Sample records for fshr genotype status

  1. Relationship Between Genotype Variants Follicle-stimulating Hormone Receptor Gene Polymorphisms (FSHR) and Morphology of Oocytes Prior to ICSI Procedures


    Gashi, Zafer; Elezaj, Shkelzen; Zeqiraj, Afrim; Grabanica, Driton; Shabani, Isak; Gruda, Bujar; Gashi, Fitore


    Introduction: This study investigated association of Asn680Ser FSHR polymorphism with the ovarian response in 104 women of Albanian ethnic population enrolled in ICSI program. The reason of infertility in all cases has been identified as male factor. Methods: Analysis of the Asn680Ser polymorphism was performed using TaqMan? SNP Genotyping Assay. Clinical and endocrinologic parameters were analyzed based on the genotype, age, BMI, oocyte yield, number of transferred embryos and pregnancy rate...

  2. Relationship Between Genotype Variants Follicle-stimulating Hormone Receptor Gene Polymorphisms (FSHR) and Morphology of Oocytes Prior to ICSI Procedures (United States)

    Gashi, Zafer; Elezaj, Shkelzen; Zeqiraj, Afrim; Grabanica, Driton; Shabani, Isak; Gruda, Bujar; Gashi, Fitore


    Introduction: This study investigated association of Asn680Ser FSHR polymorphism with the ovarian response in 104 women of Albanian ethnic population enrolled in ICSI program. The reason of infertility in all cases has been identified as male factor. Methods: Analysis of the Asn680Ser polymorphism was performed using TaqMan® SNP Genotyping Assay. Clinical and endocrinologic parameters were analyzed based on the genotype, age, BMI, oocyte yield, number of transferred embryos and pregnancy rate. Results: The frequencies of the Asn680 Ser genotype variants were as follows: Asn/Asn 22.1%, Asn/Ser 47.1%, and Ser/Ser 30.8%, respectively. BMI was significantly higher in the Ser/Ser group as compared to those from the Asn/Ser or the Asn/Asn group (p= 0.0010). The genotype variants Ser/Ser indicates a higher rate of oocyte retrieval (25.9%) in the immature form, metaphase I (MI) as opposed to the other two groups (Asn/Asn 23.7 % vs. Asn/Ser 21.9%), which was statistically significant (p = 0.3020). Conclusions: FSH receptor polymorphism is associated with different ovarian response to controlled ovarian stimulation (COS), but is not an important factor in increasing the degree of pregnancy. Polymorphisms of the FSH receptor is associated with normal morphology and genetic maturation (metaphase II) oocytes in dependence of genotypic variation polymorphisms. PMID:27994298


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    E. Andreas


    Full Text Available Follicle stimulating hormone (FSH is a pituitary expressed glycoprotein hormone that regulatesreproduction in mammals which composed of α and β-sub unit. The β-sub unit dictates its bindingspecificity with their receptor (FSHR. This study aimed to identify polymorphism of FSH β-sub unitand FSHR genes, and its effect to superovulatory response traits on superovulated cows. Study was doneon 32 cows including Angus, Friesian Holstein (FH, Limousin, Simmental and Brahman in CipelangLivestock Embryo Center. Cows used have been treated superovulation and mated by artificialinsemination. Superovulation response (SR, ovulation rate (OR, fertilization percentage (FP andviable transfer embryo percentage (VP were analyzed to investigate the effect of FSH β-sub unit andFSHR polymorphism. Allele frequency of FSH β-sub unit|PstI and FSH|AluI were opposite withinspecies. Mostly B allele and C allele for FSH β-sub unit and FSHR respectively have a high number inBos taurus species while those were in contrast in Bos indicus species. The highest heterozygosity wasfound in FH cattle (0.250 for FSH β-sub unit and Brahman (0.333 for FSHR. Significant effect was found between FSHR gene polymorphism with ovulation rate where CC genotype was higher (P<0.05than CG and GG genotypes.

  4. The Common Follicle-Stimulating Hormone Receptor (FSHR Promoter Polymorphism FSHR −29G > A Affects Androgen Production in Normal Human Small Antral Follicles

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    Tanni Borgbo


    Full Text Available Follicle-stimulating hormone receptors (FSHRs are almost exclusively expressed on granulosa cells, and FSH action is probably most clearly reflected in intrafollicular hormone milieu of antral follicles. Little is known about the possible effects of the common single nucleotide polymorphism (SNP FSHR −29G > A (rs1394205 on hormonal conditions in humsan small antral follicles (hSAFs obtained from women in the natural menstrual cycle. This study investigated the follicle fluid (FF concentrations of anti-Müllerian hormone, estradiol, progesterone, androstenedione, and testosterone in hSAF in relation to the different genotypes of FSHR −29G > A. FF from 362 follicles was collected in 95 women undergoing fertility preservation, who did not suffer from a disease that directly affected ovarian function. The testosterone levels of the minor A/A genotype were significantly increased compared to the A/G and the G/G genotype. Furthermore, significantly reduced androstenedione levels were observed for the G/G genotype, as compared to the A/G genotype, while the other hormones did not show statistical significant differences. In conclusion, the androgen levels of hSAF were significantly elevated in the minor SNP genotype in the FSHR promoter polymorphism FSHR −29G > A.

  5. A novel homozygous mutation in the FSHR gene is causative for primary ovarian insufficiency. (United States)

    Liu, Hongli; Xu, Xiaofei; Han, Ting; Yan, Lei; Cheng, Lei; Qin, Yingying; Liu, Wen; Zhao, Shidou; Chen, Zi-Jiang


    To identify the potential FSHR mutation in a Chinese woman with primary ovarian insufficiency (POI). Genetic and functional studies. University-based reproductive medicine center. A POI patient, her family members, and another 192 control women with regular menstruation. Ovarian biopsy was performed in the patient. Sanger sequencing was carried out for the patient, her sister, and parents. The novel variant identified was further confirmed with the use of control subjects. Sanger sequencing and genotype analysis to identify the potential variant of the FSHR gene; hematoxylin and eosin staining of the ovarian section to observe the follicular development; Western blotting and immunofluorescence to detect FSH receptor (FSHR) expression; and cyclic adenosine monophosphate (cAMP) assay to monitor FSH-induced signaling. Histologic examination of the ovaries in the patient revealed follicular development up to the early antral stage. Mutational screening and genotype analysis of the FSHR gene identified a novel homozygous mutation c.175C>T (p.R59X) in exon 2, which was inherited in the autosomal recessive mode from her heterozygous parents but was absent in her sister and the 192 control women. Functional studies demonstrated that in vitro the nonsense mutation caused the loss of full-length FSHR expression and that p.R59X mutant showed no response to FSH stimulation in the cAMP level. The mutation p.R59X in FSHR is causative for POI by means of arresting folliculogenesis. Copyright © 2017 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  6. Relationship of status of polymorphic rapd bands with genotypic ...

    African Journals Online (AJOL)

    Relationship of status of polymorphic rapd bands with genotypic adaptation in early finger millet genotypes. S Das, RC Misra, GR Rout, MC Pattanaik, S Aparajita. Abstract. Molecular characterisation of the 15 early duration finger millet (Eleusine coracana G) genotypes was done through RAPD markers. Twenty-five ...


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    Stephania Madrid Gaviria


    Full Text Available Because FSH and its receptor play a fundamental role in reproduction, the objective of this research was determining the effect of the A-320T polymorphism in productive and reproductive traits in Antioquia Holstein cows. The PCR-RFLP was used to amplify a segment of 970 bp of the bovine follicle stimulating hormone receptor gene (FSHR which was digested with the restriction enzyme TaqI. The effect of the FSHR genotypes on productive and reproductive traits was determinate by a Mixed Linear Model and Tukey Test was used to establish significant differences between means for the three genotypes. The effect of allelic substitution was studied through a linear regression model where the genotypes AA, AT and TT were transformed into a quantitative scale of 0, 1 and 2, respectively according to the number of possessed T alleles. In Antioquia Holstein cattle the most common genotype was the AT (0.485 followed by TT (0.417 and AA (0.096 genotypes. Allele frequencies were 0.339 for A and 0.660 for T, respectively. The FSHR genotypes did not exert a significant effect on the principal productive parameters, except for fat percentage (P<0.01 where the TT individuals presented the highest percent. Results showed that T allele seems to improve the solids in milk while A allele improves dairy yield. The reproductive parameters were not affected by this SNP but AT animals showed a higher number of services per conception. Further studies are required to determine whether this SNP may be used as a molecular marker

  8. Effect of the FSH receptor single nucleotide polymorphisms (FSHR 307/680) on the follicular fluid hormone profile and the granulosa cell gene expression in human small antral follicles

    DEFF Research Database (Denmark)

    Borgbo, Tanni Kjær; Jeppesen, J V; Lindgren, I


    ), by evaluating the hormone and gene expression profiles of human small antral follicles collected under physiological conditions in connection with fertility preservation. In total 69 women at various time during the menstrual cycle were included in this study. The intrafollicular hormone content of 179...... was significantly increased, whereas AMH gene expression was significantly reduced for the G/G genotype. In follicles >6 mm, estradiol and CYP19A1 gene expression levels were significantly higher for the G/G genotype. In conclusion, significant changes were observed between the FSHR 307/680 polymorphisms in human......The most pronounced effects of FSH signalling are potentially displayed in the follicle fluid, which acts as a reservoir for FSH-induced granulosa cell (GC) secreted hormones. This study investigates the effects of two common polymorphisms of FSHR, FSHR 307 (rs6165) and FSHR 680 (rs6166...

  9. The susceptibility of FSHB -211G > T and FSHR G-29A, 919A > G, 2039A > G polymorphisms to men infertility: an association study and meta-analysis. (United States)

    Wu, Qiuyue; Zhang, Jing; Zhu, Peiran; Jiang, Weijun; Liu, Shuaimei; Ni, Mengxia; Zhang, Mingchao; Li, Weiwei; Zhou, Qing; Cui, Yingxia; Xia, Xinyi


    Male infertility is a complex disorder caused by genetic, developmental, endocrine, or environmental factors as well as unknown etiology. Polymorphisms in the follicle stimulating hormone beta subunit (FSHB) (rs10835638, c.-211G > T) and follicle stimulating hormone receptor (FSHR) (rs1394205, c.-29G > A; rs6165, c.919A > G; rs6166, c.2039 A > G) genes might disturb normal spermatogenesis and affect male reproductive ability. To further ascertain the aforementioned effects, we conducted a case-control study of 255 infertile men and 340 fertile controls from South China using the Mass ARRAY method, which was analyzed by the t-tests and logistic regression analysis using SPSS for Windows 14.0. In addition, a meta-analysis was performed by combining our results with previous reports using STATA 12.0. In the FSHB or FSHR gene single nucleotide polymorphism (SNP) evaluation, no statistically-significant difference was found in the frequency of allelic variants or in genotype distribution between cases and controls. However, a significant association for the comparison of GAA (P: 0.022, OR: 0.63, 95%CI: 0.43-0.94) was seen between the oligozoospermia and controls in haplotype analysis of rs1394205/rs6165/rs6166. In the meta-analysis, rs6165G allele and rs6166 GG genotype were associated with increased risk of the male infertility. This study suggested that FSHR GAA haplotype would exert protective effects against male sterility, which indicated that the combination of three SNP genotypes of FSHR was predicted to have a much stronger impact than either one alone. Then in the meta-analysis, a significant association was seen between FSHR rs6165, rs6166 polymorphisms and male infertility. In terms of male infertility with multifactorial etiology, further studies with larger sample sizes and different ethnic backgrounds or other risk factors are warranted to clarify the potential role of FSHB and FSHR polymorphisms in the pathogenesis of male infertility.

  10. The Common Follicle-Stimulating Hormone Receptor (FSHR) Promoter Polymorphism FSHR -29G > A Affects Androgen Production in Normal Human Small Antral Follicles

    DEFF Research Database (Denmark)

    Borgbo, Tanni; Klučková, Hana; Macek, Milan


    ) FSHR -29G > A (rs1394205) on hormonal conditions in humsan small antral follicles (hSAFs) obtained from women in the natural menstrual cycle. This study investigated the follicle fluid (FF) concentrations of anti-Müllerian hormone, estradiol, progesterone, androstenedione, and testosterone in h...

  11. Combined assessment of polymorphisms in the LHCGR and FSHR genes predict chance of pregnancy after in vitro fertilization

    DEFF Research Database (Denmark)

    Lindgren, I; Bååth, M; Uvebrant, K


    -stimulating hormone receptor (FSHR) variant N680S can be utilized for the prediction of pregnancy chances in women undergoing IVF. WHAT IS KNOWN ALREADY: The FSHR N680S polymorphism has been shown to affect the ovarian response in response to gonadotrophin treatment, while no information is currently available...... regarding variants of the LHCGR in this context. STUDY DESIGN, SIZE, DURATION: Cross-sectional study, duration from September 2010 to February 2015. Women undergoing IVF were consecutively enrolled and genetic variants compared between those who became pregnant and those who did not. The study...... was subsequently replicated in an independent sample. Granulosa cells from a subset of women were investigated regarding functionality of the genetic variants. PARTICIPANTS/MATERIALS, SETTING, METHODS: Women undergoing IVF (n = 384) were enrolled in the study and genotyped. Clinical variables were retrieved from...

  12. Vitamin d status, filaggrin genotype, and cardiovascular risk factors

    DEFF Research Database (Denmark)

    Skaaby, Tea; Husemoen, Lise Lotte Nystrup; Martinussen, Torben


    Vitamin D deficiency is associated with increased cardiovascular disease risk in observational studies. Whether these associations are causal is not clear. Loss-of-function mutations in the filaggrin gene result in up to 10% higher serum vitamin D concentrations, supposedly due to a decreased UV......-protection of the keratinocytes. We used a Mendelian randomization approach to estimate the causal effect of vitamin D status on serum lipids, blood pressure, body mass index, waist circumference, and the metabolic syndrome....

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

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    Anne Marie Minihane


    Full Text Available 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.

  14. To Screen Inactivation Mutation of Exon 1 of FSHR Gene in Polycystic Ovarian Syndrome: A South Indian Cohort Study (United States)

    Sekar, Nishu; Yeole, Samiksha; Pradeep, Rashmi; Prabhu, Yogamaya D.; Renu, Kaviyarasi; Ramgir, Shalaka S.; Abilash, V. G.


    Polycystic ovary syndrome is an endocrine disorder. Irregular menstrual cycle, acne, facial hair and elevated androgen levels are the most common signs for PCOS. PCOS has an estimated prevalence of 4-12% among reproductive age women, thus making it a forerunner in female infertility. FSHR plays an important role in FSH signaling pathway making it an important gene for PCOS. In this study, we aim to focus on any association between the FSHR gene and PCOS. Our study was to evaluate any polymorphism of exon 1 of FSHR gene associated with PCOS.PCR-RFLP technique was performed on the PCOS samples. Hormonal changes were found in the patients. Exon 1 inactivation mutation of FSHR gene was not observed in the patient sample. A study of this association needs to be done using large sample size.

  15. Hepatitis B virus in Pakistan: a systematic review of prevalence, risk factors, awareness status and genotypes. (United States)

    Ali, Muhammad; Idrees, Muhammad; Ali, Liaqat; Hussain, Abrar; Ur Rehman, Irshad; Saleem, Sana; Afzal, Samia; Butt, Sadia


    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%.

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

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    Afzal Samia


    Full Text Available Abstract 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%.

  17. Arsenate exposure affects amino acids, mineral nutrient status and antioxidants in rice (Oryza sativa L.) genotypes. (United States)

    Dwivedi, S; Tripathi, R D; Tripathi, P; Kumar, A; Dave, R; Mishra, S; Singh, R; Sharma, D; Rai, U N; Chakrabarty, D; Trivedi, P K; Adhikari, B; Bag, M K; Dhankher, O P; Tuli, R


    Simulated pot experiments were conducted on four rice (Oryza sativa L.) genotypes (Triguna, IR-36, PNR-519, and IET-4786) to examine the effects of As(V) on amino acids and mineral nutrient status in grain along with antioxidant response to arsenic exposure. Rice genotypes responded differentially to As(V) exposure in terms of amino acids and antioxidant profiles. Total amino acid content in grains of all rice genotypes was positively correlated with arsenic accumulation. While, most of the essential amino acids increased in all cultivars except IR-36, glutamic acid and glycine increased in IET-4786 and PNR-519. The level of nonprotein thiols (NPTs) and the activities of superoxide dismutase (SOD; EC, glutathione reductase (GR; EC and ascorbate peroxidase (APX; EC increased in all rice cultivars except IET-4786. A significant genotypic variation was also observed in specific arsenic uptake (SAU; mg kg(-1)dw), which was in the order of Triguna (134) > IR-36 (71) > PNR-519 (53) > IET-4786 (29). Further, application of As(V) at lower doses (4 and 8 mg L(-1) As) enhanced the accumulation of selenium (Se) and other nutrients (Fe, P, Zn, and S), however, higher dose (12 mg L(-1) As) limits the nutrient uptake in rice. In conclusion, low As accumulating genotype, IET-4786, which also had significantly induced level of essential amino acids, seems suitable for cultivation in moderately As contaminated soil and would be safe for human consumption.

  18. Is the FSHR 2039A>G variant associated with susceptibility to testicular germ cell cancer?

    DEFF Research Database (Denmark)

    Bang, A K; Busch, A S; Almstrup, K


    Testicular germ cell cancer (TGCC) is derived from germ cell neoplasia in situ (GCNIS), which arises due to niche disturbances affecting the Sertoli cells. It is believed that exogenous endocrine factors have a crucial role in governing neoplastic transformation but on a strong hereditary...... background. Follicle-stimulating hormone (FSH) is the major regulatory hormone of the Sertoli cells. FSH signalling-related single-nucleotide polymorphisms (SNPs) have previously been shown to affect FSH action in men at different levels. We aimed to investigate whether three FSH-related SNPs (FSHR 2039A......>G, FSHR -29G>A and FSHB -211G>T) are associated with development of TGCC. A total of 752 Danish and German patients with TGCC from two tertiary andrological referral centres were included. Three control groups comprising 2020 men from the general population, 679 fertile men and 417 infertile men, were...

  19. The contribution of diet and genotype to iron status in women: a classical twin study. (United States)

    Fairweather-Tait, Susan J; Guile, Geoffrey R; Valdes, Ana M; Wawer, Anna A; Hurst, Rachel; Skinner, Jane; Macgregor, Alexander J


    This is the first published report examining the combined effect of diet and genotype on body iron content using a classical twin study design. The aim of this study was to determine the relative contribution of genetic and environmental factors in determining iron status. The population was comprised of 200 BMI- and age-matched pairs of MZ and DZ healthy twins, characterised for habitual diet and 15 iron-related candidate genetic markers. Variance components analysis demonstrated that the heritability of serum ferritin (SF) and soluble transferrin receptor was 44% and 54% respectively. Measured single nucleotide polymorphisms explained 5% and selected dietary factors 6% of the variance in iron status; there was a negative association between calcium intake and body iron (p = 0.02) and SF (p = 0.04).

  20. Interactions between C-Reactive Protein Genotypes with Markers of Nutritional Status in Relation to Inflammation

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    Cornelie Nienaber-Rousseau


    Full Text Available Inflammation, as indicated by C-reactive protein concentrations (CRP, is a risk factor for chronic diseases. Both genetic and environmental factors affect susceptibility to inflammation. As dietary interventions can influence inflammatory status, we hypothesized that dietary effects could be influenced by interactions with single nucleotide polymorphisms (SNPs in the CRP gene. We determined 12 CRP SNPs, as well as various nutrition status markers in 2010 black South Africans and analyzed their effect on CRP. Interactions were observed for several genotypes with obesity in determining CRP. Lipid intake modulated the pro-inflammatory effects of some SNPs, i.e., an increase in both saturated fatty acid and monounsaturated fatty acid intake in those homozygous for the polymorphic allele at rs2808630 was associated with a larger increase in CRP. Those harboring the minor alleles at rs3093058 and rs3093062 presented with significantly higher CRP in the presence of increased triglyceride or cholesterol intake. When harboring the minor allele of these SNPs, a high omega-6 to -3 ratio was, however, found to be anti-inflammatory. Carbohydrate intake also modulated CRP SNPs, as HbA1C and fasting glucose levels interacted with some SNPs to influence the CRP. This investigation highlights the impact that nutritional status can have on reducing the inherent genetic susceptibility to a heightened systemic inflammatory state.

  1. Riboflavin status, MTHFR genotype and blood pressure: current evidence and implications for personalised nutrition. (United States)

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


    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.

  2. Relationship between Helicobacter pylori vacA genotypes status and risk of peptic ulcer in Saudi patients

    International Nuclear Information System (INIS)

    Momenah, Aiman M.; Tayeb, Mohammad T.


    To determine if there is a significant correlation between different Helicobacter pylori (H. pylori) vacA genotypes strains and severe gastric clinical outcomes. A total of 1104 gastric biopsies from 368 patients who presented with symptoms suggestive of chronic gastritis or peptic ulcer were taken from the main hospitals in the western region of Saudi Arabia from July 2004 to July 2005. These samples were cultured for H. pylori, and a polymerase chain reaction (PCR) was carried out to determine vacA genotypes status. One hundred and three (28%) patients were positive for H. pylori using culture technique. The distribution of vacA genotypes was 13 for vacAs1m1, 47 for vacAs1m2 and 43 for vacAs2m2. None of the clinical isolates were vacAs2m1 positive. The study showed a significant correlation between the vacAs1m2 genotype and gastritis cases, and a significant correlation between vacAs1m1 genotype and ulcer cases. The results of this study might be used for the identification of high-risk patients who are infected by vacAs1m1 genotype H. pylori strains. (author)

  3. The G protein-coupled receptor FSHR-1 is required for the Caenorhabditis elegans innate immune response. (United States)

    Powell, Jennifer R; Kim, Dennis H; Ausubel, Frederick M


    Innate immunity is an ancient defense system used by both vertebrates and invertebrates. Previously characterized innate immune responses in plants and animals are triggered by detection of pathogens using specific receptors, which typically use a leucine-rich repeat (LRR) domain to bind molecular patterns associated with infection. The nematode Caenorhabditis elegans uses defense pathways conserved with vertebrates; however, the mechanism by which C. elegans detects pathogens is unknown. We screened all LRR-containing transmembrane receptors in C. elegans and identified the G protein-coupled receptor FSHR-1 as an important component of the C. elegans immune response to Gram-negative and Gram-positive bacterial pathogens. FSHR-1 acts in the C. elegans intestine, the primary site of exposure to ingested pathogens. FSHR-1 signals in parallel to the known p38 MAPK pathway but converges to regulate the transcriptional induction of an overlapping but nonidentical set of antimicrobial effectors. FSHR-1 may act generally to boost the nematode immune response, or it may function as a pathogen receptor.

  4. TGF-β signaling controls FSHR signaling-reduced ovarian granulosa cell apoptosis through the SMAD4/miR-143 axis. (United States)

    Du, Xing; Zhang, Lifan; Li, Xinyu; Pan, Zengxiang; Liu, Honglin; Li, Qifa


    Follicle-stimulating hormone receptor (FSHR) and its intracellular signaling control mammalian follicular development and female infertility. Our previous study showed that FSHR is downregulated during follicular atresia of porcine ovaries. However, its role and regulation in follicular atresia remain unclear. Here, we showed that FSHR knockdown induced porcine granulosa cell (pGC) apoptosis and follicular atresia, and attenuated the levels of intracellular signaling molecules such as PKA, AKT and p-AKT. FSHR was identified as a target of miR-143, a microRNA that was upregulated during porcine follicular atresia. miR-143 enhanced pGC apoptosis by targeting FSHR, and reduced the levels of intracellular signaling molecules. SMAD4, the final molecule in transforming growth factor (TGF)-β signaling, bound to the promoter and induced significant downregulation of miR-143 in vitro and in vivo. Activated TGF-β signaling rescued miR-143-reduced FSHR and intracellular signaling molecules, and miR-143-induced pGC apoptosis. Overall, our findings offer evidence to explain how TGF-β signaling influences and FSHR signaling for regulation of pGC apoptosis and follicular atresia by a specific microRNA, miR-143.

  5. Docosahexaenoic acid (DHA) supplementation in pregnancy differentially modulates arachidonic acid and DHA status across FADS genotypes in pregnancy. (United States)

    Scholtz, S A; Kerling, E H; Shaddy, D J; Li, S; Thodosoff, J M; Colombo, J; Carlson, S E


    Some FADS alleles are associated with lower DHA and ARA status assessed by the relative amount of arachidonic acid (ARA) and docosahexaenoic acid (DHA) in plasma and red blood cell (RBC) phospholipids (PL). We determined two FADS single nucleotide polymorphisms (SNPs) in a cohort of pregnant women and examined the relationship of FADS1rs174533 and FADS2rs174575 to DHA and ARA status before and after supplementation with 600mg per day of DHA. The 205 pregnant women studied were randomly assigned to placebo (mixed soy and corn oil) (n=96) or 600mg algal DHA (n=109) in 3 capsules per day for the last two trimesters of pregnancy. Women homozygous for the minor allele of FADS1rs174533 (but not FADS2rs174575) had lower DHA and ARA status at baseline. At delivery, minor allele homozygotes of FADS1rs174533 in the placebo group had lower RBC-DHA compared to major-allele carriers (P=0.031), while in the DHA-supplemented group, all genotypes had higher DHA status compared to baseline (P=0.001) and status did not differ by genotype (P=0.941). Surprisingly, DHA but not the placebo decreased ARA status of minor allele homozygotes of both FADS SNPs but not major allele homozygotes at delivery. Any physiological effects of changing the DHA to ARA ratio by increasing DHA intake appears to be greater in minor allele homozygotes of some FADS SNPs. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. FSH-FSHR3-stem cells in ovary surface epithelium: basis for adult ovarian biology, failure, aging, and cancer. (United States)

    Bhartiya, Deepa; Singh, Jarnail


    Despite extensive research, genetic basis of premature ovarian failure (POF) and ovarian cancer still remains elusive. It is indeed paradoxical that scientists searched for mutations in FSH receptor (FSHR) expressed on granulosa cells, whereas more than 90% of cancers arise in ovary surface epithelium (OSE). Two distinct populations of stem cells including very small embryonic-like stem cells (VSELs) and ovarian stem cells (OSCs) exist in OSE, are responsible for neo-oogenesis and primordial follicle assembly in adult life, and are modulated by FSH via its alternatively spliced receptor variant FSHR3 (growth factor type 1 receptor acting via calcium signaling and the ERK/MAPK pathway). Any defect in FSH-FSHR3-stem cell interaction in OSE may affect folliculogenesis and thus result in POF. Ovarian aging is associated with a compromised microenvironment that does not support stem cell differentiation into oocytes and further folliculogenesis. FSH exerts a mitogenic effect on OSE and elevated FSH levels associated with advanced age may provide a continuous trigger for stem cells to proliferate resulting in cancer, thus supporting gonadotropin theory for ovarian cancer. Present review is an attempt to put adult ovarian biology, POF, aging, and cancer in the perspective of FSH-FSHR3-stem cell network that functions in OSE. This hypothesis is further supported by the recent understanding that: i) cancer is a stem cell disease and OSE is the niche for ovarian cancer stem cells; ii) ovarian OCT4-positive stem cells are regulated by FSH; and iii) OCT4 along with LIN28 and BMP4 are highly expressed in ovarian cancers. © 2015 Society for Reproduction and Fertility.

  7. GnRH-agonist implants suppress reproductive function and affects ovarian LHR and FSHR expression in prepubertal female cats. (United States)

    Mehl, N S; Srisuwatanasagul, S; Swangchan-Uthai, T; Sirivaidyapong, S; Khalid, M


    Effect of a GnRH-agonist (deslorelin) was studied on reproductive function and ovarian luteinizing hormone receptor (LHR) and follicle stimulating hormone receptor (FSHR) expression in prepubertal female cats that were either implanted with 4.7-mg deslorelin (implanted: n = 6) or not (controls: n = 18) or ovariohysterectomized at prepubertal age (prepubertal OVH: n = 6). Body weights, fecal estradiol, and sexual behavior of implanted and control cats were monitored for 48 weeks followed by collection of ovaries and uteri. Ovaries and uteri were collected from control cats at follicular, luteal, and inactive stage (n = 6/group) and from prepubertal OVH cats at prepubertal age. Ovaries and uteri were analyzed for anatomical/histological characteristics. Ovaries were also analyzed for LHR and FSHR expression. Statistical analysis showed higher (P ≤ 0.05) body weight in control than implanted cats only during 22nd to 26th weeks of the study. Estrus was observed in control cats only. Deslorelin reduced (P ≤ 0.05) ovarian weight and number of antral follicles but did not affect endometrial thickness and gland diameter. However, myometrial thickness of implanted cats was significantly lower than control cats at follicular and luteal stage. Ovarian LHR mRNA expression was lower (P ≤ 0.05) in implanted cats than control cats at follicular stage. FSHR mRNA and LHR protein expression did not differ among the three groups. FSHR protein expression was lower (P ≤ 0.05) in prepubertal OVH cats and was not affected by deslorelin. In conclusion, deslorelin suppresses reproductive function in prepubertal female cats for at least 48 weeks possibly through a change in the ovarian mRNA expression of LHR. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Flow cytometric analysis of FSHR, BMRR1B, LHR and apoptosis in granulosa cells and ovulation rate in merino sheep. (United States)

    Regan, Sheena L P; McFarlane, James R; O'Shea, Tim; Andronicos, Nicholas; Arfuso, Frank; Dharmarajan, Arun; Almahbobi, Ghanim


    The aim of the present study was to determine the direct cause of the mutation-induced, increased ovulation rate in Booroola Merino (BB) sheep. Granulosa cells were removed from antral follicles before ovulation and post-ovulation from BB (n=5) and WT (n=12) Merino ewes. Direct immunofluorescence measurement of mature cell surface receptors using flow cytometry demonstrated a significant up-regulation of FSH receptor (FSHR), transforming growth factor beta type 1, bone morphogenetic protein receptor (BMPR1B), and LH receptor (LHR) in BB sheep. The increased density of FSHR and LHR provide novel evidence of a mechanism for increasing the number of follicles that are recruited during dominant follicle selection. The compounding increase in receptors with increasing follicle size maintained the multiple follicles and reduced the apoptosis, which contributed to a high ovulation rate in BB sheep. In addition, we report a mutation-independent mechanism of down-regulation to reduce receptor density of the leading dominant follicle in sheep. The suppression of receptor density coincides with the cessation of mitogenic growth and steroidogenic differentiation as part of the luteinization of the follicle. The BB mutation-induced attenuation of BMPR1B signaling led to an increased density of the FSHR and LHR and a concurrent reduction in apoptosis to increase the ovulation rate. The role of BMPs in receptor modulation is implicated in the development of multiple ovulations. © 2015 Society for Reproduction and Fertility.

  9. vacA Genotype Status of Helicobacter pylori Isolated from Foods with Animal Origin

    Directory of Open Access Journals (Sweden)

    Elnaz Saeidi


    Full Text Available According to controversial theories and results of studies, foods with animal origins play an important role in the transmission of H. pylori to human. The aim of this study was to determine the distribution of vacA genotypes of H. pylori, isolated from milk and meat samples of cow, sheep, goat, camel, and buffalo. Eight hundred and twenty raw milk and meat samples were collected from various parts of Iran. Samples were cultured and those found positive for H. pylori were analyzed for the presence of various genotypes of vacA gene. Out of 420 milk and 400 meat samples, 92 (21.90% and 105 (26.25% were positive for H. pylori, respectively. The most commonly detected genotypes in the vacA gene were s1a (86.80%, m1a (79.18%, s1b (69.54%, and m1b (63.45% and detected combined genotypes were mostly m1as1a (68.52%, m1as1b (60.40%, m1bs1b (55.83%, and m1bs1a (53.29%. High presence of bacteria in the milk and meat samples of sheep represents that sheep may be the natural host of H. pylori. High presence of H. pylori strains in milk and meat samples similar to vacA genotypes in human being suggests that milk and meat samples could be the sources of bacteria for human.

  10. vacA Genotype Status of Helicobacter pylori Isolated from Foods with Animal Origin. (United States)

    Saeidi, Elnaz; Sheikhshahrokh, Amirhossein


    According to controversial theories and results of studies, foods with animal origins play an important role in the transmission of H. pylori to human. The aim of this study was to determine the distribution of vacA genotypes of H. pylori, isolated from milk and meat samples of cow, sheep, goat, camel, and buffalo. Eight hundred and twenty raw milk and meat samples were collected from various parts of Iran. Samples were cultured and those found positive for H. pylori were analyzed for the presence of various genotypes of vacA gene. Out of 420 milk and 400 meat samples, 92 (21.90%) and 105 (26.25%) were positive for H. pylori, respectively. The most commonly detected genotypes in the vacA gene were s1a (86.80%), m1a (79.18%), s1b (69.54%), and m1b (63.45%) and detected combined genotypes were mostly m1as1a (68.52%), m1as1b (60.40%), m1bs1b (55.83%), and m1bs1a (53.29%). High presence of bacteria in the milk and meat samples of sheep represents that sheep may be the natural host of H. pylori. High presence of H. pylori strains in milk and meat samples similar to vacA genotypes in human being suggests that milk and meat samples could be the sources of bacteria for human.

  11. Helicobacter pylori cagA and iceA genotypes status and risk of peptic ulcer in Saudi patients

    International Nuclear Information System (INIS)

    Momenah, Aiman M.; Tayeb, Mohammad T.


    Objective was to determine the prevalence of cagA+ and iceA genotypes among Helicobacter pylori (H. pylori) isolates from a group of Saudi patients with gastric complaints, and to find out any significant correlation between these strains and severe gastric clinical outcomes such as peptic ulcer and gastric cancer in Saudi population. A total of 1104 gastric biopsies from 368 patients who presented with symptoms suggestive of chronic gastritis, peptic ulcer disease, or gastric carcinoma were taken from the main hospitals in the Western region of Saudi Arabia from July 2004 to July 2005. We cultured the samples for H. pylori and a polymerase chain reaction was carried out to check for the presence or absence of cagA gene and the status of iceA genotypes. Among the 368 suspected patients to be infected with H. pylori by means of clinical features and endoscopic findings; 103 (28%) were positive using culture technique. The relation of the presence of cagA and the development of cases to gastritis and ulcer was statistically significant (p=0.0001). Furthermore, this study revealed that 100% of ulcer cases were infected with iceA1 with a statistically significant correlation (p=0.0001), while 94.6% of gastritis and 90.9% of normal were infected with iceA2 (p=0.0001). Moreover cagA+/iceA1 combined genotypes was statistically correlated with peptic ulcer (100%) but not cagA-/iceA1 (0%; p=0.0001).Certain H. pylori genotypes were more virulent than others. Multiple clinical implications based on these finding might be studied further.(author)

  12. Hepatitis B virus: molecular genotypes and HBeAg serological status among HBV-infected patients in the southeast of Brazil

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    Gonçales Fernando L


    Full Text Available Abstract Background Knowledge of HBV genotype is very important for clinical treatment. Studies have suggested possible pathogenic and therapeutic differences among HBV genotypes. The aim of this study was to determine HBV subtypes and genotypes in HBV-infected patients in our region (southeast Brazil and to correlate results with clinical and histopathological data. Methods One hundred and thirty-nine HBsAg-positive patients were included in the study. All patients were anti-HCV and anti-HIV negative (64% male; mean age 42 ± 14.5 years; range 7-80 years; 84% Caucasian and were followed up at the University Hospital. A method for genotyping and subtyping HBV by partial HBsAg gene sequencing with primers common to all known genotypes was used. The viral load was measured by Amplicor Monitor assay (Roche. Results HBV genotype A was the most prevalent (55%, while genotypes C, D and F were found in 3%, 38% and 4% of HBV-infected patients, respectively. Among the patients infected by genotype A, 18.3% (14/76 were African descendents and, among the patients infected by genotype D, 11.3% (6/53 were also African descendents. In the four patients infected with genotype C, 2 were Asian descendents and 2 were Caucasians. All (7 genotype F infected patients were Caucasians. Seventy percent of our HBsAg-positive patients were HBeAg negative (62% genotypes A; 26.2% D; 7.1% C and 4.7%F. The viral load of HBV-DNA was about 5 times higher in HBeAg-positive than in HBeAg-negative patients. About 40% of these patients had alanine aminotransferase of up to 1.5 times the normal level. The mean stage of fibrosis in genotype A patients (2.8 was significantly higher than the mean stage of fibrosis in genotype D patients (2.0 (P = 0.0179. Conclusion The genotypes encountered in our HBV-infected patients were apparently a consequence of the types of immigration that occurred in our region, where European and African descendents predominate. The HBeAg-negative status

  13. Inactivating Mutation screening of Exon 6 and Exon 10E of FSHR gene in women with Polycystic Ovarian Syndrome in Vellore population (United States)

    Sekar, Nishu; Sapre, Madhura; Kale, Vaikhari; Prabhu, Yogamaya D.; Renu, Kaviyarasi; Ramgir, Shalaka S.; Abilash, V. G.


    Polycystic Ovarian syndrome (PCOS) is a major cause of infertility in females of reproducing age and is typified by oligo-anovulation, hyperandrogenism, hirsutism and polycystic ovaries. FSHR gene located on chromosome 2 p21 is responsible for the normal follicular development and any deletion or mutation in the gene affects the interaction of FSH with its receptor. Thus, it becomes the candidate gene for PCOS study. Inactivating mutation in FSHR gene limits the receptor’s function by creating a complete block, changing the receptor-ligand complex or the basic hormone signal transduction.To screen the inactivating mutations in Exon 6 and Exon 10E of FSHR gene in women diagnosed with PCOS.PCR-RFLP analysis indicated that there were no inactivating mutations found in Exon 6 and Exon 10E. Variations in hormone levels were seen amongst the PCOS patients. There were no inactivating mutations found in FSHR gene of the women diagnosed with PCOS according to the Rotterdam criteria in Vellore population.

  14. Disruption of Zebrafish Follicle-Stimulating Hormone Receptor (fshr) But Not Luteinizing Hormone Receptor (lhcgr) Gene by TALEN Leads to Failed Follicle Activation in Females Followed by Sexual Reversal to Males. (United States)

    Zhang, Zhiwei; Lau, Shuk-Wa; Zhang, Lingling; Ge, Wei


    Gonadotropins are primary hormones that control vertebrate reproduction. In a recent study, we analyzed the impacts of FSH and LH on zebrafish reproduction by disrupting FSH and LH-β genes (fshb and lhb) using transcription activator-like effector nuclease (TALEN) technology. Using the same approach, we successfully deleted FSH and LH receptor genes (fshr and lhcgr) in the present study. In contrast to the deficiency of its cognate ligand FSH, the fshr-deficient females showed a complete failure of follicle activation with all ovarian follicles arrested at the primary growth-previtellogenic transition, which is the marker for puberty onset in females. Interestingly, after blockade at the primary growth stage for varying times, all females reversed to males, and all these males were fertile. In fshr-deficient males, spermatogenesis was normal in adults, but the initiation of spermatogenesis in juveniles was retarded. In contrast to fshr, the deletion of the lhcgr gene alone caused no obvious phenotypes in both males and females; however, double mutation of fshr and lhcgr resulted in infertile males. In summary, our results in the present study showed that Fshr was indispensable to folliculogenesis and the disruption of the fshr gene resulted in a complete failure of follicle activation followed by masculinization into males. In contrast, lhcgr does not seem to be essential to zebrafish reproduction in both males and females. Neither Fshr nor Lhcgr deficiency could phenocopy the deficiency of their cognate ligands FSH and LH, which is likely due to the fact that Fshr can be activated by both FSH and LH in the zebrafish.

  15. Cd Toxicity and Accumulation in Rice Plants Vary with Soil Nitrogen Status and Their Genotypic Difference can be Partly Attributed to Nitrogen Uptake Capacity

    Directory of Open Access Journals (Sweden)

    Qin DU


    Full Text Available Two indica rice genotypes, viz. Milyang 46 and Zhenshan 97B differing in Cd accumulation and tolerance were used as materials in a hydroponic system consisting of four Cd levels (0, 0.1, 1.0 and 5.0 µmol/L and three N levels (23.2, 116.0 and 232.0 mg/L to study the effects of nitrogen status and nitrogen uptake capacity on Cd accumulation and tolerance in rice plants. N-efficient rice genotype, Zhenshan 97B, accumulated less Cd and showed higher Cd tolerance than N-inefficient rice genotype, Milyang 46. There was consistency between nitrogen uptake capacity and Cd tolerance in rice plants. Increase of N level in solution slightly increased Cd concentration in shoots but significantly increased in roots of both genotypes. Compared with the control at low N level, Cd tolerance in both rice genotypes could be significantly enhanced under normal N level, but no significant difference was observed between the Cd tolerances under normal N (116.0 mg/L and high N (232.0 mg/L conditions. The result proved that genotypic differences in Cd accumulation and toxicity could be, at least in part, attributed to N uptake capacity in rice plants.

  16. Contribution of polymorphisms in ESR1, ESR2, FSHR, CYP19A1 ...

    Indian Academy of Sciences (India)


    Mar 4, 2016 ... 1Department of Medical Genetics, and 2Department of Neurology, Dicle University, Medical Faculty, ... analysis was performed only in women, the GG genotype of ... tor interacting protein 1 (NRIP1) negatively regulates the ... High FSH levels and low oestrogen levels have been asso- ...... meta-analysis.

  17. The influence of CYP1A2 genotype in the blood pressure response to caffeine ingestion is affected by physical activity status and caffeine consumption level. (United States)

    Soares, Rogerio Nogueira; Schneider, Augusto; Valle, Sandra Costa; Schenkel, Paulo Cavalheiro


    This study aimed to investigate whether the influence of CYP1A2 genotype in the blood pressure (BP) response to caffeine ingestion was affected by physical activity status and habitual caffeine consumption. Thirty-seven participants (19-50 years old) took place in the study and were categorized according to i) genotype: CYP1A2 (AA) "fast metabolizer", and CYP1A2 (AC) "slow metabolizer"; ii) physical activity level: sedentary (S) and physically active (A); and iii) caffeine consumption level: non-habitual caffeine consumer (NC) and habitual heavy caffeine consumer (C). All groups had BP assessed before (basal) and 1 hourh after (post) caffeine ingestion (6 mg·kg -1 ). It was observed that AC genotype individuals had increased basal-DBP and post-caffeine SBP when compared to AA individuals. Additionally, acute caffeine ingestion increased SBP only in the AC group. It was also found that physical activity only modulated the BP responses to acute caffeine ingestion in AC individuals. Furthermore, the results indicated that the habitual heavy caffeine consumers AC individuals had increased basal-DBP when compared to the AA ones. Our results suggest that the influence of CYP1A2 genotype in the basal and post-caffeine BP response to caffeine ingestion is modified by physical activity status and caffeine consumption level. Copyright © 2018 Elsevier Inc. All rights reserved.

  18. VacA and cagA genotypes status and antimicrobial resistance properties of Helicobacter pylori strains isolated from meat products in Isfahan province, Iran. (United States)

    Gilani, A; Razavilar, V; Rokni, N; Rahimi, E


    Although Helicobacter pylori has a significant impact on the occurrence of severe clinical syndromes, its exact ways of transmission and origin have not been identified. According to the results of some previously published articles, foods with animal origins play a substantial role in the transmission of H. pylori to humans. The present investigation was carried out to study the vacuolating cytotoxin A ( vacA ) and cytotoxin associated gene A ( cagA ) genotypes status and antibiotic resistance properties of H. pylori strains recovered from minced-meat and hamburger samples. A total of 150 meat product samples were collected from supermarkets. All samples were cultured and the susceptive colonies were then subjected to nested-PCR, PCR-based genotyping and disk diffusion methods. 11 out of 150 samples (7.33%) were positive for H. pylori . All the isolates were further identified using the nested-PCR assay. Prevalence of H. pylori in hamburger and minced-meat samples was 1.42% and 12.5%, respectively. S1a , m1a and cagA were the most commonly detected genotypes. The most commonly detected combined genotypes in the H. pylori strains of minced-meat were s1am1a (10%), s1am1b (10%) and s2m1a (10%). Helicobacter pylori strains of meat products harbored the highest levels of resistance against ampicillin (90.90%), erythromycin (72.72%), amoxicillin (72.72%), trimethoprim (63.63%), tetracycline (63.63%), and clarithromycin (63.63%). Hamburger and minced-meat samples may be the sources of virulent and resistant strains of H. pylori . Meat products are possible sources of resistant and virulent strains of H. pylori similar to those vacA and cagA genotypes. Using healthy raw materials and observation of personal hygiene can reduce the risk of H. pylori in meat products.

  19. Effect of genotype, Cr(III and Cr(VI on plant growth and micronutrient status in Silene vulgaris (Moench

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    A. E. Pradas-del-Real


    Full Text Available Chromium released into the environment from industrial activities has become an important environmental concern. Silene vulgaris has been proven to be tolerant to many heavy metals, so it is considered an interesting species in the revegetation and restoration of polluted soils, but no information is available about its response to Cr. The objective of this work was to study uptake and influence on plant growth of Cr(III and Cr(VI in six genotypes (four hermaphrodites and two females of S. vulgaris from different sites of Madrid (Spain. Plants were treated for 12 days with 60 µM of Cr(III or Cr(VI in semihydroponics. Dry weights, soil-plant analysis development values (SPAD reading with chlorophylls and micronutrient and total Cr concentrations were determined. Metal uptake was higher in presence of Cr(VI than of Cr(III and poorly translocated to the shoots. In both cases S. vulgaris did not show visual toxicity symptoms, biomass reduction, or differences among SPAD values as consequence of Cr additions. However genotypes SV36 and SV38 showed Fe and Mn imbalance. This is the first report on the relatively good performance of hermaphrodite and female S. vulgaris genotypes in Cr uptake and physiological traits, but further studies will be necessary to elucidate the mechanisms by which the gender may influence these variables. S. vulgaris presented high diversity at genotypic level; the treatment with hexavalent Cr increased the differences among genotypes so the use of cuttings from an homogeneous genotype seems to be an adequate method for the study of this species.

  20. VacA, CagA, IceA and OipA Genotype Status of Helicobacter pylori ...

    African Journals Online (AJOL)

    Purpose: To investigate the state of vacA, cagA, oipA and iceA genotypes of H. pylori isolated from gastric biopsy samples of dogs. Methods: A total of 240 gastric biopsy samples were taken from 240 dogs using gastric endoscope. All the samples were cultured and H. pylori-positive samples were analyzed for the presence ...

  1. APOE genotype and age modifies the correlation between cognitive status and metabolites from hippocampus by a 2D 1H-MRS in non-demented elders

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    Zhenyu Yin


    Full Text Available Purpose. To examine the associations among age, Apolipoprotein E (APOE genotype, metabolic changes in the hippocampus detected by 2D 1H magnetic resonance spectroscopy (MRS, and neuropsychological measures of cognition in non-demented elders.Materials and Methods. We studied a cohort of 16 cognitively normal controls (CN and 11 amnestic mild cognitive impairment (aMCI patients between 66 and 88 years old who were genotyped for APOE genetic polymorphism. Measurements of 2D1H-MRS metabolites were obtained in the hippocampus region. Adjusting by age among all subjects, the association between metabolic changes and cognitive function was measured by Spearman partial rank-order correlation. The effect of APOE status was measured by separating the subjects into APOE genotype subgroups, including the APOEε4 carriers and APOEε4 non-carriers.Results. In contrast to the CN group matched with age, gender, and education, aMCI patients showed increased myo-inositol (mI/Creatine (Cr ratio only in the right hippocampus. No differences were noted on N-acetylaspartate (NAA/Cr and mI/NAA from bilateral hippocampus, and so was mI/Cr ratio in left hippocampus between aMCI and CN. The mI/Cr ratio from the right hippocampus in non-demented elders was negatively correlated with Montreal Cognitive Assessment (MoCA scores. Whether ε4 genotype or age was added as a covariate, none of the correlation effects remained significant. Additionally, adjusting for age and APOE genotype together, there was no significant correlation between them.Conclusion. Since the higher mI/Cr from the right hippocampus of the patients with aMCI than those from CN, the mI/Cr could be a more specific predictor of general cognitive function in aMCI patients. There is an association between higher mI/Cr in right hippocampus and worse cognitive function for the non-demented older adults, and the correlation could be modified by APOE status and age. That provided a window on objectively

  2. Vitamin D status in relation to obesity, bone mineral density, bone turnover markers and vitamin D receptor genotypes in healthy Saudi pre- and postmenopausal women. (United States)

    Ardawi, M-S M; Qari, M H; Rouzi, A A; Maimani, A A; Raddadi, R M


    The various factors that may contribute to vitamin D deficiency or insufficiency were examined among healthy Saudi pre- and postmenopausal women. Vitamin D deficiency was highly prevalent among studied Saudi women with obesity, poor sunlight exposure, poor dietary vitamin D supplementation and age as the main risk factors. The various factors that may contribute to vitamin D deficiency or insufficiency in relation to bone health among Saudi women are not known. The main objectives of the present study were to determine the factors influencing vitamin D status in relation to serum 25-hydroxyvitamin D (25(OH)D), intact parathyroid hormone (PTH), bone turnover markers (BTMs), bone mineral density (BMD), and vitamin D receptor genotype (VDR) in healthy Saudi pre- and postmenopausal women. A total number of 1,172 healthy Saudi women living in the Jeddah area were randomly selected and studied. Anthropometric parameters, socioeconomic status, sun exposure index together with serum levels of 25(OH)D, calcitriol, intact PTH, Ca, PO4, Mg, creatinine, albumin, and biochemical BTMs were measured. BMD was measured by a dual energy X-ray absorptiometry and VDR genotypes were also determined. About 80.0% of Saudi women studied exhibited vitamin D deficiency (serum 25(OH)D75 nmol/L). Secondary hyperparathyroidism was evident in 18.5% and 24.6% in pre- and postmenopausal women with 25(OH)Dobesity, poor exposure to sunlight, poor dietary vitamin D supplementation, and age.

  3. FSHR and LHR Expression and Signaling as Well as Maturation and Apoptosis of Cumulus-Oocyte Complexes Following Treatment with FSH Receptor Binding Inhibitor in Sheep

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    Suocheng Wei


    Full Text Available Background/Aims: Currently, it remains unknown whether FSH receptor binding inhibitor (FRBI influences follicular development and reproduction functions in humans and animals. The present study aimed to investigate FRBI effects on in vitro maturation (IVM and apoptosis of cumulus-oocyte complexes (COCs of sheep, to determine the effect of FRBI on mRNA and protein levels of FSHR and LHR in COCs, and to elucidate the signal pathway of FRBI effects. Methods: COCs were in vitro cultured for 24h in the IVM media supplemented with varying concentrations of FRBI (0, 10, 20, 30 and 40µg/mL and FSH (10IU/mL. The harvested COCs were observed under an inverted microscope and maturation rates of COCs were determined. Real time RT-PCR and Western blotting were utilized to detect mRNA and protein levels of FSHR and LHR. The concentrations of FSH, LH and caspase-3 were determined using especial ELISA kits for sheep, respectively. Results: Maturation rates of COCs decreased gradually as FRBI concentrations increased from 0 to 40µg/mL, reaching a bottom value of 23.76% of the FRBI-4 group. The maximal apoptosis rate was detected in the FRBI-4 group. IP3 contents of FRBI-3 and FRBI-4 groups were reduced as compared to control group (CG and FSH groups (P<0.05. Levels of FSHR protein of FRBI-3 and FRBI-4 groups as well as LHR protein of FRBI-4 group were significantly less than that of CG and FSH group. FSH contents of four FRBI treatment groups were gradually decreased along with the supplementation doses of FRBI. Caspase-3 contents of FRBI groups were reduced with a maximum reduction of the FRBI-2 group. Conclusion: Our results revealed supplement of FRBI into IVM media could dose-dependently decrease the maturation rate and increase apoptosis rate of sheep COCs. A lower dose of FRBI treatment slightly promoted IP3 production, but a higher dose of FRBI reduced IP3 production. FRBI suppressed the mRNA and protein expression levels of FSHR and LHR in sheep COCs

  4. Polimorfismos de DNA nos genes dos receptores de estrogênio e FSHR e associação com resposta superovulatória em bovinos


    Valeriano, Ana Cláudia de Melo


    Estudos baseados em genes candidatos buscam identificar polimorfismos e a prospecção de genes candidatos que estão envolvidos no processo de ovulação são ferramentas de importantes quando se pretende incrementar a eficiência reprodutiva de rebanhos e melhorar as respostas das biotécnicas de multiplicação animal. Sendo assim, o objetivo deste estudo foi sequenciar e detectar polimorfismos em parte do “exon” 10 do gene do receptor do hormônio folículo estimulante (FSHR); genotipar doadoras de e...

  5. Association of Exon 10A and 10B inactivating mutation of follicle stimulating hormone receptor gene (FSHR) and Polycystic Ovarian Syndrome in Vellore cohort (United States)

    Sekar, Nishu; Kulkarni, Rucha; Ozalkar, Sharvari; Prabhu, Yogamaya D.; Renu, Kaviyarasi; Ramgir, Shalaka S.; Abilash, V. G.


    Polycystic ovarian syndrome is the most common heterogenous endocrine disorder in women. Follicle stimulating hormone receptor is associated with normal development as well as maturation of follicles and triggers estrogen production in granulosa cells of the ovary. Inactivating mutation in FSHR gene correlated with reduction of ovarian function in women is due to damage to receptor function. This study aims to investigate whether inactivating mutations, in follicle stimulating hormone receptor gene is related to polycystic ovarian morphology in women with PCOS. Genomic DNA isolated from 15 subjects from Sandhya Hospital, Vellore (10 patients with PCOS and 5 healthy controls) was taken for this study. Patient data included a clinical report, hormonal levels, and ovarian morphological details. DNA isolation was followed by DNA amplification by polymerase chain reaction using Exon 10 A and Exon 10 B primers. The PCR-RFLP analysis was performed using Dde1 restriction enzyme. Here we discuss inactivating mutation found in Exon 10 of FSHR gene in patients with PCOS.The absence of inactivating mutation was observed through PCR-RFLP study on Exon 10A and Exon 10B.

