimum irinotecan administration. In order to determine the performance of laboratories with regard to the whole testing process for UGT1A1 to ensure the consistency and accuracy of the test results, the National Center for Clinical Laboratories conducted an external quality assessment program for UGT1A1*28 genotyping in 2015. The panel, which comprised of four known mutational samples and six wild-type samples, was distributed to 45 laboratories that test for the presence of UGT1A1*28 polymorphisms. Participating laboratories were allowed to perform polymorphism analysis by using their routine methods. The accuracy of the genotyping and reporting of results was analyzed. Other information from the individual laboratories, including the number of samples tested each month, accreditation/certification status, and test methodology, was reviewed. Forty-four of the 45 participants reported the correct results for all samples. There was only one genotyping error, with a corresponding analytical sensitivity of 99.44% (179/180 challenges; 95% confidence interval: 96.94−99.99%) and an analytical specificity of 100% (270/270 challenges; 95% confidence interval: 98.64−100%). Both commercial kits and laboratory development tests were commonly used by the laboratories, and pyrosequencing was the main methodology used (n = 26, 57.8%). The style of the written reports showed large variation, and many reports showed a shortage of information. In summary, the first UGT1A1 genotyping external quality assessment result demonstrated that UGT1A1 genotype analysis of good quality was performed in the majority of pharmacogenetic testing centers that were investigated. However, greater education on the reporting of UGT1A1 genetic testing results is needed. PMID:26820647

  17. Cigarette smoking, N-acetyltransferase 2 genotypes, and breast cancer risk: pooled analysis and meta-analysis.

    PubMed

    Ambrosone, Christine B; Kropp, Silke; Yang, Jun; Yao, Song; Shields, Peter G; Chang-Claude, Jenny

    2008-01-01

    Approximately 10 years ago, it was noted that smoking increased risk of breast cancer among women with N-acetyltransferase 2 (NAT2) slow acetylation genotypes. This report was followed by a number of studies to address this question. We pooled data from 10 existing studies and also conducted a meta-analysis of 13 studies published from 1996 to October 2006 that were conducted among women, were published in English, and had adequate information on smoking and NAT2 genotyping. Raw data were requested from authors. Unconditional logistic regression was done for pooled analysis, and random effect models was done for meta-analysis. Study heterogeneity was assessed, and sensitivity tests were done when subgroups were excluded from the analysis. In the pooled analysis, there was a significant interaction between smoking, NAT2 genotype, and risk of breast cancer [pack-years (continuous variable, P(interaction) = 0.03)], with higher pack-years significantly associated with an increased risk of breast cancer among women with NAT2 slow genotypes (pooled analysis relative risk, 1.49; 95% confidence interval, 1.08-2.04). These findings were supported by the meta-analysis including all studies; pack-years were significantly associated with risk among slow acetylators in a dose-dependent fashion (meta-analysis relative risk, 1.44; 95% confidence interval, 1.23-1.68 for > or =20 pack-years versus never smokers), but not among rapid acetylators. Similar relationships were noted for smoking status (ever, never) and duration of smoking. Our results show that cigarette smoking is associated with an increase in breast cancer risk among women with NAT2 slow acetylation genotypes. Because slow NAT2 genotypes are present in 50% to 60% of Caucasian populations, smoking is likely to play an important role in breast cancer etiology.

  18. Prevalence of the Helicobacter pylori babA2 gene and correlation with the degree of gastritis in infected Slovenian children.

    PubMed

    Homan, Matjaž; Šterbenc, Anja; Kocjan, Boštjan J; Luzar, Boštjan; Zidar, Nina; Orel, Rok; Poljak, Mario

    2014-10-01

    The aims of our study were to determine the prevalence of the babA2 gene within Helicobacter pylori strains circulating in the Slovenian pediatric population, to further clarify its significance in causing inflammation of gastric mucosa in children and to verify whether cagA, vacA, iceA and babA genes work independently or synergistically in causing gastritis. A total of 163 H. pylori isolates obtained from the same number of children were tested for the presence of cagA, vacA and iceA genes using previously established methods, while the babA2 gene was determined using novel polymerase chain reaction assay targeting a 139-bp fragment of the central region of babA2. The babA2 gene was detected in 47.9% of H. pylori samples. The presence of the babA2 gene was strongly associated with cagA, vacA s1 and vacA m1 genotype. The babA2 status correlated positively with bacterial density score, activity of inflammation and chronic inflammation of gastric mucosa. No significant correlation was found between the babA2 status and the presence of atrophy or intestinal metaplasia. In addition, the activity of gastric inflammation and density score were significantly associated with the coexpression of the cagA, vacA s1, vacA m1 and babA2 genes. The study, which included the largest number of pediatric H. pylori samples to date, confirmed that babA2 gene plays an important role in the pathogenesis of H. pylori gastritis in children. Furthermore, our results suggest that babA2, cagA and vacA s1 and m1 gene products may work synergistically in worsening the inflammation of gastric mucosa.

  19. Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing.

    PubMed

    Mack, Steven J; Milius, Robert P; Gifford, Benjamin D; Sauter, Jürgen; Hofmann, Jan; Osoegawa, Kazutoyo; Robinson, James; Groeneweg, Mathijs; Turenchalk, Gregory S; Adai, Alex; Holcomb, Cherie; Rozemuller, Erik H; Penning, Maarten T; Heuer, Michael L; Wang, Chunlin; Salit, Marc L; Schmidt, Alexander H; Parham, Peter R; Müller, Carlheinz; Hague, Tim; Fischer, Gottfried; Fernandez-Viňa, Marcelo; Hollenbach, Jill A; Norman, Paul J; Maiers, Martin

    2015-12-01

    The development of next-generation sequencing (NGS) technologies for HLA and KIR genotyping is rapidly advancing knowledge of genetic variation of these highly polymorphic loci. NGS genotyping is poised to replace older methods for clinical use, but standard methods for reporting and exchanging these new, high quality genotype data are needed. The Immunogenomic NGS Consortium, a broad collaboration of histocompatibility and immunogenetics clinicians, researchers, instrument manufacturers and software developers, has developed the Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines. MIRING is a checklist that specifies the content of NGS genotyping results as well as a set of messaging guidelines for reporting the results. A MIRING message includes five categories of structured information - message annotation, reference context, full genotype, consensus sequence and novel polymorphism - and references to three categories of accessory information - NGS platform documentation, read processing documentation and primary data. These eight categories of information ensure the long-term portability and broad application of this NGS data for all current histocompatibility and immunogenetics use cases. In addition, MIRING can be extended to allow the reporting of genotype data generated using pre-NGS technologies. Because genotyping results reported using MIRING are easily updated in accordance with reference and nomenclature databases, MIRING represents a bold departure from previous methods of reporting HLA and KIR genotyping results, which have provided static and less-portable data. More information about MIRING can be found online at miring.immunogenomics.org.

  20. Diversity of Human Clock Genotypes and Consequences

    PubMed Central

    Zhang, Luoying; Ptáček, Louis J.; Fu, Ying-Hui

    2014-01-01

    The molecular clock consists of a number of genes that form transcriptional and post-transcriptional feedback loops, which function together to generate circadian oscillations that give rise to circadian rhythms of our behavioral and physiological processes. Genetic variations in these clock genes have been shown to be associated with phenotypic effects in a repertoire of biological processes, such as diurnal preference, sleep, metabolism, mood regulation, addiction, and fertility. Consistently, rodent models carrying mutations in clock genes also demonstrate similar phenotypes. Taken together, these studies suggest that human clock-gene variants contribute to the phenotypic differences observed in various behavioral and physiological processes, although to validate this requires further characterization of the molecular consequences of these polymorphisms. Investigating the diversity of human genotypes and the phenotypic effects of these genetic variations shall advance our understanding of the function of the circadian clock and how we can employ the clock to improve our overall health. PMID:23899594

  1. Sources of Wilhelm Johannsen's genotype theory.

    PubMed

    Roll-Hansen, Nils

    2009-01-01

    This paper describes the historical background and early formation of Wilhelm Johannsen's distinction between genotype and phenotype. It is argued that contrary to a widely accepted interpretation (For instance, W. Provine, 1971. The Origins of Theoretical Population Genetics. Chicago: The University of Chicago Press; Mayr, 1973; F. B. Churchill, 1974. Journal of the History of Biology 7: 5-30; E. Mayr, 1982. The Growth of Biological Thought, Cambridge: Harvard University Press; J. Sapp, 2003. Genesis. The Evolution of Biology. New York: Oxford University Press) his concepts referred primarily to properties of individual organisms and not to statistical averages. Johannsen's concept of genotype was derived from the idea of species in the tradition of biological systematics from Linnaeus to de Vries: An individual belonged to a group - species, subspecies, elementary species - by representing a certain underlying type (S. Müller-Wille and V. Orel, 2007. Annals of Science 64: 171-215). Johannsen sharpened this idea theoretically in the light of recent biological discoveries, not least those of cytology. He tested and confirmed it experimentally combining the methods of biometry, as developed by Francis Galton, with the individual selection method and pedigree analysis, as developed for instance by Louis Vilmorin. The term "genotype" was introduced in W. Johannsen's 1909 (Elemente der Exakten Erblichkeitslehre. Jena: Gustav Fischer) treatise, but the idea of a stable underlying biological "type" distinct from observable properties was the core idea of his classical bean selection experiment published 6 years earlier (W. Johannsen, 1903. Ueber Erblichkeit in Populationen und reinen Linien. Eine Beitrag zur Beleuchtung schwebender Selektionsfragen, Jena: Gustav Fischer, pp. 58-59). The individual ontological foundation of population analysis was a self-evident presupposition in Johannsen's studies of heredity in populations from their start in the early 1890s till his

  2. IL-10 and TNFα Genotypes in SLE

    PubMed Central

    López, Patricia; Gutiérrez, Carmen; Suárez, Ana

    2010-01-01

    The production of two regulators of the inflammatory response, interleukin 10 (IL-10) and tumor necrosis factor α (TNFα), has been found to be deeply deregulated in SLE patients, suggesting that these cytokines may be involved in the pathogenesis of the disease. Genetic polymorphisms at the promoter regions of IL-10 and TNFα genes have been associated with different constitutive and induced cytokine production. Given that individual steady-state levels of these molecules may deviate an initial immune response towards different forms of lymphocyte activation, functional genetic variants in their promoters could influence the development of SLE. The present review summarizes the information previously reported about the involvement of IL-10 and TNFα genetic variants on SLE appearance, clinical phenotype, and outcome. We show that, in spite of the heterogeneity of the populations studied, the existing knowledge points towards a relevant role of IL-10 and TNFα genotypes in SLE. PMID:20625422

  3. The Genotype-Tissue Expression (GTEx) project

    PubMed Central

    2014-01-01

    Genome-wide association studies have identified thousands of loci for common diseases, but for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions are likely to contribute to many disease phenotypes. The careful examination of gene expression and its relationship to genetic variation has thus become a critical next step in the elucidation of the genetic basis of common disease. Cell context is a key determinant of gene regulation; but to date, the challenge of collecting large numbers of diverse tissues in humans has largely precluded such studies outside of a few easily sampled cell types. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues. PMID:23715323

  4. The Blood Group A Genotype Determines the Level of Expression of the Blood Group A on Platelets But Not the Anti-B Isotiter

    PubMed Central

    Lehner, Barbara; Eichelberger, Beate; Jungbauer, Christof; Panzer, Simon

    2015-01-01

    Summary Background The extent of expression of the blood group A on platelets is controversial. Further, the relation between platelets' blood group A expression and the titers of isoagglutinins has not been thoroughly investigated, so far. Methods We evaluated the relation between the genotype with platelets' blood group A and H expression estimated by flow cytometry and the titers of isoagglutinins. Results The A expression varied between genotypes and within genotypes. However, the expression in A1 was stronger than in all other genotypes (p < 0.0001). An overlap of expression levels was apparent between homozygous A1A1 and heterozygous A1 individuals. Still, The A1A1 genotype is associated with a particularly high antigen expression (p = 0.009). Platelets' A expression in A2 versus blood group O donors was also significant (p = 0.007), but there was again an overlap of expression. The secretor status had only little influence on the expression (p = 0.18). Also, isoagglutinin titers were not associated with genotypes. Conclusion: To distinguish between A1 and A2 donors may reduce incompatible platelet transfusions and therefore be favorable on platelet transfusion increment. Clinical data are needed to support this notion. PMID:26733767

  5. Does Apolipoprotein E Genotype Increase Risk of Postoperative Delirium?

    PubMed Central

    Vasunilashorn, Sarinnapha; Ngo, Long; Kosar, Cyrus M.; Fong, Tamara G.; Jones, Richard N.

    2015-01-01

    Objectives To determine whether Apolipoprotein E (ApoE) is associated with postoperative delirium incidence, severity, and duration in older patients free of dementia at baseline. Design, Setting, Participants We examined 557 non-demented patients age ≥70 undergoing major non-cardiac surgery enrolled in the Successful Aging after Elective Surgery (SAGES) Study. Measurements We considered three ApoE measures: ε2, ε4 carriers vs. non-carriers, and a three-category ApoE measure. Delirium was determined using the Confusion Assessment Method (CAM) and chart review. We used generalized linear models to estimate the association between ApoE and delirium incidence, severity (peak CAM Severity [CAM-S] score), and days. Results ApoE ε2 and ε4 was present in 15% and 19% respectively, and postoperative delirium occurred in 24%. Among patients with delirium, the mean peak CAM-S score was 8.0 (standard deviation 4), with most patients experiencing one or two delirium days (51% or 28%, respectively). After adjusting for age, sex, surgical procedure, and preoperative cognitive function, ApoE ε4 and ε2 carrier status were not associated with postoperative delirium: RR for ε4=1.0, 95% confidence interval (CI) 0.7-1.5 and RR for ε2=0.9, 95% CI 0.6-1.4. No association between ApoE and delirium severity or number of delirium days was observed. Conclusions In older surgery patients free of dementia, our findings do not support the hypothesis that the ApoE genotype does not confer either risk or protection in postoperative delirium incidence, severity, or duration. Thus, an important genetic risk factor for Alzheimer's Disease does not affect risk of delirium. PMID:26238230

  6. Targeted stock identification using multilocus genotype 'familyprinting'

    USGS Publications Warehouse

    Letcher, B.H.; King, T.L.

    1999-01-01

    We present an approach to stock identification of small, targeted populations that uses multilocus microsatellite genotypes of individual mating adults to uniquely identify first- and second-generation offspring in a mixture. We call the approach 'familyprinting'; unlike DNA fingerprinting where tissue samples of individuals are matched, offspring from various families are assigned to pairs of parents or sets of four grandparents with known genotypes. The basic unit of identification is the family, but families can be nested within a variety of stock units ranging from naturally reproducing groups of fish in a small tributary or pond from which mating adults can be sampled to large or small collections of families produced in hatcheries and stocked in specific locations. We show that, with as few as seven alleles per locus using four loci without error, first-generation offspring can be uniquely assigned to the correct family. For second-generation applications in a hatchery more alleles per locus (10) and loci (10) are required for correct assignment of all offspring to the correct set of grandparents. Using microsatellite DNA variation from an Atlantic salmon (Salmo solar) restoration river (Connecticut River, USA), we also show that this population contains sufficient genetic diversity in sea-run returns for 100% correct first, generation assignment and 97% correct second-generation assignment using 14 loci. We are currently using first- and second-generation familyprinting in this population with the ultimate goal of identifying stocking tributary. In addition to within-river familyprinting, there also appears to be sufficient genetic diversity within and between Atlantic salmon populations for identification of 'familyprinted' fish in a mixture of multiple populations. We also suggest that second-generation familyprinting with multiple populations may also provide a tool for examining stock structure. Familyprinting with microsatellite DNA markers is a viable

  7. Automated genotyping of dinucleotide repeat markers

    SciTech Connect

    Perlin, M.W.; Hoffman, E.P. |

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  8. Experimental evidence for competitive growth advantage of genotype VII over VI: implications for foot-and-mouth disease virus serotype A genotype turnover in nature.

    PubMed

    Mohapatra, J K; Subramaniam, S; Singh, N K; Sanyal, A; Pattnaik, B

    2012-04-01

    In India, systematic genotype replacement has been observed for serotype A foot-and-mouth disease virus. After a decade of co-circulation of genotypes VI and VII, genotype VII emerged as the single dominant genotype since 2001. To derive possible explanations for such epochal evolution dynamics, in vitro intergenotype growth competition experiments involving both co- and superinfection regimes were conducted. Coinfection of BHK-21 cells demonstrated abrupt loss in the genotype VI viral load with commensurate increase in the load of genotype VII as measured by the genotype differentiating ELISA, RT-PCR and real-time RT-PCR. The superinfection dynamics was shaped by temporal spacing of infection, where the invading genotype VII took more number of passages than coinfection to eventually overtake the resident genotype VI. It was speculated that such superior replicative fitness of genotype VII could have been a possible factor for the ultimate dominance of genotype VII in nature.

  9. SNP discovery and genotyping using Genotyping-by-Sequencing in Pekin ducks

    PubMed Central

    Zhu, Feng; Cui, Qian-Qian; Hou, Zhuo-Cheng

    2016-01-01

    Genomic selection and genome-wide association studies need thousands to millions of SNPs. However, many non-model species do not have reference chips for detecting variation. Our goal was to develop and validate an inexpensive but effective method for detecting SNP variation. Genotyping by sequencing (GBS) can be a highly efficient strategy for genome-wide SNP detection, as an alternative to microarray chips. Here, we developed a GBS protocol for ducks and tested it to genotype 49 Pekin ducks. A total of 169,209 SNPs were identified from all animals, with a mean of 55,920 SNPs per individual. The average SNP density reached 1156 SNPs/MB. In this study, the first application of GBS to ducks, we demonstrate the power and simplicity of this method. GBS can be used for genetic studies in to provide an effective method for genome-wide SNP discovery. PMID:27845353

  10. A Tale of Two Genotypes: Consistency between Two High-Throughput Genotyping Centers

    PubMed Central

    Weeks, Daniel E.; Conley, Yvette P.; Ferrell, Robert E.; Mah, Tammy S.; Gorin, Michael B.

    2002-01-01

    Multiple genome-wide scans involving sib-pairs or limited pedigrees have been extensively used for a wide number of complex genetic conditions. Comparing data from two or more scans, as well as combining data, require an understanding of the sources of genotyping errors and data discrepancies. We have conducted two genome-wide scans for age-related maculopathy using the Center for Inherited Disease Research (CIDR) and the Mammalian Genotyping Service (MGS). Thirty individuals were typed in common, in order to allow for the alignment of alleles and comparison of the data sets. The analysis of these 8914 genotypes distributed over 321 markers in common demonstrated excellent agreement between these two laboratories, which have low rates of internal errors. Under the assumption that within each genotype, the smaller MGS allele should correspond to the smaller CIDR allele, the alleles align well between the two centers, with only a small fraction (less than 0.65%) of the aligned alleles showing large differences in sizes. However, since called allele sizes are integer “labels” which may not directly reflect the true underlying allele sizes, it is important to carefully prepare in advance if one wishes to merge data from different laboratories. In particular, it would not suffice to attempt to align alleles by typing only one or two controls in common. Fortunately, for the purposes of linkage analysis, one can avoid merging difficulties by simply carrying out linkage analyses using laboratory-specific allele labels and allele frequencies for each laboratory-specific subset of the data. PMID:11875031

  11. The mode of insertion of umbilical cord and vessels: association with maternal haemoglobin genotype, neonatal factors, and placental component volumes.

    PubMed

    Addai, F K; Quashie, F J; Ockleford, C D

    1994-02-01

    We investigated whether variations in mode of attachment of umbilical cords and vessels coincided with differences in maternal haemoglobin genotype and neonatal factors or placental micro-volumetric composition. The incidence of placentae with marginally inserted cords, or those in which umbilical vessels separated prior to insertion, was not statistically different in samples from sickle cell patients having haemoglobin-SS and haemoglobin-SC genotypes, as compared with haemoglobin-AA controls. Results obtained from analysis of variance (ANOVA) suggest that the mode of insertion (status) of umbilical vessels may have clinical significance, because it produced differences in the main effects associated with neonatal gestational age, placental weight, and placental index. Point counting stereology was employed to estimate the microscopic compartment volumes of placentae prior to an assessment of statistical association between the data obtained and the status of umbilical vessels and maternal haemoglobin genotype. Furcate placentae (with separated umbilical vessels) had statistically greater than normal volumes of villi, villous trophoblast, and syncytial knots. We deduce that furcate placentae are prone to early delivery, because they are heavier, having more voluminous villi with more trophoblast and syncytial knots than controls.

  12. Novel Hepatitis E Virus Genotype in Norway Rats, Germany

    PubMed Central

    Johne, Reimar; Heckel, Gerald; Plenge-Bönig, Anita; Kindler, Eveline; Maresch, Christina; Reetz, Jochen; Schielke, Anika

    2010-01-01

    Human hepatitis E virus infections may be caused by zoonotic transmission of virus genotypes 3 and 4. To determine whether rodents are a reservoir, we analyzed the complete nucleotide sequence of a hepatitis E–like virus from 2 Norway rats in Germany. The sequence suggests a separate genotype for this hepatotropic virus. PMID:20735931

  13. Systems properties of the Haemophilus influenzae Rd metabolic genotype.

    PubMed

    Edwards, J S; Palsson, B O

    1999-06-18

    Haemophilus influenzae Rd was the first free-living organism for which the complete genomic sequence was established. The annotated sequence and known biochemical information was used to define the H. influenzae Rd metabolic genotype. This genotype contains 488 metabolic reactions operating on 343 metabolites. The stoichiometric matrix was used to determine the systems characteristics of the metabolic genotype and to assess the metabolic capabilities of H. influenzae. The need to balance cofactor and biosynthetic precursor production during growth on mixed substrates led to the definition of six different optimal metabolic phenotypes arising from the same metabolic genotype, each with different constraining features. The effects of variations in the metabolic genotype were also studied, and it was shown that the H. influenzae Rd metabolic genotype contains redundant functions under defined conditions. We thus show that the synthesis of in silico metabolic genotypes from annotated genome sequences is possible and that systems analysis methods are available that can be used to analyze and interpret phenotypic behavior of such genotypes.

  14. Paternity testing and delivering trait-predictive genotypic data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the RosBREED project, the Genotyping Team (Team Leader: Nahla Bassil) leads the effort to obtain DNA data needed to enable marker-assisted breeding for critical fruit quality traits. These data are obtained from reference genotypes of apple, peach, cherry and strawberry carefully chosen to repres...

  15. Protein profiles and immunoreactivities of Acanthamoeba morphological groups and genotypes.

    PubMed

    Pumidonming, Wilawan; Koehsler, Martina; Leitsch, David; Walochnik, Julia

    2014-11-01

    Acanthamoeba is a free-living protozoan found in a wide variety of habitats. A classification of Acanthamoeba into currently eighteen genotypes (T1-T18) has been established, however, data on differences between genotypes on the protein level are scarce. The aim of this study was to compare protein and immunoreactivity profiles of Acanthamoeba genotypes. Thirteen strains, both clinical and non-clinical, from genotypes T4, T5, T6, T7, T9, T11 and T12, representing three morphological groups, were investigated for their protein profiles and IgG, IgM and IgA immunoreactivities. It was shown that protein and immunoreactivity profiles of Acanthamoeba genotypes T4, T5, T6, T7, T9, T11 and T12 are clearly distinct from each other, but the banding patterns correlate to the morphological groups. Normal human sera revealed anti-Acanthamoeba antibodies against isolates of all investigated genotypes, interestingly, however only very weak IgM and virtually no IgA immunoreactivity with T7 and T9, both representing morphological group I. The strongest IgG, IgM and IgA immunoreactivities were observed for genotypes T4, T5 and T6. Differences of both, protein and immunological patterns, between cytopathic and non-cytopathic strains, particularly within genotype T4, were not at the level of banding patterns, but rather in expression levels.

  16. Caffeoylquinic Acids in Storage Roots of Sixteen Sweetpotato Genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The contents of chlorogenic acid and the 3,4-, 3,5- and 4,5- isomers of dicaffeoylquinic acid (DCQA) in the storage root tissues of sixteen sweetpotato genotypes were determined. Averaged over genotypes, the contents of the four compounds were highest in the cortex, intermediate in the stele and lo...

  17. The genotype-phenotype map of an evolving digital organism.

    PubMed

    Fortuna, Miguel A; Zaman, Luis; Ofria, Charles; Wagner, Andreas

    2017-02-01

    To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.

  18. Genotype calling and haplotyping in parent-offspring trios

    PubMed Central

    Chen, Wei; Li, Bingshan; Zeng, Zhen; Sanna, Serena; Sidore, Carlo; Busonero, Fabio; Kang, Hyun Min; Li, Yun; Abecasis, Gonçalo R.

    2013-01-01

    Emerging sequencing technologies allow common and rare variants to be systematically assayed across the human genome in many individuals. In order to improve variant detection and genotype calling, raw sequence data are typically examined across many individuals. Here, we describe a method for genotype calling in settings where sequence data are available for unrelated individuals and parent-offspring trios and show that modeling trio information can greatly increase the accuracy of inferred genotypes and haplotypes, especially on low to modest depth sequencing data. Our method considers both linkage disequilibrium (LD) patterns and the constraints imposed by family structure when assigning individual genotypes and haplotypes. Using simulations, we show that trios provide higher genotype calling accuracy across the frequency spectrum, both overall and at hard-to-call heterozygous sites. In addition, trios provide greatly improved phasing accuracy—improving the accuracy of downstream analyses (such as genotype imputation) that rely on phased haplotypes. To further evaluate our approach, we analyzed data on the first 508 individuals sequenced by the SardiNIA sequencing project. Our results show that our method reduces the genotyping error rate by 50% compared with analysis using existing methods that ignore family structure. We anticipate our method will facilitate genotype calling and haplotype inference for many ongoing sequencing projects. PMID:23064751

  19. Ant colony optimization as a method for strategic genotype sampling.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A simulation study was carried out to develop an alternative method of selecting animals to be genotyped. Simulated pedigrees included 5000 animals, each assigned genotypes for a bi-allelic single nucleotide polymorphism (SNP) based on assumed allelic frequencies of 0.7/ 0.3 and 0.5/0.5. In addition...

  20. The genotype-phenotype map of an evolving digital organism

    PubMed Central

    Zaman, Luis; Wagner, Andreas

    2017-01-01

    To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable. PMID:28241039

  1. Genotype III Saint Louis Encephalitis Virus Outbreak, Argentina, 2005

    PubMed Central

    Ré, Viviana; Almirón, Walter R.; Farías, Adrián; Vázquez, Ana; Sanchez-Seco, María Paz; Aguilar, Javier; Spinsanti, Lorena; Konigheim, Brenda; Visintin, Andrés; García, Jorge; Morales, Maria Alejandra; Tenorio, Antonio; Contigiani, Marta

    2006-01-01

    Twenty-six years after it was last detected, Saint Louis encephalitis virus (SLEV) genotype III reemerged in 2005 in Córdoba, Argentina, where it caused an outbreak. Two genotype III SLEV strains were isolated from Culex quinquefasciatus. A 71.43% prevalence for neutralizing antibodies was found in domestic fowl in the homestead of a patient with encephalitis. PMID:17283629

  2. Preference of Gossypium genotypes to Bemisia argentifolii (Homoptera: Aleyrodidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several Gossypium species and genotypes were evaluated by in field and greehouse tests in the Lower Rio Grande Valley, Texas, for preference to the whitefly. Genotypes with G.hirsutum, G. barabadense, G. herbaceum, and G. arboreum were examined, including commercial and obsolete cultivars,(cultivar...

  3. Screening of Wheat Genotypes for Boron Efficiency in Bangladesh

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A number of Bangladeshi wheat genotypes (varieties and advanced lines) have been tested for boron efficiency through sand culture experiments over two years (2007-08 & 2008-09) against two Thai check varieties ‘Fang 60’ (boron efficient) and ‘SW41’ (boron inefficient). Performances of the genotypes ...

  4. Association of caveolin-1 genotypes with gastric cancer in Taiwan.

    PubMed

    Lin, Chih-Hsueh; Lin, Cheng-Chieh; Tsai, Chia-Wen; Chang, Wen-Shin; Yang, Chuan-Wei; Bau, Da-Tian

    2014-05-01

    Gastric cancer is one of the leading causes of tumor-related death worldwide, for which the prevalence and mortality rates are very high in developed countries. Caveolin-1 (Cav-1) is the main protein in the caveolin family and plays a role in tumorigenesis signaling. The contribution of CAV1 genetic variants to gastric cancer is still largely unknown. In the present study, we aimed to investigate the role of CAV1 genotypes in gastric cancer risk. We recruited 358 gastric patients and 358 cancer-free controls for CAV1 genotyping analysis. Six single-nucleotide polymorphisms (SNPs) of CAV1, C521A (rs1997623), G14713A (rs3807987), G21985A (12672038), T28608A (rs3757733), T29107A (rs7804372), and G32124A (rs3807992), were genotyped by the polymerase chain reaction-restriction fragment length polymorphism method. There was a significant difference between the gastric cancer and control groups in the genotypic frequency distribution of the CAV1 G14713A genotypes (p=1.24*10(-5)), with those carrying the A allele having a higher risk for gastric cancer compared to those with the GG genotype (p=0.0001). Our findings suggested that CAV1 genotype may determine the individual susceptibility to gastric cancer, and that the CAV1 G14713A genotype may serve as a novel biomarker for early detection and prediction of gastric cancer.

  5. Clonal propagation of walnut rootstock genotypes for genetic improvement 2011

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This year we produced more than 9700 liner-sized plantlets of 83 genotypes for use in greenhouse and field pest and disease resistance screening, growth in nurseries, and development of orchard trials. These included 6200 plants of 33 new Juglans microcarpa x ‘Serr’ paradox genotypes and 230 plants ...

  6. Spectral reflectance models for characterizing winter wheat genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Optimum wheat yield can be achieved by developing and growing the best genotype in the most suited environment. However, exhaustive field measurements are required to characterize plants in breeder plots for screening genotypes with desirable traits. Remote sensing tools have been shown to provide r...

  7. Regional selection of hybrid Nacional cacao genotypes in Coastal Ecuador

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent international demand for “nacional” flavour cacao has increased the need for local cacao producers in Ecuador to use high-yielding “nacional” hybrid genotypes. The relative potential of cacao genotypes over various environments needs to be assessed prior to final selection of potential candid...

  8. A new statistic and its power to infer membership in a genome-wide association study using genotype frequencies.

    PubMed

    Jacobs, Kevin B; Yeager, Meredith; Wacholder, Sholom; Craig, David; Kraft, Peter; Hunter, David J; Paschal, Justin; Manolio, Teri A; Tucker, Margaret; Hoover, Robert N; Thomas, Gilles D; Chanock, Stephen J; Chatterjee, Nilanjan

    2009-11-01

    Aggregate results from genome-wide association studies (GWAS), such as genotype frequencies for cases and controls, were until recently often made available on public websites because they were thought to disclose negligible information concerning an individual's participation in a study. Homer et al. recently suggested that a method for forensic detection of an individual's contribution to an admixed DNA sample could be applied to aggregate GWAS data. Using a likelihood-based statistical framework, we developed an improved statistic that uses genotype frequencies and individual genotypes to infer whether a specific individual or any close relatives participated in the GWAS and, if so, what the participant's phenotype status is. Our statistic compares the logarithm of genotype frequencies, in contrast to that of Homer et al., which is based on differences in either SNP probe intensity or allele frequencies. We derive the theoretical power of our test statistics and explore the empirical performance in scenarios with varying numbers of randomly chosen or top-associated SNPs.

  9. HPV genotypes detected in the oropharyngeal mucosa of HIV-infected men who have sex with men in Northern Italy.

    PubMed

    Martinelli, M; Mazza, F; Frati, E R; Fasolo, M M; Colzani, D; Bianchi, S; Fasoli, E; Amendola, A; Orlando, G; Tanzi, E

    2016-09-01

    The aim of this study was to investigate the epidemiological profile of HPV oropharyngeal infections in HIV-infected men who have sex with men. A total of 135 subjects were enrolled at the L. Sacco University Hospital (Milan, Italy) to evaluate their HPV oropharyngeal infection status at baseline and at a follow-up visit at least 12 months later. HPV DNA was detected from oropharyngeal swabs using an in-house nested PCR that amplifies a segment of the L1 gene. The PCR products were then sequenced and genotyped. A greater percentage of high-risk genotypes was identified compared to low-risk genotypes (13·7% vs. 6·9%, P < 0·05), and two uncommon alpha-HPV genotypes were detected, i.e. HPV-102 and HPV-114. HPV infection prevalence was 24·4% and the cumulative incidence was 24·1%. During the follow-up period, one case of HPV infection (HPV-33) persisted, while the overall rate of infection clearance was 58·3%. HPV oropharyngeal infection was widespread in the cohort examined, and most of the infections were transient and cleared within 12 months. These results may help to clarify the role of HPV in the oropharynx and may also improve our understanding of the need to implement preventive strategies in at-risk populations.

  10. Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype.

    PubMed

    Rausch, Philipp; Rehman, Ateequr; Künzel, Sven; Häsler, Robert; Ott, Stephan J; Schreiber, Stefan; Rosenstiel, Philip; Franke, Andre; Baines, John F

    2011-11-22

    The FUT2 (Secretor) gene is responsible for the presence of ABO histo-blood group antigens on the gastrointestinal mucosa and in bodily secretions. Individuals lacking a functional copy of FUT2 are known as "nonsecretors" and display an array of differences in susceptibility to infection and disease, including Crohn disease. To determine whether variation in resident microbial communities with respect to FUT2 genotype is a potential factor contributing to susceptibility, we performed 454-based community profiling of the intestinal microbiota in a panel of healthy subjects and Crohn disease patients and determined their genotype for the primary nonsecretor allele in Caucasian populations, W143X (G428A). Consistent with previous studies, we observe significant deviations in the microbial communities of individuals with Crohn disease. Furthermore, the FUT2 genotype explains substantial differences in community composition, diversity, and structure, and we identified several bacterial species displaying disease-by-genotype associations. These findings indicate that alterations in resident microbial communities may in part explain the variety of host susceptibilities surrounding nonsecretor status and that FUT2 is an important genetic factor influencing host-microbial diversity.

  11. Environmental metabolomics links genotype to phenotype and predicts genotype abundance in wild plant populations.

    PubMed

    Field, Katie J; Lake, Janice A

    2011-08-01

    'The Holy Grail' of plant ecology is to uncover rules that associate species and traits with environmental constraints, community composition and subsequent ecosystem functioning. These aims have been crystallized in recent years within the context of global climate change and environmental pollution, increasing the urgency of the need to predict how vegetation will respond across spatial scales. We investigated whether genetic diversity is associated with the way in which phenotypic plasticity within plant populations is realized and whether this is related to genotype abundance. We used environmental metabolomics to demonstrate biochemical variation between co-occurring genotypes of Carex caryophyllea L. A novel combined metabolomic/functional trait analysis was used to test the functionality of this variation in governing plasticity to variation in edaphic conditions, with particular reference to metabolic pathways that play important roles in growth-related traits. We show that genetic diversity within a wild C. caryophyllea population relates to differences in metabolic composition and functional traits in response to soil nutrient variation, influencing genotype abundance within a community. Our findings highlight the vital role genetic diversity plays within a population in facilitating plant phenotypic plasticity and the potential usefulness of environmental metabolomics to future ecological studies.

  12. Association of water spectral indices with plant and soil water relations in contrasting wheat genotypes

    PubMed Central

    Gutierrez, Mario; Reynolds, Matthew P.; Klatt, Arthur R.

    2010-01-01

    Spectral reflectance indices can be used to estimate the water status of plants in a rapid, non-destructive manner. Water spectral indices were measured on wheat under a range of water-deficit conditions in field-based yield trials to establish their relationship with water relations parameters as well as available volumetric soil water (AVSW) to indicate soil water extraction patterns. Three types of wheat germplasm were studied which showed a range of drought adaptation; near-isomorphic sister lines from an elite/elite cross, advanced breeding lines, and lines derived from interspecific hybridization with wild relatives (synthetic derivative lines). Five water spectral indices (one water index and four normalized water indices) based on near infrared wavelengths were determined under field conditions between the booting and grain-filling stages of crop development. Among all water spectral indices, one in particular, which was denominated as NWI-3, showed the most consistent associations with water relations parameters and demonstrated the strongest associations in all three germplasm sets. NWI-3 showed a strong linear relationship (r2 >0.6–0.8) with leaf water potential (ψleaf) across a broad range of values (–2.0 to –4.0 MPa) that were determined by natural variation in the environment associated with intra- and inter-seasonal affects. Association observed between NWI-3 and canopy temperature (CT) was consistent with the idea that genotypes with a better hydration status have a larger water flux (increased stomatal conductance) during the day. NWI-3 was also related to soil water potential (ψsoil) and AVSW, indicating that drought-adapted lines could extract more water from deeper soil profiles to maintain favourable water relations. NWI-3 was sufficiently sensitive to detect genotypic differences (indicated by phenotypic and genetic correlations) in water status at the canopy and soil levels indicating its potential application in precision phenotyping

  13. Genotyping of benzimidazole resistant and susceptible isolates of Haemonchus contortus from sheep by allele specific PCR.

    PubMed

    Mohanraj, Karthik; Subhadra, Subhra; Kalyanasundaram, Aravindan; Ilangopathy, Manikkavasagan; Raman, Muthusamy

    2017-03-01

    Extensive and indiscriminate use of the benzimidazole class of drugs has led to the onset of anthelmintic resistance. In tropical countries like India, Haemonchus contortus is the most pathogenic parasite infecting sheep and goats. The widespread presence of resistant helminths (especially H. contortus) threatens the livestock farming. The use of various drugs has led to single nucleotide polymorphism that causes specific amino acid substitutions in β-tubulin protein of H. contortus to confer resistance. This emphasizes the need for a survey on the present status of resistance in India. In this study, allele specific PCR was employed to screen the presence of a SNP, a thymine-to-adenine transversion which leads to substitution of amino acid in codon 200 of β-tubulin gene that is correlated specifically with BZ resistance. Third stage larvae (L3) from pooled faecal cultures of four organized sheep farms served as a source of genomic DNA for identification of H. contortus and further genotype analysis. A total of 1000 larvae was screened, out of which 673 larvae were identified as H. contortus. Among 673 H. contortus larvae, 539 larvae (80 %) were genotyped as homozygous resistant (rr) and remaining 134 (20 %) were heterozygous susceptible (Sr) by allele specific PCR. The concluded resistance status reasons out the failure of anthelmintic drug in treating ruminants. Immediate steps are needed to avoid further aggravation of the problem. Target selective treatment by reviewing the resistance status of individual drugs, appropriate use of anthelmintic drugs and other control strategies will provide a pragmatic option for delaying the further spread of anthelmintic resistance.

  14. National Tuberculosis Genotyping and Surveillance Network: Design and Methods

    PubMed Central

    Braden, Christopher R.; Schable, Barbara A.; Onorato, Ida M.

    2002-01-01

    The National Tuberculosis Genotyping and Surveillance Network was established in 1996 to perform a 5-year, prospective study of the usefulness of genotyping Mycobacterium tuberculosis isolates to tuberculosis control programs. Seven sentinel sites identified all new cases of tuberculosis, collected information on patients and contacts, and obtained patient isolates. Seven genotyping laboratories performed DNA fingerprinting analysis by the international standard IS6110 method. BioImage Whole Band Analyzer software was used to analyze patterns, and distinct patterns were assigned unique designations. Isolates with six or fewer bands on IS6110 patterns were also spoligotyped. Patient data and genotyping designations were entered in a relational database and merged with selected variables from the national surveillance database. In two related databases, we compiled the results of routine contact investigations and the results of investigations of the relationships of patients who had isolates with matching genotypes. We describe the methods used in the study. PMID:12453342

  15. Genotyping and phylogenetic analysis of Acanthamoeba isolates associated with keratitis.

    PubMed

    Risler, Arnaud; Coupat-Goutaland, Bénédicte; Pélandakis, Michel

    2013-11-01

    We examined a partial SSU-rDNA sequence from 20 Acanthamoeba isolates associated with keratitis infections. The phylogenetic tree inferred from this partial sequence allowed to assign isolates to genotypes. Among the 20 isolates examined, 16 were found to be of the T4 genotype, 2 were T3, 1 was a T5, and 1 was a T2, confirming the predominance of T4 in infections. However, the study highlighted other genotypes more rarely associated with infections, particularly the T2 genotype. Our study is the second one to detect that this genotype is associated with keratitis. Additionally, the phylogenetic analyses showed five main emerging clusters, T4/T3/T11, T2/T6, T10/T12/T14, T13/T16, and T7/T8/T9/T17, regularly obtained whichever method was used. A similar branching pattern was found when the full rDNA sequence was investigated.

