WorldWideScience

Sample records for s-variant sert genotype

  1. Ontogeny of SERT Expression and Antidepressant-like Response to Escitalopram in Wild-Type and SERT Mutant Mice.

    Science.gov (United States)

    Mitchell, Nathan C; Gould, Georgianna G; Koek, Wouter; Daws, Lynette C

    2016-08-01

    Depression is a disabling affective disorder for which the majority of patients are not effectively treated. This problem is exacerbated in children and adolescents for whom only two antidepressants are approved, both of which are selective serotonin reuptake inhibitor (SSRIs). Unfortunately SSRIs are often less effective in juveniles than in adults; however, the mechanism(s) underlying age-dependent responses to SSRIs is unknown. To this end, we compared the antidepressant-like response to the SSRI escitalopram using the tail suspension test and saturation binding of [(3)H]citalopram to the serotonin transporter (SERT), the primary target of SSRIs, in juvenile [postnatal day (P)21], adolescent (P28), and adult (P90) wild-type (SERT+/+) mice. In addition, to model individuals carrying low-expressing SERT variants, we studied mice with reduced SERT expression (SERT+/-) or lacking SERT (SERT-/-). Maximal antidepressant-like effects were less in P21 mice relative to P90 mice. This was especially apparent in SERT+/- mice. However, the potency for escitalopram to produce antidepressant-like effects in SERT+/+ and SERT+/- mice was greater in P21 and P28 mice than in adults. SERT expression increased with age in terminal regions and decreased with age in cell body regions. Binding affinity values did not change as a function of age or genotype. As expected, in SERT-/- mice escitalopram produced no behavioral effects, and there was no specific [(3)H]citalopram binding. These data reveal age- and genotype-dependent shifts in the dose-response for escitalopram to produce antidepressant-like effects, which vary with SERT expression, and may contribute to the limited therapeutic response to SSRIs in juveniles and adolescents. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

  2. Sertões desvendados

    Directory of Open Access Journals (Sweden)

    Wegner Robert

    2000-01-01

    Full Text Available This essay presents readers with the central argument from three books, ranging from Euclides da Cunha to Guimarães Rosa and the hygienist movement of the 1920s, focusing on the theme of the sertão (backlands in Brazilian literature and social thought. Based on this presentation, the essay emphasizes that linked to the topic under review, Brazilian intellectual tradition has nearly always encompassed classical themes from sociology and political science, like incorporation and nation-building. After digressing to the three authors' styles, the essay concludes by suggesting the validity of performing comparative studies on approaches to the Brazilian backlands and those conducted by North American scholars.

  3. A ontologia discursiva de Os sertões The discursive ontology of Os sertões

    Directory of Open Access Journals (Sweden)

    Leopoldo M. Bernucci

    1998-07-01

    Full Text Available Este artigo discute atributos de Os sertões, analisando sua ontologia discursiva, em particular os aspectos ligados às narrativas imaginárias e literárias. Mostra que a principal obra de Euclides conjuga pelo menos dois modos discursivos: o das ciências e um outro que caracteriza as narrativas sobre realidades imaginárias e literárias. Trechos são destacados com o objetivo de demonstrar que na sua construção híbrida participam elementos que poderiam pertencer tanto à ficção como à historiografia. Apoiando-se em Hayden White, o autor contempla três modos interpretativos da história de Canudos em Os sertões: o argumentativo, o explicativo e o ideológico. Finalmente, realiza breve comparação com A guerra do fim do mundo, de Vargas Llosa, quanto ao modo e a seqüência como são narrados os fatos.This analysis of the discursive ontology of Os sertões is particularly concerned with the book’s imaginary and literary narratives. Cunha’s main work combines at least two discursive styles: the discourse of the sciences and the discourse that characterizes narratives dealing with imaginary and literary realities. Selected excerpts show how the hybrid construction of Os sertões relies on elements which may belong to the realm of either fiction or historiography. Based on the ideas of Hayden White, the article detects three ways in which Os sertões interprets the history of Canudos: argumentative, explanatory, and ideological. The text ends with a brief comparison of the narration and sequencing of facts in Vargas Llosa’s La guerra del fin del mundo and Cunha’s Os sertões.