  6. 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. (United States)

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


    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.

  7. Genotyping, levels of expression and physical status of human papilloma virus in oropharyngeal squamous cell carcinoma among Colombian patients. (United States)

    Erira, Alveiro; Motta, Leidy Angélica; Chala, Andrés; Moreno, Andrey; Gamboa, Fredy; García, Dabeiba Adriana


    One of the risk factors for squamous cell oropharyngeal carcinoma is infection with the human papilloma virus (HPV), with prevalences that vary depending on the geographical region.  To identify the most frequent HPV viral types in oropharyngeal cancer, the levels of expression and the physical condition of the viral genome.  Forty-six patients were included in the study from among those attending head and neck surgical services in the cities of Bogotá, Manizales and Bucaramanga. In the histopathological report all study samples were characterized as oropharyngeal squamous cell carcinoma. DNA extraction was subsequently performed for HPV genotyping and to determine the physical state of the viral genome, as well as RNA to determine viral transcripts using real-time PCR.  HPV prevalence in tumors was 21.74% (n=10) and the most common viral type was HPV-16 (nine cases). Viral expression for HPV-16 was low (one of 11 copies) and the predominant physical state of the virus was mixed (eight cases), with disruption observed at the E1 - E2 binding site (2525 - 3720 nucleotides).  The prevalence of HPV associated with oropharyngeal carcinoma among the Colombian study population was 21.7%, which is relatively low. The most frequent viral type was HPV-16, found in a mixed form and with low expression of E7, possibly indicating a poor prognosis for these patients.

  8. The prevalence of the HPV 16 genome, integrated viral status and p53 genotype in cervical cancer population of north-eastern Hungary, the correlation with the established markers of tumour progression. (United States)

    Hernádi, Zoltán; Sápy, Tamás; Krasznai, Zoárd T


    To evaluate the prevalence of the HPV 16 integrated status and the p53 genotype in cervical cancer in north-eastern Hungary and their correlation with the established prognostic factors. Parallel with the routine histological examination, Southern blot hybridisation and multiplex PCRs were used to detect type/physical state of HPV DNA in primary tumours and in regional lymph nodes combined with p53 genotyping of 83 patients. 46.9% (39/83) prevalence rate of HPV 16 genome was found. The frequency of viral integration (76.9% in primary tumours and 95.2% in regional lymph nodes) and that of the p53Arg homozygous genotype (64.1%) proved to be higher than reported from other parts of the world. The HPV 16 integration and the p53 genotype, failed to correlate with the FIGO stage and lymphatic spread. The prevalence of the integrated status of the HPV 16 genome combined with homozygous p53Arg genotype is relatively high in Hungary. These factors however failed to show a strong correlation with the established markers of tumour progression.

  9. Genotypic status of the TbAT1/P2 adenosine transporter of Trypanosoma brucei gambiense isolates from Northwestern Uganda following melarsoprol withdrawal.

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    Anne J N Kazibwe

    Full Text Available BACKGROUND: The development of arsenical and diamidine resistance in Trypanosoma brucei is associated with loss of drug uptake by the P2 purine transporter as a result of alterations in the corresponding T. brucei adenosine transporter 1 gene (TbAT1. Previously, specific TbAT1 mutant type alleles linked to melarsoprol treatment failure were significantly more prevalent in T. b. gambiense from relapse patients at Omugo health centre in Arua district. Relapse rates of up to 30% prompted a shift from melarsoprol to eflornithine (alpha-difluoromethylornithine, DFMO as first-line treatment at this centre. The aim of this study was to determine the status of TbAT1 in recent isolates collected from T. b. gambiense sleeping sickness patients from Arua and Moyo districts in Northwestern Uganda after this shift in first-line drug choice. METHODOLOGY AND RESULTS: Blood and cerebrospinal fluids of consenting patients were collected for DNA preparation and subsequent amplification. All of the 105 isolates from Omugo that we successfully analysed by PCR-RFLP possessed the TbAT1 wild type allele. In addition, PCR/RFLP analysis was performed for 74 samples from Moyo, where melarsoprol is still the first line drug; 61 samples displayed the wild genotype while six were mutant and seven had a mixed pattern of both mutant and wild-type TbAT1. The melarsoprol treatment failure rate at Moyo over the same period was nine out of 101 stage II cases that were followed up at least once. Five of the relapse cases harboured mutant TbAT1, one had the wild type, while no amplification was achieved from the remaining three samples. CONCLUSIONS/SIGNIFICANCE: The apparent disappearance of mutant alleles at Omugo may correlate with melarsoprol withdrawal as first-line treatment. Our results suggest that melarsoprol could successfully be reintroduced following a time lag subsequent to its replacement. A field-applicable test to predict melarsoprol treatment outcome and identify

  10. Desmanthus GENOTYPES

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    Full Text Available Desmanthus is a genus of forage legumes with potential to improve pastures and livestock produc-tion on clay soils of dry tropical and subtropical regions such as the existing in Brazil and Australia. Despite this patterns of natural or enforced after-ripening of Desmanthus seeds have not been well established. Four year old seed banks of nine Desmanthus genotypes at James Cook University were accessed for their patterns of seed softe-ning in response to a range of temperatures. Persistent seed banks were found to exist under all of the studied ge-notypes. The largest seeds banks were found in the genotypes CPI 78373 and CPI 78382 and the smallest in the genotypes CPI’s 37143, 67643, and 83563. An increase in the percentage of softened seeds was correlated with higher temperatures, in two patterns of response: in some accessions seeds were not significantly affected by tempe-ratures below 80º C; and in others, seeds become soft when temperature rose to as little as 60 ºC. At 80 °C the heat started to depress germination. High seed production of Desmanthus associated with dependence of seeds on eleva-ted temperatures to softening can be a very important strategy for plants to survive in dry tropical regions.

  11. The -29G/A FSH receptor gene polymorphism is associated with higher FSH and LH levels in normozoospermic men. (United States)

    Tamburino, L; La Vignera, S; Tomaselli, V; Condorelli, R A; Cannarella, R; Mongioì, L M; Calogero, A E


    The functional role of the FSHR promoter -29G/A polymorphism (rs1394205) in men is not clear. Some studies failed to find a relationship between the FSHR -29G/A and follicle-stimulating hormone (FSH) levels and did not associate the SNP with male infertility. Only one study showed that the FSHR -29 SNP modulates serum FSH levels in Baltic young male cohort. Because the SNP -29G/A has to be shown to have a strong effect on in vitro transcription activity of the FSHR promoter and the activation of FSHR is necessary for a normal FSH function, this study was undertaken to assess whether the FSHR -29G/A SNP modulates the gonadal endocrine function in men. A total of 200 men with alteration of conventional sperm parameters or normozoospermia (according to the parameters WHO 2010), were genotyped by TaqMan Assay. Hormone levels were measured by immunoassay, and sperm analysis was performed according to the World Health Organization criteria. A significant gradient of increasing FSH levels across the FSHR -29G/A genotypes was observed (p men (n = 110), those with FSHR -29A-allele carriers (GA + AA and AA) had higher serum FSH (p men with the GG genotype. The carrier status of rs1394205 genotypes did not affect the other endocrine parameters neither in men with altered sperm parameters nor in normozoospermic men. The FSHR -29G/A polymorphism modulates FSH and, for the first time, LH serum levels and BMI in normozoospermic men. These findings underline the importance to pay close attention to the studies of genetic variations associated with clinical-endocrine parameters.

  12. VacA, cagA, iceA and oipA genotypes status and antimicrobial resistance properties of Helicobacter pylori isolated from various types of ready to eat foods. (United States)

    Hemmatinezhad, Behsan; Momtaz, Hassan; Rahimi, Ebrahim


    Despite the high clinical standing of Helicobacter pylori, its exact routes of transmission and origin have not been determined. Based on the contentious hypothesis, foods play an important roles in the transmission of H. pylori to humans. The present study was carried out to investigate the vacA, cagA, oipA and iceA genotypes status of H. pylori isolated from the various types of ready to eat foods. A total of 550 ready to eat food samples were cultured and tested. H. pylori-positive strains were analyzed for the presence of various genotypes and antimicrobial resistance pattern. Seventy four out of 550 (13.45 %) samples were positive for H. pylori. Olvie salad (36 %), restaurant salad (30 %), fruit salad (28 %) and soup (22 %) were the most commonly contaminated. H. pylori strains harbored the highest levels of resistance against amoxicillin (94.59 %), ampicillin (93.24 %), metronidazole (89.18 %) and tetracycline (72.97 %). The most commonly detected genotypes were vacA s1a (78.37 %), vacA m2 (75.67 %), vacA m1a (51.35 %) and cagA (41.89 %). The prevalence of iceA1, iceA2 and oipA genotypes were 13.51, 4.05 and 18.91 %, respectively. S1am2 (70.27 %), s1am1a (39.18 %) and m1am2 (31.08 %) were the most commonly detected combined genotypes. Of 40 different genotypic combinations, s1a/cagA+/iceA1/oipA- (12.16 %), s1a/cagA+/iceA1/oipA+ (10.81 %) and s1a/cagA-/iceA1/oipA+ (10.81 %) were the most prevalent. The present investigation showed that some types of ready to eat food samples maybe the sources of resistant and virulent strains of H. pylori. Warily use of antibiotics with respect to the results of disk diffusion method and careful health monitoring on food and staffs of food producing companies maybe reduce the risk of H. pylori in foods.

  13. FADS genotype and diet are important determinants of DHA status: a cross-sectional study in Danish infants1-3

    DEFF Research Database (Denmark)

    Harsløf, Laurine Bente Schram; Larsen, Lesli Hingstrup; Ritz, Christian


    Background: Infant docosahexaenoic acid (DHA) status is supported by the DHA content of breast milk and thus can decrease once complementary feeding begins. Furthermore, it is unclear to what extent endogenous DHA synthesis contributes to status. Objective: We investigated several determinants, i...

  14. The Immunoexpression of FSH-R in the Ductuli Efferentes and the Epididymis of Men and Rat: Effect of FSH on the Morphology and Steroidogenic Activity of Rat Epididymal Epithelial Cells In Vitro

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    Małgorzata Świder-Al-Amawi


    Full Text Available The Sertoli cells were regarded as the only target for FSH in male reproductive system. The expression of FSH receptor (FSH-R was detected also in epithelial cells of the caput epididymis of rat and monkey. We showed in the immunohistochemistry study the expression of FSH-R in rat and human ductuli efferentes and the caput, corpus, and cauda epididymis, moreover, by Western blot analysis in the caput and cauda epididymis of rat. Additionally, we presented that the morphology of rat epididymal epithelial cells in vitro was affected by FSH, and FSH stimulation resulted in the increase of 17β-estradiol synthesis by rat caput epididymal cells in dose-depended manner. In conclusion, the identification of FSH receptors in human and rat epididymides supports our results that the epididymis is a target organ not only for LH but additionally for FSH. On the basis of the results we showed for the first time that morphology of epididymal epithelial cells and epididymal steroidogenesis can be regulated by FSH.

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

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


    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. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

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    Brian O'Farrell

    Full Text Available 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 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.

  17. The Association of Combined GSTM1 and CYP2C9 Genotype Status with the Occurrence of Hemorrhagic Cystitis in Pediatric Patients Receiving Myeloablative Conditioning Regimen Prior to Allogeneic Hematopoietic Stem Cell Transplantation

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    Chakradhara Rao S. Uppugunduri


    Full Text Available Hemorrhagic cystitis (HC is one of the complications of busulfan-cyclophosphamide (BU-CY conditioning regimen during allogeneic hematopoietic stem cell transplantation (HSCT in children. Identifying children at high risk of developing HC in a HSCT setting could facilitate the evaluation and implementation of effective prophylactic measures. In this retrospective analysis genotyping of selected candidate gene variants was performed in 72 children and plasma Sulfolane (Su, water soluble metabolite of BU levels were measured in 39 children following treatment with BU-CY regimen. The cytotoxic effects of Su and acrolein (Ac, water soluble metabolite of CY were tested on human urothelial cells (HUCs. The effect of Su was also tested on cytochrome P 450 (CYP function in HepaRG hepatic cells. Cumulative incidences of HC before day 30 post HSCT were estimated using Kaplan–Meier curves and log-rank test was used to compare the difference between groups in a univariate analysis. Multivariate Cox regression was used to estimate hazard ratios with 95% confidence intervals (CIs. Multivariate analysis included co-variables that were significantly associated with HC in a univariate analysis. Cumulative incidence of HC was 15.3%. In the univariate analysis, HC incidence was significantly (p < 0.05 higher in children older than 10 years (28.6 vs. 6.8% or in children with higher Su levels (>40 vs. <11% or in carriers of both functional GSTM1 and CYP2C9 (33.3 vs. 6.3% compared to the other group. In a multivariate analysis, combined GSTM1 and CYP2C9 genotype status was associated with HC occurrence with a hazards ratio of 4.8 (95% CI: 1.3–18.4; p = 0.02. Ac was found to be toxic to HUC cells at lower concentrations (33 μM, Su was not toxic to HUC cells at concentrations below 1 mM and did not affect CYP function in HepaRG cells. Our observations suggest that pre-emptive genotyping of CYP2C9 and GSTM1 may aid in selection of more effective prophylaxis to

  18. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52)


    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja


    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  19. Expressão relativa de fator semelhante a insulina (IGFI e receptor do homômonio folículo estimulante (FSHR em folículos e tecido ovariano de Bos primigenius (Nelore

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    Jorge Luís Ferreira


    Full Text Available O aperfeiçoamento das técnicas que objetivam a exploração do potencial reprodutivo das fêmeas requer a compreensão mais ampla dos mecanismos de controle de desenvolvimento folicular. Uma alternativa de estudo nesta esfera, é a quantificação da expressão relativa de genes envolvidos nos processos de recrutamento, seleção e desenvolvimento folicular, pelo emprego da técnica de transcrição - reversa associado a reação em cadeia pela polimerase (RT - PCR. O presente trabalho objetivou quantificar a expressão relativa dos genes insulin-like growth factor I (IGF-I e do receptor do hormônio folículo estimulante (FSHR, tendo como controle interno o gene da gliceraldeído 3-fosfato desidrogenase (GAPDH. Foram utilizados ovários bovinos de animais de matadouro em diferentes fases do ciclo estral. O RNA total dos folículos e tecido ovarianos foi purificado por TRIZOL. As reações de RT-PCR foram realizadas com o "kit" SuperScriptTM First-Strand. Os produtos de PCR foram analisados em gel de agarose e as bandas submetidas à análise densitométrica. Todos os genes foram amplificados observando-se a curva exponencial de amplificação, a validação do método foi realizada através de análise de regressão, sendo estabelecido o coeficiente de amplificação (E. A expressão relativa de mRNA para cada gene de interesse foi calculada pela fórmula estabelecida por Prelle et al.12. Em todos os tecidos analisados, todos os genes foram expressos, sobressaltando-se diferenças nos diferentes ciclos estudados. Com relação os dados referentes ao coeficiente de amplificação (E, observou-se tanto para gene controle (GAPDH, como para o gene IGF-I concordância nos valores encontrados para as diferentes classes analisadas. Quanto ao gene IGF-I, a interpretação dos achados para a expressão relativa de mRNA pode está relacionada ao caráter constitutivo dessa proteína ou devido os transcritos não serem dependentes dos níveis de FSH

  20. The frequency of genotypes for the SNP Ser/Ser in the studied population of Albanian women is higher in the Balkan region

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    Zafer Gashi


    Full Text Available In women undergoing natural cycles, just one oocyte is usually selected for ovulation, yet routine clinical techniques to support the development of multiple follicles using additional gonadotrophins result in numerous ovulations. Several parameters have been postulated as predictors of ovarian response (inhibin B, 17-β-estradiol and antiMüllerian hormone. Nevertheless, the FSH level on the day 3 of menstrual cycle remains, the most widely used biomarker due to its low cost, although, the genetic background of individuals seems to determine the response of patients to rFSH stimulation better than the stimulation design. Consequently, the variants of FSHR were explored and they may be involved in the role of FSH receptor in mediated signal transduction and with ovarian response in infertile women submitted to ovarian stimulation. In this study we examined, for the first time, the prevalence of genotype variants Asn680Ser in population Albanian women from Kosovo Dukagjin region who took part in IVF / ICSI program. The frequencies of the Asn680Ser genotype variants were as follows: Asn/Asn 22.1%, Asn/Ser 47.1%, and Ser/Ser 30.8%, respectively (Table 1. bE2 levels between the three genotype variants showed slight but statistically significant difference (p= 0.0308. No difference was also found between the genotype groups either in terms of AFC, amount of the FSH required for ovulation induction, stimulation length days, number of dominant follicles, oocyte retrieval number or endometrial thickness (Table 2. BMI was significantly higher in the Ser/Ser group as compared to those from the Asn/Ser or the Asn/Asn group (p= 0.0010 (Table 2. In the study population of Albanian women Dukagjin region of Kosovo had a higher incidence of Ser / SER genotype compared to Asn / Asn genotype. Our research results in the Albanian population differ from published data for other ethnic groups in the Balkans.

  1. APOE Genotyping, Cardiovascular Disease (United States)

    ... Resources For Health Professionals Subscribe Search APOE Genotyping, Cardiovascular Disease Send Us Your Feedback Choose Topic At a ... help understand the role of genetic factors in cardiovascular disease . However, the testing is sometimes used in clinical ...

  2. Radiosensitivity of fingermillet genotypes

    Energy Technology Data Exchange (ETDEWEB)

    Raveendran, T S; Nagarajan, C; Appadurai, R; Prasad, M N; Sundaresan, N [Tamil Nadu Agricultural Univ., Coimbatore (India)


    Varietal differences in radiosensitivity were observed in a study involving 4 genotypes of fingermillet (Eleusine coracana (Linn.) Gaertn.) subjected to gamma-irradiation. Harder seeds were found to tolerate a higher dose of the mutagen.

  3. Applications of blood group genotyping

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    Mariza A. Mota


    Full Text Available Introduction: The determination of blood group polymorphism atthe genomic level facilitates the resolution of clinical problemsthat cannot be addressed by hemagglutination. They are useful to(a determine antigen types for which currently available antibodiesare weakly reactive; (b type patients who have been recentlytransfused; (c identify fetuses at risk for hemolytic disease of thenewborn; and (d to increase the reliability of repositories of antigennegative RBCs for transfusion. Objectives: This review assessedthe current applications of blood group genotyping in transfusionmedicine and hemolytic disease of the newborn. Search strategy:Blood group genotyping studies and reviews were searched ingeneral database (MEDLINE and references were reviewed.Selection criteria: All published data and reviews were eligible forinclusion provided they reported results for molecular basis ofblood group antigens, DNA analysis for blood group polymorphisms,determination of fetal group status and applications of blood groupgenotyping in blood transfusion. Data collection: All data werecollected based on studies and reviews of blood grouppolymorphisms and their clinical applications.

  4. Genetic modifiers of nutritional status in cystic fibrosis1234


    Bradley, Gia M; Blackman, Scott M; Watson, Christopher P; Doshi, Vishal K; Cutting, Garry R


    Background: Improved nutrition early in life is associated with better pulmonary function for patients with cystic fibrosis (CF). However, nutritional status is poorly correlated with the CFTR genotype.

  5. Haemoglobin genotype of children with severe malaria seen at the ...

    African Journals Online (AJOL)

    Prof Ezechukwu


    Oct 23, 2011 ... malaria seen in University of Benin. Teaching Hospital (UBTH), Benin. City. Patients and methods: ... gested to play crucial role in the defense of host against malaria infection and reduce susceptibility to severe .... Binary logistic regression model using Hb genotype status (abnormal Hb versus HbAA) as the ...

  6. Identification of polymorphic inversions from genotypes

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    Cáceres Alejandro


    Full Text Available Abstract Background Polymorphic inversions are a source of genetic variability with a direct impact on recombination frequencies. Given the difficulty of their experimental study, computational methods have been developed to infer their existence in a large number of individuals using genome-wide data of nucleotide variation. Methods based on haplotype tagging of known inversions attempt to classify individuals as having a normal or inverted allele. Other methods that measure differences between linkage disequilibrium attempt to identify regions with inversions but unable to classify subjects accurately, an essential requirement for association studies. Results We present a novel method to both identify polymorphic inversions from genome-wide genotype data and classify individuals as containing a normal or inverted allele. Our method, a generalization of a published method for haplotype data 1, utilizes linkage between groups of SNPs to partition a set of individuals into normal and inverted subpopulations. We employ a sliding window scan to identify regions likely to have an inversion, and accumulation of evidence from neighboring SNPs is used to accurately determine the inversion status of each subject. Further, our approach detects inversions directly from genotype data, thus increasing its usability to current genome-wide association studies (GWAS. Conclusions We demonstrate the accuracy of our method to detect inversions and classify individuals on principled-simulated genotypes, produced by the evolution of an inversion event within a coalescent model 2. We applied our method to real genotype data from HapMap Phase III to characterize the inversion status of two known inversions within the regions 17q21 and 8p23 across 1184 individuals. Finally, we scan the full genomes of the European Origin (CEU and Yoruba (YRI HapMap samples. We find population-based evidence for 9 out of 15 well-established autosomic inversions, and for 52 regions

  7. Common genotypes of hepatitis B virus

    International Nuclear Information System (INIS)

    Idrees, M.; Khan, S.; Riazuddin, S.


    Objective: To find out the frequency of common genotypes of hepatitis-B virus (HBV). Subjects and Methods: HBV genotypes were determined in 112 HBV DNA positive sera by a simple and precise molecular genotyping system base on PCR using type-specific primers for the determination of genotypes of HBV A through H. Results: Four genotypes (A,B,C and D) out of total eight reported genotypes so far were identified. Genotypes A, B and C were predominant. HBV genotype C was the most predominant in this collection, appearing in 46 samples (41.7%). However, the genotypes of a total of 5 (4.46%) samples could not be determined with the present genotyping system. Mixed genotypes were seen in 8(7.14% HBV) isolates. Five of these were infected with genotypes A/D whereas two were with genotypes C/D. One patient was infected with 4 genotypes (A/B/C/D). Genotype A (68%) was predominant in Sindh genotype C was most predominant in North West Frontier Province (NWFP) (68.96) whereas genotype C and B were dominant in Punjab (39.65% and 25.86% respectively). Conclusion: All the four common genotypes of HBV found worldwide (A,B,C and D) were isolated. Genotype C is the predominant Genotypes B and C are predominant in Punjab and N.W.F.P. whereas genotype A is predominant in Sindh. (author)

  8. HBV genotypic variability in Cuba.

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    Carmen L Loureiro

    Full Text Available 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.

  9. HBV Genotypic Variability in Cuba (United States)

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


    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

  10. The JP2 genotype of Aggregatibacter actinomycetemcomitans and marginal periodontitis in the mixed dentition

    DEFF Research Database (Denmark)

    Jensen, Anne Birkeholm; Ennibi, Oum Keltoum; Ismaili, Zouheir


    AIM: To perform a cross-sectional study on the carrier frequency of JP2 and non-JP2 genotypes of A. actinomycetemcomitans in Moroccan schoolchildren and relate the presence of these genotypes to the periodontal status in the mixed dentition. MATERIAL AND METHODS: A plaque sample from 513 children...... the JP2 genotype and 186 (36.3%) were positive for non-JP2 genotypes, whereas A. actinomycetemcomitans could not be detected in the remaining 281 subjects. Among 75 subjects with mixed dentition and selected for clinical examination, clinical attachment loss (CAL) ≥3 mm at two or more periodontal sites...

  11. Echinococcus granulosus genotypes in Iran (United States)

    Sharafi, Seyedeh Maryam; Rostami-Nejad, Mohammad; Moazeni, Mohammad; Yousefi, Morteza; Saneie, Behnam; Hosseini-Safa, Ahmad


    Hydatidosis, caused by Echinococcus granulosus is one of the most important zoonotic diseases, throughout most parts of the world. Hydatidosis is endemic in Iran and responsible for approximately 1% of admission to surgical wards. There are extensive genetic variations within E. granulosus and 10 different genotypes (G1–G10) within this parasite have been reported. Identification of strains is important for improvement of control and prevention of the disease. No new review article presented the situation of Echinococcus granulosus genotypes in Iran in the recent years; therefore in this paper we reviewed the different studies regarding Echinococcus granulosus genotypes in Iran. PMID:24834298

  12. Representativeness of Tuberculosis Genotyping Surveillance in the United States, 2009-2010. (United States)

    Shak, Emma B; France, Anne Marie; Cowan, Lauren; Starks, Angela M; Grant, Juliana


    Genotyping of Mycobacterium tuberculosis isolates contributes to tuberculosis (TB) control through detection of possible outbreaks. However, 20% of U.S. cases do not have an isolate for testing, and 10% of cases with isolates do not have a genotype reported. TB outbreaks in populations with incomplete genotyping data might be missed by genotyping-based outbreak detection. Therefore, we assessed the representativeness of TB genotyping data by comparing characteristics of cases reported during January 1, 2009-December 31, 2010, that had a genotype result with those cases that did not. Of 22,476 cases, 14,922 (66%) had a genotype result. Cases without genotype results were more likely to be patients <19 years of age, with unknown HIV status, of female sex, U.S.-born, and with no recent history of homelessness or substance abuse. Although cases with a genotype result are largely representative of all reported U.S. TB cases, outbreak detection methods that rely solely on genotyping data may underestimate TB transmission among certain groups.

  13. Representativeness of Tuberculosis Genotyping Surveillance in the United States, 2009–2010 (United States)

    Shak, Emma B.; Cowan, Lauren; Starks, Angela M.; Grant, Juliana


    Genotyping of Mycobacterium tuberculosis isolates contributes to tuberculosis (TB) control through detection of possible outbreaks. However, 20% of U.S. cases do not have an isolate for testing, and 10% of cases with isolates do not have a genotype reported. TB outbreaks in populations with incomplete genotyping data might be missed by genotyping-based outbreak detection. Therefore, we assessed the representativeness of TB genotyping data by comparing characteristics of cases reported during January 1, 2009–December 31, 2010, that had a genotype result with those cases that did not. Of 22,476 cases, 14,922 (66%) had a genotype result. Cases without genotype results were more likely to be patients <19 years of age, with unknown HIV status, of female sex, U.S.-born, and with no recent history of homelessness or substance abuse. Although cases with a genotype result are largely representative of all reported U.S. TB cases, outbreak detection methods that rely solely on genotyping data may underestimate TB transmission among certain groups. PMID:26556930

  14. Plant genotype, microbial recruitment and nutritional security. (United States)

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


    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).

  15. Possible Synergistic Interactions Among Multiple HPV Genotypes in Women Suffering from Genital Neoplasia (United States)

    Hajia, Massoud; Sohrabi, Amir


    Objective: Persistence of HPV infection is the true cause of cervical disorders. It is reported that competition may exist among HPV genotypes for colonization. This survey was designed to establish the multiple HPV genotype status in our community and the probability of multiple HPV infections involvement. Methods: All multiple HPV infections were selected for investigation in women suffering from genital infections referred to private laboratories in Tehran, Iran. A total of 160 multi HPV positive specimens from cervical scraping were identified by the HPV genotyping methods, "INNO-LiPA and Geno Array". Result: In present study, HPV 6 (LR), 16 (HR), 53 (pHR), 31 (HR) and 11 (LR) were included in 48.8% of detected infections as the most five dominant genotypes. HPV 16 was detected at the highest rate with genotypes 53, 31 and 52, while HPV 53 appeared linked with HPV 16, 51 and 56 in concurrent infections. It appears that HPV 16 and 53 may have significant tendencies to associate with each other rather than with other genotypes. Analysis of the data revealed there may be some synergistic interactions with a few particular genotypes such as "HPV 53". Conclusion: Multiple HPV genotypes appear more likely to be linked with development of cervical abnormalities especially in patients with genital infections. Since, there are various patterns of dominant HPV genotypes in different regions of world, more investigations of this type should be performed for careHPV programs in individual countries. Creative Commons Attribution License

  16. relationship of status of polymorphic rapd bands with genotypic

    African Journals Online (AJOL)


    Department of Plant Breeding and Genetics, College of Agriculture, Orissa University of Agriculture and. Technology .... Amplified Polymorphic DNA) have been ... DNA quantification was done by visualising under UV light after electrophoresis on 0.8% (w/v) agarose gel. The. DNA was again diluted in TE buffer to 5 μg μl-1.

  17. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D


    : Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. ELIGIBILITY CRITERIA FOR STUDY SELECTION: Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after...

  18. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D


    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURC...

  19. Are men carrying the apolipoprotein epsilon 4- or epsilon 2 allele less fertile than epsilon 3 epsilon 3 genotypes?

    DEFF Research Database (Denmark)

    Gerdes, Lars Ulrik; Gerdes, C; Hansen, P S


    may affect reproductive efficiency, and we therefore compared the distributions of 40-year-old married men with known genotypes by the numbers of their biological children. The distributions were statistically significantly different (P = 0.0026). On average, men with the epsilon 3 epsilon 3 genotype....... These findings are unlikely to be due to gross error in the reported prevalence of childlessness, differences in socioeconomic status or other likely sources of bias. They are compatible with higher fertility in men with the epsilon 3 epsilon 3 genotype than in those with the other common apoE genotypes....

  20. Hepatitis C Virus: Virology and Genotypes

    KAUST Repository

    Abdelaziz, Ahmed


    Hepatitis C virus (HCV) is a major causative agent of chronic liver disease worldwide. HCV is characterized by genetic heterogeneity, with at least six genotypes identified. The geographic distribution of genotypes has shown variations in different

  1. Prevalence and genotypes of Enterocytozoon bieneusi in China. (United States)

    Wang, Sha-Sha; Wang, Rong-Jun; Fan, Xian-Cheng; Liu, Ting-Li; Zhang, Long-Xian; Zhao, Guang-Hui


    Enterocytozoon bieneusi has been considered as the most frequently diagnosed microsporidian species in humans and various animal species, accounting for more than 90% of the cases of human microsporidiosis. Spores of this pathogen excreted from both symptomatic and asymptomatic hosts into environment also would be an important source of waterborne outbreak of microsporidiosis. Due to limited effective drugs available but with too much side effects to mammals (eg. toxic), accurate characterization of E. bieneusi in both humans and animals is essential to implement effective control strategies to this pathogen. In China, E. bieneusi infection was presented in humans and some animals with high prevalence. Analysis of genetic variations of the internal transcribed spacer (ITS) sequences found 361 genotypes in China, and some novel genotypes were identified in some specific hosts. Additionally, associations between infections and some risk factors were also observed. In the present article, we reviewed the current status of prevalence, genotypes, multilocus genotypes (MLGs) in humans, various animals and waters in China. These findings will provide basic information for developing effective control strategies against E. bieneusi infection in China as well as other countries. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. AGT M235T genotype/anxiety interaction and gender in the HyperGEN study.

    Directory of Open Access Journals (Sweden)

    Sarah S Knox


    Full Text Available Both anxiety and elevated heart rate (HR have been implicated in the development of hypertension. The HyperGen cohort, consisting of siblings with severe and mild hypertension, an age-matched random sample of persons from the same base populations, and unmedicated adult offspring of the hypertensive siblings (N = 1,002 men and 987 women, was analyzed for an association of the angiotenisinogen AGTM235T genotype (TT, MT, MM with an endophenotype, heart rate (HR in high and low anxious groups.The interaction of AGTM genotype with anxiety, which has been independently associated with hypertension, was investigated adjusting for age, hypertension status, smoking, alcohol consumption, beta blocker medication, body mass index, physical activity and hours of television viewing (sedentary life style.Although there was no main effect of genotype on HR in men or women, high anxious men with the TT genotype had high HR, whereas high anxious men with the MM genotype had low HR. In women, HR was inversely associated with anxiety but there was no interaction with genotype.The results suggest that high anxiety in men with the TT genotype may increase risk for hypertension whereas the MM genotype may be protective in high anxious men. This type of gene x environment interaction may be one reason why genome wide association studies sometimes fail to replicate. The locus may be important only in combination with certain environmental factors.

  3. Distribution of hepatitis C virus genotypes among injecting drug users in Lebanon

    Directory of Open Access Journals (Sweden)

    Shamra Sarah


    Full Text Available Abstract Background The aim of this study is to determine the prevalence of anti-HCV among injecting drug users (IDUs in Lebanon, to establish the current prevalence of HCV genotypes in this population and to determine whether demographic characteristics and behavioral variables differ between participants who were HCV-RNA positive and those who were HCV-RNA negative or between the different genotypes. Participants were recruited using respondent-driven sampling method. The blood samples were collected as dried blood spots and then eluted to be tested for HCV, HBV and HIV by ELISA. Anti-HCV positive samples were subjected to RNA extraction followed by qualitative detection and genotyping. Results Among 106 IDUs, 56 (52.8% were anti-HCV-positive. The two groups did not differ in terms of age, marital status, and nationality. As for the behavioral variable, there was a trend of increased risky behaviors among the HCV-RNA positive group as compared to the HCV-RNA negative group but none of the variables reached statistical significance. Half (50% of the 56 anti-HCV-positive were HCV-RNA positive. Genotype 3 was the predominant one (57.1% followed by genotype 1 (21% and genotype 4 (18%. Conclusions The predominance of genotype 3 seems to be the predominant genotype among IDUs in Lebanon, a situation similar to that among IDUs in Western Europe. This study provides a base-line against possible future radical epidemiological variant that might occur in IDUs.

  4. AGT M235T genotype/anxiety interaction and gender in the HyperGEN study. (United States)

    Knox, Sarah S; Guo, Xinxin; Zhang, Yuqing; Weidner, G; Williams, Scott; Ellison, R Curtis


    Both anxiety and elevated heart rate (HR) have been implicated in the development of hypertension. The HyperGen cohort, consisting of siblings with severe and mild hypertension, an age-matched random sample of persons from the same base populations, and unmedicated adult offspring of the hypertensive siblings (N = 1,002 men and 987 women), was analyzed for an association of the angiotenisinogen AGTM235T genotype (TT, MT, MM) with an endophenotype, heart rate (HR) in high and low anxious groups. The interaction of AGTM genotype with anxiety, which has been independently associated with hypertension, was investigated adjusting for age, hypertension status, smoking, alcohol consumption, beta blocker medication, body mass index, physical activity and hours of television viewing (sedentary life style). Although there was no main effect of genotype on HR in men or women, high anxious men with the TT genotype had high HR, whereas high anxious men with the MM genotype had low HR. In women, HR was inversely associated with anxiety but there was no interaction with genotype. The results suggest that high anxiety in men with the TT genotype may increase risk for hypertension whereas the MM genotype may be protective in high anxious men. This type of gene x environment interaction may be one reason why genome wide association studies sometimes fail to replicate. The locus may be important only in combination with certain environmental factors.

  5. Genotype x environment interaction and optimum resource ...

    African Journals Online (AJOL)

    ... x E) interaction and to determine the optimum resource allocation for cassava yield trials. The effects of environment, genotype and G x E interaction were highly significant for all yield traits. Variations due to G x E interaction were greater than those due to genotypic differences for all yield traits. Genotype x location x year ...

  6. Hepatitis virus genotyping by Polymerase Chain Reaction and DNA Enzyme immunoassay among Saudi patients in the Western Province, Saudi Arabia

    International Nuclear Information System (INIS)

    Osoba, A.O.; Ibrahim, M.; Abdelaal, M.A.; Al-Mowallad, A.; Al-Shareef, B.; Hussein, B.A.


    The distribution of hepatitis C virus (HCV) genotypes in the Western Province of Saudi Arabia is unknown. The purpose of our study was to determine the prevalent HCV genotypes among HCV seropositive Saudi patients in the Western Province and to study the relationship between types/subtypes, clinical status and liver histology. Serum samples were collected from 140 consecutive patients attending the Hematology Clinic with varying grades of liver diseases, high almandine transferees (ALT) for > 6 months, positive HCV, qualitative PCR and who had liver biopsy. HCV genotyping was determined on patients who had tested positive by both HCV enzyme immunoassay (EIA) and the recombinant immunoblot assay (RIBA). Of the 140 patients, 97 (69.2%) had genotype 4, 18 (12.8%) had genotype 1a, and 16 (11.4%) had genotype 1b. Genotype 2b and 5 were found in two patients (1.4%) each, while 5 patients (3.6%) had mixed infections with genotype 4 and 5. Of the 97 patients infected with genotype 4, 84 (86.6%) had chronic active hepatitis (CAH), two (2.1%) had CAH with active cirrhosis, 9(9.3%) had cirrhosis and two (2.1%) had normal liver histology (NLH). The most prevalent HCV genotype in the Western Province of Saudi Arabia was genotype 4 (69.2%). Genotype 1b was encountered in 16 (11.4%) patients. For the first time, genotype 5 was identified in the Western Province of Saudi Arabia. Genotype 1b and 4 were associated with different histological grades of liver disease. (author)

  7. Genetic Divergence in Sugarcane Genotypes


    Tahir, Mohammad; Rahman, Hidayatur; Gul, Rahmani; Ali, Amjad; Khalid, Muhammad


    To assess genetic divergence of sugarcane germplasm, an experiment comprising 25 sugarcane genotypes was conducted at Sugar Crops Research Institute (SCRI), Mardan, Khyber Pakhtunkhwa, Pakistan, in quadruple lattice design during 2008-09. Among the 14 parameters evaluated, majority exhibited significant differences while some showed nonsignificant mean squares. The initial correlation matrix revealed medium to high correlations. Principal Component Analysis (PCA) showed that there were two pr...

  8. Measles Outbreak with Unique Virus Genotyping, Ontario, Canada, 2015. (United States)

    Thomas, Shari; Hiebert, Joanne; Gubbay, Jonathan B; Gournis, Effie; Sharron, Jennifer; Severini, Alberto; Jiaravuthisan, Manisa; Shane, Amanda; Jaeger, Valerie; Crowcroft, Natasha S; Fediurek, Jill; Sander, Beate; Mazzulli, Tony; Schulz, Helene; Deeks, Shelley L


    The province of Ontario continues to experience measles virus transmissions despite the elimination of measles in Canada. We describe an unusual outbreak of measles in Ontario, Canada, in early 2015 that involved cases with a unique strain of virus and no known association among primary case-patients. A total of 18 cases of measles were reported from 4 public health units during the outbreak period (January 25-March 23, 2015); none of these cases occurred in persons who had recently traveled. Despite enhancements to case-patient interview methods and epidemiologic analyses, a source patient was not identified. However, the molecular epidemiologic analysis, which included extended sequencing, strongly suggested that all cases derived from a single importation of measles virus genotype D4. The use of timely genotype sequencing, rigorous epidemiologic investigation, and a better understanding of the gaps in surveillance are needed to maintain Ontario's measles elimination status.

  9. Decoding noises in HIV computational genotyping. (United States)

    Jia, MingRui; Shaw, Timothy; Zhang, Xing; Liu, Dong; Shen, Ye; Ezeamama, Amara E; Yang, Chunfu; Zhang, Ming


    Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline. Results showed that mis-genotyped cases occurred at 4.6% globally, with some regional and high-risk population heterogeneities. Results also revealed a consistent mis-genotyping pattern in gp120 in all studied populations except the group of men who have sex with men. Our study also suggests novel virus diversities in the mis-genotyped cases. Finally, this study reemphasizes the importance of implementing a standardized genotyping pipeline to avoid genotyping disparity and to advance our understanding of virus evolution in various epidemiological settings. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Postmortem Changes in Pork Muscle Protein Phosphorylation in Relation to the RN Genotype

    DEFF Research Database (Denmark)

    Lametsch, René; Larsen, Martin Røssel; Essén-Gustavsson, Birgitta


    Postmortem changes in pork muscle protein phosphorylation in relation to the RN(-) genotype were investigated using one-dimensional gel electrophoresis and a phosphor specific staining. The phosphorylation levels of several protein bands were found to be affected by the RN(-) genotype and to change...... of phosphorylation of these key enzymes during the postmortem metabolism. The results illustrate that the protein phosphorylation level of the muscle proteins could be interpreted as a global metabolic fingerprint containing information about the activity status of the enzymes in the postmortem metabolism....... during postmortem development. Glycogen phosphorylase, phosphofructokinase, and pyruvate kinase were found in protein bands affected by the RN(-) genotype, and the phosphorylation profile indicates that part of the increased rate and extended pH decline of the RN(-) genotype could be a consequence...

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

    Directory of Open Access Journals (Sweden)

    Specht Günther


    Full Text Available Abstract 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

  12. Grain yield stability of early maize genotypes

    Directory of Open Access Journals (Sweden)

    Chitra Bahadur Kunwar


    Full Text Available The objective of this study was to estimate grain yield stability of early maize genotypes. Five early maize genotypes namely Pool-17, Arun1EV, Arun-4, Arun-2 and Farmer’s variety were evaluated using Randomized Complete Block Design along with three replications at four different locations namely Rampur, Rajahar, Pakhribas and Kabre districts of Nepal during summer seasons of three consecutive years from 2010 to 2012 under farmer’s fields. Genotype and genotype × environment (GGE biplot was used to identify superior genotype for grain yield and stability pattern. The genotypes Arun-1 EV and Arun-4 were better adapted for Kabre and Pakhribas where as pool-17 for Rajahar environments. The overall findings showed that Arun-1EV was more stable followed by Arun-2 therefore these two varieties can be recommended to farmers for cultivation in both environments.

  13. Heterogeneous recombination among Hepatitis B virus genotypes. (United States)

    Castelhano, Nadine; Araujo, Natalia M; Arenas, Miguel


    The rapid evolution of Hepatitis B virus (HBV) through both evolutionary forces, mutation and recombination, allows this virus to generate a large variety of adapted variants at both intra and inter-host levels. It can, for instance, generate drug resistance or the diverse viral genotypes that currently exist in the HBV epidemics. Concerning the latter, it is known that recombination played a major role in the emergence and genetic diversification of novel genotypes. In this regard, the quantification of viral recombination in each genotype can provide relevant information to devise expectations about the evolutionary trends of the epidemic. Here we measured the amount of this evolutionary force by estimating global and local recombination rates in >4700 HBV complete genome sequences corresponding to nine (A to I) HBV genotypes. Counterintuitively, we found that genotype E presents extremely high levels of recombination, followed by genotypes B and C. On the other hand, genotype G presents the lowest level, where recombination is almost negligible. We discuss these findings in the light of known characteristics of these genotypes. Additionally, we present a phylogenetic network to depict the evolutionary history of the studied HBV genotypes. This network clearly classified all genotypes into specific groups and indicated that diverse pairs of genotypes are derived from a common ancestor (i.e., C-I, D-E and, F-H) although still the origin of this virus presented large uncertainty. Altogether we conclude that the amount of observed recombination is heterogeneous among HBV genotypes and that this heterogeneity can influence on the future expansion of the epidemic. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Serotonin Transporter Genotype (5HTTLPR) Moderates the Longitudinal Impact of Atypical Attachment on Externalizing Behavior. (United States)

    Humphreys, Kathryn L; Zeanah, Charles H; Nelson, Charles A; Fox, Nathan A; Drury, Stacy S


    To test whether genotype of the serotonin transporter-linked polymorphic region (5HTTLPR) and atypical attachment interact to predict externalizing psychopathology prospectively in a sample of children with a history of early institutional care. Caregiver report of externalizing behavior at 54 months was examined in 105 children initially reared in institutional care and enrolled in the Bucharest Early Intervention Project, a randomized controlled trial of high quality foster care. 5HTTLPR genotype, attachment status at 42 months of age (typical [secure, avoidant, or ambivalent] or atypical [disorganized-controlling, insecure-other]), and their interaction were examined as predictors of externalizing behavior at age 54 months. 5HTTLPR genotype and atypical attachment at age 42 months interacted to predict externalizing behavior at age 54 months. Specifically, children with the s/s genotype with an atypical attachment had the highest externalizing scores. However, s/s children with a typical attachment demonstrated the lowest externalizing scores, even after controlling for intervention group status. There was no association between attachment status and externalizing behavior among children carrying at least 1 copy of the l allele. These findings indicate that genetic variation in the serotonergic system moderates the association between atypical attachment status and externalizing in young children. Our findings suggest that children, as a result of genetic variability in the serotonergic system, demonstrate differential sensitivity to the attachment relationship.

  15. Serotonin Transporter Genotype (5HTTLPR) Moderates the Longitudinal Impact of Atypical Attachment on Externalizing Behavior (United States)

    Humphreys, Kathryn L.; Zeanah, Charles H.; Nelson, Charles A.; Fox, Nathan A.; Drury, Stacy S.


    Objective To test whether genotype of the serotonin transporter-linked polymorphic region (5HTTLPR) and atypical attachment interact to predict externalizing psychopathology prospectively in a sample of children with a history of early institutional care. Methods Caregiver report of externalizing behavior at 54 months was examined in 105 children initially reared in institutional care and enrolled in the Bucharest Early Intervention Project, a randomized controlled trial of high quality foster care. 5HTTLPR genotype, attachment status at 42 months of age (typical [secure, avoidant, or ambivalent] or atypical [disorganized-controlling, insecure-other]), as well as their interaction, were examined as predictors of externalizing behavior at age 54 months. Results 5HTTLPR genotype and atypical attachment at age 42 months interacted to predict externalizing behavior at age 54 months. Specifically, children with the s/s genotype with an atypical attachment had the highest externalizing scores. However, s/s children with a typical attachment demonstrated the lowest externalizing scores, even after controlling for intervention group status. There was no association between attachment status and externalizing behavior among children carrying at least one copy of the l allele. Discussion These findings indicate that genetic variation in the serotonergic system moderates the association between atypical attachment status and externalizing in young children. Our findings suggest that children, as a result of genetic variability in the serotonergic system, demonstrate differential sensitivity to the attachment relationship. PMID:25933228

  16. Hepatitis C virus genotypes in Myanmar. (United States)

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


    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.

  17. Hepatitis C Virus: Virology and Genotypes

    KAUST Repository

    Abdelaziz, Ahmed


    Hepatitis C virus (HCV) is a major causative agent of chronic liver disease worldwide. HCV is characterized by genetic heterogeneity, with at least six genotypes identified. The geographic distribution of genotypes has shown variations in different parts of the world over the past decade because of variations in population structure, immigration, and routes of transmission. Genotype differences are of epidemiologic interest and help the study of viral transmission dynamics to trace the source of HCV infection in a given population. HCV genotypes are also of considerable clinical importance because they affect response to antiviral therapy and represent a challenging obstacle for vaccine development.

  18. First insight into the genotypic diversity of clinical Mycobacterium tuberculosis isolates from Gansu Province, China.

    Directory of Open Access Journals (Sweden)

    Jie Liu

    Full Text Available BACKGROUND: Investigations of Mycobacterium tuberculosis genetic diversity in China have indicated a significant regional distribution. The aim of this study was to characterize the genotypes of clinical M. tuberculosis isolates obtained from Gansu, which has a special geographic location in China. METHODOLOGY/PRINCIPAL FINDINGS: A total of 467 clinical M. tuberculosis strains isolated in Gansu Province were genotyped by 15-locus mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR and spoligotyping. The results showed that 445 isolates belonged to six known spoligotype lineages, whereas 22 isolates were unknown. The Beijing genotype was the most prevalent (87.58%, n = 409, while the shared type 1 was the dominant genotype (80.94%, n = 378. The second most common lineage was the T lineage, with 25 isolates (5.35%, followed by the H lineage with 5 isolates (1.07%, the MANU family (0.64%, 3 isolates, the U family (0.43%, 2 isolates and the CAS lineage with 1 isolate (0.21%. By using the VNTR15China method, we observed 15 groups and 228 genotypes among the 467 isolates. We found no association between the five larger groups (including the Beijing genotype and sex, age, or treatment status, and there was no noticeable difference in the group analysis in different areas. In the present study, seven of the 15 MIRU-VNTR loci were highly or moderately discriminative according to their Hunter-Gaston discriminatory index. CONCLUSIONS/SIGNIFICANCE: The Beijing genotype is the predominant genotype in Gansu province. We confirm that VNTR15China is suitable for typing Beijing strains in China and that it has a better discriminatory power than spoligotyping. Therefore, the use of both methods is the most suitable for genotyping analysis of M. tuberculosis.

  19. Evaluation of the Abbott Real Time HCV genotype II assay for Hepatitis C virus genotyping. (United States)

    Sariguzel, Fatma Mutlu; Berk, Elife; Gokahmetoglu, Selma; Ercal, Baris Derya; Celik, Ilhami


    The determination of HCV genotypes and subtypes is very important for the selection of antiviral therapy and epidemiological studies. The aim of this study was to evaluate the performance of Abbott Real Time HCV Genotype II assay in HCV genotyping of HCV infected patients in Kayseri, Turkey. One hundred patients with chronic hepatitis C admitted to our hospital were evaluated between June 2012 and December 2012, HCV RNA levels were determined by the COBAS® AmpliPrep/COBAS® TaqMan® 48 HCV test. HCV genotyping was investigated by the Abbott Real Time HCV Genotype II assay. With the exception of genotype 1, subtypes of HCV genotypes could not be determined by Abbott assay. Sequencing analysis was used as the reference method. Genotypes 1, 2, 3 and 4 were observed in 70, 4, 2 and 24 of the 100 patients, respectively, by two methods. The concordance between the two systems to determine HCV major genotypes was 100%. Of 70 patients with genotype 1, 66 showed infection with subtype 1b and 4 with subtype 1a by Abbott Real Time HCV Genotype II assay. Using sequence analysis, 61 showed infection with subtype 1b and 9 with subtype 1a. In determining of HCV genotype 1 subtypes, the difference between the two methods was not statistically significant (P>0.05). HCV genotype 4 and 3 samples were found to be subtype 4d and 3a, respectively, by sequence analysis. There were four patients with genotype 2. Sequence analysis revealed that two of these patients had type 2a and the other two had type 2b. The Abbott Real Time HCV Genotype II assay yielded results consistent with sequence analysis. However, further optimization of the Abbott Real Time HCV Genotype II assay for subtype identification of HCV is required.

  20. Genotyping isolates of the entomopathogenic fungus Beauveria ...

    African Journals Online (AJOL)

    Multi-locus denaturing gradient gel electrophoresis (DGGE) analysis was developed to investigate the genotypes of Beauveria bassiana sensu lato. ... These results demonstrated that multi-locus DGGE is a potentially useful molecular marker for genotyping, identifying and tracking the fates of experimentally released ...

  1. Genetic relationship among Musa genotypes revealed by ...

    African Journals Online (AJOL)



    Mar 29, 2012 ... A banana germplasm was established containing 44 Musa genotypes collected from various locations in Malaysia. To detect their genetic variation and to rule out duplicates among cultivar, microsatellite markers were used in their analysis. The microsatellite profiles of 44 Musa genotypes of various origins.

  2. Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)


    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){sub 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. 32 refs., 5 figs., 3 tabs.

  3. Helicobacter pylori genotyping from positive clotests in patients with duodenal ulcer

    Directory of Open Access Journals (Sweden)

    Mattar Rejane


    Full Text Available Even though the seroprevalence of H. pylori may be high in the normal population, a minority develops peptic ulcer. Colonization of the gastric mucosa by more pathogenic vacA strains of H. pylori seems to be associated with enhanced gastric inflammation and duodenal ulcer. H. pylori genotyping from positive CLOtests was developed to determine the vacA genotypes and cagA status in 40 duodenal ulcer patients and for routine use. The pathogenic s1b/ m1/ cagA genotype was the most frequently occurring strain (17/42.5%; only two (5% patients presented the s2/ m2 genotype, the less virulent strain. Multiple strains were also detected in 17 (42.5% patients. Multiple strains of H. pylori colonizing the human stomach have been underestimated, because genotyping has been performed from cultures of H. pylori. We concluded that genotyping of H. pylori from a positive CLOtest had the advantages of reducing the number of biopsies taken during endoscopy, eliminating the step of culturing H. pylori, and assuring the presence of H. pylori in the specimen being processed.

  4. Genomic evaluations with many more genotypes

    Directory of Open Access Journals (Sweden)

    Wiggans George R


    Full Text Available Abstract Background Genomic evaluations in Holstein dairy cattle have quickly become more reliable over the last two years in many countries as more animals have been genotyped for 50,000 markers. Evaluations can also include animals genotyped with more or fewer markers using new tools such as the 777,000 or 2,900 marker chips recently introduced for cattle. Gains from more markers can be predicted using simulation, whereas strategies to use fewer markers have been compared using subsets of actual genotypes. The overall cost of selection is reduced by genotyping most animals at less than the highest density and imputing their missing genotypes using haplotypes. Algorithms to combine different densities need to be efficient because numbers of genotyped animals and markers may continue to grow quickly. Methods Genotypes for 500,000 markers were simulated for the 33,414 Holsteins that had 50,000 marker genotypes in the North American database. Another 86,465 non-genotyped ancestors were included in the pedigree file, and linkage disequilibrium was generated directly in the base population. Mixed density datasets were created by keeping 50,000 (every tenth of the markers for most animals. Missing genotypes were imputed using a combination of population haplotyping and pedigree haplotyping. Reliabilities of genomic evaluations using linear and nonlinear methods were compared. Results Differing marker sets for a large population were combined with just a few hours of computation. About 95% of paternal alleles were determined correctly, and > 95% of missing genotypes were called correctly. Reliability of breeding values was already high (84.4% with 50,000 simulated markers. The gain in reliability from increasing the number of markers to 500,000 was only 1.6%, but more than half of that gain resulted from genotyping just 1,406 young bulls at higher density. Linear genomic evaluations had reliabilities 1.5% lower than the nonlinear evaluations with 50

  5. Developmental plasticity: re-conceiving the genotype. (United States)

    Sultan, Sonia E


    In recent decades, the phenotype of an organism (i.e. its traits and behaviour) has been studied as the outcome of a developmental 'programme' coded in its genotype. This deterministic view is implicit in the Modern Synthesis approach to adaptive evolution as a sorting process among genetic variants. Studies of developmental pathways have revealed that genotypes are in fact differently expressed depending on environmental conditions. Accordingly, the genotype can be understood as a repertoire of potential developmental outcomes or norm of reaction. Reconceiving the genotype as an environmental response repertoire rather than a fixed developmental programme leads to three critical evolutionary insights. First, plastic responses to specific conditions often comprise functionally appropriate trait adjustments, resulting in an individual-level, developmental mode of adaptive variation. Second, because genotypes are differently expressed depending on the environment, the genetic diversity available to natural selection is itself environmentally contingent. Finally, environmental influences on development can extend across multiple generations via cytoplasmic and epigenetic factors transmitted to progeny individuals, altering their responses to their own, immediate environmental conditions and, in some cases, leading to inherited but non-genetic adaptations. Together, these insights suggest a more nuanced understanding of the genotype and its evolutionary role, as well as a shift in research focus to investigating the complex developmental interactions among genotypes, environments and previous environments.