  16. Genetic relationships among some hawthorn (Crataegus spp.) species and genotypes.

    PubMed

    Yilmaz, Kadir Ugurtan; Yanar, Makbule; Ercisli, Sezai; Sahiner, Hatice; Taskin, Tuncer; Zengin, Yasar

    2010-10-01

    The genus Crataegus is well distributed in Turkey as a wild plant, with numerous, inherently variable species and genotypes. RAPD markers were used to study 17 hawthorn genotypes belonging to Crataegus monogyna ssp. monogyna Jacq (2 genotypes), C. monogyna ssp. azarella Jacq (1), Crataegus pontica K.Koch (3), Crataegus orientalis var. orientalis Pallas Ex Bieb (3), Crataegus pseudoheterophylla Pojark (1), Crataegus aronia var. dentata Browicz (1), C. aronia var. aronia Browicz (4), and Crateagus x bornmuelleri Zabel (2). The 10 RAPD primers produced 72 polymorphic bands (88% polymorphism). A dendrogram based on Jaccard's index included four major groups and one outgroup according to taxa. The lowest genetic variability was observed within C. aronia var. aronia genotypes. The study demonstrated that RAPD analysis is efficient for genotyping wild-grown hawthorns.

  17. Civil Navigation Signal Status

    DTIC Science & Technology

    2015-04-29

    2015 04 29 _GPS Civil Navigation Signal Status UNCLASSIFIED/APPROVED FOR PUBLIC RELEASE UNCLASSIFIED/APPROVED FOR PUBLIC RELEASE Space and Missile...Systems Center Maj Michael Zollars 29 Apr 15 Civil Navigation Signal Status Report Documentation Page Form ApprovedOMB No. 0704-0188 Public...2015 4. TITLE AND SUBTITLE Civil Navigation Signal Status 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d

  18. Changing genotypes of cholera toxin (CT) of Vibrio cholerae O139 in Bangladesh and description of three new CT genotypes.

    PubMed

    Bhuiyan, Nurul A; Nusrin, Suraia; Alam, Munirul; Morita, Masatomo; Watanabe, Haruo; Ramamurthy, Thandavarayan; Cravioto, Alejandro; Nair, Gopinath Balakrish

    2009-11-01

    We determined the genotype of cholera toxin by amplifying and sequencing the B-subunit in a sequential collection of 90 strains of Vibrio cholerae O139 isolated over the past 13 years since its first description in 1992. Representative strains isolated during 1993-1997 harboured ctxB of El Tor type (genotype 3). Twenty-six strains isolated during 1999, 2001, 2005 and three strains isolated in 1998, 2000 and 2002 were identified to belong to new ctxB genotypes 4 and 5, respectively. Genotype 5 was similar to genotype 1 except at position 28 (D-->A). The genotype 6 was similar to genotype 4 except at position 34 (H-->P). The implication of switch in terms of function of the toxin and its impact on human disease is unclear. How this change has influenced their prevalence relative to that of V. cholerae O1 in human infection is also not clear. The other common virulence gene clusters including the Vibrio pathogenicity island-1, Vibrio seventh pandemic island (VSP)-I and VSP-II of V. cholerae O139 did not show any remarkable difference from that of the O1 El Tor strains. Overall, the majority of the O139 strains tested in this study were similar to the El Tor strains but had altered ctxB genotype. This change and the impact that it causes to the epidemiology of cholera caused by O139 should be closely monitored.

  19. Identification of a novel t17 genotype of acanthamoeba from environmental isolates and t10 genotype causing keratitis in Thailand.

    PubMed

    Nuprasert, Warisa; Putaporntip, Chaturong; Pariyakanok, Lalida; Jongwutiwes, Somchai

    2010-12-01

    We analyzed the nuclear small-subunit rRNA genes of Acanthamoeba isolates from freshwater sources (n=16) and from patients (n=6) in Bangkok and surrounding areas. The T10 genotype from a keratitis patient and a novel T17 genotype from water samples were diagnosed for the first time in this study.

  20. Comparing genotyping-by-sequencing and Single Nucleotide Polymorphism chip genotyping in Quantitive Trait Loci mapping in wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Array- or chip-based single nucleotide polymorphism (SNP) markers are widely used in genomic studies because of their abundance in a genome and cost less per data point compared to older marker technologies. Genotyping by sequencing (GBS), a relatively newer approach of genotyping, suggests equal or...

  1. CALIPSO Mission Status Update: Payload Status

    NASA Technical Reports Server (NTRS)

    Verhappen, Ron; Borchardt, Robert; MacDonnell, David; Cisewski, Mike

    2007-01-01

    The CALIPSO mission payload status update is presented. The contents include: 1) Wide Field Camera Overview; 2) WFC Temperatures; 3) WFC Voltages; 4) Imaging Infrared Radiometer (IIR) Health; 5) IIR Voltages; 6) Payload Control (PLC) Voltages; 7) PLC Temperatures; 8) Low Voltage Power Supply (LVPS) (CALOPS0025N); 9) PLC Radiation Effects; 10) SDS Status (CALOPS0020N); 11) CALIOP LIDAR; 12) Laser Energy Trends; 13) Laser Energy Zoom; 14) Laser Management Approach; 15) Green / Red Ratio; 16) Pedestal @ SHG Temperature Trends; 17) LOM Heater Duty Cycle Trends; 18) LOM Pressure Trends; 19) Boresight Trend; 20) 1064 Dark Noise Trend; 21) 532 SNR Trend; 22) Spike Trends; 23) LIDAR Highlights; 24) Backup Laser Status; and 25) Future Plans.

  2. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing.

    PubMed

    Campbell, Nathan R; Harmon, Stephanie A; Narum, Shawn R

    2015-07-01

    Genotyping-in-Thousands by sequencing (GT-seq) is a method that uses next-generation sequencing of multiplexed PCR products to generate genotypes from relatively small panels (50-500) of targeted single-nucleotide polymorphisms (SNPs) for thousands of individuals in a single Illumina HiSeq lane. This method uses only unlabelled oligos and PCR master mix in two thermal cycling steps for amplification of targeted SNP loci. During this process, sequencing adapters and dual barcode sequence tags are incorporated into the amplicons enabling thousands of individuals to be pooled into a single sequencing library. Post sequencing, reads from individual samples are split into individual files using their unique combination of barcode sequences. Genotyping is performed with a simple perl script which counts amplicon-specific sequences for each allele, and allele ratios are used to determine the genotypes. We demonstrate this technique by genotyping 2068 individual steelhead trout (Oncorhynchus mykiss) samples with a set of 192 SNP markers in a single library sequenced in a single Illumina HiSeq lane. Genotype data were 99.9% concordant to previously collected TaqMan(™) genotypes at the same 192 loci, but call rates were slightly lower with GT-seq (96.4%) relative to Taqman (99.0%). Of the 192 SNPs, 187 were genotyped in ≥90% of the individual samples and only 3 SNPs were genotyped in <70% of samples. This study demonstrates amplicon sequencing with GT-seq greatly reduces the cost of genotyping hundreds of targeted SNPs relative to existing methods by utilizing a simple library preparation method and massive efficiency of scale.

  3. Molecular characterization of the Hepatitis B virus genotypes in Colombia: a Bayesian inference on the genotype F.

    PubMed

    Alvarado Mora, Mónica Viviana; Romano, Camila Malta; Gomes-Gouvêa, Michele Soares; Gutierrez, Maria Fernanda; Botelho, Livia; Carrilho, Flair José; Pinho, João Renato Rebello

    2011-01-01

    Hepatitis B is a worldwide health problem affecting about 2 billion people and more than 350 million are chronic carriers of the virus. Nine HBV genotypes (A to I) have been described. The geographical distribution of HBV genotypes is not completely understood due to the limited number of samples from some parts of the world. One such example is Colombia, in which few studies have described the HBV genotypes. In this study, we characterized HBV genotypes in 143 HBsAg-positive volunteer blood donors from Colombia. A fragment of 1306 bp partially comprising HBsAg and the DNA polymerase coding regions (S/POL) was amplified and sequenced. Bayesian phylogenetic analyses were conducted using the Markov Chain Monte Carlo (MCMC) approach to obtain the maximum clade credibility (MCC) tree using BEAST v.1.5.3. Of all samples, 68 were positive and 52 were successfully sequenced. Genotype F was the most prevalent in this population (77%) - subgenotypes F3 (75%) and F1b (2%). Genotype G (7.7%) and subgenotype A2 (15.3%) were also found. Genotype G sequence analysis suggests distinct introductions of this genotype in the country. Furthermore, we estimated the time of the most recent common ancestor (TMRCA) for each HBV/F subgenotype and also for Colombian F3 sequences using two different datasets: (i) 77 sequences comprising 1306 bp of S/POL region and (ii) 283 sequences comprising 681 bp of S/POL region. We also used two other previously estimated evolutionary rates: (i) 2.60 × 10(-4)s/s/y and (ii) 1.5 × 10(-5)s/s/y. Here we report the HBV genotypes circulating in Colombia and estimated the TMRCA for the four different subgenotypes of genotype F.

  4. [Chemical characterization of Brazilian oat genotypes].

    PubMed

    Beber, Rosane Costa; de Francisco, Alicia; Alves, Antonio Carlos; de Sá, Roberta Marins; Ogliari, Paulo

    2002-01-01

    The chemical composition of oats has been poorly studied in Brazil. Therefore, the objective of this study was to characterize the main chemical constituents of Brazilian oat cultivars. This knowledge is essential for the utilization of this cereal in balanced diets, specially for individuals with high blood cholesterol, where the beta-glucans contribute to it's reduction. The analyzed genotipes were recommended by the Brazilian Oat Research Commission. The cultivars studied (CTC3, UFRGS7, UFRGS14, UPF7 and UPF16) showed high levels of protein (16.8%), lipids (6.84%) and beta-glucans (4.89%). The aminoacid profil of these samples was limiting only for lyisine, threonine and isoleucine. The other aminoacids had similar values to those recommended by the FAO. It was observed that all the studied variables suffered changes according to the interactions between genotype, locality and year of production. Cultivars UFRGS14, UFRGS7 and UPF16 were differentiated for their high contents of protein, lipids and beta-glucans, respectively.

  5. Genotyping of Canine parvovirus in western Mexico.

    PubMed

    Pedroza-Roldán, César; Páez-Magallan, Varinia; Charles-Niño, Claudia; Elizondo-Quiroga, Darwin; De Cervantes-Mireles, Raúl Leonel; López-Amezcua, Mario Alberto

    2015-01-01

    Canine parvovirus (CPV) is one of the most common infectious agents related to high morbidity rates in dogs. In addition, the virus is associated with severe gastroenteritis, diarrhea, and vomiting, resulting in high death rates, especially in puppies and nonvaccinated dogs. To date, there are 3 variants of the virus (CPV-2a, CPV-2b, and CPV-2c) circulating worldwide. In Mexico, reports describing the viral variants circulating in dog populations are lacking. In response to this deficiency, a total of 41 fecal samples of suspected dogs were collected from October 2013 through April 2014 in the Veterinary Hospital of the University of Guadalajara in western Mexico. From these, 24 samples resulted positive by polymerase chain reaction, and the viral variant was determined by restriction fragment length polymorphism. Five positive diagnosed samples were selected for partial sequencing of the vp2 gene and codon analysis. The results demonstrated that the current dominant viral variant in Mexico is CPV-2c. The current study describes the genotyping of CPV strains, providing valuable evidence of the dominant frequency of this virus in a dog population from western Mexico.

  6. Understanding Genotypes and Phenotypes in Epileptic Encephalopathies

    PubMed Central

    Helbig, Ingo; Tayoun, Abou Ahmad N.

    2016-01-01

    Epileptic encephalopathies are severe often intractable seizure disorders where epileptiform abnormalities contribute to a progressive disturbance in brain function. Often, epileptic encephalopathies start in childhood and are accompanied by developmental delay and various neurological and non-neurological comorbidities. In recent years, this concept has become virtually synonymous with a group of severe childhood epilepsies including West syndrome, Lennox-Gastaut syndrome, Dravet syndrome, and several other severe childhood epilepsies for which genetic factors are increasingly recognized. In the last 5 years, the field has seen a virtual explosion of gene discovery, raising the number of bona fide genes and possible candidate genes for epileptic encephalopathies to more than 70 genes, explaining 20-25% of all cases with severe early-onset epilepsies that had otherwise no identifiable causes. This review will focus on the phenotypic variability as a characteristic aspect of genetic epilepsies. For many genetic epilepsies, the phenotypic presentation can be broad, even in patients with identical genetic alterations. Furthermore, patients with different genetic etiologies can have seemingly similar clinical presentations, such as in Dravet syndrome. While most patients carry mutations in SCN1A, similar phenotypes can be seen in patients with mutations in PCDH19, CHD2, SCN8A, or in rare cases GABRA1 and STXBP1. In addition to the genotypic and phenotypic heterogeneity, both benign phenotypes and severe encephalopathies have been recognized in an increasing number of genetic epilepsies, raising the question whether these conditions represent a fluid continuum or distinct entities. PMID:27781027

  7. Porphyromonas gingivalis Fim-A genotype distribution among Colombians

    PubMed Central

    Jaramillo, Adriana; Parra, Beatriz; Botero, Javier Enrique; Contreras, Adolfo

    2015-01-01

    Introduction: Porphyromonas gingivalis is associated with periodontitis and exhibit a wide array of virulence factors, including fimbriae which is encoded by the FimA gene representing six known genotypes. Objetive: To identify FimA genotypes of P. gingivalis in subjects from Cali-Colombia, including the co-infection with Aggregatibacter actinomycetemcomitans, Treponema denticola, and Tannerella forsythia. Methods: Subgingival samples were collected from 151 people exhibiting diverse periodontal condition. The occurrence of P. gingivalis, FimA genotypes and other bacteria was determined by PCR. Results: P. gingivalis was positive in 85 patients. Genotype FimA II was more prevalent without reach significant differences among study groups (54.3%), FimA IV was also prevalent in gingivitis (13.0%). A high correlation (p= 0.000) was found among P. gingivalis, T. denticola, and T. forsythia co-infection. The FimA II genotype correlated with concomitant detection of T. denticola and T. forsythia. Conclusions: Porphyromonas gingivalis was high even in the healthy group at the study population. A trend toward a greater frequency of FimA II genotype in patients with moderate and severe periodontitis was determined. The FimA II genotype was also associated with increased pocket depth, greater loss of attachment level, and patients co-infected with T. denticola and T. forsythia. PMID:26600627

  8. Bayesian Gaussian Mixture Models for High-Density Genotyping Arrays

    PubMed Central

    Sabatti, Chiara; Lange, Kenneth

    2011-01-01

    Affymetrix's SNP (single-nucleotide polymorphism) genotyping chips have increased the scope and decreased the cost of gene-mapping studies. Because each SNP is queried by multiple DNA probes, the chips present interesting challenges in genotype calling. Traditional clustering methods distinguish the three genotypes of an SNP fairly well given a large enough sample of unrelated individuals or a training sample of known genotypes. This article describes our attempt to improve genotype calling by constructing Gaussian mixture models with empirically derived priors. The priors stabilize parameter estimation and borrow information collectively gathered on tens of thousands of SNPs. When data from related family members are available, our models capture the correlations in signals between relatives. With these advantages in mind, we apply the models to Affymetrix probe intensity data on 10,000 SNPs gathered on 63 genotyped individuals spread over eight pedigrees. We integrate the genotype-calling model with pedigree analysis and examine a sequence of symmetry hypotheses involving the correlated probe signals. The symmetry hypotheses raise novel mathematical issues of parameterization. Using the Bayesian information criterion, we select the best combination of symmetry assumptions. Compared to Affymetrix's software, our model leads to a reduction in no-calls with little sacrifice in overall calling accuracy. PMID:21572926

  9. Illumina human exome genotyping array clustering and quality control

    PubMed Central

    Guo, Yan; He, Jing; Zhao, Shilin; Wu, Hui; Zhong, Xue; Sheng, Quanhu; Samuels, David C; Shyr, Yu; Long, Jirong

    2015-01-01

    With the rise of high-throughput sequencing technology, traditional genotyping arrays are gradually being replaced by sequencing technology. Against this trend, Illumina has introduced an exome genotyping array that provides an alternative approach to sequencing, especially suited to large-scale genome-wide association studies (GWASs). the exome genotyping array targets the exome plus rare single-nucleotide polymorphisms (SNPs), a feature that makes it substantially more challenging to process than previous genotyping arrays that targeted common SNPs. Researchers have struggled to generate a reliable protocol for processing exome genotyping array data. The Vanderbilt epidemiology center, in cooperation with Vanderbilt Technologies for Advanced Genomics Analysis and Research Design (VANGARD), has developed a thorough exome chip–processing protocol. The protocol was developed during the processing of several large exome genotyping array-based studies, which included over 60,000 participants combined. The protocol described herein contains detailed clustering techniques and robust quality control procedures, and it can benefit future exome genotyping array–based GWASs. PMID:25321409

  10. Ovine prion protein genotype frequencies in northwestern China.

    PubMed

    Zhao, C-L; Wu, R; Liu, L; Li, F-D; Zhang, X-L; Wang, C; Wang, F; Diao, X-L; Guan, H-W; Wang, X; Zhou, L

    2012-06-21

    Anti-scrapie breeding programs have been initiated to screen for scrapie-resistant sheep based on ovine prion protein gene (PRNP) genotypes at codons 136, 154 and 171 in many countries, especially European Union member states. However, investigation of sheep PRNP genotypes is limited in China, despite the large number of sheep breeds. We analyzed 432 sheep of five different breeds from farms in northwestern China, using PCR-single-strand conformational polymorphism analysis (PCR-SSCP); the corresponding haplotypes of different PRNP alleles were cloned. PRNP allele genotyping was done by amplification refractory mutation system-PCR (ARMS-PCR), according to the haplotype clones of each PRNP allele. The validity of ARMS-PCR was checked by PCR-SSCP. Another 325 unknown PRNP genotypes of other sheep breeds were analyzed according to the established ARMS-PCR. Genotype frequencies of 757 sheep were analyzed with these two methods to evaluate susceptibility to scrapie in northwestern China. Relevant mutations were also detected at other sites. Both methods were effective for ovine PRNP allele genotyping, and the results of the analysis completely coincided. Scrapie-resistant genotypes were found to be uncommon, indicating a high risk for ovine scrapie in northwest China. In addition to codons 136, 154 and 171, we found numerous new mutations; nearly half of them were previously unreported. These sheep populations have a high degree of polymorphism at the PRNP locus.

  11. National Prociency Testing Result of CYP2D6*10 Genotyping for Adjuvant Tamoxifen Therapy in China

    PubMed Central

    Lin, Guigao; Zhang, Kuo; Yi, Lang; Han, Yanxi; Xie, Jiehong; Li, Jinming

    2016-01-01

    Tamoxifen has been successfully used for treating breast cancer and preventing cancer recurrence. Cytochrome P450 2D6 (CYP2D6) plays a key role in the process of metabolizing tamoxifen to its active moiety, endoxifen. Patients with variants of the CYP2D6 gene may not receive the full benefit of tamoxifen treatment. The CYP2D6*10 variant (the most common variant in Asians) was analyzed to optimize the prescription of tamoxifen in China. To ensure referring clinicians have accurate information for genotype-guided tamoxifen treatment, the Chinese National Center for Clinical Laboratories (NCCL) organized a national proficiency testing (PT) to evaluate the performance of laboratories providing CYP2D6*10 genotyping. Ten genomic DNA samples with CYP2D6 wild-type or CYP2D6*10 variants were validated by PCR-sequencing and sent to 28 participant laboratories. The genotyping results and pharmacogenomic test reports were submitted and evaluated by NCCL experts. Additional information regarding the number of samples tested, the accreditation/certification status, and detecting technology was also requested. Thirty-one data sets were received, with a corresponding analytical sensitivity of 98.2% (548/558 challenges; 95% confidence interval: 96.7–99.1%) and an analytic specificity of 96.5% (675/682; 95% confidence interval: 97.9–99.5%). Overall, 25/28 participants correctly identified CYP2D6*10 status in 10 samples; however, two laboratories made serious genotyping errors. Most of the essential information was included in the 20 submitted CYP2D6*10 test reports. The majority of Chinese laboratories are reliable for detecting the CYP2D6*10 variant; however, several issues revealed in this study underline the importance of PT schemes in continued external assessment and provision of guidelines. PMID:27603206

  12. Challenges in CYP2D6 phenotype assignment from genotype data: a critical assessment and call for standardization.

    PubMed

    Hicks, J Kevin; Swen, Jesse J; Gaedigk, Andrea

    2014-02-01

    The cytochrome P450 2D6 (CYP2D6) enzyme contributes to the metabolism and/or bioactivation of approximately 25% of clinically used drugs. The CYP2D6 gene locus is highly polymorphic and complex, and variants within this gene locus affect CYP2D6 enzymatic function resulting in a wide range of metabolic activity from little to no activity to ultrarapid metabolism. For many of the drugs metabolized by CYP2D6, the variation in metabolic activity is one of the most important factors responsible for interindividual drug response. Therefore, determining an individual's CYP2D6 phenotype, or metabolic status, will help identify individuals that may benefit from a change in drug or drug dosage. Genotype analysis has become the method of choice to predict a person's metabolic status. Numerous reference laboratories now offer CYP2D6 genotyping; however, there can be substantial differences in the number of genetic variants interrogated as well as test interpretation. Furthermore, there is no standardized process of how a CYP2D6 genotype result is translated into a phenotype assignment. This review summarizes the complexity of CYP2D6 genotyping and highlights the major challenges for phenotype classification. We call for the implementation of a universally accepted system for CYP2D6 phenotype assignment to promote consistency of test interpretation among reference laboratories and medical institutions. We propose a system that utilizes the CYP2D6 activity score system to place individuals into a continuum of activity scores - rather than using the traditional poor, intermediate, extensive and ultra-rapid metabolizer categorizations - and directly translating activity scores into clinically actionable recommendations.

  13. Nuclear proliferation status report. Status report

    SciTech Connect

    1992-07-01

    This report contains information concerning the nuclear proliferation status of the following countries: (1) Russia, (2) Ukraine, (3) Belarus, (4) Kazakhstan, (5) Israel, (6) India, (7) Pakistan, (8) South Africa, (9) North Korea, (10) Iraq, (11) Iran, (12) Lybia, (13) Algeria, (14) Syria, (15) Brazil, (16) Argentina, and (17) Taiwan.

  14. Genotype and Phenotype Analysis in Pediatric Patients with Cystinuria

    PubMed Central

    2017-01-01

    Cystinuria is an inherited disorder characterized by defective renal reabsorption of cystine and dibasic amino acids leading to nephrolithiasis. This study was conducted to analyze the genotypes and phenotypes of pediatric patients with cystinuria. Eight children from Seoul National University Hospital and Asan Medical Center presenting with cystinuria from January 2003 to June 2016 were retrospectively analyzed. Mutational studies were performed by direct sequencing. Two of the 8 were male and 6 were female. The median ages at onset and diagnosis were 1.5 (range, 0.3–13.6) and 2.6 (range, 0.7–16.7) years, respectively. The median followed up was 7.7 (range, 3.4–14.0) years. Mutational analyses were performed in 7 patients and revealed biallelic SLC3A1 mutations (AA genotype) in 4 patients, a single heterozygous SLC3A1 mutation (A- genotype) in 1 patient, biallelic SLC7A9 mutations (BB genotype) in 1 patient, and a single heterozygous SLC7A9 mutation (B- genotype) in 1 patient. Two of the mutations were novel. No genotype-phenotype correlations were observed, except for earlier onset age in patients with non-AA genotypes than in patients with the AA genotype. All patients suffered from recurrent attacks of symptomatic nephrolithiasis, which lead to urologic interventions. At the last follow-up, 3 patients had a mild-to-moderate degree of renal dysfunction. This is the first study of genotypic and phenotypic analyses of patients with cystinuria in Korea. PMID:28049243

  15. Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity.

    PubMed

    Parra, Gabriel I; Squires, R Burke; Karangwa, Consolee K; Johnson, Jordan A; Lepore, Cara J; Sosnovtsev, Stanislav V; Green, Kim Y

    2017-01-01

    Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII.4. The non-GII.4 genotypes were comprised of one or more intra-genotypic variants, with each variant containing strains that differed by only a few residues over several decades (remaining "static") and that have co-circulated with no clear epidemiologic pattern. In contrast, the GII.4 genotype presented the largest number of variants (>10) that have evolved over time with a clear pattern of periodic variant replacement. To expand our understanding of these two patterns of diversification ("static" versus "evolving"), we analyzed using NGS the nearly full-length norovirus genome in healthy individuals infected with GII.4, GII.6 or GII.17 viruses in different outbreak settings. The GII.4 viruses accumulated mutations rapidly within and between hosts, while the GII.6 and GII.17 viruses remained relatively stable, consistent with their diversification patterns. Further analysis of genetic relationships and natural history patterns identified groupings of certain genotypes into larger related clusters designated here as "immunotypes". We propose that "immunotypes" and their evolutionary patterns influence the prevalence of a particular norovirus genotype in the human population.

  16. Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity

    PubMed Central

    Karangwa, Consolee K.; Sosnovtsev, Stanislav V.

    2017-01-01

    Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII.4. The non-GII.4 genotypes were comprised of one or more intra-genotypic variants, with each variant containing strains that differed by only a few residues over several decades (remaining “static”) and that have co-circulated with no clear epidemiologic pattern. In contrast, the GII.4 genotype presented the largest number of variants (>10) that have evolved over time with a clear pattern of periodic variant replacement. To expand our understanding of these two patterns of diversification (“static” versus “evolving”), we analyzed using NGS the nearly full-length norovirus genome in healthy individuals infected with GII.4, GII.6 or GII.17 viruses in different outbreak settings. The GII.4 viruses accumulated mutations rapidly within and between hosts, while the GII.6 and GII.17 viruses remained relatively stable, consistent with their diversification patterns. Further analysis of genetic relationships and natural history patterns identified groupings of certain genotypes into larger related clusters designated here as “immunotypes”. We propose that “immunotypes” and their evolutionary patterns influence the prevalence of a particular norovirus genotype in the human population. PMID:28103318

  17. Imputation of missing genotypes: an empirical evaluation of IMPUTE

    PubMed Central

    Zhao, Zhenming; Timofeev, Nadia; Hartley, Stephen W; Chui, David HK; Fucharoen, Supan; Perls, Thomas T; Steinberg, Martin H; Baldwin, Clinton T; Sebastiani, Paola

    2008-01-01

    Background Imputation of missing genotypes is becoming a very popular solution for synchronizing genotype data collected with different microarray platforms but the effect of ethnic background, subject ascertainment, and amount of missing data on the accuracy of imputation are not well understood. Results We evaluated the accuracy of the program IMPUTE to generate the genotype data of partially or fully untyped single nucleotide polymorphisms (SNPs). The program uses a model-based approach to imputation that reconstructs the genotype distribution given a set of referent haplotypes and the observed data, and uses this distribution to compute the marginal probability of each missing genotype for each individual subject that is used to impute the missing data. We assembled genome-wide data from five different studies and three different ethnic groups comprising Caucasians, African Americans and Asians. We randomly removed genotype data and then compared the observed genotypes with those generated by IMPUTE. Our analysis shows 97% median accuracy in Caucasian subjects when less than 10% of the SNPs are untyped and missing genotypes are accepted regardless of their posterior probability. The median accuracy increases to 99% when we require 0.95 minimum posterior probability for an imputed genotype to be acceptable. The accuracy decreases to 86% or 94% when subjects are African Americans or Asians. We propose a strategy to improve the accuracy by leveraging the level of admixture in African Americans. Conclusion Our analysis suggests that IMPUTE is very accurate in samples of Caucasians origin, it is slightly less accurate in samples of Asians background, but substantially less accurate in samples of admixed background such as African Americans. Sample size and ascertainment do not seem to affect the accuracy of imputation. PMID:19077279

  18. Yugoslavia: Country Status Report.

    ERIC Educational Resources Information Center

    Robson, Barbara

    A survey of the status of language usage in Yugoslavia begins with an overview of the distribution of Serbo-Croatian, Croato-Serbian, Slovene, Macedonian, Albanian, and Hungarian, noting the status of all languages spoken there as nationality languages and as official languages in their speakers' republics. The equality of languages and cultures,…

  19. Morocco: Country Status Report.

    ERIC Educational Resources Information Center

    McFerren, Margaret

    A survey of the status of language usage in Morocco begins with an overview of the distribution and usage of Arabic, the official language, the Berber dialects, and French, an unofficial second language. The continuing high status and widespread use of French despite arabization efforts is discussed. A matrix follows that rates these languages and…

  20. X-33 Program Status

    NASA Technical Reports Server (NTRS)

    Dill, Charlie C.; Austin, Robert E. (Technical Monitor)

    2000-01-01

    The presentation briefly presents the current status of the program. The program's objectives and near term plans are stated. A brief description of the vehicle configuration, the technologies to be demonstrated and the missions to be flown are presented. Finally, a status of the vehicle assembly, the launch control center development and the significant test programs' accomplishments are presented.

  1. Genotype by Sex and Genotype by Age Interactions with Sedentary Behavior: The Portuguese Healthy Family Study

    PubMed Central

    Santos, Daniel M. V.; Katzmarzyk, Peter T.; Diego, Vincent P.; Blangero, John; Souza, Michele C.; Freitas, Duarte L.; Chaves, Raquel N.; Gomes, Thayse N.; Santos, Fernanda K.; Maia, José A. R.

    2014-01-01

    Sedentary behavior (SB) expression and its underlying causal factors have been progressively studied, as it is a major determinant of decreased health quality. In the present study we applied Genotype x Age (GxAge) and Genotype x Sex (GxSex) interaction methods to determine if the phenotypic expression of different SB traits is influenced by an interaction between genetic architecture and both age and sex. A total of 1345 subjects, comprising 249 fathers, 327 mothers, 334 sons and 325 daughters, from 339 families of The Portuguese Healthy Family Study were included in the analysis. SB traits were assessed by means of a 3-d physical activity recall, the Baecke and IPAQ questionnaires. GxAge and GxSex interactions were analyzed using SOLAR 4.0 software. Sedentary behaviour heritability estimates were not always statistically significant (p>0.05) and ranged from 3% to 27%. The GxSex and GxAge interaction models were significantly better than the single polygenic models for TV (min/day), EEsed (kcal/day), personal computer (PC) usage and physical activty (PA) tertiles. The GxAge model is also significantly better than the polygenic model for Sed (min/day). For EEsed, PA tertiles, PC and Sed, the GxAge interaction was significant because the genetic correlation between SB environments was significantly different from 1. Further, PC and Sed variance heterogeneity among distinct ages were observed. The GxSex interaction was significant for EEsed due to genetic variance heterogeneity between genders and for PC due to a genetic correlation less than 1 across both sexes. Our results suggest that SB expression may be influenced by the interactions between genotype with both sex and age. Further, different sedentary behaviors seem to have distinct genetic architectures and are differentially affected by age and sex. PMID:25302714

  2. Sympatric speciation: compliance with phenotype diversification from a single genotype.

    PubMed Central

    Kaneko, K; Yomo, T

    2000-01-01

    A novel mechanism for sympatric speciation that takes into account complex bioprocesses within each individual organism is proposed. According to dynamical systems theory, organisms with identical genotypes can possess differentiated physiological states and may coexist 'symbiotically' through appropriate mutual interaction. With mutations, the phenotypically differentiated organisms gradually come to possess distinct genotypes while maintaining their symbiotic relationship. This symbiotic speciation is robust against sexual recombination, because offspring of mixed parentage with intermediate genotypes are less fit than their parents. This leads to sterility of the hybrid. Accordingly, a basis for mating preference also arises. PMID:11133025

  3. Genotype-phenotype correlation in long QT syndrome

    PubMed Central

    Baskar, Shankar; Aziz, Peter F.

    2015-01-01

    Congenital long QT syndrome, caused by a cardiac channelopathy, is a leading cause of sudden cardiac death in the young population. In total, 16 genes have been implicated in this condition, with three genes being the most commonly affected. Long QT syndrome is one of the earliest conditions for which a genotype specific treatment was designed. This genotype-phenotype correlation extends to involve the clinical presentation, electrocardiographic manifestation and treatment strategies. It is necessary for the clinician treating these patients to be cognizant of the important role played by the genotype in order to best provide counseling and treatment options to this unique population. PMID:26779509

  4. From genotype to phenotype in Dravet disease.

    PubMed

    Gataullina, Svetlana; Dulac, Olivier

    2017-01-01

    Dravet syndrome combines clonic generalized, focal or unilateral seizures, beginning within the first year of life, often triggered by hyperthermia whatever its cause, including pertussis vaccination. Long-lasting febrile seizures are frequent in infancy and repeat status epilepticus (SE) has negative prognostic value. Massive myoclonus, rare absences, complex partial seizures and generalized spikes may appear several years later. Myoclonic status may occur in childhood, but acute encephalopathy with febrile SE followed by ischemic lesions and psychomotor impairment, the most severe condition, occurs mainly within the first five years of life. Generalized tonic-clonic and tonic seizures in sleep predominate in adulthood. Non epileptic manifestations appear with age, including intellectual disability, ataxia and crouching gait. Incidence of SUDEP is high, whatever the age. SCN1A haploinsufficiency producing NaV1.1 dysfunction mainly affects GABAergic neurons. In cortical interneurons it explains epilepsy, in cerebellum the ataxia, in basal ganglia and motor neurons the crouching gait, in hypothalamus the thermodysregulation and sleep troubles, and dysfunction in all these structures contributes to psychomotor delay. Valproate, stiripentol, topiramate and bromide are the basis of antiepileptic treatment, whereas inhibitors of sodium channel worsen the condition. Benzodiazepines seem to facilitate acute encephalopathy when given chronically, and they should be restricted to SE. Ketogenic diet is useful in both chronic and acute conditions. Only targeting SCN1A haploinsufficiency and NaV1.1 dysfunction could improve non epileptic manifestations of this condition that deserves being considered as a disease, not only as an epilepsy syndrome.

  5. Differing Von Hippel Lindau Genotype in Paired Primary and Metastatic Tumors in Patients with Clear Cell Renal Cell Carcinoma

    PubMed Central

    Vaziri, Susan A. J.; Tavares, Emmanuel J.; Golshayan, Ali R.; Rini, Brian I.; Aydin, Hakan; Zhou, Ming; Sercia, Linda; Wood, Laura; Ganapathi, Mahrukh K.; Bukowski, Ronald M.; Ganapathi, Ram

    2012-01-01

    In sporadic clear cell renal cell carcinoma (CCRCC), the von Hippel Lindau (VHL) gene is inactivated by mutation or methylation in the majority of primary (P) tumors. Due to differing effects of wild-type (WT) and mutant (MT) VHL gene on downstream signaling pathways regulating angiogenesis, VHL gene status could impact clinical outcome. In CCRCC, comparative genomic hybridization analysis studies have reported genetic differences between paired P and metastatic (M) tumors. We thus sequenced the VHL gene in paired tumor specimens from 10 patients to determine a possible clonal relationship between the P tumor and M lesion(s) in patients with CCRCC. Using paraffin-embedded specimens, genomic DNA from microdissected samples (>80% tumor) of paired P tumor and M lesions from all 10 patients, as well as in normal tissue from 6 of these cases, was analyzed. The DNA was used for PCR-based amplification of each of the 3 exons of the VHL gene. Sequences derived from amplified samples were compared to the wild-type VHL gene sequence (GenBank Accession No. AF010238). Methylation status of the VHL gene was determined using VHL methylation-specific PCR primers after DNA bisulfite modification. In 4/10 (40%) patients the VHL gene status differed between the P tumor and the M lesion. As expected, when the VHL gene was mutated in both the P tumor and M lesion, the mutation was identical. Further, while the VHL genotype differed between the primary tumor in different kidneys or multiple metastatic lesions in the same patient, the VHL germline genotype in the normal adjacent tissue was always wild-type irrespective of the VHL gene status in the P tumor. These results demonstrate for the first time that the VHL gene status can be different between paired primary and metastatic tissue in patients with CCRCC. PMID:22655276

  6. Phasing of many thousands of genotyped samples.

    PubMed

    Williams, Amy L; Patterson, Nick; Glessner, Joseph; Hakonarson, Hakon; Reich, David

    2012-08-10

    Haplotypes are an important resource for a large number of applications in human genetics, but computationally inferred haplotypes are subject to switch errors that decrease their utility. The accuracy of computationally inferred haplotypes increases with sample size, and although ever larger genotypic data sets are being generated, the fact that existing methods require substantial computational resources limits their applicability to data sets containing tens or hundreds of thousands of samples. Here, we present HAPI-UR (haplotype inference for unrelated samples), an algorithm that is designed to handle unrelated and/or trio and duo family data, that has accuracy comparable to or greater than existing methods, and that is computationally efficient and can be applied to 100,000 samples or more. We use HAPI-UR to phase a data set with 58,207 samples and show that it achieves practical runtime and that switch errors decrease with sample size even with the use of samples from multiple ethnicities. Using a data set with 16,353 samples, we compare HAPI-UR to Beagle, MaCH, IMPUTE2, and SHAPEIT and show that HAPI-UR runs 18× faster than all methods and has a lower switch-error rate than do other methods except for Beagle; with the use of consensus phasing, running HAPI-UR three times gives a slightly lower switch-error rate than Beagle does and is more than six times faster. We demonstrate results similar to those from Beagle on another data set with a higher marker density. Lastly, we show that HAPI-UR has better runtime scaling properties than does Beagle so that for larger data sets, HAPI-UR will be practical and will have an even larger runtime advantage. HAPI-UR is available online (see Web Resources).

  7. Host determinants of DNA alkylation and DNA repair activity in human colorectal tissue: O(6)-methylguanine levels are associated with GSTT1 genotype and O(6)-alkylguanine-DNA alkyltransferase activity with CYP2D6 genotype.

    PubMed

    Povey, A C; Hall, C N; Badawi, A F; Cooper, D P; Guppy, M J; Jackson, P E; O'Connor, P J; Margison, G P

    2001-08-22

    There is increasing evidence that alkylating agent exposure may increase large bowel cancer risk and factors which either alter such exposure or its effects may modify risk. Hence, in a cross-sectional study of 78 patients with colorectal disease, we have examined whether (i) metabolic genotypes (GSTT1, GSTM1, CYP2D6, CYP2E1) are associated with O(6)-methyldeoxyguanosine (O(6)-MedG) levels, O(6)-alkylguanine-DNA alkyltransferase (ATase) activity or K-ras mutations, and (ii) there was an association between ATase activity and O(6)-MedG levels. Patients with colon tumours and who were homozygous GSTT1(*)2 genotype carriers were more likely than patients who expressed GSTT1 to have their DNA alkylated (83 versus 32%, P=0.03) and to have higher O(6)-MedG levels (0.178+/-0.374 versus 0.016+/-0.023 micromol O(6)-MedG/mol dG, P=0.04) in normal, but not tumour, DNA. No such association was observed between the GSTT1 genotype and the frequency of DNA alkylation or O(6)-MedG levels in patients with benign colon disease or rectal tumours. Patients with colon tumours or benign colon disease who were CYP2D6-poor metabolisers had higher ATase activity in normal tissue than patients who were CYP2D6 extensive metabolisers or CYP2D6 heterozygotes. Patients with the CYP2E1 Dra cd genotype were less likely to have a K-ras mutation: of 55 patients with the wild-type CYP2E1 genotype (dd), 23 had K-ras mutations, whereas none of the 7 individuals with cd genotype had a K-ras mutation (P=0.04). No other associations were observed between GSTT1, GSTM1, CYP2D6 and CYP2E1 Pst genotypes and adduct levels, ATase activity or mutational status. O(6)-MedG levels were not associated with ATase activity in either normal or tumour tissue. However, in 15 patients for whom both normal and tumour DNA contained detectable O(6)-MedG levels, there was a strong positive association between the normal DNA/tumour DNA adduct ratio and the normal tissue/tumour tissue ATase ratio (r(2)=0.66, P=0.001). These

  8. Differential effects of the APOE genotype on brain function across the lifespan.

    PubMed

    Filippini, N; Ebmeier, K P; MacIntosh, B J; Trachtenberg, A J; Frisoni, G B; Wilcock, G K; Beckmann, C F; Smith, S M; Matthews, P M; Mackay, C E

    2011-01-01

    Increasing age and carrying an APOE ε4 allele are well established risk factors for Alzheimer's disease (AD). The earlier age of onset of AD observed in ε4-carriers may reflect an accelerated aging process. We recently reported that APOE genotype modulates brain function decades before the appearance of any cognitive or clinical symptoms. Here we test the hypothesis that APOE influences brain aging by comparing healthy ε4-carriers and non-carriers, using the same imaging protocol in distinct groups of younger and older healthy volunteers. A cross-sectional factorial design was used to examine the effects of age and APOE genotype, and their interaction, on fMRI activation during an encoding memory task. The younger (N=36; age range 20-35; 18 ε4-carriers) and older (35 middle-age/elderly; age range 50-78 years; 15 ε4-carriers) healthy volunteers taking part in the study were cognitively normal. We found a significant interaction between age and ε4-status in the hippocampi, frontal pole, subcortical nuclei, middle temporal gyri and cerebellum, such that aging was associated with decreased activity in e4-carriers and increased activity in non-carriers. Reduced cerebral blood flow was found in the older ε4-carriers relative to older non-carriers despite preserved grey matter volume. Overactivity of brain function in young ε4-carriers is disproportionately reduced with advancing age even before the onset of measurable memory impairment. The APOE genotype determines age-related changes in brain function that may reflect the increased vulnerability of ε4-carriers to late-life pathology or cognitive decline.