  4. IDOL N342S Variant, Atherosclerosis Progression and Cardiovascular Disorders in the Italian General Population.

    Directory of Open Access Journals (Sweden)

    Ashish Dhyani

    Full Text Available Inducible degrader of the low density lipoprotein receptor (IDOL, is an E3 ubiquitin ligase that negatively modulates low density lipoprotein receptor (LDL-R expression. Genome-wide association studies (GWAS indicated that genetic variants in IDOL gene contributes to variation in LDL-C plasma levels and the detailed analysis of a specific locus resulted in the identification of the functional common single nucleotide polymorphism (SNP rs9370867 (c.G1025A, p.N342S associates with increased LDL-R degradation and increased LDL-C levels. These findings, however, were not confirmed in two other independent cohorts and no data about the impact of this variant on atherosclerosis progression and cardiovascular risk are available. Aim of this study was to investigate the association between a functional variant in IDOL and atherosclerosis progression in an Italian general population. 1384 subjects enrolled in the PLIC study (Progression of Lesions in the Intima of Carotid were genotyped by Q-PCR allelic discrimination and the association with anthropometric parameters, plasma lipids and the carotid intima media thickness (cIMT and the impact on cardiovascular disease (CVD incidence were investigated. The N342S variant was not associated with changes of the plasma lipid profile among GG, AG or AA carriers, including total cholesterol (249±21, 249±19 and 248±21 mg/dl respectively, LDL-C (158±25, 161±22 and 160±23 mg/dL, cIMT (0.74±0.14, 0.75±0.17 and 0.77±0.15 mm and CVD incidence. In agreement, the expression of LDLR and the uptake of LDL was similar in macrophages derived from GG and AA carriers. Taken together our findings indicate that the N342S variant does not impact plasma lipid profile and is not associated with atherosclerosis progression and CVD in the general population, suggesting that other variants in the IDOL gene might be functionally linked with cholesterol metabolism.

  5. IDOL N342S Variant, Atherosclerosis Progression and Cardiovascular Disorders in the Italian General Population.

    Science.gov (United States)

    Dhyani, Ashish; Tibolla, Gianpaolo; Baragetti, Andrea; Garlaschelli, Katia; Pellegatta, Fabio; Grigore, Liliana; Norata, Giuseppe Danilo; Catapano, Alberico Luigi

    2015-01-01

    Inducible degrader of the low density lipoprotein receptor (IDOL), is an E3 ubiquitin ligase that negatively modulates low density lipoprotein receptor (LDL-R) expression. Genome-wide association studies (GWAS) indicated that genetic variants in IDOL gene contributes to variation in LDL-C plasma levels and the detailed analysis of a specific locus resulted in the identification of the functional common single nucleotide polymorphism (SNP) rs9370867 (c.G1025A, p.N342S) associates with increased LDL-R degradation and increased LDL-C levels. These findings, however, were not confirmed in two other independent cohorts and no data about the impact of this variant on atherosclerosis progression and cardiovascular risk are available. Aim of this study was to investigate the association between a functional variant in IDOL and atherosclerosis progression in an Italian general population. 1384 subjects enrolled in the PLIC study (Progression of Lesions in the Intima of Carotid) were genotyped by Q-PCR allelic discrimination and the association with anthropometric parameters, plasma lipids and the carotid intima media thickness (cIMT) and the impact on cardiovascular disease (CVD) incidence were investigated. The N342S variant was not associated with changes of the plasma lipid profile among GG, AG or AA carriers, including total cholesterol (249±21, 249±19 and 248±21 mg/dl respectively), LDL-C (158±25, 161±22 and 160±23 mg/dL), cIMT (0.74±0.14, 0.75±0.17 and 0.77±0.15 mm) and CVD incidence. In agreement, the expression of LDLR and the uptake of LDL was similar in macrophages derived from GG and AA carriers. Taken together our findings indicate that the N342S variant does not impact plasma lipid profile and is not associated with atherosclerosis progression and CVD in the general population, suggesting that other variants in the IDOL gene might be functionally linked with cholesterol metabolism.