  6. Genotype X/C recombinant (putative genotype I) of hepatitis B virus is rare in Hanoi, Vietnam--genotypes B4 and C1 predominate. (United States)

    Phung, Thi Bich Thuy; Alestig, Erik; Nguyen, Thanh Liem; Hannoun, Charles; Lindh, Magnus


    There are eight known genotypes of hepatitis B virus, A-H, and several subgenotypes, with rather well-defined geographic distributions. HBV genotypes were evaluated in 153 serum samples from Hanoi, Vietnam. Of the 87 samples that could be genotyped, genotype B was found in 67 (77%) and genotype C in 19 (22%). All genotype C strains were of subgenotype C1, and the majority of genotype B strains were B4, while a few were B2. The genotype X/C recombinant strain, identified previously in Swedish patients of indigenous Vietnamese origin, was found in one sample. This variant, proposed to be classified as genotype I, has been found recently also by others in Vietnam and Laos. The current study indicates that the genotype X/C recombinant may represent approximately 1% of the HBV strains circulating in Vietnam. (c) 2010 Wiley-Liss, Inc.

  7. Molecular characterization, expression profile of the FSHR gene and ...

    Indian Academy of Sciences (India)



    Jun 17, 2017 ... 1National-Local Joint Engineering Research Center for Livestock Breeding, College of Animal ... mal ovarian follicle development by stimulating ovarian .... primers were designed using Primer Premier software ... Application.

  8. Molecular characterization, expression profile of the FSHR gene and ...

    Indian Academy of Sciences (India)


    Oct 24, 2016 ... Muscovy duckswere lived under the same normal conditions of management and feeding ..... The authors declare that they have no conflict of interest. .... acid: functional expression of alternatively spliced variants and receptor.

  9. Molecular characterization, expression profile of the FSHR gene and ...

    Indian Academy of Sciences (India)


    Oct 24, 2016 ... gene(internal control), respectively.P5~P13 ... The obtained RNA quality was detected by 1.5% agarose gel electrophoresis and the concentration was ... sequenced by a commercial service (Majorbio Co. Ltd, Shanghai).

  10. Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates

    Directory of Open Access Journals (Sweden)

    Virgolino Helaine A


    Full Text Available Abstract Background Hepatitis B virus (HBV isolates have been classified in eight genotypes, A to H, which exhibit distinct geographical distributions. Genotypes A, D and F are predominant in Brazil, a country formed by a miscegenated population, where the proportion of individuals from Caucasian, Amerindian and African origins varies by region. Genotype F, which is the most divergent, is considered indigenous to the Americas. A systematic molecular characterization of HBV isolates from different parts of the world would be invaluable in establishing HBV evolutionary origins and dispersion patterns. A large-scale study is needed to map the region-by-region distribution of the HBV genotypes in Brazil. Results Genotyping by PCR-RFLP of 303 HBV isolates from HBsAg-positive blood donors showed that at least two of the three genotypes, A, D, and F, co-circulate in each of the five geographic regions of Brazil. No other genotypes were identified. Overall, genotype A was most prevalent (48.5%, and most of these isolates were classified as subgenotype A1 (138/153; 90.2%. Genotype D was the most common genotype in the South (84.2% and Central (47.6% regions. The prevalence of genotype F was low (13% countrywide. Nucleotide sequencing of the S gene and a phylogenetic analysis of 32 HBV genotype F isolates showed that a great majority (28/32; 87.5% belonged to subgenotype F2, cluster II. The deduced serotype of 31 of 32 F isolates was adw4. The remaining isolate showed a leucine-to-isoleucine substitution at position 127. Conclusion The presence of genotypes A, D and F, and the absence of other genotypes in a large cohort of HBV infected individuals may reflect the ethnic origins of the Brazilian population. The high prevalence of isolates from subgenotype A1 (of African origin indicates that the African influx during the colonial slavery period had a major impact on the circulation of HBV genotype A currently found in Brazil. Although most genotype F

  11. Status epilepticus

    NARCIS (Netherlands)

    Hensiek, AE; Absalom, Anthony


    Status epilepticus is defined as epileptic activity that continues for more than 30 minutes as a single seizure or as recurrent seizures without inter-ictal return of consciousness. The seizure activity is usually classified as partial or generalized. Although status epilepticus is an uncommon

  12. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C


    to routine STR profiling, use of SNaPshot is an important part of the development of SNP sets for a wide range of forensic applications with these markers, from genotyping highly degraded DNA with very short amplicons to the introduction of SNPs to ascertain the ancestry and physical characteristics......This review explores the key factors that influence the optimization, routine use, and profile interpretation of the SNaPshot single-base extension (SBE) system applied to forensic single-nucleotide polymorphism (SNP) genotyping. Despite being a mainly complimentary DNA genotyping technique...... of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides...

  13. HMSRP Hawaiian Monk Seal Microsatellite Genotypes (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Currently ~2,400 Hawaiian monk seal specimens have been analyzed genetically, providing genotypes at 18 microsatellite loci. These data are organized by individual,...

  14. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie


    Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years Udgivelsesdato...

  15. Assessment of antibiotic susceptibilities, genotypic characteristics ...

    African Journals Online (AJOL)



    Sep 28, 2011 ... Staphylococcus aureus and Salmonella Typhimurium ... This study was designed to evaluate the antibiotic susceptibilities, genotypic characteristics and ..... Distribution of reference and virulence genes among antibiotic-sensitive S. aureus (SAS), .... environmental factors such as temperature, water activity,.

  16. Hepatitis C Virus: Viral Quasispecies and Genotypes

    Directory of Open Access Journals (Sweden)

    Kyoko Tsukiyama-Kohara


    Full Text Available Hepatitis C virus (HCV mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs, which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

  17. Hepatitis C Virus: Viral Quasispecies and Genotypes. (United States)

    Tsukiyama-Kohara, Kyoko; Kohara, Michinori


    Hepatitis C virus (HCV) mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs), which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

  18. Early seedling development of Medicago truncatula genotypes ...

    African Journals Online (AJOL)



    Jan 8, 2014 ... heat shock proteins; ABA, abscisic acid. Page 2. Amar et al. 323. Figure 1. Seed vigor of M. truncatula genotypes under different salt stress conditions. Results are means ..... (HSPs) that accumulate during seed late maturation.

  19. Hearing impairment in genotyped Wolfram syndrome patients.

    NARCIS (Netherlands)

    Plantinga, R.F.; Pennings, R.J.E.; Huygen, P.L.M.; Bruno, R.; Eller, P.; Barrett, T.G.; Vialettes, B.; Paquis-Fluklinger, V.; Lombardo, F.; Cremers, C.W.R.J.


    OBJECTIVES: Wolfram syndrome is a progressive neurodegenerative syndrome characterized by the features "DIDMOAD" (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness). We sought to study the audiometric data of genotyped Wolfram syndrome patients with sensorineural hearing impairment.

  20. Existence of various human parvovirus B19 genotypes in Chinese plasma pools: genotype 1, genotype 3, putative intergenotypic recombinant variants and new genotypes. (United States)

    Jia, Junting; Ma, Yuyuan; Zhao, Xiong; Huangfu, Chaoji; Zhong, Yadi; Fang, Chi; Fan, Rui; Lv, Maomin; Zhang, Jingang


    Human parvovirus B19 (B19V) is a frequent contaminant of blood and plasma-derived medicinal products. Three distinct genotypes of B19V have been identified. The distribution of the three B19V genotypes has been investigated in various regions or countries. However, in China, data on the existence of different B19V genotypes are limited. One hundred and eighteen B19V-DNA positive source plasma pool samples collected from three Chinese blood products manufacturers were analyzed. The subgenomic NS1/VP1u region junction of B19V was amplified by nested PCR. These amplified products were then cloned and subsequently sequenced. For genotyping, their phylogenetic inferences were constructed based on the NS1/VP1-unique region. Then putative recombination events were analyzed and identified. Phylogenetic analysis of 118 B19V sequences attributed 61.86 % to genotype 1a, 10.17 % to genotype 1b, and 17.80 % to genotype 3b. All the genotype 3b sequences obtained in this study grouped as a specific, closely related cluster with B19V strain D91.1. Four 1a/3b recombinants and 5 new atypical B19V variants with no recombination events were identified. There were at least 3 subtypes (1a, 1b and 3b) of B19V circulating in China. Furthermore, putative B19V 1a/3b recombinants and unclassified strains were identified as well. Such recombinant and unclassified strains may contribute to the genetic diversity of B19V and consequently complicate the B19V infection diagnosis and NAT screening. Further studies will be required to elucidate the biological significance of the recombinant and unclassified strains.

  1. Popcorn genotypes resistance to fall armyworm

    Directory of Open Access Journals (Sweden)

    Nádia Cristina de Oliveira


    Full Text Available ABSTRACT: The aim of this study was to evaluate popcorn genotypes for resistance to the fall armyworm, Spodoptera frugiperda. The experiment used a completely randomized design with 30 replicates. The popcorn genotypes Aelton, Arzm 05 083, Beija-Flor, Colombiana, Composto Chico, Composto Gaúcha, Márcia, Mateus, Ufvm Barão Viçosa, Vanin, and Viviane were evaluated,along with the common maize variety Zapalote Chico. Newly hatched fall armyworm larvae were individually assessed with regard to biological development and consumption of food. The data were subjected to multivariate analyses of variance and genetic divergence among genotypes was evaluated through the clustering methods of Tocher based on generalized Mahalanobis distances and canonical variable analyses. Seven popcorn genotypes, namely, Aelton, Arzm 05 083, Composto Chico, Composto Gaúcha, Márcia, Mateus, and Viviane,were shown to form a cluster (cluster I that had antibiosis as the mechanism of resistance to the pest. Cluster I genotypes and the Zapalote Chico genotype could be used for stacking genes for antibiosis and non-preference resistance.

  2. Plasma signaling proteins in persons at genetic risk for Alzheimer disease: influence of APOE genotype. (United States)

    Ringman, John M; Elashoff, David; Geschwind, Daniel H; Welsh, Brian T; Gylys, Karen H; Lee, Cathy; Cummings, Jeffrey L; Cole, Greg M


    To study the effect of familial Alzheimer disease (FAD) mutations and APOE genotype on plasma signaling protein levels. Cross-sectional comparison of plasma levels of 77 proteins measured using multiplex immune assays. A tertiary referral dementia research center. Thirty-three persons from families harboring PSEN1 or APP mutations, aged 19 to 59 years. Protein levels were compared between FAD mutation carriers (MCs) and noncarriers (NCs) and among APOE genotype groups, using multiple linear regression models. Twenty-one participants were FAD MCs and 12 were NCs. Six had the APOE ε2/3, 6 had the ε3/4, and 21 had the ε3/3 genotype. Levels of 17 proteins differed among APOE genotype groups, and there were significant interactions between age and APOE genotype for 12 proteins. Plasma levels of apolipoprotein E and superoxide dismutase 1 were highest in the ε2 carriers, lowest in ε4 carriers, and intermediate in the ε3 carriers. Levels of multiple interleukins showed the opposite pattern and, among the ε4 carriers, demonstrated significant negative correlations with age. Although there were no significant differences between FAD MCs and NCs, there were interactions between mutation status and APOE genotype for 13 proteins. We found different patterns of inflammatory markers in young and middle-aged persons among APOE genotype groups. The APOE ε4 carriers had the lowest levels of apolipoprotein E. Young ε4 carriers have increased inflammatory markers that diminish with age. We demonstrated altered inflammatory responses in young and middle adulthood in ε4 carriers that may relate to AD risk later in life.

  3. Genotypic characterization of initial acquisition of Streptococcus mutans in American Indian children

    Directory of Open Access Journals (Sweden)

    David J. Lynch


    Full Text Available Background: Severe-early childhood caries (S-ECC is one of the most common infectious diseases in children and is prevalent in lower socio-economic populations. American Indian children suffer from the highest levels of S-ECC in the United States. Members of the mutans streptococci, Streptococcus mutans, in particular, are key etiologic agents in the development of caries. Children typically acquire S. mutans from their mothers and early acquisition is often associated with higher levels of tooth decay. Methods: We have conducted a 5-year birth cohort study with a Northern Plains Tribe to determine the temporality and fidelity of S. mutans transmission from mother to child in addition to the genotypic diversity of S. mutans in this community. Plaque samples were collected from 239 mother/child dyads at regular intervals from birth to 36 months and S. mutans were isolated and genotyped by arbitrarily primed-polymerase chain reaction (AP-PCR. Results: Here we present preliminary findings from a subset of the cohort. The focus for this paper is on initial acquisition events in the children. We identified 17 unique genotypes in 711 S. mutans isolates in our subset of 40 children, 40 mothers and 14 primary caregivers. Twelve of these genotypes were identified in more than one individual. S. mutans colonization occurred by 16 months in 57.5% of the children and early colonization was associated with higher decayed, missing and filled surface (DMFS scores (p=0.0007. Children colonized by S. mutans shared a common genotype with their mothers 47.8% of the time. While multiple genotypes were common in adults, only 10% of children harbored multiple genotypes. Conclusion: These children acquire S. mutans at an earlier age than the originally described ‘window of infectivity’ and often, but not exclusively, from their mothers. Early acquisition is associated with both the caries status of the children and the mothers.

  4. Cotton genotypes selection through artificial neural networks. (United States)

    Júnior, E G Silva; Cardoso, D B O; Reis, M C; Nascimento, A F O; Bortolin, D I; Martins, M R; Sousa, L B


    Breeding programs currently use statistical analysis to assist in the identification of superior genotypes at various stages of a cultivar's development. Differently from these analyses, the computational intelligence approach has been little explored in genetic improvement of cotton. Thus, this study was carried out with the objective of presenting the use of artificial neural networks as auxiliary tools in the improvement of the cotton to improve fiber quality. To demonstrate the applicability of this approach, this research was carried out using the evaluation data of 40 genotypes. In order to classify the genotypes for fiber quality, the artificial neural networks were trained with replicate data of 20 genotypes of cotton evaluated in the harvests of 2013/14 and 2014/15, regarding fiber length, uniformity of length, fiber strength, micronaire index, elongation, short fiber index, maturity index, reflectance degree, and fiber quality index. This quality index was estimated by means of a weighted average on the determined score (1 to 5) of each characteristic of the HVI evaluated, according to its industry standards. The artificial neural networks presented a high capacity of correct classification of the 20 selected genotypes based on the fiber quality index, so that when using fiber length associated with the short fiber index, fiber maturation, and micronaire index, the artificial neural networks presented better results than using only fiber length and previous associations. It was also observed that to submit data of means of new genotypes to the neural networks trained with data of repetition, provides better results of classification of the genotypes. When observing the results obtained in the present study, it was verified that the artificial neural networks present great potential to be used in the different stages of a genetic improvement program of the cotton, aiming at the improvement of the fiber quality of the future cultivars.

  5. Stock Status (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data inform the public of the most recent stock status for all stocks (FSSI and non-FSSI) in the fishery management unit contained in a fishery managment plan....

  6. Hepatitis C virus genotypes in Bahawalpur

    International Nuclear Information System (INIS)

    Qazi, M.A.; Fayyaz, M.; Chaudhry, G.M.D.; Jamil, A.


    This study was conducted at Medical Unit-II Bahawal Victoria Hospital / Quaid-e-Azam Medical College Bahawalpur from May 1st , 2005 to December 31st 2005. The objective of this study was to determine hepatitis C virus (HCV) genotypes in Bahawalpur, Pakistan. In consecutive 105 anti-HCV (ELISA-3) positive patients, complete history and physical examination was performed. Liver function tests, complete blood counts and platelet count, blood sugar fasting and 2 hours after breakfast, prothrombin time, serum albumin, serum globulin and abdominal ultrasound were carried out in all the patients. Tru cut biopsy was performed on 17 patients. We studied HCV RNA in all these patients by Nested PCR method. HCV RNA was detected in 98 patients and geno typing assay was done by genotype specific PCR. Among total of 105 anti-HCV positive patients, HCV-RNA was detected in 98 patients. Out of these 98 patients there were 57 (58.2%) males and 41 (42.8%) females. Their age range was 18-75 years. The age 18-29 years 26 (26.5%), 30-39 years 35 (35.7%) and 40-75 37 (37.8%), while 10 (10.2%) patients were diabetics and 34 (34.7%) patients were obese. Liver cirrhosis was present in 10 (10.2%) patients. Forty two (43.9%) patients were symptomatic while 56 (57.1%) were asymptomatic. Out of 98 patients 11 (11.2%) were un type-able and 87 (88.8%) were type able. 70/98 (71.4%) were genotype 3; 10/98 (10.2%) were genotype 1; 03/98 (3.1%) were genotype 2; 03/98 (3.1%) were mixed genotype 2 and 3; 01/98 (1%) were mixed genotype 3a and 3b. Genotype 3 is the most common HCV virus in our area which shows that both virological and biochemical response will be better. Because HCV genotype 3 is more frequent among the drug users which points towards unsafe injection practices in our area. (author)

  7. Phenotypic and genotypic variation in Iranian Pistachios

    Directory of Open Access Journals (Sweden)

    Somayeh Tayefeh Aliakbarkhani


    Full Text Available As Iran is one of the richest pistachio germplasms a few studies have been conducted on different sexes of pistachio trees, in areas where this crop emerged. To this end, 40 male and female Iranian pistachio genotypes from Feizabad region, Khorasan, Iran; were evaluated using morphological characters and randomly amplified polymorphic DNA (RAPD markers. For morphological assessments, 54 variables were considered to investigate similarities between and among the studied genotypes. Morphological data indicated relative superiority in some female genotypes (such as Sefid 1, Sefid Sabuni 2, Garmesiah, and Ghermezdorosht Z regarding characters such as halfcrackedness, the percentages of protein and fat content. 115 polymorphic bands were recorded with 92.83% average polymorphism among all primers. The total resolving power (Rp of the primers was 74.54. The range of genetic similarity varied from about 0.31 to about 0.70. Genotypes were segregated into eight groups at the similarity limit of 0.41. Results of present investigation could be helpful for strategic decisions for maintaining Iranian pistachio genotypes.

  8. Precise genotyping and recombination detection of Enterovirus (United States)


    Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception,, for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution. PMID:26678286

  9. Genetic diversity of "Pimenta Longa" genotypes (Piper spp., Piperaceae) of the Embrapa Acre germplasm collection


    Wadt, Lúcia Helena de Oliveira; Ehringhaus, Christiane; Kageyama, Paulo Yoshio


    The commonly known Pimenta longa is a commercially valuable natural resource found wild in Acre, Brazil. Specifically, three Piperaceae species with contested taxonomic status were studied, Piper hispidinervum, Piper aduncum, and Piper hispidum, to assesses the inter- and intra-specific genetic relationship of 49 Piper genotypes kept in the Pimenta longa germplasm collection at Embrapa Acre, using sixty six Random Amplified Polymorphic DNA (RAPD) markers. The DNA polymorphism level detected w...

  10. Saponin profile of green asparagus genotypes. (United States)

    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


    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.

  11. Carcass traits of four rabbit genotypes

    Directory of Open Access Journals (Sweden)

    Ajda Kermauner


    Full Text Available Seventy-three rabbits of four genotypes (A - SIKA maternal line; C - SIKA sire line; AxC - hybrids between line A and C; AxCal - crossbreds between line A and the Californian breed were used to evaluate the effect of genotype on carcass traits. Rabbits were weaned at 35 days and slaughtered at 93 days of age. Rabbits were fed standard feed mixture ad libitum. The highest live weight at slaughter and dressing percentage was achieved by line C, and the lowest in line A. Hybrids between line A and C exhibited slightly worse carcass traits than rabbits in line C, but the differences were not statistically significant. The Californian breed gave worse results than crossbreeding with line C, though in most cases the differences between AxC and AxCal were not significant. The differences between genotypes in hind leg tissue composition, pH and meat colour were not statistically significant.

  12. Genotype x environment interaction for grain yield of wheat genotypes tested under water stress conditions

    International Nuclear Information System (INIS)

    Sail, M.A.; Dahot, M.U.; Mangrio, S.M.; Memon, S.


    Effect of water stress on grain yield in different wheat genotypes was studied under field conditions at various locations. Grain yield is a complex polygenic trait influenced by genotype, environment and genotype x environment (GxE) interaction. To understand the stability among genotypes for grain yield, twenty-one wheat genotypes developed Through hybridization and radiation-induced mutations at Nuclear Institute of Agriculture (NIA) TandoJam were evaluated with four local check varieties (Sarsabz, Thori, Margalla-99 and Chakwal-86) in multi-environmental trails (MET/sub s/). The experiments were conducted over 5 different water stress environments in Sindh. Data on grain yield were recorded from each site and statistically analyzed. Combined analysis of variance for all the environments indicated that the genotype, environment and genotype x environment (GxE) interaction were highly significant (P greater then 0.01) for grain yield. Genotypes differed in their response to various locations. The overall highest site mean yield (4031 kg/ha) recorded at Moro and the lowest (2326 kg/ha) at Thatta. Six genotypes produced significantly (P=0.01) the highest grain yield overall the environments. Stability analysis was applied to estimate stability parameters viz., regression coefficient (b), standard error of regression coefficient and variance due to deviation from regression (S/sub 2/d) genotypes 10/8, BWS-78 produced the highest mean yield over all the environments with low regression coefficient (b=0.68, 0.67 and 0.63 respectively and higher S/sup 2/ d value, showing specific adaptation to poor (un favorable) environments. Genotype 8/7 produced overall higher grain yield (3647 kg/ha) and ranked as third high yielding genotype had regression value close to unity (b=0.9) and low S/sup d/ value, indicating more stability and wide adaptation over the all environments. The knowledge of the presence and magnitude of genotype x environment (GE) interaction is important to

  13. Imputation across genotyping arrays for genome-wide association studies: assessment of bias and a correction strategy. (United States)

    Johnson, Eric O; Hancock, Dana B; Levy, Joshua L; Gaddis, Nathan C; Saccone, Nancy L; Bierut, Laura J; Page, Grier P


    A great promise of publicly sharing genome-wide association data is the potential to create composite sets of controls. However, studies often use different genotyping arrays, and imputation to a common set of SNPs has shown substantial bias: a problem which has no broadly applicable solution. Based on the idea that using differing genotyped SNP sets as inputs creates differential imputation errors and thus bias in the composite set of controls, we examined the degree to which each of the following occurs: (1) imputation based on the union of genotyped SNPs (i.e., SNPs available on one or more arrays) results in bias, as evidenced by spurious associations (type 1 error) between imputed genotypes and arbitrarily assigned case/control status; (2) imputation based on the intersection of genotyped SNPs (i.e., SNPs available on all arrays) does not evidence such bias; and (3) imputation quality varies by the size of the intersection of genotyped SNP sets. Imputations were conducted in European Americans and African Americans with reference to HapMap phase II and III data. Imputation based on the union of genotyped SNPs across the Illumina 1M and 550v3 arrays showed spurious associations for 0.2 % of SNPs: ~2,000 false positives per million SNPs imputed. Biases remained problematic for very similar arrays (550v1 vs. 550v3) and were substantial for dissimilar arrays (Illumina 1M vs. Affymetrix 6.0). In all instances, imputing based on the intersection of genotyped SNPs (as few as 30 % of the total SNPs genotyped) eliminated such bias while still achieving good imputation quality.

  14. Detection and gB genotyping of CMV in Mexican preterm infants in the context of maternal seropositivity. (United States)

    Arellano-Galindo, José; Villanueva-García, Dina; Cruz-Ramirez, José Luis; Yalaupari-Mejìa, Juan Pablo; Uribe-Gutiérrez, Gabriel; Velazquez-Guadarrama, Norma; Nava-Frias, Margarita; Munoz-Hernández, Onofre; Mejía-Arangure, Juan Manuel


    Congenital (CI) and perinatal cytomegalovirus (CMV) infections (PI) can be linked to maternal CMV seropositivity, with fatal consequences in preterm newborns. GB genotyping has been used to analyze genotypic similarity in mothers and infants. The frequency of CMV infection in the context of maternal seropositivity and the viral gB genotypes as well as the genotypic similarity in mothers and preterm infants were investigated. Saliva samples and dry blood spots (DBS) were taken weekly from preterm newborns  from birth until the first month of life, and breast milk samples were taken from their mothers weekly during the first month of lactation. CMV IgG seroprevalence of the mothers and CI or PI in the infants were established. The gB status and genotypic similarities were established retrospectively in DBS and in the breast milk samples. In total, 387 neonates and 375 mothers were enrolled. The maternal CMV-positive IgG serology was 97.3% (365/375). Neonatal CMV was found in 5.1% (20/387) of newborns, and one infant presented with CMV-compatible symptoms. CI was 2.5% and PI in the first month after birth was 11.8%. GB2 was the most prevalent genotype and was also the genotype preferentially transmitted to newborns by mothers with mixed infections. CMV PI and CI in preterm infants from highly seropositive mothers was high, but the rate of symptomatic infection was low. The prevalent genotype was gB2, and this genotype was preferentially transmitted to newborns by mothers with mixed infections.

  15. Oilseed rape genotypes response to boron toxicity

    Directory of Open Access Journals (Sweden)

    Savić Jasna


    Full Text Available Response of 16 oilseed rape genotypes to B (boron toxicity was analyzed by comparing the results of two experiments conducted in a glasshouse. In Experiment 1 plants were grown in standard nutrient solutions with 10 µMB (control and 1000 µM B. Relative root and shoot growth varied from 20-120% and 31-117%, respectively. Variation in B concentration in shoots was also wide (206.5-441.7 µg B g-1 DW as well as total B uptake by plant (62.3-281.2 µg B g1. Four selected genotypes were grown in Experiment 2 in pots filled with high B soil (8 kg ha-1 B; B8. Shoot growth was not affected by B8 treatment, while root and shoot B concentration was significantly increased compared to control. Genotypes Panther and Pronto which performed low relative root and shoot growth and high B accumulation in plants in Experiment 1, had good growth in B8 treatment. In Experiment 2 genotype NS-L-7 had significantly lower B concentration in shots under treatment B8, but also very high B accumulation in Experiment 1. In addition, cluster analyses classified genotypes in three groups according to traits contrasting in their significance for analyzing response to B toxicity. The first group included four varieties based on their shared characteristics that have small value for the relative growth of roots and shoots and large values of B concentration in shoot. In the second largest group were connected ten genotypes that are heterogeneous in traits and do not stand out on any characteristic. Genotypes NS-L-7 and Navajo were separated in the third group because they had big relative growth of root and shoot, but also a high concentration of B in the shoot, and high total B uptake. Results showed that none of tested genotypes could not be recommended for breeding process to tolerance for B toxicity. [Projekat Ministarstva nauke Republike Srbije, br. OI 173028

  16. Compliance status

    International Nuclear Information System (INIS)

    Black, D.G.


    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

  17. Compliance status

    Energy Technology Data Exchange (ETDEWEB)

    Black, D.G.


    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.


    Indian Academy of Sciences (India)

    First page Back Continue Last page Graphics. STATUS REPORT. Raman scattering observed – 90, 135, 180 degrees and back scattering. Traditionally specific angle dependence to learn about polarization response. Learn molecular information from the surface or materials just below the surface (upto 12 mm depth) ...

  19. An Affymetrix Microarray Design for Microbial Genotyping (United States)


    les échantillons qui ne se prêtent pas aux méthodes culturales de la microbiologie classique. La puce à ADN est une technologie qui permet la... area of microbial genotyping there are multiple platforms that can identify one or a few microbial targets in a single assay iteration. For most

  20. Human papillomavirus genotyping by multiplex pyrosequencing in ...

    Indian Academy of Sciences (India)


    malignant cervical samples ... low- and high-risk HPV genotypes without identifying ... Since these samples were not from “healthy .... major capsid protein, any variation in its coding sequence is .... worldwide: a meta-analysis; Br. J. Cancer 88 63–73.

  1. Physicochemical and sensorial quality of banana genotypes

    Directory of Open Access Journals (Sweden)

    Ronielli Cardoso Reis


    Full Text Available Despite the diversity of banana varieties in Brazil, only a few cultivars have the proper agronomic traits and fruit quality for commercial exploitation. This study aimed at evaluating the physicochemical traits and sensorial acceptance of banana genotypes, in order to identify those with potential for commercial growing. Six improved banana genotypes were assessed (BRS Maravilha, PC 0101, FHIA 18, TM 2803, YB 4203 and BRS Caipira, as well as three commercial cultivars (Grand Naine, Pacovan and Prata Anã. Analyses of peel and pulp color, peel thickness, pulp yield, moisture, pH, soluble solids, titratable acidity, total carotenoids and sensorial acceptance were performed. The BRS Maravilha, FHIA 18, YB 4203 and BRS Caipira genotypes presented physicochemical traits similar to the Grand Naine, Pacovan and Prata Anã commercial cultivars. The BRS Maravilha and TM 2803 genotypes had sensorial acceptance similar to the Prata Anã and Grand Naine cultivars, and are therefore promising for commercial growing, with the advantage of being resistant to the black Sigatoka and Panama disease.

  2. Genotyping of human pappilomavirus in cervical precancerous ...

    African Journals Online (AJOL)

    Background: Cervical cancer caused by human papilloma virus (HPV), is the second most common cancer for women. This cancer is distributed worldwide, with ~80% of cases are found in the developing countries. In Indonesia, data of HPV genotypes are still limited and do not represent all regions of the country. Thus ...

  3. Cryptosporidium Pig Genotype II in Immunocompetent Man

    Czech Academy of Sciences Publication Activity Database

    Kváč, Martin; Květoňová, Dana; Sak, Bohumil; Ditrich, Oleg


    Roč. 15, č. 6 (2009), s. 982-983 ISSN 1080-6040 R&D Projects: GA ČR GP523/07/P117 Institutional research plan: CEZ:AV0Z60220518 Keywords : immunocompetent patients * cryptosporidiosis * Cryptosporidium pig genotype II Subject RIV: GJ - Animal Vermins ; Diseases , Veterinary Medicine Impact factor: 6.794, year: 2009

  4. Morphometric characteristics of Lotus corniculatus L. genotypes ...

    African Journals Online (AJOL)

    The aim of this study was to examine the degree of variability in morphological and agronomic characteristics of 20 Lotus corniculatus L. local genotypes, and also to set aside germplasm that will be used as a source of genetic basis for improvement of the studied properties. In poor quality soils, L. corniculatus L. plays an ...

  5. Genotype X Fertility Interactions in Seedling Sweetgum (United States)

    Scott X. Chang; Daniel J. Robison


    Genotype x fertility interactions may affect the suitability of sweetgum (Liquidambar styraciflua L.) for specific sites or the efficiency of nutrient use. To gain a better understanding of these interactions, 2-year-old sweetgum seedlings from two half-sib families were tested for growth response to N (0 and 100 kg/ha equivalent) and P (0 and 50 kg...

  6. (AMMI) and genotype by environment interaction

    African Journals Online (AJOL)



    Apr 30, 2014 ... Background and justification: Lack of stable high yielding cultivars is one ... of advanced finger millet genotypes evaluated in multiple environments, and (ii) identify stable high yielding .... for interaction principal component axis (IPCA) n, γgn ..... Table 2: Analysis of variance for grain yield using AMMI model.

  7. Captive-bred neotropical birds diagnosed with Cryptosporidium Avian genotype III. (United States)

    Silva Novaes, Ricardo; Pires, Marcus Sandes; Sudré, Adriana Pittella; Bergamo do Bomfim, Teresa Cristina


    Currently, there are only three valid species of Cryptosporidium infecting avian hosts, namely, Cryptosporidium meleagridis, Cryptosporidium baileyi, Cryptosporidium galli and Cryptosporidium avium in addition to 12 genotypes of unknown species status. The objectives of this study were to microscopically diagnose the presence of Cryptosporidium in birds from a commercial aviary located in Rio de Janeiro, Brazil; genotypically characterize species and/or genotypes of genus Cryptosporidum; and conduct sequencing and phylogenetic analyses to compare the obtained DNA sequences with those deposited in GenBank. A total of 85 fecal samples were collected from wild captive-bred birds: 48 of family Psittacidae and 37 of family Ramphastidae. Initially, a search for the presence of Cryptosporidium sp. oocysts was conducted using the centrifugal-flotation in saturated sugar solution technique, after that, the collected samples were analyzed microscopically. Cryptosporidium infections were only detected in 24.32% of samples belonging to the family Ramphastidae. DNA was extracted from positive samples and molecular diagnostics was applied targeting the 18S rRNA gene, followed by sequencing and phylogenetic analysis. The Cryptosporidium Avian genotype III was diagnosed in this study more closely related to the gastric species. This is the first record of Cryptosporidium Avian genotype III in order Piciformes and family Ramphastidae, where three host species (Ramphastus toco, Ramphastus tucanus, and Pteroglossus bailloni) were positive for the etiologic agent. Based on the molecular data obtained, these wild birds raised in captivity do not represent a source of human cryptosporidiosis, considering that Cryptosporidium Avian genotype III does not constitute a zoonosis. Copyright © 2017. Published by Elsevier B.V.

  8. BDNF genotype interacts with motor-function to influence rehabilitation responsiveness post-stroke

    Directory of Open Access Journals (Sweden)

    Christine T Shiner


    Full Text Available Background. Persistent motor impairment is common but highly heterogeneous post-stroke. Genetic polymorphisms, including those identified on the brain derived neurotrophic factor (BDNF and apolipoprotein E (APOE genes, may contribute to this variability by limiting the capacity for use-dependent neuroplasticity, and hence rehabilitation responsiveness.Objective. To determine whether BDNF and APOE genotypes influence motor improvement facilitated by post-stroke upper-limb rehabilitation. Methods. BDNF Val66Met and APOE isoform genotypes were determined using leukocyte DNA for 55 community-dwelling patients 2-123 months post-stroke. All patients completed a dose-matched upper-limb rehabilitation program of either Wii-based Movement Therapy or Constraint-induced Movement Therapy. Upper-limb motor-function was assessed pre- and post-therapy using a suite of functional measures. Results. Motor-function improved for all patients post-therapy, with no difference between therapy groups. In the pooled data, there was no significant effect of BDNF or APOE genotype on motor-function at baseline, or following the intervention. However, a significant interaction between the level of residual motor-function and BDNF genotype was identified (p=0.029, whereby post-therapy improvement was significantly less for Met allele carriers with moderate and high, but not low motor-function. There was no significant association between APOE genotype and therapy outcomes. Conclusions. This study identified a novel interaction between the BDNF Val66Met polymorphism, motor-function status and the magnitude of improvement with rehabilitation in chronic stroke. This polymorphism does not preclude, but may reduce, the magnitude of motor improvement with therapy, particularly for patients with higher but not lower residual motor-function. BDNF genotype should be considered in the design and interpretation of clinical trials.

  9. Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping. (United States)

    Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung


    The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018 Elsevier Inc. All rights reserved.

  10. Hereditary Hemochromatosis (HFE genotypes in heart failure: Relation to etiology and prognosis

    Directory of Open Access Journals (Sweden)

    Torp-Pedersen Christian


    Full Text Available Abstract Background It is believed that hereditary hemochromatosis (HH might play a role in cardiac disease (heart failure (HF and ischemia. Mutations within several genes are HH-associated, the most common being the HFE gene. In a large cohort of HF patients, we sought to determine the etiological role and the prognostic significance of HFE genotypes. Methods We studied 667 HF patients (72.7% men with depressed systolic function, enrolled in a multicentre trial with a follow-up period of up to 5 years. All were genotyped for the known HFE variants C282Y, H63D and S65C. Results The genotype and allele frequencies in the HF group were similar to the frequencies determined in the general Danish population. In multivariable analysis mortality was not predicted by C282Y-carrier status (HR 1.2, 95% CI: 0.8-1.7; H63D-carrier status (HR 1.0, 95% CI: 0.7-1.3; nor S65C-carrier status (HR 1.2, 95% CI: 0.7-2.0. We identified 27 (4.1% homozygous or compound heterozygous carriers of HFE variants. None of these carriers had a clinical presentation suggesting hemochromatosis, but hemoglobin and ferritin levels were higher than in the rest of the cohort. Furthermore, a trend towards reduced mortality was seen in this group in univariate analyses (HR 0.4, 95% CI: 0.2-0.9, p = 0.03, but not in multivariate (HR 0.5, 95% CI: 0.2-1.2. Conclusion HFE genotypes do not seem to be a significant contributor to the etiology of heart failure in Denmark. HFE variants do not affect mortality in HF.

  11. In Vitro Conservation of Sweet Potato Genotypes

    Directory of Open Access Journals (Sweden)

    Maria de Fátima Arrigoni-Blank


    Full Text Available 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.

  12. The potential of plant viruses to promote genotypic diversity via genotype x environment interactions

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Stuefer, Josef F.


    † Background and Aims Genotype by environment (G × E) interactions are important for the long-term persistence of plant species in heterogeneous environments. It has often been suggested that disease is a key factor for the maintenance of genotypic diversity in plant populations. However, empirical...... and the G × E interactions were examined with respect to genotypespecific plant responses to WClMV infection. Thus, the environment is defined as the presence or absence of the virus. † Key Results WClMV had a negative effect on plant performance as shown by a decrease in biomass and number of ramets...... evidence for this contention is scarce. Here virus infection is proposed as a possible candidate for maintaining genotypic diversity in their host plants. † Methods The effects of White clover mosaic virus (WClMV) on the performance and development of different Trifolium repens genotypes were analysed...

  13. Genotypic Variation of Early Maturing Soybean Genotypes for Phosphorus Utilization Efficiency under Field Grown Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Abaidoo, R. C. [Kwame Nkrumah University of Technology, Kumasi (Ghana); International Institute of Tropical Agriculture, Ibadan (Nigeria); Opoku, A.; Boahen, S. [Kwame Nkrumah University of Technology, Kumasi (Ghana); Dare, M. O. [Federal University of Agriculture, Abeokuta (Nigeria)


    Variability in the utilization of phosphorus (P) by 64 early-maturing soybean (Glycine max L. Merr.) genotypes under low-P soil conditions were evaluated in 2009 and 2010 at Shika, Nigeria. Fifteen phenotypic variables; number of nodules, nodule dry weight, grain yield, plant biomass, total biomass, biomass N and P content, Phosphorus Utilization Index (PUI), shoot P Utilization efficiency (PUIS), grain P Utilization efficiency (PUIG), Harvest Index (HI), Biological N fixed (BNF), total N fixed and N and P uptake were measured. The four clusters revealed by cluster analysis were basically divided along (1) plant biomass and uptake, (2) nutrient acquisition and utilization and (3) nodulation components. Three early maturing genotypes, TGx1842-14E, TGx1912-11F and TGx1913-5F, were identified as having high P utilization index and low P uptake. These genotypes could be a potential source for breeding for P use efficiency in early maturing soybean genotypes. (author)

  14. Effect of lifestyle factors on plasma total homocysteine concentrations in relation to MTHFR(C677T) genotype. Inter99 (7)

    DEFF Research Database (Denmark)

    Husemoen, L L N; Thomsen, T F; Fenger, M


    a Fluorescent Polarization Immuno Assay. MTHFR-genotype was determined by PCR and RFLP analysis. Information about lifestyle factors was obtained from a self-administered questionnaire. RESULTS: Daily smoking, less healthy dietary habits, and coffee drinking were associated with elevated tHcy concentrations...... independent of other determinants. Wine consumption was related to tHcy in a J-shaped manner, whereas beer consumption was negatively associated with tHcy after multiple adjustments. Interaction was observed between smoking status and MTHFR-genotype, smoking status and sex, and beer consumption and age....... The effect of smoking was more pronounced in persons with the TT genotype and in women. The effect of beer consumption was more pronounced at younger than at older ages. CONCLUSIONS: Smoking status, dietary habits, coffee intake, wine, and beer consumption were major lifestyle determinants of tHcy. Changes...

  15. Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps. (United States)

    Manrubia, Susanna; Cuesta, José A


    An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences. Here, we analytically derive the distribution of genotype network sizes for a hierarchy of models which successively incorporate features of increasingly realistic sequence-to-structure genotype-phenotype maps. The main feature of these models relies on the characterization of each phenotype through a prototypical sequence whose sites admit a variable fraction of letters of the alphabet. Our models interpolate between two limit distributions: a power-law distribution, when the ordering of sites in the prototypical sequence is strongly constrained, and a lognormal distribution, as suggested for RNA, when different orderings of the same set of sites yield different phenotypes. Our main result is the qualitative and quantitative identification of those features of sequence-to-structure maps that lead to different distributions of genotype network sizes. © 2017 The Author(s).

  16. Status Epilepticus (United States)

    Seinfeld, Syndi; Goodkin, Howard P.; Shinnar, Shlomo


    Although the majority of seizures are brief and cause no long-term consequences, a subset is sufficiently prolonged that long-term consequences can result. These very prolonged seizures are termed “status epilepticus” (SE) and are considered a neurological emergency. The clinical presentation of SE can be diverse. SE can occur at any age but most commonly occurs in the very young and the very old. There are numerous studies on SE in animals in which the pathophysiology, medication responses, and pathology can be rigorously studied in a controlled fashion. Human data are consistent with the animal data. In particular, febrile status epilepticus (FSE), a form of SE common in young children, is associated with injury to the hippocampus and subsequent temporal lobe epilepsy (TLE) in both animals and humans. PMID:26931807

  17. Pollen diversity, viability and floral structure of some Musa genotypes

    African Journals Online (AJOL)

    Pollen diversity, viability and floral structure of some Musa genotypes. ... This experiment was designed to study the floral structure, pollen morphology and the potential pollen viability of five Musa genotypes obtained ... HOW TO USE AJOL.

  18. Behavior of durum wheat genotypes under normal irrigation and ...

    African Journals Online (AJOL)

    Behavior of durum wheat genotypes under normal irrigation and drought stress conditions in the greenhouse. ... African Journal of Biotechnology ... Genotypes were grouped in cluster analysis (using Ward's method) based on Yp, Ys and ...

  19. Genetic variability in cowpea (Vigna unguiculata (L.) Walp.) genotypes

    African Journals Online (AJOL)

    sive protein in human diets with grains containing about. 23–25% protein ... Keywords: heritability, phenotype, principal component analysis, variance. Introduction .... be due to genotype, environment, and the interaction of genotype and ...

  20. magnitude of genotype x environment interaction for bacterial leaf

    African Journals Online (AJOL)


    African Crop Science Journal, Vol. ... effects of treatments into genotype, environment, and genotype x environment (G x E) interactions. Results .... method is economically effective (Niño-Liu et al., ..... This phenomenon indicated differences in.

  1. Genotype 3 is the predominant hepatitis C genotype in a multi-ethnic Asian population in Malaysia. (United States)

    Ho, Shiaw-Hooi; Ng, Kee-Peng; Kaur, Harvinder; Goh, Khean-Lee


    Genotypes of hepatitis C virus (HCV) are distributed differently across the world. There is a paucity of such data in a multi-ethnic Asian population like Malaysia. The objectives of this study were to determine the distribution of HCV genotypes between major ethnic groups and to ascertain their association with basic demographic variables like age and gender. This was a cross-sectional prospective study conducted from September 2007 to September 2013. Consecutive patients who were detected to have anti-HCV antibodies in the University of Malaya Medical Centre were included and tested for the presence of HCV RNA using Roche Cobas Amplicor Analyzer and HCV genotype using Roche single Linear Array HCV Genotyping strip. Five hundred and ninety-six subjects were found to have positive anti-HCV antibodies during this period of time. However, only 396 (66.4%) were HCV RNA positive and included in the final analysis. Our results showed that HCV genotype 3 was the predominant genotype with overall frequency of 61.9% followed by genotypes 1 (35.9%), 2 (1.8%) and 6 (0.5%). There was a slightly higher prevalence of HCV genotype 3 among the Malays when compared to the Chinese (P=0.043). No other statistical significant differences were observed in the distribution of HCV genotypes among the major ethnic groups. There was also no association between the predominant genotypes and basic demographic variables. In a multi-ethnic Asian society in Malaysia, genotype 3 is the predominant genotype among all the major ethnic groups with genotype 1 as the second commonest genotype. Both genotypes 2 and 6 are uncommon. Neither genotype 4 nor 5 was detected. There is no identification of HCV genotype according to ethnic origin, age and gender.

  2. Sleep duration, depression, and oxytocinergic genotype influence prepulse inhibition of the startle reflex in postpartum women. (United States)

    Comasco, Erika; Gulinello, Maria; Hellgren, Charlotte; Skalkidou, Alkistis; Sylven, Sara; Sundström-Poromaa, Inger


    The postpartum period is characterized by a post-withdrawal hormonal status, sleep deprivation, and susceptibility to affective disorders. Postpartum mothering involves automatic and attentional processes to screen out new external as well as internal stimuli. The present study investigated sensorimotor gating in relation to sleep duration, depression, as well as catecholaminergic and oxytocinergic genotypes in postpartum women. Prepulse inhibition (PPI) of the startle reflex and startle reactivity were assessed two months postpartum in 141 healthy and 29 depressed women. The catechol-O-methyltransferase (COMT) Val158Met, and oxytocin receptor (OXTR) rs237885 and rs53576 polymorphisms were genotyped, and data on sleep duration were collected. Short sleep duration (less than four hours in the preceding night) and postpartum depression were independently associated with lower PPI. Also, women with postpartum depression had higher startle reactivity in comparison with controls. The OXTR rs237885 genotype was related to PPI in an allele dose-dependent mode, with T/T healthy postpartum women carriers displaying the lowest PPI. Reduced sensorimotor gating was associated with sleep deprivation and depressive symptoms during the postpartum period. Individual neurophysiological vulnerability might be mediated by oxytocinergic genotype which relates to bonding and stress response. These findings implicate the putative relevance of lower PPI of the startle response as an objective physiological correlate of liability to postpartum depression. Copyright © 2016 Elsevier B.V. and ECNP. All rights reserved.

  3. Association Between Early Childhood Caries and Colonization with Streptococcus mutans Genotypes From Mothers. (United States)

    Childers, Noel K; Momeni, Stephanie S; Whiddon, Jennifer; Cheon, Kyounga; Cutter, Gary R; Wiener, Howard W; Ghazal, Tariq S; Ruby, John D; Moser, Stephen A


    The purpose of this study was to evaluate Streptococcus mutans genotypes (GT) between mother and child (M-C) in a high caries risk cohort to explore the association with early childhood caries (ECC). Sixty-nine infants (each approximately one year old) had periodic oral examinations (dmfs) and microbial samples collected from dental plaque, saliva, and other oral surfaces. Their mothers had an examination and plaque collected. S mutans isolates were genotyped using repetitive extragenic palindromic-PCR (rep-PCR). Statistical analyses were conducted for associations of S mutans in M-C dyads with caries outcomes. Twenty-seven S mutans genotypes (GT) from 3,414 isolates were identified. M-C were categorized as GT match (n equals 40) or no-match (n equals 29). When modeling the severity of ECC at 36 months (approximately four years old), the estimated dmfs in the match group was 2.61 times that of the no-match group (P=.014). Colonization of children with Streptococcus mutans genotypes that matched with mothers was shown to be highly associated with early childhood caries. Although the data suggest vertical transmission of S mutans in 40 of 69 children that shared GT with their mother, it is possible that other individuals transmitted the S mutans. Nonetheless, these findings support the importance of the mother's oral microbial status as a contributing influence to their children's oral health.

  4. HFE gene mutations and iron status of Brazilian blood donors. (United States)

    Santos, P C J L; Cançado, R D; Terada, C T; Rostelato, S; Gonzales, I; Hirata, R D C; Hirata, M H; Chiattone, C S; Guerra-Shinohara, E M


    Mutations of the HFE and TFR2 genes have been associated with iron overload. HFE and TFR2 mutations were assessed in blood donors, and the relationship with iron status was evaluated. Subjects (N = 542) were recruited at the Hemocentro da Santa Casa de São Paulo, São Paulo, Brazil. Iron status was not influenced by HFE mutations in women and was independent of blood donation frequency. In contrast, men carrying the HFE 282CY genotype had lower total iron-binding capacity (TIBC) than HFE 282CC genotype carriers. Men who donated blood for the first time and were carriers of the HFE 282CY genotype had higher transferrin saturation values and lower TIBC concentrations than those with the homozygous wild genotype for the HFE C282Y mutation. Moreover, in this group of blood donors, carriers of HFE 63DD plus 63HD genotypes had higher serum ferritin values than those with the homozygous wild genotype for HFE H63D mutation. Multiple linear regression analysis showed that HFE 282CY leads to a 17.21% increase (P = 0.018) and a 83.65% decrease (P = 0.007) in transferrin saturation and TIBC, respectively. In addition, serum ferritin is influenced by age (3.91%, P = 0.001) and the HFE 63HD plus DD genotype (55.84%, P = 0.021). In conclusion, the HFE 282Y and 65C alleles were rare, while the HFE 63D allele was frequent in Brazilian blood donors. The HFE C282Y and H63D mutations were associated with alterations in iron status in blood donors in a gender-dependent manner.

  5. HFE gene mutations and iron status of Brazilian blood donors

    Directory of Open Access Journals (Sweden)

    P.C.J.L. Santos


    Full Text Available Mutations of the HFE and TFR2 genes have been associated with iron overload. HFE and TFR2 mutations were assessed in blood donors, and the relationship with iron status was evaluated. Subjects (N = 542 were recruited at the Hemocentro da Santa Casa de São Paulo, São Paulo, Brazil. Iron status was not influenced by HFE mutations in women and was independent of blood donation frequency. In contrast, men carrying the HFE 282CY genotype had lower total iron-binding capacity (TIBC than HFE 282CC genotype carriers. Men who donated blood for the first time and were carriers of the HFE 282CY genotype had higher transferrin saturation values and lower TIBC concentrations than those with the homozygous wild genotype for the HFE C282Y mutation. Moreover, in this group of blood donors, carriers of HFE 63DD plus 63HD genotypes had higher serum ferritin values than those with the homozygous wild genotype for HFE H63D mutation. Multiple linear regression analysis showed that HFE 282CY leads to a 17.21% increase (P = 0.018 and a 83.65% decrease (P = 0.007 in transferrin saturation and TIBC, respectively. In addition, serum ferritin is influenced by age (3.91%, P = 0.001 and the HFE 63HD plus DD genotype (55.84%, P = 0.021. In conclusion, the HFE 282Y and 65C alleles were rare, while the HFE 63D allele was frequent in Brazilian blood donors. The HFE C282Y and H63D mutations were associated with alterations in iron status in blood donors in a gender-dependent manner.

  6. Determinants of selenium status in healthy adults

    Directory of Open Access Journals (Sweden)

    Hoeg Antonia


    Full Text Available Abstract Background Selenium (Se status in non-deficient subjects is typically assessed by the Se contents of plasma/serum. That pool comprises two functional, specific selenoprotein components and at least one non-functional, non-specific components which respond differently to changes in Se intake. A more informative means of characterizing Se status in non-deficient individuals is needed. Methods Multiple biomarkers of Se status (plasma Se, serum selenoprotein P [SEPP1], plasma glutathione peroxidase activity [GPX3], buccal cell Se, urinary Se were evaluated in relation to selenoprotein genotypes (GPX1, GPX3, SEPP1, SEP15, dietary Se intake, and parameters of single-carbon metabolism in a cohort of healthy, non-Se-deficient men (n = 106 and women (n = 155. Conclusions Plasma Se concentration was 142.0 ± 23.5 ng/ml, with GPX3 and serum-derived SEPP1 calculated to comprise 20% and 34%, respectively, of that total. The balance, comprised of non-specific components, accounted for virtually all of the interindividual variation in total plasma Se. Buccal cell Se was associated with age and plasma homocysteine (hCys, but not plasma Se. SEPP1 showed a quadratic relationship with body mass index, peaking at BMI 25-30. Urinary Se was greater in women than men, and was associated with metabolic body weight (kg0.75, plasma folate, vitamin B12 and hCys (negatively. One GPX1 genotype (679T/T was associated with significantly lower plasma Se levels than other allelic variants. Selenium intake, estimated from food frequency questionnaires, did not predict Se status as indicated by any biomarker. These results show that genotype, methyl-group status and BMI contribute to variation in Se biomarkers in Se-adequate individuals.

  7. HPV genotypes in invasive cervical cancer in Danish women

    DEFF Research Database (Denmark)

    Kirschner, Benny; Junge, Jette; Holl, Katsiaryna


    Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer.......Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer....

  8. Evaluation of promising sweetpotato genotypes for high altitude ...

    African Journals Online (AJOL)

    The trials were set up to identify sweetpotato genotypes with adaptation to highland agroecologies with special reference to resistance to Ahemaria blight ... growth and at harvest, four genotypes and the local check, Magabari, bad high levels of resistance toA/Jemaria blight. Eight genotypes had total storage root yield ...

  9. Hepatitis B virus Genotypes in West Azarbayjan Province, Northwest Iran

    Directory of Open Access Journals (Sweden)

    Mohammad Hasan Khadem Ansari


    CONCLUSIONS: The results reveal that D genotype is the main genotype of HBV in West Azarbayjan province. Presence of this genotype conformed with the low rate of acute liver diseases caused by hepatitis B chronic infection, cirrhosis of the liver and hepatocellular carcinoma.

  10. Genotype-based personalised nutrition for obesity prevention and ...

    African Journals Online (AJOL)

    Typically, genotype-based personalised nutrition involves genotyping for a number of susceptibility SNPs associated with the prevention, or management, of a particular disease. Dietary advice is then personalised to the individual's genotype to ensure optimal prevention or treatment outcomes. To ensure evidence-based ...