  9. Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria.

    PubMed

    Daniels, Rachel; Hamilton, Elizabeth J; Durfee, Katelyn; Ndiaye, Daouda; Wirth, Dyann F; Hartl, Daniel L; Volkman, Sarah K

    2015-11-10

    Despite decades of eradication efforts, malaria remains a global burden. Recent renewed interest in regional elimination and global eradication has been accompanied by increased genomic information about Plasmodium parasite species responsible for malaria, including characteristics of geographical populations as well as variations associated with reduced susceptibility to anti-malarial drugs. One common genetic variation, single-nucleotide polymorphisms (SNPs), offers attractive targets for parasite genotyping. These markers are useful not only for tracking drug resistance markers but also for tracking parasite populations using markers not under drug or other selective pressures. SNP genotyping methods offer the ability to track drug resistance as well as to fingerprint individual parasites for population surveillance, particularly in response to malaria control efforts in regions nearing elimination status. While informative SNPs have been identified that are agnostic to specific genotyping technologies, high-resolution melting (HRM) analysis is particularly suited to field-based studies. Compared to standard fluorescent-probe based methods that require individual SNPs in a single labeled probe and offer at best 10% sensitivity to detect SNPs in samples that contain multiple genomes (polygenomic), HRM offers 2-5% sensitivity. Modifications to HRM, such as blocked probes and asymmetric primer concentrations as well as optimization of amplification annealing temperatures to bias PCR towards amplification of the minor allele, further increase the sensitivity of HRM. While the sensitivity improvement depends on the specific assay, we have increased detection sensitivities to less than 1% of the minor allele. In regions approaching malaria eradication, early detection of emerging or imported drug resistance is essential for prompt response. Similarly, the ability to detect polygenomic infections and differentiate imported parasite types from cryptic local reservoirs

  10. Reduced Uptake of Family Screening in Genotype-Negative Versus Genotype-Positive Long QT Syndrome.

    PubMed

    Hanninen, Mikael; Klein, George J; Laksman, Zachary; Conacher, Susan S; Skanes, Allan C; Yee, Raymond; Gula, Lorne J; Leong-Sit, Peter; Manlucu, Jaimie; Krahn, Andrew D

    2015-08-01

    The acceptance and yield of family screening in genotype-negative long QT syndrome (LQTS) remains incompletely characterized. In this study of family screening for phenotype-definite Long QT Syndrome (LQTS, Schwartz score ≥3.5), probands at a regional Inherited Cardiac Arrhythmia clinic were reviewed. All LQTS patients were offered education by a qualified genetic counselor, along with materials for family screening including electronic and paper correspondence to provide to family members. Thirty-eight qualifying probands were identified and 20 of these had family members who participated in cascade screening. The acceptance of screening was found to be lower among families without a known pathogenic mutation (33 vs. 77 %, p = 0.02). A total of 52 relatives were screened; fewer relatives were screened per index case when the proband was genotype-negative (1.7 vs. 3.1, p = 0.02). The clinical yield of screening appeared to be similar irrespective of gene testing results (38 vs. 33 %, p = 0.69). Additional efforts to promote family screening among gene-negative long QT families may be warranted.

  11. Marker density and read depth for genotyping populations using genotyping-by-sequencing.

    PubMed

    Beissinger, Timothy M; Hirsch, Candice N; Sekhon, Rajandeep S; Foerster, Jillian M; Johnson, James M; Muttoni, German; Vaillancourt, Brieanne; Buell, C Robin; Kaeppler, Shawn M; de Leon, Natalia

    2013-04-01

    Genotyping-by-sequencing (GBS) approaches provide low-cost, high-density genotype information. However, GBS has unique technical considerations, including a substantial amount of missing data and a nonuniform distribution of sequence reads. The goal of this study was to characterize technical variation using this method and to develop methods to optimize read depth to obtain desired marker coverage. To empirically assess the distribution of fragments produced using GBS, ∼8.69 Gb of GBS data were generated on the Zea mays reference inbred B73, utilizing ApeKI for genome reduction and single-end reads between 75 and 81 bp in length. We observed wide variation in sequence coverage across sites. Approximately 76% of potentially observable cut site-adjacent sequence fragments had no sequencing reads whereas a portion had substantially greater read depth than expected, up to 2369 times the expected mean. The methods described in this article facilitate determination of sequencing depth in the context of empirically defined read depth to achieve desired marker density for genetic mapping studies.

  12. Genotypes are useful for more than genomic evaluation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New services that provide pedigree discovery, breed composition, mating programs, genomic inbreeding, fertility defects, and inheritance tracking all are possible from low cost genotyping, in addition to genomic evaluation. Genetic markers let breeders select among sibs before their phenotypes becam...

  13. Molecular methods for genotyping complex copy number polymorphisms.

    PubMed

    Cantsilieris, Stuart; Baird, Paul N; White, Stefan J

    2013-02-01

    Genome structural variation shows remarkable complexity with respect to copy number, sequence content and distribution. While the discovery of copy number polymorphisms (CNP) has increased exponentially in recent years, the transition from discovery to genotyping has proved challenging, particularly for CNPs embedded in complex regions of the genome. CNPs that are collectively common in the population and possess a dynamic range of copy numbers have proved the most difficult to genotype in association studies. This is in some part due to technical limitations of genotyping assays and the sequence properties of the genomic region being analyzed. Here we describe in detail the basis of a number of molecular techniques used to genotype complex CNPs, compare and contrast these approaches for determination of multi-allelic copy number, and discuss the potential application of these techniques in genetic studies.

  14. Special features of RAD Sequencing data: implications for genotyping

    PubMed Central

    Davey, John W; Cezard, Timothée; Fuentes-Utrilla, Pablo; Eland, Cathlene; Gharbi, Karim; Blaxter, Mark L

    2013-01-01

    Restriction site-associated DNA Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases and that most RAD loci will be accurately genotyped by existing tools. PMID:23110438

  15. A Genotyping Exercise for Pharmacogenetics in Pharmacy Practice

    PubMed Central

    Johnston, Jeffrey S.; Bao, Shengying; Kelley, Katherine A.

    2009-01-01

    Objective To develop a genotype exercise to improve pharmacy students’ comprehension of pharmacogenetic principles that apply to patient care. Design Deoxyribonucleic acid (DNA) was collected during class from 10 student volunteers and subjected to genotype analysis. The results were presented to the class and discussed in the context of a patient genetic counseling session. Students completed a survey instrument regarding their attitudes toward this learning experience. Assessment Students indicated that the exercise engaged them with the course content and would positively influence their ability to apply pharmacogenetic principles to patient care. Conclusion An applied genotype exercise enhanced learning of pharmacogenetic principles. Based on these findings, conducting a genotype exercise in a large classroom setting is feasible in terms of time and expense, and meaningful in terms of student satisfaction. PMID:19564986

  16. Forensic SNP Genotyping using Nanopore MinION Sequencing

    PubMed Central

    Cornelis, Senne; Gansemans, Yannick; Deleye, Lieselot; Deforce, Dieter; Van Nieuwerburgh, Filip

    2017-01-01

    One of the latest developments in next generation sequencing is the Oxford Nanopore Technologies’ (ONT) MinION nanopore sequencer. We studied the applicability of this system to perform forensic genotyping of the forensic female DNA standard 9947 A using the 52 SNP-plex assay developed by the SNPforID consortium. All but one of the loci were correctly genotyped. Several SNP loci were identified as problematic for correct and robust genotyping using nanopore sequencing. All these loci contained homopolymers in the sequence flanking the forensic SNP and most of them were already reported as problematic in studies using other sequencing technologies. When these problematic loci are avoided, correct forensic genotyping using nanopore sequencing is technically feasible. PMID:28155888

  17. The HIVdb system for HIV-1 genotypic resistance interpretation.

    PubMed

    Tang, Michele W; Liu, Tommy F; Shafer, Robert W

    2012-01-01

    The Stanford HIV Drug Resistance Database hosts a freely available online genotypic resistance interpretation system called HIVdb to help clinicians and laboratories interpret HIV-1 genotypic resistance tests. These tests are designed to assess susceptibility to nucleoside and nonnucleoside reverse transcriptase inhibitors (NRTI and NNRTI), protease inhibitors and integrase inhibitors. The HIVdb genotypic resistance interpretation system output consists of (1) a list of penalty scores for each antiretroviral (ARV) resistance mutation in a submitted sequence, (2) estimates of decreased NRTI, NNRTI, protease and integrase inhibitor susceptibility, and (3) comments about each ARV resistance mutation in the submitted sequence. The application's strengths are its convenience for submitting sequences, its quality control analysis, its transparency and its extensive comments. The Sierra Web service is an extension that enables laboratories analyzing many sequences to individualize the format of their results. The algorithm specification interface compiler makes it possible for HIVdb to provide results using a variety of different HIV-1 genotypic resistance interpretation algorithms.

  18. Forensic SNP Genotyping using Nanopore MinION Sequencing.

    PubMed

    Cornelis, Senne; Gansemans, Yannick; Deleye, Lieselot; Deforce, Dieter; Van Nieuwerburgh, Filip

    2017-02-03

    One of the latest developments in next generation sequencing is the Oxford Nanopore Technologies' (ONT) MinION nanopore sequencer. We studied the applicability of this system to perform forensic genotyping of the forensic female DNA standard 9947 A using the 52 SNP-plex assay developed by the SNPforID consortium. All but one of the loci were correctly genotyped. Several SNP loci were identified as problematic for correct and robust genotyping using nanopore sequencing. All these loci contained homopolymers in the sequence flanking the forensic SNP and most of them were already reported as problematic in studies using other sequencing technologies. When these problematic loci are avoided, correct forensic genotyping using nanopore sequencing is technically feasible.

  19. Special features of RAD Sequencing data: implications for genotyping.

    PubMed

    Davey, John W; Cezard, Timothée; Fuentes-Utrilla, Pablo; Eland, Cathlene; Gharbi, Karim; Blaxter, Mark L

    2013-06-01

    Restriction site-associated DNA Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases and that most RAD loci will be accurately genotyped by existing tools.

  20. Circulation of genotype-I hepatitis B virus in the primitive tribes of Arunachal Pradesh in early sixties and molecular evolution of genotype-I.

    PubMed

    Haldipur, Bangari P; Walimbe, Atul M; Arankalle, Vidya A

    2014-10-01

    Retrospective serologic screening of 1077 serum samples collected from the primitive tribe from north-eastern India in 1963 revealed high prevalence of HBV (15% HBsAg carrier rate) and HCV (7% anti-HCV positivity) and co-circulation of multiple HBV genotypes-A, C, D and G. Full genome sequencing classified all the G-genotype samples as genotype-I. Comparison of genotype-I-HBV full-genome sequences representing 1963 (n=5, this study) and 2005 (reported earlier) showed identical recombination break-points of genotypes-A/G/C. Genotype-C and genotype-C-fragment of I-genotype circulating in 1963 were distinctly different. The data demonstrates that the recombination events were not recent. Molecular clock analysis predicted existence of genotype-I in this tribe during 1920s.

  1. Advanced onset of puberty after metformin therapy in swine with thrifty genotype.

    PubMed

    Astiz, S; Gonzalez-Bulnes, A; Astiz, I; Barbero, A; Perez-Solana, M L; Garcia-Real, I

    2014-09-01

    The prevention and treatment of obesity in children is based on adequate nutrition and exercise plus antihyperglycaemic drugs. Currently, the incidence of childhood obesity is aggravated in ethnicities with thrifty genotype, but there is no available information on the effects of metformin therapy. The relative effects of lifestyle and metformin on patterns of growth, fattening, metabolic status and attainment of puberty were assessed in females of an obese swine model (Iberian gilts), allocated to three experimental groups (group A, obesogenic diet and scarce exercise; group DE, adequate diet and opportunity for exercise; and group DEM, adequate diet and opportunity for exercise plus metformin). Group A evidenced high weight, corpulence and adiposity, high plasma triglycerides and impairments of glucose regulation predisposing to insulin resistance. These features were favourably modulated by adequate lifestyle (group DE), and these effects were strengthened by metformin treatment (group DEM), which induced an improvement in body development by favouring muscle deposition. However, contrary to expectations, metformin advanced the onset of puberty. Metformin treatments would have positive effects on growth patterns, adiposity and metabolic features of young females from ethnicities with thrifty genotype or developing leptin resistance, but a negative effect by advancing the attainment of puberty. This study provides a warning regarding the use of metformin, without further studies, in girls from these ethnicities.

  2. A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites

    PubMed Central

    Côté, Nathalie M. L.; Daligault, Julien; Pruvost, Mélanie; Bennett, E. Andrew; Gorgé, Olivier; Guimaraes, Silvia; Capelli, Nicolas; Le Bailly, Matthieu; Geigl, Eva-Maria; Grange, Thierry

    2016-01-01

    Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies. PMID:26752051

  3. HIV infection among U.S. Army and Air Force military personnel: sociodemographic and genotyping analysis.

    PubMed

    Singer, Darrell E; Bautista, Christian T; O'Connell, Robert J; Sanders-Buell, Eric; Agan, Brian K; Kijak, Gustavo H; Hakre, Shilpa; Sanchez, Jose L; Sateren, Warren B; McCutchan, Francine E; Michael, Nelson L; Scott, Paul T

    2010-08-01

    Since 1985, the U.S. Department of Defense has periodically screened all military personnel for HIV allowing for the monitoring of the infection in this dynamic cohort population. A nested case-control study was performed to study sociodemographics, overseas assignment, and molecular analysis of HIV. Cases were newly identified HIV infections among U.S. Army and Air Force military personnel from 2000 to 2004. Controls were frequency matched to cases by gender and date of case first positive HIV screening test. Genotyping analysis was performed using high-throughput screening assays and partial genome sequencing. HIV was significantly associated with black race [odds ratio (OR) = 6.65], single marital status (OR = 4.45), and age (OR per year = 1.07). Ninety-seven percent were subtype B and 3% were non-B subtypes (A3, CRF01_AE, A/C recombinant, G, CRF02_AG). Among cases, overseas assignment in the period at risk prior to their first HIV-positive test was associated with non-B HIV subtype infection (OR = 8.44). Black and single military personnel remain disproportionately affected by HIV infection. Most non-B HIV subtypes were associated with overseas assignment. Given the increased frequency and length of assignments, and the expanding HIV genetic diversity observed in this population, there is a need for active HIV genotyping surveillance and a need to reinforce primary HIV prevention efforts.

  4. Molecular detection and genotyping of Acanthamoeba spp. among stray dogs using conjunctival swab sampling.

    PubMed

    Karakuş, Mehmet; Aykur, Mehmet; Özbel, Yusuf; Töz, Seray; Dağcı, Hande

    2016-12-01

    Acanthamoeba is one of the most common free-living amoebas (FLA) that present in environment. In humans, Acanthamoeba can cause an infection of the eye termed Acanthamoeba keratitis, which mostly occurs in contact lens wearers. In the present study, we aimed to screen the presence of Acanthamoeba DNA in stray dogs using previously collected conjunctival swab samples in a hyper-endemic area for canine leishmaniasis. Totally, 184 dogs were included in the study and 27 of them (14.6%) were found positive for Acanthamoeba according to the 18s rRNA gene sequencing. Two different genotypes (T4 and T5) were identified and T5 was firstly reported in Turkey in the present study. Statistical analysis was performed and no correlation was found between Leishmania and Acanthamoeba positivity (P<0.05). To best of our knowledge, this is the first study conducted to screen Acanthamoeba among stray dogs. Further studies are necessary to reveal the infection status and genotypes among dogs and its possible correlation with leishmaniasis.

  5. Two major mumps genotype G variants dominated recent mumps outbreaks in the Netherlands (2009-2012).

    PubMed

    Gouma, Sigrid; Sane, Jussi; Gijselaar, Daphne; Cremer, Jeroen; Hahné, Susan; Koopmans, Marion; van Binnendijk, Rob

    2014-05-01

    During three seasons of mumps outbreaks in the Netherlands (September 2009-August 2012), 822 mumps cases were laboratory-confirmed at the National Institute for Public Health and the Environment (RIVM). Most patients were vaccinated young adults. Given the protracted endemic circulation, we studied the genetic diversity and changes of mumps virus over a period of 3 years. Phylogenetic analysis of the small hydrophobic (SH) gene (316 bp) was performed on a representative set of 808 specimens that tested positive for mumps via PCR. Additionally, the haemagglutinin/neuraminidase (HN) gene (1749 bp) and fusion (F) gene (1617 bp) were sequenced for a subset of samples (n = 17). Correlations between different sequence types and epidemiological and clinical data were investigated. The outbreaks in the Netherlands were dominated by two SH gene sequence types within genotype G, termed MuVs/Delft.NLD/03.10 (variant 1) and MuVs/Scheemda.NLD/12.10 (variant 2). Sequence analysis of the HN and F genes indicated that the outbreaks were initiated by separately introduced genetic lineages. The predominance of variant 2 by the end of the first outbreak season could not be explained by any of the epidemiological factors investigated. Orchitis was more frequently reported in males infected with variant 2, irrespective of age and vaccination status. These findings illustrate genetic heterogeneity of an emerging mumps genotype, and raise questions about the mechanisms driving mumps epidemiology and immunity in relation to vaccination.

  6. Apolipoprotein E genotype may influence urinary gammacarboxyglutamate (Gla) concentrations in young individuals.

    PubMed

    Crăciun, Alexandra M; Vermeer, Cees

    2013-09-01

    Upon degradation of vitamin K-dependent proteins (known as Gla-proteins) the free aminoacid Gla cannot be re-utilized and is excreted in the urine, where it can be used as an overall marker for vitamin K status. We report the urinary Gla excretion values in first morning void urine for healthy young Romanian subjects from birth, childhood and young adulthood. In these subjects we have evaluated age, gender and apo E genotype as potential confounders. The urinary free Gla/creat ratio (Gla/creat, mg/g) was highest in newborns (34.8 ± 19.5; p < 0.001), than fell in the group 4 to 48 months old (13.1 ± 11.1) to levels that were not significantly different from the young adult group (18.3 ± 5.5). No gender-related differences were observed in Gla/creat in newborns and young children, but Gla excretion in women was higher than in men (28.6%; p < 0.029). Remarkably, Gla excretion in subjects bearing the apo ε2+ allele was significantly lower (11.9 ± 4.2) than in those bearing combinations of the ε3+ and ε4+ alleles (20.3 ± 4.1). The novelty of this study resides in the evaluation of urinary Gla excretion in relation with apo E genotype, suggesting that apo ε2 allele is a risk factor for developing vitamin K insufficiency.

  7. Phenotypic variability in X-linked ocular albinism: Relationship to linkage genotypes

    SciTech Connect

    Schnur, R.E. |; Wick, P.A.; Bailey, C.; Rebbeck, T.; Weleber, R.G.; Wagstaff, J.; Grix, A.W.; Pagon, R.A.; Hockey, A.; Edwards, M.J.

    1994-09-01

    One hundred nineteen individuals from 11 families with X-linked ocular albinism (OA1) were studied with respect to both their clinical phenotypes and their linkage genotypes. In a four-generation Australian family, two affected males and an obligatory carrier lacked cutaneous melanin macroglobules (MMGs); ocular features were identical to those of Nettleship-Falls OA1. Four other families had more unusual phenotypic features in addition to OA1. All OA1 families were genotyped at DXS16, DXS85, DXS143, STS, and DXS452 and for a CA-repeat polymorphism at the Kallmann syndrome locus (KAL). Separate two-point linkage analyses were performed for the following: group A, six families with biopsy-proved MMGs in at least one affected male; group B, four families whose biopsy status was not known; and group C, OA-9 only (16 samples), the family without MMGs. At the set of loci closest to OA1, there is no clear evidence in our data set for locus heterogeneity between groups A and C or among the four other families with complex phenotypes. Combined multipoint analysis (LINKMAP) in the 11 families and analysis of individual recombination events confirms that the major locus for OA1 resides within the DXS85-DXS143 interval. The authors suggest that more detailed clinical evaluations of OA1 individuals and families should be performed for future correlation with specific mutations in candidate OA1 genes. 29 refs., 5 figs., 4 tabs.

  8. Variation in genotype and higher virulence of a strain of Sporothrix schenckii causing disseminated cutaneous sporotrichosis.

    PubMed

    Zhang, Zhenying; Liu, Xiaoming; Lv, Xuelian; Lin, Jingrong

    2011-12-01

    Sporotrichosis is usually a localized, lymphocutaneous disease, but its disseminated type was rarely reported. The main objective of this study was to identify specific DNA sequence variation and virulence of a strain of Sporothrix schenckii isolated from the lesion of disseminated cutaneous sporotrichosis. We confirmed this strain to be S. schenckii by(®) tubulin and chitin synthase gene sequence analysis in addition to the routine mycological and partial ITS and NTS sequencing. We found a 10-bp deletion in the ribosomal NTS region of this strain, in reference to the sequence of control strains isolated from fixed cutaneous sporotrichosis. After inoculated into immunosuppressed mice, this strain caused more extensive system involvement and showed stronger virulence than the control strain isolated from a fixed cutaneous sporotrichosis. Our study thus suggests that different clinical manifestation of sporotrichosis may be associated with variation in genotype and virulence of the strain, independent of effects due to the immune status of the host.

  9. Status Epilepticus and Refractory Status Epilepticus Management

    PubMed Central

    Abend, Nicholas S.; Bearden, David; Helbig, Ingo; McGuire, Jennifer; Narula, Sona; Panzer, Jessica A.; Topjian, Alexis; Dlugos, Dennis J.

    2014-01-01

    Status epilepticus (SE) describes persistent or recurring seizures without a return to baseline mental status, and is a common neurologic emergency. SE can occur in the context of epilepsy or may be symptomatic of a wide range of underlying etiologies. The clinician’s aim is to rapidly institute care that simultaneously stabilizes the patient medically, identifies and manages any precipitant conditions, and terminates seizures. Seizure management involves “emergent” treatment with benzodiazepines followed by “urgent” therapy with other anti-seizure medications. If seizures persist then refractory SE is diagnosed and management options include additional anti-seizure medications or infusions of midazolam or pentobarbital. This paper reviews the management of pediatric SE and RSE. PMID:25727508

  10. Genotyping of Global Yersinia Pestis Isolates by Using IS285

    DTIC Science & Technology

    2006-11-01

    ecological variants. In this work , we consider literature data, as well as our previous and new results on genotyping of global Y. pestis strains. We come...as a biological weapon, one should have efficient tools of genotyping. In this work , we analyze literature data and present our results of Y...GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S

  11. Tissue persistence of parvovirus B19 genotypes in asymptomatic persons.

    PubMed

    Corcioli, Fabiana; Zakrzewska, Krystyna; Rinieri, Alessio; Fanci, Rosa; Innocenti, Massimo; Civinini, Roberto; De Giorgi, Vincenzo; Di Lollo, Simonetta; Azzi, Alberta

    2008-11-01

    Parvovirus B19 (B19V) can persist in immunocompetent symptomatic and non-symptomatic individuals, as demonstrated by the finding of viral DNA in different tissues, in absence of viremia and of anti-B19V IgM. The spread and the nature of this phenomenon have not been clearly determined. In order to investigate the frequency of persistence and the tissue distribution of the three genotypes of B19V, the viral load of the persistent virus and its expression in the affected tissues, 139 tissue samples and 102 sera from 139 asymptomatic individuals have been analyzed by consensus PCRs and genotype specific PCRs for B19V detection and genotyping. Viral load was measured by real time PCR and viral mRNAs were detected by RT-PCR. Altogether, 51% individuals carried B19V DNA, more frequently in solid tissues (65%) than in bone marrow (20%). Genotype 1 was found in 28% tissue samples, genotype 2 in 68% and genotype 3 in 3% only. Viral load ranged from less then 10 copies to 7 x 10(4) copies per 10(6) cells, with the exception of two samples of myocardium with about 10(6) copies per 10(6) cells. mRNA of capsid proteins was present in two bone marrow samples only. In conclusion, in asymptomatic individuals B19V persistence is more common in solid tissues than in bone marrow, and genotype 2 persists more frequently than genotype 1. The results suggest that the virus persists without replicating, at sub-immunogenic levels.

  12. Sex and PRNP genotype determination in preimplantation caprine embryos.

    PubMed

    Guignot, F; Perreau, C; Cavarroc, C; Touzé, J-L; Pougnard, J-L; Dupont, F; Beckers, J-F; Rémy, B; Babilliot, J-M; Bed'Hom, B; Lamorinière, J M; Mermillod, P; Baril, G

    2011-08-01

    The objective of this study was to test the accuracy of genotype diagnosis after whole amplification of DNA extracted from biopsies obtained by trimming goat embryos and to evaluate the viability of biopsied embryos after vitrification/warming and transfer. Whole genome amplification (WGA) was performed using Multiple Displacement Amplification (MDA). Sex and prion protein (PRNP) genotypes were determined. Sex diagnosis was carried out by PCR amplification of ZFX/ZFY and Y chromosome-specific sequences. Prion protein genotype determination was performed on codons 142, 154, 211, 222 and 240. Embryos were collected at day 7 after oestrus and biopsied either immediately after collection (blastocysts and expanded blastocysts) or after 24 h of in vitro culture (compacted morulae). Biopsied embryos were frozen by vitrification. Vitrified whole embryos were kept as control. DNA of biopsies was extracted and amplified using MDA. Sex diagnosis was efficient for 97.4% of biopsies and PRNP genotyping was determined in 78.7% of biopsies. After embryo transfer, no significant difference was observed in kidding rate between biopsied and vitrified control embryos, whereas embryo survival rate was different between biopsied and whole vitrified embryos (p = 0.032). At birth, 100% of diagnosed sex and 98.2% of predetermined codons were correct. Offspring PRNP profiles were in agreement with parental genotype. Whole genome amplification with MDA kit coupled with sex diagnosis and PRNP genotype predetermination are very accurate techniques to genotype goat embryos before transfer. These novel results allow us to plan selection of scrapie-resistant genotypes and kid sex before transfer of cryopreserved embryo.

  13. Global Surveillance of Emerging Influenza Virus Genotypes by Mass Spectrometry

    DTIC Science & Technology

    2007-05-30

    seasons (2005–2006) showed evidence for emergence and establishment of new genotypes of circulating H3N2 strains worldwide. Mixed viral quasispecies were...showedevidence for emergence and establishment of new genotypes of circulating H3N2 strains worldwide. Mixed viral quasispecies were found in approximately 1 % of...type AADFAA and single-nucleotide variations AAHFAA and AADFBB, respectively, providing a snapshot of enduring ‘‘fit’’ quasispecies contributors and of

  14. The value of molecular stratification for CEBPA(DM) and NPM1(MUT) FLT3(WT) genotypes in older patients with acute myeloid leukaemia.

    PubMed

    Dickson, Glenda J; Bustraan, Sophia; Hills, Robert K; Ali, Akbar; Goldstone, Anthony H; Burnett, Alan K; Linch, David C; Gale, Rosemary E

    2016-02-01

    Older adult patients (≥60 years) with acute myeloid leukaemia (AML) are generally considered to be poor-risk and there is limited information available regarding risk stratification based on molecular characterization in this age group, particularly for the double-mutant CEBPA (CEBPA(DM) ) genotype. To investigate whether a molecular favourable-risk genotype can be identified, we investigated CEBPA, NPM1 and FLT3 status and prognostic impact in a cohort of 301 patients aged 60 years or more with intermediate-risk cytogenetics, all treated intensively. Overall survival (OS) at 1 year was highest in the 12 patients (4%) that were CEBPA(DM) compared to the 76 (28%) with a mutant NPM1 and wild-type FLT3 (NPM1(MUT) FLT3(WT) ) genotype or all other patients (75%, 54%, 33% respectively), with median survival 15·2, 13·6 and 6·6 months, although the benefit was short-term (OS at 3 years 17%, 29%, 12% respectively). Combination of the CEBPA(DM) and NPM1(MUT) FLT3(WT) genotype patients defined a molecular group with favourable prognosis (P < 0·0001 in multivariate analysis), with 57% of patients alive at 1 year compared to 33% for all other patients. Knowledge of genotype in older cytogenetically intermediate-risk patients might influence therapy decisions.

  15. Spatial analysis to support geographic targeting of genotypes to environments

    PubMed Central

    Hyman, Glenn; Hodson, Dave; Jones, Peter

    2013-01-01

    Crop improvement efforts have benefited greatly from advances in available data, computing technology, and methods for targeting genotypes to environments. These advances support the analysis of genotype by environment interactions (GEI) to understand how well a genotype adapts to environmental conditions. This paper reviews the use of spatial analysis to support crop improvement research aimed at matching genotypes to their most appropriate environmental niches. Better data sets are now available on soils, weather and climate, elevation, vegetation, crop distribution, and local conditions where genotypes are tested in experimental trial sites. The improved data are now combined with spatial analysis methods to compare environmental conditions across sites, create agro-ecological region maps, and assess environment change. Climate, elevation, and vegetation data sets are now widely available, supporting analyses that were much more difficult even 5 or 10 years ago. While detailed soil data for many parts of the world remains difficult to acquire for crop improvement studies, new advances in digital soil mapping are likely to improve our capacity. Site analysis and matching and regional targeting methods have advanced in parallel to data and technology improvements. All these developments have increased our capacity to link genotype to phenotype and point to a vast potential to improve crop adaptation efforts. PMID:23515351

  16. Optimal genotype determination in highly multiplexed SNP data.

    PubMed

    Moorhead, Martin; Hardenbol, Paul; Siddiqui, Farooq; Falkowski, Matthew; Bruckner, Carsten; Ireland, James; Jones, Hywel B; Jain, Maneesh; Willis, Thomas D; Faham, Malek

    2006-02-01

    High-throughput genotyping technologies that enable large association studies are already available. Tools for genotype determination starting from raw signal intensities need to be automated, robust, and flexible to provide optimal genotype determination given the specific requirements of a study. The key metrics describing the performance of a custom genotyping study are assay conversion, call rate, and genotype accuracy. These three metrics can be traded off against each other. Using the highly multiplexed Molecular Inversion Probe technology as an example, we describe a methodology for identifying the optimal trade-off. The methodology comprises: a robust clustering algorithm and assessment of a large number of data filter sets. The clustering algorithm allows for automatic genotype determination. Many different sets of filters are then applied to the clustered data, and performance metrics resulting from each filter set are calculated. These performance metrics relate to the power of a study and provide a framework to choose the most suitable filter set to the particular study.

  17. High-Throughput Genotyping with Single Nucleotide Polymorphisms

    PubMed Central

    Ranade, Koustubh; Chang, Mau-Song; Ting, Chih-Tai; Pei, Dee; Hsiao, Chin-Fu; Olivier, Michael; Pesich, Robert; Hebert, Joan; Chen, Yii-Der I.; Dzau, Victor J.; Curb, David; Olshen, Richard; Risch, Neil; Cox, David R.; Botstein, David

    2001-01-01

    To make large-scale association studies a reality, automated high-throughput methods for genotyping with single-nucleotide polymorphisms (SNPs) are needed. We describe PCR conditions that permit the use of the TaqMan or 5′ nuclease allelic discrimination assay for typing large numbers of individuals with any SNP and computational methods that allow genotypes to be assigned automatically. To demonstrate the utility of these methods, we typed >1600 individuals for a G-to-T transversion that results in a glutamate-to-aspartate substitution at position 298 in the endothelial nitric oxide synthase gene, and a G/C polymorphism (newly identified in our laboratory) in intron 8 of the 11–β hydroxylase gene. The genotyping method is accurate—we estimate an error rate of fewer than 1 in 2000 genotypes, rapid—with five 96-well PCR machines, one fluorescent reader, and no automated pipetting, over one thousand genotypes can be generated by one person in one day, and flexible—a new SNP can be tested for association in less than one week. Indeed, large-scale genotyping has been accomplished for 23 other SNPs in 13 different genes using this method. In addition, we identified three “pseudo-SNPs” (WIAF1161, WIAF2566, and WIAF335) that are probably a result of duplication. PMID:11435409

  18. Safety system status monitoring

    SciTech Connect

    Lewis, J.R.; Morgenstern, M.H.; Rideout, T.H.; Cowley, P.J.

    1984-03-01

    The Pacific Northwest Laboratory has studied the safety aspects of monitoring the preoperational status of safety systems in nuclear power plants. The goals of the study were to assess for the NRC the effectiveness of current monitoring systems and procedures, to develop near-term guidelines for reducing human errors associated with monitoring safety system status, and to recommend a regulatory position on this issue. A review of safety system status monitoring practices indicated that current systems and procedures do not adequately aid control room operators in monitoring safety system status. This is true even of some systems and procedures installed to meet existing regulatory guidelines (Regulatory Guide 1.47). In consequence, this report suggests acceptance criteria for meeting the functional requirements of an adequate system for monitoring safety system status. Also suggested are near-term guidelines that could reduce the likelihood of human errors in specific, high-priority status monitoring tasks. It is recommended that (1) Regulatory Guide 1.47 be revised to address these acceptance criteria, and (2) the revised Regulatory Guide 1.47 be applied to all plants, including those built since the issuance of the original Regulatory Guide.

  19. Rapid replacement of prevailing genotype of human respiratory syncytial virus by genotype ON1 in Beijing, 2012-2014.

    PubMed

    Cui, Guanglin; Zhu, Runan; Deng, Jie; Zhao, Linqing; Sun, Yu; Wang, Fang; Qian, Yuan

    2015-07-01

    Human respiratory syncytial virus (HRSV) is the most common viral pathogen causing lower respiratory infections in infants and young children worldwide. HRSV ON1 genotype in subgroup A with a characteristic of a 72 nucleotide duplication in the second highly variable region of attachment glycoprotein gene, has been reported in some countries since it was first detected in clinical samples collected in Canada in 2010. In this study, 557 HRSV antigen-positive nasopharyngeal aspirates were randomly selected during 2012/2013 to 2013/2014 HRSV seasons in Beijing for subgroup typing and for ON1 genotype screening by using a PCR based method developed for easily identifying genotype ON1 out of strains of subtype A. It was found that subgroup B was dominant in the 2012/2013 season and sudden shift of subgroup dominance from B to A and rapid replacement of previously prevailing NA1 genotype by ON1 genotype occurred in the 2013/2014 season. Reversible amino acid replacement in the G protein gene was found in a new branch of ON1 genotype. The evolutionary rate of the 351 global ON1 sequences was estimated to 7.34 × 10(-3) nucleotide substitutions per site per year (95% highest probability density intervals, HPD, 5.71 × 10(-3) to 9.04 × 10(-3)), with the time of most recent common ancestor dating back to June 2009.

  20. Folate status and neural tube defects.

    PubMed

    Molloy, A M; Mills, J L; Kirke, P N; Weir, D G; Scott, J M

    1999-01-01

    Periconceptional folic acid supplementation prevents approximately 70% of neural tube defects (NTDs). While most women carrying affected fetuses do not have deficient blood folate levels, the risk of having an NTD affected child is inversely correlated with pregnancy red cell folate levels. Current research is focused on the discovery of genetic abnormalities in folate related enzymes which might explain the role of folate in NTD prevention. The first candidate gene to emerge was the C677T variant of 5,10-methylenetetrahydrofolate reductase. Normal subjects who are homozygous for the mutation (TT) have red cell folate status some 20% lower than expected. It is now established that the prevalence of the TT genotype is significantly higher among spina bifida cases and their parents. Nevertheless, our studies show that the variant does not account for the reduced blood folate levels in many NTD affected mothers. We conclude that low maternal folate status may in itself be the most important risk factor for NTDs and that food fortification may be the only population strategy of benefit in the effort to eliminate NTDs.

  1. Genetic Variations Involved in Vitamin E Status

    PubMed Central

    Borel, Patrick; Desmarchelier, Charles

    2016-01-01

    Vitamin E (VE) is the generic term for four tocopherols and four tocotrienols that exhibit the biological activity of α-tocopherol. VE status, which is usually estimated by measuring fasting blood VE concentration, is affected by numerous factors, such as dietary VE intake, VE absorption efficiency, and VE catabolism. Several of these factors are in turn modulated by genetic variations in genes encoding proteins involved in these factors. To identify these genetic variations, two strategies have been used: genome-wide association studies and candidate gene association studies. Each of these strategies has its advantages and its drawbacks, nevertheless they have allowed us to identify a list of single nucleotide polymorphisms associated with fasting blood VE concentration and α-tocopherol bioavailability. However, much work remains to be done to identify, and to replicate in different populations, all the single nucleotide polymorphisms involved, to assess the possible involvement of other kind of genetic variations, e.g., copy number variants and epigenetic modifications, in order to establish a reliable list of genetic variations that will allow us to predict the VE status of an individual by knowing their genotype in these genetic variations. Yet, the potential usefulness of this area of research is exciting with regard to personalized nutrition and for future clinical trials dedicated to assessing the biological effects of the various isoforms of VE. PMID:27983595

  2. Rationale and methods for the National Tuberculosis Genotyping and Surveillance Network.

    PubMed

    Castro, Kenneth G; Jaffe, Harold W

    2002-11-01

    Our understanding of tuberculosis (TB) transmission dynamics has been refined by genotyping of Mycobacterium tuberculosis strains. The National Tuberculosis Genotyping and Surveillance Network was designed and implemented to systematically evaluate the role of genotyping technology in improving TB prevention and control activities. Genotyping proved a useful adjunct to investigations of outbreaks, unusual clusters, and laboratory cross-contamination.

  3. Rapid typing of Mannheimia haemolytica major genotypes 1 and 2 using MALDI-TOF mass spectrometry.

    PubMed

    Loy, John Dustin; Clawson, Michael L

    2017-05-01

    Genotype 2M. haemolytica predominantly associate over genotype 1 with the lungs of cattle with respiratory disease and ICEs containing antimicrobial resistance genes. Distinct protein masses were detected by MALDI-TOF MS between genotype 1 and 2 strains. MALDI-TOF MS could rapidly differentiate genotype 2 strains in veterinary diagnostic laboratories.

  4. General-Purpose Genotype or How Epigenetics Extend the Flexibility of a Genotype

    PubMed Central

    Massicotte, Rachel; Angers, Bernard

    2012-01-01

    This project aims at investigating the link between individual epigenetic variability (not related to genetic variability) and the variation of natural environmental conditions. We studied DNA methylation polymorphisms of individuals belonging to a single genetic lineage of the clonal diploid fish Chrosomus eos-neogaeus sampled in seven geographically distant lakes. In spite of a low number of informative fragments obtained from an MSAP analysis, individuals of a given lake are epigenetically similar, and methylation profiles allow the clustering of individuals in two distinct groups of populations among lakes. More importantly, we observed a significant pH variation that is consistent with the two epigenetic groups. It thus seems that the genotype studied has the potential to respond differentially via epigenetic modifications under variable environmental conditions, making epigenetic processes a relevant molecular mechanism contributing to phenotypic plasticity over variable environments in accordance with the GPG model. PMID:22567383

  5. Web Operational Status Boards

    SciTech Connect

    Millard, W. David; Stoops, LaMar R.; Dorow, Kevin E.

    2004-04-16

    Web Operational Status Boards (WebOSB)is a web-based application designed to acquire, display, and update highly dynamic status information between multiple users and jurisdictions. WebOSB is able to disseminate real-time status information—support the timely sharing of information—with constant, dynamic updates via personal computers and the Internet between emergency operations centers (EOCs), incident command centers, and to users outside the EOC who need to know the information (hospitals, shelters, schools). The WebOSB application far exceeds outdated information-sharing methods used by emergency workers: whiteboards, Word and Excel documents, or even locality-specific Web sites. WebOSB’s capabilities include the following elements: - Secure access. Multiple users can access information on WebOSB from any personal computer with Internet access and a secure ID. Privileges are use to control access and distribution of status information and to identify users who are authorized to add or edit information. - Simultaneous update. WebOSB provides options for users to add, display, and update dynamic information simultaneously at all locations involved in the emergency management effort, A single status board can be updated from multiple locations enabling shelters and hospitals to post bed availability or list decontamination capability. - On-the-fly modification. Allowing the definition of an existing status board to be modified on-the-fly can be an asset during an emergency, where information requirements can change quickly. The status board designer feature allows an administrator to quickly define, modi,, add to, and implement new status boards in minutes without needing the help of Web designers and computer programmers. - Publisher/subscriber notification. As a subscriber, each user automatically receives notification of any new information relating to specific status boards. The publisher/subscriber feature automatically notified each user of any new

  6. Epidemiology and genetic characterization of hepatitis A virus genotype IIA.

    PubMed

    Desbois, Delphine; Couturier, Elisabeth; Mackiewicz, Vincent; Graube, Arielle; Letort, Marie-José; Dussaix, Elisabeth; Roque-Afonso, Anne-Marie

    2010-09-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5' untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored.