  6. The (disorder in the sertão: violence and survival in Grande sertão: veredas A (desordem no sertão: violência e sobrevivência em Grande sertão: veredas

    Directory of Open Access Journals (Sweden)

    Regina Crispim e Rogério Santana

    2009-01-01

    Full Text Available This article analyses two episodes from the novel Grande sertão: Veredas,written by João Guimarães Rosa: Zé Bebelo’s judgment and the pact made byRiobaldo. In the first episode, one examines the peculiar society constitutedin the “sertão” by “coronéis” and “jagunços”; in the second one, the notionof pact is broadened beyond the symbolic deal made with the devil, showingits development as strategies of survival in an environment in which theapparent disorder reveals itself as the essence of the order devised and keptby violence.Este artigo analisa dois episódios do romance Grande sertão: veredas, de JoãoGuimarães Rosa: o julgamento de Zé Bebelo e o pacto feito por Riobaldo.No primeiro, examina-se a peculiar organização da sociedade formada nosertão pelos coronéis e jagunços; no segundo, amplia-se a noção de pacto paraalém do simbólico trato com o diabo, mostrando seus desdobramentos comoestratégias de sobrevivência num meio em que a aparente desordem se revelaa essência de uma ordem forjada e mantida pela violência.

  7. Serotonin Transporter-Independent Actions of the Antidepressant Vortioxetine As Revealed Using the SERT Met172 Mouse.

    OpenAIRE

    Nackenoff Alex G; Simmler Linda D; Baganz Nicole L; Pehrson Alan L; Sánchez Connie; Blakely Randy D

    2017-01-01

    Selective serotonin (5 HT SERT) reuptake inhibitors (SSRIs) are the most commonly prescribed treatments for depression. However they have delayed efficacy and can induce side effects that can encourage discontinuation. Recently agents have been developed including vortioxetine (Trintellix) that augment SERT blockade with interactions at other targets. At therapeutic doses vortioxetine interacts with SERT as well as 5 HT1A 5 HT1B 5 HT3 and 5 HT7 receptors. We assessed the SERT dependency of vo...

  8. Self-Explanation and Reading Strategy Training (SERT) Improves Low-Knowledge Students' Science Course Performance

    Science.gov (United States)

    McNamara, Danielle S.

    2017-01-01

    This study demonstrates the generalization of previous laboratory results showing the benefits of Self-Explanation Reading Training (SERT) to college students' course exam performance. The participants were 265 students enrolled in an Introductory Biology course, 59 of whom were provided with SERT. The results showed that SERT benefited students…

  9. Grande sertão: a escrita de uma leitura

    Directory of Open Access Journals (Sweden)

    Lisa Carvalho Vasconcellos

    2005-10-01

    Full Text Available O presente  traba lho,  resultado parcial da pesquisa  que desenvolvo em meu Mestrado, vem abordar alguns questionamentos sobre  a lei­tura que acredito se rem intrínsecos a Grande sertão:veredas. Atra vés de uma analogia entre o narratário, ou seja o visitante para quem Riobaldo  conta  sua história, e o leitor  empírico da obra,  abordo o romance rosiano como uma na rrativa que reflete metalinguisticamente sobre a problemática  da leitura. A partir  dessa idéia, passo a a nalisar que tipo de leitura nos propõe o protagonista do romance.