  11. Introduction to a special issue on genotype by environment interaction (United States)

    Expression of a phenotype is a function of the genotype, the environment, and the differential sensitivity of certain genotypes to different environments, also known as genotype by environment (G × E) interaction. This special issue of Crop Science includes a collection of manuscripts that reviews t...

  12. Core Gene Expression and Association of Genotypes with Viral ...

    African Journals Online (AJOL)

    Purpose: To determine genotypic distribution, ribonucleic acid (RNA) RNA viral load and express core gene from Hepatitis C Virus (HCV) infected patients in Punjab, Pakistan. Methods: A total of 1690 HCV RNA positive patients were included in the study. HCV genotyping was tested by type-specific genotyping assay, viral ...

  13. Effect of Genotype and Age on Some Morphometric, Body Linear ...

    African Journals Online (AJOL)

    A population of 231 roosters of the Nigerian indigenous chickens of normal feathered frizzle feathered and naked neck genotypes was evaluated for the effect of genotype and age on some morphometric body linear measurements and semen characteristics of three Nigerian chicken genotypes. 20 roosters from each ...

  14. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system. (United States)


    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 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 (DNA...

  15. Genotype x Environment Interaction for Tuber Yield, Dry Matter ...

    African Journals Online (AJOL)

    A study was conducted to determine stability of tuber yield, dry matter content and specific gravity, and the nature and magnitude of genotype x environment (G x E) interaction in elite tetraploid potato genotypes. Eleven potato genotypes including two standard checks were evaluated in the eastern part of Ethiopia at ...

  16. [Evaluation of hepatitis B virus genotyping EIA kit]. (United States)

    Tanaka, Yasuhito; Sugauchi, Fuminaka; Matsuuraa, Kentaro; Naganuma, Hatsue; Tatematsu, Kanako; Takagi, Kazumi; Hiramatsu, Kumiko; Kani, Satomi; Gotoh, Takaaki; Wakimoto, Yukio; Mizokami, Masashi


    Clinical significance of Hepatitis B virus(HBV) genotyping is increasingly recognized. The aim of this study was to evaluate reproducibility, accuracy, and sensitivity of an enzyme immunoassay (EIA) based HBV genotyping kit, which designed to discriminate between genotypes to A, B, C, or D by detecting genotype-specific epitopes in PreS2 region. Using the four genotypes panels, the EIA demonstrated complete inter and intra-assay genotyping reproducibility. Serum specimens had stable results after 8 days at 4 degrees C, or 10 cycles of freezing-thawing. In 91 samples that have been genotyped by DNA sequencing, 87(95.6%) were in complete accordance with EIA genotyping. Of examined 344 HBsAg-positive serum specimens, genotypes A, B, C and D were determined in 26 (7.6%), 62 (18.0%), 228 (66.3%), and 9 (2.6%) cases, respectively. Of 19 (5.5%) specimens unclassified by the EIA, 13 were found to have low titer of HBsAg concentration (< 3 IU/ml), and the other 5 had amino acid mutations or deletions within targeted PreS2 epitopes. The EIA allowed genotyping even in HBV DNA negative samples (96.2%). In conclusion, HBV genotype EIA is reliable, sensitive and easy assay for HBV genotyping. The assay would be useful for clinical use.

  17. Genotype by environment interactions and yield stability of stem ...

    African Journals Online (AJOL)

    In a maize breeding program, potential genotypes are usually evaluated in different environments before desirable ones are selected. Genotype x environment (G x E) interaction is associated with the differential performance of genotypes tested at different locations and in different years, and influences selection and ...

  18. Genotype x environment interaction and stability analysis for yield ...

    African Journals Online (AJOL)

    Chickpea is the major pulse crop cultivated in Ethiopia. However, its production is constrained due to genotype instability and environmental variability. This research was carried out to examine the magnitude of environmental effect on yield of chickpea genotypes and to investigate the stability and adaptability of genotypes ...

  19. Reactions of some potato genotypes to late blight in Cameroon ...

    African Journals Online (AJOL)

    Reactions of some potato genotypes to late blight in Cameroon. D. K. Njualem, P. Demo, H. A. Mendoza, J. T. Koi, S. F. Nana. Abstract. Field experiments were conducted in Cameroon in 1995 and 1996 to evaluate reactions of different potato genotypes to late blight. There were significant differences among genotypes for ...

  20. Association of OCT derived drusen measurements with AMD associated-genotypic SNPs in Amish population. (United States)

    Chavali, Venkata Ramana Murthy; Diniz, Bruno; Huang, Jiayan; Ying, Gui-Shuang; Sadda, SriniVas R; Stambolian, Dwight

    To investigate the association of OCT derived drusen measures in Amish age-related macular degeneration (AMD) patients with known loci for macular degeneration. Members of the Old Order Amish community in Pennsylvania ages 50 and older were assessed for drusen area, volume and regions of retinal pigment epithelium (RPE) atrophy using a Cirrus High- Definition-OCT. Measurements were obtained in the macula region within a central circle (CC) of 3 mm diameter and a surrounding perifoveal ring (PR) of 3 to 5 mm diameter using the Cirrus OCT RPE analysis software. Other demographic information including age, gender and smoking status were collected. Study subjects were further genotyped to determine their risk for the AMD associated SNPs in SYN3, LIPC, ARMS2, C3, CFB, CETP, CFI and CFH genes using TaqMan genotyping assays. The association of genotypes with OCT measures were assessed using linear trend p-values calculated from univariate and multivariate generalized linear models. 432 eyes were included in the analysis. Multivariate analysis (adjusted by age, gender and smoking status) confirmed the known significant association between AMD and macular drusen with the number of CFH risk alleles for drusen area (area increased 0.12 mm 2 for a risk allele increase, pAmish AMD population.

  1. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

    Directory of Open Access Journals (Sweden)

    Didion John P


    Full Text Available Abstract Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing

  2. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

    Grant, Jon E; Leppink, Eric W; Redden, Sarah A


    adjustment and delay aversion) and the Spatial Working Memory task (total errors). This study adds to the growing literature on the role of COMT in impulsive behaviors by showing that the Val/Val genotype was associated with specific clinical and cognitive elements among young adults who gamble......Neuropsychological studies of adults with problem gambling indicate impairments across multiple cognitive domains. Catechol-O-methyltransferase (COMT) plays a unique role in the regulation of dopamine in the prefrontal cortex, and has been implicated in the cognitive dysfunction evident in problem...... gambling. This study examined adults with varying levels of gambling behavior to determine whether COMT genotype was associated with differences in gambling symptoms and cognitive functioning. 260 non-treatment-seeking adults aged 18-29 years with varying degrees of gambling behavior provided saliva...


    Directory of Open Access Journals (Sweden)

    Irina Ancu


    Full Text Available In Romania the blueberry breeding program started in 1982 and till now was conducted by dr. Paulina Mladin. For inducing the variability, different genetic resources of American blueberry cultivars (V. corymbosum, V. angustifolium were involved in a high number of crosses. For identify the genotype with the best fruit quality, some biometric quality indicators (average fruit weight, size index and basically chemical compounds of fruits including ascorbic acid, dry matter, ash, soluble solids, total sugar, titratable acidity, tanoid substances, pectic substances, protein crude, phosphorus and potassium were determined. Of the eleven chemical studied properties who reflected the fruits quality, for five of them were found no statistically significant differences. The purpose of this paper work was to evaluate fruit quality and to identify the valuable genotypes resulted from Romanian blueberry breeding program.

  4. BCL2 genotypes and prostate cancer survival

    Energy Technology Data Exchange (ETDEWEB)

    Renner, Wilfried [Medical University of Graz, Clinical Institute of Medical and Chemical Laboratory Diagnostics, Graz (Austria); Langsenlehner, Uwe [GKK Outpatient Department, Division of Internal Medicine, Graz (Austria); Krenn-Pilko, Sabine; Langsenlehner, Tanja [Medical University of Graz, Department of Therapeutic Radiology and Oncology, Graz (Austria); Eder, Petra [University Hospital Wuerzburg, Department of Internal Medicine I, Wuerzburg (Germany)


    The antiapoptotic B-cell lymphoma 2 (BCL2) gene is a key player in cancer development and progression. A functional single-nucleotide polymorphism (c.-938C>A, rs2279115) in the inhibitory P2 BCL2 gene promoter has been associated with clinical outcomes in various types of cancer. Aim of the present study was to analyze the role of BCL2-938C>A genotypes in prostate cancer mortality. The association between BCL2-938C>A (rs2279115) genotypes and prostate cancer outcome was studied within the prospective PROCAGENE study comprising 702 prostate cancer patients. During a median follow-up time of 92 months, 120 (17.1%) patients died. A univariate Cox regression model showed a significant association of the CC genotype with reduced cancer-specific survival (CSS; hazard ratio, HR, 2.13, 95% confidence interval, CI, 1.10-4.12; p = 0.024) and overall survival (OS; HR 2.34, 95% CI 1.58-3.47; p < 0.001). In a multivariate Cox regression model including age at diagnosis, risk group, and androgen deprivation therapy, the CC genotype remained a significant predictor of poor CSS (HR 2.05, 95% CI 1.05-3.99; p = 0.034) and OS (HR 2.25, 95% CI 1.51-3.36; p < 0.001). This study provides evidence that the homozygous BCL2-938 CC genotype is associated with OS and C in prostate cancer patients. (orig.) [German] Das antiapoptotische Gen B cell lymphoma 2 (BCL2) spielt eine Schluesselrolle in der Entstehung und Progression von Krebserkrankungen. Ein funktioneller Einzelnukleotid-Polymorphismus (c.-938C>A, rs2279115) im inhibitorischen P2-BCL2-Promotor wurde mit dem klinischen Outcome verschiedener Krebserkrankungen verknuepft. Ziel der vorliegenden Studie war die Untersuchung der Rolle von BCL2-938C>A-Genotypen fuer die Mortalitaet bei Patienten mit Prostatakarzinom. Der Zusammenhang zwischen BCL2-938C>A-Genotypen (rs2279115) und dem Outcome bei Prostatakrebs wurde in der prospektiven PROCAGENE-Studie, die 702 Patienten mit Prostatakarzinom umfasste, untersucht. Waehrend der medianen

  5. Comparative characteristics of immune answers indicators depending on the replicative activity and genotype of hepatitis c virus

    Directory of Open Access Journals (Sweden)

    Олеся Василівна Гололобова


    Full Text Available Aim. To analyze the character of changes and disorders of immune system with the help of complex study of indicators of cellular and humor section of immunity, cytokine status in patients with HCV-infection taking into account the replicative activity, genotype of virus and to formulate the possible causes of chronization.Methods. There were examined 155 patients with HCV-infection. An acute hepatitis C AHC was fixed in 23,9 %, chronic hepatitis C (CHC– in 76,1 %, 18–70 years old. Among examined patients with AHC and CHC prevailed men (67,6 and 72 % respectively. Diagnosis was set on the base of clinic and amnestic, epidemiologic, laboratory and instrumental data. Epidemiologic verification of diagnosis was realized by detection the specific serologic markers of HC (anti-HCV (sum, anti-HCV IgM and Ig G, anti-HCV core and anti-HCV NS-3, NS-4, NS-5 in blood serum using ELISA method. Molecular and genetic studies that included definition of replicative activity of HCV evaluated on the base of detection of RNA HCV in blood serum using the qualitative PCR method were carried out in 126 patients (31 with AHC and 95 with CHC. At the same time RNA of HCV was detected in peripheral blood in all (31 patients with AHC and in 74 (77,89 % patients with CHC. Using the method of restriction analysis we carried out the genetic typing of HCV in 90 patients with AHC and 60 with CHC. We carried out the comparative characteristics of the content of immunologic indicators in 45 (75 % patients with CHC with positive and 15 (25 % patients with negative results of PCR-study (polymerase chain reaction of HCV RNA in blood. For detection of regularities of changes of immune status depending on virus genotype there was carried out the comparative assessment of the content of immunologic indicators in patients with AHC and CHC with the most widespread genotypes of HVC– 1b and 3a. Immunologic studies included the definitions of the main subpopulations of lymphocytes

  6. Novel approach for CES1 genotyping

    DEFF Research Database (Denmark)

    Bjerre, Ditte; Berg Rasmussen, Henrik


    AIM: Development of a specific procedure for genotyping of CES1A1 (CES1) and CES1A2, a hybrid of CES1A1 and the pseudogene CES1P1. MATERIALS & METHODS: The number of CES1A1 and CES1A2 copies and that of CES1P1 were determined using real-time PCR. Long range PCRs followed by secondary PCRs allowed...

  7. Screening cotton genotypes for seedling drought tolerance

    Directory of Open Access Journals (Sweden)

    Penna Julio C. Viglioni


    Full Text Available The objectives of this study were to adapt a screening method previously used to assess seedling drought tolerance in cereals for use in cotton (Gossypium hirsutum L. and to identify tolerant accessions among a wide range of genotypes. Ninety genotypes were screened in seven growth chamber experiments. Fifteen-day-old seedlings were subjected to four 4-day drought cycles, and plant survival was evaluated after each cycle. Three cycles are probably the minimum required in cotton work. Significant differences (at the 0.05 level or lower among entries were obtained in four of the seven experiments. A "confirmation test" with entries previously evaluated as "tolerant" (high survival and "susceptible" (low survival was run. A number of entries duplicated their earlier performance, but others did not, which indicates the need to reevaluate selections. Germplasms considered tolerant included: `IAC-13-1', `IAC-RM4-SM5', `Minas Sertaneja', `Acala 1517E-1' and `4521'. In general, the technique is simple, though time-consuming, with practical value for screening a large number of genotypes. Results from the screening tests generally agreed with field information. The screening procedure is suitable to select tolerant accessions from among a large number of entries in germplasm collections as a preliminary step in breeding for drought tolerance. This research also demonstrated the need to characterize the internal lack of uniformity in growth chambers to allow for adequate designs of experiments.

  8. CMS Status

    International Nuclear Information System (INIS)

    Dobrzynski, L.


    The status of the construction and installation of CMS detector is reviewed. The 4T magnet is cold since end of February 2006. Its commissioning up to the nominal field started in July 2006 allowing a Cosmic Challenge in which elements of the final detector are involved. All big mechanical pieces equipped with muons chambers have been assembled in the surface hall SX5. Since mid July the detector is closed with commissioned HCAL, two ECAL supermodules and representative elements of the silicon tracker. The trigger system as well as the DAQ are tested. After the achievement of the physics TDR, CMS is now ready for the promising signal hunting. (author)

  9. Identification of zoonotic genotypes of Giardia duodenalis.

    Directory of Open Access Journals (Sweden)

    Hein Sprong

    Full Text Available 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

  10. Genotypic diversity of root and shoot characteristics of

    Directory of Open Access Journals (Sweden)

    ali ganjali


    Full Text Available Root and shoot characteristics of chickpea (Cicer arietinum L. genotypes are believed to be important in drought tolerance. There is a little information about the response of genotypes root growth in hydroponics and greenhouse culture, also the relationships between root size and drought tolerance. This study was conducted to observe whether genotypes differ in root size, and to see that root size is associated with drought tolerance during early vegetative growth. We found significant differences (p0.01 in root dry weight, total root length, tap root length, root area, leaf dry weight, leaf area and shoot biomass per plant among 30 genotypes of chickpea grown in hydroponics culture for three weeks. Each of these parameters correlated with all others, positively. Among 30 genotypes, 10 genotypes with different root sizes were selected and were grown in a greenhouse in sand culture experiment under drought stress (FC %30 for three weeks. There were not linear or non-linear significant correlations between root characters in hydroponics and greenhouse environments. It seems that environmental factors are dominant on genetic factors in seedling stage and so, the expression of genotypics potential for root growth characteristics of genotypes are different in hydroponic and greenhouse conditions. In this study, the selection of genotypes with vigorous roots system in hydroponic condition did not lead to genotypes with the same root characters in greenhouse environment. The genotype×drought interactions for root characters of chickpea seedlings in 30 days were not significant (p

  11. Performance of chickpea genotypes under Swat valley conditions

    International Nuclear Information System (INIS)

    Khan, A.; Rahim, M.; Ahmad, F.; Ali, A.


    Twenty-two genetically diverse chickpeas genotypes were studied for their physiological efficiency to select the most desirable genotype/genotypes for breeding program on chickpea. Genotype 'CM7-1' was found physiologically efficient stain with maximum harvest index (37.33%) followed by genotype 'CM1571-1-A' with harvest index of 35.73%. Genotype '90206' produced maximum biological yield (7463 kg ha/sup -1/) followed by genotypes 'CM31-1' and 'E-2034' with biological yield of 7352 and 7167 kg ha/sup -1/, respectively. Harvest index and economic yield showed significant positive correlation value of (r=+0.595), while negative correlation value of (r = -0.435) was observed between harvest index and biological yield. (author)

  12. PAI-1 gain-of-function genotype, factors increasing PAI-1 levels, and airway obstruction: The GALA II Cohort. (United States)

    Sherenian, M G; Cho, S H; Levin, A; Min, J-Y; Oh, S S; Hu, D; Galanter, J; Sen, S; Huntsman, S; Eng, C; Rodriguez-Santana, J R; Serebrisky, D; Avila, P C; Kalhan, R; Smith, L J; Borrell, L N; Seibold, M A; Keoki Williams, L; Burchard, E G; Kumar, R


    PAI-1 gain-of-function variants promote airway fibrosis and are associated with asthma and with worse lung function in subjects with asthma. We sought to determine whether the association of a gain-of-function polymorphism in plasminogen activator inhibitor-1 (PAI-1) with airway obstruction is modified by asthma status, and whether any genotype effect persists after accounting for common exposures that increase PAI-1 level. We studied 2070 Latino children (8-21y) with genotypic and pulmonary function data from the GALA II cohort. We estimated the relationship of the PAI-1 risk allele with FEV1/FVC by multivariate linear regression, stratified by asthma status. We examined the association of the polymorphism with asthma and airway obstruction within asthmatics via multivariate logistic regression. We replicated associations in the SAPPHIRE cohort of African Americans (n=1056). Secondary analysis included the effect of the at-risk polymorphism on postbronchodilator lung function. There was an interaction between asthma status and the PAI-1 polymorphism on FEV 1 /FVC (P=.03). The gain-of-function variants, genotypes (AA/AG), were associated with lower FEV 1 /FVC in subjects with asthma (β=-1.25, CI: -2.14,-0.35, P=.006), but not in controls. Subjects with asthma and the AA/AG genotypes had a 5% decrease in FEV 1 /FVC (P<.001). In asthmatics, the risk genotype (AA/AG) was associated with a 39% increase in risk of clinically relevant airway obstruction (OR=1.39, CI: 1.01, 1.92, P=.04). These associations persisted after exclusion of factors that increase PAI-1 including tobacco exposure and obesity. The decrease in the FEV 1 /FVC ratio associated with the risk genotype was modified by asthma status. The genotype increased the odds of airway obstruction by 75% within asthmatics only. As exposures known to increase PAI-1 levels did not mitigate this association, PAI-1 may contribute to airway obstruction in the context of chronic asthmatic airway inflammation. © 2017

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

    Directory of Open Access Journals (Sweden)

    Prasanth VP


    Full Text Available Abstract 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

  14. Prediction of male-pattern baldness from genotypes. (United States)

    Liu, Fan; Hamer, Merel A; Heilmann, Stefanie; Herold, Christine; Moebus, Susanne; Hofman, Albert; Uitterlinden, André G; Nöthen, Markus M; van Duijn, Cornelia M; Nijsten, Tamar Ec; Kayser, Manfred


    The global demand for products that effectively prevent the development of male-pattern baldness (MPB) has drastically increased. However, there is currently no established genetic model for the estimation of MPB risk. We conducted a prediction analysis using single-nucleotide polymorphisms (SNPs) identified from previous GWASs of MPB in a total of 2725 German and Dutch males. A logistic regression model considering the genotypes of 25 SNPs from 12 genomic loci demonstrates that early-onset MPB risk is predictable at an accuracy level of 0.74 when 14 SNPs were included in the model, and measured using the area under the receiver-operating characteristic curves (AUC). Considering age as an additional predictor, the model can predict normal MPB status in middle-aged and elderly individuals at a slightly lower accuracy (AUC 0.69-0.71) when 6-11 SNPs were used. A variance partitioning analysis suggests that 55.8% of early-onset MPB genetic liability can be explained by common autosomal SNPs and 23.3% by X-chromosome SNPs. For normal MPB status in elderly individuals, the proportion of explainable variance is lower (42.4% for autosomal and 9.8% for X-chromosome SNPs). The gap between GWAS findings and the variance partitioning results could be explained by a large body of common DNA variants with small effects that will likely be identified in GWAS of increased sample sizes. Although the accuracy obtained here has not reached a clinically desired level, our model was highly informative for up to 19% of Europeans, thus may assist decision making on early MPB intervention actions and in forensic investigations.

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

    Directory of Open Access Journals (Sweden)

    Astobiza Ianire


    Full Text Available Abstract 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

  16. Audioprofiles and antioxidant enzyme genotypes in presbycusis. (United States)

    Angeli, Simon I; Bared, Anthony; Ouyang, Xiaomei; Du, Li Lin; Yan, Denise; Zhong Liu, Xue


    Audiometric patterns have been shown to indirectly provide information regarding the pathophysiology of presbycusis and be useful in the phenotyping of hereditary deafness. Hospital-based cohort study of adults with presbycusis, comparing the association of audiometric patterns and polymorphisms of antioxidant enzymes that have been linked to presbycusis: GSTT1, GSTM1 and NAT2. All subjects underwent a clinical evaluation and completed questionnaires regarding ototoxicity and noise exposure. Pure-tone threshold audiometry was obtained and subjects' audiograms were classified into specific patterns. DNA was extracted from blood and the polymorphisms of GSTT1, GSTM1, and the NAT2 variants (NAT2* 5A; NAT2* 6A,B) were analyzed by PCR. The audiometric patterns that were more prevalent in our cohort were "High-Frequency Steeply Sloping" or HFSS (33%), "High-Frequency Gently Sloping" or HFGS (31%), and "Flat" (27%), with other patterns being rare. We did not find a statistical significant effect of gender, age, hearing level, and ear side on the audiometric pattern. Subjects with mutant alleles for GSTT1 were more likely to have a HFSS audiogram than subjects with the wild type genotype. In this cohort, there was a similar prevalence for the three audiometric configurations HFSS, HFGS, and Flat, with other configurations being rare. Subjects with mutant alleles for GSTT1 were more likely to have a HFSS audiogram than subjects with the wild type genotype, suggesting that the basal turn of the cochlea is susceptible to GSTT1 regulated oxidative stress. However, further studies of audioprofiles with larger sample sizes may be needed to establish phenotype-genotype correlations in presbycusis. Copyright © 2012 The American Laryngological, Rhinological, and Otological Society, Inc.

  17. Genotyping Cryptosporidium andersoni in cattle in Shaanxi Province, Northwestern China.

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    Guang-Hui Zhao

    Full Text Available The present study examined the prevalence and genotypes of Cryptosporidium andersoni in cattle in Shaanxi province, China. A total of 2071 fecal samples (847 from Qinchuan cattle and 1224 from dairy cattle were examined for the presence of Cryptosporidium oocysts, and 70 samples (3.4% were C. andersoni-positive and those positive samples were identified by PCR amplification of the small subunit ribosomal RNA (SSU rRNA and the Cryptosporidium oocyst wall protein (COWP genes. C. andersoni was the only species found in the examined cattle in this province. Fifty-seven C. andersoni isolates were characterized into 5 MLST subtypes using multilocus sequence typing analysis, including a new subtype in the native beef breed Qinchuan cattle. All of these C. andersoni isolates presented a clonal genetic structure. These findings provide new insights into the genetic structure of C. andersoni isolates in Shaanxi province and basic data of Cryptosporidium prevalence status, which in turn have implications for controlling cryptosporidiosis in this province.

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

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


    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.

  19. Plant genotypic diversity reduces the rate of consumer resource utilization. (United States)

    McArt, Scott H; Thaler, Jennifer S


    While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore--the Japanese beetle (Popillia japonica)--increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore.

  20. Relationship of some upland rice genotype after gamma irradiation (United States)

    Suliartini, N. W. S.; Wijayanto, T.; Madiki, A.; Boer, D.; Muhidin; Juniawan


    The objective of the research was to group local upland rice genotypes after being treated with gamma irradiation. The research materials were upland rice genotypes resulted from mutation of the second generation and two parents: Pae Loilo (K3D0) and Pae Pongasi (K2D0) Cultivars. The research was conducted at the Indonesian Sweetener and Fiber Crops Research Institute, Malang Regency, and used the augmented design method. Research data were analyzed with R Program. Eight hundred and seventy one genotypes were selected with the selection criteria were based on yields on the average parents added 1.5 standard deviation. Based on the selection, eighty genotypes were analyzed with cluster analyses. Nine observation variables were used to develop cluster dendrogram using average linked method. Genetic distance was measured by euclidean distance. The results of cluster dendrogram showed that tested genotypes were divided into eight groups. Group 1, 2, 7, and 8 each had one genotype, group 3 and 6 each had two genotypes, group 4 had 25 genotypes, and group 5 had 51 genotypes. Check genotypes formed a separate group. Group 6 had the highest yield per plant of 126.11 gram, followed by groups 5 and 4 of 97.63 and 94.08 gram, respectively.

  1. VacA and cagA genotypes of Helicobacter pylori isolated from raw meat in Isfahan province, Iran. (United States)

    Gilani, Ali; Razavilar, Vadood; Rokni, Nordahr; Rahimi, Ebrahim


    Foods with animal origins play a substantial role in the transmission of Helicobacter pylori . The present investigation was carried out to study the vacA and cagA genotypes status of H. pylori isolated from various types of meat samples. Two hundred and twenty meat samples were collected and cultured. H. pylori -positive strains were analyzed for the presence of vacA and cagA genotypes. Eleven out of 220 (5.00%) samples were positive for H. pylori . Findings were confirmed by nested PCR. Prevalence of H. pylori in the meat samples of slaughterhouses and butcheries were 72.20% and 27.70%, respectively. The most commonly detected genotypes in the meat samples of slaughterhouses and butcheries were vacA m1a (66.66%) and vacA s1a (37.50%), respectively. The S1am1a was the most commonly detected genotype. Meat sampled from butcheries had the higher prevalence of H. pylori and its genotypes than those of slaughterhouses ( p meat samples could be the potential sources of virulent strains of H. pylori . Application of sanitary measures in the storage, transportation and sale of meat is essential for reducing the levels of H. pylori cross contamination.

  2. Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria. (United States)

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


    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.

  3. Antioxidant capacity of anthocyanins from acerola genotypes

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    Vera Lúcia Arroxelas Galvão De Lima


    Full Text Available Anthocyanins from 12 acerola genotypes cultivated at the Active Germplasm Bank at Federal Rural University of Pernambuco were isolated for antioxidant potential evaluation. The antioxidant activity and radical scavenging capacity of the anthocyanin isolates were measured according to the β-carotene bleaching method and 1,1-diphenyl-2-picrylhydrazyl (DPPH free radical scavenging assay, respectively. The antioxidant activity varied from 25.58 to 47.04% at 0.2 mg.mL-1, and it was measured using the β-carotene bleaching method. The free radical scavenging capacity increased according to the increase in concentration and reaction time by the DPPH assay. At 16.7 μg.mL-1 concentration and after 5 minutes and 2 hours reaction time, the percentage of scavenged radicals varied from 36.97 to 63.92% and 73.27 to 94.54%, respectively. Therefore, the antioxidant capacity of acerola anthocyanins varied amongst acerola genotypes and methods used. The anthocyanins present in this fruit may supply substantial dietary source of antioxidant which may promote health and produce disease prevention effects.

  4. [Mexican phenotype and genotype Vibrio cholerae 01]. (United States)

    Giono, S; Gutiérrez Cogno, L; Rodríguez Angeles, G; del Rio Zolezzi, A; Valdespino González, J L; Sepúlveda Amor, J


    This paper presents the phenotypical and genotypical characterization of 26922 Vibrio cholerae 01 strains isolated in Mexico from 1991 to 1993. All strains isolated were El Tor biovar. Strains were sensitive to antibiotics excluding furazolidone, streptomycin and sulfisoxasole to which we found resistance in 97% and we are using this characteristic as epidemiological markers. We detected a marked change in frequency of Inaba serotype from 1991, when it was dominant, with 99.5%, until 1992 when Ogawa serotype turned to be dominant with 95% of isolates. All Vibrio cholerae 01 strains, except one Ogawa strain, were to igenic, and V. choleraeno 01 were not toxigenic by ELISA, PCR and cell culture tests. Dominant ribotype was 5, but we found some strains with 6a pattern and two with ribotype 12. We are searching for ribotype 2 among hemolytic strains in order to learn if there is any relation to Gulf Coast strains prevalent in the USA, but until now we have not found any V. cholerae ribotype 2 in our isolates. Even if rapid tests are recommended for immediate diagnosis of cholera, it is necessary to continue bacterial isolation in order to have strains for phenotyping and genotyping studies that may support epidemiological analysis.

  5. HFE genotype affects exosome phenotype in cancer. (United States)

    Mrowczynski, Oliver D; Madhankumar, A B; Slagle-Webb, Becky; Lee, Sang Y; Zacharia, Brad E; Connor, James R


    Neuroblastoma is the third most common childhood cancer, and timely diagnosis and sensitive therapeutic monitoring remain major challenges. Tumor progression and recurrence is common with little understanding of mechanisms. A major recent focus in cancer biology is the impact of exosomes on metastatic behavior and the tumor microenvironment. Exosomes have been demonstrated to contribute to the oncogenic effect on the surrounding tumor environment and also mediate resistance to therapy. The effect of genotype on exosomal phenotype has not yet been explored. We interrogated exosomes from human neuroblastoma cells that express wild-type or mutant forms of the HFE gene. HFE, one of the most common autosomal recessive polymorphisms in the Caucasian population, originally associated with hemochromatosis, has also been associated with increased tumor burden, therapeutic resistance boost, and negative impact on patient survival. Herein, we demonstrate that changes in genotype cause major differences in the molecular and functional properties of exosomes; specifically, HFE mutant derived exosomes have increased expression of proteins relating to invasion, angiogenesis, and cancer therapeutic resistance. HFE mutant derived exosomes were also shown to transfer this cargo to recipient cells and cause an increased oncogenic functionality in those recipient cells. Copyright © 2017. Published by Elsevier B.V.

  6. Haplotype-Based Genotyping in Polyploids

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    Josh P. Clevenger


    Full Text Available Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads. Implementing a haplotype-based method in contrasting subgenome-specific sequences leads to higher accuracy of SNP identification in polyploids. To test this method, a large-scale 48K SNP array (Axiom Arachis2 was developed for Arachis hypogaea (peanut, an allotetraploid, in which 1,674 haplotype-based SNPs were included. Results of the array show that 74% of the haplotype-based SNP markers could be validated, which is considerably higher than previous methods used for peanut. The haplotype method has been implemented in a standalone program, HAPLOSWEEP, which takes as input bam files and a vcf file and identifies haplotype-based markers. Haplotype discovery can be made within single reads or span paired reads, and can leverage long read technology by targeting any length of haplotype. Haplotype-based genotyping is applicable in all allopolyploid genomes and provides confidence in marker identification and in silico-based genotyping for polyploid genomics.

  7. Hearing impairment in genotyped Wolfram syndrome patients. (United States)

    Plantinga, Rutger F; Pennings, Ronald J E; Huygen, Patrick L M; Bruno, Rocco; Eller, Philipp; Barrett, Timothy G; Vialettes, Bernard; Paquis-Fluklinger, Veronique; Lombardo, Fortunato; Cremers, Cor W R J


    Wolfram syndrome is a progressive neurodegenerative syndrome characterized by the features "DIDMOAD" (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness). We sought to study the audiometric data of genotyped Wolfram syndrome patients with sensorineural hearing impairment. Pure tone threshold data of 23 Wolfram syndrome patients were used for cross-sectional analysis in subgroups (age less than 16 years or between 19 and 25 years, gender, and origin). All subgroups, with 1 exception, showed a fairly similar type of hearing impairment with, on average, thresholds of about 25 dB (range, 0 to 65 dB) at 0.25 to 1 kHz, gently sloping downward to about 60 dB (range, 25 to 95 dB) at 8 kHz. The subgroup of Dutch women, which was excluded from the calculations of the average hearing thresholds, showed a higher degree of hearing impairment. Only the latter subgroup showed progression; however, contrary to the previous longitudinal analysis, progression was not significant in the present cross-sectional analysis, presumably because of the high degree of cross-subject variability. This unique collection of audiometric data from genotyped Wolfram syndrome patients shows no substantial progression in sensorineural hearing impairment with advancing age, no relation to the types of WFS1 mutations identified, and, with exclusion of the subgroup of Dutch female patients, no significant sex-related differences.

  8. Deep sequencing analysis of HBV genotype shift and correlation with antiviral efficiency during adefovir dipivoxil therapy.

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    Yuwei Wang

    Full Text Available Viral genotype shift in chronic hepatitis B (CHB patients during antiviral therapy has been reported, but the underlying mechanism remains elusive.38 CHB patients treated with ADV for one year were selected for studying genotype shift by both deep sequencing and Sanger sequencing method.Sanger sequencing method found that 7.9% patients showed mixed genotype before ADV therapy. In contrast, all 38 patients showed mixed genotype before ADV treatment by deep sequencing. 95.5% mixed genotype rate was also obtained from additional 200 treatment-naïve CHB patients. Of the 13 patients with genotype shift, the fraction of the minor genotype in 5 patients (38% increased gradually during the course of ADV treatment. Furthermore, responses to ADV and HBeAg seroconversion were associated with the high rate of genotype shift, suggesting drug and immune pressure may be key factors to induce genotype shift. Interestingly, patients with genotype C had a significantly higher rate of genotype shift than genotype B. In genotype shift group, ADV treatment induced a marked enhancement of genotype B ratio accompanied by a reduction of genotype C ratio, suggesting genotype C may be more sensitive to ADV than genotype B. Moreover, patients with dominant genotype C may have a better therapeutic effect. Finally, genotype shifts was correlated with clinical improvement in terms of ALT.Our findings provided a rational explanation for genotype shift among ADV-treated CHB patients. The genotype and genotype shift might be associated with antiviral efficiency.

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


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


    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 fr...

  10. Molecular genotyping of HCV infection in seropositive blood donor (United States)

    Zarin, Siti Noraziah Abu; Ibrahim, Nazlina


    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.

  11. Echinococcus canadensis (Cestoda: Taeniidae) is a valid species consisting of the mitochondrial genotypes G6, G7, G8 and G10 (United States)

    The species status of Echinococcus canadensis has long been controversial, mainly because it consists of the mitochondrial genotypes G6, G7, G8 and G10 with different host affinity: G6 (camel strain) and G7 (pig strain) with domestic cycles and G8 (cervid strain) and G10 (Fennoscandian cervid strain...

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

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    Joaquim Manoel da Silva

    Full Text Available 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.

  13. Phosphorus use efficiency in pima cotton (Gossypium barbadense L. genotypes

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    Elcio Santos


    Full Text Available In the Brazilian Cerrado, P deficiency restricts cotton production, which requires large amounts of phosphate fertilizer. To improve the yield of cotton crops, genotypes with high P use efficiency must be identified and used. The present study evaluated P uptake and use efficiency of different Gossypium barbadense L. genotypes grown in the Cerrado. The experiment was carried out in a greenhouse with a completely randomized design, 15 x 2 factorial treatment structure (15 genotypes x 2 P levels, and four replicates. The genotypes were MT 69, MT 70, MT 87, MT 91, MT 92, MT 94, MT 101, MT 102, MT 103, MT 105, MT 106, MT 110, MT 112, MT 124, and MT 125; P levels were sufficient (1000 mg pot-1, PS treatment or deficient (PD treatment. Dry matter (DM and P levels were determined in cotton plant parts and used to calculate plant P content and use efficiency. In general, DM and P content were higher in the PS than in the PD treatment, with the exception of root DM and total DM in some genotypes. Genotypes also differed in terms of P uptake and use capacity. In the PS treatment, genotypes MT 92 and MT 102 had the highest response to phosphate fertilization. Genotype MT 69 exhibited the most efficient P uptake in the PD treatment. Genotype MT 124 showed the best shoot physiological efficiency, apparent recovery efficiency, and utilization efficiency, whereas MT 110 exhibited the highest root physiological efficiency.

  14. Welcome to the neighbourhood: interspecific genotype by genotype interactions in Solidago influence above- and belowground biomass and associated communities. (United States)

    Genung, Mark A; Bailey, Joseph K; Schweitzer, Jennifer A


    Intra- and interspecific plant-plant interactions are fundamental to patterns of community assembly and to the mixture effects observed in biodiversity studies. Although much research has been conducted at the species level, very little is understood about how genetic variation within and among interacting species may drive these processes. Using clones of both Solidago altissima and Solidago gigantea, we found that genotypic variation in a plant's neighbours affected both above- and belowground plant traits, and that genotype by genotype interactions between neighbouring plants impacted associated pollinator communities. The traits for which focal plant genotypic variation explained the most variation varied by plant species, whereas neighbour genotypic variation explained the most variation in coarse root biomass. Our results provide new insight into genotypic and species diversity effects in plant-neighbour interactions, the extended consequences of diversity effects, and the potential for evolution in response to competitive or to facilitative plant-neighbour interactions. © 2011 Blackwell Publishing Ltd/CNRS.

  15. Mathematical Ability and Socio-Economic Background: IRT Modeling to Estimate Genotype by Environment Interaction. (United States)

    Schwabe, Inga; Boomsma, Dorret I; van den Berg, Stéphanie M


    Genotype by environment interaction in behavioral traits may be assessed by estimating the proportion of variance that is explained by genetic and environmental influences conditional on a measured moderating variable, such as a known environmental exposure. Behavioral traits of interest are often measured by questionnaires and analyzed as sum scores on the items. However, statistical results on genotype by environment interaction based on sum scores can be biased due to the properties of a scale. This article presents a method that makes it possible to analyze the actually observed (phenotypic) item data rather than a sum score by simultaneously estimating the genetic model and an item response theory (IRT) model. In the proposed model, the estimation of genotype by environment interaction is based on an alternative parametrization that is uniquely identified and therefore to be preferred over standard parametrizations. A simulation study shows good performance of our method compared to analyzing sum scores in terms of bias. Next, we analyzed data of 2,110 12-year-old Dutch twin pairs on mathematical ability. Genetic models were evaluated and genetic and environmental variance components estimated as a function of a family's socio-economic status (SES). Results suggested that common environmental influences are less important in creating individual differences in mathematical ability in families with a high SES than in creating individual differences in mathematical ability in twin pairs with a low or average SES.

  16. Genotyping in the Brazilian Criollo Horse Stud Book: resources and perspectives. (United States)

    Costa, M A P; Bressel, R M C; Almeida, D B; Oliveira, P A; Bassini, L N; Moreira, C G A; Manzke, V H B; Siewerdt, F; Moreira, H L M


    The goal of this research was to evaluate the ability of the genotyping information available in the Brazilian Criollo Horse Stud Book to describe the genetic variability of the breed and the exclusion probability determined in comparative tests. Altogether, two softwares were used in the analyses of the available genotypes: Cervus 3.0.3 and Genepop 4.0. Eight microsatellite markers totaled 109 alleles, with an average of 13.6 +/- 0.6 alleles per locus. Large differences between expected and observed heterozygosity were ubiquitous (0.821 +/- 0.07 and 0.470 +/- 0.17, respectively). Although the estimated null allele frequency caused initial concern (0.284 +/- 0.199), it is likely that it was a reflection of the inbreeding coefficients found (0.432 +/- 0.184). All loci showed significant deviation from Hardy-Weinberg equilibrium, with heterozygote deficit (P < 0.0001) and genotypic linkage disequilibrium with at least one marker. The high polymorphic information content (0.798 +/- 0.088) could not warrant exclusion power for three loci (HMS7, HMS6 and HTG4) above 50% (0.491 +/- 0.158). However, combined exclusion probability reached 99.61%, a level close to ideal. The results demonstrate the excellent performance of the markers assessed in describing the genetic status of the breed and suggest the considerable ability to establish parentage.

  17. KIR-HLA genotypes in HIV-infected patients lacking immunological recovery despite effective antiretroviral therapy.

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    Alessandro Soria

    Full Text Available BACKGROUND: In HIV-infected individuals, mechanisms underlying unsatisfactory immune recovery during effective combination antiretroviral therapy (cART have yet to be fully understood. We investigated whether polymorphism of genes encoding immune-regulating molecules, such as killer immunoglobulin-like receptors (KIR and their ligands class I human leukocyte antigen (HLA, could influence immunological response to cART. METHODS: KIR and HLA frequencies were analyzed in 154 HIV-infected and cART-treated patients with undetectable viral load divided into two groups: 'immunological non responders' (INR, N = 50, CD4(+ T-cell count 350/mm(3. Molecular KIR were typed using polymerase chain reaction-based genotyping. Comparisons were adjusted for baseline patient characteristics. RESULTS: The frequency of KIR2DL3 allele was significantly higher in FR than in INR (83.7% vs. 62%, P = 0.005. The functional compound genotype HLA-C1(+/KIR2DL3(+, even at multivariable analysis, when adjusted for nadir CD4(+ T-cell count, was associated with reduced risk of INR status: odds ratio (95% Confidence Intervals 0.34 (0.13-0.88, P = 0.03. CONCLUSIONS: Reduced presence of the inhibitory KIR2DL3 genotype detected in INR might provoke an imbalance in NK function, possibly leading to increased immune activation, impaired killing of latently infected cells, and higher proviral burden. These factors would hinder full immune recovery during therapy.

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

    Ashworth, V E T M; Clegg, M T


    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.

  19. Prevalence and clinical utility of human papilloma virus genotyping in patients with cervical lesions. (United States)

    Kaur, Parminder; Aggarwal, Aruna; Nagpal, Madhu; Oberoi, Loveena; Sharma, Swati


    Cervical cancer is the commonest cancer among Indian women. High-risk human papilloma virus (HPV) detection holds the potential to be used as a tool to identify women, at risk of subsequent development of cervical cancer. There is a pressing need to identify prevalence of asymptomatic cervical HPV infection in local population. In our study, we explored the prevalence of HPV genotypes and their distribution in women with cervical lesions. Scrape specimens were obtained from 100 women (study group) with cervical abnormalities. HPV was detected with amplicor HPV tests, and the individual genotypes in these specimens were identified by Hybribio Genoarray test kit. Fifty specimens were also collected from females with healthy cervix (control group). The present study also aimed to determine the status of HPV prevalence and its association with different sociodemographic factors. Out of the total number of 100 samples, 10 (10 %) women tested positive for HPV DNA. Among them, HPV 18 was observed in 6, HPV 16 in 2, HPV 52 and HPV 39 in one each. Fifty specimens collected from patients with healthy cervix were not infected with any of the HPV genotype. Our study generates data of HPV prevalence in patients with cervical lesions visiting tertiary care institute. The data generated will be useful for laying guidelines for mass screening of HPV detection, treatment, and prophylaxis.

  20. Apolipoprotein E Genotype and Sex Influence Glucose Tolerance in Older Adults: A Cross-Sectional Study

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    Angela J. Hanson


    Full Text Available Background: Glucose intolerance and apolipoprotein ε4 allele (E4+ are risk factors for Alzheimer's disease (AD. Insulin sensitizers show promise for treating AD, but are less effective in E4+ individuals. Little is known about how the APOE genotype influences glucose metabolism. Methods: Cross-sectional analysis of 319 older adults who underwent oral glucose tolerance tests; a subset had insulin, amyloid beta (Aβ42, and Mini Mental Status Examination. Glucose and insulin patterns with respect to cognitive diagnosis, E4 status, and sex were examined with analysis of covariance and Pearson correlation. Results: People with cognitive impairment had higher fasting insulin levels. E4 status did not affect fasting glucose values, whereas men had higher fasting glucose levels than women. E4+ men had the lowest and E4+ women had the highest glucose levels, compared to E4- groups; insulin did not differ by sex or E4 group. E4 status and sex moderated correlations between metabolic measures and AD risk factors including age and Aβ. Conclusions: Insulin resistance was associated with cognitive impairment, and sex, E4 status, and glucose values are interrelated in older adults at risk of AD. Understanding glucose metabolism for different APOE and sex groups may help elucidate differences in therapeutic responses.

  1. Sources of Wilhelm Johannsen's genotype theory. (United States)

    Roll-Hansen, Nils


    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. Identification of Zoonotic Genotypes of Giardia duodenalis

    DEFF Research Database (Denmark)

    Sprong, H.; Cacciò, S.M.; van der Giessen, J.W.B


    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......, 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...

  3. Automated genotyping of dinucleotide repeat markers

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)


    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.

  4. Spatial overlap links seemingly unconnected genotype-matched TB cases in rural Uganda (United States)

    Kato-Maeda, Midori; Emperador, Devy M.; Wandera, Bonnie; Mugagga, Olive; Crandall, John; Janes, Michael; Marquez, Carina; Kamya, Moses R.; Charlebois, Edwin D.; Havlir, Diane V.


    Introduction Incomplete understanding of TB transmission dynamics in high HIV prevalence settings remains an obstacle for prevention. Understanding where transmission occurs could provide a platform for case finding and interrupting transmission. Methods From 2012–2015, we sought to recruit all adults starting TB treatment in a Ugandan community. Participants underwent household (HH) contact investigation, and provided names of social contacts, sites of work, healthcare and socializing, and two sputum samples. Mycobacterium tuberculosis culture-positive specimens underwent 24-loci MIRU-VNTR and spoligotyping. We sought to identify epidemiologic links between genotype-matched cases by analyzing social networks and mapping locations where cases reported spending ≥12 hours over the one-month pre-treatment. Sites of spatial overlap (≤100m) between genotype-matched cases were considered potential transmission sites. We analyzed social networks stratified by genotype clustering status, with cases linked by shared locations, and compared network density by location type between clustered vs. non-clustered cases. Results Of 173 adults with TB, 131 (76%) were enrolled, 108 provided sputum, and 84/131 (78%) were MTB culture-positive: 52% (66/131) tested HIV-positive. Of 118 adult HH contacts, 105 (89%) were screened and 3 (2.5%) diagnosed with active TB. Overall, 33 TB cases (39%) belonged to 15 distinct MTB genotype-matched clusters. Within each cluster, no cases shared a HH or reported shared non-HH contacts. In 6/15 (40%) clusters, potential epidemiologic links were identified by spatial overlap at specific locations: 5/6 involved health care settings. Genotype-clustered TB social networks had significantly greater network density based on shared clinics (p<0.001) and decreased density based on shared marketplaces (p<0.001), compared to non-clustered networks. Conclusions In this molecular epidemiologic study, links between MTB genotype-matched cases were only

  5. Differential response of kabuli and desi chickpea genotypes toward inoculation with PGPR in different soils (United States)

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


    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

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

    Directory of Open Access Journals (Sweden)

    Krystle A Lang Kuhs

    Full Text Available 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

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

    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


    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. Epidemiological evaluation of spatiotemporal and genotypic clustering of Mycobacterium tuberculosis in Ontario, Canada. (United States)

    Tuite, A R; Guthrie, J L; Alexander, D C; Whelan, M S; Lee, B; Lam, K; Ma, J; Fisman, D N; Jamieson, F B


    In Canada, tuberculosis (TB) rates are at a historic low, with the remaining risk concentrated in a few vulnerable population subgroups. To describe the epidemiology of TB in the Canadian province of Ontario and to characterise risk factors associated with transmission events, identified using genetic typing techniques. Retrospective analysis of 2186 culture-positive TB cases between August 2007 and December 2011. Temporal trends and risk of spatiotemporal and genotypic clustering were evaluated using Poisson and logistic regression models. Being in a spatiotemporal cluster was associated with Aboriginal status (odds ratio [OR] 3.63, 95% confidence interval [CI] 1.23-10.71). Cases in genotypic clusters were more likely to report homelessness as a risk factor (adjusted OR [aOR] 2.92, 95%CI 1.74-4.90) or be male (aOR 1.35, 95%CI 1.09-1.68), and were less likely to be aged ≥ 65 years (aOR 0.63, 95%CI 0.49-0.82), foreign-born (aOR 0.32, 95%CI 0.24-0.43) or Aboriginal (aOR 0.40, 95%CI 0.16-0.99). The Beijing lineage had an annual rate of increase of almost 10% (P = 0.047), and was associated with genotypic clustering (aOR 2.84, 95%CI 2.19-3.67). Genotypic data suggest that disease clusters are smaller, but far more common, than would be estimated using spatiotemporal clustering.

  9. A measles outbreak in Sindh, Pakistan caused by a genotype B3 virus. (United States)

    Zaidi, Syed Sohail Zahoor; Hameed, Abdul; Ali, Naeem; Umair, Massab; Alam, Muhammad Masroor; Rana, Muhammad Suleman; Sharif, Salmaan; Aamir, Uzma Bashir; Shaukat, Shahzad; Angez, Mehar; Khurshid, Adnan; Akhtar, Ribqa; Mehmood, Nayab; Badar, Nazish


    Measles continues to be a major public health issue causing substantial outbreaks worldwide, mostly affecting young children. Molecular analysis of measles viruses provides important information on outbreak linkages and transmission pathways that can be helpful towards implementation of appropriate control programs. In Pakistan, the control of measles is still tenuous, and progress towards elimination has been irregular and challenging. In the 2013 measles outbreak we received 4,682 sera collected from suspected patients in 23 districts across Sindh. A total of 3,283 samples were confirmed measles positive using IgM ELISA with the highest infection rate in children aged 1-12 months. Males were more affected than females and a visible peak was observed from January to April. Among the 3,283 cases, 59.1% were unvaccinated, 29.6% had received 1 dose and 10.3% had received 2 doses of measles vaccine while 0.85% had an unknown vaccination status. For genotype detection and phylogenetic analysis, 60 throat swab samples were collected from suspected patients below 15 years of age in eight districts of Sindh province. Forty four (73%; 44/60) throat swab samples were successfully genotyped using RT-PCR. Phylogenetic analyses based on partial sequences of the nucleocapsid protein gene revealed that all Pakistani measles virus strains belonged to genotype B3 and were closely related to those isolated from neighboring countries such as Iran, Afghanistan (99.1-100%) and India with 98.6 - 99.6% nucleotide homology. This is the first report on the phylogenetic analysis of measles B3 genotype strains from Pakistan and highlights the need for strengthening the surveillance systems and improving immunization coverage across the country.

  10. Riboflavin, MTHFR genotype and blood pressure: A personalized approach to prevention and treatment of hypertension. (United States)

    McNulty, Helene; Strain, J J; Hughes, Catherine F; Ward, Mary


    Hypertension is the leading risk factor contributing to mortality worldwide, primarily from cardiovascular disease (CVD), while effective treatment of hypertension is proven to reduce CVD events. Along with the well recognized nutrition and lifestyle determinants, genetic factors are implicated in the development and progression of hypertension. In recent years genome-wide association studies have identified a region near the gene encoding the folate-metabolizing enzyme methylenetetrahydrofolate reductase (MTHFR) among eight loci associated with blood pressure. Epidemiological studies, which provide a separate line of evidence to link this gene with blood pressure, show that the 677C→T polymorphism in MTHFR increases the risk of hypertension by 24-87% and CVD by up to 40%, albeit with a large geographical variation in the extent of excess disease risk suggestive of a gene-environment interaction. Emerging evidence indicates that the relevant environmental factor may be riboflavin, the MTHFR co-factor, via a novel and genotype-specific effect on blood pressure. Randomized trials conducted in hypertensive patients (with and without overt CVD) pre-screened for this polymorphism show that targeted riboflavin supplementation in homozygous individuals (MTHFR 677TT genotype) lowers systolic blood pressure by 6 to 13 mmHg, independently of the effect of antihypertensive drugs. The latest evidence, that the blood pressure phenotype associated with this polymorphism is modifiable by riboflavin, has important clinical and public health implications. For hypertensive patients, riboflavin supplementation can offer a non-drug treatment to effectively lower blood pressure in those identified with the MTHFR 677TT genotype. For sub-populations worldwide with this genotype, better riboflavin status may prevent or delay the development of high blood pressure. Thus riboflavin, targeted at those homozygous for a common polymorphism in MTHFR, may offer a personalized treatment or

  11. Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation (United States)

    Wang, Chaolong; Zhan, Xiaowei; Liang, Liming; Abecasis, Gonçalo R.; Lin, Xihong


    Accurate estimation of individual ancestry is important in genetic association studies, especially when a large number of samples are collected from multiple sources. However, existing approaches developed for genome-wide SNP data do not work well with modest amounts of genetic data, such as in targeted sequencing or exome chip genotyping experiments. We propose a statistical framework to estimate individual ancestry in a principal component ancestry map generated by a reference set of individuals. This framework extends and improves upon our previous method for estimating ancestry using low-coverage sequence reads (LASER 1.0) to analyze either genotyping or sequencing data. In particular, we introduce a projection Procrustes analysis approach that uses high-dimensional principal components to estimate ancestry in a low-dimensional reference space. Using extensive simulations and empirical data examples, we show that our new method (LASER 2.0), combined with genotype imputation on the reference individuals, can substantially outperform LASER 1.0 in estimating fine-scale genetic ancestry. Specifically, LASER 2.0 can accurately estimate fine-scale ancestry within Europe using either exome chip genotypes or targeted sequencing data with off-target coverage as low as 0.05×. Under the framework of LASER 2.0, we can estimate individual ancestry in a shared reference space for samples assayed at different loci or by different techniques. Therefore, our ancestry estimation method will accelerate discovery in disease association studies not only by helping model ancestry within individual studies but also by facilitating combined analysis of genetic data from multiple sources. PMID:26027497

  12. Genotypic and phenotypic characterization of Chikungunya virus of different genotypes from Malaysia.

    Directory of Open Access Journals (Sweden)

    I-Ching Sam

    Full Text Available BACKGROUND: Mosquito-borne Chikungunya virus (CHIKV has recently re-emerged globally. The epidemic East/Central/South African (ECSA strains have spread for the first time to Asia, which previously only had endemic Asian strains. In Malaysia, the ECSA strain caused an extensive nationwide outbreak in 2008, while the Asian strains only caused limited outbreaks prior to this. To gain insight into these observed epidemiological differences, we compared genotypic and phenotypic characteristics of CHIKV of Asian and ECSA genotypes isolated in Malaysia. METHODS AND FINDINGS: CHIKV of Asian and ECSA genotypes were isolated from patients during outbreaks in Bagan Panchor in 2006, and Johor in 2008. Sequencing of the CHIKV strains revealed 96.8% amino acid similarity, including an unusual 7 residue deletion in the nsP3 protein of the Asian strain. CHIKV replication in cells and Aedes mosquitoes was measured by virus titration. There were no differences in mammalian cell lines. The ECSA strain reached significantly higher titres in Ae. albopictus cells (C6/36. Both CHIKV strains infected Ae. albopictus mosquitoes at a higher rate than Ae. aegypti, but when compared to each other, the ECSA strain had much higher midgut infection and replication, and salivary gland dissemination, while the Asian strain infected Ae. aegypti at higher rates. CONCLUSIONS: The greater ability of the ECSA strain to replicate in Ae. albopictus may explain why it spread far more quickly and extensively in humans in Malaysia than the Asian strain ever did, particularly in rural areas where Ae. albopictus predominates. Intergenotypic genetic differences were found at E1, E2, and nsP3 sites previously reported to be determinants of host adaptability in alphaviruses. Transmission of CHIKV in humans is influenced by virus strain and vector species, which has implications for regions with more than one circulating CHIKV genotype and Aedes species.