  7. Is incidence of multiple HPV genotypes rising in genital infections?

    PubMed

    Sohrabi, Amir; Hajia, Masoud; Jamali, Firouzeh; Kharazi, Faranak

    2017-02-16

    Frequency of cervical cancer related to Human Papilloma Virus (HPV) has increased remarkably in less-developed countries. Hence, applying capable diagnostic methods is urgently needed, as is having a therapeutic strategy as an effective step for cervical cancer prevention. The aim of this study was to investigate the prevalence of various multi-type HPV infection patterns and their possible rising incidence in women with genital infections. This descriptive study was conducted on women who attended referral clinical laboratories in Tehran for genital infections from January 2012 until December 2013. A total of 1387 archival cervical scraping and lesion specimens were collected from referred women. HPV genotyping was performed using approved HPV commercial diagnostic technologies with either INNO-LiPA HPV or Geno Array Test kits. HPV was positive in 563 cases (40.59%) with mean age of 32.35±9.96. Single, multiple HPV genotypes and untypable cases were detected in 398 (70.69%), 160 (28.42%) and 5 (0.89%) cases, respectively. Multiple HPV infections were detected in 92 (57.5%), 42 (26.2%), 17 (10.6%) and 9 (5.7%) cases as two, three, four and five or more genotypes, respectively. The prevalence of 32 HPV genotypes was determined one by one. Seventeen HPV genotypes were identified in 95.78% of all positive infections. Five dominant genotypes, HPV6, 16, 53, 11 and 31, were identified in a total of 52.35%of the HPV positive cases. In the present study, we were able to evaluate the rate of multiple HPV types in genital infections. Nevertheless, it is necessary to evaluate the role of the dominant HPV low-risk types and the new probably high-risk genotypes, such as HPV53, in the increasing incidences of genital infections.

  8. Assessment of HCV genotypes in Yunnan Province of Southwest China.

    PubMed

    Li, Qiongfen; Yao, Yufeng; Shen, Yunsong; Cao, Danfeng; Li, Yalin; Zhang, Shuqiong; Cun, Wei; Sun, Mingbo; Yu, Jiankun; Shi, Li; Dong, Shaozhong

    2016-12-23

    Recently, we reported that the frequency of hepatitis C virus (HCV) genotypes and subtypes has rapidly changed among intravenous drug users (IDUs) in Yunnan Province over the last 5 years; this is especially true for subtype 6a which has increased in frequency from 5 to 15%. Here, we assessed 120 HCV-positive plasma samples from the general population (GP). HCV NS5B fragments were amplified and sequenced by PCR. We identified four HCV genotypes (1, 2, 3 and 6) and seven HCV subtypes (1b, 2a, 3a, 3b, 6a, 6n, and 6k) in this population. Genotype 3 was predominant, with a distribution frequency of 0.484, followed by genotype 1 (0.283), genotype 6 (0.133) and genotype 2 (0.100). HCV subtypes 3b (frequency 0.292) and 1b (frequency 0.283) were the most common subtypes. A comparison of the current data with previous results reported for IDUs showed that the distribution frequencies of genotypes 1, 2 and 6 were significantly different between patients in the GP and IDUs (P < 0.05). Among the HCV subtypes, the distribution frequencies of 1b, 2a, 6a, and 6n were significantly different between patients in the GP and IDU groups (P < 0.05). Moreover, Phylogenetic analyses showed that HCV subtype 6a strains isolated from IDUs and the GP were intermixed and not separately clustered. HCV subtype 6a was predominant not only among IDUs but also among those in the GP in the Guangdong Province and Vietnam. However, HCV subtype 6a was predominant only among IDUs and not among those in the GP in the Yunnan and Guangxi Provinces. Our results indicate that the HCV subtype 6a could rapidly spread across China.

  9. HCV genotype distribution and possible transmission risks in Lahore, Pakistan

    PubMed Central

    Ahmad, Waqar; Ijaz, Bushra; Javed, Fouzia Tahir; Jahan, Shah; Shahid, Imran; Khan, Fawad Mumtaz; Hassan, Sajida

    2010-01-01

    AIM: To investigate the prevalence of hepatitis C virus (HCV) genotypes and their association with possible transmission routes in the general population of Lahore, as the data exclusively related to this city is limited. METHODS: Complete data regarding patient’s history, possible route of infection and biochemical tests was collected from the public hospital for 1364 patients. SPSS version 16 windows software was used for data analysis by univariate and multivariate techniques. RESULTS: Age range ≤ 40 years showed high prevalence of HCV infection. HCV genotype 3a was dominant (55.9%), followed by 1a (23.6%), 4a (12.5%), 3b (3.2%), untypable (2.5%), 4b (1.2%) and mixed type (1.2%). Blood transfusion, dental surgery and barber shops were the main risk factors for HCV transmission. Genotype prevalence was independent of age (P = 0.971) and gender (P = 0.122) while risk factors showed a significant association with age (P = 0.000) and genotypes (P = 0.000). We observed an independent association of risk factors and genotype 3a, while patients with genotype 1 and 4 were mostly infected due to dental surgery blood transfusion and barber shops. Risk factors of intravenous drug use and sexual exposure were exclusively found in ≤ 40 years age group. CONCLUSION: An increase in genotypes 1a and 4a suggest migration of people, possibly from Balochistan and the northern war-zone area. Government should focus on public education regarding infection routes. PMID:20818816

  10. Influence of Acanthamoeba genotype on clinical course and outcomes for patients with Acanthamoeba keratitis in Spain.

    PubMed

    Arnalich-Montiel, Francisco; Lumbreras-Fernández, Blanca; Martín-Navarro, Carmen M; Valladares, Basilio; Lopez-Velez, Rogelio; Morcillo-Laiz, Rafael; Lorenzo-Morales, Jacob

    2014-04-01

    Genotype T4 is by far the most frequent genotype of Acanthamoeba keratitis (AK) and therefore has been considered the most virulent. This study included 14 cases of AK of genotype T4 and three cases of non-T4 genotype. We found that cases of non-T4 genotype had a worse response to medical therapy, greater need for surgical intervention, greater risk of extracorneal involvement, and remarkably poorer final visual outcome than those of T4 genotype, suggesting an association between Acanthamoeba virulence and genotype that requires additional case investigation.

  11. Influence of Acanthamoeba Genotype on Clinical Course and Outcomes for Patients with Acanthamoeba Keratitis in Spain

    PubMed Central

    Lumbreras-Fernández, Blanca; Martín-Navarro, Carmen M.; Valladares, Basilio; Lopez-Velez, Rogelio; Morcillo-Laiz, Rafael; Lorenzo-Morales, Jacob

    2014-01-01

    Genotype T4 is by far the most frequent genotype of Acanthamoeba keratitis (AK) and therefore has been considered the most virulent. This study included 14 cases of AK of genotype T4 and three cases of non-T4 genotype. We found that cases of non-T4 genotype had a worse response to medical therapy, greater need for surgical intervention, greater risk of extracorneal involvement, and remarkably poorer final visual outcome than those of T4 genotype, suggesting an association between Acanthamoeba virulence and genotype that requires additional case investigation. PMID:24430449

  12. Auto-interpreter for CYP2D6 SNaPshot genotyping.

    PubMed

    Ong, Sungmoon; Jeong, Hye-Eun; Lee, Sang Seop; Shon, Ji-Hong; Shin, Jae-Gook; Kim, Eun-Young

    2008-11-06

    CYP2D6 genotyping using SNaPshot method is a very useful tool clinically. However it's hard to interpret the obtained data as a genotype without training. Thus SNaPshot auto-interpreter for the genotype was designed to interpret obtained raw data to a genotype. The auto-interpreter showed good concordance with experts' reading. The validated auto-interpreter of CYP2D6 genotyping using SNaPshot can contribute to accelerating the clinical use.

  13. Detection and integration of genotyping errors in statistical genetics.

    PubMed

    Sobel, Eric; Papp, Jeanette C; Lange, Kenneth

    2002-02-01

    Detection of genotyping errors and integration of such errors in statistical analysis are relatively neglected topics, given their importance in gene mapping. A few inopportunely placed errors, if ignored, can tremendously affect evidence for linkage. The present study takes a fresh look at the calculation of pedigree likelihoods in the presence of genotyping error. To accommodate genotyping error, we present extensions to the Lander-Green-Kruglyak deterministic algorithm for small pedigrees and to the Markov-chain Monte Carlo stochastic algorithm for large pedigrees. These extensions can accommodate a variety of error models and refrain from simplifying assumptions, such as allowing, at most, one error per pedigree. In principle, almost any statistical genetic analysis can be performed taking errors into account, without actually correcting or deleting suspect genotypes. Three examples illustrate the possibilities. These examples make use of the full pedigree data, multiple linked markers, and a prior error model. The first example is the estimation of genotyping error rates from pedigree data. The second-and currently most useful-example is the computation of posterior mistyping probabilities. These probabilities cover both Mendelian-consistent and Mendelian-inconsistent errors. The third example is the selection of the true pedigree structure connecting a group of people from among several competing pedigree structures. Paternity testing and twin zygosity testing are typical applications.

  14. Super-genotype: global monoclonality defies the odds of nature.

    PubMed

    Le Roux, Johannes J; Wieczorek, Ania M; Wright, Mark G; Tran, Carol T

    2007-07-04

    The ability to respond to natural selection under novel conditions is critical for the establishment and persistence of introduced alien species and their ability to become invasive. Here we correlated neutral and quantitative genetic diversity of the weed Pennisetum setaceum Forsk. Chiov. (Poaceae) with differing global (North American and African) patterns of invasiveness and compared this diversity to native range populations. Numerous molecular markers indicate complete monoclonality within and among all of these areas (F(ST) = 0.0) and is supported by extreme low quantitative trait variance (Q(ST) = 0.00065-0.00952). The results support the general-purpose-genotype hypothesis that can tolerate all environmental variation. However, a single global genotype and widespread invasiveness under numerous environmental conditions suggests a super-genotype. The super-genotype described here likely evolved high levels of plasticity in response to fluctuating environmental conditions during the Early to Mid Holocene. During the Late Holocene, when environmental conditions were predominantly constant but extremely inclement, strong selection resulted in only a few surviving genotypes.

  15. Development of SNP-genotyping arrays in two shellfish species.

    PubMed

    Lapègue, S; Harrang, E; Heurtebise, S; Flahauw, E; Donnadieu, C; Gayral, P; Ballenghien, M; Genestout, L; Barbotte, L; Mahla, R; Haffray, P; Klopp, C

    2014-07-01

    Use of SNPs has been favoured due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the design of medium-throughput genotyping arrays for two oyster species, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markers were designed for two Illumina GoldenGate arrays and genotyped on more than 1000 samples for each species. In each case, oyster samples were obtained from wild and selected populations and from three-generation families segregating for traits of interest in aquaculture. The rate of successfully genotyped polymorphic SNPs was about 60% for each species. Effects of SNP origin and quality on genotyping success (Illumina functionality Score) were analysed and compared with other model and nonmodel species. Furthermore, a simulation was made based on a subset of the C. gigas SNP array with a minor allele frequency of 0.3 and typical crosses used in shellfish hatcheries. This simulation indicated that at least 150 markers were needed to perform an accurate parental assignment. Such panels might provide valuable tools to improve our understanding of the connectivity between wild (and selected) populations and could contribute to future selective breeding programmes.

  16. Clusters of incompatible genotypes evolve with limited dispersal

    PubMed Central

    Landguth, Erin L.; Johnson, Norman A.; Cushman, Samuel A.

    2015-01-01

    Theoretical and empirical studies have shown heterogeneous selection to be the primary driver for the evolution of reproductively isolated genotypes in the absence of geographic barriers. Here, we ask whether limited dispersal alone can lead to the evolution of reproductively isolated genotypes despite the absence of any geographic barriers or heterogeneous selection. We use a spatially-explicit, individual-based, landscape genetics program to explore the influences of dispersal strategies on reproductive isolation. We simulated genetic structure in a continuously distributed population and across various dispersal strategies (ranging from short- to long-range individual movement), as well as potential mate partners in entire population (ranging from 20 to 5000 individuals). We show that short-range dispersal strategies lead to the evolution of clusters of reproductively isolated genotypes despite the absence of any geographic barriers or heterogeneous selection. Clusters of genotypes that are reproductively isolated from other clusters can persist when migration distances are restricted such that the number of mating partners is below about 350 individuals. We discuss how our findings may be applicable to particular speciation scenarios, as well as the need to investigate the influences of heterogeneous gene flow and spatial selection gradients on the emergence of reproductively isolating genotypes. PMID:25954302

  17. Zoonotic Enterocytozoon bieneusi genotypes found in brazilian sheep.

    PubMed

    Fiuza, Vagner Ricardo da Silva; Lopes, Carlos Wilson Gomes; Cosendey, Rachel Ingrid Juliboni; de Oliveira, Francisco Carlos Rodrigues; Fayer, Ronald; Santín, Monica

    2016-08-01

    The presence of Enterocytozoon bieneusi in sheep has been reported in only three countries worldwide. The present study has found E. bieneusi in Brazilian sheep for the first time; in 24/125 (19.2%) fecal samples by PCR and on 8/10 (80%) farms from three diverse locations. A significantly greater number of lambs (34.1%) were found infected than older sheep (11.1%) (P=0.0036); most of the lambs were less than 6months of age. Farms with an intensive production system had a lower infection rate (10.5%) of infection than semi-intensive farms (23%), but this difference was not statistically significant. Sequencing analysis of the internal transcribed spacer (ITS) region of the rRNA gene revealed four known E. bieneusi genotypes (BEB6, BEB7, I, and LW1) and two novel genotypes (BEB18 and BEB19). Genotypes LW1 and BEB19 clustered within designated zoonotic Group 1 while genotypes BEB6, BEB7, I, and BEB18, and clustered within Group 2. BEB6 was the most prevalent (45.8%), followed by BEB7 (33.3%). Genotypes BEB6, I, and LW1 are zoonotic and can pose a risk to human health for immunocompromised individuals.

  18. Biolistic transformation of elite genotypes of switchgrass (Panicum virgatum L.).

    PubMed

    King, Zachary R; Bray, Adam L; Lafayette, Peter R; Parrott, Wayne A

    2014-02-01

    Transformation of elite switchgrass (Panicum virgatum L.) genotypes would facilitate the characterization of genes related to cell wall recalcitrance to saccharification. However, transformation of explants from switchgrass plants has remained difficult. Therefore, the objective of this study was to develop a biolistic transformation protocol for elite genotypes. Three switchgrass genotypes (ST1, ST2, and AL2) were previously selected for tissue culture responsiveness. One genotype, SA37, was selected for further use due to its improved formation of callus amenable to transformation. Various medium sets were compared and a previously published medium set provided cultures with >96 % embryogenic callus, and data on transient and stable gene expression of RFP were used to optimize biolistic parameters, and further validate the switchgrass (PvUbi1) promoter. SA37 proved to be the most transformable, whereas eight transgenic calli on average were recovered per bombardment of 20 calli (40 % efficiency) when using a three-day day preculture step, 0.6 M osmotic adjustment medium, 4,482 kPa rupture disks and 0.4 μm gold particles which traveled 9 cm before hitting the target callus tissue. Regenerability was high, especially for ST2, for which it is possible to recover on average over 400 plants per half-gram callus tissue. It is now possible to routinely and efficiently engineer elite switchgrass genotypes using biolistic transformation.

  19. Novel genotype of Tritrichomonas foetus from cattle in Southern Africa.

    PubMed

    Casteriano, Andrea; Molini, Umberto; Kandjumbwa, Kornelia; Khaiseb, Siegfried; Frey, Caroline F; Šlapeta, Jan

    2016-12-01

    Bovine trichomonosis caused by Tritrichomonas foetus is a significant reproductive disease of cattle. Preputial samples were collected using sheath washing technique in bulls in Namibia. Thirty-six trichomonad cultures were characterized using the TaqMan-probe commercial real-time polymerase chain reaction (PCR) diagnostic assay (VetMAX™-Gold Trich Detection Kit) and CYBR real-time PCR assay based on TFR3/4 primers. Diagnostic real-time PCRs and DNA sequencing of the internal transcribed region confirmed presence of T. foetus in 35 out of 36 samples. Multilocus genotyping using cysteine proteases (CP1, CP2, CP4, CP5, CP6, CP7, CP8, CP9) and malate dehydrogenase (MDH1) gene sequences demonstrate that the T. foetus in Namibia are genetically distinct from those characterized elsewhere. We report the discovery of a novel genotype of T. foetus in Namibian cattle, distinct from other T. foetus genotypes in Europe, South and North America and Australia. We suggest recognition of a 'Southern African' genotype of T. foetus. Identification of the new genotype of T. foetus demonstrates the need for wider global sampling to fully understand the diversity and origin of T. foetus causing disease in cattle or cats.

  20. The relationship between Obsessive-Compulsive symptoms and PARKIN genotype: The CORE-PD study

    PubMed Central

    Sharp, ME; Caccappolo, E; Mejia-Santana, H; Tang, M–X; Rosado, L; Orbe Reilly, M; Ruiz, D; Louis, ED; Comella, C; Nance, M; Bressman, S; Scott, WK; Tanner, C; Waters, C; Fahn, S; Cote, L; Ford, B; Rezak, M; Novak, K; Friedman, JH; Pfeiffer, R; Payami, H; Molho, E; Factor, SA; Nutt, J; Serrano, C; Arroyo, M; Pauciulo, MW; Nichols, WC; Clark, LN; Alcalay, RN; Marder, KS

    2014-01-01

    Background Few studies have systematically investigated the association between PARKIN genotype and psychiatric co-morbidities of PD. PARKIN-associated PD is characterized by severe nigral dopaminergic neuronal loss, a finding that may have implications for behaviors rooted in dopaminergic circuits such as obsessive-compulsive symptoms (OCS). Methods The Schedule of Compulsions and Obsessions Patient Inventory (SCOPI) was administered to 104 patients with early-onset PD and 257 asymptomatic first-degree relatives. Carriers of one and two PARKIN mutations were compared to non-carriers. Results Among patients, carriers scored lower than non-carriers in adjusted models (one-mutation: 13.9 point difference, p=0.03; two-mutation: 24.1, p=0.001), where lower scores indicate less OCS. Among asymptomatic relatives, there was a trend towards the opposite: mutation carriers scored higher than non-carriers (one mutation p = 0.05; two mutations p = 0.13). Conclusions First, there was a significant association between PARKIN mutation status and obsessive-compulsive symptom level in both PD and asymptomatics, suggesting that OCS might represent an early non-motor dopamine-dependent feature. Second, irrespective of disease status, heterozygotes were significantly different that non-carriers suggesting that PARKIN heterozygosity may contribute to phenotype. PMID:25393808

  1. System status display evaluation

    NASA Technical Reports Server (NTRS)

    Summers, Leland G.

    1988-01-01

    The System Status Display is an electronic display system which provides the crew with an enhanced capability for monitoring and managing the aircraft systems. A flight simulation in a fixed base cockpit simulator was used to evaluate alternative design concepts for this display system. The alternative concepts included pictorial versus alphanumeric text formats, multifunction versus dedicated controls, and integration of the procedures with the system status information versus paper checklists. Twelve pilots manually flew approach patterns with the different concepts. System malfunctions occurred which required the pilots to respond to the alert by reconfiguring the system. The pictorial display, the multifunction control interfaces collocated with the system display, and the procedures integrated with the status information all had shorter event processing times and lower subjective workloads.

  2. Differences between spent hens of different genotype in performance, meat yield and suitability of the meat for sausage production.

    PubMed

    Loetscher, Y; Albiker, D; Stephan, R; Kreuzer, M; Messikommer, R E

    2015-02-01

    The valorization of spent hens via the food chain has some major limitations, which include low meat yield and tough meat. The latter issue can be overcome by producing convenience foods; the first may be alleviated by employing a genotype with higher meatiness. To quantitatively compare two common layer genotypes in production performance, meat yield and sausage quality, 2200 57 weeks old Institut de Sélection Animale (ISA) Warren and Dekalb White hens each were investigated during the last 60 days of egg laying. The hens were housed in an aviary system in 2×10 compartments (10 compartments/each genotype). Measurements included feed intake, laying performance, egg weight and feed conversion ratio as measured per compartment. BW was determined twice on 10 animals per compartment. Finally, two sub-groups of five hens per compartment were slaughtered, meat yield was recorded and bratwurst-type sausages were produced (n=20 per genotype). Fat proportion, cooking loss, connective tissue properties and Kramer shear energy were measured. After 1, 4, 7 and 10 months of frozen storage, oxidative stability (thiobarbituric acid reactive substances (TBARS)) and microbiological status were determined as shelf-life related criteria. ANOVA was performed considering genotype as the main effect. The ISA Warren hens were inferior in laying performance (-11%) and feed conversion ratio (+10%) compared with Dekalb White, but had the same feed intake. The ISA Warren had higher BW and carcass weight than the Dekalb White. Carcass yield was higher by 5.9%. There were 80 g (23%) more meat available for sausage production from ISA Warren compared with Dekalb White. Sausages prepared from meat of ISA Warren hens contained less fat than those from Dekalb White, but showed the same cooking loss. Although the collagen proportion of the sausages produced from ISA Warren was lower than from Dekalb White, collagen solubility was lower and shear energy was higher. During the 10 months of frozen

  3. Equine cryptosporidial infection associated with Cryptosporidium hedgehog genotype in Algeria.

    PubMed

    Laatamna, Abd Elkarim; Wagnerová, Pavla; Sak, Bohumil; Květoňová, Dana; Aissi, Miriem; Rost, Michael; Kváč, Martin

    2013-10-18

    Faecal samples from two horse farms in Algeria keeping Arabian, Thoroughbred, and Barb horses were examined for the presence of Cryptosporidium in 2010-2011. A total of 138 faecal samples (16 from a farm keeping 50 animals and 122 from a farm with 267 horses) were screened for Cryptosporidium spp. infection using molecular tools. DNA was extracted from all samples. Nested PCR was performed to amplify fragments of the SSU rDNA and gp60 genes to determine the presence of Cryptosporidium species and genotypes. Sequence analyses of SSU and gp60 genes revealed four animals positive for the presence of subtype XIIIa A22R9 of the Cryptosporidium hedgehog genotype. The infections were not associated with diarrhoea. This study reports, for the first time, the occurrence of Cryptosporidium in Algeria and the first occurrence of the hedgehog genotype in horses. These findings support the potential role of infected horses in sylvatic-domestic transmission of Cryptosporidium.

  4. From genotype to apricot fruit quality: the antioxidant properties contribution.

    PubMed

    Leccese, Annamaria; Bartolini, Susanna; Viti, Raffaella

    2012-12-01

    Apricot fruit (Prunus armeniaca L.) quality strictly relates to the eating quality of fresh produce. Since consumers are more and more interested in healthy food, and apricot germplasm shows a wide choice of new selections and cultivars, apricot nutraceutical properties are under evaluation in order to select outstanding genotypes, which may link breeding and marketing. In the present study, 18 apricot genotypes of the Italian and international germplasm were evaluated over three years according to pomological, total antioxidant and total phenols attributes using principal component and hierarchical cluster analyses. The antioxidant capacity ranged from 1.24 to 11.47 μmolTE gFW⁻¹ and total phenols from 0.22 to 1.58 mgGAE gFW⁻¹. Four outstanding genotypes stood out as healthy food for fresh consumption which may also be introduced in breeding programs to produce new cultivars with improved nutraceutical values in addition to fruit qualitative attributes.

  5. Noninvasive genotyping of common marmoset (Callithrix jacchus) by fingernail PCR.

    PubMed

    Takabayashi, Shuji; Katoh, Hideki

    2015-07-01

    The common marmoset (Callithrix jacchus) is a New World primate that is a useful model for medical studies. In this study, we report a convenient, reliable, and noninvasive procedure to genotype a living common marmoset by using fingernails. This method was used to successfully genotype DNA by restriction fragment length polymorphism (RFLP) PCR without prior purification, by using the KOD FX PCR enzyme kit. Additionally, there is no sample contamination from hematopoietic chimera derived from fused placenta in utero. We compared chimeric levels between various tissues in females with male littermates using quantitative fluorescent (QF)-PCR to prepare a reliable DNA source for genetic analyses, such as genotyping, gene mapping, or genomic sequencing. The chimerism detected appeared to be restricted to lymphatic tissues, such as bone marrow, thymus, spleen, lymph nodes and blood cells. As a result, DNA from fingernails with the quick is the best DNA source for genetic research in living marmosets.

  6. Acanthamoeba T4 genotype associated with keratitis infections in Tunisia.

    PubMed

    Dendana, F; Sellami, H; Trabelsi, H; Neji, S; Cheikhrouhou, F; Makni, F; Ayadi, A

    2013-01-01

    Acanthamoeba keratitis (AK) is a sight-threatening infection. We report five cases of AK diagnosed from 2005 to 2009 in the Laboratory of Parasitology-Mycology at Habib Bourguiba Sfax Hospital, Tunisia. All were associated with improper care of contact lenses (rinsing of contact lenses with tap water and inappropriate cleaning) and lens storage. The patients displayed different clinical presentations: corneal inflammation, corneal ulceration, and corneal abscess. The diagnosis was made after direct examination, culture, and polymerase chain reaction amplification with specific primers. The genotype classification was based on the highly variable DF3 region in the 18S rRNA gene. This is the first study characterizing Acanthamoeba genotype in Tunisia and North Africa. All Acanthamoeba isolates were associated to the T4 genotype. Three different DF3 sequence types were related to AK infections T4/10, T4/15, and T4/16.

  7. Genotype identification of human cystic echinococcosis in Isfahan, central Iran.

    PubMed

    Kia, Eshrat Bigom; Rahimi, Hamidreza; Sharbatkhori, Mitra; Talebi, Ardeshir; Fasihi Harandi, Majid; Mirhendi, Hossein

    2010-08-01

    Echinococcosis/hydatidosis is one of the most important zoonotic diseases commonly found in different regions of Iran with a major economic and public health importance. In the current study, Echinococcus granulosus isolates were collected from hospitalized patients in Isfahan, central Iran. The genotypes of 30 samples were determined by polymerase chain reaction amplification of internal transcribed spacer-1 region of ribosomal DNA, followed by restriction fragment length polymorphism (RFLP) with two restriction enzymes namely AluI and MspI. As expected, each isolate yielded an approximately 1-kbp DNA fragment on the electrophoresis gel. According to RFLP results for both enzymes, all isolates had an equal pattern indicating the G1 genotype. Our findings confirmed that G1 is the dominant genotype of cystic echinococcosis in human in central Iran, with predilection to different organs including liver, lung, and brain, and warrants the importance of sheep dog cycle in public health.

  8. Inference of kinship coefficients from Korean SNP genotyping data.

    PubMed

    Park, Seong-Jin; Yang, Jin Ok; Kim, Sang Cheol; Kwon, Jekeun; Lee, Sanghyuk; Lee, Byungwook

    2013-06-01

    The determination of relatedness between individuals in a family is crucial in analysis of common complex diseases. We present a method to infer close inter-familial relationships based on SNP genotyping data and provide the relationship coefficient of kinship in Korean families. We obtained blood samples from 43 Korean individuals in two families. SNP data was obtained using the Affymetrix Genome-wide Human SNP array 6.0 and the Illumina Human 1M-Duo chip. To measure the kinship coefficient with the SNP genotyping data, we considered all possible pairs of individuals in each family. The genetic distance between two individuals in a pair was determined using the allele sharing distance method. The results show that genetic distance is proportional to the kinship coefficient and that a close degree of kinship can be confirmed with SNP genotyping data. This study represents the first attempt to identify the genetic distance between very closely related individuals.

  9. Bridging the Gap between Genotype and Phenotype via Network Approaches

    PubMed Central

    Kim, Yoo-Ah; Przytycka, Teresa M.

    2013-01-01

    In the last few years we have witnessed tremendous progress in detecting associations between genetic variations and complex traits. While genome-wide association studies have been able to discover genomic regions that may influence many common human diseases, these discoveries created an urgent need for methods that extend the knowledge of genotype-phenotype relationships to the level of the molecular mechanisms behind them. To address this emerging need, computational approaches increasingly utilize a pathway-centric perspective. These new methods often utilize known or predicted interactions between genes and/or gene products. In this review, we survey recently developed network based methods that attempt to bridge the genotype-phenotype gap. We note that although these methods help narrow the gap between genotype and phenotype relationships, these approaches alone cannot provide the precise details of underlying mechanisms and current research is still far from closing the gap. PMID:23755063

  10. Maintenance and stability of introduced genotypes in groundwater aquifer material.

    PubMed Central

    Jain, R K; Sayler, G S; Wilson, J T; Houston, L; Pacia, D

    1987-01-01

    Three indigenous groundwater bacterial strains and Pseudomonas putida harboring plasmids TOL (pWWO) and RK2 were introduced into experimentally contaminated groundwater aquifer microcosms. Maintenance of the introduced genotypes was measured over time by colony hybridization with gene probes of various specificity. On the basis of the results of colony hybridization quantitation of the introduced organisms and genes, all introduced genotypes were stably maintained at approximately 10(5) positive hybrid colonies g-1 of aquifer microcosm material throughout an 8-week incubation period. Concomitant removal of the environmental contaminants, viz., toluene, chlorobenzene, and styrene, in both natural (uninoculated) and inoculated aquifer microcosms was also demonstrated. The results indicate that introduced catabolic plasmids, as well as indigenous organisms, can be stably maintained in groundwater aquifer material without specific selective pressure for the introduced genotypes. These results have positive implications for in situ treatment and biodegradation in contaminated aerobic groundwater aquifers. Images PMID:3300546

  11. Sources of Hepatitis E Virus Genotype 3 in the Netherlands

    PubMed Central

    Lodder, Willemijn J.; Lodder-Verschoor, Froukje; van den Berg, Harold H.J.L.; Vennema, Harry; Duizer, Erwin; Koopmans, Marion; de Roda Husman, Ana Maria

    2009-01-01

    Non–travel-related hepatitis E virus (HEV) genotype 3 infections in persons in the Netherlands may have a zoonotic, foodborne, or water-borne origin. Possible reservoirs for HEV transmission by water, food, and animals were studied. HEV genotype 3/open reading frame 2 sequences were detected in 53% of pig farms, 4% of wild boar feces, and 17% of surface water samples. HEV sequences grouped within 4 genotype 3 clusters, of which 1 is so far unique to the Netherlands. The 2 largest clusters contained 35% and 43% of the animal and environmental sequences and 75% and 6%, respectively, of human HEV sequences obtained from a study on Dutch hepatitis E patients. This finding suggests that infection risk may be also dependent on transmission routes other than the ones currently studied. Besides the route of exposure, virus characteristics may be an important determinant for HEV disease in humans. PMID:19239749

  12. Genome-Wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions

    PubMed Central

    Wang, Wensheng; Qin, Qiao; Sun, Fan; Wang, Yinxiao; Xu, Dandan; Li, Zhikang; Fu, Binying

    2016-01-01

    Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions. The introgression of donor genomic DNA induced genome-wide DNA methylation changes in DK151 plants. A total of 1190 differentially methylated regions (DMRs) were detected between the two genotypes under normal growth conditions, and the DMR-associated genes in DK151 plants were mainly related to stress response, programmed cell death, and nutrient reservoir activity, which are implicated to constitutive drought stress tolerance. A comparison of the DNA methylation changes in the two genotypes under drought conditions indicated that DK151 plants have a more stable methylome, with only 92 drought-induced DMRs, than IR64 plants with 506 DMRs. Gene ontology analyses of the DMR-associated genes in drought-stressed plants revealed that changes to the DNA methylation status of genotype-specific genes are associated with the epigenetic regulation of drought stress responses. Transcriptome analysis further helped to identify a set of 12 and 23 DMR-associated genes that were differentially expressed in DK151 and IR64, respectively, under drought stress compared with respective controls. Correlation analysis indicated that DNA methylation has various effects on gene expression, implying that it affects gene expression directly or indirectly through diverse regulatory pathways. Our results indicate that drought-induced alterations to DNA methylation may influence

  13. FRIB Cryogenic Plant Status

    SciTech Connect

    Dixon, Kelly D.; Ganni, Venkatarao; Knudsen, Peter N.; Casagranda, Fabio

    2015-12-01

    After practical changes were approved to the initial conceptual design of the cryogenic system for MSU FRIB and an agreement was made with JLab in 2012 to lead the design effort of the cryogenic plant, many activities are in place leading toward a cool-down of the linacs prior to 2018. This is mostly due to using similar equipment used at CHLII for the 12 GeV upgrade at JLab and an aggressive schedule maintained by the MSU Conventional Facilities department. Reported here is an updated status of the cryogenic plant, including the equipment procurement status, plant layout, facility equipment and project schedule.

  14. Nutritional Status Assessment

    NASA Technical Reports Server (NTRS)

    Smith, Scott M.

    2008-01-01

    Nutritional Status Assessment (Nutrition) is the most comprehensive inflight study done by NASA to date of human physiologic changes during long-duration space flight; this includes measures of bone metabolism, oxidative damage, nutritional assessments, and hormonal changes. This study will impact both the definition of nutritional requirements and development of food systems for future space exploration missions to the Moon and Mars. This experiment will also help to understand the impact of countermeasures (exercise and pharmaceuticals) on nutritional status and nutrient requirements for astronauts.

  15. Genotype matching in a parasitoid-host genotypic food web: an approach for measuring effects of environmental change.

    PubMed

    Lavandero, Blas; Tylianakis, Jason M

    2013-01-01

    Food webs typically quantify interactions between species, whereas evolution operates through the success of alleles within populations of a single species. To bridge this gap, we quantify genotypic interaction networks among individuals of a single specialized parasitoid species and its obligate to cyclically parthenogenetic aphid host along a climatic gradient. As a case study for the kinds of questions genotype food webs could be used to answer, we show that genetically similar parasitoids became more likely to attack genetically similar hosts in warmer sites (i.e. there was network-wide congruence between the within-species shared allelic distance of the parasitoid and that of its host). Narrowing of host-genotype-niche breadth by parasitoids could reduce resilience of the network to changes in host genetic structure or invasion by novel host genotypes and inhibit biological control. Thus, our approach can be easily used to detect changes to sub-species-level food webs, which may have important ecological and evolutionary implications, such as promoting host-race specialization or the accelerated loss of functional diversity following extinctions of closely related genotypes.

  16. Newcastle disease: evolution of genotypes and the related diagnostic challenges.

    PubMed

    Miller, Patti J; Decanini, Eduardo Lucio; Afonso, Claudio L

    2010-01-01

    Since the discovery of Newcastle disease virus (NDV) in 1926, nine genotypes of class I viruses and ten of class II have been identified, representing a diverse and continually evolving group of viruses. The emergence of new virulent genotypes from global epizootics and the year-to-year changes observed in the genomic sequence of NDV of low and high virulence implies that distinct genotypes of NDV are simultaneously evolving at different geographic locations across the globe. This vast genomic diversity may be favored by the large variety of avian species susceptible to NDV infection and by the availability of highly mobile wild bird reservoirs. The genomic diversity of NDV increases the possibility of diagnostic failures, resulting in unidentified infections. Constant epidemiological surveillance and pro-active characterization of circulating strains are needed to ensure that the immunological and PCR reagents are effective in identifying NDV circulating worldwide. For example, in the United States, the widely used real-time reverse transcription polymerase chain reaction (RRT-PCR) matrix gene assay for the identification of NDV often fails to detect low virulence APMV-1 from waterfowl, while the RRT-PCR fusion gene assay, used to identify virulent isolates, often fails to detect certain virulent NDV genotypes. A new matrix-polymerase multiplex test that detects most of the viruses currently circulating worldwide and a modified fusion test for the identification of virulent pigeon viruses circulating in the U.S. and Europe have recently been developed. For newly isolated viruses with unknown sequences, recently developed random priming sequencing methods need to be incorporated into the diagnostic arsenal. In addition, the current system of classifying NDV into genotypes or lineages is inadequate. Here, we review the molecular epidemiology and recent diagnostic problems related to viral evolution of NDV and explain why a new system, based on objective criteria, is

  17. Human papillomavirus genotyping and integration in ovarian cancer Saudi patients

    PubMed Central

    2013-01-01

    Background Human papillomavirus (HPV) is associated with different malignancies but its role in the pathogenesis of ovarian cancer is controversial. This study investigated the prevalence, genotyping and physical state of HPV in ovarian cancer Saudi patients. Methods Hundred formalin fixed paraffin embedded (FFPE) ovarian carcinoma tissues and their normal adjacent tissues (NAT) were included in the study. HPV was detected by nested polymerase chain reaction (PCR) using degenerated HPVL1 consensus primer pairs MY09/MY11 and GP5+/GP6 + to amplify a broad spectrum of HPV genotypes in a single reaction. The HPV positive samples were further genotyped using DNA sequencing. The physical state of the virus was identified using Amplification of Papillomavirus Oncogene Transcripts (APOT) assay in the samples positive for HPV16 and/or HPV18. Results High percentage of HPV (42%) was observed in ovarian carcinoma compared to 8% in the NAT. The high-risk HPV types 16, 18 and 45 were highly associated with the advanced stages of tumor, while low-risk types 6 and 11 were present in NAT. In malignant tissues, HPV-16 was the most predominant genotype followed by HPV-18 and -45. The percentage of viral integration into the host genome was significantly high (61.1%) compared to 38.9% episomal in HPV positive tumors tissues. In HPV18 genotype the percentage of viral integration was 54.5% compared to 45.5% episomal. Conclusion The high risk HPV genotypes in ovarian cancer may indicate its role in ovarian carcinogenesis. The HPV vaccination is highly recommended to reduce this type of cancer. PMID:24252426

  18. Chimpanzee Personality and the Arginine Vasopressin Receptor 1A Genotype.

    PubMed

    Wilson, V A D; Weiss, A; Humle, T; Morimura, N; Udono, T; Idani, G; Matsuzawa, T; Hirata, S; Inoue-Murayama, M

    2017-03-01

    Polymorphisms of the arginine vasopressin receptor 1a (AVPR1a) gene have been linked to various measures related to human social behavior, including sibling conflict and agreeableness. In chimpanzees, AVPR1a polymorphisms have been associated with traits important for social interactions, including sociability, joint attention, dominance, conscientiousness, and hierarchical personality dimensions named low alpha/stability, disinhibition, and negative emotionality/low dominance. We examined associations between AVPR1a and six personality domains and hierarchical personality dimensions in 129 chimpanzees (Pan troglodytes) living in Japan or in a sanctuary in Guinea. We fit three linear and three animal models. The first model included genotype, the second included sex and genotype, and the third included genotype, sex, and sex × genotype. All personality phenotypes were heritable. Chimpanzees possessing the long form of the allele were higher in conscientiousness, but only in models that did not include the other predictors; however, additional analyses suggested that this may have been a consequence of study design. In animal models that included sex and sex × genotype, chimpanzees homozygous for the short form of the allele were higher in extraversion. Taken with the findings of previous studies of chimpanzees and humans, the findings related to conscientiousness suggest that AVPR1a may be related to lower levels of impulsive aggression. The direction of the association between AVPR1a genotype and extraversion ran counter to what one would expect if AVPR1a was related to social behaviors. These results help us further understand the genetic basis of personality in chimpanzees.

  19. Photosynthesis, photorespiration and productivity of wheat and soybean genotypes.

    PubMed

    Aliyev, Jalal A

    2012-07-01

    The results of the numerous measurements obtained during the last 40 years on gas exchange rate, photosynthetic carbon metabolism by exposition in ¹⁴CO₂ and activities of primary carbon fixation enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPC/O), in various wheat and soybean genotypes grown over a wide area in the field and contrasting in photosynthetic traits and productivity are presented in this article. It was established that high productive wheat genotypes (7-9 t ha⁻¹) with the optimal architectonics possess higher rate of CO₂ assimilation during the leaf ontogenesis. Along with the high rate of photosynthesis, high values of photorespiration are characteristic for the high productive genotypes. Genotypes with moderate (4-5 t ha⁻¹) and low (3 t ha⁻¹) grain yield are characterized by relatively low rates of both CO₂ assimilation and photorespiration. A value of photorespiration constitutes 28-35% of photosynthetic rate in contrasting genotypes. The activities of RuBPC and RuBPO were changing in a similar way in the course of the flag leaf and ear elements development. High productive genotypes are also characterized by a higher rate of biosynthesis and total value of glycine-serine and a higher photosynthetic rate. Therefore, contrary to conception arisen during many years on the wastefulness of photorespiration, taking into account the versatile investigations on different aspects of photorespiration, it was proved that photorespiration is one of the evolutionarily developed vital metabolic processes in plants and the attempts to reduce this process with the purpose of increasing the crop productivity are inconsistent.