  10. Mechanisms of Intestinal Serotonin Transporter (SERT Upregulation by TGF-β1 Induced Non-Smad Pathways.

    Directory of Open Access Journals (Sweden)

    Saad Nazir

    Full Text Available TGF-β1 is an important multifunctional cytokine with numerous protective effects on intestinal mucosa. The influence of TGF-β1 on serotonin transporter (SERT activity, the critical mechanism regulating the extracellular availability of serotonin (5-HT, is not known. Current studies were designed to examine acute effects of TGF-β1 on SERT. Model human intestinal Caco-2 cells grown as monolayer's or as cysts in 3D culture and ex vivo mouse model were utilized. Treatment of Caco-2 cells with TGF-β1 (10 ng/ml, 60 min stimulated SERT activity (~2 fold, P<0.005. This stimulation of SERT function was dependent upon activation of TGF-β1 receptor (TGFRI as SB-431542, a specific TGF-βRI inhibitor blocked the SERT stimulation. SERT activation in response to TGF-β1 was attenuated by inhibition of PI3K and occurred via enhanced recruitment of SERT-GFP to apical surface in a PI3K dependent manner. The exocytosis inhibitor brefeldin A (2.5 μM attenuated the TGF-β1-mediated increase in SERT function. TGF-β1 increased the association of SERT with the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE syntaxin 3 (STX3 and promoted exocytosis of SERT. Caco-2 cells grown as cysts in 3D culture recapitulated the effects of TGF-β1 showing increased luminal staining of SERT. Ussing chamber studies revealed increase in 3H-5-HT uptake in mouse ileum treated ex vivo with TGF-β1 (10 ng/ml, 1h. These data demonstrate a novel mechanism rapidly regulating intestinal SERT via PI3K and STX3. Since decreased SERT is implicated in various gastro-intestinal disorders e.g IBD, IBS and diarrhea, understanding mechanisms stimulating SERT function by TGF-β1 offers a novel therapeutic strategy to treat GI disorders.

  11. Serotonin Transporter-Independent Actions of the Antidepressant Vortioxetine As Revealed Using the SERT Met172 Mouse.

    Science.gov (United States)

    Nackenoff, Alex G; Simmler, Linda D; Baganz, Nicole L; Pehrson, Alan L; Sánchez, Connie; Blakely, Randy D

    2017-05-17

    Selective serotonin (5-HT, SERT) reuptake inhibitors (SSRIs) are the most commonly prescribed treatments for depression. However, they have delayed efficacy and can induce side-effects that can encourage discontinuation. Recently, agents have been developed, including vortioxetine (Trintellix), that augment SERT blockade with interactions at other targets. At therapeutic doses, vortioxetine interacts with SERT as well as 5-HT 1A , 5-HT 1B , 5-HT 3 , and 5-HT 7 receptors. We assessed the SERT-dependency of vortioxetine action using the SERT Met172 mouse model, which disrupts high-affinity interactions of many antidepressants with the transporter. We demonstrate that the SERT Met172 substitution induces an ∼19-fold loss in vortioxetine potency for SERT inhibition in midbrain synaptosomes. Moreover, in these mice, we observed reduced SERT occupancy, a diminished ability to prolong 5-HT clearance, and a reduced capacity to elevate extracellular 5-HT. Despite reduced interactions with SERT, vortioxetine maintained its ability to enhance mobility in tail suspension and forced swim tests, reduce consumption latency in the novelty induced hypophagia test, and promoted proliferation and survival of subgranular zone hippocampal stem cells. Our findings suggest that the antidepressant actions of vortioxetine may be SERT-independent, and encourage consideration of agents that mimic one or more actions of the drug in the development of improved depression treatments.

  12. Brain SERT Expression of Male Rats Is Reduced by Aging and Increased by Testosterone Restitution

    Science.gov (United States)

    Herrera-Pérez, José Jaime; Fernández-Guasti, Alonso; Martínez-Mota, Lucía

    2013-01-01

    In preclinical and clinical studies aging has been associated with a deteriorated response to antidepressant treatment. We hypothesize that such impairment is explained by an age-related decrease in brain serotonin transporter (SERT) expression associated with low testosterone (T) levels. The objectives of this study were to establish (1) if brain SERT expression is reduced by aging and (2) if the SERT expression in middle-aged rats is increased by T-restitution. Intact young rats (3–5 months) and gonad-intact middle-aged rats with or without T-restitution were used. The identification of the brain SERT expression was done by immunofluorescence in prefrontal cortex, lateral septum, hippocampus, and raphe nuclei. An age-dependent reduction of SERT expression was observed in all brain regions examined, while T-restitution recovered the SERT expression only in the dorsal raphe of middle-aged rats. This last action seems relevant since dorsal raphe plays an important role in the antidepressant action of selective serotonin reuptake inhibitors. All data suggest that this mechanism accounts for the T-replacement usefulness to improve the response to antidepressants in the aged population. PMID:26317087