  13. Methods for discovering and validating relationships among genotyped animals (United States)

    Genomic selection based on single-nucleotide polymorphisms (SNPs) has led to the collection of genotypes for over 2.2 million animals by the Council on Dairy Cattle Breeding in the United States. To assure that a genotype is assigned to the correct animal and that the animal’s pedigree is correct, t...

  14. Variation of meat quality traits among five genotypes of chicken. (United States)

    Tang, H; Gong, Y Z; Wu, C X; Jiang, J; Wang, Y; Li, K


    The main objective of this study was to examine the diversity of meat quality traits among 5 chicken genotypes. The genotypes included 2 Chinese native breeds (Wenchang,WCH, and Xianju), 1 commercial broiler line (Avian, AV), 1 commercial layer line (Hy-Line Brown, HLB), and 1 Chinese commercial broiler line (Lingnanhuang, LNH) synthesized by exotic and native breeds, which were slaughtered at their market ages: 16, 7, 16, and 8 wk, respectively. The effects of genotype, muscle type, and sex on meat quality traits were examined. Birds from slow-growing genotypes (WCH, Xianju, and HLB) exhibited higher shear value, inosine-5'-monophosphate concentration, lower cook loss, and more fat than those from fast-growing genotypes (AV and LNH). Chickens from WCH possessed the lowest expressible moisture, cook loss, and the highest lipid (%) among the 3 slow-growing genotypes. The HLB birds were intermediate in expressible moisture and cook loss and lowest in lipid among all genotypes. The LNH cross birds were similar to AV broilers in most meat quality parameters, although they had a lower shear force value and higher fat content than AV broilers. Breast muscle had higher expressible moisture, shear force, protein (%), inosine-5'-monophosphate content, lower cook loss, and lipid (%) than leg muscle. Muscles from male chickens had higher expressible moisture than those from the females. Variability of meat quality characteristics is mainly related to genotype and muscle type differences.

  15. Screening of Wheat Genotypes for Boron Efficiency in Bangladesh (United States)

    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 ...

  16. Crossbreeding of large white and Nsukka local pigs: Genotype and ...

    African Journals Online (AJOL)

    5-Blood samples from 80 pigs of 4 genotypes - the Nsukka local (Lo), the exotic Large White (LW), the one-way F1 (LW x Lo) and the F2 crosses belonging to 5 age groups, were analyzed, to determine the mean values of the haematological parameters in the genotypes and different age groups and to check if and how the ...

  17. Enhanced fodder yield of maize genotypes under saline irrigation is ...

    African Journals Online (AJOL)

    Poor quality irrigation water adversely affects the growth and yield of crops. This study was designed to evaluate the growth, fodder yield and ionic concentration of three promising maize (Zea mays L.) genotypes under the influence of varying quality irrigation water, with different salinity levels. The genotypes, such as ...

  18. Breeding of a Tomato Genotype Readily Accessible to Genetic Manipulation

    NARCIS (Netherlands)

    Koornneef, Maarten; Hanhart, Corrie; Jongsma, Maarten; Toma, Ingrid; Weide, Rob; Zabel, Pim; Hille, Jacques


    A tomato genotype, superior in regenerating plants from cell cultures, was obtained by transferring regeneration capacity from Lycopersicon peruvianum into L. esculentum by classical breeding. This genotype, MsK93, greatly facilitates genetic manipulation of tomato, as was demonstrated by successful

  19. Application of mixed models for the assessment genotype and ...

    African Journals Online (AJOL)

    Application of mixed models for the assessment genotype and environment interactions in cotton ( Gossypium hirsutum ) cultivars in Mozambique. ... The cultivars ISA 205, STAM 42 and REMU 40 showed superior productivity when they were selected by the Harmonic Mean of Genotypic Values (HMGV) criterion in relation ...

  20. The influence of host genotype X environment Interactions on the ...

    African Journals Online (AJOL)

    Mean squares for environments, genotypes and G x E interactions were highly significant (P<0.0001) for anthracnose infection. Significant G x E interactions, accounting for 19% of the treatment sums of squares, indicated that genotypes responded differentially to anthracnose infection across environments. The additive ...

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

    Directory of Open Access Journals (Sweden)

    Miguel A Fortuna


    Full Text Available 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.

  2. The genotype-phenotype map of an evolving digital organism. (United States)

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


    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.

  3. The influence of temperature on photosynthesis of different tomato genotypes

    NARCIS (Netherlands)

    Gosiewski, W.; Nilwik, H.J.M.; Bierhuizen, J.F.


    Net photosynthesis and dark respiration from whole plants of various tomato genotypes were measured in a closed system. At low irradiance (27 W m−2) and low external CO2 concentration (550 mg m−3), net photosynthesis of 10 genotypes was found to vary between 0.122 and 0.209 mg CO2 m−2 s−1.

  4. characterisation of common bean genotypes based on storage

    African Journals Online (AJOL)


    of pliers and then ground to fine powder with a ... segregation of genotypes were Rm 23.75, 32.50,. 33.75, 22.50 ... Figure 1. Positions of Phaseolus vulgarisL. genotypes on the first and second correspondence scores based on storage protein.

  5. Integrated analysis for genotypic adaptation in rice | Das | African ...

    African Journals Online (AJOL)

    Integrated analysis for genotypic adaptation in rice. S Das, RC Misra, MC Pattnaik, SK Sinha. Abstract. Development of varieties with high yield potential coupled with wide adaptability is an important plant breeding objective. The presence of genotype by environment (GxE) interaction plays a crucial role in determining the ...

  6. Characteristics of Streptococcus mutans genotypes and dental caries in children (United States)

    Cheon, Kyounga; Moser, Stephen A.; Wiener, Howard W.; Whiddon, Jennifer; Momeni, Stephanie S.; Ruby, John D.; Cutter, Gary R.; Childers, Noel K.


    This longitudinal cohort study evaluated the diversity, commonality, and stability of Streptococcus mutans genotypes associated with dental caries history. Sixty-seven 5 and 6 yr-old children, considered being at high caries risk, had plaque collected from baseline through 36 months for S. mutans isolation and genotyping with repetitive extragenic palindromic-PCR (4,392 total isolates). Decayed, missing, filled surfaces (dmfs/DMFS) for each child were recorded at baseline. At baseline, 18 distinct genotypes were found among 911 S. mutans isolates from 67 children (diversity) and 13 genotypes were shared by at least 2 children (commonality). The number of genotypes per individual was positively associated with the proportion of decayed surfaces (p-ds) at baseline. Twenty-four of the 39 children who were available at follow-up visits maintained a predominant genotype for the follow-up periods (stability) and was negatively associated with p-ds. The observed diversity, commonality, and stability of S. mutans genotypes represent a pattern of dental caries epidemiology in this high caries risk community, which suggest fewer decayed surfaces are significantly associated with lower diversity and stability of S. mutans genotypes. PMID:23659236

  7. Beijing/W genotype Mycobacterium tuberculosis and drug resistance.

    NARCIS (Netherlands)

    Glynn, Judith R; Kremer, Kristin; Borgdorff, Martien W; Rodriguez, Mar Pujades; Soolingen, Dick van


    Beijing/W genotype Mycobacterium tuberculosis is widespread, may be increasing, and may have a predilection for drug resistance. Individual-level data on >29,000 patients from 49 studies in 35 countries were combined to assess the Beijing genotype's prevalence worldwide, trends over time and with

  8. Apolipoprotein E genotype, cardiovascular biomarkers and risk of stroke

    DEFF Research Database (Denmark)

    Khan, Tauseef A; Shah, Tina; Prieto, David


    At the APOE gene, encoding apolipoprotein E, genotypes of the ε2/ε3/ε4 alleles associated with higher LDL-cholesterol (LDL-C) levels are also associated with higher coronary risk. However, the association of APOE genotype with other cardiovascular biomarkers and risk of ischaemic stroke is less c...

  9. Genotype dependent callus induction and shoot regeneration in ...

    African Journals Online (AJOL)

    This study aims to observe the effect of genotype, hormone and culture conditions on sunflower (Helianthus annuus L.) callus induction and indirect plant regeneration. Calli were obtained from hypocotyl and cotyledon explants of five different sunflower genotypes; Trakya 80, Trakya 129, Trakya 259, Trakya 2098 and ...

  10. Efficiency and response of conilon coffee genotypes to nitrogen supply

    African Journals Online (AJOL)

    The objective of the study was to differentiate genotypes with higher efficiency and responsiveness to nitrogen supply, to understand how the nitrogen supply can impact the dry matter allocation and the accumulation of this nutrient in the different plant compartments of genotypes of conilon coffee, cultivated under ...

  11. Haemoglobin genotype of children with severe malaria seen at the ...

    African Journals Online (AJOL)

    Abstract: Introduction: Types of haemoglobin (Hb) genotype have been found to be crucial to the rate of red blood cell parasite invasion, multiplication, and destruction as well as outcome of malaria disease. In a bid to provide more information on the relationship between Hb genotype and level of protection conferred by ...

  12. participatory selection of mungbean genotypes in uganda abstract

    African Journals Online (AJOL)



    May 29, 2017 ... that there were no significant differences in genotype choices based on gender ... However, there were significant genotype preference differences between eastern and northern regions (χ2 = ..... for southern Ethiopia. ... of improved cowpea cultivars in the Guinea and Sudan savanna zones of north east.

  13. Genetic variation of response to water deficit in parental genotypes ...

    African Journals Online (AJOL)


    In this study, we investigated morphological and photosynthetic responses to water deficit in parental genotypes of M. ... for adaptation to water deficit in legumes is a prerequisite for any research aiming to improve legume yields. ...... tolerant genotypes in rainfed lowland rice. Field Crop. Res. 99:48-58. Rouached A, Slama I, ...

  14. Clusters of incompatible genotypes evolve with limited dispersal (United States)

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


    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...

  15. Evaluation of sorghum genotypes under drought stress conditions ...

    African Journals Online (AJOL)

    Seven genotypes of sorghum (Sorghum bicolour (L.) Moench) were studied in both drought and normal conditions. In each condition, the genotypes were evaluated using a split plot based randomized complete block design with three replications. Drought tolerance indices including stability tolerance index (STI), mean ...

  16. Cell Line Controls for the Genotyping of a Spectrum of Human Single Nucleotide Polymorphisms in the Clinical Laboratory. (United States)

    Kimbacher, Christine; Paar, Christian; Freystetter, Andrea; Berg, Joerg


    Genotyping for clinically important single nucleotide polymorphisms (SNPs) is performed by many clinical routine laboratories. To support testing, quality controls and reference materials are needed. Those may be derived from residual patient samples, left over samples of external quality assurance schemes, plasmid DNA or DNA from cell lines. DNAs from cell lines are commutable and available in large amounts. DNA from 38 cell lines were examined for suitability as controls in 11 SNP assays that are frequently used in a clinical routine laboratory: FV (1691G>A), FII (20210G>A), PAI-1 4G/5G polymorphism, MTHFR (677C>T, 1298A>C), HFE (H63D, S65C, C282Y), APOE (E2, E3, E4), LPH (-13910C>T), UGT1A1 (*28, *36, *37), TPMT (*2, *3A, *3B, *3C), VKORC1 (-1639G>A, 1173C>T), CYP2C9 (*2, *3, *5). Genotyping was performed by real-time PCR with melting curve analysis and confirmed by bi-directional sequencing. We find an almost complete spectrum of genotypic constellations within these 38 cell lines. About 12 cell lines appear sufficient as genotypic controls for the 11 SNP assays by covering almost all of the genotypes. However, hetero- and homozygous genotypes for FII and the alleles TPMT*2, UGT1A1*37 and CYP2C9*5 were not detected in any of the cell lines. DNA from most of the examined cell lines appear suitable as quality controls for these SNP assays in the laboratory routine, as to the implementation of those assays or to prepare samples for quality assurance schemes. Our study may serve as a pilot to further characterize these cell lines to arrive at the status of reference materials.

  17. Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping

    Directory of Open Access Journals (Sweden)

    Gregory W. Peterson


    Full Text Available Genotyping-by-sequencing (GBS has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L. accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.

  18. Genotypic character relationship and phenotypic path coefficient analysis in chili pepper genotypes grown under tropical condition. (United States)

    Usman, Magaji G; Rafii, Mohd Y; Martini, Mohammad Y; Oladosu, Yusuff; Kashiani, Pedram


    Studies on genotypic and phenotypic correlations among characters of crop plants are useful in planning, evaluating and setting selection criteria for the desired characters in a breeding program. The present study aimed to estimate the phenotypic correlation coefficients among yield and yield attributed characters and to work out the direct and indirect effects of yield-related characters on yield per plant using path coefficient analysis. Twenty-six genotypes of chili pepper were laid out in a randomized complete block design with three replications. Yield per plant showed positive and highly significant (P ≤ 0.01) correlations with most of the characters studied at both the phenotypic and genotypic levels. By contrast, disease incidence and days to flowering showed a significant negative association with yield. Fruit weight and number of fruits exerted positive direct effect on yield and also had a positive and significant (P ≤ 0.01) correlation with yield per plant. However, fruit length showed a low negative direct effect with a strong and positive indirect effect through fruit weight on yield and had a positive and significant association with yield. Longer fruits, heavy fruits and a high number of fruits are variables that are related to higher yields of chili pepper under tropical conditions and hence could be used as a reliable indicator in indirect selection for yield. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  19. Genotypic diversity of european Phytophthora ramorum isolates based on SSR analysis (United States)

    Kris Van Poucke; Annelies Vercauteren; Martine Maes; Sabine Werres; Kurt Heungens


    in Scotland were genotyped using seven microsatellite markers as described by Vercauteren et al. (2010). Thirty multilocus genotypes were identified within the Scottish population, with 51 percent of the isolates belonging to the main European genotype EU1MG1 and 13 unique detected genotypes. Ten of those genotypes were site specific, often represented by...

  20. SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays

    Directory of Open Access Journals (Sweden)

    Stephen W. Erickson


    Full Text Available SNPMClust is an R package for genotype clustering and calling with Illumina microarrays. It was originally developed for studies using the GoldenGate custom genotyping platform but can be used with other Illumina platforms, including Infinium BeadChip. The algorithm first rescales the fluorescent signal intensity data, adds empirically derived pseudo-data to minor allele genotype clusters, then uses the package mclust for bivariate Gaussian model fitting. We compared the accuracy and sensitivity of SNPMClust to that of GenCall, Illumina's proprietary algorithm, on a data set of 94 whole-genome amplified buccal (cheek swab DNA samples. These samples were genotyped on a custom panel which included 1064 SNPs for which the true genotype was known with high confidence. SNPMClust produced uniformly lower false call rates over a wide range of overall call rates.

  1. Micropropagation of six Paulownia genotypes through tissue culture

    Directory of Open Access Journals (Sweden)

    Lydia Shtereva


    Full Text Available We investigated the effect of genotype and culture medium on the in vitro germination and development of plantlets from seeds of 6 different Paulownia genotypes (P. tomentosa, hybrid lines P. tomentosa P. fortunei (Mega, Ganter and Caroline, P. elongata and hybrid line P. elongata P. fortunei. Nodal and shoot tip explants were used for micropropagation of Paulownia genotypes by manipulating plant growth regulators. The highest germination percentage for all genotypes was obtained for seeds inoculated on medium supplemented with 50 mg*L GA3 (MSG2. On Thidiazuron containing media, the explants of hybrid line P. elongata P. fortunei exhibited the highest frequency of axillary shoot proliferation following by P. tomentosa P. fortunei. The results are discussed with the perspective of applying an improved protocol for in vitro seed germination and plantlet formation in several economically valuable Paulownia genotypes.

  2. Test of IL28B polymorphisms in chronic hepatitis C patients treated with PegIFN and ribavirin depends on HCV genotypes: results from a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Zhifang Jia

    Full Text Available Many studies have been published on the association between single nucleotide polymorphisms (SNP near the IL28B gene and response to the combined treatments of pegylated-interferon (PegIFN and ribavirin (RBV in chronic HCV-infected patients, but without identical conclusions. The aim of this study was to assess impact of the IL28B polymorphisms on the effect of HCV standard treatment using meta-analysis based method.Association studies between polymorphisms of rs12979860 or rs8099917 and response to PegIFN/RBV treatment in chronic HCV patients were retrieved from PubMed. Data of qualified studies on sustained virological response (SVR in different genotypes were extracted and analyzed using meta-analysis method in Stata 10 software.Thirty-four papers, containing 46 independent studies, were included in the analysis. In the HCV G1/4 patients without treatment history, individuals carrying rs12979860 CC genotype were more likely to achieve SVR (OR 3.97, 95%CI 3.29-4.80 compared to those carrying CT/TT genotypes. Similar results were observed in the HCV G1/4 patients with unsuccessful or unknown treatment history (OR 3.76, 95%CI 2.67-5.28 or in the patients co-infected with human immunodeficiency virus (OR 5.20, 95%CI 3.04-8.90. However, associations could not be observed in HCV G2/3 patients. For rs8099917, similar results were obtained for genotype TT compared to genotypes TG/GG, indicating that TT genotype was significantly associated with better treatment response in patients infected with genotype 1 or 4 HCV, but not genotype 2 or 3 HCV.Polymorphisms of rs12979860 and rs8099917 near IL28B only associate with the treatment response to PegIFN/RBV in patients infected with HCV genotype 1 or 4 but not with genotype 2 or 3, irrespective of the previous treatment history or HIV co-infected status. Therefore, identification of IL28B genotypes is necessary only in patients infected with relatively difficult-to-treat genotype 1 or 4 HCV.

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

    Directory of Open Access Journals (Sweden)

    Maryam Niyyati


    Full Text Available 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.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.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.Overall, the present review will focus on present status of genotypes of Acanthamoeba in Iran during recent years.

  4. [Software for performing a global phenotypic and genotypic nutritional assessment]. (United States)

    García de Diego, L; Cuervo, M; Martínez, J A


    The nutritional assessment of a patient needs the simultaneous managing a extensive information and a great number of databases, as both aspects of the process of nutrition and the clinical situation of the patient are analyzed. The introduction of computers in the nutritional area constitutes an extraordinary advance in the administration of nutrition information, providing a complete assessment of nutritional aspects in a quick and easy way. To develop a computer program that can be used as a tool for assessing the nutritional status of the patient, the education of clinical staff, for epidemiological studies and for educational purposes. Based on a computer program which assists the health specialist to perform a full nutritional evaluation of the patient, through the registration and assessment of the phenotypic and genotypic features. The application provides nutritional prognosis based on anthropometric and biochemical parameters, images of states of malnutrition, questionnaires to characterize diseases, diagnostic criteria, identification of alleles associated with the development of specific metabolic illnesses and questionnaires of quality of life, for a custom actuation. The program includes, as part of the nutritional assessment of the patient, food intake analysis, design of diets and promotion of physical activity, introducing food frequency questionnaires, dietary recalls, healthy eating indexes, model diets, fitness tests, and recommendations, recalls and questionnaires of physical activity. A computer program performed under Java Swing, using SQLite database and some external libraries such as JfreeChart for plotting graphs. This brand new designed software is composed of five blocks categorized into ten modules named: Patients, Anthropometry, Clinical History, Biochemistry, Dietary History, Diagnostic (with genetic make up), Quality of life, Physical activity, Energy expenditure and Diets. Each module has a specific function which evaluates a

  5. The phenotype, psychotype and genotype of bruxism (United States)

    Cruz-Fierro, Norma; Martínez-Fierro, Margarita; Cerda-Flores, Ricardo M.; Gómez-Govea, Mayra A.; Delgado-Enciso, Iván; Martínez-De-Villarreal, Laura E.; González-Ramírez, Mónica T.; Rodríguez-Sánchez, Irám Pablo


    Bruxism is a jaw muscle activity that involves physio-pathological, psycho-social, hereditary and genetic factors. The purpose of this study was to determine the associations between self-reported bruxism, anxiety, and neuroticism personality trait with the rs6313 polymorphism in the gene HTR2A. A sample of 171 subjects of both sexes (14–53 years of age) was included. The control group (group 1, n=60) exhibited no signs or symptoms of bruxism. The case group had signs and symptoms of bruxism (n=112) and was subdivided into group 2, bruxism during sleep (n=22); group 3, awake bruxism (n=44); and group 4 combined bruxism (n=46). As diagnostic tools, the Self-Reported Bruxism Questionnaire (SBQ), the Beck Anxiety Inventory (BAI) and the Eysenck Personality Questionnaire Revised-Abbreviated (EPQR-A) were used. HTR2A (rs6313) SNPs were determined by qPCR for all the participants. The packages SPSS, maxLik and EPI-INFO were used for data analysis. The combined bruxism group reported higher scores in bruxism symptoms, mean = 32.21; anxiety symptoms, mean = 14.80; and neuroticism, mean = 3.26. Combined bruxism was associated with a higher degree of neuroticism (OR=15.0; CI 1.52–148.32) and anxiety in grade 3-moderate (OR=3.56; CI 1.27–10.03), and grade 4-severe (OR=8.40; CI 1.45–48.61), as determined using EPISODE computer software. Genotypic homogeneity analysis revealed no significant differences in allele frequency (P=0.612) among the four groups. The population was in Hardy-Weinberg equilibrium (maxLik package). In conclusion, the three instruments confirm traits of bruxism, anxiety and neuroticism in individuals with bruxism. These data were ratified when the sample was divided by genotypic homogeneity. On the other hand, there was no significant difference between the groups in the SNPs rs6313 from the HTR2A gene. PMID:29599979

  6. Rotavirus genotype shifts among Swedish children and adults-Application of a real-time PCR genotyping. (United States)

    Andersson, Maria; Lindh, Magnus


    It is well known that human rotavirus group A is the most important cause of severe diarrhoea in infants and young children. Less is known about rotavirus infections in other age groups, and about how rotavirus genotypes change over time in different age groups. Develop a real-time PCR to easily genotype rotavirus strains in order to monitor the pattern of circulating genotypes. In this study, rotavirus strains in clinical samples from children and adults in Western Sweden during 2010-2014 were retrospectively genotyped by using specific amplification of VP 4 and VP 7 genes with a new developed real-rime PCR. A genotype was identified in 97% of 775 rotavirus strains. G1P[8] was the most common genotype representing 34.9%, followed by G2P[4] (28.3%), G9P[8] (11.5%), G3P[8] (8.1%), and G4P[8] (7.9%) The genotype distribution changed over time, from predominance of G1P[8] in 2010-2012 to predominance of G2P[4] in 2013-2014. There were also age-related differences, with G1P[8] being the most common genotype in children under 2 years (47.6%), and G2P[4] the most common in those over 70 years of age (46.1%.). The shift to G2P[4] in 2013-2014 was associated with a change in the age distribution, with a greater number of rotavirus positive cases in elderly than in children. By using a new real-time PCR method for genotyping we found that genotype distribution was age related and changed over time with a decreasing proportion of G1P[8]. Copyright © 2017. Published by Elsevier B.V.

  7. A prospective study on symptom generation according to spicy food intake and TRPV1 genotypes in functional dyspepsia patients. (United States)

    Lee, S-Y; Masaoka, T; Han, H S; Matsuzaki, J; Hong, M J; Fukuhara, S; Choi, H S; Suzuki, H


    Capsaicin is an ingredient of red peppers that binds to transient receptor potential vanilloid subtype 1 (TRPV1), and Koreans eat more capsaicin-rich food than do Japanese. This study aimed to compare symptom generation according to TRPV1 genotypes and the intake of spicy foods. Consecutive functional dyspepsia (FD) patients who were evaluated at Konkuk University Medical Centre (Korea) and Keio University Hospital (Japan) were included. Questionnaires on spicy food intake, patient assessment of gastrointestinal symptoms (PAGI-SYM), patient assessment of quality of life, and hospital anxiety and depression scale were provided. Blood was sampled for the detection of TRPV1 polymorphisms, and upper gastrointestinal endoscopy was performed with biopsies. Of 121 included subjects, 35 and 28 carried the TRPV1 CC and GG genotypes, respectively, with the prevalence rates not differing between Japan and Korea. The prevalence of FD subtypes did not differ with the spicy food intake, TRPV1 genotypes, or Helicobacter pylori infection. Neither TRPV1 polymorphisms nor H. pylori infections were related to scores on the PAGI-SYM questionnaires, but spicy food intake was positively correlated with the scores for stomach fullness (p = 0.001) and retching (p = 0.001). Using the linear regression analysis, stomach fullness was associated with spicy food intake (p = 0.007), whereas retching was related to younger age (p foods, younger age and female gender, regardless of TRPV1 genotypes and the H. pylori infection status. Capsaicin-rich foods may induce stomach fullness. © 2016 John Wiley & Sons Ltd.

  8. Genotyping of vacA alleles of Helicobacter pylori strains recovered ...

    African Journals Online (AJOL)

    commonly detected genotypes in the meat-based foods, viz, vegetable sandwich and ready to eat fish, were vacA ... Keywords: Helicobacter pylori, VacA genotypes, Genotyping, Food items ..... Microbiology and Quality Control, Islamic Azad.

  9. Multiple sclerosis prevalence in Ireland: relationship to vitamin D status and HLA genotype.

    LENUS (Irish Health Repository)

    Lonergan, R


    BACKGROUND: The relationship between prevalence of multiple sclerosis (MS) and latitude may be due to both genetic and environmental factors. The hypothesis that, in Ireland, MS prevalence is increasing and that north-south differences relate to variation in serum 25-hydroxyvitamin D (25(OH)D) levels was tested in this study. PATIENTS AND METHODS: Patients and matched control subjects were identified in counties Donegal, Wexford and South Dublin through multiple sources. Prevalence was determined. Blood samples were taken for serum 25(OH)D and serum intact parathyroid hormone measurement, and DNA was extracted. RESULTS: Prevalence in 2007 was significantly greater in Donegal (northwest) (290.3\\/105, 95% CI 262.3 to 321.7) compared with 2001 (184.6\\/105; 162 to 209.5). In Wexford (southeast), there was a non-significant increase in prevalence in 2007 compared with 2001. Prevalence was significantly higher in Donegal than in Wexford (144.8\\/105; 126.7 to 167.8, p<0.0001) and South Dublin (127.8\\/105; 111.3 to 148.2, p<0.0001). Overall, mean 25(OH)D levels were low and did not differ between patients (38.6 nmol\\/l) and controls (36.4 nmol\\/l) However, significantly more patients than controls had 25(OH)D levels <25 nmol\\/l (deficiency) (p=0.004). Levels of 25(OH)D (mean 50.74 nmol\\/l) were significantly higher in South Dublin (area with lowest prevalence) (p<0.0001) than in Donegal or Wexford. HLA DRB1*15 occurred most frequently in Donegal (greatest MS prevalence) and least frequently in South Dublin. CONCLUSION: Vitamin D deficiency is common in Ireland. Latitudinal variation in MS probably relates to an interaction between genetic factors and environment (25(OH)D levels), and MS risk may be modified by vitamin D in genetically susceptible individuals.

  10. Physical status of multiple human papillomavirus genotypes in flow-sorted cervical cancer cells

    NARCIS (Netherlands)

    Vermeulen, Christine F. W.; Jordanova, Ekaterina S.; Szuhai, Karoly; Kolkman-Uljee, Sandra; Vrede, M. Albert; Peters, Alexander A. W.; Schtturing, Ed; Fleuren, Gert Jan

    Multiple human papilloma virus (HPV) infections have been detected in cervical cancer. To investigate the significance of multiple HPV infections, we studied their prevalence in cancer samples from a low-risk (Dutch) and a high-risk (Surinamese) population and the correlation of HPV infection with

  11. A SNP Genotyping Array for Hexaploid Oat

    Directory of Open Access Journals (Sweden)

    Nicholas A. Tinker


    Full Text Available Recognizing a need in cultivated hexaploid oat ( L. for a reliable set of reference single nucleotide polymorphisms (SNPs, we have developed a 6000 (6K BeadChip design containing 257 Infinium I and 5486 Infinium II designs corresponding to 5743 SNPs. Of those, 4975 SNPs yielded successful assays after array manufacturing. These SNPs were discovered based on a variety of bioinformatics pipelines in complementary DNA (cDNA and genomic DNA originating from 20 or more diverse oat cultivars. The array was validated in 1100 samples from six recombinant inbred line (RIL mapping populations and sets of diverse oat cultivars and breeding lines, and provided approximately 3500 discernible Mendelian polymorphisms. Here, we present an annotation of these SNPs, including methods of discovery, gene identification and orthology, population-genetic characteristics, and tentative positions on an oat consensus map. We also evaluate a new cluster-based method of calling SNPs. The SNP design sequences are made publicly available, and the full SNP genotyping platform is available for commercial purchase from an independent third party.

  12. Genotyping of Canine parvovirus in western Mexico. (United States)

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


    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. © 2014 The Author(s).

  13. Forage yield and nitrogen nutrition dynamics of warm-season native forage genotypes under two shading levels and in full sunlight

    Directory of Open Access Journals (Sweden)

    Raquel Santiago Barro


    Full Text Available The successful achievement of a highly productive understorey pasture in silvopastoral systems depends on the use of well-adapted forage genotypes, showing good agronomic performance and persistence under shading and grazing. In this study, the herbage dry matter yield (DMY and nitrogen nutrition dynamics were determined in three native warm-season grasses (Paspalum regnellii, Paspalum dilatatum and Paspalum notatum and a forage legume (Arachis pintoi under two shading levels compared with full sun. The experiment was conducted in the Campanha region, Bagé, state of Rio Grande do Sul, Brazil, during two evaluation cycles (2008/2009 and 2009/2010. Three shade cloth levels (0%, 50% and 80% of light restriction were applied to the forage genotypes in a split plot design, in which shading levels were the main plot and forage genotypes were the subplots, with three replications. P. regnellii showed the highest accumulated DMY (1500 and 1700 g m-2, respectively, for the first and second evaluation cycles at all shading levels and showed no DMY decreased under the heavy shade (80%. Average DMY over the four genotypes under the 50% shade level was higher or equal compared with full sun. Influence of rainfall was observed on the DMY performance of all genotypes: the positive effect of moderate shading (50% on P. dilatatum and P. notatum DMY was associated to a low soil water availability status. Increased shading level resulted in high nitrogen nutrition index values on grasses, in comparison with full sun. All genotypes performed well under the moderate shading level, but the DMY of both P. regnellii and P. dilatatum and the herbage N content in P. notatum and A. pintoi of all genotypes stood out, showing that those main genotypes are promising to grow in silvopastoral systems at the Campanha region in southern Brazil.

  14. Antixenosis of bean genotypes to Chrysodeixis includens (Lepidoptera: Noctuidae

    Directory of Open Access Journals (Sweden)

    Rafaela Morando


    Full Text Available The objective of this work was to evaluate bean genotypes for resistance to soybean looper (Chrysodeixis includens. Initially, free-choice tests were carried out with 59 genotypes, divided into three groups according to leaf color intensity (dark green, light green, and medium green, in order to evaluate oviposition preference. Subsequently, 12 genotypes with high potential for resistance were selected, as well as two susceptible commercial standards. With these genotypes, new tests were performed for oviposition in a greenhouse, besides tests for attractiveness and consumption under laboratory conditions (26±2ºC, 65±10% RH, and 14 h light: 10 h dark photophase. In the no-choice test with adults, in the greenhouse, the 'IAC Jabola', Arcelina 1, 'IAC Boreal', 'Flor de Mayo', and 'IAC Formoso' genotypes were the least oviposited, showing antixenosis-type resistance for oviposition. In the free-choice test with larvae, Arcelina 4, 'BRS Horizonte', 'Pérola', H96A102-1-1-1-52, 'IAC Boreal', 'IAC Harmonia', and 'IAC Formoso' were the less consumed genotypes, which indicates antixenosis to feeding. In the no-choice test, all genotypes (except for 'IAPAR 57' expressed moderate levels of antixenosis to feeding against C. includens larvae.

  15. Porphyromonas gingivalis Fim-A genotype distribution among Colombians (United States)

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


    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

  16. Assessing accuracy of genotype imputation in American Indians.

    Directory of Open Access Journals (Sweden)

    Alka Malhotra

    Full Text Available Genotype imputation is commonly used in genetic association studies to test untyped variants using information on linkage disequilibrium (LD with typed markers. Imputing genotypes requires a suitable reference population in which the LD pattern is known, most often one selected from HapMap. However, some populations, such as American Indians, are not represented in HapMap. In the present study, we assessed accuracy of imputation using HapMap reference populations in a genome-wide association study in Pima Indians.Data from six randomly selected chromosomes were used. Genotypes in the study population were masked (either 1% or 20% of SNPs available for a given chromosome. The masked genotypes were then imputed using the software Markov Chain Haplotyping Algorithm. Using four HapMap reference populations, average genotype error rates ranged from 7.86% for Mexican Americans to 22.30% for Yoruba. In contrast, use of the original Pima Indian data as a reference resulted in an average error rate of 1.73%.Our results suggest that the use of HapMap reference populations results in substantial inaccuracy in the imputation of genotypes in American Indians. A possible solution would be to densely genotype or sequence a reference American Indian population.

  17. Genetic similarity of soybean genotypes revealed by seed protein

    Directory of Open Access Journals (Sweden)

    Nikolić Ana


    Full Text Available More accurate and complete descriptions of genotypes could help determinate future breeding strategies and facilitate introgression of new genotypes in current soybean genetic pool. The objective of this study was to characterize 20 soybean genotypes from the Maize Research Institute "Zemun Polje" collection, which have good agronomic performances, high yield, lodging and drought resistance, and low shuttering by seed proteins as biochemical markers. Seed proteins were isolated and separated by PAA electrophoresis. On the basis of the presence/absence of protein fractions coefficients of similarity were calculated as Dice and Roger and Tanamoto coefficient between pairs of genotypes. The similarity matrix was submitted for hierarchical cluster analysis of un weighted pair group using arithmetic average (UPGMA method and necessary computation were performed using NTSYS-pc program. Protein seed analysis confirmed low level of genetic diversity in soybean. The highest genetic similarity was between genotypes P9272 and Kador. According to obtained results, soybean genotypes were assigned in two larger groups and coefficients of similarity showed similar results. Because of the lack of pedigree data for analyzed genotypes, correspondence with marker data could not be determined. In plant with a narrow genetic base in their gene pool, such as soybean, protein markers may not be sufficient for characterization and study of genetic diversity.

  18. Glutathione S-transferase M1 null genotype: lack of association with tumour characteristics and survival in advanced breast cancer

    International Nuclear Information System (INIS)

    Lizard-Nacol, Sarab; Coudert, Bruno; Colosetti, Pascal; Riedinger, Jean-Marc; Fargeot, Pierre; Brunet-Lecomte, Patrick


    Glutathione S-transferase (GST)M1, a member of the μ class GST gene family, has been shown to be polymorphic because of a partial gene deletion. This results in a failure to express the GSTM1 gene in 50-60% of individuals. Several studies have demonstrated a possible link with the GSTM1-null genotype and susceptibility to cancer. Furthermore, a GSTM1 isoenzyme has been positively associated with protective effect against mutagenic drugs, such as alkylating agents and anthracyclines. To determine whether GSTM1 polymorphisms are associated with tumour characteristics and survival in advanced breast cancer patients, and whether it may constitute a prognostic factor. We genotyped 92 patients receiving primary chemotherapy, which included cyclophosphamide, doxorubicine and 5-fluorouracil. The relationships between allelism at GSTM1 and clinicopathological parameters including age, menopausal status, tumour size, grade hormone receptors, involved nodes and p53 gene mutations were analysed. Of the patients with GSTM1-positive genotype, tissue samples obtained before and after treatment were available from 28 cases, allowing RNA extraction and GSTM1 expression by reverse transcription polymerase chain reaction. Relationships with clinical response to chemotherapy, and disease-free and overall survival were also evaluated. The data obtained was analysed using logistic regression to estimate the odds ratio and 95% confidence interval. Of 92 patients, 57.6% (n = 53) were classified as heritably GSTM1-deficient, and 42.4% (n = 39) were of the GSTM1-positive genotype. There were no statistically significant relationships between GSTM1-null genotype and the clinicopathological parameters analysed. No relationship was observed between GSTM1 RNA expression and objective clinical response to chemotherapy. Objective clinical response to chemotherapy was related only to clinical tumour size (P = 0.0177) and to the absence of intraductal carcinoma (P = 0.0013). GSTM1-null genotype

  19. MMP-8 genotypes influence the inflammatory response in human endotoxemia. (United States)

    Rella, Judith M; Jilma, Bernd; Fabry, Astrid; Kaynar, A Murat; Mayr, Florian B


    Clinical studies have reported associations between MMP-8 genotypes and clinical outcomes without exploring underlying mechanisms. This study aims to understand the influence of the rs1940475 SNP on downstream chemokine and cytokine response in human endotoxemia. Rs1940475 was genotyped in 44 healthy Caucasian males, who were challenged with an intravenous bolus of 2 ng/kg lipopolysaccharide (LPS). Plasma levels of tumor necrosis factor (TNF), interleukin (IL)-6, IL-8, and macrophage inflammatory protein (MIP)-1α were measured at baseline and 2, 4, 6, and 24 h after LPS infusion with high-sensitivity enzyme immunoassays. Peak TNF levels at 2 h after LPS infusion were significantly higher in subjects with AA genotype compared to subjects with AG or GG genotypes (185 pg/mL [IQR, 154-234] vs. 94 pg/mL [IQR, 65-125] vs. 107 pg/mL [IQR, 80-241], respectively; p = 0.03 between groups). Peak IL-6 levels were trend-wise higher in subjects with AA genotype compared to those with AG or GG genotypes (566 pg/mL [IQR, 294-644] vs. 278 pg/mL [IQR, 184-539] and 329 pg/mL [IQR, 240-492], respectively; p = 0.15 between groups). In contrast, peak MIP-1α at 2 h was highest in GG genotype carriers compared to those with AG or AA genotypes (602 pg/mL [IQR, 449-727] vs. 389 pg/mL [IQR, 375-490] and 510 pg/mL [425-813], respectively; p < 0.03 between groups). AA genotype carriers had highest peak TNF and IL-6 levels after LPS challenge, whereas peak MIP-1α levels were highest in GG carriers. This indicates that the rs1940475 SNP modifies the host response to inflammatory stimuli, which may in part explain previously shown associations with clinical outcomes.

  20. Genotype by sex and genotype by age interactions with sedentary behavior: the Portuguese Healthy Family Study.

    Directory of Open Access Journals (Sweden)

    Daniel M V Santos

    Full Text Available 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.

  1. Evaluation of Soybean and Cowpea Genotypes for Phosphorus Use Efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Kumaga, F. K.; Ofori, K.; Adiku, S. K.; Kugblenu, Y. O.; Asante, W.; Seidu, H. [College of Agriculture and Consumer Sciences, University of Ghana, Legon, Accra (Ghana); Adu-Gyamfi, J. J. [Soil and Water Management and Crop Nutrition Laboratory, International Atomic Energy Agency, Vienna (Austria)


    Initial screening of one hundred and fifty-two (152) and fifty (50) genotypes of soybean and cowpea, respectively, were conducted at the early growth stage to evaluate root traits associated with phosphorus (P) efficiency. Fifty soybean genotypes were subsequently selected and evaluated on a tropical low P soil (Lixisol) for growth and yield under low and adequate P availability. Plants were sampled at twelve and thirty days after sowing and at maturity. Six cowpea genotypes were also selected and evaluated in pots filled with Alfisol under low, moderate and high P availability. Plants were sampled at forty days and assessed for shoot yield and nodulation under low P availability. Using Principal Component Analysis (PCA), Phosphorus Efficiency Index (PEI) was used to determine P efficiency of soybean and cowpea genotypes. A wide variation in root traits for soybean and cowpea at the early growth stage was found, and allometric analysis showed a significant correlation between the root and shoot parameters at this stage. The study provided an opportunity to compare root traits of newly developed cowpea genotypes (early maturing, medium maturing, dual purpose and Striga resistant lines) with older released cultivars. There were significant differences in root length among the groups. In general, dual purpose, Striga resistant and medium/early maturing genotypes showed the longest roots while the older varieties showed the least total root length. Field and pot results also showed differential growth of soybean and cowpea with low P availability. Further, PCA of the results indicated that soybean genotypes could be grouped into three distinct P efficiency categories. Retaining the PC and the relative weight for each genotype in combination with yield potential under high P, four categories of responsiveness to P were obtained. Cowpea genotypes were grouped into three P efficiency categories and two categories of responsiveness to P. The study also found genetic

  2. Association of water spectral indices with plant and soil water relations in contrasting wheat genotypes. (United States)

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


    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 (r(2) >0.6-0.8) with leaf water potential (psi(leaf)) 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 (psi(soil)) 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

  3. IL28B genotype is not useful for predicting treatment outcome in Asian chronic hepatitis B patients treated with pegylated interferon-α. (United States)

    Holmes, Jacinta A; Nguyen, Tin; Ratnam, Dilip; Heerasing, Neel M; Tehan, Jane V; Bonanzinga, Sara; Dev, Anouk; Bell, Sally; Pianko, Stephen; Chen, Robert; Visvanathan, Kumar; Hammond, Rachel; Iser, David; Rusli, Ferry; Sievert, William; Desmond, Paul V; Bowden, D Scott; Thompson, Alexander J


    IL28B genotype predicts response to pegylated interferon (peg-IFN)-based therapy in chronic hepatitis C. However, the utility of IL28B genotyping in chronic hepatitis B (CHB) cohorts treated with peg-IFN is unclear. It was investigated whether IL28B genotype is associated with peg-IFN treatment outcomes in a predominantly Asian CHB cohort. This was a retrospective analysis of CHB patients treated with 48 weeks of peg-IFN monotherapy. IL28B genotype (rs12979860) was determined (TaqMan allelic discrimination kit). Baseline hepatitis B virus (HBV)-DNA, alanine aminotransferase, and liver histology were available. The primary end-points were HBV e antigen (HBeAg) seroconversion with HBV-DNA < 2000 IU/mL 24 weeks post-therapy (HBeAg-positive patients) and HBV-DNA < 2000 IU/mL 24 weeks after peg-IFN (HBeAg-negative patients). The association between IL28B genotype and peg-IFN outcomes was analyzed. IL28B genotype was determined for 96 patients. Eighty-eight percent were Asian, 62% were HBeAg positive, and 13% were METAVIR stage F3-4. Median follow-up time was 39.3 months. The majority of patients carried the CC IL28B genotype (84%). IL28B genotype did not differ according to HBeAg status. The primary end-points were achieved in 27% of HBeAg-positive and 61% of HBeAg-negative patients. There was no association between IL28B genotype and the primary end-point in either group. Furthermore, there was no difference in HBeAg loss alone, HBV surface antigen, alanine aminotransferase normalization, or on-treatment HBV-DNA levels according to IL28B genotype. In the context of a small possible effect size and high frequency in Asian populations, IL28B genotyping is likely to have, at best, limited clinical utility for predicting peg-IFN treatment outcome for CHB patients in the Asia-Pacific region. © 2013 Journal of Gastroenterology and Hepatology Foundation and Wiley Publishing Asia Pty Ltd.

  4. Genotyping-by-sequencing data of 272 crested wheatgrass (Agropyron cristatum genotypes

    Directory of Open Access Journals (Sweden)

    Pingchuan Li


    Full Text Available Crested wheatgrass [Agropyron cristatum L. (Gaertn.] is an important cool-season forage grass widely used for early spring grazing. However, the genomic resources for this non-model plant are still lacking. Our goal was to generate the first set of next generation sequencing data using the genotyping-by-sequencing technique. A total of 272 crested wheatgrass plants representing seven breeding lines, five cultivars and five geographically diverse accessions were sequenced with an Illumina MiSeq instrument. These sequence datasets were processed using different bioinformatics tools to generate contigs for diploid and tetraploid plants and SNPs for diploid plants. Together, these genomic resources form a fundamental basis for genomic studies of crested wheatgrass and other wheatgrass species. The raw reads were deposited into Sequence Read Archive (SRA database under NCBI accession SRP115373 ( and the supplementary datasets are accessible in Figshare (10.6084/m9.figshare.5345092. Keywords: Crested wheatgrass, Genotyping-by-sequencing, Diploid, Tetraploid, Raw sequence data

  5. Hepatitis E Virus Genotype 3 in Sewage and Genotype 1 in Acute Hepatitis Cases, Israel (United States)

    Ram, Daniela; Manor, Yossi; Gozlan, Yael; Schwartz, Eli; Ben-Ari, Ziv; Mendelson, Ella; Mor, Orna


    Hepatitis E virus (HEV) is an emerging infectious agent in developed countries. HEV genotypes 1 (G1) and 3 (G3) have been identified in environmental and clinical samples in Europe. In Israel, the overall prevalence of anti-HEV IgG antibodies was found to be 10.6%; however, reports of HEV infection are scarce. In this study, the presence of HEV in Israel was investigated using 169 sewage samples from 32 treatment facilities and 49 samples from acute hepatitis patients, all collected between 2013 and 2015. Fourteen sewage samples, from Haifa (11/18 samples), Tel Aviv (2/29 samples), and Beer Sheva (1/17 samples), regions with good sanitary conditions and middle-high socioeconomic populations, were HEV positive. Among the patient samples, 6.1% (3/49) were HEV positive, all returning travelers from India. Genotype analysis revealed G1 HEV in patients and G3 HEV sequences in sewage. Evidence that HEV could be establishing itself in our region may justify more active surveillance to monitor its spread. PMID:27246446

  6. Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies

    Directory of Open Access Journals (Sweden)

    Katy Denise Heath


    Full Text Available Predicting how species interactions evolve requires that we understand the mechanistic basis of coevolution, and thus the functional genotype-by-genotype interactions (G × G that drive reciprocal natural selection. Theory on host-parasite coevolution provides testable hypotheses for empiricists, but depends upon models of functional G × G that remain loosely tethered to the molecular details of any particular system. In practice, reciprocal cross-infection studies are often used to partition the variation in infection or fitness in a population that is attributable to G × G (statistical G × G. Here we use simulations to demonstrate that within-population statistical G × G likely tells us little about the existence of coevolution, its strength, or the genetic basis of functional G × G. Combined with studies of multiple populations or points in time, mapping and molecular techniques can bridge the gap between natural variation and mechanistic models of coevolution, while model-based statistics can formally confront coevolutionary models with cross-infection data. Together these approaches provide a robust framework for inferring the infection genetics underlying statistical G × G, helping unravel the genetic basis of coevolution.

  7. Analysis of the genetic diversity of four rabbit genotypes using ...

    African Journals Online (AJOL)



    May 15, 2013 ... consumption and low cost, it has been widely utilized in genetics analysis in ... isozyme variation among the selected individuals within each rabbit genotype. ... with different embryo survival (Bolet and Theau-Clement, 1994).

  8. Genotype x environment interaction and stability analysis for yield ...

    African Journals Online (AJOL)



    . Combined analysis of variance (ANOVA) for yield and yield components revealed highly significant .... yield stability among varieties, multi-location trials with ... Mean grain yield (kg/ha) of 17 Kabuli-type chickpea genotypes ...

  9. Sofosbuvir based treatment of chronic hepatitis C genotype 3 infections

    DEFF Research Database (Denmark)

    Dalgard, Olav; Weiland, Ola; Noraberg, Geir


    BACKGROUND AND AIMS: Chronic hepatitis C virus (HCV) genotype 3 infection with advanced liver disease has emerged as the most challenging to treat. We retrospectively assessed the treatment outcome of sofosbuvir (SOF) based regimes for treatment of HCV genotype 3 infections in a real life setting...... in Scandinavia. METHODS: Consecutive patients with chronic HCV genotype 3 infection were enrolled at 16 treatment centers in Denmark, Sweden, Norway and Finland. Patients who had received a SOF containing regimen were included. The fibrosis stage was evaluated by liver biopsy or transient liver elastography...... was similar for all treatment regimens, but lower in men (p = 0.042), and in patients with decompensated liver disease (p = 0.004). CONCLUSION: We found that sofosbuvir based treatment in a real-life setting could offer SVR rates exceeding 90% in patients with HCV genotype 3 infection and advanced liver...

  10. Evaluation of 14 winter bread wheat genotypes in normal irrigation ...

    African Journals Online (AJOL)

    Evaluation of 14 winter bread wheat genotypes in normal irrigation and stress conditions after anthesis stage. ... African Journal of Biotechnology ... Using biplot graphic method, comparison of indices amounts and mean rating of indices for ...

  11. adaptation of introduced mungbean genotypes in uganda abstract

    African Journals Online (AJOL)


    locations in Uganda, to determine the adaptability of introduced mungbean genotypes, and identify ... The six test multi-locations were grouped into two candidate mega-environments for ..... interactions: Challenges and opportunities for.

  12. cyanide cassava genotypes in acid ultisols of south eastern Nigeria

    African Journals Online (AJOL)

    ENGR C.J


    Jan 29, 2014 ... Thirty-eight high and low cyanide cassava genotypes were evaluated for growth and .... sium (K) and sodium (Na) were determined by Flamephoto-metory .... outlined for randomized complete block design (Steel et al., 1997).

  13. Molecular methods for bacterial genotyping and analyzed gene regions

    Directory of Open Access Journals (Sweden)

    İbrahim Halil Yıldırım1, Seval Cing Yıldırım2, Nadir Koçak3


    Full Text Available Bacterial strain typing is an important process for diagnosis, treatment and epidemiological investigations. Current bacterial strain typing methods may be classified into two main categories: phenotyping and genotyping. Phenotypic characters are the reflection of genetic contents. Genotyping, which refers discrimination of bacterial strains based on their genetic content, has recently become widely used for bacterial strain typing. The methods already used in genotypingof bacteria are quite different from each other. In this review we tried to summarize the basic principles of DNA-based methods used in genotyping of bacteria and describe some important DNA regions that are used in genotyping of bacteria. J Microbiol Infect Dis 2011;1(1:42-46.

  14. Effects of nutritional supplementation and genotype on milk ...

    African Journals Online (AJOL)

    Effects of nutritional supplementation and genotype on milk production and fertility of lactating dairy ... Bulletin of Animal Health and Production in Africa ... The objective of this study was to determine effects of nutrition on milk production and ...

  15. Effects of genotype x bradyrhizobium inoculation or x fertilizer n ...

    African Journals Online (AJOL)

    Genotype x inoculation interaction was significant only for protein and oil content in one year. .... main-plot factor. ... components and expected genetic gains invoiving yield srrnin. ... Combined analysis of the cu ltivar experiment was carried.

  16. Characterization of cowpea genotype resistance to Callosobruchus maculatus

    Directory of Open Access Journals (Sweden)

    Maria de Jesus Passos de Castro


    Full Text Available The objective of this work was to characterize the resistance of 50 cowpea (Vigna unguiculata genotypes to Callosobruchus maculatus. A completely randomized design with five replicates per treatment (genotype was used. No-choice tests were performed using the 50 cowpea genotypes to evaluate the preference for oviposition and the development of the weevil. The genotypes IT85 F-2687, MN05-841 B-49, MNC99-508-1, MNC99-510-8, TVu 1593, Canapuzinho-1-2, and Sanzi Sambili show non-preference-type resistance (oviposition and feeding. IT81 D-1045 Ereto and IT81 D-1045 Enramador exhibit antibiosis against C. maculatus and descend from resistant genitors, which grants them potential to be used in future crossings to obtain cowpea varieties with higher levels of resistance.

  17. Multiple centroid method to evaluate the adaptability of alfalfa genotypes

    Directory of Open Access Journals (Sweden)

    Moysés Nascimento


    Full Text Available This study aimed to evaluate the efficiency of multiple centroids to study the adaptability of alfalfa genotypes (Medicago sativa L.. In this method, the genotypes are compared with ideotypes defined by the bissegmented regression model, according to the researcher's interest. Thus, genotype classification is carried out as determined by the objective of the researcher and the proposed recommendation strategy. Despite the great potential of the method, it needs to be evaluated under the biological context (with real data. In this context, we used data on the evaluation of dry matter production of 92 alfalfa cultivars, with 20 cuttings, from an experiment in randomized blocks with two repetitions carried out from November 2004 to June 2006. The multiple centroid method proved efficient for classifying alfalfa genotypes. Moreover, it showed no unambiguous indications and provided that ideotypes were defined according to the researcher's interest, facilitating data interpretation.

  18. A preliminary investigation into genotype x environment interaction ...

    African Journals Online (AJOL)



    Aug 24, 2014 ... Genotype x environment interaction (G x E) in dairy cattle is a contentious ... environments, if it exists, with a negative impact on genetic response ..... interaction for Holstein milk yield in Colombia, Mexico and Puerto Rico.