  20. Duarte GALT genotypes are not associated with ovarian cancer risk

    PubMed Central

    Merritt, Melissa A.; Kotsopoulos, Joanne; Cramer, Daniel W.; Hankinson, Susan E.; Terry, Kathryn L.; Tworoger, Shelley S.

    2012-01-01

    Objective To investigate whether Galactose-1-phosphate uridyl transferase (GALT) variant genotypes were associated with epithelial ovarian cancer risk and to determine if this association was modified by lactose intake. Design two prospective cohort studies and a case-control study. Setting Academic institution. Patient(s) 992 cases and 1050 population-based controls from a New England case-control study and 240 cases and 900 controls from the Nurses’ Health Studies. Intervention(s) None. Main Outcome Measure(s) Genotyping of the N314D variant and the 4-bp deletion (-119delGTCA) of GALT using the Taqman 5′ nuclease assay. Duarte1 (D1) genotype individuals have a missense mutation (N314D) associated with normal GALT activity unless it occurs together with an associated 4-bp deletion leading to reduced GALT activity (Duarte2 or D2). Result(s) Logistic regression analysis identified no association between D1/D2 genotypes and ovarian cancer risk (pooled RR, 1.1 (95% CI, 0.8–1.5) for D1 and 1.0 (95% CI, 0.7–1.4) for D2). We did not observe a significant interaction between D1 and D2 genotypes in analyses stratified by level of lactose intake (Pinteraction ≥ 0.3). Conclusion(s) D1 and D2 genotypes do not appear to play a role in the association between galactose intake, possible ovarian dysfunction and the link with ovarian cancer. PMID:22749219

  1. PEPA-1* genotype affects return rate for hatchery steelhead

    USGS Publications Warehouse

    Reisenbichler, R.R.; Hayes, M.C.; Rubin, S.P.; Wetzel, L.A.; Baker, B.M.

    2006-01-01

    Allozymes continue to be useful as genetic markers in a variety of studies; however, their utility often hinges on the selective neutrality of the allelic variation. Our study tested for neutrality between the two most common alleles (*100 and *110) at the cytosol nonspecific dipeptidase locus (PEPA-1*) in steelhead Oncorhynchus mykiss from Dworshak National Fish Hatchery in Idaho. We tested for differential growth and survival among fish with the * 100/100, *100/ 110, and *110/110 genotypes rearing in a hatchery or a natural stream. We repeated the study for two year-classes, using heterozygous (*100/110) adults to make the experimental crosses. This design avoided differences in family contribution among genotypes because each cross produced all three genotypes. We divided the progeny from each family into two groups. One group was reared in a hatchery for 1 year and then released for migration to the sea and subsequent return to the hatchery as adults. The other group was released into a natural stream and monitored for 3 years. We found no significant differences in size or survival among PEPA-1* genotypes for either the naturally reared fish or the hatchery-reared fish immediately prior to release as smolts. For females, survival to returning adult also was similar among genotypes; however, hatchery-reared males with the *110/110 genotype returned at a higher rate than did males with the *100/ 100 genotype; heterozygous males were intermediate. These results indicate that selection occurs at the PEPA-1* locus or at one or more loci tightly linked to it. The finding of nearly equal frequencies for these two alleles in the source population suggests that selection differentials among genotypes reverse or vary from year to year; otherwise, steady directional selection would drive the *100 allele to low frequencies or extinction. Locus PEPA-1* seems inappropriate for genetic marks in studies of steelhead that span the full life cycle and probably should be avoided

  2. Two-temperature LATE-PCR endpoint genotyping

    PubMed Central

    Sanchez, J Aquiles; Abramowitz, Jessica D; Salk, Jesse J; Reis, Arthur H; Rice, John E; Pierce, Kenneth E; Wangh, Lawrence J

    2006-01-01

    Background In conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay. Results Two-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE)-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA) and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of 2:1 and 1:2 ratios of the

  3. reGenotyper: Detecting mislabeled samples in genetic data

    PubMed Central

    Snoek, Basten L.; Elvin, Mark; Rodriguez, Miriam; Arends, Danny; Swertz, Morris A.; Kammenga, Jan E.; Li, Yang

    2017-01-01

    In high-throughput molecular profiling studies, genotype labels can be wrongly assigned at various experimental steps; the resulting mislabeled samples seriously reduce the power to detect the genetic basis of phenotypic variation. We have developed an approach to detect potential mislabeling, recover the “ideal” genotype and identify “best-matched” labels for mislabeled samples. On average, we identified 4% of samples as mislabeled in eight published datasets, highlighting the necessity of applying a “data cleaning” step before standard data analysis. PMID:28192439

  4. Nephele: genotyping via complete composition vectors and MapReduce

    PubMed Central

    2011-01-01

    Background Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences. Results Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on traditional hardware. Nephele

  5. Mitochondrial genotyping of an endangered bitterling Acheilognathus typus (Cyprinidae)

    PubMed Central

    Saitoh, Kenji; Shindo, Kentaro; Fujimoto, Yasufumi; Takahashi, Kiyotaka; Shimada, Tetsuo

    2016-01-01

    Abstract Genotyping of endangered species is helpful for establishing and evaluating conservation strategies. Mitochondrial sequence data was analyzed from 541 individuals of a critically endangered fish, Acheilognathus typus from present-day range-wide localities to re-evaluate an in-progress restoration program around Lake Izunuma-Uchinuma, Miyagi, Japan. Acheilognathus typus showed low sequence diversity with only eight haplotypes and π and ĥ values of 0.59129 and 0.00118 respectively. Genetic data suggests Acheilognathus typus is adapted to pulsed environments and prone to population flush and crash. Genotyping of populations in introduced localities revealed that their source is not from nearby localities. PMID:27843393

  6. Phylogenetic evidence for a new genotype of Acanthamoeba (Amoebozoa, Acanthamoebida).

    PubMed

    Corsaro, Daniele; Venditti, Danielle

    2010-06-01

    Acanthamoeba are widespread free-living amoebae, able to cause infection in animals, with keratitis and granulomatous encephalitis as major diseases in humans. Recent developments in the subgenus classification are based on the determination of the nucleotide sequence of the 18S rDNA. By this mean, Acanthamoeba have been clustered into 15 sequence types or genotypes, called T1 to T15. In this study, we analysed near full 18S rDNA of an Acanthamoeba recovered from an environmental sample and various unidentified Acanthamoeba sequences retrieved from GenBank. We provided phylogenetic evidence for a new genotype, which we proposed to name T16.

  7. Genotype specific peripheral lipid profile changes with hepatitis C therapy

    PubMed Central

    Pedersen, Mark R; Patel, Amit; Backstedt, David; Choi, Myunghan; Seetharam, Anil B

    2016-01-01

    AIM To evaluate magnitude/direction of changes in peripheral lipid profiles in patients undergoing direct acting therapy for hepatitis C by genotype. METHODS Mono-infected patients with hepatitis C were treated with guideline-based DAAs at a university-based liver clinic. Patient characteristics and laboratory values were collected before and after the treatment period. Baseline demographics included age, ethnicity, hypertension, diabetes, hyperlipidemia, treatment regimen, and fibrosis stage. Total cholesterol (TCHOL), high density lipoprotein (HDL), low density lipoprotein (LDL), triglycerides (TG), and liver function tests were measured prior to treatment and ETR. Changes in lipid and liver function were evaluated by subgroups with respect to genotype. Mean differences were calculated for each lipid profile and liver function component (direction/magnitude). The mean differences in lipid profiles were then compared between genotypes for differences in direction/magnitude. Lipid profile and liver function changes were evaluated with Levene’s test and student’s t test. Mean differences in lipid profiles were compared between genotypes using ANOVA, post hoc analysis via the Bonferroni correction or Dunnett T3. RESULTS Three hundred and seventy five patients enrolled with 321 (85.6%) achieving sustained-viral response at 12 wk. 72.3% were genotype 1 (GT1), 18.1% genotype 2 (GT2), 9.7% genotype 3 (GT3). Baseline demographics were similar. Significant change in lipid profiles were seen with GT1 and GT3 (ΔGT1, p and ΔGT3, p), with TCHOL increasing (+5.3, P = 0.005 and +16.1, P < 0.001), HDL increasing (+12.5, P < 0.001 and +7.9, P = 0.038), LDL increasing (+7.4, P = 0.058 and +12.5, P < 0.001), and TG decreasing (-5.9, P = 0.044 and -9.80 P = 0.067). Among genotypes (ΔGT1 v. ΔGT2 v. ΔGT3, ANOVA), significant mean differences were seen with TCHOL (+5.3 v. +0.1 v. +16.1, P = 0.017) and HDL (+12.3 v. +2 v. +7.9, P = 0.040). Post-hoc, GT3 was associated with a

  8. Genotypic structure of a Drosophila population for adult locomotor activity

    SciTech Connect

    Grechanyi, G.V.; Korzun, V.M.

    1995-01-01

    Analysis of the variation of adult locomotor activity in four samples taken at different times from a natural population of Drosophila melanogaster showed that the total variation of this trait is relatively stable in time and has a substantial genetic component. Genotypic structure of the population for locomotor activity is characterized by the presence of large groups of genotypes with high and low values of this trait. A possible explanation for the presence of such groups in a population is cyclic density-dependent selection.

  9. The division of labor: genotypic versus phenotypic specialization.

    PubMed

    Wahl, L M

    2002-07-01

    A model of the division of labor in simple evolving systems is explored to compare two strategies evident in natural populations: phenotypic specialization (such as differentiation by regulated gene expression) and genotypic specialization (such as co-infection by complementary covirus populations). While genotypic specialization is vulnerable to the chance extinction of an essential specialist type and to parasitism, phenotypic specialization is able to overcome these hurdles. When simple spatial effects are included, phenotypic specialization has further benefits, protecting against destructive dynamic patterns. Many of the advantages of phenotypic specialization, however, can only be realized when a high degree of relatedness within groups is ensured.

  10. Behavior, Expectations and Status

    ERIC Educational Resources Information Center

    Webster, Jr, Murray; Rashotte, Lisa Slattery

    2010-01-01

    We predict effects of behavior patterns and status on performance expectations and group inequality using an integrated theory developed by Fisek, Berger and Norman (1991). We next test those predictions using new experimental techniques we developed to control behavior patterns as independent variables. In a 10-condition experiment, predictions…

  11. Status, Numbers and Influence

    ERIC Educational Resources Information Center

    Melamed, David; Savage, Scott V.

    2013-01-01

    We develop a theoretical model of social influence in n-person groups. We argue that disagreement between group members introduces uncertainty into the social situation, and this uncertainty motivates people to use status characteristics to evaluate the merits of a particular opinion. Our model takes the numerical distribution of opinions and the…

  12. Algeria: Country Status Report.

    ERIC Educational Resources Information Center

    McFerren, Margaret

    A survey of the status of language usage in Algeria begins with an overview of the usage patterns of Arabic, the Berber languages, and French. The country's return to Arabic as its official language after independence from France in 1962 is discussed along with the resultant language planning, issues of language of instruction at the elementary,…

  13. Mongolian. Materials Status Report.

    ERIC Educational Resources Information Center

    Center for Applied Linguistics, Washington, DC. Language/Area Reference Center.

    The materials status report for Mongolian, the official standard language of the Mongolian People's Republic, is one of a series intended to provide the nonspecialist with a picture of the availability and quality of texts for teaching various languages to English speakers. The report consists of: (1) a brief narrative description of Mongolain,…

  14. Angola: Country Status Report.

    ERIC Educational Resources Information Center

    Bruhn, Thea C.

    A survey of the status of language usage in Angola begins with an overview of the usage and distribution of Portuguese as the official language, and the four most significant native languages and dialects spoken there: Umbundu, Kimbundu, Kikongo, and Lunda-Chokwe. The introduction of Spanish through Cuban trainers, teachers, and military advisors…

  15. Uigur. Materials Status Report.

    ERIC Educational Resources Information Center

    Center for Applied Linguistics, Washington, DC. Language/Area Reference Center.

    The materials status report for Uigur, a Turkic language spoken in the Sinkiang-Uigur Autonomous Region in northwest China and in the Soviet Socialist Republics of Kazakh and Uzbek, is one of a series intended to provide the nonspecialist with a picture of the availability and quality of texts for teaching various languages to English speakers.…

  16. NASA Armstrong Status

    NASA Technical Reports Server (NTRS)

    Jacobson, Steven R.

    2014-01-01

    Armstrong (formerly Dryden) Flight Research Center continues it's legacy of exciting work in the area of dynamics and control of advanced vehicle concepts. This status presentation highlights the research and technology development that Armstrong's Control and Dynamics branch is performing in the areas of Control of Flexible Structures and Automated Cooperative Trajectories.

  17. Singapore: Country Status Report.

    ERIC Educational Resources Information Center

    Christian, Donna

    A survey of the status of language usage in Singapore begins with an overview of patterns of usage of Malay, English, Mandarin Chinese, and Tamil. The function of English as a primary language along with the official language, Malay, is discussed, along with the history of the dominance of English since Singapore's role as a British colony despite…

  18. Glueballs: a status report

    SciTech Connect

    Scharre, D.L.

    1982-01-01

    It is expected from quantum chromodynamics (QCD) that glueballs, bound states which contain gluons but no valence quarks, should exist. To date, no conclusive evidence for glueballs has been presented. After a brief review of the expected properties and experimental signatures of glueballs the status of some glueball candidate states are discussed.

  19. Chad: Country Status Report.

    ERIC Educational Resources Information Center

    McFerren, Margaret

    A survey of the status of language usage in Chad begins with an overview of the usage patterns of four languages. They include: French, designated the official language as a practical necessity; Chadian Arabic and Sara, important popularly spoken languages in their respective regions; and Toubou, a less prevalent language but one that is spoken by…

  20. Mexico: Country Status Report.

    ERIC Educational Resources Information Center

    McFerren, Margaret

    A survey of the status of language usage in Mexico begins with an overview of language distribution among the population, mono- and multilingualism, changes in patterns of usage between the 1970 and 1980 censuses, and linguistic issues related to assimilation of the Indian population and the role and philosophy of the Instituto Nacional…

  1. Amharic. Materials Status Report.

    ERIC Educational Resources Information Center

    Center for Applied Linguistics, Washington, DC. Language/Area Reference Center.

    The materials status report for Amharic, the dominant language of Ethiopia, is one of a series intended to provide the nonspecialist with a picture of the availability and quality of texts for teaching various languages to English speakers. The report consists of: (1) a brief narrative description of Amharic, the areas where it is spoken, its…

  2. The status of GALLEX

    SciTech Connect

    Wink, R. )

    1991-01-01

    We describe the status of G A L L E X solar neutrino experiment until the end of June 1991. Since June 1990 31 desorptions with the full equipment have been done. The results of the first 27 desorptions are presented. We also describe our low level proportional counters including the counting system.

  3. The status of GALLEX

    SciTech Connect

    Wink, R.; The GALLEX Collaboration

    1991-12-31

    We describe the status of G A L L E X solar neutrino experiment until the end of June 1991. Since June 1990 31 desorptions with the full equipment have been done. The results of the first 27 desorptions are presented. We also describe our low level proportional counters including the counting system.

  4. The Status of Teachers

    ERIC Educational Resources Information Center

    Banerji, R. C.

    1976-01-01

    Various factors related to the decline in social status by teachers are examined, with special consideration given to reasons for this decline in India. It is suggested that the community, government, and educational administrators must bring about changes in attitudes and relationships that affect public opinion of teachers. (LBH)

  5. NASA Dryden Status

    NASA Technical Reports Server (NTRS)

    Bosworth, John T.

    2009-01-01

    This slide presentation reviews the status of several NASA Dryden projects. These include: the Lift And Nozzle Change Effects on Tail Shock (LANCETS), Integrated Resilient Aircraft Control (IRAC) F-18 #853 Testbed X-48B, Blended Wing Body flights, Stratospheric Observatory for Infrared Astronomy (SOFIA), Ikhana Project, and the Orion Crew Exploration Vehicle (CEV) Launch Abort Systems Tests

  6. Somali. Materials Status Report.

    ERIC Educational Resources Information Center

    Center for Applied Linguistics, Washington, DC. Language/Area Reference Center.

    The materials status report for Somali, the official language of Somalia, is one of a series intended to provide the nonspecialist with a picture of the availability and quality of texts for teaching various languages to English speakers. The report consists of: (1) a brief narrative description of Somali, the areas where it is spoken, its major…

  7. Somalia: Country Status Report.

    ERIC Educational Resources Information Center

    McFerren, Margaret

    A survey of the status of language usage in Somalia begins with an overview of the usage patterns of Somali, the official language, and three languages previously used officially: English, Italian, and Arabic. The cultural context that for many years has supported the usage of a single native language for communication and administration is also…

  8. Stellarator status, 1989

    SciTech Connect

    Lyon, J.F. ); Grieger, G.; Rau, F. ); Iiyoshi, A. ); Navarro, A.P. ); Kovrizhnykh, L.M. . Inst. Obshchey Fiziki); Pavlichenko, O.S. (AN Ukrain

    1990-07-01

    The present status of stellarator experiments and recent progress in stellarator research (both experimental and theoretical) are reported by groups in the United States, the USSR, Japan, Australia, and the European Community (the Federal Republic of Germany and Spain). Experiments under construction and studies of large, next-generation stellarators are also described. 73 refs., 11 figs., 4 tabs.

  9. Innate Susceptibility to Norovirus Infections Influenced by FUT2 Genotype in a United States Pediatric Population

    PubMed Central

    Currier, Rebecca L.; Payne, Daniel C.; Staat, Mary A.; Selvarangan, Rangaraj; Shirley, S. Hannah; Halasa, Natasha; Boom, Julie A.; Englund, Janet A.; Szilagyi, Peter G.; Harrison, Christopher J.; Klein, Eileen J.; Weinberg, Geoffrey A.; Wikswo, Mary E.; Parashar, Umesh; Vinjé, Jan; Morrow, Ardythe L.

    2015-01-01

    Background. Norovirus is a leading cause of acute gastroenteritis (AGE). Noroviruses bind to gut histo-blood group antigens (HBGAs), but only 70%–80% of individuals have a functional copy of the FUT2 (“secretor”) gene required for gut HBGA expression; these individuals are known as “secretors.” Susceptibility to some noroviruses depends on FUT2 secretor status, but the population impact of this association is not established. Methods. From December 2011 to November 2012, active AGE surveillance was performed at 6 geographically diverse pediatric sites in the United States. Case patients aged <5 years were recruited from emergency departments and inpatient units; age-matched healthy controls were recruited at well-child visits. Salivary DNA was collected to determine secretor status and genetic ancestry. Stool was tested for norovirus by real-time reverse transcription polymerase chain reaction. Norovirus genotype was then determined by sequencing. Results. Norovirus was detected in 302 of 1465 (21%) AGE cases and 52 of 826 (6%) healthy controls. Norovirus AGE cases were 2.8-fold more likely than norovirus-negative controls to be secretors (P < .001) in a logistic regression model adjusted for ancestry, age, site, and health insurance. Secretors comprised all 155 cases and 21 asymptomatic infections with the most prevalent norovirus, GII.4. Control children of Meso-American ancestry were more likely than children of European or African ancestry to be secretors (96% vs 74%; P < .001). Conclusions. FUT2 status is associated with norovirus infection and varies by ancestry. GII.4 norovirus exclusively infected secretors. These findings are important to norovirus vaccine trials and design of agents that may block norovirus-HBGA binding. PMID:25744498

  10. Differential association for N-acetyltransferase 2 genotype and phenotype with bladder cancer risk in Chinese population

    PubMed Central

    Quan, Lei; Chattopadhyay, Koushik; Nelson, Heather H.; Chan, Kenneth K.; Xiang, Yong-Bing; Zhang, Wei; Wang, Renwei; Gao, Yu-Tang; Yuan, Jian-Min

    2016-01-01

    Background N-acetyltransferase 2 (NAT2) is involved in both carcinogen detoxification through hepatic N-acetylation and carcinogen activation through local O-acetylation. NAT2 slow acetylation status is significantly associated with increased bladder cancer risk among European populations, but its association in Asian populations is inconclusive. Methods NAT2 acetylation status was determined by both single nucleotide polymorphisms (SNPs) and caffeine metabolic ratio (CMR), in a population-based study of 494 bladder cancer patients and 507 control subjects in Shanghai, China. Results The CMR, a functional measure of hepatic N-acetylation, was significantly reduced in a dose-dependent manner among both cases and controls possessing the SNP-inferred NAT2 slow acetylation status (all P-values<5.0×10−10). The CMR-determined slow N-acetylation status (CMR<0.34) was significantly associated with a 50% increased risk of bladder cancer (odds ratio = 1.50, 95% confidence interval = 1.10-2.06) whereas the SNP-inferred slow acetylation statuses were significantly associated with an approximately 50% decreased risk of bladder cancer. The genotype-disease association was strengthened after the adjustment for CMR and was primarily observed among never smokers. Conclusions The apparent differential associations for phenotypic and genetic measures of acetylation statuses with bladder cancer risk may reflect dual functions of NAT2 in bladder carcinogenesis because the former only measures the capacity of carcinogen detoxification pathway while the latter represents both carcinogen activation and detoxification pathways. Future studies are warranted to ascertain the specific role of N- and O-acetylation in bladder carcinogenesis, particularly in populations exposed to different types of bladder carcinogens. PMID:27223070

  11. Laser capture microdissection as a tool to evaluate human papillomavirus genotyping and methylation as biomarkers of persistence and progression of anal lesions

    PubMed Central

    Cornall, Alyssa M; Roberts, Jennifer M; Molano, Monica; Machalek, Dorothy A; Phillips, Samuel; Hillman, Richard J; Grulich, Andrew E; Jin, Fengyi; Poynten, I Mary; Templeton, David J; Garland, Suzanne M; Tabrizi, Sepehr N

    2015-01-01

    Introduction Anal squamous cell carcinoma is preceded by persistent infection with high-risk human papillomavirus (HPV) and the cancer precursor, high-grade squamous intraepithelial lesion (HSIL). Detection of specific HPV genotypes and HPV-related biomarkers may be an option for primary anal screening. However, more data on the natural history of HPV-related anal lesions are required. The outcomes from this study will enhance our understanding of the clinical and biological behaviour of HPV-related anal lesions and inform the development of future HPV genotype and/or biomarker screening tests. Methods and analysis HIV-negative and HIV-positive men who have sex with men, aged 35 years and over, recruited from community-based settings in Sydney, Australia, attend 6 clinic visits over 3 years. At the first 5 visits, participants undergo a digital anorectal examination, an anal swab for HPV genotyping and anal cytology, and high-resolution anoscopy with directed biopsy of any visible abnormalities that are suggestive of any abnormality suspicious of SIL. Tissue sections from participants diagnosed with histologically confirmed HSIL at the baseline clinic visit will undergo laser capture microdissection, HPV detection and genotyping, and quantitation of CpG methylation in baseline and follow-up biopsies. Histological and cytological findings in combination with HPV genotyping data will be used to identify persistent HSIL. HSIL will be stratified as non-persistent and persistent based on their status at 12 months. The performance of HPV genotype and methylation status in predicting disease persistence at 12 months will be assessed, along with associations with HIV status and other covariates such as age. Ethics and dissemination The St Vincent's Hospital Ethics Committee granted ethics approval for the study. Written informed consent is obtained from all individuals before any study-specific procedures are performed. Findings from this study will be disseminated

  12. Actinobacillus actinomycetemcomitans serotype e--biotypes, genetic diversity and distribution in relation to periodontal status.

    PubMed

    Doğan, B; Saarela, M H; Jousimies-Somer, H; Alaluusua, S; Asikainen, S

    1999-04-01

    Actinobacillus actinomycetemcomitans isolates from 356 individuals were screened for identification of serotype e in order to investigate its distribution in relation to periodontal status. From subjects with serotype e, 1-6 isolates per subject (n = 61) were genotyped using arbitrarily primed-polymerase chain reaction (AP-PCR) and apaH gene polymerase chain reaction-restriction fragment-length polymorphism (PCR-RFLP) analysis to determine the genetic heterogeneity within the serotype. Furthermore, one serotype e strain per subject was tested for fermentation of 8 carbohydrates for biotyping. Among patients with adult periodontitis (n = 219), localized juvenile periodontitis (n = 55) and other forms of early-onset periodontitis (n = 18) serotypes b, a and c, respectively, were the most frequently detected serotypes. Non-periodontitis subjects (n = 64) were predominantly colonized with serotype c. Serotype e was found in 30 (14%) adult periodontitis patients, 2 (11%) early-onset periodontitis patients and in 5 (8%) non-periodontitis individuals, but in none of the 55 localized juvenile periodontitis patients. AP-PCR distinguished 3 and apaH gene PCR-RFLP analysis 2 genotypes among the 61 A. actinomycetemcomitans serotype e isolates, one genotype per subject. The AP-PCR genotypes 1 and 3 represented the apaH genotype 1 and the AP-PCR genotype 2 the apaH genotype 2. On the basis of variable fermentation of galactose and xylose, 3 biotypes among A. actinomycetemcomitans serotype e were established. Contrary to the absence of A. actinomycetemcomitans serotype e in localized juvenile periodontitis patients, its detection frequency was comparable among other forms of periodontitis and periodontal health. Clinical serotype e isolates form at least 2 genetic types and 3 biotypes.

  13. Genotypic Variation for Drought Tolerance in Beta vulgaris

    PubMed Central

    OBER, E. S.; LUTERBACHER, M. C.

    2002-01-01

    Insufficient soil moisture during summer months is now the major cause of sugar beet yield losses in the UK. However, selection for increased drought tolerance has not been a breeding priority until recently. Genetic variation for drought tolerance is an essential prerequisite for the development of more stress‐tolerant varieties, but commercial sugar beet varieties seem to have similar yield responses to drought. The objective of this study was to assess the degree of genotypic variation for drought tolerance within a wide range of sugar beet germplasm and genebank accessions within Beta. Thirty sugar beet genotypes were screened under field drought conditions, and putative drought tolerant and sensitive lines (in terms of yield reduction in polythene‐covered vs. irrigated plots) were identified. Significant genotype × water treatment interactions were found for dry matter yield and relative leaf expansion rate. Genotypic differences for drought susceptibility index were also significant. Differential sensitivity of seedling shoot growth to water deficit was examined by comparing 350 genebank accessions in a simple growth chamber screen. Methods of data management were devised to highlight lines for entry into subsequent field tests. The results of the field and seedling screens indicate that there is variation for tolerance to water deficits within sugar beet and related types, and that there are lines that show greater drought tolerance than selected commercial varieties. Divergent lines showing contrasting behaviour should aid in the identification of key morpho‐physiological traits that confer drought tolerance. PMID:12102517

  14. IMPROVING TALL FESCUE SHADE TOLERANCE: IDENTIFYING CANDIDATE GENOTYPES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tall fescue (Schedonorus arundinaceus) is genetically variable for many agronomic traits, so it might be possible to increase its persistence and productivity in shaded agroforestry applications. The objective of this research was to identify high yielding, shade-tolerant genotypes. Seed was obtaine...

  15. Improving Tall Fescue Shade Tolerance: Identifying Candidate Genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tall fescue (Schedonorus arundinaceus) is genetically variable for many agronomic traits, so it might be possible to increase its persistence and productivity in shaded agroforestry applications. The objective of this research was to identify high yielding, shade-tolerant genotypes. Seed was obtai...

  16. Comparing performance of modern genotype imputation methods in different ethnicities

    NASA Astrophysics Data System (ADS)

    Roshyara, Nab Raj; Horn, Katrin; Kirsten, Holger; Ahnert, Peter; Scholz, Markus

    2016-10-01

    A variety of modern software packages are available for genotype imputation relying on advanced concepts such as pre-phasing of the target dataset or utilization of admixed reference panels. In this study, we performed a comprehensive evaluation of the accuracy of modern imputation methods on the basis of the publicly available POPRES samples. Good quality genotypes were masked and re-imputed by different imputation frameworks: namely MaCH, IMPUTE2, MaCH-Minimac, SHAPEIT-IMPUTE2 and MaCH-Admix. Results were compared to evaluate the relative merit of pre-phasing and the usage of admixed references. We showed that the pre-phasing framework SHAPEIT-IMPUTE2 can overestimate the certainty of genotype distributions resulting in the lowest percentage of correctly imputed genotypes in our case. MaCH-Minimac performed better than SHAPEIT-IMPUTE2. Pre-phasing always reduced imputation accuracy. IMPUTE2 and MaCH-Admix, both relying on admixed-reference panels, showed comparable results. MaCH showed superior results if well-matched references were available (Nei’s GST ≤ 0.010). For small to medium datasets, frameworks using genetically closest reference panel are recommended if the genetic distance between target and reference data set is small. Our results are valid for small to medium data sets. As shown on a larger data set of population based German samples, the disadvantage of pre-phasing decreases for larger sample sizes.

  17. Genotypic variation for drought tolerance in Beta vulgaris.

    PubMed

    Ober, E S; Luterbacher, M C

    2002-06-01

    Insufficient soil moisture during summer months is now the major cause of sugar beet yield losses in the UK. However, selection for increased drought tolerance has not been a breeding priority until recently. Genetic variation for drought tolerance is an essential prerequisite for the development of more stress-tolerant varieties, but commercial sugar beet varieties seem to have similar yield responses to drought. The objective of this study was to assess the degree of genotypic variation for drought tolerance within a wide range of sugar beet germplasm and genebank accessions within Beta. Thirty sugar beet genotypes were screened under field drought conditions, and putative drought tolerant and sensitive lines (in terms of yield reduction in polythene-covered vs. irrigated plots) were identified. Significant genotype x water treatment interactions were found for dry matter yield and relative leaf expansion rate. Genotypic differences for drought susceptibility index were also significant. Differential sensitivity of seedling shoot growth to water deficit was examined by comparing 350 genebank accessions in a simple growth chamber screen. Methods of data management were devised to highlight lines for entry into subsequent field tests. The results of the field and seedling screens indicate that there is variation for tolerance to water deficits within sugar beet and related types, and that there are lines that show greater drought tolerance than selected commercial varieties. Divergent lines showing contrasting behaviour should aid in the identification of key morpho-physiological traits that confer drought tolerance.

  18. Prolonged Incubation Time in Sheep with QK171 Genotype

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Sheep scrapie susceptibility or resistance is a function of genotype with polymorphisms at codon 171 playing a major role. Glutamine (Q) at 171 contributes to scrapie susceptibility while arginine (R) is associated with resistance. In some breeds, lysine (K) occurs at 171, but its affe...

  19. Genotypic diversity of environmental Cryptococcus neoformans isolates from Northern Portugal.

    PubMed

    Ferreira, Ana Sofia; Sampaio, Ana; Maduro, Ana Paula; Silva, Inês; Teles, Fernando; Martins, Maria da Luz; Inácio, João

    2014-02-01

    The Cryptococcus neoformans/C. gattii species complex members are the main agents of systemic cryptococcosis. This disease is believed to be acquired from the environment via fungal cell inhalation. Often, isolates recovered from environmental and clinical sources have proven to be genotypically similar. We assessed the occurrence of C. neoformans and C. gattii in environmental substrates collected in a Portuguese region. Twenty-eight isolates were identified as C. neoformans - five from decaying Eucalyptus leaves and 23 from domestic pigeon droppings. The isolates were genotyped using a URA5-RFLP approach. The C. neoformans VNIV (53.6%, n = 15) and VNI (32.1%, n = 9) genotypes were abundantly present among environmental isolates. The hybrid VNIII (14.3%, n = 4) genotype was underrepresented and the VNII was not found. Cryptococcus gattii was also not found although some isolates yielded a positive canavanine-glycine-bromothymol blue test.

  20. Ecosystem recovery after climatic extremes enhanced by genotypic diversity

    PubMed Central

    Reusch, Thorsten B. H.; Ehlers, Anneli; Hämmerli, August; Worm, Boris

    2005-01-01

    Contemporary climate change is characterized both by increasing mean temperature and increasing climate variability such as heat waves, storms, and floods. How populations and communities cope with such climatic extremes is a question central to contemporary ecology and biodiversity conservation. Previous work has shown that species diversity can affect ecosystem functioning and resilience. Here, we show that genotypic diversity can replace the role of species diversity in a species-poor coastal ecosystem, and it may buffer against extreme climatic events. In a manipulative field experiment, increasing the genotypic diversity of the cosmopolitan seagrass Zostera marina enhanced biomass production, plant density, and faunal abundance, despite near-lethal water temperatures due to extreme warming across Europe. Net biodiversity effects were explained by genotypic complementarity rather than by selection of particularly robust genotypes. Positive effects on invertebrate fauna suggest that genetic diversity has second-order effects reaching higher trophic levels. Our results highlight the importance of maintaining genetic as well as species diversity to enhance ecosystem resilience in a world of increasing uncertainty. PMID:15710890

  1. Comparing performance of modern genotype imputation methods in different ethnicities

    PubMed Central

    Roshyara, Nab Raj; Horn, Katrin; Kirsten, Holger; Ahnert, Peter; Scholz, Markus

    2016-01-01

    A variety of modern software packages are available for genotype imputation relying on advanced concepts such as pre-phasing of the target dataset or utilization of admixed reference panels. In this study, we performed a comprehensive evaluation of the accuracy of modern imputation methods on the basis of the publicly available POPRES samples. Good quality genotypes were masked and re-imputed by different imputation frameworks: namely MaCH, IMPUTE2, MaCH-Minimac, SHAPEIT-IMPUTE2 and MaCH-Admix. Results were compared to evaluate the relative merit of pre-phasing and the usage of admixed references. We showed that the pre-phasing framework SHAPEIT-IMPUTE2 can overestimate the certainty of genotype distributions resulting in the lowest percentage of correctly imputed genotypes in our case. MaCH-Minimac performed better than SHAPEIT-IMPUTE2. Pre-phasing always reduced imputation accuracy. IMPUTE2 and MaCH-Admix, both relying on admixed-reference panels, showed comparable results. MaCH showed superior results if well-matched references were available (Nei’s GST ≤ 0.010). For small to medium datasets, frameworks using genetically closest reference panel are recommended if the genetic distance between target and reference data set is small. Our results are valid for small to medium data sets. As shown on a larger data set of population based German samples, the disadvantage of pre-phasing decreases for larger sample sizes. PMID:27698363

  2. Speech Characteristics Associated with Three Genotypes of Ataxia

    ERIC Educational Resources Information Center

    Sidtis, John J.; Ahn, Ji Sook; Gomez, Christopher; Sidtis, Diana

    2011-01-01

    Purpose: Advances in neurobiology are providing new opportunities to investigate the neurological systems underlying motor speech control. This study explores the perceptual characteristics of the speech of three genotypes of spino-cerebellar ataxia (SCA) as manifest in four different speech tasks. Methods: Speech samples from 26 speakers with SCA…

  3. Genotyping by sequencing of a diploid potato F2 population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genotyping-by-sequencing (GBS) of multiplexed, restriction-site associated DNA (RAD) libraries is an attractive technology for generating genome-wide markers because of its technical simplicity and low costs per sample. To investigate its feasibility for potato, a diploid F2 population (S. tuberosum...

  4. Genotypic characterization of amoeba isolated from Acanthamoeba keratitis in Poland.

    PubMed

    Derda, Monika; Solarczyk, Piotr; Cholewiński, Marcin; Hadaś, Edward

    2015-03-01

    Free-living amoebae belonging to the genus Acanthamoeba are the causative factor of many diseases. Among others, they cause Acanthamoeba keratitis (AK), a condition that usually occurs in contact lens wearers, though it is also observed in non-wearers. The number of diagnosed cases of AK increased more than eightfold during 8 years in the USA, and a proportional increase in frequency also occurred in Poland and Europe. Cases of AK are usually diagnosed late, and their therapy is difficult and rarely successful. AK is an uncommon diagnosis in Poland. The increased number of positive cases observed in our laboratory may reflect the growing at-risk population of contact lens wearers. Acanthamoeba as a genus of facultative human parasites is currently classified into 17 genotypes. Isolates belonging to seven genotypes were found to be associated with AK. One genotype in particular, T4, was found to be overrepresented in human disease. The main finding of our study is that in Poland, AK is almost always associated with the T4 genotype.

  5. Genotypes are useful for more than genomic evaluation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New services that provide pedigree discovery, breed composition, mating programs, genomic inbreeding, fertility defects, and inheritance tracking all are possible from low-cost genotyping in addition to genomic evaluation. Genetic markers let breeders select among sibs before their phenotypes became...

  6. Iterative combination of national phenotype, genotype, pedigree, and foreign information

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Single step methods can combine all sources of information into accurate rankings for animals with and without genotypes. Equations that require inverting the genomic relationship matrix G work well with limited numbers of animals, but equivalent models without inversion are needed as numbers increa...

  7. Rice Genotype Variation in Leaf-Grain Element Concentration Associations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As a major food crop of the world, rice can also be a major source of mineral nutrients for much of the world's population. The control of accumulation of particular elements in the grain varies by element. There is considerable variation among rice genotypes for concentrations of specific elements ...

  8. Potential antioxidant response to coffee — A matter of genotype?

    PubMed Central

    Hassmann, Ute; Haupt, Larisa M.; Smith, Robert A.; Winkler, Swantje; Bytof, Gerhard; Lantz, Ingo; Griffiths, Lyn R.; Marko, Doris

    2014-01-01

    In a human intervention study, coffee combining natural green coffee bean constituents and dark roast products was identified as a genotype-dependent inducer of the Nrf2/ARE pathway, significantly affecting Nrf2 gene expression and downstream GST1A1 and UGT1A1 gene transcription. The observed transcriptional changes correlated with the presence of specific Nrf2 genotypes suggesting their influence on both Nrf2 and subsequent ARE-dependent GST1A1 and UGT1A1 transcription. While the presence of the − 653 SNP seems to be advantageous, resulting in higher Nrf2, GST1A1 and UGT1A1 gene transcription following coffee consumption, in contrast, the presence of the − 651 SNP significantly down-regulated the response to the study coffee. Furthermore, the presence of the B/B genotype in GST1A1 along with the frequency of the [TA]6/6 and [TA]7/7 polymorphisms in UGT1A1 appeared to significantly increase sensitivity toward coffee-induced gene transcription. This data suggests that when examining the role of the Nrf2/ARE pathway in the regulation of antioxidative and chemopreventive phase II efficacy, individual genotypes should be included when considering the potency of bioactive food/food constituents and their therapeutic potential. PMID:25606436

  9. Comprehensive genotyping of the USA national maize inbred seed bank

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The germplasm bank at the USDA-ARS North Central Regional Plant Introduction Station (NCRPIS) in Ames, Iowa, preserves maize inbred lines from breeding programs from all over the world, including some of the key lines from the breeding history of maize. We genotyped 2,815 maize inbred accessions, mo...

  10. Tissue fractions of cadmium in two hyperaccumulating Jerusalem artichoke genotypes.

    PubMed

    Long, Xiaohua; Ni, Ni; Liu, Zhaopu; Rengel, Zed; Jiang, Xin; Shao, Hongbo

    2014-01-01

    In order to investigate the mechanisms in two Jerusalem artichoke (Helianthus tuberosus L.) genotypes that hyperaccumulate Cd, a sand-culture experiment was carried out to characterize fractionation of Cd in tissue of Cd-hyperaccumulating genotypes NY2 and NY5. The sequential extractants were: 80% v/v ethanol (FE), deionized water (FW), 1 M NaCl (FNaCl), 2% v/v acetic acid (FAcet), and 0.6 M HCl (FHCl). After 20 days of treatments, NY5 had greater plant biomass and greater Cd accumulation in tissues than NY2. In both genotypes the FNaCl fraction was the highest in roots and stems, whereas the FAcet and FHCl fractions were the highest in leaves. With an increase in Cd concentration in the culture solution, the content of every Cd fraction also increased. The FW and FNaCl ratios in roots were lower in NY5 than in NY2, while the amount of other Cd forms was higher. It implied that, in high accumulator, namely, NY5, the complex of insoluble phosphate tends to be shaped more easily which was much better for Cd accumulation. Besides, translocation from plasma to vacuole after combination with protein may be one of the main mechanisms in Cd-accumulator Jerusalem artichoke genotypes.