  13. Brain SERT Expression of Male Rats Is Reduced by Aging and Increased by Testosterone Restitution

    Directory of Open Access Journals (Sweden)

    José Jaime Herrera-Pérez

    2013-01-01

    Full Text Available In preclinical and clinical studies aging has been associated with a deteriorated response to antidepressant treatment. We hypothesize that such impairment is explained by an age-related decrease in brain serotonin transporter (SERT expression associated with low testosterone (T levels. The objectives of this study were to establish (1 if brain SERT expression is reduced by aging and (2 if the SERT expression in middle-aged rats is increased by T-restitution. Intact young rats (3–5 months and gonad-intact middle-aged rats with or without T-restitution were used. The identification of the brain SERT expression was done by immunofluorescence in prefrontal cortex, lateral septum, hippocampus, and raphe nuclei. An age-dependent reduction of SERT expression was observed in all brain regions examined, while T-restitution recovered the SERT expression only in the dorsal raphe of middle-aged rats. This last action seems relevant since dorsal raphe plays an important role in the antidepressant action of selective serotonin reuptake inhibitors. All data suggest that this mechanism accounts for the T-replacement usefulness to improve the response to antidepressants in the aged population.

  14. Développer le désert : anciennes et nouvelles utopies

    OpenAIRE

    Henry, J.R.; Marçot, J.L.; Moisseron, Jean-Yves

    2011-01-01

    sert et développement : deux termes en apparence antinomiques, mais qui ont souvent été associés étroitement dans les imaginaires et les pratiques. Aussi bien dans les traditions religieuses méditerranéennes que sous les habits successifs de « progrès », de « développement » et de « mondialisation », l’idée de civilisation a maintes fois trouvé dans la référence au désert son contraire, son révélateur et son complément : quand la civilisation échoue à conquérir le désert, c’est à celui-ci q...

  15. Characterization of a Novel Drosophila SERT Mutant: Insights on the Contribution of the Serotonin Neural System to Behaviors.

    Science.gov (United States)

    Hidalgo, Sergio; Molina-Mateo, Daniela; Escobedo, Pía; Zárate, Rafaella V; Fritz, Elsa; Fierro, Angélica; Perez, Edwin G; Iturriaga-Vasquez, Patricio; Reyes-Parada, Miguel; Varas, Rodrigo; Fuenzalida-Uribe, Nicolás; Campusano, Jorge M

    2017-10-18

    A better comprehension on how different molecular components of the serotonergic system contribute to the adequate regulation of behaviors in animals is essential in the interpretation on how they are involved in neuropsychiatric and pathological disorders. It is possible to study these components in "simpler" animal models including the fly Drosophila melanogaster, given that most of the components of the serotonergic system are conserved between vertebrates and invertebrates. Here we decided to advance our understanding on how the serotonin plasma membrane transporter (SERT) contributes to serotonergic neurotransmission and behaviors in Drosophila. In doing this, we characterized for the first time a mutant for Drosophila SERT (dSERT) and additionally used a highly selective serotonin-releasing drug, 4-methylthioamphetamine (4-MTA), whose mechanism of action involves the SERT protein. Our results show that dSERT mutant animals exhibit an increased survival rate in stress conditions, increased basal motor behavior, and decreased levels in an anxiety-related parameter, centrophobism. We also show that 4-MTA increases the negative chemotaxis toward a strong aversive odorant, benzaldehyde. Our neurochemical data suggest that this effect is mediated by dSERT and depends on the 4-MTA-increased release of serotonin in the fly brain. Our in silico data support the idea that these effects are explained by specific interactions between 4-MTA and dSERT. In sum, our neurochemical, in silico, and behavioral analyses demonstrate the critical importance of the serotonergic system and particularly dSERT functioning in modulating several behaviors in Drosophila.