  19. Giardia and Cryptosporidium species and genotypes in coyotes (Canis latrans). (United States)

    Trout, James M; Santín, Mónica; Fayer, Ronald


    Feces and duodenal scrapings were collected from 22 coyotes (Canis latrans) killed in managed hunts in northeastern Pennsylvania. Polymerase chain reaction (PCR) methods were used to detect Giardia and Cryptosporidium spp. PCR-amplified fragments of Giardia and Cryptosporidium spp. SSU-rRNA genes were subjected to DNA sequence analysis for species/genotype determination. Seven coyotes (32%) were positive for G. duodenalis: three assemblage C, three assemblage D, and one assemblage B. Six coyotes (27%) were positive for Cryptosporidium spp. One isolate shared 99.7% homology with C. muris, whereas five others (23%) shared 100% homology with C. canis, coyote genotype. This is the first report on multiple genotypes of Giardia spp. in coyotes and on the prevalence of Cryptosporidium spp. genotypes in coyotes.

  20. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)


    Oct 15, 2012 ... in human has been paralleled by the simultaneous develop- ment of ... In crop plants, the development of large genotyping arrays started much ..... via deep resequencing of reduced representation libraries with the Illumina ...

  1. Efficiency and response of conilon coffee genotypes to nitrogen supply

    African Journals Online (AJOL)



    Aug 31, 2016 ... tolerance to the deficit of these nutrients in the soil. (Colodetti et al., 2014; ... be passive of exploration using genotypes of rapid growth and low nutritional ... amino acids, proteins, nucleotides, hormones and chlorophyll ...

  2. Pollen diversity, viability and floral structure of some Musa genotypes

    African Journals Online (AJOL)

    Prof. Ogunji

    Pollen diversity, viability and floral structure of some Musa genotypes ... at the Faculty of Agriculture & Natural Resources Management farm, Ebonyi State University,. Abakaliki. ..... Roots, tuber, plantains and bananas in human nutrition. Rome,.

  3. High-throughput mouse genotyping using robotics automation. (United States)

    Linask, Kaari L; Lo, Cecilia W


    The use of mouse models is rapidly expanding in biomedical research. This has dictated the need for the rapid genotyping of mutant mouse colonies for more efficient utilization of animal holding space. We have established a high-throughput protocol for mouse genotyping using two robotics workstations: a liquid-handling robot to assemble PCR and a microfluidics electrophoresis robot for PCR product analysis. This dual-robotics setup incurs lower start-up costs than a fully automated system while still minimizing human intervention. Essential to this automation scheme is the construction of a database containing customized scripts for programming the robotics workstations. Using these scripts and the robotics systems, multiple combinations of genotyping reactions can be assembled simultaneously, allowing even complex genotyping data to be generated rapidly with consistency and accuracy. A detailed protocol, database, scripts, and additional background information are available at

  4. Genotype x environment interaction and stability analysis for yield ...

    African Journals Online (AJOL)



    May 6, 2015 ... 4Ethiopian Institute of Agriculture Research, Debre Zeit Agriculture Research Center, Ethiopia. Received .... interaction on seed yield of Kabuli -chickpea genotypes .... becomes important for the chickpea breeders in terms of.

  5. Assessment of genotype x environment interaction on yield and ...

    African Journals Online (AJOL)



    Apr 11, 2011 ... yield and yield components of durum wheat genotypes ... The results of combined analysis of variance showed a strong influence of the ... Stability is defined as the early prediction of environmental im- ... Many resear-.

  6. Genetic diversity of maize genotypes on the basis of morpho ...

    African Journals Online (AJOL)

    Genetic diversity of maize genotypes on the basis of morpho-physiological and simple sequence repeat (SSR) markers. Ashish Kumar, Arunita Rakshit, Naresh K Mangilipelli, Y Varalaxmi, T Vijayalakshmi, Jainender M Vanaja, SK Yadav, B Venkateswarlu, M Maheswari ...

  7. The Comparison of Growth, Slaughter and Carcass Traits of Meat Chicken Genotype Produced by Back-Crossing with A Commercial Broiler Genotype

    Directory of Open Access Journals (Sweden)

    Musa Sarıca


    Full Text Available This study was conducted to determine the growth and some slaughter traits between commercial fast growing chickens and three-way cross M2 genotypes. 260 male female mixed chickens from each genotype was reared 10 replicate per genotype in the same house. Two different slaughtering ages were applied to commercial chickens and slaughtered at 6 and 7 weeks of age for comparing with cross genotypes. F chickens reached to slaughtering age at 42 days, whereas cross groups reached at 49 days. Genotypes consumed same amount of feed until slaughtering ages, but F genotype had better feed conversion ratio. The differences between dressing percentage and carcass parts ratios of genotypes were found significant, and F genotype had higher dressing percentage. Carcass parts of all genotypes were found in acceptable limits.

  8. Effect of lifestyle factors on plasma total homocysteine concentrations in relation to MTHFR(C677T) genotype. Inter99 (7)

    DEFF Research Database (Denmark)

    Husemoen, L L N; Thomsen, T F; Fenger, M


    a Fluorescent Polarization Immuno Assay. MTHFR-genotype was determined by PCR and RFLP analysis. Information about lifestyle factors was obtained from a self-administered questionnaire. RESULTS: Daily smoking, less healthy dietary habits, and coffee drinking were associated with elevated tHcy concentrations......OBJECTIVE: To examine the associations between various lifestyle factors--smoking habits, physical activity, dietary habits, coffee, tea, and alcohol consumption--and homocysteine (tHcy) in relation to MTHFR(C677T) genotype. DESIGN: Cross-sectional population-based study. SETTING: Residents....... The effect of smoking was more pronounced in persons with the TT genotype and in women. The effect of beer consumption was more pronounced at younger than at older ages. CONCLUSIONS: Smoking status, dietary habits, coffee intake, wine, and beer consumption were major lifestyle determinants of tHcy. Changes...


    Directory of Open Access Journals (Sweden)

    Heni Safitri


    Full Text Available Salinity is one of the most serious problems in rice cultivation. Salinity drastically reduced plant growth and yield, especially at seedling stage. Several rice genotypes have been produced, but their tolerance to salinity has not yet been evaluated. The study aimed to evaluate salinity tolerance of rice genotypes at seedling stage. The glasshouse experiment was conducted at Cimanggu Experimental Station, Bogor, from April to May 2013. Thirteen rice genotypes and two check varieties, namely Pokkali (salt tolerant and IR29 (salt sensitive were tested at seedling stage. The experiment was arranged in a randomized complete block design with three replications and two factors, namely the levels of NaCl (0 and 120 mM and 13 genotypes of rice. Rice seedlings were grown in the nutrient culture (hydroponic supplemented with NaCl at different levels. The growth and salinity injury levels of the genotypes were recorded periodically. The results showed that salinity level of 120 mM NaCl reduced seedling growth of all rice genotypes, but the tolerant ones were survived after 14 days or until the sensitive check variety died. Based on the visual injury symptoms on the leaves, five genotypes, i.e. Dendang, Inpara 5, Inpari 29, IR77674-3B-8-2-2-14-4-AJY2, and IR81493-BBB-6-B- 2-1-2 were tolerant to 120 mM salinity level, while Inpara 4 was comparable to salt sensitive IR29. Hence, Inpara 4 could be used as a salinity sensitive genotype for future research of testing tolerant variety. Further evaluation is needed to confirm their salinity tolerance under field conditions. 

  10. Antioxidant Defense Mechanisms of Salinity Tolerance in Rice Genotypes

    Directory of Open Access Journals (Sweden)

    Mohammad Golam Kibria


    Full Text Available In order to elucidate the role of antioxidant responses in salinity tolerance in rice genotypes under salt stress, experiments were conducted using four rice varieties, including salt-sensitive BRRI dhan 28 and three salt-tolerant varieties BRRI dhan 47, BINA dhan 8 and BINA dhan 10. Thirty-day-old rice seedlings were transplanted into pots. At the active tillering stage (35 d after transplanting, plants were exposed to different salinity levels (0, 20, 40 and 60 mmol/L NaCl. Salt stress caused a significant reduction in growth for all the rice genotypes. Growth reduction was higher in the salt-sensitive genotype than in the salt-tolerant ones, and BINA dhan 10 showed higher salt tolerance in all measured physiological parameters. The reduction in shoot and root biomass was found to be minimal in BINA dhan 10. Chlorophyll content significantly decreased under salt stress except for BINA dhan 10. Proline content significantly increased in salt-tolerant rice genotypes with increased salt concentration, and the highest proline content was obtained from BINA dhan 10 under salt stress. Catalase and ascorbate peroxidase activities significantly decreased in salt-sensitive genotype whereas significantly increased in salt-tolerant ones with increasing salt concentration. However, salt stress significantly decreased guaiacol peroxidase activity in all the rice genotypes irrespective of salt tolerance. K+/Na+ ratio also significantly decreased in shoots and roots of all the rice genotypes. The salt-tolerant genotype BINA dhan 10 maintained higher levels of chlorophyll and proline contents as well as catalase and ascorbate peroxidase activities under salt stress, thus, this might be the underlying mechanism for salt tolerance.

  11. Comparative salinity responses among tomato genotypes and rootstocks

    International Nuclear Information System (INIS)

    Oztekin, G.B.; Tuzel, Y.


    Salinity is a major constraint limiting agricultural crop productivity in the world. However, plant species and cultivars differ greatly in their response to salinity. This study was conducted in a greenhouse to determine the response of 4 commercial tomato rootstocks, 21 cultivars and 8 candidate varieties to salinity stress. Seeds were germinated in peat and when the plants were at the fifth-true leaf stage, salt treatment was initiated except control treatment. NaCl was added to nutrient solution daily with 25 mM concentration and had been reached to 200 mM final concentration. On harvest day, genotypes were classified based on the severity of leaf symptoms caused by NaCl treatment. After symptom scoring, the plants were harvested and leaf number, root length, stem length and diameter per plant were measured. The plants were separated into shoots and roots for dry matter production. Our results showed that, on average, NaCl stress decreased all parameters and the rootstocks gave the highest performance than genotypes. Among all rootstocks, three varieties (2211 and 2275) and ten genotypes (Astona, Astona RN, Caracas, Deniz, Durinta, Export, Gokce, Target, Yeni Talya and 144 HY) were selected as tolerant with slight chlorosis whereas the genotype Malike was selected as sensitive with severe chlorosis. Candidate varieties 2316 and 1482 were the most sensitive ones. Plant growth and dry matter production differed among the tested genotypes. However no correlation was found between plant growth and dry matter production. Rootstock Beaufort gave the highest shoot dry matter although Heman had highest root dry matter. Newton showed more shoot and root dry matter than other genotypes. It is concluded that screening of genotypes based on severity of symptoms at early stage of development and their dry matter production could be used as a tool to indicate genotypic variation to salt stress. (author)

  12. Prevalence of American Foulbrood and Paenibacillus Larvae Genotypes in Bulgaria


    RUSENOVA, Nikolina; PARVANOV, Parvan


    This study aimed to analyse the prevalence of American foulbrood and Paenibacillus larvae genotypes in Bulgaria. For this purpose, data concerning American foulbrood outbreaks were used. Also, available data on the number of destroyed bee families covering a twenty-five-year period (1989 - 2013) was collected from the register of Bulgarian Food Safety Agency. In addition, Paenibacillus larvae genotypes in 15 apiaries were established by rep - PCR with BOXA1R and MBOREP1 primers. Results showe...

  13. Genotype-Specific Measles Transmissibility: A Branching Process Analysis. (United States)

    Ackley, Sarah F; Hacker, Jill K; Enanoria, Wayne T A; Worden, Lee; Blumberg, Seth; Porco, Travis C; Zipprich, Jennifer


    Substantial heterogeneity in measles outbreak sizes may be due to genotype-specific transmissibility. Using a branching process analysis, we characterize differences in measles transmission by estimating the association between genotype and the reproduction number R among postelimination California measles cases during 2000-2015 (400 cases, 165 outbreaks). Assuming a negative binomial secondary case distribution, we fit a branching process model to the distribution of outbreak sizes using maximum likelihood and estimated the reproduction number R for a multigenotype model. Genotype B3 is found to be significantly more transmissible than other genotypes (P = .01) with an R of 0.64 (95% confidence interval [CI], .48-.71), while the R for all other genotypes combined is 0.43 (95% CI, .28-.54). This result is robust to excluding the 2014-2015 outbreak linked to Disneyland theme parks (referred to as "outbreak A" for conciseness and clarity) (P = .04) and modeling genotype as a random effect (P = .004 including outbreak A and P = .02 excluding outbreak A). This result was not accounted for by season of introduction, age of index case, or vaccination of the index case. The R for outbreaks with a school-aged index case is 0.69 (95% CI, .52-.78), while the R for outbreaks with a non-school-aged index case is 0.28 (95% CI, .19-.35), but this cannot account for differences between genotypes. Variability in measles transmissibility may have important implications for measles control; the vaccination threshold required for elimination may not be the same for all genotypes or age groups.

  14. The genetic diversity of hepatitis A genotype I in Bulgaria. (United States)

    Cella, Eleonora; Golkocheva-Markova, Elitsa N; Trandeva-Bankova, Diljana; Gregori, Giulia; Bruni, Roberto; Taffon, Stefania; Equestre, Michele; Costantino, Angela; Spoto, Silvia; Curtis, Melissa; Ciccaglione, Anna Rita; Ciccozzi, Massimo; Angeletti, Silvia


    The purpose of this study was to analyze sequences of hepatitis A virus (HAV) Ia and Ib genotypes from Bulgarian patients to investigate the molecular epidemiology of HAV genotype I during the years 2012 to 2014. Around 105 serum samples were collected by the Department of Virology of the National Center of Infectious and Parasitic Diseases in Bulgaria. The sequenced region encompassed the VP1/2A region of HAV genome. The sequences obtained from the samples were 103. For the phylogenetic analyses, 5 datasets were built to investigate the viral gene in/out flow among distinct HAV subpopulations in different geographic areas and to build a Bayesian dated tree, Bayesian phylogenetic and migration pattern analyses were performed. HAV Ib Bulgarian sequences mostly grouped into a single clade. This indicates that the Bulgarian epidemic is partially compartmentalized. It originated from a limited number of viruses and then spread through fecal-oral local transmission. HAV Ia Bulgarian sequences were intermixed with European sequences, suggesting that an Ia epidemic is not restricted to Bulgaria but can affect other European countries. The time-scaled phylogeny reconstruction showed the root of the tree dating in 2008 for genotype Ib and in 1999 for genotype Ia with a second epidemic entrance in 2003. The Bayesian skyline plot for genotype Ib showed a slow but continuous growth, sustained by fecal-oral route transmission. For genotype Ia, there was an exponential growth followed by a plateau, which suggests better infection control. Bidirectional viral flow for Ib genotype, involving different Bulgarian areas, was observed, whereas a unidirectional flow from Sofia to Ihtiman for genotype Ia was highlighted, suggesting the fecal-oral transmission route for Ia. Copyright © 2017 The Authors. Published by Wolters Kluwer Health, Inc. All rights reserved.

  15. Sex and PRNP genotype determination in preimplantation caprine embryos. (United States)

    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


    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. © 2010 Blackwell Verlag GmbH.

  16. Evaluation of allelopathic potential of safflower genotypes (Carthamus tinctorius L.

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    Motamedi Marzieh


    Full Text Available Forty safflower genotypes were grown under normal irrigation and drought stress. In the first experiment, the allelopathic potential of shoot residues was evaluated using the sandwich method. Each genotype residue (0.4 g was placed in a sterile Petri dish and two layers of agar were poured on that. Radish seeds were placed on agar medium. The radish seeds were cultivated without safflower residues as the controls. The length of the radicle, hypocotyl, and fresh biomass weight and seed germination percentages were measured. A pot experiment was also done on two genotypes with the highest and two with the lowest allelopathic activity selected after screening genotypes in the first experiment. Before entering the reproductive phase, irrigation treatments (normal irrigation and drought stress were applied. Shoots were harvested, dried, milled and mixed with the topsoil of new pots and then radish seeds were sown. The pots with safflower genotypes were used to evaluate the effect of root residue allelopathy. The shoot length, fresh biomass weight, and germination percentage were measured. Different safflower genotypes showed varied allelopathic potential. The results of the first experiment showed that Egypt and Iran-Khorasan genotypes caused maximum inhibitory responses and Australia and Iran-Kerman genotypes resulted in minimum inhibitory responses on radish seedling growth. Fresh biomass weight had the most sensitivity to safflower residues. The results of the pot experiment were consistent with the results of in vitro experiments. Residues produced under drought stress had more inhibitory effects on the measured traits. Safflower root residue may have a higher level of allelochemicals or different allelochemicals than shoot residue.

  17. Prevalence of Helicobacter pylori vacA Genotypes and cagA Gene in Dental Plaque of Asymptomatic Mexican Children (United States)

    Mendoza-Cantú, Alejandra; Urbina-Ríos, Cynthia Sofía; García-Martínez, Martha Elena; Torre-Martínez, Hilda H. H.


    The variability in Helicobacter pylori vacA and cagA genes has been related to the progression of the gastrointestinal disease; also the presence of H. pylori in the oral cavity has been associated with periodontal disease in adults, but, in children without dyspeptic symptoms, little is known about this. We evaluated the prevalence of H. pylori and the presence of vacA/cagA genotypes in the oral cavity of Mexican children without dyspeptic symptoms. The gingival status was measured, and dental plaque samples (n = 100) were taken. 38% of children were positive for H. pylori 16S rRNA gene by qPCR. A significant association between H. pylori oral infection and gingival status was observed (P < 0.001). In 34.6% (9/26) of mild gingivitis cases, s1m2 genotype was found, while s1m1 was typed in 50% (3/6) of moderate gingivitis. The cagA prevalence among H. pylori-positive children was 80.8% (21/26), 83.3% (5/6), and 16.7% (1/6) of cases of mild gingivitis, moderate gingivitis, and nongingivitis, respectively (P < 0.001). The s1m1/cagA+ combinational genotype was the most detected in children with gingivitis. Our results suggest that the prevalence of H. pylori and detection of vacA/cagA genotypes-associated gastrointestinal disease in the oral cavity could be related to the progression of gingivitis in asymptomatic children. PMID:29226140

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

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    Guigao Lin

    Full Text Available 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.

  19. Prevalence of Helicobacter pylori vacA Genotypes and cagA Gene in Dental Plaque of Asymptomatic Mexican Children

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    Alejandra Mendoza-Cantú


    Full Text Available The variability in Helicobacter pylori vacA and cagA genes has been related to the progression of the gastrointestinal disease; also the presence of H. pylori in the oral cavity has been associated with periodontal disease in adults, but, in children without dyspeptic symptoms, little is known about this. We evaluated the prevalence of H. pylori and the presence of vacA/cagA genotypes in the oral cavity of Mexican children without dyspeptic symptoms. The gingival status was measured, and dental plaque samples (n=100 were taken. 38% of children were positive for H. pylori 16S rRNA gene by qPCR. A significant association between H. pylori oral infection and gingival status was observed (P<0.001. In 34.6% (9/26 of mild gingivitis cases, s1m2 genotype was found, while s1m1 was typed in 50% (3/6 of moderate gingivitis. The cagA prevalence among H. pylori-positive children was 80.8% (21/26, 83.3% (5/6, and 16.7% (1/6 of cases of mild gingivitis, moderate gingivitis, and nongingivitis, respectively (P<0.001. The s1m1/cagA+ combinational genotype was the most detected in children with gingivitis. Our results suggest that the prevalence of H. pylori and detection of vacA/cagA genotypes-associated gastrointestinal disease in the oral cavity could be related to the progression of gingivitis in asymptomatic children.

  20. Genotypic differences in phosphate nutrition of rice (Oryza Sativa L.)

    International Nuclear Information System (INIS)

    Bui Thi Hong Thanh; Zapata, F.; Bowen, G.D.; Kumarasinghe, K.S.


    Phosphate uptake and use by five genotypes of paddy rice were studied at five phosphate levels in pot studies for 49 days. For all five P levels there were marked genotypic differences in shoot growth, plant dry weight, root/shoot ratios, phosphate uptake and translocation, P content of roots and shoots, and phosphorus use efficiency of shoots (PUE, g shoot mg P -1 in shoot). There were significant genotypic differences in root weight (4 P levels) and in uptake/mg root (all P levels). These latter may have resulted from differences in root weight/root length conversion, root hair development or uptake characteristics, factors which were not studied specifically. Differences between genotypes and P levels in the percentage translocation were partly explicable by differences in P uptake/plant (r = 0.72) but especially by differences in root/shoot ratios (r = 0.89). Differences in PUE were largely a factor of P percentage of the tops (r = 0.94) but significant differences between genotypes were shown as a function of % P. Differences in net photosynthesis rates were largely, but not entirely, due to differences in P % of the shoots. Key factors in P uptake and use and genotypic differences are root growth, uptake/mg root, root/shoot ratios and PUE. (author). 9 refs, 2 figs, 3 tabs


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    Glenn eHyman


    Full Text Available 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 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 five or ten 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.

  2. High prevalence of Hepatitis C virus genotype 6 in Vietnam. (United States)

    Pham, Duc Anh; Leuangwutiwong, Pornsawan; Jittmittraphap, Akanitt; Luplertlop, Nattanej; Bach, Hoa Khanh; Akkarathamrongsin, Srunthron; Theamboonlers, Apiradee; Poovorawan, Yong


    This study aimed to update the prevalence of the various Hepatitis C virus genotypes in Vietnamese blood donors. One hundred and three HCV antibody-positive plasma samples were collected from blood donors at the National Institute of Hematology and Blood Transfusion, Hanoi, Vietnam. All specimens were subjected to RT-PCR of the 5' untranslated region (UTR) to confirm the presence of HCV RNA. The core and NS5B regions of thh positive samples were subsequently amplified by RT-PCR followed by direct sequencing and phylogenetic analysis. Seventy out of 103 samples (68.0%) were RNA positive. Core and NS5B were successfully amplified and sequences were obtained for 70 and 65 samples, respectively. Phylogenetic analysis revealed that genotype 6a was the most predominant among Vietnamese blood donors with a prevalence of 37.1% (26/70), followed by genotype 1a at 30.0% (21/70) and genotype 1b at 17.1% (12/70). The prevalence of two other genotype 6 variants, 6e and 61 was 8.6% and 1.4%, respectively. Further analysis of recent studies showed that the geographic distribution of genotype 6 covered mainly southern China and the mainland of Southeast Asia including Vietnam, Laos, Thailand, and Myanmar. The GenBank accession numbers for the sequences reported in this study are FJ768772-FJ768906.

  3. Evaluation of Different Rice Genotypes Tolerance to Saline Irrigation Water

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    S. Jafari Rad


    Full Text Available To study the responses of seven rice genotypes (Khazar, SA13, Deylam, Sange Joe, Sepidrud, 831 and T5 to different levels of irrigation water salinity, and determining grain yield based on tolerance indices, a CRD based factorial pot experiment with five levels of irrigation water salinity (1, 2, 4, 6 and 8 dSm-1 and three replications was carried out at Rice Research Institute of Iran in 2011. Indices such as SSI, TOL, MP, GMP, HM, STI, YI and YSI were calculated and their correlations with grain yield were estimated for both stress and non-stress conditions. Results indicated significant differences among genotypes and the indices within both conditions. Results also showed that STI and MP indices could be considered as the best indices to screen salt tolerant genotypes. Among the genotypes used in the experiment, T5 produced the highest yield in both non-stress (19.71 g/plant and stress (10.69 g/plant conditions, while the lowest yield in normal (11.84 g/plant and stressful (4.29 g/plant conditions was recorded for Deylam and Khazar, respectively. The highest and the lowest percentage of yield reduction were found in Khazar (69.49% and Sange Joe (31.48% in stressful conditions, respectively. Overall, genotypes T5, 831, Sepidrud and Sange Joe can probably be considered as superior high yielding genotypes in both saline and non-saline conditions for further research.

  4. Genotypic differences in phosphate nutrition of rice (Oryza Sativa L.)

    Energy Technology Data Exchange (ETDEWEB)

    Hong Thanh, Bui Thi; Zapata, F [FAO/IAEA Agriculture and Biotechnology Lab., Seibersdorf (Austria). Soils Science Unit; Bowen, G D; Kumarasinghe, K S [Joint FAO/IAEA Div. of Nuclear Techniques in Food and Agriculture, Vienna (Austria). Soil Fertility, Irrigation and Crop Production Section


    Phosphate uptake and use by five genotypes of paddy rice were studied at five phosphate levels in pot studies for 49 days. For all five P levels there were marked genotypic differences in shoot growth, plant dry weight, root/shoot ratios, phosphate uptake and translocation, P content of roots and shoots, and phosphorus use efficiency of shoots (PUE, g shoot mg P{sup -1} in shoot). There were significant genotypic differences in root weight (4 P levels) and in uptake/mg root (all P levels). These latter may have resulted from differences in root weight/root length conversion, root hair development or uptake characteristics, factors which were not studied specifically. Differences between genotypes and P levels in the percentage translocation were partly explicable by differences in P uptake/plant (r = 0.72) but especially by differences in root/shoot ratios (r = 0.89). Differences in PUE were largely a factor of P percentage of the tops (r = 0.94) but significant differences between genotypes were shown as a function of % P. Differences in net photosynthesis rates were largely, but not entirely, due to differences in P % of the shoots. Key factors in P uptake and use and genotypic differences are root growth, uptake/mg root, root/shoot ratios and PUE. (author). 9 refs, 2 figs, 3 tabs.

  5. Distribution of HCV genotypes among different exposure categories in Brazil

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    Oliveira M.L.A.


    Full Text Available Hepatitis C virus (HCV infection is widespread and responsible for more than 60% of chronic hepatitis cases. HCV presents a genetic variability which has led to viral classification into at least 6 genotypes and a series of subtypes. These variants present characteristic geographical distribution, but their association with different responses to treatment with interferon and severity of disease still remains controversial. The aim of this study was to investigate the patterns of distribution of HCV genotypes among different exposure categories in Brazil. Two hundred and fifty anti-HCV positive samples were submitted to HCV-RNA detection by RT-PCR and their genotype was determined by restriction fragment length polymorphism (RFLP analysis. In addition, the genotype/subtype of 60 samples was also determined by a reverse hybridization assay. HCV 1 was the most prevalent (72.0%, followed by type 3 (25.3%, HCV 2 (2.0% and HCV 4 (0.7%. The HCV genotype distribution varied among the different exposure categories, with HCV 1 being more frequent among blood donors, hemophiliacs and hemodialysis patients. A high frequency of HCV 3 was observed in cirrhotic patients, blood donors from the South of Brazil and injecting drug users (IDUs. The general distribution of the HCV genotype in Brazil is similar to that in other regions of the world.

  6. Genetic diversity of some chili (Capsicum annuum L. genotypes

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    M.J. Hasan


    Full Text Available A study on genetic diversity was conducted with 54 Chili (Capsicum annuum L. genotypes through Mohalanobis’s D2 and principal component analysis for twelve quantitative characters viz. plant height, number of secondary branch/plant, canopy breadth , days to first flowering, days to 50% flowering, fruits/plant, 5 fruits weight, fruit length, fruit diameter, seeds/fruit, 1000 seed weight and yield/plant were taken into consideration. Cluster analysis was used for grouping of 54 chili genotypes and the genotypes were fallen into seven clusters. Cluster II had maximum (13 and cluster III had the minimum number (1 of genotypes. The highest inter-cluster distance was observed between cluster I and III and the lowest between cluster II and VII. The characters yield/plant, canopy breadth, secondary branches/plant, plant height and seeds/fruit contributed most for divergence in the studied genotypes. Considering group distance, mean performance and variability the inter genotypic crosses between cluster I and cluster III, cluster III and cluster VI, cluster II and cluster III and cluster III and cluster VII may be suggested to use for future hybridization program.

  7. Genotyping panel for assessing response to cancer chemotherapy

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    Hampel Heather


    Full Text Available Abstract Background Variants in numerous genes are thought to affect the success or failure of cancer chemotherapy. Interindividual variability can result from genes involved in drug metabolism and transport, drug targets (receptors, enzymes, etc, and proteins relevant to cell survival (e.g., cell cycle, DNA repair, and apoptosis. The purpose of the current study is to establish a flexible, cost-effective, high-throughput genotyping platform for candidate genes involved in chemoresistance and -sensitivity, and treatment outcomes. Methods We have adopted SNPlex for genotyping 432 single nucleotide polymorphisms (SNPs in 160 candidate genes implicated in response to anticancer chemotherapy. Results The genotyping panels were applied to 39 patients with chronic lymphocytic leukemia undergoing flavopiridol chemotherapy, and 90 patients with colorectal cancer. 408 SNPs (94% produced successful genotyping results. Additional genotyping methods were established for polymorphisms undetectable by SNPlex, including multiplexed SNaPshot for CYP2D6 SNPs, and PCR amplification with fluorescently labeled primers for the UGT1A1 promoter (TAnTAA repeat polymorphism. Conclusion This genotyping panel is useful for supporting clinical anticancer drug trials to identify polymorphisms that contribute to interindividual variability in drug response. Availability of population genetic data across multiple studies has the potential to yield genetic biomarkers for optimizing anticancer therapy.

  8. Performance of Garden Pea Genotypes in Eastern Hills of Nepal

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    Krishna Poudel


    Full Text Available Garden pea (Pisum sativum L is an important winter legume used as fresh vegetables and other drier food products. Despite of its importance as cash crop in many parts of Nepal, much study on various aspects for enhancing production and productivity has yet to be done. Therefore, to evaluate the production performance different genotypes of garden pea in eastern hills agro-ecological conditions present experiments were carried out consecutively for two years (2015 and 2016 at Agricultural Research Station, Pakhribas. The experiment comprised of 11 different genotypes of garden pea including a check variety Arkel. The production performance was evaluated in a completely randomized block design with three replications. The seeds were sown at 50 × 10 cm spacing during first week of October for two years. The result showed that DGP-05 genotype had earliest 104 days after sowing. The DGP-08 genotype showed 13 which were the maximum numbers of pods per plant (13, while DGP-01 showed 8 numbers of seeds as the maximum per pod. The DGP-03 genotype had the longest pod of 9.78 cm among others. The highest fresh pod yield of 18.14 t/ha was achieved from genotype DGP-09 followed by Arkel with (16.32 t/ha.

  9. Characterization of some sunflower genotypes using ISSR markers

    International Nuclear Information System (INIS)

    Mokrani, L.; Nabulsi, I.; MirAli, N.


    Sunflower (Helianthus annuus L.) is grown mostly as a source of vegetable oil of high quality and is especially used in food industry. It is generally produced by multinationals and sold as hybrids. Our research, based on two techniques (ISSR and RAPD), is considered as the first one to be interested in molecular characterization of sunflower genotypes in Syria. We used 25 ISSR primers and 13 RAPD primers to study 29 sunflower genotypes and two reference controls belonging to the same family (Calendula officinalis L. and Targets erecta L.). ISSR results revealed a low polymorphism when compared to other studies. We noticed also 11 genotypes genetically related where percent disagreement values (PDV) didn't exceed 1%, they are 7189 - 7191 - 7184 - 7183 - 443 - 441 - Ghab1 -Ghab2 - Ghab3 - Ghab4 - Ghab5 - Madakh halab - Sarghaya4 -Tarkibi knitra. Sarghaya4 and Tarkibi knitra have indeed the lowest yield and some common morphological characters. At the opposite, the genotype Hysum33 has the highest yield and is genetically distant from the other genotypes. All the genotypes could be used in QTL detection as we didn't notice any similarity between them. (author)

  10. Direct maximum parsimony phylogeny reconstruction from genotype data. (United States)

    Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell


    Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

  11. Role of Helicobacter pylori cagA EPIYA motif and vacA genotypes for the development of gastrointestinal diseases in Southeast Asian countries: a meta-analysis

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    Sahara Shu


    Full Text Available Abstract Background Infection with cagA-positive, cagA EPIYA motif ABD type, and vacA s1, m1, and i1 genotype strains of Helicobacter pylori is associated with an exacerbated inflammatory response and increased risk of gastroduodenal diseases. However, it is unclear whether the prevalence and virulence factor genotypes found in Southeast Asia are similar to those in Western countries. Here, we examined the cagA status and prevalence of cagA EPIYA motifs and vacA genotypes among H. pylori strains found in Southeast Asia and examined their association with gastroduodenal disease. Methods To determine the cagA status, cagA EPIYA motifs, and vacA genotypes of H. pylori, we conducted meta-analyses of 13 previous reports for 1,281 H. pylori strains detected from several Southeast Asian countries. Results The respective frequencies of cagA-positive and vacA s1, m1, and i1 genotypes among examined subjects were 93% (1,056/1,133, 98% (1,010/1,033, 58% (581/1,009, and 96% (248/259, respectively. Stratification showed significant variation in the frequencies of cagA status and vacA genotypes among countries and the individual races residing within each respective country. The frequency of the vacA m-region genotype in patients infected with East Asian-type strains differed significantly between the northern and southern areas of Vietnam (p vacA m1 type or cagA-positive strains was associated with an increased risk of peptic ulcer disease (odds ratio: 1.46, 95%CI: 1.01-2.12, p = 0.046 and 2.83, 1.50-5.34, p = 0.001, respectively in the examined Southeast Asian populations. Conclusions Both Western- and East Asian-type strains of H. pylori are found in Southeast Asia and are predominantly cagA-positive and vacA s1 type. In Southeast Asia, patients infected with vacA m1 type or cagA-positive strains have an increased risk of peptic ulcer disease. Thus, testing for this genotype and the presence of cagA may have clinical usefulness.

  12. Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions. (United States)

    Luijckx, Pepijn; Ben-Ami, Frida; Mouton, Laurence; Du Pasquier, Louis; Ebert, Dieter


    The degree of specificity in host-parasite interactions has important implications for ecology and evolution. Unfortunately, specificity can be difficult to determine when parasites cannot be cultured. In such cases, studies often use isolates of unknown genetic composition, which may lead to an underestimation of specificity. We obtained the first clones of the unculturable bacterium Pasteuria ramosa, a parasite of Daphnia magna. Clonal genotypes of the parasite exhibited much more specific interactions with host genotypes than previous studies using isolates. Clones of P. ramosa infected fewer D. magna genotypes than isolates and host clones were either fully susceptible or fully resistant to the parasite. Our finding enhances our understanding of the evolution of virulence and coevolutionary dynamics in this system. We recommend caution when using P. ramosa isolates as the presence of multiple genotypes may influence the outcome and interpretation of some experiments. © 2010 Blackwell Publishing Ltd/CNRS.

  13. Innovations, status, and networks

    NARCIS (Netherlands)

    P. Wang (Pengfei)


    markdownabstractTo obtain and maintain competitive advantage, firms need to implement appropriate innovation strategies (i.e. exploration or exploitation) and acquire status in external networks. In this dissertation, I investigate how innovation strategy, status, and network structure jointly

  14. USCIS My Case Status (United States)

    Department of Homeland Security — USCIS provide a way for the public who applied for U.S. citizenship to check the status of their application online. To view the status of a case, the application...

  15. Root phosphatase activity, plant growth and phosphorus accumulation of maize genotypes

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    Machado Cynthia Torres de Toledo


    Full Text Available The activity of the enzyme phosphatase (P-ase is a physiological characteristic related to plant efficiency in relation to P acquisition and utilization, and is genetically variable. As part of a study on maize genotype characterization in relation to phosphorus (P uptake and utilization efficiency, two experiments were set up to measure phosphatase (P-ase activity in intact roots of six local and improved maize varieties and two sub-populations. Plants were grown at one P level in nutrient solution (4 mg L-1 and the P-ase activity assay was run using 17-day-old plants for varieties and 24-day-old plants for subpopulations. Shoot and root dry matter yields and P concentrations and contents in plant parts were determined, as well as P-efficiency indexes. Root P-ase activity differed among varieties, and highest enzimatic activities were observed in two local varieties -'Catetão' and 'Caiano' -and three improved varieties -'Sol da Manhã', 'Nitrodente' and 'BR 106'. 'Carioca', a local variety, had the lowest activity. Between subpopulations, 'ND2', with low yielding and poorly P-efficient plants, presented higher root P-ase activity as compared to 'ND10', high yielding and highly P-efficient plants. In general, subpopulations presented lower P-ase activities as compared to varieties. Positive and/or negative correlations were obtained between P-ase activity and P-efficiency characteristics, specific for the genotypes, not allowing inference on a general and clear association between root-secreted phosphatase and dry matter production or P acquisition. Genotypic variability must be known and considered before using P-ase activity as an indicator of P nutritional status, or P tolerance, adaptation and efficiency under low P conditions.

  16. In vitro screening of potato genotypes for osmotic stress tolerance

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    Gelmesa Dandena


    Full Text Available Potato (Solanum tuberosum L. is a cool season crop which is susceptible to both drought and heat stresses. Lack of suitable varieties of the crop adapted to drought-prone areas of the lowland tropics deprives farmers living in such areas the opportunity to produce and use the crop as a source of food and income. As a step towards developing such varieties, the present research was conducted to evaluate different potato genotypes for osmotic stress tolerance under in vitro conditions and identify drought tolerant genotypes for future field evaluation. The experiment was carried out at the Leibniz University of Hannover, Germany, by inducing osmotic stress using sorbitol at two concentrations (0.1 and 0.2 M in the culture medium. A total of 43 genotypes collected from different sources (27 advanced clones from CIP, nine improved varieties, and seven farmers’ cultivars were used in a completely randomized design with four replications in two rounds. Data were collected on root and shoot growth. The results revealed that the main effects of genotype, sorbitol treatment, and their interactions significantly (P < 0.01 influenced root and shoot growthrelated traits. Under osmotic stress, all the measured root and shoot growth traits were significantly correlated. The dendrogram obtained from the unweighted pair group method with arithmetic mean allowed grouping of the genotypes into tolerant, moderately tolerant, and susceptible ones to a sorbitol concentration of 0.2 M in the culture medium. Five advanced clones (CIP304350.100, CIP304405.47, CIP392745.7, CIP388676.1, and CIP388615.22 produced shoots and rooted earlier than all other genotypes, with higher root numbers, root length, shoot and root mass under osmotic stress conditions induced by sorbitol. Some of these genotypes had been previously identified as drought-tolerant under field conditions, suggesting the capacity of the in vitro evaluation method to predict drought stress tolerant

  17. Hepatitis C virus genotypes: A plausible association with viral loads

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    Salma Ghulam Nabi


    Full Text Available Background and Aim: The basic aim of this study was to find out the association of genotypes with host age, gender and viral load. Material and Methods: The present study was conducted at Social Security Hospital, Pakistan. This study included 320 patients with chronic hepatitis C virus (HCV infection who were referred to the hospital between November 2011 and July 2012. HCV viral detection and genotyping was performed and the association was seen between genotypes and host age, gender and viral load. Results : The analysis revealed the presence of genotypes 1 and 3 with further subtypes 1a, 1b, 3a, 3b and mixed genotypes 1b + 3a, 1b + 3b and 3a + 3b. Viral load quantification was carried out in all 151 HCV ribonucleic acid (RNA positive patients. The genotype 3a was observed in 124 (82.12% patients, 3b was found in 21 (13.91%, 1a was seen in 2 (1.32%, 1b in 1 (0.66%, mixed infection with 1b + 3a in 1 (0.66%, 1b + 3b in 1 (0.66% and 3a + 3b was also found in 1 (0.66% patient. Viral load quantification was carried out in all 151 HCV RNA positive patients and was compared between the various genotypes. The mean viral load in patients infected with genotype 1a was 2.75 × 10 6 , 1b 3.9 × 10 6 , 3a 2.65 × 10 6 , 3b 2.51 × 10 6 , 1b + 3a 3.4 × 106, 1b + 3b 2.7 × 106 and 3a + 3b 3.5 × 10 6 . An association between different types of genotypes and viral load was observed. Conclusion : Further studies should be carried out to determine the association of viral load with different genotypes so that sufficient data is available and can be used to determine the type and duration of therapy needed and predict disease outcome.

  18. A window into the transcriptomic basis of genotype-by-genotype interactions in the legume-rhizobia mutualism. (United States)

    Wood, Corlett W; Stinchcombe, John R


    The maintenance of genetic variation in the benefits provided by mutualists is an evolutionary puzzle (Heath & Stinchcombe, ). Over time, natural selection should favour the benefit strategy that confers the highest fitness, eroding genetic variation in partner quality. Yet abundant genetic variation in partner quality exists in many systems (Heath & Stinchcombe, ). One possible resolution to this puzzle is that the genetic identity of both a host and its partner affects the benefits each mutualist provides to the other, a pattern known as a genotype-by-genotype interaction (Figure ). Mounting evidence suggests that genotype-by-genotype interactions between partners are pervasive at the phenotypic level (Barrett, Zee, Bever, Miller, & Thrall, ; Heath, ; Hoeksema & Thompson, ). Ultimately, however, to link these phenotypic patterns to the maintenance of genetic variation in mutualisms we need to answer two questions: How much variation in mutualism phenotypes is attributable to genotype-by-genotype interactions, and what mutualistic functions are influenced by each partner and by the interaction between their genomes? In this issue of Molecular Ecology, Burghardt et al. (2017) use transcriptomics to address both questions in the legume-rhizobia mutualism. © 2017 John Wiley & Sons Ltd.

  19. integrated analysis for genotypic adaptation in rice abstract résumé

    African Journals Online (AJOL)


    The presence of genotype by environment (GxE) interaction plays a crucial role in determining the performance of ... assess yield performance, stability and adaptability of thirty-six rice genotypes of three different maturity groups evaluated ..... Pooled analysis of variance for grain yield in mid-early rice genotypes. Genotypes ...

  20. Evaluation of genotype-phenotype relationships in patients referred for endocrine assessment in suspected Pendred syndrome. (United States)

    Soh, Lip Min; Druce, Maralyn; Grossman, Ashley B; Differ, Ann-Marie; Rajput, Liala; Bitner-Glindzicz, Maria; Korbonits, Márta


    Patients with Pendred syndrome have genotypic and phenotypic variability, leading to challenges in definitive diagnosis. Deaf children with enlarged vestibular aqueducts are often subjected to repeated investigations when tests for mutations in SLC26A4 are abnormal. This study provides genotype and phenotype information from patients with suspected Pendred syndrome referred to a single clinical endocrinology unit. A retrospective analysis of 50 patients with suspected Pendred syndrome to investigate the correlation between genetic, perchlorate discharge test (PDT) and endocrine status. Eight patients with monoallelic SLC26A4 mutations had normal PDT. Of the 33 patients with biallelic mutations, ten of 12 patients with >30% discharge developed hypothyroidism. In our cohort, c.626G>T and c.3-2A>G result in milder clinical presentations with lower median perchlorate discharge of 9.3% (interquartile range 4-15%) compared with 40% (interquartile range 21-60%) for the remaining mutations. Eight novel mutations were detected. All patients with PDT 30% have a high risk of developing goitre and hypothyroidism, and should have lifelong monitoring. © 2015 European Society of Endocrinology.

  1. Genetic diversity of "Pimenta Longa" genotypes (Piper spp., Piperaceae of the Embrapa Acre germplasm collection

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    Lúcia Helena de Oliveira Wadt


    Full Text Available The commonly known Pimenta longa is a commercially valuable natural resource found wild in Acre, Brazil. Specifically, three Piperaceae species with contested taxonomic status were studied, Piper hispidinervum, Piper aduncum, and Piper hispidum, to assesses the inter- and intra-specific genetic relationship of 49 Piper genotypes kept in the Pimenta longa germplasm collection at Embrapa Acre, using sixty six Random Amplified Polymorphic DNA (RAPD markers. The DNA polymorphism level detected was high (96.97%, but the marker frequencies for each species showed polymorphism levels of 79.4% for Piper hispidinervum and 5.3% for P. aduncum. The genetic similarity clustering analysis resulted in three distinct groups corresponding to Piper hispidinervum, Piper aduncum, and Piper hispidum. Four and nine characteristic RAPD markers were identified for P. hispidinervum and P. aduncum, respectively, supporting the existence of two separate species. However, six genotypes collected in Tarauacá county formed a distinct subgroup within the P. hispidinervum group and may be considered as an ecotype of this species or an intermediate between the P. hispidinervum and P. aduncum groups. More extensive sampling of both P. hispidinervum and P. aduncum populations throughout the region are needed to further establish their relation and its implication for breeding efforts.

  2. A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites. (United States)

    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


    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.

  3. Phenotypic and genotypic profile of clinical and animal multidrug-resistant Salmonella enterica isolates from Mexico. (United States)

    Aguilar-Montes de Oca, S; Talavera-Rojas, M; Soriano-Vargas, E; Barba-León, J; Vázquez-Navarrete, J; Acosta-Dibarrat, J; Salgado-Miranda, C


    The objective of this study was to obtain a phenotypic and genotypic profile of Salmonella enterica including multidrug-resistant (MDR) isolates from food-producing animals and clinical isolates, as well as their genetic relatedness in two different States of Mexico (Jalisco and State of Mexico). A total of 243 isolates were evaluated in terms of antimicrobial resistance (AMR) and related genes through a disk diffusion method and PCR respectively; we found 16 MDR isolates, all of them harbouring the bla CMY gene but not qnr genes, these isolates represent less than 10% of the collection. The pulsed-field gel electrophoresis revealed a higher genotypic similitude within isolates of State of Mexico than Jalisco. A low percentage of Salmonella isolates were resistant to relevant antibiotics in human health, nevertheless, the AMR and involved genes were similar despite the different serovars and origin of the isolates. This investigation provided an insight of the current status of AMR of Salmonella isolates in two States of Mexico and pinpoint the genes involved in AMR and their epidemiological relationship, the information could help to determine an adequate therapy in human and veterinary medicine. © 2017 The Society for Applied Microbiology.

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

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    Rachel Massicotte


    Full Text Available 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.

  5. Associations between apolipoprotein E genotypes and serum levels of glucose, cholesterol, and triglycerides in a cognitively normal aging Han Chinese population. (United States)

    Tao, Qing-Qing; Chen, Yan; Liu, Zhi-Jun; Sun, Yi-Min; Yang, Ping; Lu, Shen-Ji; Xu, Miao; Dong, Qin-Yun; Yang, Jia-Jun; Wu, Zhi-Ying


    To determine the associations between apolipoprotein E (APOE) genotypes and serum levels of glucose, total cholesterol, and triglycerides in a cognitively normal aging Han Chinese population. There were 1,003 cognitively normal aging subjects included in this study. APOE genotypes were analyzed and biochemical parameters were tested. All the subjects were divided into three groups according to APOE genotypes: (1) E2/2 or E2/3 (APOE E2); (2) E3/3 (APOE E3); and (3) E2/4, E3/4, or E4/4 (APOE E4). Correlations of serum levels of glucose, total cholesterol, and triglycerides with APOE genotypes were assessed. E2, E3, and E4 allele frequencies were found to be 6.2%, 82.1%, and 11.7%, respectively. Serum levels of total cholesterol were higher in the APOE E4 group (Ptriglycerides (adjusted odds ratio 1.042, 95% confidence interval 0.759-1.429, P=0.800). A higher serum level of total cholesterol was significantly correlated with APOE E4 status in a cognitively normal, nondiabetic aging population. However, there was no correlation between APOE genotypes and serum levels of glucose or total triglycerides.

  6. Screening of cotton (gossypium hirsutum l.) genotypes for heat tolerance

    International Nuclear Information System (INIS)

    Abro, S.; Khan, M.A.; Sial, M.A.


    Cotton yield is highly affected due to biotic (diseases and pests) and abiotic (heat, dought and salinity) Stresses. Among them, high temperature is the main environmental constraint which adversely reduces cotton yield and quality. High temperature above 36 degree C affects plant growth and development especially during reproductive phase. Present studies were carried out to assess the tolerance of fifty-eight newly evolved cotton genotypes to heat stresses, based on agronomic and physiological characteristics. The genotypes were screened in field conditions under two temperature regimes. The studies were conducted at experimental farm of Nuclear Institute of Agriculture, Tando Jam, Pakistan. The results showed that March sown crop experienced high temperature (i.e. > 44 degree C in May and June), which significantly affected crop growth and productivity. The genotypes were identified as heat-tolerant on the basis of relative cell injury percentage (RCI %), heat susceptibility index (HSI) values, boll retention and seed cotton yield (kg/ha). RCI level in cotton genotypes ranged from 39.0 to 86.0%. Out of 58, seventeen genotypes (viz.NIA-80, NIA-81, NIA-83, NIA-84, NIA-M-30, NIA-M31, NIA-HM-48, NIA-HM-327, NIA-H-32, NIA-HM-2-1, NIA-Bt1, NIA-Bt2, NIA-Perkh, CRIS-342, CRIS-134, NIAB-111 and check variety Sadori indicated high level of heat tolerance at both (heat-stressed and non-stressed) temperature regimes; as shown the lowest relative injury level and relatively heat resistant index (HSI<1) values. Such genotypes could be used as heattolerant genotypes under heat-stressed environments. (author)

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

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    Amir Sohrabi


    Full Text Available 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. Keywords: Multiple HPV Types, Incidence, Genital infection, Cervical cancer, Iran

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

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


    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. The Comparison of Growth, Slaughter and Carcass Traits of Meat Chicken Genotype Produced by Back-Crossing with A Commercial Broiler Genotype


    Musa Sarıca; Umut Sami Yamak; Mehmet Akif Boz; Ahmet Uçar


    This study was conducted to determine the growth and some slaughter traits between commercial fast growing chickens and three-way cross M2 genotypes. 260 male female mixed chickens from each genotype was reared 10 replicate per genotype in the same house. Two different slaughtering ages were applied to commercial chickens and slaughtered at 6 and 7 weeks of age for comparing with cross genotypes. F chickens reached to slaughtering age at 42 days, whereas cross groups reached at 49 days. Genot...

  10. Physiological responses of genotypes soybean to simulated drought stress

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    Eleonóra Krivosudská


    Full Text Available The objective of this research was to investigate possible genetic variation in the sensitivity of soybean cultivars for nitrogen fixation rates in response to soil drying. The work confirmed that the selected physiological characteristics (RWC, osmotic potential, stress index and created nodules on roots are good evaluating parameters for the determination of water stress in plant. In the floricultural year 2014 an experiment with four genetic resources of soybean was launched. Sowing of Maverick (USA, Drina (HRV, Nigra (SVK and Polanka (CZK genotypes was carried out in the containers of 15 l capacity. This stress had a negative impact on the physiological parameters. By comparing the RWC values, the decrease was more significant at the end of dehydration, which was monitored in Maverick and Drina genotypes using the Nitrazon inoculants and water stress effect. Inoculated stressed Nigra and Polanka genotypes have kept higher water content till the end of dehydration period. Also the proline accumulation was monitored during the water stress, whilst higher content of free proline reached of Maverick. More remarkable decrease of osmotic potential was again registered in a foreign Drina and Maverick genotypes in the inoculated variations. Nigra and Polanka genotypes responses not so significant in the given conditions.

  11. Resistance of citrus genotypes to Phyllocnitis citrella Stainton (Lepidoptera: Gracillariidae). (United States)

    Santos, M S; Vendramim, J D; Lourenção, A L; Pitta, R M; Martins, E S


    The development and reproduction of the citrus leafminer (CLM), Phyllocnistis citrella Stainton, were evaluated in six citrus genotypes in order to identify genotypes with resistance traits that could be applied in a program for the development of citrus varieties resistant to the citrus leafminer. Tests were conducted under controlled laboratory conditions (25 ± 1ºC, 70 ± 10% RH, and 14h photophase). Seedlings of each genotype tested were infested with eggs obtained from a stock colony of CLM maintained on 'Cravo' lemon (Citrus limonia L. Osbeck), and the duration and survival of the eggs, larval and pupal stages, pupal size and weight, fecundity and longevity of adults, and sex ratio were evaluated. No influence was observed on the duration and survival of eggs, larvae and pupae of P. citrella. However, pupae obtained in the hybrid C x R(4) were significantly smaller and lighter than pupae from the remaining treatments. Adult females from the hybrids C x R(4) and C x R(315) were the least fecund. However, the lowest value for the corrected reproductive potential (CRP) was recorded in the hybrid C x R(315), suggesting that this genotype is the least favorable for the development and reproduction of CLM. On the other hand, the highest CRP value obtained in the 'Rugoso' lemon confirms the susceptibility of this genotype, indicating it as the most suitable for CLM.

  12. Phenotypic characterization of papaya genotypes to determine powdery mildew resistance

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    Marcelo Vivas


    Full Text Available In support of breeding of papaya (Carica papaya, the disease incidence and severity of powdery mildew (Ovulariopsis caricicola were evaluated in papaya genotypes. Two experiments in complete randomized blocks were carried out, one in the field and the other in a greenhouse. In field experiments, the lowest mean disease incidence was observed on the genotypes ‘Costa Rica’ and ‘Baixinho Super’, and the lowest mean disease severity on ‘Caliman M5’, ‘GTF’, ‘SH 11-08’, and ‘JS 11’. In the greenhouse experiment, the genotypes ‘Caliman M5’, ‘Golden’, ‘Kapoho Solo’, ‘Waimanalo’, ‘Mamão Bené’, ‘SH 12-07’, ‘JS 12’, and ‘GTF’ had the lowest mean incidence in at least one evaluation. On the other hand, for severity, the genotypes ‘Diva’, ‘Sunrise Solo 72/12’, ‘Kapoho Solo PA’, ‘Waimanalo’, ‘Maradol’, ‘Maradol GL’, ‘SH 15-04’, ‘FMV, ‘JS 12-4’, ‘SH 12-07’ and ‘Sekati FLM’ had the lowest means. These results indicate these genotypes for a possible use in breeding for reduction of powdery mildew intensity

  13. Methods for MHC genotyping in non-model vertebrates. (United States)

    Babik, W


    Genes of the major histocompatibility complex (MHC) are considered a paradigm of adaptive evolution at the molecular level and as such are frequently investigated by evolutionary biologists and ecologists. Accurate genotyping is essential for understanding of the role that MHC variation plays in natural populations, but may be extremely challenging. Here, I discuss the DNA-based methods currently used for genotyping MHC in non-model vertebrates, as well as techniques likely to find widespread use in the future. I also highlight the aspects of MHC structure that are relevant for genotyping, and detail the challenges posed by the complex genomic organization and high sequence variation of MHC loci. Special emphasis is placed on designing appropriate PCR primers, accounting for artefacts and the problem of genotyping alleles from multiple, co-amplifying loci, a strategy which is frequently necessary due to the structure of the MHC. The suitability of typing techniques is compared in various research situations, strategies for efficient genotyping are discussed and areas of likely progress in future are identified. This review addresses the well established typing methods such as the Single Strand Conformation Polymorphism (SSCP), Denaturing Gradient Gel Electrophoresis (DGGE), Reference Strand Conformational Analysis (RSCA) and cloning of PCR products. In addition, it includes the intriguing possibility of direct amplicon sequencing followed by the computational inference of alleles and also next generation sequencing (NGS) technologies; the latter technique may, in the future, find widespread use in typing complex multilocus MHC systems. © 2009 Blackwell Publishing Ltd.