  11. Root response of Jerusalem artichoke genotypes to different water regimes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to determine effects of drought on selected root growth parameters and develop relationships between root parameters and tuber yield for selected Jerusalem artichoke (JA) genotypes. Three water regimes (Field capacity, 50% available water (AW) and 25% AW) and five JA...

  12. The magnitude of local adaptation under genotype-dependent dispersal

    PubMed Central

    Bolnick, Daniel I; Otto, Sarah P

    2013-01-01

    Dispersal moves individuals from patches where their immediate ancestors were successful to sites where their genotypes are untested. As a result, dispersal generally reduces fitness, a phenomenon known as “migration load.” The strength of migration load depends on the pattern of dispersal and can be dramatically lessened or reversed when individuals move preferentially toward patches conferring higher fitness. Evolutionary ecologists have long modeled nonrandom dispersal, focusing primarily on its effects on population density over space, the maintenance of genetic variation, and reproductive isolation. Here, we build upon previous work by calculating how the extent of local adaptation and the migration load are affected when individuals differ in their dispersal rate in a genotype-dependent manner that alters their match to their environment. Examining a one-locus, two-patch model, we show that local adaptation occurs through a combination of natural selection and adaptive dispersal. For a substantial portion of parameter space, adaptive dispersal can be the predominant force generating local adaptation. Furthermore, genetic load may be largely averted with adaptive dispersal whenever individuals move before selective deaths occur. Thus, to understand the mechanisms driving local adaptation, biologists must account for the extent and nature of nonrandom, genotype-dependent dispersal, and the potential for adaptation via spatial sorting of genotypes. PMID:24363900

  13. Determining self-incompatibility genotypes in Belgian wild cherries.

    PubMed

    De Cuyper, B; Sonneveld, T; Tobutt, K R

    2005-04-01

    ABSTRACT The self-incompatibility (S) genotypes of a collection of 65 Belgian accessions of wild cherry, selected within two populations and planted in a seed orchard, were determined using polymerase chain reaction (PCR) methods. Initially, DNA extracts were amplified with consensus primers that amplify across the second intron of the S-ribonuclease gene which shows considerable length polymorphism. The provisional genotypes deduced were checked with the appropriate allele-specific primers for the known alleles S(1) to S(16). Putative new alleles were subjected to PCR with consensus primers amplifying across the first intron. Six new alleles, S(17) to S(22), were thus indicated on the basis of the estimated lengths of the first and second intron PCR products. Examples of these alleles were partially sequenced and were indeed mutually distinct and different from the known alleles. The incompatibility genotypes of all 65 accessions were determined and one triploid individual was found. Seventeen alleles were detected in all. Allele frequencies differed between samples and the expected total number of alleles in the underlying populations was estimated. The wild cherry populations differed significantly with respect to allelic frequencies from sweet cherry cultivars; alleles S(4) and S(5), which are moderately frequent in sweet cherry, were absent from the wild cherry accessions. The knowledge of the S genotypes will be useful for studying the gene flow within the seed orchard and these approaches should also be informative in wild populations.

  14. Murine models susceptibility to distinct Trypanosoma cruzi I genotypes infection.

    PubMed

    León, Cielo M; Montilla, Marleny; Vanegas, Ricardo; Castillo, Maria; Parra, Edgar; Ramírez, Juan David

    2017-04-01

    Chagas disease is a complex zoonosis that affects around 8 million people worldwide. This pathology is caused by Trypanosoma cruzi, a kinetoplastid parasite that shows tremendous genetic diversity evinced in six distinct Discrete Typing Units (TcI-TcVI) including a recent genotype named as TcBat and associated with anthropogenic bats. TcI presents a broad geographical distribution and has been associated with chronic cardiomyopathy. Recent phylogenetic studies suggest the existence of two genotypes (Domestic (TcIDom) and sylvatic TcI) within TcI. The understanding of the course of the infection in different mouse models by these two genotypes is not yet known. Therefore, we infected 126 animals (ICR-CD1, National Institute of Health (NIH) and Balb/c) with two TcIDom strains and one sylvatic strain for a follow-up period of 60 days. We quantified the parasitaemia, immune response and histopathology observing that the maximum day of parasitaemia was achieved at day 21 post-infection. Domestic strains showed higher parasitaemia than the sylvatic strain in the three mouse models; however in the survival curves Balb/c mice were less susceptible to infection compared with NIH and ICR-CD1. Our results suggest that the genetic background plays a fundamental role in the natural history of the infection and the sympatric TcI genotypes have relevant implications in disease pathogenesis.

  15. Assessing allelic dropout and genotype reliability using maximum likelihood.

    PubMed Central

    Miller, Craig R; Joyce, Paul; Waits, Lisette P

    2002-01-01

    A growing number of population genetic studies utilize nuclear DNA microsatellite data from museum specimens and noninvasive sources. Genotyping errors are elevated in these low quantity DNA sources, potentially compromising the power and accuracy of the data. The most conservative method for addressing this problem is effective, but requires extensive replication of individual genotypes. In search of a more efficient method, we developed a maximum-likelihood approach that minimizes errors by estimating genotype reliability and strategically directing replication at loci most likely to harbor errors. The model assumes that false and contaminant alleles can be removed from the dataset and that the allelic dropout rate is even across loci. Simulations demonstrate that the proposed method marks a vast improvement in efficiency while maintaining accuracy. When allelic dropout rates are low (0-30%), the reduction in the number of PCR replicates is typically 40-50%. The model is robust to moderate violations of the even dropout rate assumption. For datasets that contain false and contaminant alleles, a replication strategy is proposed. Our current model addresses only allelic dropout, the most prevalent source of genotyping error. However, the developed likelihood framework can incorporate additional error-generating processes as they become more clearly understood. PMID:11805071

  16. Genotypic response to multiple abiotic stresses: Functional relationships among nutrients

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Macro- and micro-nutrients estimated in leaves, stems and seed of eleven genotypes of five physiologically diverse crop species (chickpeas, corn, safflower, soybean, and wheat, respectively producing protein, carbohydrates, oil, protein-oil, and carbohydrates-protein, as main seed storage macromolec...

  17. Immune Response Genotypes and Risk of Young Adult Hodgkin Lymphoma

    DTIC Science & Technology

    2008-09-01

    1) To identify, enroll and collect blood specimens from 368 adolescents and young adults 18 years of age or older at the time of participation... Young Adult Hodgkin Lymphoma PRINCIPAL INVESTIGATOR: Wendy Cozen, Victoria Cortessis...COVERED 1 Sep 2007 – 31 Aug 2008 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Immune Response Genotypes and Risk of Young Adult Hodgkin Lymphoma 5b

  18. Surveillance for Echinococcus canadensis genotypes in Canadian ungulates.

    PubMed

    Schurer, Janna; Shury, Todd; Leighton, Frederick; Jenkins, Emily

    2013-12-01

    The geographic and host distribution, prevalence and genotypes of Echinococcus canadensis in wild ungulates in Canada are described to better understand the significance for wildlife and public health. We observed E. canadensis in 10.5% (11/105) of wild elk (wapiti; Cervus canadensis) in Riding Mountain National Park, Manitoba, examined at necropsy, over two consecutive years (2010-2011). Molecular characterization of hydatid cyst material from these elk, as well as three other intermediate wildlife host species, was based on sequence of a 470 bp region of the NADH dehydrogenase subunit 1 (NAD1) mitochondrial gene. In moose [Alces alces], elk, and caribou [Rangifer tarandus] from northwestern Canada, the G10 genotype was the only one present, and the G8 genotype was detected in a muskox (Ovibos moschatus) from northeastern Canada. On a search of the national wildlife health database (1992-2010), cervids with hydatid cysts were reported in all provinces and territories except the Atlantic provinces, from which wolves [Canis lupis] are historically absent. Of the 93 cervids with records of hydatid cysts, 42% were elk, 37% were moose, 14% were caribou, and 6% were white-tailed and mule deer [Odocoileus virginianus and Odocoileus hemonius]. In these animals, 83% of cysts were detected in lungs alone, 8% in both lungs and liver, 3% in liver alone, and 6% in other organs. These observations can help target surveillance programs and contribute to a better understanding of ecology, genetic diversity, and genotype pathogenicity in the Echinococcus granulosus species complex.

  19. Evaluation of soybean genotypes for resistance to charcoal rot

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Charcoal rot caused by Macrophomina phaseolina causes more yield loss in soybean than most other diseases in the southern U.S.A. There are no commercial genotypes marketed as resistant to charcoal rot of soybean. Reactions of 27 maturity group (MG) III, 29 Early MG IV, 34 Late MG IV, and 59 MG V gen...

  20. Comparative analysis of African swine fever virus genotypes and serogroups.

    PubMed

    Malogolovkin, Alexander; Burmakina, Galina; Titov, Ilya; Sereda, Alexey; Gogin, Andrey; Baryshnikova, Elena; Kolbasov, Denis

    2015-02-01

    African swine fever virus (ASFV) causes highly lethal hemorrhagic disease among pigs, and ASFV's extreme antigenic diversity hinders vaccine development. We show that p72 ASFV phylogenetic analysis does not accurately define ASFV hemadsorption inhibition assay serogroups. Thus, conventional ASFV genotyping cannot discriminate between viruses of different virulence or predict efficacy of a specific ASFV vaccine.

  1. Genotype and ancestry modulate brain's DAT availability in healthy humans

    SciTech Connect

    Shumay, E.; Shumay, E.; Chen, J.; Fowler, J.S.; Volkow, N.D.

    2011-08-01

    The dopamine transporter (DAT) is a principal regulator of dopaminergic neurotransmission and its gene (the SLC6A3) is a strong biological candidate gene for various behavioral- and neurological disorders. Intense investigation of the link between the SLC6A3 polymorphisms and behavioral phenotypes yielded inconsistent and even contradictory results. Reliance on objective brain phenotype measures, for example, those afforded by brain imaging, might critically improve detection of DAT genotype-phenotype association. Here, we tested the relationship between the DAT brain availability and the SLC6A3 genotypes using an aggregate sample of 95 healthy participants of several imaging studies. These studies employed positron emission tomography (PET) with [{sup 11}C] cocaine wherein the DAT availability was estimated as Bmax/Kd; while the genotype values were obtained on two repeat polymorphisms - 3-UTR- and intron 8- VNTRs. The main findings are the following: (1) both polymorphisms analyzed as single genetic markers and in combination (haplotype) modulate DAT density in midbrain; (2) ethnic background and age influence the strength of these associations; and (3) age-related changes in DAT availability differ in the 3-UTR and intron8 - genotype groups.

  2. Coral host transcriptomic states are correlated with Symbiodinium genotypes.

    PubMed

    DeSalvo, M K; Sunagawa, S; Fisher, P L; Voolstra, C R; Iglesias-Prieto, R; Medina, M

    2010-03-01

    A mutualistic relationship between reef-building corals and endosymbiotic dinoflagellates (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. In this study, we monitored Symbiodinium physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered fragments of the coral Montastraea faveolata using a custom cDNA gene expression microarray. Interestingly, gene expression was more similar among samples with the same Symbiodinium content rather than the same experimental condition. In order to discount for host-genotypic effects, we sampled fragments from a single colony of M. faveolata containing different symbiont types, and found that the host transcriptomic states grouped according to Symbiodinium genotype rather than thermal stress. As the first study that links coral host transcriptomic patterns to the clade content of their Symbiodinium community, our results provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-Symbiodinium partnerships.

  3. Nutrient uptake of peanut genotypes under different water regimes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Drought is a serious environmental stress limiting growth and productivity in peanut and other crops. Nutrient uptake of peanut is reduced under drought conditions, which reduces yield. The objectives of this study were to investigate nutrient uptake of peanut genotypes in response to drought and ...

  4. Accuracy of genotype imputation in Swiss cattle breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to evaluate the accuracy of imputation from Illumina Bovine3k Bead Chip (3k) and Illumina BovineLD (6k) to 54k chip information in Swiss dairy cattle breeds. Genotype data comprised of 54k SNP chip data of Original Braunvieh (OB), Brown Swiss (BS), Swiss Fleckvieh (SF...

  5. Genotyping by sequencing in grape - stacks or tassel?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genotyping by sequencing (GBS) is a powerful method for assaying populations of individuals for hundreds of thousands of genetic markers. The optimal strategy employed for data collection and analysis depends on the kind of biological question being asked and the genomic resources already available...

  6. Genotype-phenotype correlation for pulmonary function in cystic fibrosis

    PubMed Central

    de Gracia, J; Mata, F; Alvarez, A; Casals, T; Gatner, S; Vendrell, M; de la Rosa, D; Guarner, L; Hermosilla, E

    2005-01-01

    Background: Since the CFTR gene was cloned, more than 1000 mutations have been identified. To date, a clear relationship has not been established between genotype and the progression of lung damage. A study was undertaken of the relationship between genotype, progression of lung disease, and survival in adult patients with cystic fibrosis (CF). Methods: A prospective cohort of adult patients with CF and two CFTR mutations followed up in an adult cystic fibrosis unit was analysed. Patients were classified according to functional effects of classes of CFTR mutations and were grouped based on the CFTR molecular position on the epithelial cell surface (I–II/I–II, I–II/III–V). Spirometric values, progression of lung disease, probability of survival, and clinical characteristics were analysed between groups. Results: Seventy four patients were included in the study. Patients with genotype I–II/I–II had significantly lower current spirometric values (p<0.001), greater loss of pulmonary function (p<0.04), a higher proportion of end-stage lung disease (p<0.001), a higher risk of suffering from moderate to severe lung disease (odds ratio 7.12 (95% CI 1.3 to 40.5)) and a lower probability of survival than patients with genotype I–II/III, I–II/IV and I–II/V (p<0.001). Conclusions: The presence of class I or II mutations on both chromosomes is associated with worse respiratory disease and a lower probability of survival. PMID:15994263

  7. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Drug metabolizing enzyme genotyping system. 862.3360 Section 862.3360 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... drug metabolizing enzyme. This device is used as an aid in determining treatment choice...

  8. LHRH and LHR genotypes and prostate cancer incidence and survival.

    PubMed

    Ingles, Sue Ann; Liu, Stephen V; Pinski, Jacek

    2013-01-01

    Despite their crucial role in initiating steroid-hormone synthesis, the hypothalamic and pituitary hormones (LH, LHRH) and their receptors have received scant attention in genetic studies of hormone-related diseases. This study included 1,170 men diagnosed with prostate cancer (PC) in Los Angeles County between 1999 and 2003. LHRH and LH receptor genotypes were examined for association with PC survival. Additionally, associations with PC incidence were examined by comparing PC cases to control men of similar age and race/ethnicity. The LHR 312 G allele was found to be associated with increased PC mortality (p=0.01). Ten years after diagnosis, 16% of men carrying two copies of the G allele (genotype GG) had died of PC, compared to 11% of those with genotype AG and 9% of those with AA. In a case-control comparison, this same allele was significantly associated with decreased PC risk: OR=0.68 (95% CI: 0.49, 0.93) for genotype GG vs. AA. These results suggest that androgens may play opposing roles in PC initiation and progression, and highlight the need to include these important but overlooked genes in future studies of PC etiology, prognosis, and treatment.

  9. Genotype 3 Infection: The Last Stand of Hepatitis C Virus.

    PubMed

    Chan, Austin; Patel, Keyur; Naggie, Susanna

    2017-02-01

    Hepatitis C virus (HCV) represents a significant global disease burden, with an estimated 130-150 million people worldwide living with chronic HCV infection. Within the six major clinical HCV genotypes, genotype 3 represents 22-30% of all infection and is described as a unique entity with higher rates of steatosis, faster progression to cirrhosis, and higher rates of hepatocellular carcinoma. Hepatic steatosis in the setting of hepatitis C genotype 3 (HCV-3) is driven by viral influence on three major pathways: microsomal triglyceride transfer protein, sterol regulatory element-binding protein-1c, and peroxisome proliferator-associated receptor-α. Historically with direct-acting antivirals, the rates of cure for HCV-3 therapies lagged behind the other genotypes. As current therapies for HCV-3 continue to close this gap, it is important to be cognizant of common drug interactions such as acid-suppressing medication and amiodarone. In this review, we discuss the rates of steatosis in HCV-3, the mechanisms behind HCV-3-specific steatosis, and current and future therapies.

  10. Tamarix (Tamaricaceae) hybrids: most dominant invasive genotype in southern Africa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hybridization can potentially enhance invasiveness. Tamarix (Tamaricaceae) hybrids appear to be the dominant genotypes in their invasions. Exotic Tamarix are declared invasive in South Africa and the exotic T. chinensis and T. ramosissima are known to hybridize between themselves, and with the nativ...

  11. Differential soil acidity tolerance of dry bean genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil acidity is a major yield limiting factors for bean production in the tropical regions. Using soil acidity tolerant genotypes is an important strategy in improving bean yields and reducing cost of production. A greenhouse experiment was conducted with the objective of evaluating 20 dry bean geno...

  12. Distribution of Candida albicans genotypes among family members

    NASA Technical Reports Server (NTRS)

    Mehta, S. K.; Stevens, D. A.; Mishra, S. K.; Feroze, F.; Pierson, D. L.

    1999-01-01

    Thirty-three families (71 subjects) were screened for the presence of Candida albicans in mouthwash or stool specimens; 12 families (28 subjects) were culture-positive for this yeast. An enrichment procedure provided a twofold increase in the recovery of C. albicans from mouthwash specimens. Nine of the twelve culture-positive families had two positive members each, two families had three positive members each, and one family had four positive members. Genetic profiles were obtained by three methods: pulsed-field gel electrophoresis; restriction endonuclease analysis, and random amplification of polymorphic DNA analysis. DNA fingerprinting of C. albicans isolated from one body site three consecutive times revealed that each of the 12 families carried a distinct genotype. No two families shared the same strain, and two or more members of a family commonly shared the same strain. Intrafamily genotypic identity (i.e., each member within the family harbored the same strain) was demonstrated in six families. Genotypes of isolates from husband and wife differed from one another in five families. All three methods were satisfactory in determining genotypes; however, we concluded that restriction endonuclease analysis provided adequate resolving power.

  13. Detection of genotype recycling fraud in U.S. immigrants.

    PubMed

    Wenk, Robert E

    2011-01-01

    Relationship testing laboratories provide genetic evidence to support or refute claims of kinship between U.S. citizen petitioners and potential immigrant beneficiaries. One female beneficiary presented a male amelogenin type and alleles at 15 autosomal loci that were identical to an alleged brother's. Laboratory records showed that her alleged father had petitioned to have 15 children emigrate from Ghana. The petitioner's 15 paternity indices exceeded 10⁵, but the children shared only four short tandem repeat (STR) profiles, suggesting fraudulent reuse of genotypes in this alleged pedigree (AP). To determine the extent of this "genotype recycling," I examined the laboratory's 555 APs from Ghana and 532 control APs from Nigeria. Seventeen Ghanaian APs (3.1%) but no Nigerian APs showed genotype recycling. Of 90 tested people in the 17 APs, 56 shared identical STR profiles with others in their AP. Of these 56 people, 10 were petitioners with unexpectedly high parentage indices. Seven of 56 had amelogenin types that disagreed with their declared genders. Database searches for identical multilocus genotypes in allegedly different people would best detect this fraud.

  14. Racial differences in seroprevalence of HAV and HEV in blood donors in the Western Cape, South Africa: a clue to the predominant HEV genotype?

    PubMed

    Lopes, T; Cable, R; Pistorius, C; Maponga, T; Ijaz, S; Preiser, W; Tedder, R; Andersson, M I

    2017-03-30

    Hepatitis E virus (HEV) infection is a major cause of acute hepatitis worldwide. This infection causes major water-borne outbreaks in low- and middle-income countries, whilst in industrialised countries this infection is zoonotic. These differences in epidemiology are related to different HEV genotypes. HEV genotype 3 is a zoonotic infection, whilst genotype 2 causes large outbreaks. This study determined the seroprevalence of HEV in blood donors from the Western Cape. Anti-hepatitis A virus (anti-HAV) antibody was detected in 184/300 (61%) donors. Antibody to HEV (anti-HEV) was detected in 78 of 300 donors (26%). It was highest in mixed race donors (62/100), followed by white donors (23/100) and lowest in black donors (19/100) P = 0.019. Since it is thought that genotypes 1 and 2 predominate both viruses would be acquired by the oro-faecal route, it is surprising that HEV seroprevalence does not mirror that of HAV. We postulate that this may reflect differences in socio-economic status and consumption of dietary meat. So the marked divergence between HEV and HAV seroprevalence may be the result of different routes of transmission. Further data are needed to explore the risk factors associated with HEV infection.

  15. Thermolabile MTHFR genotype and retinal vascular occlusive disease

    PubMed Central

    Cahill, M; Karabatzaki, M; Donoghue, C; Meleady, R; Mynett-Johnson, L; Mooney, D; Graham, I; Whitehead, A; Shields, D

    2001-01-01

    BACKGROUND—Raised levels of total plasma homocysteine (tHcy) are associated with an increased risk of retinal vascular occlusive disease. A thermolabile form of a pivotal enzyme in homocysteine metabolism, methylenetetrahydrofolate reductase (MTHFR), has been associated with vascular occlusive disease and raised tHcy levels. The relation between thermolabile MTHFR genotype, tHcy, and retinal vascular occlusive disease has not been determined.
METHODS—A retrospective case-control study involving hospital based controls and cases with retinal vascular occlusions in whom tHcy levels had been determined was undertaken. Genotyping for the MTHFR 677 C-T mutation that specifies the thermolabile form of the enzyme was performed by established methods in all subjects. The relation between homozygosity for thermolabile MTHFR genotype (TT), raised tHcy levels, and risk of retinal vascular occlusive disease was examined.
RESULTS—87 cases of retinal vascular occlusive disease (mean age 68.7 years) comprising 26 cases of retinal artery occlusion and 61 of retinal vein occlusion were compared with 87 controls (mean age 70.2 years). The TT genotype did not confer a significantly increased risk of retinal vascular occlusive disease. The mean tHcy level was significantly higher in the cases than in the controls (p<0.0001). Overall, and in both the cases and controls, the frequency of the TT genotype was higher in those with normal tHcy levels than in those with increased levels of tHcy. However, the TT genotype did not significantly alter the risk of increased tHcy levels in these patients.
CONCLUSIONS—The TT genotype is not associated with an increased risk of retinal vascular occlusive disease or increased tHcy levels in this group of elderly patients. In older patients, nutritional rather than genetic factors may be more important in increasing tHcy levels, a known risk factor for retinal vascular occlusive disease.

 PMID:11133719

  16. Pollen-Stigma Adhesion in Kale Is Not Dependent on the Self-(In)Compatibility Genotype.

    PubMed Central

    Luu, D. T.; Heizmann, P.; Dumas, C.

    1997-01-01

    The adhesion of pollen on the stigmas of flowering plants is a critical step for the success of reproduction in angiosperms, long considered to present some specificity in terms of self-incompatibility. We carried out quantitative measurements of the pollen-stigma adhesion (expressed in Newtons) in kale (Brassica oleracea), using the flotation force of Archimedes exerted by dense sucrose solutions (50%, w/v) to release pollen grains fixed on the surface of stigmas. We demonstrate that pollen adhesion varies with the genotypes of the plants used as partners, but increases with time in all cases for about 30 to 60 min after pollination. There is no correlation with the self- or cross-status of the pollinations, nor with the self-compatible or -incompatible genotypes of the parents. Only late events of pollination, after the germination or arrest of the pollen tube, depend on compatibility type. Biochemical and physiological dissection of pollen-stigma adhesion points to major components of this interaction: among male components, the pollen coating, eliminated by delipidation (or modified by mutation in the case of the cer mutants of the related species Arabidopsis thaliana), plays a major role in adhesion; the genetic background of the pollen parent is also of some importance. On the female side, the developmental stage of the stigma and the protein constituents of the stigmatic pellicle are critical for pollen capture. The SLG and SLR1 proteins are not involved in the initial stages of pollen adhesion on the stigma but one or both may be involved in the later stages. PMID:12223868

  17. Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet.

    PubMed

    Wedrowicz, Faye; Karsa, Mawar; Mosse, Jennifer; Hogan, Fiona E

    2013-07-01

    The koala, an Australian icon, has been added to the threatened species list. Rationale for the listing includes proposed declines in population size, threats to populations (e.g. disease) and loss and fragmentation of habitat. There is now an urgent need to obtain accurate data to assess the status of koala populations in Australia, to ensure the long-term viability of this species. Advances in genetic techniques have enabled DNA analysis to study and inform the management of wild populations; however, sampling of individual koalas is difficult in tall, often remote, eucalypt forest. The collection of faecal pellets (scats) from the forest floor presents an opportunistic sampling strategy, where DNA can be collected without capturing or even sighting an individual. Obtaining DNA via noninvasive sampling can be used to rapidly sample a large proportion of a population; however, DNA from noninvasively collected samples is often degraded. Factors influencing DNA quality and quantity include environmental exposure, diet and methods of sample collection, storage and DNA isolation. Reduced DNA quality and quantity can introduce genotyping errors and provide inaccurate DNA profiles, reducing confidence in the ability of such data to inform management/conservation strategies. Here, we present a protocol that produces a reliable individual koala genotype from a single faecal pellet and highlight the importance of optimizing DNA isolation and analysis for the species of interest. This method could readily be adapted for genetic studies of mammals other than koalas, particularly those whose diet contains high proportions of volatile materials that are likely to induce DNA damage.

  18. Genetic diversity of popcorn genotypes using molecular analysis.

    PubMed

    Resh, F S; Scapim, C A; Mangolin, C A; Machado, M F P S; do Amaral, A T; Ramos, H C C; Vivas, M

    2015-08-19

    In this study, we analyzed dominant molecular markers to estimate the genetic divergence of 26 popcorn genotypes and evaluate whether using various dissimilarity coefficients with these dominant markers influences the results of cluster analysis. Fifteen random amplification of polymorphic DNA primers produced 157 amplified fragments, of which 65 were monomorphic and 92 were polymorphic. To calculate the genetic distances among the 26 genotypes, the complements of the Jaccard, Dice, and Rogers and Tanimoto similarity coefficients were used. A matrix of Dij values (dissimilarity matrix) was constructed, from which the genetic distances among genotypes were represented in a more simplified manner as a dendrogram generated using the unweighted pair-group method with arithmetic average. Clusters determined by molecular analysis generally did not group material from the same parental origin together. The largest genetic distance was between varieties 17 (UNB-2) and 18 (PA-091). In the identification of genotypes with the smallest genetic distance, the 3 coefficients showed no agreement. The 3 dissimilarity coefficients showed no major differences among their grouping patterns because agreement in determining the genotypes with large, medium, and small genetic distances was high. The largest genetic distances were observed for the Rogers and Tanimoto dissimilarity coefficient (0.74), followed by the Jaccard coefficient (0.65) and the Dice coefficient (0.48). The 3 coefficients showed similar estimations for the cophenetic correlation coefficient. Correlations among the matrices generated using the 3 coefficients were positive and had high magnitudes, reflecting strong agreement among the results obtained using the 3 evaluated dissimilarity coefficients.

  19. Examination of resistance of potato genotypes to Erwinia ssp.

    PubMed

    Kállai, Mónika; Csitári, Gábor; Sipos, Elvira; Polgár, Zsolt

    2007-01-01

    Potato can be attacked by several economically important pathogens. From the various diseases, in our experiment we dealt with the bacterial soft rot of potato caused by Erwinia species. In the experiments back cross progenies (BC1, BC2, BC3 and BC4) of Solanum brevidens + Solanum tuberosum somatic hybrids produced by the Potato Research Centre, Keszthely were tested to the infection of E carotovora ssp. atroseptica (Eca), E. carotovora ssp. carotovora (Ecc) and E. chrysanthemi (Echr). All together 11 BC genotypes pre selected from several hundred breeding lines based on their preferred agronomical appearance and virus resistance characters as well as 4 Hungarian potato cultivar (Rioja, Desiree, White lady and Hópehely) as controls were involved into the experiments. Tuber slices from each genotype were artificially infected with bacteria suspension Ecc strain D3, and Echr strain CHR 1492, and Eca strain BN3) and incubated at 27 degrees C with 100% relative air humidity for 48 h before evaluation. Dry matter and starch content of tubers were determined right before the tests. Volume of rotted tuber tissue was determined in mm3 and used for comparison of the level of resistance or susceptibility of the genotypes. Relationship between the reaction to the bacteria strains and dry matter content was examined also. Tested genotypes showed the highest resistance to Eca, while the highest susceptibility to Echr. By the increase of BC level the susceptibility of the genotypes significantly increased as well regardless of the tested bacteria. No direct correlation was found between the dry matter content of tubers and their reaction to tested bacteria.

  20. PCR Primers for identification of high sucrose Saccharum genotypes.

    PubMed

    Vinayak, Vandana; Dhawan, Ashok K; Gupta, V K

    2010-01-01

    The progeny of a cross between high sucrose sugarcane clone S. officinarum 'Gungera' and a low sucrose clone S. spontaneum 'SES 603' resulted in interspecific hybrids that were named as ISH-1 to ISH-29 and graded on the basis of sucrose content. Hybrids ISH-1, ISH-5, ISH-17 and ISH-23 were selected as very high sucrose (65 to 100 mg/g tissue) genotypes, whereas ISH-10, ISH-11, ISH-12 and ISH-25 were very low sucrose (2 to 25 mg/g tissue) genotypes. DNA from leaves of both the parent clones, as also the progeny hybrids, was amplified using selected primers, in order to identify markers for sucrose content. Ten specific primers were examined: primers 'A' and 'B' that detect polymorphism in promoter region of sucrose synthase-2 gene; primers AI, SS and SPS that were designed on the basis of nucleotide sequences of genes for acid invertase, sucrose synthase and sucrose phosphate synthase enzymes, respectively and primers MSSCIR43, MSSCIRI, SMC226CG, SMC1039CG and SCB07 selected for relation to sucrose accumulation process. DNA products specific to low or high sucrose clones were identified. Primer 'A' and AI amplified DNA products of size 230 and 500 bp, respectively only in high sucrose genotypes ('Gungera', ISH-1, ISH-5, ISH-17 and ISH-23), while primer SMC226CG generated a DNA product of size 920 bp only in low sucrose genotypes ('SES 603', ISH-10, ISH-11, ISH-12 and ISH-25). Ten random decamer primers were also examined, but their products did not show relationship to sucrose content of genotypes.

  1. Epigenomics and bolting tolerance in sugar beet genotypes.

    PubMed

    Hébrard, Claire; Peterson, Daniel G; Willems, Glenda; Delaunay, Alain; Jesson, Béline; Lefèbvre, Marc; Barnes, Steve; Maury, Stéphane

    2016-01-01

    In sugar beet (Beta vulgaris altissima), bolting tolerance is an essential agronomic trait reflecting the bolting response of genotypes after vernalization. Genes involved in induction of sugar beet bolting have now been identified, and evidence suggests that epigenetic factors are involved in their control. Indeed, the time course and amplitude of DNA methylation variations in the shoot apical meristem have been shown to be critical in inducing sugar beet bolting, and a few functional targets of DNA methylation during vernalization have been identified. However, molecular mechanisms controlling bolting tolerance levels among genotypes are still poorly understood. Here, gene expression and DNA methylation profiles were compared in shoot apical meristems of three bolting-resistant and three bolting-sensitive genotypes after vernalization. Using Cot fractionation followed by 454 sequencing of the isolated low-copy DNA, 6231 contigs were obtained that were used along with public sugar beet DNA sequences to design custom Agilent microarrays for expression (56k) and methylation (244k) analyses. A total of 169 differentially expressed genes and 111 differentially methylated regions were identified between resistant and sensitive vernalized genotypes. Fourteen sequences were both differentially expressed and differentially methylated, with a negative correlation between their methylation and expression levels. Genes involved in cold perception, phytohormone signalling, and flowering induction were over-represented and collectively represent an integrative gene network from environmental perception to bolting induction. Altogether, the data suggest that the genotype-dependent control of DNA methylation and expression of an integrative gene network participate in bolting tolerance in sugar beet, opening up perspectives for crop improvement.

  2. Epigenomics and bolting tolerance in sugar beet genotypes

    PubMed Central

    Hébrard, Claire; Peterson, Daniel G.; Willems, Glenda; Delaunay, Alain; Jesson, Béline; Lefèbvre, Marc; Barnes, Steve; Maury, Stéphane

    2016-01-01

    In sugar beet (Beta vulgaris altissima), bolting tolerance is an essential agronomic trait reflecting the bolting response of genotypes after vernalization. Genes involved in induction of sugar beet bolting have now been identified, and evidence suggests that epigenetic factors are involved in their control. Indeed, the time course and amplitude of DNA methylation variations in the shoot apical meristem have been shown to be critical in inducing sugar beet bolting, and a few functional targets of DNA methylation during vernalization have been identified. However, molecular mechanisms controlling bolting tolerance levels among genotypes are still poorly understood. Here, gene expression and DNA methylation profiles were compared in shoot apical meristems of three bolting-resistant and three bolting-sensitive genotypes after vernalization. Using Cot fractionation followed by 454 sequencing of the isolated low-copy DNA, 6231 contigs were obtained that were used along with public sugar beet DNA sequences to design custom Agilent microarrays for expression (56k) and methylation (244k) analyses. A total of 169 differentially expressed genes and 111 differentially methylated regions were identified between resistant and sensitive vernalized genotypes. Fourteen sequences were both differentially expressed and differentially methylated, with a negative correlation between their methylation and expression levels. Genes involved in cold perception, phytohormone signalling, and flowering induction were over-represented and collectively represent an integrative gene network from environmental perception to bolting induction. Altogether, the data suggest that the genotype-dependent control of DNA methylation and expression of an integrative gene network participate in bolting tolerance in sugar beet, opening up perspectives for crop improvement. PMID:26463996

  3. Molecular Characterization of Prunus angustifolia Genotypes from Turkey.

    PubMed

    Akbulut, Mustafa; Polat, Mehmet; Ercisli, Sezai; Sorkheh, Karim

    2016-08-25

    Prunus angustifolia var. angustifolia is a deciduous shrub with 1.5-3.0 m plant height and mostly found in rural areas between 1400 and 1600 m in northeastern Turkey including Bayburt, Gumushane, and Kars provinces. The plant has multistems and well known to adapt severe winter and dry-hot summer conditions. In this study, we aimed to explore the genetic diversity within this specie and also to investigate its phylogenetic relationship with economically important the other cherry species; Prunus avium, Prunus cerasus, Prunus laurocerasus, and Prunus mahaleb. A total of 50 simple sequence repeats (SSRs) markers used to elucidate the genetic variation among 32 P. angustifolia var. angustifolia genotypes selected from three locations (Bayburt, Gumushane, and Kars) in northeastern Turkey. The cross-species transportability of used 50 SSRs was 80 % indicating a high degree of homology between P. angustifolia and the other Prunus species. The genetic distance between P. angustifolia var. angustifolia genotypes belonging to a particular geographic site was lower than that between genotypes of different geographic origins. Cluster analysis in general differentiated P. angustifolia var. angustifolia genotypes according to their geographic sites and separated them from the other Prunus species. P. angustifolia found more closer to P. mahaleb and P. cerasus, in the subgenus Cerasus, The analysis of molecular variance revealed that genetic variation among individuals within populations was much higher than among Prunus groups and among P. angustifolia var. angustifolia populations of different geographic sites. The results indicate a substantial genetic diversity in P. angustifolia var. angustifolia and the need of exploring a wider area to increase the chance of finding a particular genotype.

  4. BK Polyomavirus Genotypes Represent Distinct Serotypes with Distinct Entry Tropism

    PubMed Central

    Pastrana, Diana V.; Ray, Upasana; Magaldi, Thomas G.; Schowalter, Rachel M.; Çuburu, Nicolas

    2013-01-01

    BK polyomavirus (BKV) causes significant urinary tract pathogenesis in immunosuppressed individuals, including kidney and bone marrow transplant recipients. It is currently unclear whether BKV-neutralizing antibodies can moderate or prevent BKV disease. We developed reporter pseudoviruses based on seven divergent BKV isolates and performed neutralization assays on sera from healthy human subjects. The results demonstrate that BKV genotypes I, II, III, and IV are fully distinct serotypes. While nearly all healthy subjects had BKV genotype I-neutralizing antibodies, a majority of subjects did not detectably neutralize genotype III or IV. Surprisingly, BKV subgenotypes Ib1 and Ib2 can behave as fully distinct serotypes. This difference is governed by as few as two residues adjacent to the cellular glycan receptor-binding site on the virion surface. Serological analysis of mice given virus-like particle (VLP)-based BKV vaccines confirmed these findings. Mice administered a multivalent VLP vaccine showed high-titer serum antibody responses that potently cross-neutralized all tested BKV genotypes. Interestingly, each of the neutralization serotypes bound a distinct spectrum of cell surface receptors, suggesting a possible connection between escape from recognition by neutralizing antibodies and cellular attachment mechanisms. The finding implies that different BKV genotypes have different cellular tropisms and pathogenic potentials in vivo. Individuals who are infected with one BKV serotype may remain humorally vulnerable to other BKV serotypes after implementation of T cell immunosuppression. Thus, prevaccinating organ transplant recipients with a multivalent BKV VLP vaccine might reduce the risk of developing posttransplant BKV disease. PMID:23843634

  5. Adapting Genotyping-by-Sequencing for Rice F2 Populations

    PubMed Central

    Furuta, Tomoyuki; Ashikari, Motoyuki; Jena, Kshirod K.; Doi, Kazuyuki; Reuscher, Stefan

    2017-01-01

    Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population, and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species O. longistaminata. While most GBS pipelines aim to analyze mainly homozygous populations, we attempted to genotype a highly heterozygous F2 population. We show how species- and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average), we were able to generate up to 8154 informative SNP markers in 1081 F2 individuals. Additionally, the effects of enzyme choice, read coverage, and data postprocessing are evaluated. Using GBS-derived markers, we were able to assemble a genetic map of 1536 cM. To demonstrate the usefulness of our GBS pipeline, we determined quantitative trait loci (QTL) for the number of tillers. We were able to map four QTL to chromosomes 1, 3, 4, and 8, and partially confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform, we show that the GBS method is flexible and cost-effective, even for smaller laboratories. PMID:28082325

  6. Mental representations of social status.

    PubMed

    Chiao, Joan Y; Bordeaux, Andrew R; Ambady, Nalini

    2004-09-01

    How do people think about social status? We investigated the nature of social status and number representations using a semantic distance latency test. In Study 1, 21 college students compared words connoting different social status as well as numbers, which served as a control task. Participants were faster at comparing occupations and numbers that were semantically farther apart relative to those more closely related. In Study 2, we examined the semantic distance effect for a social status category, for which participants have as much knowledge of, as with numbers. We asked 15 US Navy Midshipmen to compare the social status associated with different ranks in the Navy as well as compare number magnitudes. Participants were fastest when comparing ranks far in status relative to ranks close in status. These findings reveal that humans have mental representations of social status that share properties with that of number.

  7. Genotype and phylogenetic characterization of hepatitis B virus among multi-ethnic cohort in Hawaii

    PubMed Central

    Sakurai, Mayumi; Sugauchi, Fuminaka; Tsai, Naoky; Suzuki, Seiji; Hasegawa, Izumi; Fujiwara, Kei; Orito, Etsuro; Ueda, Ryuzo; Mizokami, Masashi

    2004-01-01

    AIM: Hepatitis B virus (HBV) genomes in carriers from Hawaii have not been evaluated previously. The aim of the present study was to evaluate the distribution of HBV genotypes and their clinical relevance in Hawaii. METHODS: Genotyping of HBV among 61 multi-ethnic carriers in Hawaii was performed by genetic methods. Three complete genomes and 61 core promoter/precore regions of HBV were sequenced directly. RESULTS: HBV genotype distribution among the 61 carriers was 23.0% for genotype A, 14.7% for genotype B and 62.3% for genotype C. Genotypes A, B and C were obtained from the carriers whose ethnicities were Filipino and Caucasian, Southeast Asian, and various Asian and Micronesian, respectively. All cases of genotype B were composed of recombinant strains with genotype C in the precore plus core region named genotype Ba. HBeAg was detected more frequently in genotype C than in genotype B (68.4% vs 33.3%, P < 0.05) and basal core promoter (BCP) mutation (T1762/A1764) was more frequently found in genotype C than in genotype B. Twelve of the 38 genotype C strains possessed C at nucleotide (nt) position 1858 (C -1858). However there was no significant difference in clinical characteristics between C-1858 and T-1858 variants. Based on complete genome sequences, phylogenetic analysis revealed one patient of Micronesian ethnicity as having C-1858 clustered with two isolates from Polynesia with T-1858. In addition, two strains from Asian ethnicities were clustered with known isolates in carriers from Southeast Asia. CONCLUSION: Genotypes A, B and C are predominant types among multi-ethnic HBV carriers in Hawaii, and distribution of HBV genotypes is dependent on the ethnic background of the carriers in Hawaii. PMID:15259069

  8. Exploring genotype concordance in epidemiologically linked cases of tuberculosis in New York City.

    PubMed

    Robbins, R S; Perri, B R; Ahuja, S D; Anger, H A; Sullivan Meissner, J; Shashkina, E; Kreiswirth, B N; Proops, D C

    2017-02-01

    Comparing genotype results of tuberculosis (TB) isolates from individuals diagnosed with TB can support or refute transmission; however, these conclusions are based upon the criteria used to define a genotype match. We used a genotype-match definition which allowed for variation in IS6110 restriction fragment length polymorphism (RFLP) to support transmission between epidemiologically linked persons. Contacts of individuals with infectious TB (index cases) diagnosed in New York City from 1997 to 2003 who subsequently developed TB (contact cases) from 1997 to 2007 were identified. For each contact case and index case (case-pair), isolate genotypes (spoligotype and RFLP results) were evaluated. Isolates from case-pairs were classified as exact or non-exact genotype match. Genotypes from non-exact match case-pairs were reviewed at the genotyping laboratory to determine if the isolates met the near-genotype-match criteria (exactly matching spoligotype and similar RFLP banding patterns). Of 118 case-pairs identified, isolates from 83 (70%) had exactly matching genotypes and 14 (12%) had nearly matching genotypes (supporting transmission), while the remaining 21 (18%) case-pairs had discordant genotypes (refuting transmission). Using identical genotype-match criteria for isolates from case-pairs epidemiologically linked through contact investigation may lead to underestimation of transmission. TB programmes should consider the value of expanding genotype-match criteria to more accurately assess transmission between such cases.