  16. [Study of genetic variants in the BDNF, COMT, DAT1 and SERT genes in Colombian children with attention deficit disorder].

    Science.gov (United States)

    Ortega-Rojas, Jenny; Arboleda-Bustos, Carlos E; Morales, Luis; Benítez, Bruno A; Beltrán, Diana; Izquierdo, Álvaro; Arboleda, Humberto; Vásquez, Rafael

    Attention deficit and hyperactive disorder (ADHD) is highly prevalent among children in Bogota City. Both genetic and environmental factors play a very important role in the etiology of ADHD. However, to date few studies have addressed the association of genetic variants and ADHD in the Colombian population. To test the genetic association between polymorphisms in the DAT1, HTTLPR, COMT and BDNF genes and ADHD in a sample from Bogota City. We genotyped the most common polymorphisms in DAT1, SERT, COMT and BDNF genes associated with ADHD using conventional PCR followed by restriction fragment length polymorphism (RFLP) in 97 trios recruited in a medical center in Bogota. The transmission disequilibrium test (TDT) was used to determine the association between such genetic variants and ADHD. The TDT analysis showed that no individual allele of any variant studied has a preferential transmission. Our results suggest that the etiology of the ADHD may be complex and involves several genetic factors. Further studies in other candidate polymorphisms in a larger sample size will improve our knowledge of the ADHD in Colombian population. Copyright © 2016 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

  17. Sertão e Narração: Guimarães Rosa, Glauber Rocha e seus desenredos Sertão (backland and Narration: Guimarães Rosa, Glauber Rocha and their plots

    Directory of Open Access Journals (Sweden)

    Pedro Paulo Gomes Pereira

    2008-04-01

    Full Text Available Este texto busca verificar as formas de construção da nação em Grande Sertão: veredas, de Guimarães Rosa, e Deus e o Diabo na terra do sol, de Glauber Rocha. Utilizando autores como Homi Bhabha, Stuart Hall, Walter Mignolo, Veena Das, o texto indaga de que forma esses autores construíram o sertão.This text tries to verify how the nation was constructed in Grande sertão: veredas [The Devil to Pay in the Backlands] by Guimarães Rosa, and Deus e o Diabo na terra do sol [Black God, White Devil] by Glauber Rocha. By analyzing authors as Homi Bhabha, Stuart Hall and Walter Mignolo, the text inquires how these authors had constructed the sertão (backland.

  18. Serotonin transporter (SERT and translocator protein (TSPO expression in the obese ob/ob mouse

    Directory of Open Access Journals (Sweden)

    Santini Ferruccio

    2011-02-01

    Full Text Available Abstract Background An ever growing body of evidences is emerging concerning metabolism hormones, neurotransmitters or stress-related biomarkers as effective modulators of eating behavior and body weight in mammals. The present study sought at examining the density and affinity of two proteins related to neurotransmission and cell metabolism, the serotonin transporter SERT and the cholesterol import-benzodiazepine site TSPO (translocator protein, in a rodent leptin-lacking mutant, the obese ob/ob mouse. Binding studies were thus carried out in brain or peripheral tissues, blood platelets (SERT and kidneys (TSPO, of ob/ob and WT mice supplied with a standard diet, using the selective radiochemical ligands [3H]-paroxetine and [3H]-PK11195. Results We observed comparable SERT number or affinity in brain and platelets of ob/ob and WT mice, whilst a significantly higher [3H]-PK11195 density was reported in the brain of ob/ob animals. TSPO binding parameters were similar in the kidneys of all tested mice. By [3H]-PK11195 autoradiography of coronal hypothalamic-hippocampal sections, an increased TSPO signal was detected in the dentate gyrus (hippocampus and choroids plexus of ob/ob mice, without appreciable changes in the cortex or hypothalamic-thalamic regions. Conclusions These findings show that TSPO expression is up-regulated in cerebral regions of ob/ob leptin-deficient mice, suggesting a role of the translocator protein in leptin-dependent CNS trophism and metabolism. Unchanged SERT in mutant mice is discussed herein in the context of previous literature as the forerunner to a deeper biochemical investigation.