  14. Does Sex Trade with Violence among Genotypes in Drosophila melanogaster? (United States)

    Cabral, Larry G.; Foley, Brad R.; Nuzhdin, Sergey V.


    The evolutionary forces shaping the ability to win competitive interactions, such as aggressive encounters, are still poorly understood. Given a fitness advantage for competitive success, variance in aggressive and sexual display traits should be depleted, but a great deal of variation in these traits is consistently found. While life history tradeoffs have been commonly cited as a mechanism for the maintenance of variation, the variability of competing strategies of conspecifics may mean there is no single optimum strategy. We measured the genetically determined outcomes of aggressive interactions, and the resulting effects on mating success, in a panel of diverse inbred lines representing both natural variation and artificially selected genotypes. Males of one genotype which consistently lost territorial encounters with other genotypes were nonetheless successful against males that were artificially selected for supernormal aggression and dominated all other lines. Intransitive patterns of territorial success could maintain variation in aggressive strategies if there is a preference for territorial males. Territorial success was not always associated with male mating success however and females preferred ‘winners’ among some male genotypes, and ‘losers’ among other male genotypes. This suggests that studying behaviour from the perspective of population means may provide limited evolutionary and genetic insight. Overall patterns of competitive success among males and mating transactions between the sexes are consistent with mechanisms proposed for the maintenance of genetic variation due to nonlinear outcomes of competitive interactions. PMID:18414669

  15. Lead enrichment in different genotypes of rice grains. (United States)

    Chen, Gang; Sun, Guo-rong; Liu, Ai-ping; Zhou, Wei-dong


    Using environmental scanning electron microscopy and X-ray electron probe microanalysis, the lead content was studied in inner and outer surface of rice glume, surface of caryopsis, center of caryopsis, near aleuronic layer and aleuronic layer in 21 genotypes of rice grains. The results showed that the lead content in different part of 21 genotypes of rice grains changed as inner surface of rice glume > aleuronic layer > near aleuronic layer > surface of caryopsis > outer surface of rice glume > center of caryopsis. There were genetic differences in lead enrichment in different genotypes of rice grains, which reflected as the differences of lead content in the same part and different part of rice grains. In different genotypes of rice grains, there were significant non-linear correlations between lead content in the inner surface of rice glume, center of caryopsis, aleuronic layer and that in the other parts of rice grain. The results also indicated that the lead enrichment in the center of caryopsis regulated by glume and aleuronic layer. In addition, in different genotypes of rice grains, there were differences in regulation of lead enrichment among different parts, which changed non-linearly.

  16. Productivity of Upland Rice Genotypes under Different Nitrogen Doses

    Energy Technology Data Exchange (ETDEWEB)

    Traore, K.; Traore, O. [INERA /Station de Farakoba, Bobo-Dioulasso (Burkina Faso); Bado, V. B. [Africa Rice Center (AfricaRice), Saint Louis (Senegal)


    Nitrogen (N) deficiency is one of the most yield-limiting nutrients in upland rice growing area in Burkina Faso. A field experiment was carried out from 2008 to 2010 in Farakoba research center with the objective to evaluate 200 upland rice (Oryza sativa L.) genotypes from WAB, NERICA, CNA, CNAX, IRAT and IR lines for N use efficiency. The treatments consisted of three levels of N: low, medium and high at 20, 60 and 100 kg-N h{sup a-1}, respectively. Both grain and straw yield increased with N application. The yields were highest for NERICA and WAB lines compared to the other lines, and this was consistent over the N doses. A large variability was found among the genotypes. Three groups of genotypes were identified according to N use efficiency. The high N use efficiency genotypes were found in WAB and NERICA lines. The N concentration in the shoot at flowering significantly increased with N doses and this was similar for N taken up by genotypes. (author)

  17. Cross-Sectional and Longitudinal Effects of CREB1 Genotypes on Individual Differences in Memory and Executive Function: Findings from the BLSA

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    Claudia Wolf


    Full Text Available Purpose: Previously, we have shown that the SNP rs10932201 genotype of the cyclic AMP responsive element binding protein 1 gene (CREB1 contributes to individual differences in executive and memory function at the neural system and behavioral levels in healthy, young adults. However, longitudinal effects of CREB1 genotypes on cognition have not yet been addressed. Furthermore we were interested in replicating associations between CREB1 genotypes and human cognition in previous cross-sectional studies and explore whether APOE4 status might modify these relations.Materials and Methods: We investigated whether common, independent tag SNPs within CREB1 (rs2253206, rs10932201, rs6785 influence individual differences in age-related longitudinal change and level of executive function and memory performance independent of baseline age, sex, APOE4 status, and education. Our analysis included data from cognitively unimpaired older adults participating in the Baltimore Longitudinal Study of Aging. Eleven measures from six cognitive tests (sample sizes range 617–786 were analyzed using linear mixed effects and generalized estimating equations models. Mean baseline age ranged from 50 to 69 years and mean time of follow-up (interval ranged from 8 to 22 years.Results: We found significant effects of all three CREB1 SNPs on performance level and/or longitudinal change in performance based on eight measures assessing semantic memory, episodic memory, or both executive function and semantic memory. SNP rs10932201 showed the most significant and largest effect (Cohen’s d = -0.70, p < 0.01 on age-related longitudinal decline of semantic memory. Additionally, we show interactions between all three CREB1 SNPs and APOE4 status on age-related longitudinal declines and levels of memory and executive function.Conclusion: Our results suggest that CREB1 genotypes independently and by interactions with APOE4 status contribute to individual differences in cognitive aging.

  18. Epstein-Barr virus and human papillomavirus infections and genotype distribution in head and neck cancers.

    Directory of Open Access Journals (Sweden)

    Zeyi Deng

    Full Text Available To investigate the prevalence, genotypes, and prognostic values of Epstein-Barr virus (EBV and human papillomavirus (HPV infections in Japanese patients with different types of head and neck cancer (HNC.HPV and EBV DNA, EBV genotypes and LMP-1 variants, and HPV mRNA expression were detected by PCR from fresh-frozen HNC samples. HPV genotypes were determined by direct sequencing, and EBV encoded RNA (EBER was examined by in situ hybridization.Of the 209 HNC patients, 63 (30.1% had HPV infection, and HPV-16 was the most common subtype (86.9%. HPV E6/E7 mRNA expression was found in 23 of 60 (38.3% HPV DNA-positive cases detected. The site of highest prevalence of HPV was the oropharynx (45.9%. Among 146 (69.9% HNCs in which EBV DNA was identified, 107 (73.3% and 27 (18.5% contained types A and B, respectively, and 124 (84.9% showed the existence of del-LMP-1. However, only 13 (6.2% HNCs were positive for EBER, 12 (92.3% of which derived from the nasopharynx. Co-infection of HPV and EBER was found in only 1.0% of HNCs and 10.0% of NPCs. Kaplan-Meier survival analysis showed significantly better disease-specific and overall survival in the HPV DNA+/mRNA+ oropharyngeal squamous cell carcinoma (OPC patients than in the other OPC patients (P = 0.027 and 0.017, respectively. Multivariate analysis showed that stage T1-3 (P = 0.002 and HPV mRNA-positive status (P = 0.061 independently predicted better disease-specific survival. No significant difference in disease-specific survival was found between the EBER-positive and -negative NPC patients (P = 0.155.Our findings indicate that co-infection with HPV and EBV is rare in HNC. Oropharyngeal SCC with active HPV infection was related to a highly favorable outcome, while EBV status was not prognostic in the NPC cohort.

  19. Genetic and epigenetic transgenerational implications related to omega-3 fatty acids. Part II: maternal FADS2 rs174575 genotype and DNA methylation predict toddler cognitive performance. (United States)

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


    Maternal transfer of fatty acids is important to fetal brain development. The prenatal environment may differentially affect the substrates supporting declarative memory abilities, as the level of fatty acids transferred across the placenta may be affected by the maternal fatty acid desaturase 2 (FADS2) rs174575 single nucleotide polymorphism. In this study, we hypothesized that toddler and maternal rs174575 genotype and FADS2 promoter methylation would be related to the toddlers' declarative memory performance. Seventy-one 16-month-old toddlers participated in an imitation paradigm designed to test immediate and long-term declarative memory abilities. FADS2 rs174575 genotype was determined and FADS2 promoter methylation was quantified from blood by bisulfite pyrosequencing for the toddlers and their natural mothers. Toddlers of GG mothers at the FADS2 rs174575 single nucleotide polymorphism did not perform as well on memory assessments as toddlers of CC or CG mothers when controlling for plasma α-linolenic acid and child genotype. Toddler methylation status was related to immediate memory performance, whereas maternal methylation status was related to delayed memory performance. Thus, prenatal experience and maternal FADS2 status have a pervasive, long-lasting influence on the brain development of the offspring, but as the postnatal environment becomes more primary, the offsprings' own biology begins to have an effect. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Agronomical and phytochemical evaluation of Stevia rebaudiana genotypes

    Directory of Open Access Journals (Sweden)

    Vouillamoz, José F.


    Full Text Available The agronomical potential and the phytochemical variability of 18 genotypes of the Paraguayan plant Stevia rebaudiana have been investigated in Switzerland in order identify the best genotype for local cultivation. Over a two years period, yields in dry leaves ranged from 10 to 170 g m-2, with a percentage of leaves ranging from 53 to 75 %. HPLC analyses showed a notable variability in phytochemical composition, with stevioside content ranging from 0.3 to 7.9 % w/w and rebaudioside A from 0.3 to 6.5 % w/w. Cultivation of S. rebaudiana in Switzerland is feasible. With a density of 10 plants per m2, the potential yields of dry matter are approximately 1-2 t ha-1. The most productive genotypes (Pharmasaat, Hem Zaden, Stepa and Mediplant 3 and 11 will be submitted to the industry for organoleptic evaluation.

  1. Comparative analysis of minor histocompatibility antigens genotyping methods

    Directory of Open Access Journals (Sweden)

    A. S. Vdovin


    Full Text Available The wide range of techniques could be employed to find mismatches in minor histocompatibility antigens between transplant recipients and their donors. In the current study we compared three genotyping methods based on polymerase chain reaction (PCR for four minor antigens. Three of the tested methods: allele-specific PCR, restriction fragment length polymorphism and real-time PCR with TaqMan probes demonstrated 100% reliability when compared to Sanger sequencing for all of the studied polymorphisms. High resolution melting analysis was unsuitable for genotyping of one of the tested minor antigens (HA-1 as it has linked synonymous polymorphism. Obtained data could be used to select the strategy for large-scale clinical genotyping.


    Directory of Open Access Journals (Sweden)

    Marián KOTRLA


    Full Text Available Deliberate cultivation of plants for energy biomass is becoming increasingly important. Biomass should significantly contribute to increase the share of renewable energy in the European Union. On the research locality of Slovak University of Agriculture in Nitra localized in the village Kolíňany (Slovak Republic is implemented basic research focused on the growth and production of the two genotypes energy grass Miscanthus. Research is carried out since 2010. In the third year after planting (the year 2012 were confirmed biomass production depending on the genotype of 35.45 and 36.67 t ha-1. Based on the analysis of growth and production performance of Miscanthus genotypes can be evaluated the high environmental and socio-economic aspects of growing energy crops, depending on the specific agro-ecological conditions.

  3. Models for genotype by environment interaction estimation on halomorphic soil

    Directory of Open Access Journals (Sweden)

    Dimitrijević Miodrag


    Full Text Available In genotype by environment interaction estimation, as well as, in total trial variability anal­ysis several models are in use. The most often used are Analysis of variance, Eberhart and Russell model and AMMI model. Each of the models has its own specificities, in the way of sources of varia­tion comprehension and treatment. It is known that agriculturally less productive environments increase errors, dimmish reaction differences between genotypes and decrease repeatability of conditions during years. A sample consisting on six bread wheat varieties was studied in three veg­etation periods on halomorphic soil, solonetz type in Banat (vil. Kumane. Genotype by environ­ment interaction was quantified using ANOVA, Eberhart and Russell model and AMMI model. The results were compared not only on pure solonetz soil (control, but also on two level of ameliora­tion (25 and 50t/ha phosphor-gypsum.

  4. Distribution of Human papilloma virus genotypes in cervical cancer tissues

    Directory of Open Access Journals (Sweden)

    Stamenković M.


    Full Text Available Cervical cancer incidence and mortality rates in Serbia are among the highest in Europe and data on Human papilloma virus (HPV type distribution are scarce. The aim of this study was to determine the prevalence of HPV types in archival specimens of cervical cancer tissues of women in the Serbian population. A total of 45 paraffin-embedded tissue samples of cervical carcinoma were used in this study. The procedure included deparaffinization of tissue samples, DNA extraction, PCR, gel electrophoresis and HPV genotyping by direct sequencing. HPV was detected in 32 samples (71%. Genotyping revealed the presence of 6 high-risk HPV types 16, 18, 33, 45, 53 and 58, where HPV type 16 was the most prevalent type (73.7%. The results of this study and further studies will provide more detailed information about HPV genotype distribution and may contribute to the formulation of national guidelines for the prevention of cervical cancer. [175073

  5. Carcass traits and meat quality of two different rabbit genotypes

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    Maria D'Agata


    Full Text Available To evaluate the effect of genotype on carcass traits and meat quality, thirty-two rabbits for two genotypes (local population – LP; commercial hybrids – HY were used. Rabbits were weaned at 35 days old and slaughtered at 103 days of age for LP and 87 days of age for HY. Comparing the slaughtering traits of two genotypes, LP provided higher dressing out (59.4% vs 56.2%, Pvs 14.2%, Pvs 22.3, Pvs 8,9%, Pvs 0.86%, Pvs 1.12%; Pvs 19.2%; Pvs 31.6%; Pvs 3.8%; P*, higher redness (a*, yellowness (b* and C* value than HY (P

  6. Correlation of oxidative stress in patients with HBV-induced liver disease with HBV genotypes and drug resistance mutations. (United States)

    Xianyu, Jianbo; Feng, Jiafu; Yang, Yuwei; Tang, Jie; Xie, Gang; Fan, Lingying


    This study aims to explore the correlation of oxidative stress (OxS) in patients with chronic hepatitis B (CHB) and the disease severity with HBV genotypes and drug resistance mutations. A total of 296 patients with CHB were enrolled into the study. PCR-reverse dot-blot hybridization was used to detect the HBV genotypes (B, C, and D) and the drug resistance-causing HBV mutant genes. In addition, the total oxidative stress (TOS) and total antioxidant status (TAS) were determined, and oxidative stress index (OSI) was calculated and compared. Serum levels of TOS and OSI, the B/C ratio, and drug resistance mutation rate were increased along with the elevated disease severity degree (CHBHBV mutation had higher serum TOS and OSI levels, while lower serum TAS levels (P HBV-induced liver disease, and the damage degree is correlated with the HBV genotype and drug resistance mutation. Oxidative stress might be a useful indicator of the progression of HBV-induced liver disease in patients. Copyright © 2018. Published by Elsevier Inc.

  7. Measles virus genotypes circulating in India, 2011-2015. (United States)

    Vaidya, Sunil R; Chowdhury, Deepika T


    The Government of India is accepted to participate in the measles elimination and rubella control goal 2020, hence genetic characterization of measles viruses (MeV) becomes essential. At National Reference Laboratory (National Institute of Virology, Pune), the throat swabs/urine specimens (n = 380) or PCR products (n = 219) obtained from the suspected measles cases were referred for the molecular testing and subsequently, MeV nucleoprotein (N) gene sequencing/genotyping. In addition, 2,449 suspected measles cases, mainly from the Maharashtra state were referred for the laboratory diagnosis. A detailed study was performed on N gene sequences obtained during last two decades. Indian MeV sequences obtained during 2011-2015 were compared with 1996-2010 sequences and genetic divergence was studied. Circulation of measles genotypes B3 (n = 3), D4 (n = 49), and D8 (n = 351) strains were observed in 19 States and three Union Territories of India. In addition, 64 measles viruses were isolated from 253 throat swab or urine specimens obtained from the suspected measles cases. During 2011-2015, 67.9% (1,663/2,449) suspected measles cases were laboratory confirmed. Molecular studies showed circulation of measles genotype B3 in India along with prominently circulating genotypes D4 and D8 except D7 strains. The genetic diversion within Indian B3, D4, and D8 genotypes was 0.3%, 1.1%, and 2.1%, respectively. The genetic divergence of Indian B3, D4, and D8 measles strains with the WHO reference sequences was 2.5%, 2.6%, and 1.8%, respectively. It is crucial data for national immunization program. More measles/rubella genotyping studies are necessary to track transmission and to support measles elimination and rubella control. J. Med. Virol. 89:753-758, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  8. Genomic prediction when some animals are not genotyped

    Directory of Open Access Journals (Sweden)

    Lund Mogens S


    Full Text Available Abstract Background The use of genomic selection in breeding programs may increase the rate of genetic improvement, reduce the generation time, and provide higher accuracy of estimated breeding values (EBVs. A number of different methods have been developed for genomic prediction of breeding values, but many of them assume that all animals have been genotyped. In practice, not all animals are genotyped, and the methods have to be adapted to this situation. Results In this paper we provide an extension of a linear mixed model method for genomic prediction to the situation with non-genotyped animals. The model specifies that a breeding value is the sum of a genomic and a polygenic genetic random effect, where genomic genetic random effects are correlated with a genomic relationship matrix constructed from markers and the polygenic genetic random effects are correlated with the usual relationship matrix. The extension of the model to non-genotyped animals is made by using the pedigree to derive an extension of the genomic relationship matrix to non-genotyped animals. As a result, in the extended model the estimated breeding values are obtained by blending the information used to compute traditional EBVs and the information used to compute purely genomic EBVs. Parameters in the model are estimated using average information REML and estimated breeding values are best linear unbiased predictions (BLUPs. The method is illustrated using a simulated data set. Conclusions The extension of the method to non-genotyped animals presented in this paper makes it possible to integrate all the genomic, pedigree and phenotype information into a one-step procedure for genomic prediction. Such a one-step procedure results in more accurate estimated breeding values and has the potential to become the standard tool for genomic prediction of breeding values in future practical evaluations in pig and cattle breeding.

  9. Genotyping of Brucella species using clade specific SNPs

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    Foster Jeffrey T


    Full Text Available Abstract Background Brucellosis is a worldwide disease of mammals caused by Alphaproteobacteria in the genus Brucella. The genus is genetically monomorphic, requiring extensive genotyping to differentiate isolates. We utilized two different genotyping strategies to characterize isolates. First, we developed a microarray-based assay based on 1000 single nucleotide polymorphisms (SNPs that were identified from whole genome comparisons of two B. abortus isolates , one B. melitensis, and one B. suis. We then genotyped a diverse collection of 85 Brucella strains at these SNP loci and generated a phylogenetic tree of relationships. Second, we developed a selective primer-extension assay system using capillary electrophoresis that targeted 17 high value SNPs across 8 major branches of the phylogeny and determined their genotypes in a large collection ( n = 340 of diverse isolates. Results Our 1000 SNP microarray readily distinguished B. abortus, B. melitensis, and B. suis, differentiating B. melitensis and B. suis into two clades each. Brucella abortus was divided into four major clades. Our capillary-based SNP genotyping confirmed all major branches from the microarray assay and assigned all samples to defined lineages. Isolates from these lineages and closely related isolates, among the most commonly encountered lineages worldwide, can now be quickly and easily identified and genetically characterized. Conclusions We have identified clade-specific SNPs in Brucella that can be used for rapid assignment into major groups below the species level in the three main Brucella species. Our assays represent SNP genotyping approaches that can reliably determine the evolutionary relationships of bacterial isolates without the need for whole genome sequencing of all isolates.

  10. Rotavirus genotypes associated with acute diarrhea in Egyptian infants. (United States)

    Ahmed, Salwa F; Mansour, Adel M; Klena, John D; Husain, Tupur S; Hassan, Khaled A; Mohamed, Farag; Steele, Duncan


    Before the introduction of rotavirus vaccine in Egypt, information on the burden of disease and the circulating rotavirus genotypes is critical to monitor vaccine effectiveness. A cohort of 348 Egyptian children was followed from birth to 2 years of age with twice-weekly home visits to detect diarrheal illness. VP7 and VP4 genes were genotyped by reverse-transcription polymerase chain reaction and DNA sequencing. Forty percentage of children had rotavirus-associated diarrhea at least once by their second birthday. One hundred and twelve children experienced a single rotavirus diarrheal episodes (RDE) at a median age of 9 months; while 27 infants had their second RDE at a median age of 15 months and 1 infant had 3 RDE at the age of 2, 16 and 22 months. Of the 169 RDE, 82% could be assigned a G-type, while 58% had been identified a P-type. The most prevalent genotype was G2 (32%), followed by G1 (24%) and G9 (19%). G2P[4] rotavirus episodes were significantly associated with fever (P = 0.03) and vomiting (P = 0.06) when compared with other genotypes. G2 strains were the predominant genotype causing 50% of the second RDE while G9 represented 25% of the second RDE. Genotypes identified are similar to those detected globally except for absence of G4. Our finding that 75% of the second RDE were due to G2 and G9 indicates a possible reduction in natural protection afforded by these types compared with G1, where 90% of G1 cases did not experience a second xposure, indicating greater protection against recurrent symptomatic infection.

  11. Phenotype- and genotype-specific structural alterations in spasmodic dysphonia. (United States)

    Bianchi, Serena; Battistella, Giovanni; Huddleston, Hailey; Scharf, Rebecca; Fleysher, Lazar; Rumbach, Anna F; Frucht, Steven J; Blitzer, Andrew; Ozelius, Laurie J; Simonyan, Kristina


    Spasmodic dysphonia is a focal dystonia characterized by involuntary spasms in the laryngeal muscles that occur selectively during speaking. Although hereditary trends have been reported in up to 16% of patients, the causative etiology of spasmodic dysphonia is unclear, and the influences of various phenotypes and genotypes on disorder pathophysiology are poorly understood. In this study, we examined structural alterations in cortical gray matter and white matter integrity in relationship to different phenotypes and putative genotypes of spasmodic dysphonia to elucidate the structural component of its complex pathophysiology. Eighty-nine patients with spasmodic dysphonia underwent high-resolution magnetic resonance imaging and diffusion-weighted imaging to examine cortical thickness and white matter fractional anisotropy in adductor versus abductor forms (distinct phenotypes) and in sporadic versus familial cases (distinct genotypes). Phenotype-specific abnormalities were localized in the left sensorimotor cortex and angular gyrus and the white matter bundle of the right superior corona radiata. Genotype-specific alterations were found in the left superior temporal gyrus, supplementary motor area, and the arcuate portion of the left superior longitudinal fasciculus. Our findings suggest that phenotypic differences in spasmodic dysphonia arise at the level of the primary and associative areas of motor control, whereas genotype-related pathophysiological mechanisms may be associated with dysfunction of regions regulating phonological and sensory processing. Identification of structural alterations specific to disorder phenotype and putative genotype provides an important step toward future delineation of imaging markers and potential targets for novel therapeutic interventions for spasmodic dysphonia. © 2017 International Parkinson and Movement Disorder Society. © 2017 International Parkinson and Movement Disorder Society.

  12. Direct maximum parsimony phylogeny reconstruction from genotype data

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    Ravi R


    Full Text Available Abstract Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. Results In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Conclusion Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

  13. Procedures for identifying S-allele genotypes of Brassica. (United States)

    Wallace, D H


    Procedures are described for efficient selection of: (1) homozygous and heterozygous S-allele genotypes; (2) homozygous inbreds with the strong self- and sib-incompatibility required for effective seed production of single-cross F1 hybrids; (3) heterozygous genotypes with the high self- and sib-incompatibility required for effective seed production of 3- and 4-way hybrids.From reciprocal crosses between two first generation inbred (I1) plants there are three potential results: both crosses are incompatible; one is incompatible and the other compatible; and both are compatible. Incompatibility of both crosses is useful information only when combined with data from other reciprocal crosses. Each compatible cross, depending on whether its reciprocal is incompatible or compatible, dictates alternative reasoning and additional reciprocal crosses for efficiently and simultaneously identifying: (A) the S-allele genotype of all individual I1 plants, and (B) the expressions of dominance or codominance in pollen and stigma (sexual organs) of an S-allele heterozygous genotype. Reciprocal crosses provide the only efficient means of identifying S-allele genotypes and also the sexual-organ x S-allele-interaction types.Fluorescent microscope assay of pollen tube penetration into the style facilitates quantitation within 24-48 hours of incompatibility and compatibility of the reciprocal crosses. A procedure for quantitating the reciprocal difference is described that maximizes informational content of the data about interactions between S alleles in pollen and stigma of the S-allele-heterozygous genotype.Use of the non-inbred Io generation parent as a 'known' heterozygous S-allele genotype in crosses with its first generation selfed (I1) progeny usually reduces at least 7 fold the effort required for achieving objectives 1, 2, and 3, compared to the method of making reciprocal crosses only among I1 plants.Identifying the heterozygous and both homozygous S-allele genotypes during

  14. Nephele: genotyping via complete composition vectors and MapReduce

    Directory of Open Access Journals (Sweden)

    Mardis Scott


    Full Text Available Abstract 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

  15. Use of chronic irradiation in formation of new rape genotypes

    International Nuclear Information System (INIS)

    Fabry, A.; Zukalova, H.; Cerny, J.; Folk, A.


    Chronic irradiation of hybrid plants of F 1 generation obtained by crossing the Canadian rape without erucic acid with European winter varieties containg this acid, doubled the frequency of winter genotypes and increased significantly the frequency of required recombinations of winter character and absence of erucic acid in F 2 -M 2 . Genotypes with a more favourable ratio between linoleic and linolenic acids were obtained in the irradiated F 2 -M 2 population. The obtained radio-induced mutants are used for the production of new varieties of winter rape without erucic acid at the Slapy Breeding Station. (author)

  16. Neuregulin-1 genotypes and eye movements in schizophrenia

    DEFF Research Database (Denmark)

    Haraldsson, H.M.; Ettinger, U.; Magnusdottir, B.B.


    Neuregulin-1 (NRG-1) is a putative susceptibility gene for schizophrenia but the neurocognitive processes that may involve NRG-1 in schizophrenia are unknown. Deficits in antisaccade (AS) and smooth pursuit eye movements (SPEM) are promising endophenotypes, which may be associated with brain...... dysfunctions underlying the pathophysiology of schizophrenia. The aim of this study was to investigate the associations of NRG-1 genotypes with AS and SPEM in schizophrenia patients and healthy controls. Patients (N = 113) and controls (N = 106) were genotyped for two NRG-1 single nucleotide polymorphisms...... findings of impaired AS and SPEM performance in schizophrenia patients (all P

  17. Two-temperature LATE-PCR endpoint genotyping

    Directory of Open Access Journals (Sweden)

    Reis Arthur H


    Full Text Available Abstract 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

  18. Service Level Status

    CERN Multimedia

    Lopienski, S


    Nowadays, IT departments provide, and people use, computing services of an increasingly heterogeneous nature. There is thus a growing need for a status display that groups these different services and reports status and availability in a uniform way. The Service Level Status (SLS) system addresses these needs by providing a web-based display that dynamically shows availability, basic information and statistics about various IT services, as well as the dependencies between them.

  19. Association of OCT-Derived Drusen Measurements with AMD-Associated Genotypic SNPs in the Amish Population

    Directory of Open Access Journals (Sweden)

    Venkata Ramana Murthy Chavali


    Full Text Available Purpose: To investigate the association of optical coherence tomography (OCT-derived drusen measures in Amish age-related macular degeneration (AMD patients with known loci for macular degeneration. Methods: Members of the Old Order Amish community in Pennsylvania ages 50 and older were assessed for drusen area, volume and regions of retinal pigment epithelium (RPE atrophy using a Cirrus High-Definition OCT. Measurements were obtained in the macula region within a central circle (CC of 3 mm in diameter and a surrounding perifoveal ring (PR of 3 to 5 mm in diameter using the Cirrus OCT RPE analysis software. Other demographic information, including age, gender and smoking status, were collected. Study subjects were further genotyped to determine their risk for the AMD-associated SNPs in the SYN3, LIPC, ARMS2, C3, CFB, CETP, CFI and CFH genes using TaqMan genotyping assays. The association of genotypes with OCT measures were assessed using linear trend p-values calculated from univariate and multivariate generalized linear models. Results: 432 eyes were included in the analysis. Multivariate analysis (adjusted by age, gender and smoking status confirmed the known significant association between AMD and macular drusen with the number of CFH risk alleles for the drusen area (the area increased 0.12 mm2 for a risk allele increase, p < 0.01, drusen volume (the volume increased 0.01 mm3 for a risk allele increase, p ≤ 0.05 and the area of RPE atrophy (the area increased 0.43 mm2 for a risk allele increase, p = 0.003. SYN3 risk allele G is significantly associated with larger area PR (the area increased 0.09 mm2 for a risk allele increase, p = 0.03 and larger drusen volume in the central circle (the volume increased 0.01 mm3 for a risk allele increase, p = 0.04. Conclusion: Among the genotyped SNPs tested, the CFH risk genotype appears to play a major role in determining the drusen phenotype in the Amish AMD population.

  20. SIS - Status Determination (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Status Determination dataset within the Species Information System (SIS) contains information related to overfishing, overfished, and approaching overfished...

  1. Pediatric Status Epilepticus Management (United States)

    Abend, Nicholas S; Loddenkemper, Tobias


    Purpose of Review This review discusses management of status epilepticus in children including both anticonvulsant medications and overall management approaches. Recent Findings Rapid management of status epilepticus is associated with a greater likelihood of seizure termination and better outcomes, yet data indicate there are often management delays. This review discusses an overall management approach aiming to simultaneously identify and manage underlying precipitant etiologies, administer anticonvulsants in rapid succession until seizures have terminated, and identify and manage systemic complications. An example management pathway is provided. Summary Status epilepticus is a common neurologic emergency in children and requires rapid intervention. Having a predetermined status epilepticus management pathway can expedite management. PMID:25304961

  2. Personalised nutrition: Status and perspectives

    NARCIS (Netherlands)

    Joost, H.G.; Gibney, M.J.; Cashman, K.D.; Görman, U.; Hesketh, J.E.; Mueller, M.; Ommen, B. van; Williams, C.M.; Mathers, J.C.


    Personalised, genotype-based nutrition is a concept that links genotyping with specific nutritional advice in order to improve the prevention of nutrition-associated, chronic diseases. This review describes the current scientific basis of the concept and discusses its problems. There is convincing

  3. Evaluation of some Phenological and Pomological Characteristics of Selected Walnut Genotypes from Shahroud-Iran

    Directory of Open Access Journals (Sweden)

    Sara Akhiani


    Full Text Available The first step in walnut breeding programs is to identify and evaluate superior genotypes of fruit trees. Hence, there are various walnut breeding programs in various areas of Iran. A study aimed to evaluate the morphological and chemical characteristics of selected superior genotypes of walnut was conducted in the Shahroud region in 2011-2012.  The following genotypes were selected in this study as the best walnut genotypes:  X-18 homogamous genotypes due to desirable late leafing;   genotype X-11 for its high percentage of kernel production, easily removal of shell, thin shell; genotype X-52 due to its kernel plumpness compared to other genotypes, thin shell and high percentage of kernel and genotype X-70 for its kernel brightness, easily kernel extracting and high percentage of kernels. The X-49 and X-5 genotypes had the highest amount of linoleic and linolenic fatty acids and higher nutritional quality compared to other genotypes. Three genotypes, X-3, X-11 and X-22, had the highest amount of oil. Genotypes X-9 and X-45 had the highest amount of protein. The difference between oil content and fatty acid compositions was presumably due to genetic diversity and ecological conditions of the studied genotypes cultivation.

  4. First study about the development of adult Echinococcus canadensis G6 genotype of goat origin in experimentally infected dogs. (United States)

    Soriano, Silvia Viviana; Debiaggi, María Florencia; Pierangeli, Nora Beatriz; Pianciola, Luis Alfredo; Bergagna, Héctor Fabián Jesús; Lazzarini, Lorena Evelina; Mazzeo, Melina Leonor; Basualdo, Juan Angel


    Echinococcus granulosus sensu lato (E. granulosus sl) must be considered as a species complex, comprising Echinococcus granulosus sensu stricto (E. granulosus ss, genotypes G1-G3), Echinococcus equinus (G4), Echinococcus ortleppi (G5) and Echinococcus canadensis (G6-G10) although the species status of E. canadensis is still controversial. These genotypes closely match the intermediate hosts associated strains described in earlier times among which E. canadensis G6 corresponds to the camel strain. As there are no studies concerning the development of adult stages of the G6 genotype from non-camel origin, the aims of the present study were: to characterize for the first time the development of E. canadensis G6 in dogs experimentally infected with protoscoleces derived from goats, to describe the resultant adult morphology, to evaluate the growth of their rostellar hooks from larval to adult stages and to determine the prepatent period of the strobilar stage of E. canadensis G6 derived from goats. The development of the strobilar stage of E. canadensis G6 genotype of goat origin was examined by studying the growth (variation of the total worm length) and segmentation in experimentally infected dogs at 14, 25, 35 and 56days post infection. A morphological characterization of 35-day-old worms as well as of larval and adult rostellar hooks was also carried out by conventional optical microscopic observations and/or by scanning electron microscopy. The prepatent period of the strobilar stage was assessed by microscopic examination of faeces from 2 infected dogs. Our results were compared with published data from the camel and other strains. The roles of the host, genotype and species in morphological and developmental features as well as the taxonomic position of E. canadensis G6 were discussed. The prepatent period of E. canadensis G6 genotype of goat origin was determined as at least, 41days. The obtained results contribute to increase the knowledge about the biology

  5. Differences between spent hens of different genotype in performance, meat yield and suitability of the meat for sausage production. (United States)

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


    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

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

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


    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. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. Genome-wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions

    Directory of Open Access Journals (Sweden)

    Wensheng Wang


    Full Text Available 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

  8. Ureaplasma parvum genotype, combined vaginal colonisation with Candida albicans, and spontaneous preterm birth in an Australian cohort of pregnant women. (United States)

    Payne, Matthew S; Ireland, Demelza J; Watts, Rory; Nathan, Elizabeth A; Furfaro, Lucy L; Kemp, Matthew W; Keelan, Jeffrey A; Newnham, John P


    Detection of Ureaplasma, Mycoplasma and Candida spp. in the vagina during pregnancy has previously been associated with preterm birth (PTB). However, the prevalence of these microorganisms and the associated obstetric risks (likely to be population-specific) have not been determined in Australian women; furthermore, in the case of Ureaplasma spp., very few studies have attempted characterisation at the species level and none have examined genotype/serovar status to further refine risk assessment. In order to address these issues we sampled the vaginal fluid of 191 pregnant Australian women at three time points in pregnancy. Culture methods were used for detection of Ureaplasma spp. and Candida spp., and real-time PCR was used for speciation of U. parvum and U. urealyticum, non-albicans Candida spp., Mycoplasma hominis and Mycoplasma genitalium. High-resolution melt PCR was used to genotype U. parvum. Data on various lifestyle factors (including sex during pregnancy and smoking), antimicrobial use and pregnancy outcome were collected on all participants. Chi-square tests were used to assess the association of vaginal microorganisms with PTB. Detection of Ureaplasma spp. was higher among spontaneous PTB cases, specifically in the presence of U. parvum [77 % preterm (95 % confidence interval (CI) 50-100 %) vs. 36 % term (CI: 29-43 %), p = 0.004], but not U. urealyticum. The association with PTB strengthened when U. parvum genotype SV6 was detected (54 % preterm (CI: 22-85 %) vs. 15 % term (CI: 10-20 %), p = 0.002); this genotype was also present in 80 % (4/5) of cases of PTB Ureaplasma spp. in the vagina confers an increased risk of spontaneous PTB, findings which may be useful in risk assessment for identifying women who would benefit from antimicrobial treatment.

  9. Establishment of a novel two-probe real-time PCR for simultaneously quantification of hepatitis B virus DNA and distinguishing genotype B from non-B genotypes. (United States)

    Wang, Wei; Liang, Hongpin; Zeng, Yongbin; Lin, Jinpiao; Liu, Can; Jiang, Ling; Yang, Bin; Ou, Qishui


    Establishment of a simple, rapid and economical method for quantification and genotyping of hepatitis B virus (HBV) is of great importance for clinical diagnosis and treatment of chronic hepatitis B patients. We hereby aim to develop a novel two-probe real-time PCR for simultaneous quantification of HBV viral concentration and distinguishing genotype B from non-B genotypes. Conserved primers and TaqMan probes for genotype B and non-B genotypes were designed. The linear range, detection sensitivity, specificity and repeatability of the method were assessed. 539 serum samples from HBV-infected patients were assayed, and the results were compared with commercial HBV quantification and HBV genotyping kits. The detection sensitivity of the two-probe real-time PCR was 500IU/ml; the linear range was 10(3)-10(9)IU/ml, and the intra-assay CVs and inter-assay CVs were between 0.84% and 2.80%. No cross-reaction was observed between genotypes B and non-B. Of the 539 detected samples, 509 samples were HBV DNA positive. The results showed that 54.0% (275/509) of the samples were genotype B, 39.5% (201/509) were genotype non-B and 6.5% (33/509) were mixed genotype. The coincidence rate between the method and a commercial HBV DNA genotyping kit was 95.9% (488/509, kappa=0.923, PDNA qPCR kit were achieved. A novel two-probe real-time PCR method for simultaneous quantification of HBV viral concentration and distinguishing genotype B from non-B genotypes was established. The assay was sensitive, specific and reproducible which can be applied to areas prevalent with HBV genotypes B and C, especially in China. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Development of a monoclonal antibody against viral haemorrhagic septicaemia virus (VHSV) genotype IVa

    DEFF Research Database (Denmark)

    Ito, T.; Olesen, Niels Jørgen; Skall, Helle Frank


    of the spread of genotypes to new geographical areas. A monoclonal antibody (MAb) against VHSV genotype IVa was produced, with the aim of providing a simple method of discriminating this genotype from the other VHSV genotypes (I, II, III and IVb). Balb/c mice were injected with purified VHSV-JF00Ehil (genotype...... IVa) from diseased farmed Japanese flounder. Ten hybridoma clones secreting monoclonal antibodies (MAbs) against VHSV were established. One of these, MAb VHS-10, reacted only with genotype IVa in indirect fluorescent antibody technique (IFAT) and ELISA. Using cell cultures that were transfected...

  11. Fighting status inequalities

    DEFF Research Database (Denmark)

    Nielsen, Morten Ebbe Juul; Landes, Xavier


    Status inequalities seem to play a fairly big role in creating inequalities in health. This article assumes that there can be good reasons to fight status inequalities in order to reduce inequalities in health. It examines whether the neorepublican ideal of non-dominance does a better job as a th...

  12. Morocco: Country Status Report. (United States)

    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…

  13. Adolescent Weight Status

    DEFF Research Database (Denmark)

    Hjort Kjelldgaard, Heidi; Holstein, Bjørn Evald; Due, Pernille


    day) communication with friends through cellphones, SMS messages, or Internet (1.66, 1.03-2.67). In the full population, overweight/obese weight status was associated with not perceiving best friend as a confidant (1.59, 1.11-2.28). No associations were found between weight status and number of close...

  14. Physiological response of soybean genotypes to plant density

    NARCIS (Netherlands)

    Gan, Y; Stulen, [No Value; van Keulen, H; Kuiper, PJC


    Response of soybean (Glycine max (L.) Merr.) to plant density has occupied a segment of agronomic research for most of the century. Genotype differences have been noted especially in response to planting date, lodging problems and water limitation. There is limited information on the physiological

  15. Interactions of genotype, housing and dietary calcium in layer ...

    African Journals Online (AJOL)

    The study was designed to evaluate the interactions in performance, eggshell quality and tibia traits of two laying hen genotypes, namely a commercial hybrid, Lohmann (LSL), and a traditional breed, the Czech Hen (CH), housed in conventional cages and on litter, and fed two levels of dietary calcium (Ca) (3.5% vs. 3.0%).

  16. Effect of genotype on haematology and biochemical parameters of ...

    African Journals Online (AJOL)

    Frizzle n = 33, Naked neck, n= 33 and Normal n = 33) were generated from 36 matured local chickens and used for the study to determine the effect of genotype on hematological and biochemical parameters of local chicken in the humid ...

  17. Effect of chicken genotype on growth performance and feed ...

    African Journals Online (AJOL)

    This experiment was conducted to assess the effect of chicken genotype on the growth performance, feed intake and feed efficiency of the progenies resulting from pure, straight and reciprocal cross of Giriraja (Gr) and Alpha chickens. Data obtained on body weight, body length, breast girth, keel length, feed intake and feed ...

  18. Response of Tomato Genotypes to Induced Salt Stress | Agong ...

    African Journals Online (AJOL)

    Thirteen tomato (Lycopersicon esculentum L.) genotypes were subjected to salt treatment under hydroponics and their responses monitored in a set of two experiments with the objective of advancing them as potential salt tolerant tomato scion and/or rootstocks. Salt applications ranged from 0 to 2% NaCl, with the resultant ...

  19. Nutrient composition of strawberry genotypes cultivated in a horticulture farm. (United States)

    Hossain, Ashrafi; Begum, Parveen; Salma Zannat, M; Hafizur Rahman, Md; Ahsan, Monira; Islam, Sheikh Nazrul


    This article decribes the nutrient composition of four strawberry genotypes cultivated at the Sher-e-Bangla Agriculture University horticulture farm in Dhaka (Bangladesh). AOAC and standard validated methods were employed to analyse the nutrient composition. Protein, fat and ash contents were found to be vary significantly (LSD<0.05), while the variation in moisture (LSD<1.33), dietary fibre (LSD<0.15) and total sugar (LSD<0.09) were found to be insignificant among the genotypes. Vitamin C content ranged from 26.46 mg to 37.77 mg per 100g edible strawberries (LSD<0.060). Amount of carotenoids were found to be very low being in a range of 0.99-3.30 μg per 100g edible fruit. Analysis of mineral revealed that strawberry genotypes contained a wide array of minerals including Ca, Mg, Na, K, P, Mn, Zn, Cu and Fe; most of which varied significantly (LSD<0.05) among the genotypes. Strawberries could be a potential dietary supplement for vitamin C along with minerals, particularly for the children who do not like local fruits, but love to eat the colourful strawberries. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. The influence of root rot incidence on cassava genotype on ...

    African Journals Online (AJOL)

    In Nigeria cassava root rot causes serious yield losses in cassava tuber production every year. However, the influence of root rot incidence on cassava genotype at harvest on consumers' acceptability of the gari produced from it has not been studied. A sensory evaluation was conducted on gari processed from the tuberous ...

  1. Response of cowpea genotypes to Alectra vogelii parasitism in Kenya

    African Journals Online (AJOL)

    This information showed that there is sufficient genetic variability in the cowpea genotypes studied, which can be exploited in breeding improved cowpea varieties for resistance to A. vogelii in Kenya. A great progress towards developing improved cowpea variety that meets farmer's preferences with durable resistance to A.

  2. Prevalence of heamoglobin genotype screening and awareness of ...

    African Journals Online (AJOL)

    Slightly more than half of the respondents (53.0%) had normal haemoglobin ... only a quarter (28.2%) of them had ever done their genotype test prior to the study. ... married, parental educational background and being in science-related field.

  3. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    Genotyping with large numbers of molecular markers is now an indispensable tool within plant genetics and breeding. Especially through the identification of large numbers of single nucleotide polymorphism (SNP) markers using the novel high-throughput sequencing technologies, it is now possible to reliably identify many ...

  4. Spikelet sterility in rice genotypes affected by temperature at microsporogenesis

    Directory of Open Access Journals (Sweden)

    Natalia M. de Souza

    Full Text Available ABSTRACT This study evaluated the effect of temperatures during the phase of microsporogenesis on spikelet sterility of paddy rice and identified genotypes tolerant to low temperatures at this growth stage. The inbreds SC681, SC491, and SC676 and the cultivars Epagri 109 and SCS116 Satoru were assessed. The genotypes were submitted for three days in a growth chamber to five temperatures at microsporogenesis: 9, 12, 15, 18, and 21 oC. For each tested temperature, a control was kept in the greenhouse under environmental conditions. After harvest, full and empty spikelets were counted and weighed and the percentage of spikelet sterility was determined. Data were evaluated by variance analysis using the F test. Averages were compared by Tukey’s test and regression analysis. The highest spikelet sterilities were observed when the genotypes were exposed to the temperatures of 9 and 12 oC. Genotype spikelet sterility was similar to that of the control at 21 ºC. The inbred SC 676 presented higher tolerance to lower temperatures is therefore potentially suited to generate a cultivar with adequate agronomic performance in rice growing areas prone to cold conditions at microsporogenesis.

  5. Human rotavirus genotypes causing acute watery diarrhea among ...

    African Journals Online (AJOL)

    Background: Diarrhea is a major cause of childhood morbidity and mortality in the developing countries. Rotavirus is a major cause of acute watery diarrhea. Aim: This study aims at characterizing the prevalent rotavirus G-genotypes among under.five children presenting with acute watery diarrhea in Benin City, Nigeria.

  6. DNA landmarks for genetic diversity assessment in tea genotypes ...

    African Journals Online (AJOL)

    Tea (Camellia sinensis) is one of the most important non-alcoholic beverages of the world. Natural genetic diversity in tea has been reduced due to continue selection in favor of desirable traits. The present study was conducted to estimate genetic diversity in tea genotypes cultivated in Pakistan using 20 randomly amplified ...

  7. growth and yield parameters of sorghum genotypes as affected

    African Journals Online (AJOL)


    ABSTRACT. Field trial was conducted at Bayero University, Kano research farm with the aim of determining the effect of stem injection artificial inoculation technique on the growth and yield parameters of one hundred and four sorghum genotypes against head smut. The trial was laid on a randomized complete block design ...

  8. Hepatitis E Virus Genotype 4 Outbreak, Italy, 2011 (United States)

    Garbuglia, Anna R.; Scognamiglio, Paola; Petrosillo, Nicola; Mastroianni, Claudio Maria; Sordillo, Pasquale; Gentile, Daniele; La Scala, Patrizia; Girardi, Enrico


    During 2011, 5 persons in the area of Lazio, Italy were infected with a monophyletic strain of hepatitis E virus that showed high sequence homology with isolates from swine in China. Detection of this genotype in Italy parallels findings in other countries in Europe, signaling the possible spread of strains new to Western countries. PMID:23260079

  9. Pollen diversity, viability and floral structure of some Musa genotypes

    African Journals Online (AJOL)

    Prof. Ogunji

    This is related to sterility due to triploidy, variation in genome size and structure ... Pollen grains are structures that house the male gametophytes generation of .... the mean value for all the genotypes was recorded for PITA 14, an 11TA hybrid.

  10. Potential of biofertilisers to improve performance of local genotype tomatoes

    Directory of Open Access Journals (Sweden)

    Carmen Puia


    Full Text Available Complex microbial communities in the plant rhizosphere are responsible for their success in ecosystems. Supplementary inoculation of soil with mycorrhizal fungi and rhizospheric bacteria may act as a plant growth-promoting factor. The present study aims to assess the potential use of biofertilisers on tomato as a way of increasing yield and stability of root exploration area. The experiment was set up in greenhouse, regarding the evaluation of growing dynamics of plants, mycorrhization level and obtained yield. The identification of effective inoculation variants can lead to a standardisation of technologies of growing for local plant genotypes. Data analysis was performed based on the ANOVA test, followed by Tukey HSD, principal component analysis and cluster analysis in order to identify the potential of bioproducts to stimulate the development of tomato plants. Application of bacterial biofertilisers does not stimulate enough the aboveground development of plants. An antagonistic reaction is visible between exogenous mycorrhizas and those specific in soil, acting slightly different for each genotype. Mycorrhizal level in root systems is more dependent on applied biofertilisers than on analyzed genotypes. For the variants without additional fertilisers, a high level of mycorrhization is visible only after 75 days from the transplantation. Based on results we can conclude that microbial active fertilisers may represent viable solutions to increase yield capacity and root exploration area for local tomato genotypes.

  11. `Assessment of Hybrid White Yam (Discorea Rotundata) Genotypes ...

    African Journals Online (AJOL)

    Ako-Isu had black colour while the remaining amala samples had varying shades of grey colouration. Though all the elubo samples from the experimental yam genotypes were found to be usable in amala preparation, only the amala sample made from TDr 89/02677 compared favourably (especially in the handfeel sensory ...

  12. Interaction between genotype and climates for Holstein milk ...

    African Journals Online (AJOL)

    This study was designed to investigate the interaction between genotype and climate for milk and fat production traits of Iranian Holstein dairy herds. Milk and fat production data were grouped in 5 climates, on the basis of Extended De Martonne method. (Co)Variance components and genetic parameters of first lactation ...

  13. Partitioning of copy-number genotypes in pedigrees

    Directory of Open Access Journals (Sweden)

    Andelfinger Gregor U


    Full Text Available Abstract Background Copy number variations (CNVs and polymorphisms (CNPs have only recently gained the genetic community's attention. Conservative estimates have shown that CNVs and CNPs might affect more than 10% of the genome and that they may be at least as important as single nucleotide polymorphisms in assessing human variability. Widely used tools for CNP analysis have been implemented in Birdsuite and PLINK for the purpose of conducting genetic association studies based on the unpartitioned total number of CNP copies provided by the intensities from Affymetrix's Genome-Wide Human SNP Array. Here, we are interested in partitioning copy number variations and polymorphisms in extended pedigrees for the purpose of linkage analysis on familial data. Results We have developed CNGen, a new software for the partitioning of copy number polymorphism using the integrated genotypes from Birdsuite with the Affymetrix platform. The algorithm applied to familial trios or extended pedigrees can produce partitioned copy number genotypes with distinct parental alleles. We have validated the algorithm using simulations on a complex pedigree structure using frequencies calculated from a real dataset of 300 genotyped samples from 42 pedigrees segregating a congenital heart defect phenotype. Conclusions CNGen is the first published software for the partitioning of copy number genotypes in pedigrees, making possible the use CNPs and CNVs for linkage analysis. It was implemented with the Python interpreter version 2.5.2. It was successfully tested on current Linux, Windows and Mac OS workstations.

  14. Comparative Effects of Cowpea and Soybean Genotypes on N2 ...

    African Journals Online (AJOL)


    ABSTRACT:A field trial was conducted to asses N2 - fixation and N balance in five cultivars each of soybean (TGX 1945 – 1F, ... Key words: Legume genotype, N2 fixation, N balance and Nitrogen Harvest Index (NHI) ..... subsequent maize grain yield in the guinea savanna ... On-farm evaluation of biological nitrogen fixation.

  15. β-Carotene content of selected banana genotypes from Uganda

    African Journals Online (AJOL)

    carotene with values as high as 2594.0 μg/100 g edible pulp. A positive correlation existed between pulp color intensity and β-carotene concentration. Accessions with relatively high levels of β-carotene,especially the PNG genotypes, could be ...

  16. A simple and robust approach for genotyping in Musaceae

    Czech Academy of Sciences Publication Activity Database

    Hřibová, Eva; Christelová, Pavla; Roux, N.; Doležel, Jaroslav


    Roč. 986, April 2013 (2013), s. 241-246 ISSN 0567-7572 Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional research plan: CEZ:AV0Z50380511 Keywords : fragment analysis * genotyping platform * microsatellite markers Subject RIV: EB - Genetics ; Molecular Biology

  17. Genetic diversity among some productive genotypes of tomato ...

    African Journals Online (AJOL)



    Jun 3, 2015 ... weight, cluster VIII had highest number of locules per fruit, fruit yield per plant and yield per hectare and cluster XVII was .... Cluster means for yield and quality contributing characters of 60 genotypes of tomato. Cluster lycopene β- ..... Sharma JP, Singh AK, Satesh K, Sanjeev K. (2009). Identification of.

  18. Infection of hepatitis C virus genotypes in hepatocellular carcinoma ...

    African Journals Online (AJOL)

    The aim of this retrospective study was to investigate the infection of hepatitis C virus (HCV) genotypes in hepatocellular carcinoma (HCC) patients from rural areas of Faisalabad region. Among 179 HCC subjects, men and women were 51 and 49%, respectively. All samples positive for HCV RNA by qualitative PCR were ...