  9. Further evidence of hepatitis B virus genotype I circulation in Northeast India.

    PubMed

    Ismail, Ashrafali Mohamed; Goel, Ashish; Kannangai, Rajesh; Abraham, Priya

    2013-08-01

    Hepatitis B virus (HBV) genotypes have known to show a geographical pattern in their distribution and have been used to trace the migration of populations from geographically distant regions. Novel recombinants between HBV genotypes A, G and C referred as genotype I has been recently reported from Eastern India. In our investigation to characterise antiviral resistance mutations, we identified a rare case of HBV genotype I infection in chronic hepatitis B subject. We encountered confounding results of this emerging genotype 'designated as genotype G' in three widely used HBV sequence database for genotype determination. The recombinant fragment of genotype G largely occupies the surface gene sequence of the newly identified genotype I and could hence lead to misclassification of genotype I. Additionally, recombination analysis of the generated sequences in Simplot and jpHMM model showed two different patterns of recombination events. In conclusion, the increasing recognition of genotype I in this population suggests that further studies may reveal uncommon genotypes from other geographically distant regions. Our observation of potential genotype I misclassification despite the use of public HBV sequence database and other recombination analysis tools highlights the need for updating and validating public sequence domains of diagnostic importance.

  10. Molecular Assay and Genotyping of Hepatitis C Virus among Infected Egyptian and Saudi Arabian Patients

    PubMed Central

    Farag, Mohamed MS; Sofy, Ahmed R; Mousa, Adel A; Ahmed, Mohamed A; Alganzory, Mohamed R

    2015-01-01

    Hepatitis C virus (HCV) infection is a major health problem recognized globally. HCV is a common cause of liver fibrosis that may lead to liver cirrhosis or hepatocellular carcinoma. The aim of this study was to estimate the prevalence of HCV infection and genotyping among Egyptian and Saudi Arabian chronic patients using different molecular techniques. HCV RNA viral load was assessed by real-time polymerase chain reaction (RT-PCR) technology. For HCV genotyping, RT-PCR hybridization fluorescence-based method and reverse hybridization line probe assay (INNO-LiPA) were used. A total of 40 anti-HCV-positive patients with chronic hepatitis C were examined for HCV RNA, genotyping, and different laboratory investigations. In the present study, HCV genotypes 4, mixed 4.1b, and 1 were detected in patients of both countries, while genotype 2 was only detected in Saudi Arabian patients. Genotyping methods for HCV showed no difference in the classification at the genotype level. With regard to HCV subtypes, INNO-LiPA assay was a reliable test in HCV genotyping for the detection of major genotypes and subtypes, while RT-PCR-based assay was a good test at the genotype level only. HCV genotype 4 was found to be the predominant genotype among Egyptian and Saudi Arabian chronic patients. In conclusion, data analysis for detecting and genotyping HCV was an important factor for understanding the epidemiology and treatment strategies of HCV among Egyptian and Saudi Arabian chronic patients. PMID:26512201

  11. Health status of newcomers.

    PubMed

    Matuk, L C

    1996-01-01

    This article presents and discusses findings on the health status of newcomers residing in Windsor, Ontario. The data are part of a larger study, which was based on the Ontario Health Survey's questionnaire. Data were collected from 548 newcomers through home visits, focus groups, mail surveys, and telephone interviews. Descriptive multivariate analyses focused on main areas in newcomers' physical and mental health status and their access to health services. The findings identified that most newcomers do not have acute, life-threatening physical problems or chronic illness. They do not experience major problems with access to health care or activity limitations. Men are happier, more satisfied with their health, and less stressed than women. This study has implications for adoption of sensitive transcultural approaches to promote newcomers' health. Special challenges lie in women's health and mental health.

  12. Effect of C282Y Genotype on Self-Reported Musculoskeletal Complications in Hereditary Hemochromatosis

    PubMed Central

    Simão, Márcio; Cancela, Leonor; Ottaviani, Sébastien; Cohen-Solal, Martine; Richette, Pascal

    2015-01-01

    Objective Arthropathy that mimics osteoarthritis (OA) and osteoporosis (OP) is considered a complication of hereditary hemochromatosis (HH). We have limited data comparing OA and OP prevalence among HH patients with different hemochromatosis type 1 (HFE) genotypes. We investigated the prevalence of OA and OP in patients with HH by C282Y homozygosity and compound heterozygosity (C282Y/H63D) genotype. Methods A total of 306 patients with HH completed a questionnaire. Clinical and demographic characteristics and presence of OA, OP and related complications were compared by genotype, adjusting for age, sex, body mass index (BMI), current smoking and menopausal status. Results In total, 266 of the 306 patients (87%) were homozygous for C282Y, and 40 (13%) were compound heterozygous. The 2 groups did not differ by median age [60 (interquartile range [IQR] 53 to 68) vs. 61 (55 to 67) years, P=0.8], sex (female: 48.8% vs. 37.5%, P=0.18) or current smoking habits (12.4% vs. 10%, P=0.3). As compared with compound heterozygous patients, C282Y homozygous patients had higher median serum ferritin concentration at diagnosis [1090 (IQR 610 to 2210) vs. 603 (362 to 950) µg/L, P<0.001], higher median transferrin saturation [80% (IQR 66 to 91%) vs. 63% (55 to 72%), P<0.001]) and lower median BMI [24.8 (22.1 to 26.9) vs. 26.2 (23.5 to 30.3) kg/m2, P<0.003]. The overall prevalence of self-reported OA was significantly higher with C282Y homozygosity than compound heterozygosity (53.4% vs. 32.5%; adjusted odds ratio [aOR] 2.4 [95% confidence interval 1.2–5.0]), as was self-reported OP (25.6% vs. 7.5%; aOR 3.5 [1.1–12.1]). Conclusion Patients with C282Y homozygosity may be at increased risk of musculoskeletal complications of HH. PMID:25822977

  13. Prevalence and genotyping of high risk human papillomavirus in cervical cancer samples from Punjab, Pakistan.

    PubMed

    Siddiqa, Abida; Zainab, Maidah; Qadri, Ishtiaq; Bhatti, Muhammad Faraz; Parish, Joanna L

    2014-07-17

    Cervical cancer is the third most common cause of cancer-related death in women worldwide. Infection with high-risk human papillomavirus (HPV) is established as the cause of cervical carcinoma, therefore, high risk HPV detection may have prognostic significance for the women who are at increased risk of disease progression. The paucity of data on the incidence of cervical cancer in Pakistan makes it difficult to determine disease burden. Even less information is available regarding the prevalent HPV strains in cervical specimens collected from this region. Cervical cancer is a neglected disease in Pakistan in terms of screening, prevention, and vaccination. Identification and accurate genotyping of the virus burden in cancer specimens is important to inform intervention policies for future management of HPV associated disease and to potentially stratify patients dependent on HPV status. In this study, detection and genotyping of HPV types 16 and 18 from 77 cervical specimens were carried out. Consensus primers GP5+/GP6+, which detect 44 genital HPV types, and type specific primers (TS16 and TS18) were used in conjunction with newly designed type specific primers. Using a combination of these methods of detection, a total of 94.81% (95% CI ±4.95) of cervical lesions were positive for HPV. Single infections of HPV16 were detected in 24.68% (95% CI ±9.63) of total samples and HPV18 was found in 25.97% (95% CI ±9.79) samples. Interestingly, a high proportion of samples (40.26%, 95% CI ±10.95) was positive for both HPV16 and 18, indicating a higher incidence of co-infection than previously reported for similar ethnic regions. The HPV genotype of 3.90% of HPV positive samples remained undetected, although these samples were positive with the GP5+/GP6+ primer set indicating infection with an HPV type other than 16 or 18. These data indicate that the overall incidence of high risk HPV infection in cervical cancer and intraepithelial neoplasia specimens in Punjab

  14. SalSA status

    NASA Astrophysics Data System (ADS)

    Connolly, Amy; SalSA Collaboration

    2009-06-01

    I review the status of SalSA, a proposed antenna array in a large volume salt formation for detecting ultra-high energy neutrinos. We report on measurements taken in 2007 of attenuation lengths in the 125-900 MHz frequency range at the Cote Blanche salt mine near New Iberia, Louisiana, which is the most precise in situ measurement of attenuation lengths in salt to date. We comment on the impact of these measurements on the feasibility of SalSA.

  15. Status of JUPITER Program

    SciTech Connect

    Inoue, T.; Shirakata, K.; Kinjo, K.; Ikegami, T.; Yamamoto, M.

    1981-03-10

    To obtain the data necessary for evaluating the nuclear design method of a large-scale fast breeder reactor, criticality tests with a large- scale homogeneous reactor were conducted as part of a joint research program by Japan and the U.S. Analyses of the tests are underway in both countries. The purpose of this paper is to describe the status of this project.

  16. MARS Flight Engineering Status

    SciTech Connect

    Fast, James E.; Dorow, Kevin E.; Morris, Scott J.; Thompson, Robert C.; Willett, Jesse A.

    2010-04-06

    The Multi-sensor Airborne Radiation Survey Flight Engineering project (MARS FE) has designed a high purity germanium (HPGe) crystal array for conducting a wide range of field measurements. In addition to the HPGe detector system, a platform-specific shock and vibration isolation system and environmental housing have been designed to support demonstration activities in a maritime environment on an Unmanned Surface Vehicle (USV). This report describes the status of the equipment as of the end of FY09.

  17. Electronic Status Board

    SciTech Connect

    Barnett, Clinton; Thatcher, Kyle Bryan; Andrew, Terence; Edward, William

    2004-06-02

    This software was developed to post real-time process status and building conditions to operators, system engineers, system managers, and all support personnel. Data input is via operator console, strategically located throughout the facility, or by electronic rounds tablet. The system requires a person to log in with a unique user id and password to edit data. Viewing system status does not require log in and can be done from any desktop location running FileMaker. Once logged into the system, all new records saved are stamped with date, time and user name, and a historical copy is created that can be brought up to review status. There is no limitation to the amount of records that can be saved in the historical databases. The system will flag all out of limit conditions on the screen and enter that record on a turnover summery page which displays only flagged items. System conditions are displayed on a plasma display which scrolls through the various system condition screens. The system also shows floor plans that reflect specific building radiological conditions which aides in pre job briefings to show all hazards to personnel entering specific locations. The input screen is displayed on a second standard computer monitor connected to the input PC. There are several popup screens that require user intervention to ensure that the user wants to edit the data, is editing the appropriate sytem, and if they want to continue to stay logged into the system. Each workstation is connected to a Uninterrupted Power Supply which will shut each system down safely in a power failure. The server is configured to print out current status upon notification from the UPS that power has failed. The system also has a video input card which is connected to a DVD/VCR which shows safety meetings, and images taken from a digital camera used to show specific locations/items for pre-job briefings.

  18. System status display information

    NASA Technical Reports Server (NTRS)

    Summers, L. G.; Erickson, J. B.

    1984-01-01

    The system Status Display is an electronic display system which provides the flight crew with enhanced capabilities for monitoring and managing aircraft systems. Guidelines for the design of the electronic system displays were established. The technical approach involved the application of a system engineering approach to the design of candidate displays and the evaluation of a Hernative concepts by part-task simulation. The system engineering and selection of candidate displays are covered.

  19. Status of MARS Code

    SciTech Connect

    N.V. Mokhov

    2003-04-09

    Status and recent developments of the MARS 14 Monte Carlo code system for simulation of hadronic and electromagnetic cascades in shielding, accelerator and detector components in the energy range from a fraction of an electronvolt up to 100 TeV are described. these include physics models both in strong and electromagnetic interaction sectors, variance reduction techniques, residual dose, geometry, tracking, histograming. MAD-MARS Beam Line Build and Graphical-User Interface.

  20. Automated Status Notification System

    NASA Technical Reports Server (NTRS)

    2005-01-01

    NASA Lewis Research Center's Automated Status Notification System (ASNS) was born out of need. To prevent "hacker attacks," Lewis' telephone system needed to monitor communications activities 24 hr a day, 7 days a week. With decreasing staff resources, this continuous monitoring had to be automated. By utilizing existing communications hardware, a UNIX workstation, and NAWK (a pattern scanning and processing language), we implemented a continuous monitoring system.

  1. The status of GALLEX

    SciTech Connect

    Cribier, M. . Dept. de Physique des Particules Elementaires)

    1990-01-01

    The present status of the Gallium Solar Neutrino Experiment performed by the GALLEX Collaboration in the Gran Sasso Underground Laboratory is described. The implementation phase of this experiment is now completed, the whole gallium is at hand and data taking starts now. After a short introduction and an outline of the basic experimental procedure, details will be given on different parts of the experiment and on some background. 14 refs., 2 figs.

  2. GPS Status and Modernization

    DTIC Science & Technology

    2010-03-10

    11 GPS IIA • 12 GPS IIR • 7 GPS IIR-M • 4 additional satellites in residual status • 1 additional IIR-M waiting to be set healthy • Global GPS ...AEP) Next Generation Control Segment (OCX) Legacy Control System 7 GPS Modernization – Ground • Architecture Evolution Plan (AEP) • Transitioned in 2007...Modern distributed system replaced 1970’s mainframes • Increased capacity for monitoring of GPS signals • Increased worldwide commanding

  3. Global Positioning System Status

    DTIC Science & Technology

    2011-04-27

    GPS : FREE – DEPENDABLE – RELIABLE - ACCURATE 1 GLOBAL POSITIONING SYSTEM STATUS Benjamin Barbour Major, United States Air Force Schriever AFB... Global Positioning System Service Interface Committee (CGSIC) held in Groton, CT, April 2011 14. ABSTRACT 15. SUBJECT TERMS 16. SECURITY...Continuing work with international GNSS community  Maintains Backward Compatibility  Managing GPS systems and supporting stakeholders Committed to responsible stewardship of GPS

  4. Genotyping of human rhinovirus in adult patients with acute respiratory infections identified predominant infections of genotype A21

    PubMed Central

    Ren, Lili; Yang, Donghong; Ren, Xianwen; Li, Mingkun; Mu, Xinlin; Wang, Qi; Cao, Jie; Hu, Ke; Yan, Chunliang; Fan, Hongwei; Li, Xiangxin; Chen, Yusheng; Wang, Ruiqin; An, Fucheng; An, Shuchang; Luo, Ming; Wang, Ying; Xiao, Yan; Xiang, Zichun; Xiao, Yan; Li, Li; Huang, Fang; Jin, Qi; Gao, Zhancheng; Wang, Jianwei

    2017-01-01

    Human rhinovirus (HRV) is an important causative agent of acute respiratory tract infections (ARTIs). The roles of specific HRV genotypes in patients suffering from ARTIs have not been well established. We recruited 147 adult inpatients with community-acquired pneumonia (CAP) and 291 adult outpatients with upper ARTIs (URTIs). Respiratory pathogens were screened via PCR assays. HRV was detected in 42 patients, with 35 species A, five B and two C. Seventeen genotypes were identified, and HRV-A21 ranked the highest (9/42, 21.4%). The HRV-A21-positive infections were detected in four patients with CAP and in five with URTIs, all without co-infections. The HRV-A21 genome sequenced in this study contained 12 novel coding polymorphisms in viral protein (VP) 1, VP2 EF loop, VP3 knob and 3D regions. The infections of HRV-A21 virus obtained in this study could not be neutralized by antiserum of HRV-A21 prototype strain (VR-1131), indicating remarkable antigenic variation. Metagenomic analysis showed the HRV-A21 reads were dominant in bronchoalveolar lavage fluid of the three HRV-A21-positive patients with severe CAP, in which two dead. Our results highlight an unexpected infection of genotype HRV-A21 in the clinic, indicating the necessity of precise genotyping and surveillance of HRVs to improve the clinical management of ARTIs. PMID:28128353

  5. Air-borne genotype by genotype indirect genetic effects are substantial in the filamentous fungus Aspergillus nidulans.

    PubMed

    Rode, N O; Soroye, P; Kassen, R; Rundle, H D

    2017-03-15

    Genotype by genotype indirect genetic effects (G × G IGEs) occur when the phenotype of an individual is influenced by an interaction between its own genotype and those of neighbour individuals. Little is known regarding the relative importance of G × G IGEs compared with other forms of direct and indirect genetic effects. We quantified the relative importance of IGEs in the filamentous fungus Aspergillus nidulans, a species in which IGEs are likely to be important as air-borne social interactions are known to affect growth. We used a collection of distantly related wild isolates, lab strains and a set of closely related mutation accumulation lines to estimate the contribution of direct and indirect genetic effects on mycelium growth rate, a key fitness component. We found that indirect genetic effects were dominated by G × G IGEs that occurred primarily between a focal genotype and its immediate neighbour within a vertical stack, and these accounted for 11% of phenotypic variation. These results indicate that G × G IGEs may be substantial, at least in some systems, and that the evolutionary importance of these interactions may be underappreciated, especially in microbes. We advocate for a wider use of the IGE framework in both applied (for example, choice of varietal mixtures in plant breeding) and evolutionary genetics (kin selection/kin competition studies).Heredity advance online publication, 15 March 2017; doi:10.1038/hdy.2017.9.

  6. Proteome Differences between Hepatitis B Virus Genotype-B- and Genotype-C-Induced Hepatocellular Carcinoma Revealed by iTRAQ-Based Quantitative Proteomics.

    PubMed

    Wei, Dahai; Zeng, Yongyi; Xing, Xiaohua; Liu, Hongzhi; Lin, Minjie; Han, Xiao; Liu, Xiaolong; Liu, Jingfeng

    2016-02-05

    Hepatitis B virus (HBV) is the main cause of hepatocellular carcinoma (HCC) in southeast Asia where HBV genotype B and genotype C are the most prevalent. Viral genotypes have been reported to significantly affect the clinical outcomes of HCC. However, the underlying molecular differences among different genotypes of HBV virus infected HCC have not been revealed. Here, we applied isobaric tags for relative and absolute quantitation (iTRAQ) technology integrated with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify the proteome differences between the HBV genotypes B- and C-induced HCC. In brief, a total of 83 proteins in the surrounding noncancerous tissues and 136 proteins in the cancerous tissues between HBV genotype-B- and genotype-C-induced HCC were identified, respectively. This information revealed that there might be different molecular mechanisms of the tumorigenesis and development of HBV genotypes B- and C-induced HCC. Furthermore, our results indicate that the two proteins ARFIP2 and ANXA1 might be potential biomarkers for distinguishing the HBV genotypes B- and C-induced HCC. Thus, the quantitative proteomic analysis revealed molecular differences between the HBV genotypes B- and C-induced HCC, and might provide fundamental information for further deep study.

  7. Mental Representations of Social Status

    ERIC Educational Resources Information Center

    Chiao, Joan Y.; Bordeaux, Andrew R.; Ambady, Nalni

    2004-01-01

    How do people think about social status? We investigated the nature of social status and number representations using a semantic distance latency test. In Study 1, 21 college students compared words connoting different social status as well as numbers, which served as a control task. Participants were faster at comparing occupations and numbers…

  8. Sibling Status Effects: Adult Expectations.

    ERIC Educational Resources Information Center

    Baskett, Linda Musun

    1985-01-01

    This study attempted to determine what expectations or beliefs adults might hold about a child based on his or her sibling status alone. Ratings on 50 adjective pairs for each of three sibling status types, only, oldest, and youngest child, were assessed in relation to adult expectations, birth order, and parental status of rater. (Author/DST)

  9. A Cannabis sativa STR genotype database for Australian seizures: forensic applications and limitations.

    PubMed

    Howard, Christopher; Gilmore, Simon; Robertson, James; Peakall, Rod

    2009-05-01

    A genetic database was established with the aim of documenting the genetic diversity of Cannabis sativa in Australia for future utilization in forensic investigations. The database consisted of genotypes at 10 validated short tandem repeat loci for 510 plants representing drug seizures from across Australia and 57 fiber samples. A total of 106 alleles and 314 different genotypes were detected. All fiber samples exhibited unique genotypes while 55% of the drug samples shared a genotype with one or more samples. Shared genotypes were mostly found within seizures; however, some genotypes were found among seizures. Statistical analysis indicated that genotype sharing was a consequence of clonal propagation rather than a lack of genetic resolution. Thus, the finding of shared genotypes among seizures is likely due to either a common supplier, or direct links among seizures. Notwithstanding the potential intelligence information provided by genetic analysis of C. sativa, our database analysis also reveals some present limitations.

  10. Microbe-ID: An open source toolbox for microbial genotyping and species identification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user...

  11. Biotyping and Genotyping (MLVA16) of Brucella abortus Isolated from Cattle in Brazil, 1977 to 2008

    PubMed Central

    Minharro, Sílvia; Silva Mol, Juliana P.; Dorneles, Elaine M. S.; Pauletti, Rebeca B.; Neubauer, Heinrich; Melzer, Falk; Poester, Fernando P.; Dasso, Maurício G.; Pinheiro, Elaine S.; Soares Filho, Paulo M.; Santos, Renato L.; Heinemann, Marcos B.; Lage, Andrey P.

    2013-01-01

    Brucellosis is a worldwide distributed zoonosis that causes important economic losses to animal production. In Brazil, information on the distribution of biovars and genotypes of Brucella spp. is scarce or unavailable. This study aimed (i) to biotype and genotype 137 Brazilian cattle isolates (from 1977 to 2008) of B. abortus and (ii) to analyze their distribution. B. abortus biovars 1, 2 and 3 (subgroup 3b) were confirmed and biovars 4 and 6 were first described in Brazil. Genotyping by the panel 1 revealed two groups, one clustering around genotype 40 and another around genotype 28. Panels 2A and 2B disclosed a high diversity among Brazilian B. abortus strains. Eighty-nine genotypes were found by MLVA16. MLVA16 panel 1 and 2 showed geographic clustering of some genotypes. Biotyping and MLVA16 genotyping of Brazilian B. abortus isolates were useful to better understand the epidemiology of bovine brucellosis in the region. PMID:24324670

  12. Biological and phylogenetic characterization of a genotype VII Newcastle disease virus from Venezuela: Efficacy of vaccination

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Here we describe the characterization a virulent genotype VII Newcastle disease virus (NDV) from Venezuela and evaluate the efficacy of heterologous genotype commercial vaccination under field and controlled rearing conditions. Biological pathotyping and molecular analysis were applied. Results sh...

  13. Sugarcane Genotype Performance in Three Environments (Based on Crop Cycle) at Mardan, Pakistan

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane breeders often face significant genotype x environment interactions in their trials grown under multiple environments. Hence, genotypes need to be tested for their stability across different environments keeping in view the significant interactions. An experiment comprising 28 sugarcane ge...

  14. Mechanism of the dependence of hepatitis B virus genotype G on co-infection with other genotypes for viral replication.

    PubMed

    Sakamoto, T; Tanaka, Y; Watanabe, T; Iijima, S; Kani, S; Sugiyama, M; Murakami, S; Matsuura, K; Kusakabe, A; Shinkai, N; Sugauchi, F; Mizokami, M

    2013-04-01

    Hepatitis B virus (HBV) is classified into several genotypes. Genotype G (HBV/G) is characterised by worldwide dispersion, low intragenotypic diversity and a peculiar sequence of the precore and core region (stop codon and 36-nucleotide insertion). As a rule, HBV/G is detected in co-infection with another genotype, most frequently HBV/A2. In a previous in vivo study, viral replication of HBV/G was significantly enhanced by co-infection with HBV/A2. However, the mechanism by which co-infection with HBV/A2 enhances HBV/G replication is not fully understood. In this study, we employed 1.24-fold HBV/A2 clones that selectively expressed each viral protein and revealed that the core protein expressing construct significantly enhanced the replication of HBV/G in Huh7 cells. The introduction of the HBV/A2 core promoter or core protein or both genomic regions into the HBV/G genome showed that both the core promoter and core protein are required for efficient HBV/G replication. The effect of genotype on the interaction between foreign core protein and HBV/G showed that HBV/A2 was the strongest enhancer of HBV/G replication. Furthermore, Western blot analysis of Dane particles isolated from cultures of Huh7 cells co-transfected by HBV/G and a cytomegalovirus (CMV) promoter-driven HBV/A2 core protein expression construct indicated that HBV/G employed HBV/A2 core protein during particle assembly. In conclusion, HBV/G could take advantage of core proteins from other genotypes during co-infection to replicate efficiently and to effectively package HBV DNA into virions.

  15. [Determination of hepatitis C virus genotype distribution in Mersin province, Turkey].

    PubMed

    Tezcan, Seda; Ulger, Mahmut; Aslan, Gönül; Yaraş, Serkan; Altıntaş, Engin; Sezgin, Orhan; Emekdaş, Gürol; Gürer Giray, Burcu; Sungur, Mehmet Ali

    2013-04-01

    Hepatitis C virus (HCV) is a member of the Flaviviridae family and the RNA genome e x hibit high genetic heterogeneity. Six major genotypes were phylogenetically determined and each genotype contains different subtypes. The distribution of HCV genotypes varies geographically throughout the world. Determination of viral genotype has great importance in the selection of antiviral therapy, treatment duration and monitoring the response to treatment. The aim of this study was to determine the distribution of HCV genotypes in Mersin province located at the Southern part of Turkey. A total of 236 patients (137 females, 99 males; mean age: 53.28 ± 14.99 years) with chronic HCV infection who were admitted to Mersin University Hospital Microbiology Laboratory during March 2010-May 2012 period were included in the study. The patients were anti-HCV (ELISA; Abbott Laboratories, USA) and HCV-RNA (Cobas TaqMan 48, Roche Diagnostic, USA) positive. HCV genotype analysis was determined by using a commercial LiPA kit (Line Probe Assay; AMPLIQUALITY HCV-TS; AB Analitica, Italy) based on the reverse hybridization of amplification products of viral 5'-UTR region. Out of the 236 patients, genotype 1b was observed in 84.7% (n= 200), genotype 3a in 4.2% (n= 10), genotype 1 in 3.8% (n= 9), genotype 1a/1b in 2.1% (n= 5), genotype 4a in 2% (n= 2), genotype 1a in 1.7% (n= 4), genotype 2b in 1.3% (n= 3), genotype 2 in 0.4% (n= 1), genotype 2a/2c in 0.4% (n= 1) and genotype 6 in 0.4% (n= 1). In the cases infected with genotype 1b, statistically significant differences were detected between gender distribution with the mean serum ALT (46.14 IU/L in females, 63.9 IU/L in males; p= 0.029) and HCV-RNA (634 x 103 IU/L in females, 20 x 105 IU/L in males; p= 0.005) levels. This was the first study that reflected the distribution of HCV genotypes in southern Turkey region. Genotype 1b, associated with poor prognosis and which had the highest prevalence in Turkey, was also determined as the most common

  16. Short communication: relationship of call rate and accuracy of single nucleotide polymorphism genotypes in dairy cattle.

    PubMed

    Cooper, T A; Wiggans, G R; VanRaden, P M

    2013-05-01

    Call rates on both a single nucleotide polymorphism (SNP) basis and an animal basis are used as measures of data quality and as screening tools for genomic studies and evaluations of dairy cattle. To investigate the relationship of SNP call rate and genotype accuracy for individual SNP, the correlation between percentages of missing genotypes and parent-progeny conflicts for each SNP was calculated for 103,313 Holsteins. Correlations ranged from 0.14 to 0.38 for the BovineSNP50 and BovineLD (Illumina Inc., San Diego, CA) and GeneSeek Genomic Profiler (Neogen Corp., Lincoln, NE) chips, with lower correlations for newer chips. For US genomic evaluations, genotypes are excluded for animals with a call rate of <90% across autosomal SNP or <80% across X-specific SNP. Mean call rate for 220,175 Holstein, Jersey, and Brown Swiss genotypes was 99.6%. Animal genotypes with a call rate of ≤99% were examined from the US Department of Agriculture genotype database to determine how genotype call rate is related to accuracy of calls on an animal basis. Animal call rate was determined from SNP used in genomic evaluation and is the number of called autosomal and X-specific SNP genotypes divided by the number of SNP from that type of chip. To investigate the relationship of animal call rate and parentage validation, conflicts between a genotyped animal and its sire or dam were determined through a duo test (opposite homozygous SNP genotypes between sire and progeny; 1,374 animal genotypes) and a trio test (also including conflicts with dam and heterozygous SNP genotype for the animal when both parents are the same homozygote; 482 animal genotypes). When animal call rate was ≤ 80%, parentage validation was no longer reliable with the duo test. With the trio test, parentage validation was no longer reliable when animal call rate was ≤ 90%. To investigate how animal call rate was related to genotyping accuracy for animals with multiple genotypes, concordance between genotypes

  17. Association between immunoglobulin GM and KM genotypes and placental malaria in HIV-1 negative and positive women in western Kenya.

    PubMed

    Iriemenam, Nnaemeka C; Pandey, Janardan P; Williamson, John; Blackstock, Anna J; Yesupriya, Ajay; Namboodiri, Aryan M; Rocca, Keith M; van Eijk, Anna Maria; Ayisi, John; Oteino, Juliana; Lal, Renu B; ter Kuile, Feiko O; Steketee, Richard; Nahlen, Bernard; Slutsker, Laurence; Shi, Ya Ping

    2013-01-01

    Immunoglobulin (Ig) GM and KM allotypes, genetic markers of γ and κ chains, are associated with humoral immune responsiveness. Previous studies have shown the relationships between GM6-carrying haplotypes and susceptibility to malaria infection in children and adults; however, the role of the genetic markers in placental malaria (PM) infection and PM with HIV co-infection during pregnancy has not been investigated. We examined the relationship between the gene polymorphisms of Ig GM6 and KM allotypes and the risk of PM infection in pregnant women with known HIV status. DNA samples from 728 pregnant women were genotyped for GM6 and KM alleles using polymerase chain reaction-restriction fragment length polymorphism method. Individual GM6 and KM genotypes and the combined GM6 and KM genotypes were assessed in relation to PM in HIV-1 negative and positive women, respectively. There was no significant effect of individual GM6 and KM genotypes on the risk of PM infection in HIV-1 negative and positive women. However, the combination of homozygosity for GM6(+) and KM3 was associated with decreased risk of PM (adjusted OR, 0.25; 95% CI, 0.08-0.8; P = 0.019) in HIV-1 negative women while in HIV-1 positive women the combination of GM6(+/-) with either KM1-3 or KM1 was associated with increased risk of PM infection (adjusted OR, 2.10; 95% CI, 1.18-3.73; P = 0.011). Hardy-Weinberg Equilibrium (HWE) tests further showed an overall significant positive F(is) (indication of deficit in heterozygotes) for GM6 while there was no deviation for KM genotype frequency from HWE in the same population. These findings suggest that the combination of homozygous GM6(+) and KM3 may protect against PM in HIV-1 negative women while the HIV-1 positive women with heterozygous GM6(+/-) combined with KM1-3 or KM1 may be more susceptible to PM infection. The deficit in heterozygotes for GM6 further suggests that GM6 could be under selection likely by malaria infection.

  18. Antioxidant and HSP70B responses in Chlamydomonas reinhardtii genotypes with different resistance to oxidative stress.

    PubMed

    Chankova, Stephka G; Dimova, Evgeniya G; Mitrovska, Zhana; Miteva, Daniela; Mokerova, Dariya V; Yonova, Petranka A; Yurina, Nadezhda P

    2014-03-01

    Today, the information from model species that differ in their resistance to oxidative stress and the determination of suitable plant markers for screening stress-resistant genotypes are essential for better understanding of plant stress responses and for selection. Here we aimed to assess the differences in antioxidant and HSP70B responses to paraquat treatment between genotypes susceptible and resistant to oxidative stress. Four genotypes of Chlamydomonas reinhardtii were chosen as a model of plant cells: two susceptible genotypes: wild type and paraquat-sensitive; and two paraquat-resistant genotypes: with high and moderate resistance. Varying responses to paraquat treatment were found depending on the genotype and paraquat concentrations. High paraquat concentrations (>50μM) were shown to be very stressful for all C. reinhardtii genotypes, leading to inhibition of enzyme activity. Only the paraquat-sensitive genotype responded to low-level paraquat treatment with a marked enhancement of SOD, CAT, GST activities. The lack of statistically significant response measured as SOD, CAT, GST activities in WT and resistant genotypes could be considered as an indication of absence of strong oxidative stress. This could relate to higher levels of endogenous SOD and CAT activities characteristic of moderately and highly paraquat-resistant genotypes. The response to lower paraquat concentrations evaluated as HSP70B accumulation was proportional to the level of genotype susceptibility to PQ. New evidence is provided that low-level oxidative stress impacts the antioxidant and HSP70B responses differently depending on the genotype resistance. In light of the still unresolved challenge for identification of reliable characters for screening of genotype resistance/susceptibility to oxidative stress, our study demonstrates that HSP70B accumulation could be used as an early marker for induced oxidative stress in the studied genotypes. The obtained results that the most pronounced

  19. Determination of genotypes of hepatitis C virus in Venezuela by restriction fragment length polymorphism.

    PubMed Central

    Pujol, F H; Loureiro, C L; Devesa, M; Blitz, L; Parra, K; Beker, S; Liprandi, F

    1997-01-01

    Hepatitis C virus genotypes in Venezuela were analyzed by restriction fragment length polymorphism in the 5' noncoding region. The absence of BstUI digestion was found to be a useful marker for genotype 2 specimens. From 122 serum samples, 66, 20, and 2.5% were classified as genotypes 1, 2, and 3, respectively; 0.8% were classified as genotype 4; and 10% appeared to be mixed infections. PMID:9196212

  20. High prevalence of hepatitis C virus (HCV) genotype 2 in Italian patients with chronic liver disease.

    PubMed

    Sartori, M; Andorno, S; Avogadro, E; Ballarè, M; La Terra, G; Leone, F; Quaglia, V; Fortina, G; Aglietta, M

    1996-01-01

    The prevalence of different genotypes of Hepatitis C virus may vary between geographic areas and it is possible that various genotypes have different pathogenic characteristics. Therefore, 90 consecutive Italian patients anti-Hepatitis C Virus positive with a broad spectrum of chronic liver disease, have been analysed to observe prevalence of various genotypes of Hepatitis C Virus. Genotyping was performed by polymerase chain reaction with a set of nested biotinylated primers, located in 5'UTR region. Genotype 1b and genotype 2a were the most commonly encountered (respectively, 50% and 37%) whereas other genotypes were rare. The unexpected high prevalence of genotype 2a allowed direct comparison of clinical characteristics and response to therapy between patients with genotype 2a and those with 1b. Genotype 1b was more prevalent than 2a in patients over 60 years (29 vs 12) and in those with more severe liver disease (34 vs 16). In a univariate analysis, genotype 2a was associated with less severe liver disease (p = 0.02) and younger age (p = 0.018), in comparison with genotype 1b. Patients with genotype 2a responded to interferon alpha therapy better than those with 1b (p = 0.007). In a multivariate analysis, only younger age was associated with genotype 2a. Genotype 2a (in comparison with 1b) and absence of cirrhosis were independent predictors of response to interferon alpha. In conclusion, genotype 2a is playing an emerging role in younger Italian patients and seems more sensitive than 1b to interferon alpha therapy.

  1. MICA/B genotyping of Tujias from Zhangjiajie, Hunan Province, China.

    PubMed

    Wang, Y J; Zhang, N J; Chen, E; Chen, C J; Bu, Y H; Yu, P

    2016-04-01

    One hundred eighty-seven Tujia individuals from Zhangjiajie, Hunan Province, China were genotyped at the MICA and MICB loci using polymerase chain reaction-sequence specific priming and sequencing-based typing methods. MICA and MCB genotypes are consistent with expected HW proportions. These genotype data are available in the Allele Frequencies Net Database.

  2. Aphid and ladybird beetle abundance depend on the interaction of spatial effects and genotypic diversity.

    PubMed

    Genung, Mark A; Crutsinger, Gregory M; Bailey, Joseph K; Schweitzer, Jennifer A; Sanders, Nathan J

    2012-01-01

    Intraspecific variation and genotypic diversity of host-plants can affect the structure of associated arthropod communities and the dynamics of populations. Similarly, neighboring plants can also affect interactions between host-plants and their associated arthropods. However, most studies on the effects of host-plant genotypes have largely ignored the potential effects of neighboring host-plants on arthropod communities. In this study, we used a common garden experiment to ask how spatial effects of neighboring patches, along with genotype identity and genotypic diversity in tall goldenrod (Solidago altissima), affect the abundances of a common goldenrod herbivore (Uroleucon nigrotuberculatum) and their dominant predator (Harmonia axyridis, a ladybird beetle). Aphid abundance varied 80-fold among genotypes, while ladybird beetle abundance was not affected by genotype identity. Additionally, there were strong effects of neighboring plots: aphid abundance in a focal plot was positively correlated to aphid abundance in nearby plots, suggesting strong spatial patterning in the abundance of aphids. Neither aphid nor ladybird beetle abundance was affected by genotypic diversity. However, focal plot genotypic diversity mediated the strength of the neighborhood effect (i.e., strong effects for genotype polyculture focal plots and weak effects for genotype monoculture focal plots). Our results show that aphids were directly influenced by host-plant genotype identity while ladybird beetles responded mainly to prey abundance, and suggest that genotypic diversity can influence the effects of spatial processes on the plant-herbivore interactions.

  3. Differentiation of Bovine Coronavirus (Bcov) Genotypes by a Restriction Enzyme Assay

    PubMed Central

    Pinheiro de Souza, Sibele; Miyuki Asano, Karen; Lucas Sandri, Thaisa; Nunes de Barros, Iracema; José Richtzenhain, Leonardo; Eduardo Brandão, Paulo

    2010-01-01

    This article reports the use of the GsuI restriction enzyme to differentiate genotypes of Bovine Coronavirus (BCoV), based on an 18-nucleotide deletion of S1-coding region found in one of the two genotypes. It was concluded that this assay can be used as a rapid tool for BCoV genotypes differentiation. PMID:24031559

  4. Pathogenesis of new sub-genotypes of Newcastle disease virus strains from Israel and Pakistan

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Newcastle disease (ND) is a devastating disease of poultry worldwide caused by virulent strains of Newcastle disease virus (NDV). New genotypes and sub-genotypes of NDV frequently emerge. In the past few years, NDV strains belonging to sub-genotype VIIi and XIIIb emerged in the Middle East and Asi...

  5. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... resistance genotype assay. 866.3950 Section 866.3950 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. (a) Identification. The in vitro HIV drug resistance genotype assay is a device that consists of nucleic acid...

  6. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... resistance genotype assay. 866.3950 Section 866.3950 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. (a) Identification. The in vitro HIV drug resistance genotype assay is a device that consists of nucleic acid...

  7. Short communication: Relationship of call rate and accuracy of single nucleotide polymorphism genotypes in dairy cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Call rate has been used as a measure of quality on both a single nucleotide polymorphism (SNP) and animal basis since SNP genotypes were first used in genomic evaluation of dairy cattle. The genotyping laboratories perform initial quality control screening and genotypes that fail are usually exclude...

  8. Application of genotyping-by-sequencing for mapping disease resistance in grapevine breeding families

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genotyping-by-Sequencing (GBS) is a low-cost, high-throughput, method for genome-wide polymorphism discovery and genotyping adjacent to restriction sites. Since 2010, GBS has been applied for the genotyping of over 12,000 grape breeding lines, with a primary focus on identifying markers predictive ...