  19. Recurrent myelinoclastic diffuse sclerosis: a case report of a child with Schilder's variant of multiple sclerosis

    Energy Technology Data Exchange (ETDEWEB)

    Fitzgerald, M.J.; Coleman, L.T. [Radiology Dept., Royal Children' s Hospital, Parkville, VIC (Australia)

    2000-12-01

    Myelinoclastic diffuse sclerosis (MDS, Schilder's disease) is a rare CNS demyelinating disorder affecting mainly children and usually presenting as an intracranial mass lesion. We report the first case of recurrent intracranial MDS where the third episode of demyelination involved the cervical spinal cord. This may represent a subset of the disease, which should be considered as Schilder's variant (childhood form) of multiple sclerosis. (orig.)

  20. À la découverte des eaux du désert de Jordanie | IDRC ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    17 janv. 2011 ... Pour la plupart des gens, un désert est par définition un endroit où, à toutes fins pratiques, l'eau n'existe pas. Mais une équipe de chercheurs qui étudiait la badia en Jordanie — vaste région désertique du nord-ouest du pays — a découvert un secret qui fait lentement son chemin sous cette immense ...

  1. Faca e armas brancas: um campo lexical em Grande sertão: veredas

    Directory of Open Access Journals (Sweden)

    Maria Célia de Moraes Leonel

    2001-02-01

    Full Text Available

    Estudo do campo lexical da palavra faca e de outros lexemas que se referem às armas brancas em Grande sertão: veredas de Guimarães Rosa, tendo-se em vista os significados dos vocábulos no universo de sentidos do romance. A orientação teórica centra-se, sobretudo, nas propostas de H. Geckeler e ainda nas de J. Lyons.

  2. Os sertões: atualidade e arcaísmo na representação cultural de um conflito brasileiro Os sertões: present time and archaism in the cultural representation of a Brazilian conflict

    Directory of Open Access Journals (Sweden)

    Paulo Venancio Filho

    1998-07-01

    Full Text Available Este texto busca contrapor os aspectos antagônicos da revolta de Canudos tal como percebido por Euclides da Cunha em Os sertões. A revolta revelava tragicamente a permanência de um arcaísmo irresolvido. O horror da guerra, o confronto entre a ‘civilização’ e a ‘barbárie’ ainda se manifestam cem anos depois do conflito. O mesmo confronto que a literatura já pressentia e descrevia. Aquele que, no plano não menos verdadeiro da ficção, também se revela no romance O coração das trevas, de Joseph Conrad, publicado em 1902, o mesmo ano da publicação de Os sertões.The article examines antagonistic aspects of the battle of Canudos as portrayed by Euclides da Cunha in Os sertões. In tragic fashion, the rebellion made it apparent that an archaism had not been resolved. The horror of war, the conflict between civilization and barbarism, is still with us one hundred years later - the same conflict that literature foresaw and described. In the realm of fiction (yet no less truthful, this conflict was also portrayed in Joseph Conrad’s Heart of Darkness, published in 1902, the same year as Os sertões.

  3. Regulation of extrasynaptic 5-HT by SERT function in 5-HT-absorbing neurons underscores adaptation behavior in C. elegans

    Science.gov (United States)