  19. Childhood Pompe disease: clinical spectrum and genotype in 31 patients

    NARCIS (Netherlands)

    Capelle, C.I. van; Meijden, J.C. van der; Hout, J.M. van den; Jaeken, J.; Baethmann, M.; Voit, T.; Kroos, M.A.; Derks, T.G.; Rubio-Gozalbo, M.E.; Willemsen, M.A.A.P.; Lachmann, R.H.; Mengel, E.; Michelakakis, H.; Jongste, J.C. de; Reuser, A.J.; Ploeg, A.T. van der


    BACKGROUND: As little information is available on children with non-classic presentations of Pompe disease, we wished to gain knowledge of specific clinical characteristics and genotypes. We included all patients younger than 18 years, who had been evaluated at the Pompe Center in Rotterdam, the

  20. Childhood Pompe disease: Clinical spectrum and genotype in 31 patients

    NARCIS (Netherlands)

    C.I. van Capelle (Carine); J.C. van der Meijden (Chris); J.M.P. van den Hout (Johanna); J. Jaeken; M. Baethmann; T. Voit; M.A. Kroos (Marian); T.G.J. Derks (Terry G J); M.E. Rubio-Gozalbo (Estela); M.A. Willemsen (Michél); R. Lachmann (Robin); E. Mengel; H. Michelakakis (Helen); J.C. de Jongste (Johan); A.J.J. Reuser (Arnold); A.T. van der Ploeg (Ans)


    textabstractBackground: As little information is available on children with non-classic presentations of Pompe disease, we wished to gain knowledge of specific clinical characteristics and genotypes. We included all patients younger than 18 years, who had been evaluated at the Pompe Center in

  1. Childhood Pompe disease : clinical spectrum and genotype in 31 patients

    NARCIS (Netherlands)

    van Capelle, C I; van der Meijden, J C; van den Hout, J M P; Jaeken, J; Baethmann, M; Voit, T; Kroos, M A; Derks, T G J; Rubio-Gozalbo, M E; Willemsen, M A; Lachmann, R H; Mengel, E; Michelakakis, H; de Jongste, J C; Reuser, A J J; van der Ploeg, A T


    Background: As little information is available on children with non-classic presentations of Pompe disease, we wished to gain knowledge of specific clinical characteristics and genotypes. We included all patients younger than 18 years, who had been evaluated at the Pompe Center in Rotterdam, the

  2. Synthetic microbial ecology and the dynamic interplay between microbial genotypes. (United States)

    Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R


    Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

  3. Marker assisted characterization of chickpea genotypes for wilt ...

    African Journals Online (AJOL)

    Further, the sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) analysis of seed storage protein showed a difference in protein profile among studied genotypes but none of polypeptide fragment was specific to wilt resistance or susceptibility. In present study, the reported markers linked to susceptibility ...

  4. Tamarix (Tamaricaceae) hybrids: most dominant invasive genotype in southern Africa (United States)

    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...

  5. Root response of Jerusalem artichoke genotypes to different water regimes (United States)

    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...

  6. Interaction in Short rotation coppice willow, Salix viminalis genotype mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Begley, D. [Department of Biological Sciences, Queen' s University Belfast, Newforge Lane, Belfast BT9 5PX, Northern Ireland (United Kingdom); McCracken, A.R. [Applied Plant Science and Biometrics Division, Agri-Food and Biosciences Institute, 18A Newforge Lane, Belfast BT9 5PX, Northern Ireland (United Kingdom)]|[Northern Ireland Horticulture and Plant Breeding Station, Applied Plant Science and Biometrics Division, Agri-Food and Biosciences Institute, Loughgall, Co., Armagh BT61 8JB, Northern Ireland (United Kingdom); Dawson, W.M. [Northern Ireland Horticulture and Plant Breeding Station, Applied Plant Science and Biometrics Division, Agri-Food and Biosciences Institute, Loughgall, Co., Armagh BT61 8JB, Northern Ireland (United Kingdom); Watson, S. [Applied Plant Science and Biometrics Division, Agri-Food and Biosciences Institute, 18A Newforge Lane, Belfast BT9 5PX, Northern Ireland (United Kingdom)


    Seven straight Salix viminalis genotypes with different levels of rust (Melampsora epitea) susceptibility were grown as mono-plots as well as being incorporated into a range of mixtures. Two 3-year harvests (2003 and 2006) were taken. Disease progress was followed on each of the individual genotypes throughout each growing season 2001-2006. In 2003 there were small but significant yield increases from the mixtures compared to the yield of individual components grown as mono-plots. These differences were not evident at the second harvest in 2006. No consistent effect of mixtures on reducing rust on the most susceptible genotype, Salix viminalis '77082' were observed. In some years, e.g. 2003, at certain times during the growing season, significant reductions were observed on Salix viminalis '77082' in certain 3-way mixtures compared to mono-plots. These, however, were not repeated consistently in subsequent years. It was concluded that the current commercial practice in many parts of Europe of planting mixtures as a disease control strategy will only be effective if there is sufficient genetic diversity between the Salix genotypes incorporated into the mixture. (author)

  7. Differential responses of 15 cowpea genotypes to three Striga hot ...

    African Journals Online (AJOL)

    Differential responses of 15 cowpea genotypes to three Striga hot spots in Niger. M. SALIFOU1*, J. B. L. S. TIGNEGRE2, P. TONGOONA3, S. OFFEI3,. K. OFORI3 and E. DANQUAH3. 1National Agricultural Research Institute of Niger, Maradi Regional Research Centre, Niger. 2 The world Vegetable Centre, West and Central ...

  8. Early-onset stargardt disease: phenotypic and genotypic characteristics

    NARCIS (Netherlands)

    Lambertus, S.; Huet, R.A.C. van; Bax, N.M.; Hoefsloot, L.H.; Cremers, F.P.M.; Boon, C.J.F.; Klevering, B.J.; Hoyng, C.B.


    OBJECTIVE: To describe the phenotype and genotype of patients with early-onset Stargardt disease. DESIGN: Retrospective cohort study. PARTICIPANTS: Fifty-one Stargardt patients with age at onset

  9. Tissue Fractions of Cadmium in Two Hyperaccumulating Jerusalem Artichoke Genotypes

    Directory of Open Access Journals (Sweden)

    Xiaohua Long


    Full Text Available 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.

  10. Genotype-by-environment interaction and grain yield stability of ...

    African Journals Online (AJOL)

    The objective of this paper is to identify stable and high yielding varieties among 20 Ethiopian Bread wheat (Triticum aestivum L.) genotypes on the basis of experiments conducted during the 2007 and 2008 growing seasons. The additive main effects and multiplicative interaction (ammi) model has been used to estimate ...

  11. Evaluation of bread wheat genotypes for salinity tolerance under ...

    African Journals Online (AJOL)

    In two consecutive seasons (2007-08 and 2008-09), field experiments were conducted at Soil Salinity Research Institute, Pindi Bhattian and Biosaline Agricultural Research Station, Pakka Aana, Pakistan. During 2007-08, 103 wheat landrace genotypes were evaluated for salinity tolerance. During 2008-09, 47 selected ...

  12. Approaches to genotyping individual miracidia of Schistosoma japonicum. (United States)

    Xiao, Ning; Remais, Justin V; Brindley, Paul J; Qiu, Dong-Chuan; Carlton, Elizabeth J; Li, Rong-Zhi; Lei, Yang; Blair, David


    Molecular genetic tools are needed to address questions as to the source and dynamics of transmission of the human blood fluke Schistosoma japonicum in regions where human infections have reemerged, and to characterize infrapopulations in individual hosts. The life stage that interests us as a target for collecting genotypic data is the miracidium, a very small larval stage that consequently yields very little DNA for analysis. Here, we report the successful development of a multiplex format permitting genotyping of 17 microsatellite loci in four sequential multiplex reactions using a single miracidium held on a Whatman Classic FTA indicating card. This approach was successful after short storage periods, but after long storage (>4 years), considerable difficulty was encountered in multiplex genotyping, necessitating the use of whole genome amplification (WGA) methods. WGA applied to cards stored for long periods of time resulted in sufficient DNA for accurate and repeatable genotyping. Trials and tests of these methods, as well as application to some field-collected samples, are reported, along with the discussion of the potential insights to be gained from such techniques. These include recognition of sibships among miracidia from a single host, and inference of the minimum number of worm pairs that might be present in a host.

  13. cultivars and identification of genotype-specific fingerprints using ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 89; Online resources. Diversity in Indian barley (Hordeum vulgare) cultivars and identification of genotype-specific fingerprints using microsatellite markers. S. K. Jaiswal Shree P. Pandey S. Sharma R. Prasad L. C. Prasad R. P. S. Verma Arun K. Joshi. Volume 89 Online ...

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

    Czech Academy of Sciences Publication Activity Database

    Laatamna, A.E.; Wágnerová, P.; Sak, Bohumil; Květoňová, Dana; Aissi, M.; Rost, M.; Kváč, Martin


    Roč. 197, 1-2 (2013), s. 350-353 ISSN 0304-4017 Grant - others:GAJU(CZ) 022/2010/Z; GAJU(CZ) 011/2013/Z Institutional support: RVO:60077344 Keywords : horses * Cryptosporidium hedgehog genotype * PCR * SSU * GP60 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.545, year: 2013

  15. Infection of hepatitis C virus genotypes in hepatocellular carcinoma ...

    African Journals Online (AJOL)



    Aug 8, 2011 ... East, Central Africa and Egypt (Higuchi et al., 2002). Genotypes 5 and 6 are ... routes of infection such as history of taking different injections, history of ... catheterization, abscess drainage, esophageal vortices, sclera- therapy ... 10 ml of venous blood was collected from all the study subjects and sera were ...

  16. Hepatitis E Virus Genotype 3 in Humans and Swine, Bolivia (United States)

    Cavallo, Annalisa; Gonzales, José Luis; Bonelli, Sara Irene; Valda, Ybar; Pieri, Angela; Segundo, Higinio; Ibañez, Ramón; Mantella, Antonia; Bartalesi, Filippo; Tolari, Francesco; Bartoloni, Alessandro


    We determined the seroprevalence of hepatitis E virus (HEV) in persons in 2 rural communities in southeastern Bolivia and the presence of HEV in human and swine fecal samples. HEV seroprevalence was 6.3%, and HEV genotype 3 strains with high sequence homology were detected. PMID:21801630

  17. Comparison and suitability of genotype by environment analysis ...

    African Journals Online (AJOL)

    Pearl millet (Pennisetum glaucum (L.) R. Br.) is an important food security and income crop for households living in semi-arid zones in Uganda. However, the genotype by environment interaction, in addition to the several methods used for its assessment, complicates selection of varieties adapted to such semi-arid areas.

  18. detection of the predominant microcystin-producing genotype of ...

    African Journals Online (AJOL)



    Dec 21, 2011 ... genotypes of MC-producing cyanobacteria in Mozambique. Polymerase chain ...... 1(7): 359-366. Pan H, Song L, Liu Y, Börner T (2002). ... Miles CO (2009). A convenient and cost-effective method for monitoring marine algal ...

  19. identification of common bean genotypes with dual leaf and pod ...

    African Journals Online (AJOL)




  20. Numerical and RAPD Analysis of Eight Cowpea Genotypes from ...

    African Journals Online (AJOL)

    Hence, numerical tools such as single linkage cluster analysis (SLCA) and principal component analysis (PCA) have been used to determine the extent of variability. This study was conducted to determine the performance, character contribution as well as variation pattern in eight cowpea genotypes collected in Nigeria.

  1. Genotype and ancestry modulate brain's DAT availability in healthy humans

    International Nuclear Information System (INIS)

    Shumay, E.; Chen, J.; Fowler, J.S.; Volkow, N.D.


    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 [ 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. Leaf anatomy of genotypes of banana plant grown under coloured ...

    African Journals Online (AJOL)

    This study aimed to evaluate the effect of spectral light quality on different anatomical features of banana tree plantlets grown under coloured shade nets. Banana plants of five genotypes obtained from micropropagation, were grown under white, blue, red and black nets, with shade of 50%, in a completely randomized ...

  3. Breeding value of primary synthetic wheat genotypes for grain yield (United States)

    To introduce new genetic diversity into the bread wheat gene pool from its progenitor, Aegilops tauschii (Coss.) Schmalh, 33 primary synthetic hexaploid wheat genotypes (SYN) were crossed to 20 spring bread wheat (BW) cultivars at the International Wheat and Maize Improvement Center. Modified single...

  4. Genotype identification and inference of genetic relatedness among ...

    African Journals Online (AJOL)

    Twenty-seven (27) grape genotypes representing different grape groups namely table, wine, juice grapes and rootstocks with present or potential future importance for sub-tropical viticulture were characterized with 29 microsatellite markers spanning over 15 linkage groups of 'Syrah' x 'Grenache' linkage map.

  5. Physiological responses to glyphosate are dependent on Eucalyptus urograndis genotype (United States)

    Two experiments were conducted to evaluate the response of Eucalyptus urograndis genotypes (C219 and GG100) to glyphosate in growth chambers. As glyphosate dose increased (18 up to 720 g ae ha-1), CO2 assimilation rate, transpiration rate, and stomatal conductance decreased fastest and strongest in ...

  6. Genetic diversity of Pakistani maize genotypes using chromosome ...

    African Journals Online (AJOL)

    For improvement of maize crop presence of genetic diversity in the germplasm is very important. This study was conducted to determine genetic diversity among 17 Pakistani maize genotypes using 10 simple sequence repeat (SSR) primer sets. All the amplification products were in the range of <250-750 bp. To estimate the ...

  7. Protein landmarks for diversity assessment in wheat genotypes ...

    African Journals Online (AJOL)

    Grain proteins from 20 Indian wheat genotypes were evaluated for diversity assessment based seed storage protein profiling on sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE). Genetic diversity was evaluated using Nei's index, Shannon index and Unweighted pair group method with arithmetic ...

  8. MLVA genotyping of human Brucella isolates from Peru

    NARCIS (Netherlands)

    Smits, Henk L.; Espinosa, Benjamin; Castillo, Rosa; Hall, Eric; Guillen, Alfredo; Zevaleta, Milagros; Gilman, Robert H.; Melendez, Paolo; Guerra, Carlos; Draeger, Angelika; Broglia, Alessandro; Nöckler, Karsten


    Recent human Brucella melitensis isolates from Peru were genotyped by multiple locus variable number repeat analysis. All 24 isolates originated from hospitalized patients living in the central part of Peru and consisted of six genomic groups comprising two to four isolates and nine unique

  9. Effect of Temperature and Hose Genotype on Components of ...

    African Journals Online (AJOL)

    Effect of Temperature and Hose Genotype on Components of Resistance to Groundnut Rust. P Subrahmanyam, PV Subba Rao, PM Reddy, D McDonald. Abstract. The effects of temperature on incubation period, infection frequency, lesion diameter, leaf area damage, pustule rupture, and sporulation were quantified for six ...

  10. Responses of some selected Malaysian rice genotypes to callus ...

    African Journals Online (AJOL)



    Jan 17, 2011 ... embryogenic callus culture (Yin et al., 1993). In this study, overall, the callus from the MS medium had a good texture. Furthermore, some genotypes also produced better callus in other concentrations of 2,4-D treatment, however, the quality of callus was not as good as those in. 10 µM 2,4-D. Notably, the ...

  11. Coral host transcriptomic states are correlated with Symbiodinium genotypes

    KAUST Repository

    DeSalvo, Michael K.


    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. © 2010 Blackwell Publishing Ltd.

  12. Geographical parthenogenesis: General purpose genotypes and frozen niche variation

    DEFF Research Database (Denmark)

    Vrijenhoek, Robert C.; Parker, Dave


    hypotheses concerning the evolution of niche breadth in asexual species - the "general-purpose genotype" (GPG) and "frozen niche-variation" (FNV) models. The two models are often portrayed as mutually exclusive, respectively viewing clonal lineages as generalists versus specialists. Nonetheless...

  13. Peptostreptococcus micros smooth and rough genotypes in periodontitis and gingivitis

    NARCIS (Netherlands)

    Kremer, BHA; Loos, BG; van der Velden, U; van Winkelhoff, AJ; Craandijk, J; Bulthuis, HM; Hutter, J; Varoufaki, AS; van Steenbergen, TJM

    Background: Two genotypes can be distinguished within the species Peptostreptococcus micros: a smooth (Sm) and a rough (Rg) type. To date no systematic study has been performed on the prevalence and proportion of both types in untreated periodontitis patients and subjects without destructive

  14. Field reaction of cassava genotypes to anthracnose, bacterial blight ...

    African Journals Online (AJOL)

    Field reaction of cassava genotypes to anthracnose, bacterial blight, cassava mosaic disease and their effects on yield. ... The BYDV-PAV and BYDV-RPV serotypes were identified from 9 and 10 of the 11 surveyed fields, respectively, with the two serotypes co-infecting some plants. Of the nine wheat cultivars surveyed, four ...

  15. Genetic variability of indigenous cowpea genotypes as determined ...

    African Journals Online (AJOL)

    Bayesian statistics coupled with the Markov chain Monte Carlo technique was applied to determine population structure, while the genetic variability was established by analysis of molecular variance. UPGMA analysis allowed the separation of the genotypes into three groups, but no relationship between the genetic and ...

  16. Effect of genotype on egg quality characteristics of guinea fowl ...

    African Journals Online (AJOL)

    The genotypes were Pearl x Pearl (PL x PL), Black x Black (BL x BL) and Pearl x Black (PL x BL). ... The external and shell quality parameters measured were egg weight (EWGT), egg length (ELGT), egg width (EWDT), egg shape index (ESPI), shell weight (SWGT), and shell thickness (STKN) while the internal traits were ...

  17. Assessment of genotype x environment interaction on yield and ...

    African Journals Online (AJOL)

    Days to heading, plant height, number of spikes per square meter, number of kernels per spike, spike weight, 1000 kernel weight and grain yield of the genotypes were evaluated in each location. The regression coefficient (bi) of Finlay and Wilkinson (1963) and mean square of deviation from regression (S2d) of Eberhart ...

  18. A preliminary investigation into genotype x environment interaction ...

    African Journals Online (AJOL)

    The purpose of the study was to investigate a possible genotype by environment interaction in first calf South African Holstein cows for both production and reproduction traits. Data from 100 975 cows on a total mixed ration (TMR) and 22 083 pasture based cows were used. These cows were the progeny of 4 391 sires and ...

  19. Epiphytic bacteria from various bean genotypes and their potential ...

    African Journals Online (AJOL)

    Naturally occurring epiphytic non-pathogeni bacteria were isolated from reproductive tissue of various bean genotypes grown in the field and screened for both in vitro and in vivo antagonism to Xanthomonas axonopodis pv. phaseoli (formely X. campestris pv phaseoli). Of the 22 potential bacterial antagonists screened in ...

  20. Evaluation of nutritional quality and antioxidant potential of pigeonpea genotypes. (United States)

    Sekhon, Japjot; Grewal, Satvir Kaur; Singh, Inderjit; Kaur, Jagmeet


    Three released cultivars, forty four advance breeding lines and three wild species of pigeonpea ( Cajanus cajan L. Millsp) were evaluated for nutritional, antinutritional traits and antioxidant potential so as to identify promising genotypes. The average content of total soluble sugars, starch and total soluble proteins was found to be 43.66, 360.51 and 204.54 mg/g, respectively. Antioxidant potential in terms of free radical scavenging activity (DPPH), ferric reducing antioxidant power (FRAP), reducing power, hydroxyl radical scavenging activity and superoxide anion radical scavenging activity was estimated. The diversity was observed in genotypes with all the traits. AL 1960, AL 2000, AL 2009 and AL 2046 had high total soluble proteins, medium antinutritional factors and good antioxidant potential. AL 201, AL 1931, AL 1932, AL 1960, AL 2046, AL 2049 and AL 2060 had good nutritional value as protein and starch content ranged from 20 to 23 and 42 to 52%, respectively. Wild species C. scarabaeoides 1CP15683/W15 had lower carbohydrates, proteins, and antinutritional traits while high antioxidant potential due to high total phenols, DPPH, FRAP and reducing power. The diversity observed in genotypes with all the traits could be further used to develop nutritionally important genotypes.

  1. Serotonin transporter genotype, salivary cortisol, neuroticism and life events

    DEFF Research Database (Denmark)

    Vinberg, Maj; Miskowiak, Kamilla; Kessing, Lars Vedel


    OBJECTIVE: To investigate if cortisol alone or in interaction with other risk factors (familial risk, the serotonin transporter genotype, neuroticism and life events (LEs)) predicts onset of psychiatric disorder in healthy individuals at heritable risk. MATRIAL AND METHODS: In a high-risk study...

  2. Genotyping of African swine fever virus (ASFV) isolates associated ...

    African Journals Online (AJOL)

    Four of these viruses were isolated directly from serum samples. All the viruses were classified within the domesticpig cycle-associated p72 and p54 genotype IX which also includes viruses responsible for ASF outbreaks in Kenya in 2006 and 2007 and Uganda in 2003. To define virus relationships at higher resolution, ...

  3. Leveraging from genotype by environment interaction for bread ...

    African Journals Online (AJOL)

    Developing high yielding and stable genotypes for wide and specific adaptation is ... The analysis of variance for AMMI model of grain yield showed that environment, ... The AMMI biplot, using the first two principal components, showed that testing ... However, extensive testing considering many locations across East African ...

  4. stability analysis of food barley genotypes in northern ethiopia

    African Journals Online (AJOL)


    interaction and stability for barley grain yield and yield related traits in the growing ... that the environments were diverse; causing most of the variation in grain yield. ... component axes IPCA1, IPCA2 and IPCA3, which explained 58.06, 27.11 and ..... AMMI analysis of variance for grain yield (t ha-1) of food barley genotypes ...

  5. Genotype-phenotype associations in children with congenital hyperinsulinism

    DEFF Research Database (Denmark)

    Melikyan, Maria; Brusgaard, Klaus; Petraykina, Elena

    Congenital hyperinsulinism (CHI) is a heterogeneous disease in terms of clinical presentation, genetics and histology. Mutations in eight genes are known to be a cause of CHI, of which ABCC8, KCNJ11 and GCK are among the most common. We investigated genotype-phenotype associations in a cohort...

  6. Growth response at age 10 years of five Eucalyptus genotypes ...

    African Journals Online (AJOL)

    Thus, following the 1999 drought event a trial was established in a drought-prone area, planted to a number of genotypes that were deemed to be more tolerant to water stress than Eucalyptus grandis. Each species was planted at stand densities of 816, 1 600 and 2 066 stems ha-1, where 1 600 stems ha-1 represented the ...

  7. Estimation of genetic diversity in rice ( Oryza sativa L. ) genotypes ...

    African Journals Online (AJOL)

    Thirty rice genotypes comprising land races, pure lines, somaclones, breeding lines and varieties specifically adapted to costal saline environments were characterized by SSR markers and morphological characters in this study. Out of 35 primers of SSR markers, 28 were found to be polymorphic. The PIC value ranged ...

  8. genotype by environment interaction and grain yield stability

    African Journals Online (AJOL)

    Preferred Customer

    among environments, GXE interaction and Interaction Principal Component Analysis (IPCA-I) but ... value closer to zero, Genotype Selection Index (GSI) of 4 each and AMMI stability value (ASV) of 0.124 and. 0.087 ..... Analysis of variance for grain yield using Additive Mean Effect and Multiple Interactions (AMMI) model.

  9. Interaction between a novel TGFB1 haplotype and CFTR genotype is associated with improved lung function in cystic fibrosis. (United States)

    Bremer, Lindsay A; Blackman, Scott M; Vanscoy, Lori L; McDougal, Kathryn E; Bowers, Amanda; Naughton, Kathleen M; Cutler, David J; Cutting, Garry R


    Cystic fibrosis (CF), the most common lethal single gene disorder in Caucasians, is due to mutations in the CFTR gene. Twin and sibling analysis indicates that modifier genes, rather than allelic variation in CFTR, are responsible for most of the variability in severity of lung disease, the major cause of mortality in CF patients. We used a family-based approach to test for association between lung function and two functional SNPs (rs1800469, '-509' and rs1982073, 'codon 10') in the 5' region of transforming growth factor-beta1 (TGFB1), a putative CF modifier gene. Quantitative transmission disequilibrium testing of 472 CF patient-parent-parent trios revealed that both TGFB1 SNPs showed significant transmission distortion when patients were stratified by CFTR genotype. Although lung function and nutritional status are correlated in CF patients, there was no evidence of association between the TGFB1 SNPs and variation in nutritional status. Additional tagging SNPs (rs8179181, rs2278422, rs8110090, rs4803455 and rs1982072) that capture most of the diversity in TGFB1 were also typed but none showed association with variation in lung function. However, a haplotype composed of the -509 C and codon 10 T alleles along with the C allele of the 3' SNP rs8179181 was highly associated with increased lung function in patients grouped by CFTR genotype. These results demonstrate that TGFB1 is a modifier of CF lung disease and reveal a previously unrecognized beneficial effect of TGFB1 variants upon the pulmonary phenotype.

  10. Effect of slaughtering age in different commercial chicken genotypes reared according to the organic system: 1. Welfare, carcass and meat traits

    Directory of Open Access Journals (Sweden)

    Alessandro Dal Bosco


    Full Text Available The carcass and meat quality of three different commercial chicken genotypes reared according to the organic system and slaughtered at two different ages (70 and 81 days were compared. The used genotypes were Naked Neck (CN1, Kabir (KR4 and Ross 308 (R. All animals were raised in the facilities of a big Italian company, in production units of 3000 birds. Before slaughtering, plumage conditions, foot pad dermatitis as well as qualitative traits of carcasses, such as skin damage and the presence of breast blisters, were registered (n=50. Naked Neck birds showed the best plumage conditions at both ages; the other genotypes had similar body conditions showing a dramatically worsening at the end of rearing cycle (81 days, mainly at breast level. The carcass conformation showed differences mainly for the CN1 genotype, which was more slender with higher proportions of head, neck and legs; thus, ready-to-cook-carcass yield was lower. The meat of CN1 chickens showed lower levels of lipids, pH and brightness values, but higher index of redness. Ross 308 genotype showed a bad welfare status even at 70 days, confirming that the rearing of this strain should not be permitted in organic systems. In conclusion, this study indicates that genotype deeply affects performance, welfare and qualitative characteristics of meat. Regarding the slaughtering age, although the inconsistency of European Commission rules which authorise the reduction of slaughtering age in less mature strains, at 70 days chickens show higher feed efficiency and thinness of carcass and meat.

  11. Lessons from Cuba for Global Precision Medicine: CYP2D6 Genotype Is Not a Robust Predictor of CYP2D6 Ultrarapid Metabolism. (United States)

    Dorado, Pedro; González, Idilio; Naranjo, María Eugenia G; de Andrés, Fernando; Peñas-Lledó, Eva María; Calzadilla, Luis Ramón; LLerena, Adrián


    A long-standing question and dilemma in precision medicine is whether and to what extent genotyping or phenotyping drug metabolizing enzymes such as CYP2D6 can be used in real-life global clinical and societal settings. Although in an ideal world using both genotype and phenotype biomarkers are desirable, this is not always feasible for economic and practical reasons. Moreover, an additional barrier for clinical implementation of precision medicine is the lack of correlation between genotype and phenotype, considering that most of the current methods include only genotyping. Thus, the present study evaluated, using dextromethorphan as a phenotyping probe, the relationship between CYP2D6 phenotype and CYP2D6 genotype, especially for the ultrarapid metabolizer (UM) phenotype. We report in this study, to the best of our knowledge, the first comparative clinical pharmacogenomics study in a Cuban population sample (N = 174 healthy volunteers) and show that the CYP2D6 genotype is not a robust predictor of the CYP2D6 ultrarapid metabolizer (mUM) status in Cubans. Importantly, the ultrarapid CYP2D6 phenotype can result in a host of health outcomes, such as drug resistance associated with subtherapeutic drug concentrations, overexposure to active drug metabolites, and altered sensitivity to certain human diseases by virtue of altered metabolism of endogenous substrates of CYP2D6. Hence, phenotyping tests for CYP2D6 UMs appear to be a particular necessity for precision medicine in the Cuban population. Finally, in consideration of ethical and inclusive representation in global science, we recommend further precision medicine biomarker research and funding in support of neglected or understudied populations worldwide.

  12. Genotyping and surveillance for scrapie in Finnish sheep

    Directory of Open Access Journals (Sweden)

    Hautaniemi Maria


    Full Text Available Abstract Background The progression of scrapie is known to be influenced by the amino acid polymorphisms of the host prion protein (PrP gene. There is no breeding programme for TSE resistance in sheep in Finland, but a scrapie control programme has been in place since 1995. In this study we have analysed PrP genotypes of total of 928 purebred and crossbred sheep together with the data of scrapie survey carried out in Finland during 2002–2008 in order to gain knowledge of the genotype distribution and scrapie prevalence in Finnish sheep. Results The ARQ/ARQ genotype was the most common genotype in all breeds studied. ARR allele frequency was less than 12% in purebred Finnish sheep and in most genotypes heterozygous for ARR, the second allele was ARQ. The VRQ allele was not detected in the Grey race sheep of Kainuu or in the Aland sheep, and it was present in less than 6% of the Finnish Landrace sheep. Leucine was the most prominent amino acid found in codon 141. In addition, one novel prion dimorphisms of Q220L was detected. During the scrapie survey of over 15 000 sheep in 2002–2008, no classical scrapie cases and only five atypical scrapie cases were detected. Conclusions The results indicate that the Finnish sheep populations have genetically little resistance to classical scrapie, but no classical scrapie was detected during an extensive survey in 2002–2008. However, five atypical scrapie cases emerged; thus, the disease is present in the Finnish sheep population at a low level.

  13. Lactase persistence genotypes and malaria susceptibility in Fulani of Mali

    Directory of Open Access Journals (Sweden)

    Dolo Amagana


    Full Text Available Abstract Background Fulani are a widely spread African ethnic group characterized by lower susceptibility to Plasmodium falciparum, clinical malaria morbidity and higher rate of lactase persistence compared to sympatric tribes. Lactase non-persistence, often called lactose intolerance, is the normal condition where lactase activity in the intestinal wall declines after weaning. Lactase persistence, common in Europe, and in certain African people with traditions of raising cattle, is caused by polymorphisms in the enhancer region approximately 14 kb upstream of the lactase gene. Methods To evaluate the relationship between malaria and lactase persistence genotypes, a 400 bp region surrounding the main European C/T-13910 polymorphism upstream of the lactase gene was sequenced. DNA samples used in the study originated from 162 Fulani and 79 Dogon individuals from Mali. Results Among 79 Dogon only one heterozygote of the lactase enhancer polymorphism was detected, whereas all others were homozygous for the ancestral C allele. Among the Fulani, the main European polymorphism at locus C/T-13910 was by far the most common polymorphism, with an allele frequency of 37%. Three other single-nucleotide polymorphisms were found with allele frequencies of 3.7%, 1.9% and 0.6% each. The novel DNA polymorphism T/C-13906 was seen in six heterozygous Fulani. Among the Fulani with lactase non-persistence CC genotypes at the C/T-13910 locus, 24% had malaria parasites detectable by microscopy compared to 18% for lactase persistent genotypes (P = 0.29. Pooling the lactase enhancer polymorphisms to a common presumptive genotype gave 28% microscopy positives for non-persistent and 17% for others (P = 0.11. Conclusions Plasmodium falciparum parasitaemia in asymptomatic Fulani is more common in individuals with lactase non-persistence genotypes, but this difference is not statistically significant. The potential immunoprotective properties of dietary cow milk as a reason

  14. Disclosure of APOE genotype for risk of Alzheimer's disease. (United States)

    Green, Robert C; Roberts, J Scott; Cupples, L Adrienne; Relkin, Norman R; Whitehouse, Peter J; Brown, Tamsen; Eckert, Susan LaRusse; Butson, Melissa; Sadovnick, A Dessa; Quaid, Kimberly A; Chen, Clara; Cook-Deegan, Robert; Farrer, Lindsay A


    The apolipoprotein E (APOE) genotype provides information on the risk of Alzheimer's disease, but the genotyping of patients and their family members has been discouraged. We examined the effect of genotype disclosure in a prospective, randomized, controlled trial. We randomly assigned 162 asymptomatic adults who had a parent with Alzheimer's disease to receive the results of their own APOE genotyping (disclosure group) or not to receive such results (nondisclosure group). We measured symptoms of anxiety, depression, and test-related distress 6 weeks, 6 months, and 1 year after disclosure or nondisclosure. There were no significant differences between the two groups in changes in time-averaged measures of anxiety (4.5 in the disclosure group and 4.4 in the nondisclosure group, P=0.84), depression (8.8 and 8.7, respectively; P=0.98), or test-related distress (6.9 and 7.5, respectively; P=0.61). Secondary comparisons between the nondisclosure group and a disclosure subgroup of subjects carrying the APOE epsilon4 allele (which is associated with increased risk) also revealed no significant differences. However, the epsilon4-negative subgroup had a significantly lower level of test-related distress than did the epsilon4-positive subgroup (P=0.01). Subjects with clinically meaningful changes in psychological outcomes were distributed evenly among the nondisclosure group and the epsilon4-positive and epsilon4-negative subgroups. Baseline scores for anxiety and depression were strongly associated with post-disclosure scores of these measures (Pdisclosure of APOE genotyping results to adult children of patients with Alzheimer's disease did not result in significant short-term psychological risks. Test-related distress was reduced among those who learned that they were APOE epsilon4-negative. Persons with high levels of emotional distress before undergoing genetic testing were more likely to have emotional difficulties after disclosure. ( number, NCT

  15. Identification of novel Coxiella burnetii genotypes from Ethiopian ticks.

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    Kinga M Sulyok

    Full Text Available BACKGROUND: Coxiella burnetii, the etiologic agent of Q fever, is a highly infectious zoonotic bacterium. Genetic information about the strains of this worldwide distributed agent circulating on the African continent is limited. The aim of the present study was the genetic characterization of C. burnetii DNA samples detected in ticks collected from Ethiopian cattle and their comparison with other genotypes found previously in other parts of the world. METHODOLOGY/PRINCIPAL FINDINGS: A total of 296 tick samples were screened by real-time PCR targeting the IS1111 region of C. burnetii genome and from the 32 positive samples, 8 cases with sufficient C. burnetii DNA load (Amblyomma cohaerens, n = 6; A. variegatum, n = 2 were characterized by multispacer sequence typing (MST and multiple-locus variable-number tandem repeat analysis (MLVA. One novel sequence type (ST, the proposed ST52, was identified by MST. The MLVA-6 discriminated the proposed ST52 into two newly identified MLVA genotypes: type 24 or AH was detected in both Amblyomma species while type 26 or AI was found only in A. cohaerens. CONCLUSIONS/SIGNIFICANCE: Both the MST and MLVA genotypes of the present work are closely related to previously described genotypes found primarily in cattle samples from different parts of the globe. This finding is congruent with the source hosts of the analyzed Ethiopian ticks, as these were also collected from cattle. The present study provides genotype information of C. burnetii from this seldom studied East-African region as well as further evidence for the presumed host-specific adaptation of this agent.

  16. Genetic diversity of popcorn genotypes using molecular analysis. (United States)

    Resh, F S; Scapim, C A; Mangolin, C A; Machado, M F P S; do Amaral, A T; Ramos, H C C; Vivas, M


    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.

  17. Distribution of Hepatitis C Virus Genotypes in the South Marmara Region

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    Harun Agca


    Full Text Available Aim: Hepatitis C virus (HCV is an important caustive agent of hepatitis, cirrhosis and hepatocellular carcinoma both in our country and the world. Prognosis and response to treatment is related with the genotype of HCV which has six genotypes and over a hundred quasispecies. Knowing the HCV genotype is also important for epidemiological data. In this study we aimed to investigate the HCV genotypes of samples sent to Uludag University Hospital Microbiology Laboratory which is the reference centre in the South Marmara Region. Material and Method: This study was done retrospectively to analyse the HCV patients%u2019 sera sent to our laboratory between July 2010and December 2012 for HCV genotyping. Artus HCV QS-RGQ PCR kit (Qiagene,Hilden, Germany was used in Rotor-Gene Q (Qiagene, Hilden Germany for detection of HCV RNA. HCV RNA positive samples of patients%u2019 sera were were used for genotyping by the Linear Array HCV genotyping test (Roche, NJ, USA.Results: 214 (92.6 % of total 231 patients included in the study were genotype 1, one (0.4 % was genotype 2, nine (3.9 % were genotype 3 and, seven (3.4 % were found genotype 4. Three of genotype 3 patients were of foreign nationality, two were born abroad and one of the genotype 4 patients were born abroad. Discussion: Concordant with our country data the most frequent genotype was 1, genotype 2 was seen in patients especially related with foreign countries and genotype 4 was seen rare. The importance of genotype 1, which is seen more frequent in our country and region is; resistance to antiviral treatment and prolonged treatment duration in chronic hepatitis C patients.

  18. Plant genotypes affect aboveground and belowground herbivore interactions by changing chemical defense. (United States)

    Li, Xiaoqiong; Guo, Wenfeng; Siemann, Evan; Wen, Yuanguang; Huang, Wei; Ding, Jianqing


    Spatially separated aboveground (AG) and belowground (BG) herbivores are closely linked through shared host plants, and both patterns of AG-BG interactions and plant responses may vary among plant genotypes. We subjected invasive (USA) and native (China) genotypes of tallow tree (Triadica sebifera) to herbivory by the AG specialist leaf-rolling weevil Heterapoderopsis bicallosicollis and/or the root-feeding larvae of flea beetle Bikasha collaris. We measured leaf damage and leaves rolled by weevils, quantified beetle survival, and analyzed flavonoid and tannin concentrations in leaves and roots. AG and BG herbivores formed negative feedbacks on both native and invasive genotypes. Leaf damage by weevils and the number of beetle larvae emerging as adults were higher on invasive genotypes. Beetles reduced weevil damage and weevils reduced beetle larval emergence more strongly for invasive genotypes. Invasive genotypes had lower leaf and root tannins than native genotypes. BG beetles decreased leaf tannins of native genotypes but increased root tannins of invasive genotypes. AG herbivory increased root flavonoids of invasive genotypes while BG herbivory decreased leaf flavonoids. Invasive genotypes had lower AG and BG herbivore resistance, and negative AG-BG herbivore feedbacks were much stronger for invasive genotypes. Lower tannin concentrations explained overall better AG and BG herbivore performances on invasive genotypes. However, changes in tannins and flavonoids affected AG and BG herbivores differently. These results suggest that divergent selection on chemical production in invasive plants may be critical in regulating herbivore performances and novel AG and BG herbivore communities in new environments.

  19. Neutralizing antibodies in patients with chronic hepatitis C, genotype 1, against a panel of genotype 1 culture viruses

    DEFF Research Database (Denmark)

    Pedersen, Jannie; Jensen, Tanja B; Carlsen, Thomas H R


    , infection treated with pegylated interferon-α and ribavirin. Thirty-nine patients with chronic hepatitis C, genotype 1a or 1b, with either sustained virologic response (n = 23) or non-sustained virologic response (n = 16) were enrolled. Samples taken prior to treatment were tested for their ability...... to neutralize 6 different HCV genotype 1 cell culture recombinants (1a: H77/JFH1, TN/JFH1, DH6/JFH1; 1b: J4/JFH1, DH1/JFH1, DH5/JFH1). The results were expressed as the highest dilution yielding 50% neutralization (NAb50-titer). We observed no genotype or subtype specific differences in NAb50-titers between......The correlation of neutralizing antibodies to treatment outcome in patients with chronic hepatitis C virus (HCV) infection has not been established. The aim of this study was to determine whether neutralizing antibodies could be used as an outcome predictor in patients with chronic HCV, genotype 1...

  20. Status Epilepticus and Refractory Status Epilepticus Management (United States)

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


    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

  1. Management of status epilepticus. (United States)

    Pichler, M; Hocker, S


    Status epilepticus is a neurologic and medical emergency manifested by prolonged seizure activity or multiple seizures without return to baseline. It is associated with substantial medical cost, morbidity, and mortality. There is a spectrum of severity dependent on the type of seizure, underlying pathology, comorbidities, and appropriate and timely medical management. This chapter discusses the evolving definitions of status epilepticus and multiple patient and clinical factors which influence outcome. The pathophysiology of status epilepticus is reviewed to provide a better understanding of the mechanisms which contribute to status epilepticus, as well as the potential long-term effects. The clinical presentations of different types of status epilepticus in adults are discussed, with emphasis on the hospital course and management of the most dangerous type, generalized convulsive status epilepticus. Strategies for the evaluation and management of status epilepticus are provided based on available evidence from clinical trials and recommendations from the Neurocritical Care Society and the European Federation of Neurological Societies. © 2017 Elsevier B.V. All rights reserved.

  2. DOI: 10.18697/ajfand.80.16245 12930 GENOTYPE X ...

    African Journals Online (AJOL)

    genotype x environment interaction and stability of tuber internal quality traits, and iii) ..... environment to another while the dynamic stability is when genotypic ..... TaylorPhysiological, biochemical and molecular responses of the potato.

  3. Biotyping and genotyping (MLVA16 of Brucella abortus isolated from cattle in Brazil, 1977 to 2008.

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    Sílvia Minharro

    Full Text Available 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.

  4. Biological and phylogenetic characterization of a genotype VII Newcastle disease virus from Venezuela: Efficacy of vaccination (United States)

    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...

  5. Chlamydia trachomatis Genotypes and the Swedish New Variant among Urogenital Chlamydia trachomatis Strains in Finland

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    Suvi Niemi


    Full Text Available Our aims were to genotype Chlamydia trachomatis strains present in urogenital samples and to investigate the occurrence of the Swedish new variant of C. trachomatis in Finland. We genotyped 160 C. trachomatis positive samples with ompA real-time PCR and analyzed 495 samples for the new variant. The three most prevalent genotypes were E (40%, F (28%, and G (13%. Only two specimens containing bacteria with the variant plasmid were detected. It seems that in Finland the percentage of infections due to genotypes F and G has slightly increased during the last 20 years. Genotypes E and G appear to be more common, and genotypes J/Ja and I/Ia appear to be less common in Europe than in the USA. Although the genotype E was the most common genotype among C. trachomatis strains, the new variant was rarely found in Finland.

  6. Microbe-ID: An open source toolbox for microbial genotyping and species identification (United States)

    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...

  7. Sugarcane Genotype Performance in Three Environments (Based on Crop Cycle) at Mardan, Pakistan (United States)

    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...

  8. Innate Susceptibility to Norovirus Infections Influenced by FUT2 Genotype in a United States Pediatric Population (United States)

    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.


    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

  9. Short communication: relationship of call rate and accuracy of single nucleotide polymorphism genotypes in dairy cattle. (United States)

    Cooper, T A; Wiggans, G R; VanRaden, P M


    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 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 for 1,216 animals that had a genotype with a call rate of ≤ 99

  10. Implementation of Cell Samples as Controls in National Proficiency Testing for Clopidogrel Therapy-Related CYP2C19 Genotyping in China: A Novel Approach.

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    Guigao Lin

    Full Text Available Laboratories are increasingly requested to perform CYP2C19 genetic testing when managing clopidogrel therapy, especially in patients with acute coronary syndrome undergoing percutaneous coronary intervention. To ensure high quality molecular testing and ascertain that the referring clinician has the correct information for CYP2C19 genotype-directed antiplatelet therapy, a proficiency testing scheme was set up to evaluate the laboratory performance for the entire testing process. Proficiency panels of 10 cell samples encompassing the common CYP2C19 genetic polymorphisms were distributed to 62 participating laboratories for routine molecular testing and the responses were analyzed for accuracy of genotyping and the reporting of results. Data including the number of samples tested, the accreditation/certification status, and test methodology of each individual laboratory were also reviewed. Fifty-seven of the 62 participants correctly identified the CYP2C19 variants in all samples. There were six genotyping errors, with a corresponding analytical sensitivity of 98.5% (333/338 challenges; 95% confidence interval: 96.5-99.5% and an analytic specificity of 99.6% (281/282; 95% confidence interval: 98.0-99.9%. Reports of the CYP2C19 genotyping results often lacked essential information. In conclusion, clinical laboratories demonstrated good analytical sensitivity and specificity; however, the pharmacogenetic testing community requires additional education regarding the correct reporting of CYP2C19 genetic test results.

  11. Parallel or convergent evolution in human population genomic data revealed by genotype networks


    Vahdati, Ali R; Wagner, Andreas


    Background Genotype networks are representations of genetic variation data that are complementary to phylogenetic trees. A genotype network is a graph whose nodes are genotypes (DNA sequences) with the same broadly defined phenotype. Two nodes are connected if they differ in some minimal way, e.g., in a single nucleotide. Results We analyze human genome variation data from the 1,000 genomes project, and construct haploid genotype (haplotype) networks for 12,235 protein coding genes. The struc...

  12. Prevalence of mixed hepatitis C virus (HCV genotypes among recently diagnosed dialysis patients with HCV infection

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    Mohammed A Al Balwi


    Full Text Available Hepatitis C virus (HCV infection is considered a major health problem recognized globally. HCV is a major cause of chronic liver disease that may lead to cirrhosis and hepatocellular carcinoma. The aim of this study was to investigate the prevalence of multiple (mixed HCV genotypes in Saudi patients recently diagnosed with HCV infection and their association with various clinical risk factors. We examined a total of 1,292 newly diagnosed HCV-positive cases between January 2006 and July 2009 at the Molecular Pathology Laboratory, King Abdulaziz Medical City, Riyadh. The clinical and laboratory data of the study patients were collected. The HCV-RNA viral load and its genotyping were carried out with RT-PCR technology to assist in the follow-up and management of HCV-infected patients undergoing antiviral therapy. Twenty-two patients (1.7% were found to have mixed HCV genotypes; of them, mixed genotypes associated with genotype-4 were seen in 19 patients (86%, mixed genotypes associated with genotype-1 were found in 68.4%, with genotype-3 in 26.3% and with genotype-2 in 5.3%. Additionally, mixed genotypes associated with genotype-1 were seen in three cases (13.6%; they were associated with genotype-2 in two (66.7% and with genotype-5 in one patient (33.3%. In conclusion, the prevalence rate of mixed HCV genotypes in the cohort of the newly infected Saudi patients was 1.7%, with genotype-4 being the most frequent genotype encountered.

  13. Genetic Variations Involved in Vitamin E Status

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    Patrick Borel


    Full Text Available 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.

  14. (Epi)genotype-Phenotype Analysis in 69 Japanese Patients With Pseudohypoparathyroidism Type I (United States)

    Sano, Shinichiro; Nakamura, Akie; Matsubara, Keiko; Nagasaki, Keisuke; Fukami, Maki; Kagami, Masayo


    Context: Pseudohypoparathyroidism type I (PHP-I) is divided into PHP-Ia with Albright hereditary osteodystrophy and PHP-Ib, which usually shows no Albright hereditary osteodystrophy features. Although PHP-Ia and PHP-Ib are typically caused by genetic defects involving α subunit of the stimulatory G protein (Gsα)–coding GNAS exons and methylation defects of the GNAS differentially methylated regions (DMRs) on the maternal allele, respectively, detailed phenotypic characteristics still remains to be examined. Objective: To clarify phenotypic characteristics according to underlying (epi)genetic causes. Patients and Methods: We performed (epi)genotype-phenotype analysis in 69 Japanese patients with PHP-I; that is, 28 patients with genetic defects involving Gsα-coding GNAS exons (group 1) consisting of 12 patients with missense variants (subgroup A) and 16 patients with null variants (subgroup B), as well as 41 patients with methylation defects (group 2) consisting of 21 patients with broad methylation defects of the GNAS-DMRs (subgroup C) and 20 patients with an isolated A/B-DMR methylation defect accompanied by the common STX16 microdeletion (subgroup D). Results: Although (epi)genotype-phenotype findings were grossly similar to those reported previously, several important findings were identified, including younger age at hypocalcemic symptoms and higher frequencies of hyperphosphatemia in subgroup C than in subgroup D, development of brachydactyly in four patients of subgroup C, predominant manifestation of subcutaneous ossification in subgroup B, higher frequency of thyrotropin resistance in group 1 than in group 2, and relatively low thyrotropin values in four patients with low T4 values and relatively low luteinizing hormone/follicle-stimulating hormone values in five adult females with ovarian dysfunction. Conclusion: The results imply the presence of clinical findings characteristic of each underlying cause and provide useful information on the imprinting

  15. Prevalence of fimA genotypes of Porphyromonas gingivalis in adolescent orthodontic patients.

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    Shuang Pan

    Full Text Available The placement of fixed orthodontic appliances may alter the composition of oral microbiota and has the potential risk of periodontal complication. Porphyromonas gingivalis fimbriae play a critical role in colonization of P. gingivalis in subgingival regions. In this study, we investigated the association between the prevalence of P. gingivalis-specific fimA genotypes and periodontal health status in adolescent orthodontic patients, to identify the pathogencity of P. gingivalis during orthodontic therapy.Sixty-one adolescent orthodontic patients were enrolled in the case group, while the control group consisted of 56 periodontally healthy adolescents. At baseline (T0, clinical parameter (gingival index was tested, and subgingival plaque samples were obtained from the lower incisors. The incidences of P. gingivalis and fimA genotypes were detected by polymerase chain reaction. All parameters were reassessed after 1 month (T1, 2 months (T2, 3 months (T3, and 6 months (T4 in the case group and then compared with those of the controls.Both microbiological and clinical parameters from orthodontic patients started to increase after placement of fixed appliances. Maximum values were reached at 3 months after placement and followed by their decreases at six months. However, the microbiological and clinical parameters in the case group were significantly higher than those of the control group. The GI of fimA II, IV-positive samples was significantly higher than that of negative samples.P. gingivalis carrying fimA II or IV was closely related to orthodontic gingivitis. In addition, proper oral hygiene control could lead to little increase in dental plaque accumulation, and exert a beneficial effect to periodontal tissues.

  16. Helicobacter pylori genotypes and types of gastritis in first-degree relatives of gastric cancer patients. (United States)

    Siavoshi, F; Asgharzadeh, A; Ghadiri, H; Massarrat, S; Latifi-Navid, S; Zamani, M


    The frequency of Helicobacter pylori vacA alleles, cagA, and jhp0947 and their association with types and advanced forms of gastritis in 143 first-degree relatives of gastric cancer (GC) patients was assessed. The subjects included 64/143 with antral-predominant gastritis, 68/143 with pangastritis, and 11/143 with corpus-predominant gastritis, with or without atrophy or intestinal metaplasia (IM). Further classification included the severity of atrophy or IM. Group I (40/143) included the subjects with moderate-marked atrophy or IM, group II (58/143) those with no atrophy or IM, and group III (45/143) with mild atrophy or IM. The frequency of vacA s1 was 79.7%, vacA s2 20.3%, m1 49.7%, m2 50.3%, cagA 76.2%, and jhp0947 58%. The most prevalent combination was vacAs1 cagA (+) (65.7%) (P=0.001). Of the 143 subjects, 85 (59.4%) showed atrophy or IM, and 40/85 (47%) developed the moderate-marked atrophy or IM. No significant correlation was found between genotypes and the types of gastritis, non-atrophy, atrophy, or IM and severe forms of atrophy or IM (P>0.05). It is proposed that H. pylori genotype status might not be considered as an important determinant of the types and advanced forms of gastritis in the first-degree relatives of GC patients. Copyright © 2011 Elsevier GmbH. All rights reserved.

  17. Drought induced changes of leaf-to-root relationships in two tomato genotypes. (United States)

    Moles, Tommaso Michele; Mariotti, Lorenzo; De Pedro, Leandro Federico; Guglielminetti, Lorenzo; Picciarelli, Piero; Scartazza, Andrea


    Water deficit triggers a dynamic and integrated cross-talk between leaves and roots. Tolerant plants have developed several physiological and molecular mechanisms to establish new cell metabolism homeostasis, avoiding and/or escaping from permanent impairments triggered by drought. Two tomato genotypes (a Southern Italy landrace called Ciettaicale and the well-known commercial cultivar Moneymaker) were investigated at vegetative stage to assess leaf and root metabolic strategies under 20 days of water deficit. Physiological and metabolic changes, in terms of ABA, IAA, proline, soluble sugars and phenols contents, occurred in both tomato genotypes under water stress. Overall, our results pointed out the higher plasticity of Ciettaicale to manage plant water status under drought in order to preserve the source-sink relationships. This aim was achieved by maintaining a more efficient leaf photosystem II (PSII) photochemistry, as suggested by chlorophyll fluorescence parameters, associated with a major investment towards root growth and activity to improve water uptake. On the contrary, the higher accumulation of carbon compounds, resulting from reduced PSII photochemistry and enhanced starch reserve mobilization, in leaves and roots of Moneymaker under drought could play a key role in the osmotic adjustment, although causing a feedback disruption of the source-sink relations. This hypothesis was also supported by the different drought-induced redox unbalance, as suggested by H 2 O 2 and MDA contents. This could affect both PSII photochemistry and root activity, leading to a major involvement of NPQ and antioxidant system in response to drought in Moneymaker than Ciettaicale. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  18. Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet. (United States)

    Wedrowicz, Faye; Karsa, Mawar; Mosse, Jennifer; Hogan, Fiona E


    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. © 2013 John Wiley & Sons Ltd.


    Directory of Open Access Journals (Sweden)

    Faisal Anwar


    Full Text Available 800x600 Normal 0 false false false IN X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Calibri","sans-serif"; mso-bidi-font-family:"Times New Roman";} The objectives of the study were: (1 To analyze the socio-economic and demographic characteristics of Baduy people; (2 To analyze the health status and nutritional status of Baduy people and its influential factors. This research is an explorative and descriptive study on the socio-cultural aspects of food system. The data were collected through a direct interview and discussion with respondents as well as a direct observation at the location of respondents. A sample size of 338 households was drawn from the population. To obtain the data on the cultural aspects, history and  socio aspect of food, in-depth interviews was conducted with 19 key persons. The study was last for 12 months. In Outer Baduy, the factors significantly related to nutritional status are age, number of household size, income, nutritional knowledge, and wife’s ability to read. In Moslem Baduy, only age and income are related to the nutritional status of children. In Moslem Baduy and the Outer Baduy, the correlation between age and W/A or W/H is similar: namely, the higher the age, the lower would the Z-score for the W/A or W/H. The income is significantly correlated to the child nutritional status according to Z-score for W/A with a high correlation coefficient, that is, 0.61. This means that the higher the income, the higher would be the Z-score value for the W/A.  The distribution of adults according to BMI classification in Outer Baduy it shows that 12.7% husbands and 17.6% wives are thin (wasted, while the

  20. Influence of genic status in relation to gamma ray and EMS induced pollen sterility in chillies (Capsicum Annum L.)

    International Nuclear Information System (INIS)

    Asha, M.S.; Nayar, N.K.


    Fifteen genotypes of the same species tested to study the effect of gamma rays and ethylmethane sulphonate showed wide variability in their effect. Pollen sterility increased with increase in dose. Gamma rays induced a higher per cent sterility compared to EMS. Genic status influenced variation was noted in the effect of mutagens in inducing pollen sterility. 7 refs. (author)