  9. Hepatocellular carcinoma in Sweden: its association with viral hepatitis, especially with hepatitis C viral genotypes.

    PubMed

    Widell, A; Verbaan, H; Wejstål, R; Kaczynski, J; Kidd-Ljunggren, K; Wallerstedt, S

    2000-01-01

    Viral markers of chronic hepatitis were tested for in 95 frozen serum samples from 299 patients from Malmö, Sweden, with hepatocellular carcinoma (HCC), diagnosed between 1977 and 1994. Hepatitis B analysis included anti-HBc, HBsAg and, if anti-HBc positive, HBV DNA. Hepatitis C infection analysis included anti-HCV screening, RIBA, HCV RNA and HCV genotyping. HCV genotyping was also carried out in 9 HCV-viraemic HCC-patients from Gothenburg. HCV genotype distribution in HCC cases was compared with Swedish HCV-infected blood donors. Among the 95 patients from Malmö, 28 (29%) had anti-HBc, but only 5 (5%) were chronic HBV carriers, compared with 16 (17%) with chronic hepatitis C (p = 0.021). HCV-related HCC was more common among immigrants (8/16 vs. 8/79; p < 0.001). Genotyping of 25 HCV-infected cases showed genotype 1a in 6 (24%), genotype 1b in 13 (52%), genotype 2b in 4 (16%), and genotype 3a in 2 (8.0%) patients. Genotype 1b was more common among HCC patients than among blood donors (p < 0.001), but 8 of 13 genotype 1b-infected patients were from countries where genotype 1b is predominant. Among native Swedes there was no difference between the HCV genotypes infecting blood donors and those found in HCC patients.

  10. Hepatitis B virus with a proposed genotype I was found in Sichuan Province, China.

    PubMed

    Tong, Wenbin; He, Jilan; Sun, Li; He, Shusen; Qi, Qi

    2012-06-01

    To date, eight hepatitis B virus (HBV) genotypes, A-H, have been designated, and two additional genotypes, I and J, have also been proposed. A serological survey targeting children in difficult-to-reach vaccination areas was carried out in remote counties of Sichuan Province, China. HBV genotypes and serotypes were also determined from HBsAg-positive serum samples by direct sequencing. Phylogenetic analysis showed two strains isolated from the Yi ethnic children clustered with the proposed genotype I. The pairwise genome genetic distance was 7.5% between genotypes I and C, and ranged from 8.4% to 15.2% between genotype I and other genotypes, except genotype C. Grouping Scan analyses of the two strains revealed apparent recombination events between an unknown genotype and genotype C. Two out of four HBV strains isolated from the Yi ethnic children were confirmed to be genotype I, suggesting widespread circulation and common infection with genotype I HBV in the local Yi population. High prevalence of HBsAg and low hepatitis B vaccination coverage indicated that additional efforts are needed to control HBV infection in those areas.

  11. Rapid typing of Mannheimia haemolytica major genotypes 1 and 2 using MALDI-TOF mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genotype 2 M. haemolytica predominantly associate over genotype 1 with the lungs of cattle with respiratory disease and ICEs containing antimicrobial resistance genes. Distinct protein masses were detected by MALDI-TOF MS between genotype 1 and 2 strains. MALDI-TOF MS could rapidly differentiate ge...

  12. Identification of new sub-genotypes of virulent Newcastle disease virus with potential panzootic features.

    PubMed

    Miller, Patti J; Haddas, Ruth; Simanov, Luba; Lublin, Avishay; Rehmani, Shafqat Fatima; Wajid, Abdul; Bibi, Tasra; Khan, Taseer Ahmad; Yaqub, Tahir; Setiyaningsih, Surachmi; Afonso, Claudio L

    2015-01-01

    Virulent Newcastle disease virus (NDV) isolates from new sub-genotypes within genotype VII are rapidly spreading through Asia and the Middle East causing outbreaks of Newcastle disease (ND) characterized by significant illness and mortality in poultry, suggesting the existence of a fifth panzootic. These viruses, which belong to the new sub-genotypes VIIh and VIIi, have epizootic characteristics and do not appear to have originated directly from other genotype VII NDV isolates that are currently circulating elsewhere, but are related to the present and past Indonesian NDV viruses isolated from wild birds since the 80s. Viruses from sub-genotype VIIh were isolated in Indonesia (2009-2010), Malaysia (2011), China (2011), and Cambodia (2011-2012) and are closely related to the Indonesian NDV isolated in 2007, APMV1/Chicken/Karangasem, Indonesia (Bali-01)/2007. Since 2011 and during 2012 highly related NDV isolates from sub-genotype VIIi have been isolated from poultry production facilities and occasionally from pet birds, throughout Indonesia, Pakistan and Israel. In Pakistan, the viruses of sub-genotype VIIi have replaced NDV isolates of genotype XIII, which were commonly isolated in 2009-2011, and they have become the predominant sub-genotype causing ND outbreaks since 2012. In a similar fashion, the numbers of viruses of sub-genotype VIIi isolated in Israel increased in 2012, and isolates from this sub-genotype are now found more frequently than viruses from the previously predominant sub-genotypes VIId and VIIb, from 2009 to 2012. All NDV isolates of sub-genotype VIIi are approximately 99% identical to each other and are more closely related to Indonesian viruses isolated from 1983 through 1990 than to those of genotype VII, still circulating in the region. Similarly, in addition to the Pakistani NDV isolates of the original genotype XIII (now called sub-genotype XIIIa), there is an additional sub-genotype (XIIIb) that was initially detected in India and Iran

  13. Hepatitis B virus genotype C isolates with wild-type core promoter sequence replicate less efficiently than genotype B isolates but possess higher virion secretion capacity.

    PubMed

    Qin, Yanli; Tang, Xiaoli; Garcia, Tamako; Hussain, Munira; Zhang, Jiming; Lok, Anna; Wands, Jack; Li, Jisu; Tong, Shuping

    2011-10-01

    Infection by hepatitis B virus (HBV) genotype C is associated with a prolonged viremic phase, delayed hepatitis B e antigen (HBeAg) seroconversion, and an increased incidence of liver cirrhosis and hepatocellular carcinoma compared with genotype B infection. Genotype C is also associated with the more frequent emergence of core promoter mutations, which increase genome replication and are independently associated with poor clinical outcomes. We amplified full-length HBV genomes from serum samples from Chinese and U. S. patients with chronic HBV infection and transfected circularized genome pools or dimeric constructs of individual clones into Huh7 cells. The two genotypes could be differentiated by Western blot analysis due to the reactivities of M and L proteins toward a monoclonal pre-S2 antibody and slightly different S-protein mobilities. Great variability in replication capacity was observed for both genotypes. The A1762T/G1764A core promoter mutations were prevalent in genotype C isolates and correlated with increased replication capacity, while the A1752G/T mutation frequently found in genotype B isolates correlated with a low replication capacity. Importantly, most genotype C isolates with wild-type core promoter sequence replicated less efficiently than the corresponding genotype B isolates due to less efficient transcription of the 3.5-kb RNA. However, genotype C isolates often displayed more efficient virion secretion. We propose that the low intracellular levels of viral DNA and core protein of wild-type genotype C delay immune clearance and trigger the subsequent emergence of A1762T/G1764A core promoter mutations to upregulate replication; efficient virion secretion compensates for the low replication capacity to ensure the establishment of persistent infection by genotype C.

  14. Estimation of Genetic Effects and Genotype-Phenotype Maps

    PubMed Central

    Le Rouzic, Arnaud; Álvarez-Castro, José M.

    2008-01-01

    Determining the genetic architecture of complex traits is a necessary step to understand phenotypic changes in natural, experimental and domestic populations. However, this is still a major challenge for modern genetics, since the estimation of genetic effects tends to be complicated by genetic interactions, which lead to changes in the effect of allelic substitutions depending on the genetic background. Recent progress in statistical tools aiming to describe and quantify genetic effects meaningfully improves the efficiency and the availability of genotype-to-phenotype mapping methods. In this contribution, we facilitate the practical use of the recently published ‘NOIA’ quantitative framework by providing an implementation of linear and multilinear regressions, change of reference operation and genotype-to-phenotype mapping in a package (‘noia’) for the software R, and we discuss theoretical and practical benefits evolutionary and quantitative geneticists may find in using proper modeling strategies to quantify the effects of genes. PMID:19204820

  15. Comprehensive Annotation of Mature Peptides and Genotypes for Zika Virus

    PubMed Central

    Sun, Guangyu; Baumgarth, Nicole; Klem, Edward B.; Scheuermann, Richard H.

    2017-01-01

    The rapid spread of Zika virus (ZIKV) has caused much concern in the global health community, due in part to a link to fetal microcephaly and other neurological illnesses. While an increasing amount of ZIKV genomic sequence data is being generated, an understanding of the virus molecular biology is still greatly lacking. A significant step towards establishing ZIKV proteomics would be the compilation of all proteins produced by the virus, and the resultant virus genotypes. Here we report for the first time such data, using new computational methods for the annotation of mature peptide proteins, genotypes, and recombination events for all ZIKV genomes. The data is made publicly available through the Virus Pathogen Resource at www.viprbrc.org. PMID:28125631

  16. Genotype circulation pattern of human respiratory syncytial virus in Iran.

    PubMed

    Faghihloo, Ebrahim; Yavarian, Jila; Jandaghi, Nazanin Zahra Shafiei; Shadab, Azadeh; Azad, Talat Mokhtari

    2014-03-01

    In order to have information on the molecular epidemiology and genetic circulation pattern of human respiratory syncytial virus (HRSV) in Iran, we studied the genetic variability of both group A and B HRSV strains during seven consecutive years by sequencing the hypervariable C-terminal domain of G protein. A total of 485 children <2years of age who were negative for influenza viruses, screened for the presence of HRSV in this research. HRSV was detected in 94 (19.38%) of the samples using nested RT-PCR. Group A viruses were isolated during each year, while group B viruses were isolated during 2009 and 2013. Phylogenetic analysis showed that all HRSV group A viruses belonged to three genotypes: GA1, GA2, GA5 and the group B viruses were in BA genotype.

  17. Liquid biopsy genotyping in lung cancer: ready for clinical utility?

    PubMed

    Huang, Wei-Lun; Chen, Yi-Lin; Yang, Szu-Chun; Ho, Chung-Liang; Wei, Fang; Wong, David T; Su, Wu-Chou; Lin, Chien-Chung

    2017-01-12

    Liquid biopsy is a blood test that detects evidence of cancer cells or tumor DNA in the circulation. Despite complicated collection methods and the requirement for technique-dependent platforms, it has generated substantial interest due, in part, to its potential to detect driver oncogenes such as epidermal growth factor receptor (EGFR) mutants in lung cancer. This technology is advancing rapidly and is being incorporated into numerous EGFR tyrosine kinase inhibitor (EGFR-TKI) development programs. It appears ready for integration into clinical care. Recent studies have demonstrated that biological fluids such as saliva and urine can also be used for detecting EGFR mutant DNA through application other user-friendly techniques. This review focuses on the clinical application of liquid biopsies to lung cancer genotyping, including EGFR and other targets of genotype-directed therapy and compares multiple platforms used for liquid biopsy.

  18. Genotyping of Bacillus cereus strains by microarray-based resequencing.

    PubMed

    Zwick, Michael E; Kiley, Maureen P; Stewart, Andrew C; Mateczun, Alfred; Read, Timothy D

    2008-07-02

    The ability to distinguish microbial pathogens from closely related but nonpathogenic strains is key to understanding the population biology of these organisms. In this regard, Bacillus anthracis, the bacterium that causes inhalational anthrax, is of interest because it is closely related and often difficult to distinguish from other members of the B. cereus group that can cause diverse diseases. We employed custom-designed resequencing arrays (RAs) based on the genome sequence of Bacillus anthracis to generate 422 kb of genomic sequence from a panel of 41 Bacillus cereus sensu lato strains. Here we show that RAs represent a "one reaction" genotyping technology with the ability to discriminate between highly similar B. anthracis isolates and more divergent strains of the B. cereus s.l. Clade 1. Our data show that RAs can be an efficient genotyping technology for pre-screening the genetic diversity of large strain collections to selected the best candidates for whole genome sequencing.

  19. Rationality and emotionality: serotonin transporter genotype influences reasoning bias.

    PubMed

    Stollstorff, Melanie; Bean, Stephanie E; Anderson, Lindsay M; Devaney, Joseph M; Vaidya, Chandan J

    2013-04-01

    Reasoning often occurs under emotionally charged, opinion-laden circumstances. The belief-bias effect indexes the extent to which reasoning is based upon beliefs rather than logical structure. We examined whether emotional content increases this effect, particularly for adults genetically predisposed to be more emotionally reactive. SS/SL(G) carriers of the serotonin transporter genotype (5-HTTLPR) were less accurate selectively for evaluating emotional relational reasoning problems with belief-logic conflict relative to L(A)L(A) carriers. Trait anxiety was positively associated with emotional belief-bias, and the 5-HTTLPR genotype significantly accounted for the variance in this association. Thus, deductive reasoning, a higher cognitive ability, is sensitive to differences in emotionality rooted in serotonin neurotransmitter function.

  20. Genotyping of Bacillus cereus Strains by Microarray-Based Resequencing

    PubMed Central

    Zwick, Michael E.; Kiley, Maureen P.; Stewart, Andrew C.; Mateczun, Alfred; Read, Timothy D.

    2008-01-01

    The ability to distinguish microbial pathogens from closely related but nonpathogenic strains is key to understanding the population biology of these organisms. In this regard, Bacillus anthracis, the bacterium that causes inhalational anthrax, is of interest because it is closely related and often difficult to distinguish from other members of the B. cereus group that can cause diverse diseases. We employed custom-designed resequencing arrays (RAs) based on the genome sequence of Bacillus anthracis to generate 422 kb of genomic sequence from a panel of 41 Bacillus cereus sensu lato strains. Here we show that RAs represent a “one reaction” genotyping technology with the ability to discriminate between highly similar B. anthracis isolates and more divergent strains of the B. cereus s.l. Clade 1. Our data show that RAs can be an efficient genotyping technology for pre-screening the genetic diversity of large strain collections to selected the best candidates for whole genome sequencing. PMID:18596941

  1. Influence of Gender and SNPs in GPX1 Gene on Biomarkers of Selenium Status in Healthy Brazilians.

    PubMed

    Donadio, Janaina L S; Guerra-Shinohara, Elvira M; Rogero, Marcelo M; Cozzolino, Silvia M F

    2016-05-05

    Selenium (Se) status varies worldwide as a result of natural variation of Se content in soils, dietary pattern, and the presence of SNPs. Further, Se status in Brazilians and its relationship between genetic variation and Se biomarkers is unknown. This work investigated the association between SNPs in glutathione peroxidase genes and biomarkers of Se status in healthy Brazilians. The study was conducted in 116 healthy adults in São Paulo, Brazil. Plasma and erythrocyte Se were measured by HGFAAS. Erythrocyte GPx (eGPx) activity was measured spectrometrically in a biochemical analyzer. Genotypes were determined by real-time PCR using Taqman(®) Assays. eGPx activity was higher in females compared with males. Lower erythrocyte Se concentrations were found in heterozygous GC carriers for GPX1 rs8179169. eGPx activity was higher in females with the common genotypes, except for rs8179169. GC carriers for rs8179169 had lower erythrocyte Se in both genders, and only male carriers of the variant alleles of both rs1050450 and rs1800668 had higher eGPx activity. In conclusion, the genotype for SNPs in GPX1 and gender affected biomarkers of Se status in this pilot study with healthy Brazilians.

  2. Influence of Gender and SNPs in GPX1 Gene on Biomarkers of Selenium Status in Healthy Brazilians

    PubMed Central

    Donadio, Janaina L. S.; Guerra-Shinohara, Elvira M.; Rogero, Marcelo M.; Cozzolino, Silvia M. F.

    2016-01-01

    Selenium (Se) status varies worldwide as a result of natural variation of Se content in soils, dietary pattern, and the presence of SNPs. Further, Se status in Brazilians and its relationship between genetic variation and Se biomarkers is unknown. This work investigated the association between SNPs in glutathione peroxidase genes and biomarkers of Se status in healthy Brazilians. The study was conducted in 116 healthy adults in São Paulo, Brazil. Plasma and erythrocyte Se were measured by HGFAAS. Erythrocyte GPx (eGPx) activity was measured spectrometrically in a biochemical analyzer. Genotypes were determined by real-time PCR using Taqman® Assays. eGPx activity was higher in females compared with males. Lower erythrocyte Se concentrations were found in heterozygous GC carriers for GPX1 rs8179169. eGPx activity was higher in females with the common genotypes, except for rs8179169. GC carriers for rs8179169 had lower erythrocyte Se in both genders, and only male carriers of the variant alleles of both rs1050450 and rs1800668 had higher eGPx activity. In conclusion, the genotype for SNPs in GPX1 and gender affected biomarkers of Se status in this pilot study with healthy Brazilians. PMID:27164132

  3. CHEF: a status report

    SciTech Connect

    Ostiguy, J.-F.; Michelotti, L.; /Fermilab

    2007-06-01

    CHEF refers both to a framework and to an interactive application emphasizing accelerator optics calculations. The framework supports multiple domains of applications: e.g. nonlinear analysis, perturbation theory, and tracking. Its underlying philosophy is to provide an infrastructure with minimum hidden implicit assumptions, general enough to facilitate both routine and specialized computational tasks, and to minimize the duplication of necessary, complex bookkeeping tasks. CHEF was already described in recent conferences. This paper is a status report on recent developments, including issues related to applications to high energy linacs.

  4. Model Validation Status Review

    SciTech Connect

    E.L. Hardin

    2001-11-28

    The primary objective for the Model Validation Status Review was to perform a one-time evaluation of model validation associated with the analysis/model reports (AMRs) containing model input to total-system performance assessment (TSPA) for the Yucca Mountain site recommendation (SR). This review was performed in response to Corrective Action Request BSC-01-C-01 (Clark 2001, Krisha 2001) pursuant to Quality Assurance review findings of an adverse trend in model validation deficiency. The review findings in this report provide the following information which defines the extent of model validation deficiency and the corrective action needed: (1) AMRs that contain or support models are identified, and conversely, for each model the supporting documentation is identified. (2) The use for each model is determined based on whether the output is used directly for TSPA-SR, or for screening (exclusion) of features, events, and processes (FEPs), and the nature of the model output. (3) Two approaches are used to evaluate the extent to which the validation for each model is compliant with AP-3.10Q (Analyses and Models). The approaches differ in regard to whether model validation is achieved within individual AMRs as originally intended, or whether model validation could be readily achieved by incorporating information from other sources. (4) Recommendations are presented for changes to the AMRs, and additional model development activities or data collection, that will remedy model validation review findings, in support of licensing activities. The Model Validation Status Review emphasized those AMRs that support TSPA-SR (CRWMS M&O 2000bl and 2000bm). A series of workshops and teleconferences was held to discuss and integrate the review findings. The review encompassed 125 AMRs (Table 1) plus certain other supporting documents and data needed to assess model validity. The AMRs were grouped in 21 model areas representing the modeling of processes affecting the natural and

  5. SLC - status and development

    SciTech Connect

    Fischer, G.E.

    1986-06-01

    The status of a three year construction program, begun October 1, 1983, of the SLAC Linear Collider is reviewed and evolutions of the original conceptual design are discussed. Subsystems of the project, that are described with emphasis on new or unusual technology, include: Electron Source and Injector, Damping Rings, Linear Accelerator Development, Energy (Klystron and Modulator) Upgrades, Positron Production and Reinjection, Arc Transport, Final Focus System, Control System and Conventional Facilities. Results from the commissioning program, which began in early 1986, and plans for the operation of the machine are presented.

  6. Euclid mission status

    NASA Astrophysics Data System (ADS)

    Laureijs, R.; Racca, G.; Stagnaro, L.; Salvignol, J.-C.; Lorenzo Alvarez, J.; Saavedra Criado, G.; Gaspar Venancio, L.; Short, A.; Strada, P.; Colombo, C.; Buenadicha, G.; Hoar, J.; Kohley, R.; Vavrek, R.; Mellier, Y.; Berthe, M.; Amiaux, J.; Cropper, M.; Niemi, S.; Pottinger, S.; Ealet, A.; Jahnke, K.; Maciaszek, T.; Pasian, F.; Sauvage, M.; Wachter, S.; Israelsson, U.; Holmes, W.; Seiffert, M.; Cazaubiel, V.; Anselmi, A.; Musi, P.

    2014-08-01

    In June 2012, Euclid, ESA's Cosmology mission was approved for implementation. Afterwards the industrial contracts were signed for the payload module and the spacecraft prime, and the mission requirements consolidated. We present the status of the mission in the light of the design solutions adopted by the contractors. The performances of the spacecraft in its operation, the telescope assembly, the scientific instruments as well as the data-processing have been carefully budgeted to meet the demanding scientific requirements. We give an overview of the system and where necessary the key items for the interfaces between the subsystems.

  7. Status of Wheeler Reservoir

    SciTech Connect

    Not Available

    1990-09-01

    This is one in a series of status reports prepared by the Tennessee Valley Authority (TVA) for those interested in the conditions of TVA reservoirs. This overview of Wheeler Reservoir summarizes reservoir purposes and operation, reservoir and watershed characteristics, reservoir uses and use impairments, and water quality and aquatic biological conditions. The information presented here is from the most recent reports, publications, and original data available. If no recent data were available, historical data were summarized. If data were completely lacking, environmental professionals with special knowledge of the resource were interviewed. 12 refs., 2 figs.

  8. Immune Response Genotypes and Risk of Young Adult Hodgkin Lymphoma

    DTIC Science & Technology

    2007-09-01

    TECHNICAL OBJECTIVES 1) To identify, enroll and collect blood specimens from 368 adolescents and young adults 18-to 45 years old diagnosed with Hodgkin... Young Adult Hodgkin Lymphoma PRINCIPAL INVESTIGATOR: Wendy Cozen Victoria Cortessis, Ph.D. David Conti, Ph.D. David...Genotypes and Risk of Young Adult Hodgkin Lymphoma 5b. GRANT NUMBER W81XWH-06-1-0683 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Wendy Cozen

  9. Surveillance for Echinococcus canadensis genotypes in Canadian ungulates☆

    PubMed Central

    Schurer, Janna; Shury, Todd; Leighton, Frederick; Jenkins, Emily

    2013-01-01

    The geographic and host distribution, prevalence and genotypes of Echinococcus canadensis in wild ungulates in Canada are described to better understand the significance for wildlife and public health. We observed E. canadensis in 10.5% (11/105) of wild elk (wapiti; Cervus canadensis) in Riding Mountain National Park, Manitoba, examined at necropsy, over two consecutive years (2010–2011). Molecular characterization of hydatid cyst material from these elk, as well as three other intermediate wildlife host species, was based on sequence of a 470 bp region of the NADH dehydrogenase subunit 1 (NAD1) mitochondrial gene. In moose [Alces alces], elk, and caribou [Rangifer tarandus] from northwestern Canada, the G10 genotype was the only one present, and the G8 genotype was detected in a muskox (Ovibos moschatus) from northeastern Canada. On a search of the national wildlife health database (1992–2010), cervids with hydatid cysts were reported in all provinces and territories except the Atlantic provinces, from which wolves [Canis lupis] are historically absent. Of the 93 cervids with records of hydatid cysts, 42% were elk, 37% were moose, 14% were caribou, and 6% were white-tailed and mule deer [Odocoileus virginianus and Odocoileus hemonius]. In these animals, 83% of cysts were detected in lungs alone, 8% in both lungs and liver, 3% in liver alone, and 6% in other organs. These observations can help target surveillance programs and contribute to a better understanding of ecology, genetic diversity, and genotype pathogenicity in the Echinococcus granulosus species complex. PMID:24533321

  10. Genotype-dependent expression of specific members of potato protease inhibitor gene families in different tissues and in response to wounding and nematode infection.

    PubMed

    Turrà, David; Bellin, Diana; Lorito, Matteo; Gebhardt, Christiane

    2009-05-01

    Protease inhibitors (PIs) are small ubiquitous proteins with a variety of biological functions in plants, including protein stabilization, modulation of apoptosis and defense against pathogens. Kunitz-like inhibitors (PKPIs) and proteinase inhibitors 1 (PI-1) are abundant in storage organs of potato plants and are up-regulated in other tissues in response to biotic and abiotic stress. However, little information is available on genotype-dependent regulation of individual PKPI group- and PI-1 genes. We isolated, sequenced and characterized four novel full-length PI-1 cDNAs (PPI3A2, PPI3A4, PPI2C4 and PPI2C1A) from Solanum tuberosum cv. Desirée. Specific primers were developed for PI-1 genes PPI3A2, PPI3B2 and PPI2C4 and the three PKPI homology groups A, B and C. Their expression profiles were studied by semi-quantitative RT-PCR in comparison with transcripts of the PI-1, Pin2 and PR1 gene families in various tissues, after wounding and Globodera rostochiensis infection of nematode-resistant genotypes P40 and LB7/4/c-I-7, and susceptible cv. Desirée. Individual PI-1 genes and PKPI homology groups were expressed in a tissue- and genotype-dependent manner after wounding and nematode infection. The differences in PI expression patterns were related to the intensity, type of inhibitors produced, and the kinetics of induction. Therefore, different genotype-environment combinations produce different sets of PI transcripts. Potato plants reacted to G. rostochiensis infection by modulating PKPI, PI-1 and Pin2, but not PR1 gene expression, suggesting that the jasmonic acid but not the salicylic acid defense signaling pathway is activated. PI expression profiles were not correlated with the resistance status of the potato genotype infected with G. rostochiensis.

  11. Association of susceptible genotypes to periodontal disease with the clinical outcome and tooth survival after non-surgical periodontal therapy: A systematic review and meta-analysis

    PubMed Central

    Doufexi, Aikaterini-Ellisavet; Kalogirou, Fotini

    2016-01-01

    Background The real clinical utility of genetic testing is the prognostic value of genetic factors in the clinical outcome of periodontal treatment and the tooth survival. A meta-analysis was undertaken to estimate the effect of a susceptible genotype to periodontitis on the clinical outcomes of non-surgical periodontal therapy and the tooth survival. Material and Methods A systematic search of MEDLINE-Pubmed, Cochrane Library and Scopus was performed. Additionally, a hand search was done in three journals. No specific language restriction was applied. Two reviewers screened independently titles and abstracts or full text copies. Quality assessment of all the included studies was held. Results Initial screening of electronic databases resulted in 283 articles. Ten studies met the inclusion criteria, nine of them examined the clinical outcome, while the other one investigated the tooth survival in susceptible individuals after non-surgical periodontal therapy. Eight of included studies were selected for the meta-analysis. IL-1 positive genotypes increase the risk of tooth loss, while no association found between the bleeding on probing (BOP), clinical attachment loss (CAL) and plaque index (PI) with the genotype status. Probing pocket depth (PPD) reduction in the first three months and in long-term results found to have a significant association with the genotype. Conclusions There is no difference in the clinical measurements after non-surgical periodontal treatment, apart from PPD. More publications are needed to identify a cause-effect relationship. Key words:Periodontal disease, periodontitis, periodontal therapy, clinical outcome, tooth loss, susceptibility, polymorphism, genotype, meta-analysis, systematic review. PMID:26595831

  12. Genotypes of pathogenic Leptospira spp isolated from rodents in Argentina

    PubMed Central

    Loffler, Sylvia Grune; Pavan, Maria Elisa; Vanasco, Bibiana; Samartino, Luis; Suarez, Olga; Auteri, Carmelo; Romero, Graciela; Brihuega, Bibiana

    2014-01-01

    Leptospirosis is the most widespread zoonosis in the world and significant efforts have been made to determine and classify pathogenic Leptospira strains. This zoonosis is maintained in nature through chronic renal infections of carrier animals, with rodents and other small mammals serving as the most important reservoirs. Additionally, domestic animals, such as livestock and dogs, are significant sources of human infection. In this study, a multiple-locus variable-number tandem repeat analysis (MLVA) was applied to genotype 22 pathogenic Leptospira strains isolated from urban and periurban rodent populations from different regions of Argentina. Three MLVA profiles were identified in strains belonging to the species Leptospira interrogans (serovars Icterohaemorrhagiae and Canicola); one profile was observed in serovar Icterohaemorrhagiae and two MLVA profiles were observed in isolates of serovars Canicola and Portlandvere. All strains belonging to Leptospira borgpetersenii serovar Castellonis exhibited the same MLVA profile. Four different genotypes were isolated from urban populations of rodents, including both mice and rats and two different genotypes were isolated from periurban populations. PMID:24676656

  13. Genotypes of pathogenic Leptospira spp isolated from rodents in Argentina.

    PubMed

    Loffler, Sylvia Grune; Pavan, Maria Elisa; Vanasco, Bibiana; Samartino, Luis; Suarez, Olga; Auteri, Carmelo; Romero, Graciela; Brihuega, Bibiana

    2014-04-01

    Leptospirosis is the most widespread zoonosis in the world and significant efforts have been made to determine and classify pathogenic Leptospira strains. This zoonosis is maintained in nature through chronic renal infections of carrier animals, with rodents and other small mammals serving as the most important reservoirs. Additionally, domestic animals, such as livestock and dogs, are significant sources of human infection. In this study, a multiple-locus variable-number tandem repeat analysis (MLVA) was applied to genotype 22 pathogenic Leptospira strains isolated from urban and periurban rodent populations from different regions of Argentina. Three MLVA profiles were identified in strains belonging to the species Leptospira interrogans (serovars Icterohaemorrhagiae and Canicola); one profile was observed in serovar Icterohaemorrhagiae and two MLVA profiles were observed in isolates of serovars Canicola and Portlandvere. All strains belonging to Leptospira borgpetersenii serovar Castellonis exhibited the same MLVA profile. Four different genotypes were isolated from urban populations of rodents, including both mice and rats and two different genotypes were isolated from periurban populations.

  14. Intraspecific genotypic variability determines concentrations of key truffle volatiles.

    PubMed

    Splivallo, Richard; Valdez, Nayuf; Kirchhoff, Nina; Ona, Marta Castiella; Schmidt, Jean-Pierre; Feussner, Ivo; Karlovsky, Petr

    2012-05-01

    • Aroma variability in truffles has been attributed to maturation (Tuber borchii), linked to environmental factors (Tuber magnatum), but the involvement of genetic factors has been ignored. We investigated aroma variability in Tuber uncinatum, a species with wide distribution. Our aim was to assess aroma variability at different spatial scales (i.e. trees, countries) and to quantify how aroma was affected by genotype, fruiting body maturity, and geographical origin. • A volatile fingerprinting method was used to analyze the aroma of 223 T. uncinatum fruiting bodies from seven European countries. Maturity was estimated from spore melanization. Genotypic fingerprinting was performed by amplified fragment length polymorphism (AFLP). • Discriminant analysis revealed that, regardless of the geographical origin of the truffles, most of the aroma variability was caused by eight-carbon-containing volatiles (C8-VOCs). In an orchard of T. uncinatum, truffles producing different concentrations of C8-VOCs clustered around distinct host trees. This clustering was not associated with maturity, but was associated with fungal genotype. • These results indicate that the variation in C8-VOCs in truffles is most likely under genetic control. They exemplify that understanding the factors behind aroma variability requires a holistic approach. Furthermore, they also raise new questions regarding the ecological role of 1-octen-3-ol in truffles.

  15. The Role of Haptoglobin Genotypes in Chagas Disease

    PubMed Central

    Mundaray Fernández, Ninomar; Fernández-Mestre, Mercedes

    2014-01-01

    Although the number of people infected with T. cruzi is on the rise, host genetic and immune components that are crucial in the development of the Chagas disease have been discovered. We investigated the frequency of polymorphisms in the gene encoding haptoglobin of patients with chronic Chagas disease. The results suggest that while the HP1-1 genotype may confer protection against infection and the development of chronic Chagas disease due to the rapid metabolism of the Hp1-1-Hb complex and its anti-inflammatory activity, the presence of HP2-2 genotype may increase susceptibility towards a chronic condition of the disease due to a slow metabolism of the Hp2-2-Hb complex, lower antioxidant activity, and increased inflammatory reactivity, which lead to cell damage and a deterioration of the cardiac function. Finally, correlations between HP genotypes in different age groups and cardiac manifestations suggest that HP polymorphism could influence the prognosis of this infectious disease. This study shows some of the relevant aspects of the haptoglobin gene polymorphism and its implications in the T. cruzi infection. PMID:25147423

  16. Geographical distribution of Trypanosoma cruzi genotypes in Venezuela.

    PubMed

    Carrasco, Hernán J; Segovia, Maikell; Llewellyn, Martin S; Morocoima, Antonio; Urdaneta-Morales, Servio; Martínez, Cinda; Martínez, Clara E; Garcia, Carlos; Rodríguez, Marlenes; Espinosa, Raul; de Noya, Belkisyolé A; Díaz-Bello, Zoraida; Herrera, Leidi; Fitzpatrick, Sinead; Yeo, Matthew; Miles, Michael A; Feliciangeli, M Dora

    2012-01-01

    Chagas disease is an endemic zoonosis native to the Americas and is caused by the kinetoplastid protozoan parasite Trypanosoma cruzi. The parasite is also highly genetically diverse, with six discrete typing units (DTUs) reported TcI - TcVI. These DTUs broadly correlate with several epidemiogical, ecological and pathological features of Chagas disease. In this manuscript we report the most comprehensive evaluation to date of the genetic diversity of T. cruzi in Venezuela. The dataset includes 778 samples collected and genotyped over the last twelve years from multiple hosts and vectors, including nine wild and domestic mammalian host species, and seven species of triatomine bug, as well as from human sources. Most isolates (732) can be assigned to the TcI clade (94.1%); 24 to the TcIV group (3.1%) and 22 to TcIII (2.8%). Importantly, among the 95 isolates genotyped from human disease cases, 79% belonged to TcI - a DTU common in the Americas, however, 21% belonged to TcIV- a little known genotype previously thought to be rare in humans. Furthermore, were able to assign multiple oral Chagas diseases cases to TcI in the area around the capital, Caracas. We discuss our findings in the context of T. cruzi DTU distributions elsewhere in the Americas, and evaluate the impact they have on the future of Chagas disease control in Venezuela.

  17. Phenotyping two tomato genotypes with different nitrogen use efficiency.

    PubMed

    Abenavoli, Maria Rosa; Longo, Caterina; Lupini, Antonio; Miller, Anthony J; Araniti, Fabrizio; Mercati, Francesco; Princi, Maria P; Sunseri, Francesco

    2016-10-01

    Nitrogen (N) supply usually limits crop production and optimizing N-use efficiency (NUE) to minimize fertilizer loss is important. NUE is a complex trait that can be dissected into crop N uptake from the soil (NUpE) and N utilization (NUtE). We compared NUE in 14 genotypes of three week old tomatoes grown in sand or hydroponic culture supplied with nitrate (NO3(-)). Culture method influenced measured NUE for some cultivars, but Regina Ostuni (RO) and UC82 were consistently identified as high and low NUE genotypes. To identify why these genotypes had contrasting NUE some traits were compared growing under 0.1 and 5 mM NO3(-) supply. UC82 showed greater root (15)NO3(-) influx at low and high supply, and stronger SlNRT2.1/NAR2.1 transporter expression under low supply when compared with RO. Conversely, RO showed a higher total root length and thickness compared to UC82. Compared with UC82, RO showed higher shoot SlNRT2.3 expression and NO3(-) storage at high supply, but similar NO3(-) reductase activity. After N-starvation, root cell electrical potentials of RO were significantly more negative than UC82, but nitrate elicited similar responses in both root types. Overall for UC82 and RO, NUtE may play a greater role than NUpE for improved NUE.

  18. Genotyping of clinical isolates of Acanthamoeba genus in Venezuela.

    PubMed

    Wagner, Carolina; Reyes-Batlle, María; Ysea, María Alejandra Vethencourt; Pérez, Mónica V Galindo; de Rondón, Carmen Guzmán; Paduani, Anaibeth J Nessi; Pérez, Angelyseb Dorta; López-Arencibia, Atteneri; Sifaoui, Ines; de Galindo, María Virginia Pérez; de Suárez, Eva Pérez; Martínez-Carretero, Enrique; Valladares, Basilio; Piñero, José E; Lorenzo-Morales, Jacob

    2016-12-01

    Free-living amoebae of Acanthamoeba genus are opportunistic pathogens distributed worldwide. Strains included in this genus are causative agents of a fatal encephalitis and a sight-threating keratitis in humans and other animals. In this study, 550 clinical samples which were collected between 1984 and 2014 from different patients with suspected infections due to Acanthamoeba were initially screened for the presence of this amoebic genus at the Laboratorio de Amibiasis-Escuela de Bioanálisis at the Universidad Central de Venezuela. Samples were cultured in 2% Non-Nutrient agar plates seeded with a layer of heat killed Escherichia coli. From the 550 clinical samples included in this study, 18 of them were positive for Acanthamoeba genus after culture identification. Moreover, positive samples were confirmed after amplification of the Diagnostic Fragment 3 (DF3) of the Acanthamoeba18S rDNA genus and sequencing was carried out in order to genotype the isolated strains of Acanthamoeba. Furthermore, the pathogenic potential of the strains was checked by performing thermotolerance and osmotolerance assays. Sequencing of the DF3 region resulted in the identification of genotype T4 in all the isolated strains. Moreover, most isolates were thermotolerant or both thermotolerant and osmotolerant and thus were classified as potentially pathogenic strains. To the best of our knowledge, this is the first report on the molecular characterization at the genotype level of Acanthamoeba strains in Venezuela.

  19. Histological Features of Melanoma Associated with CDKN2A Genotype

    PubMed Central

    Sargen, Michael R.; Kanetsky, Peter A.; Newton-Bishop, Julia; Hayward, Nicholas K.; Mann, Graham J.; Gruis, Nelleke A.; Tucker, Margaret A.; Goldstein, Alisa M.; Bianchi-Scarra, Giovanna; Puig, Susanna; Elder, David E.

    2014-01-01

    Background Inherited susceptibility genes have been associated with histopathologic characteristics of tumors. Objective To identify associations between histology of melanomas and CDKN2A genotype. Methods Case-control study design comparing 28 histopathologic tumor features among individuals with sporadic melanomas (N=81) and cases from melanoma families with (N=123) and without (N=120) CDKN2A germline mutations. Results Compared with CDKN2A-negative cases, mutation carriers tended to have histologic features of superficial spreading melanoma subtype including higher pigmentation (ptrend=0.02) and increased pagetoid scatter (ptrend=0.07) after adjusting for age at diagnosis, sex, and AJCC thickness category. Similar associations were observed when comparing mutation carriers to a combined group of CDKN2A-negative (wild type) and sporadic melanomas. The presence of spindle cell morphology in the vertical growth phase was also an important predictor of genotype. Of the fifteen cases with this phenotype, none were observed to harbor a CDKN2A mutation. Limitations Our study examined rare mutations and may have been underpowered to detect small, but biologically significant associations between histology and genotype. Conclusion Familial melanomas with CDKN2A mutations preferentially express a histologic phenotype of dense pigmentation, high pagetoid scatter, and a non-spindle cell morphology in the vertical growth phase. PMID:25592620

  20. Human papillomavirus genotypes and cervical cancer in northeast Thailand.

    PubMed

    Natphopsuk, Sitakan; Settheetham-Ishida, Wannapa; Pientong, Chamsai; Sinawat, Supat; Yuenyao, Pissamai; Ishida, Takafumi; Settheetham, Dariwan

    2013-01-01

    Human papillomavirus (HPV) is a major cause of cervical cancer. More than 100 HPV genotypes have been identified; however the distribution varies geographically and according to ethnicity. The purpose of this study was to investigate the prevalence and distribution of HPV subtypes among Northeast Thai women. Subjects included 198 cases of SCCA and 198 age-matched, healthy controls. HPV-DNA was amplified by PCR using the consensus primers GP5+/6+ system followed by reverse line blot hybridization genotyping. The prevalence of high-risk HPV infection was 21 (10.1%) and 152 (76.8%) in the controls and in the cases, respectively. High-risk HPV significantly increased the risk for cervical cancer with an OR of 42.4 (95%CI: 22.4-81.4, p<0.001) and an adjusted OR of 40.7-fold (95%CI: 21.5-76.8, p <0.001). HPV-16 was the most prevalent HPV type in the SCCA (56.2%) followed by HPV-58 (17.8%) and HPV-18 (13.6%); whereas HPV-58 (46.4%) was a prominent genotype in the controls followed by HPV-16 (39.3%) and unidentified HPV types (25.0%). These findings indicate that HPV infection remains a critical risk factor for SCCA; particularly, HPV-16, HPV-58 and HPV-18. In order to eradicate cervical cancer, sustained health education, promoted use of prophylactics and a HPV-58 vaccine should be introduced in this region.