    Jafarau, Gholamali; Xie, Yusu; Kullyev, Andrey; Liang, Bin; Sze, Ji Ying

    2011-01-01

    Serotonin (5-HT)-absorbing neurons use serotonin reuptake transporter (SERT) to uptake serotonin (5-HT) from extracellular space but do not synthesize it. While 5-HT-absorbing neurons have been identified in diverse organisms from C. elegans to humans, their function has not been elucidated. Here, we show that SERT in 5-HT-absorbing neurons controls behavioral response to food deprivation in C. elegans. The AIM and RIH interneurons uptake 5-HT released from chemosensory neurons and secretory neurons. Genetic analyses suggest that 5-HT secreted by both synaptic vesicles and dense core vesicles diffuse readily to the extrasynaptic space adjacent to the AIM and RIH neurons. Loss of mod-5/SERT function blocks the 5-HT absorption. mod-5/SERT mutants have been shown to exhibit exaggerated locomotor response to food deprivation. We found that transgenic expression of MOD-5/SERT in the 5-HT-absorbing neurons fully corrected the exaggerated behavior. Experiments of cell-specific inhibition of synaptic transmission suggest that the synaptic release of 5-HT from the 5-HT-absorbing neurons is not required for this behavioral modulation. Our data point to the role of 5-HT-absorbing neurons as temporal-spatial regulators of extrasynaptic 5-HT. Regulation of extrasynaptic 5-HT levels by 5-HT-absorbing neurons may represent a fundamental mechanism of 5-HT homeostasis, integrating the activity of 5-HT-producing neurons with distant targets in the neural circuits, and could be relevant to some actions of SSRIs in human. PMID:21677178

  4. François Dubet, À quoi sert vraiment un sociologue ?

    OpenAIRE

    Cochoy, Franck

    2015-01-01

    Une nouvelle collection intitulée « Dites-nous » se propose d’examiner l’utilité des sciences humaines. Cet ouvrage se présente donc de la façon suivante : « Dites-nous » M. Dubet, A quoi sert vraiment un sociologue ? La réponse de l’auteur est passionnante : utilisant à la fois son parcours personnel, ses travaux académiques ou politiques, en même temps que des références à la sociologie classique, François Dubet déploie une argumentation à la fois attrayante et instructive. Si cet ouvrage p...

  5. Agrofloresta e multifuncionalidade no Sertão de Pernambuco – Brasil

    OpenAIRE

    Teixeira, Cecilia T. M.; Silva, Thacya C. da

    2015-01-01

    O presente trabalho tem o objetivo de relatar a experiência da família de Adão de Jesus e Fabiana Duarte, protagonistas da construção de um sistema agroflorestal no sertão Pernambucano e analisar as diversas funções associadas à produção agrícola, em particular do manejo com a caatinga e a convivência com semiárido. A consciência agroecológica foi adquirida na Escola Rural de Ouricuri, através da metodologia de educação contextualizada, como também na participação em eventos de formação, que ...

  6. Índios e negros nos sertões das minas: Contatos e identidades

    Directory of Open Access Journals (Sweden)

    Marcel Mano

    2015-08-01

    Full Text Available O artigo busca resgatar parte da ocupação indígena e quilombola dos sertões das minas no segundo e terceiro quartos do século XVIII, com vistas a um mapeamento dos encontros e intersecções culturais entre esses dois coletivos. Com base na perspectiva antropológica da alteridade é realizada a análise de uma documentação histórica disponível para os atuais oeste de Minas Gerais, Triângulo Mineiro e sul de Goiás, que permite propor que as culturas e identidades coletivas de “gentios” e “calhambolas” estivessem se reelaborando num contexto de negociações e conflitos entre diferentes sujeitos históricos.

  7. Tristeza parasitária bovina no Sertão da Paraíba

    Directory of Open Access Journals (Sweden)

    V.M.M. Costa

    2011-03-01

    Full Text Available Descrevem-se 24 surtos de tristeza parasitária bovina no sertão paraibano, sendo 18 de anaplasmose por Anaplasma margimale, dois de babesiose por Babesia bigemina, dois por Babesia não identificada e dois por infecção mista de A. marginale e Babesia sp. Os surtos ocorreram entre agosto de 2007 a outubro de 2009, porém, com uma concentração dos surtos no final do período chuvoso e início do período seco de cada ano, sendo 22 em animais adultos e dois em bezerros de aproximadamente 11 meses. Dois surtos ocorreram em bovinos da raça Nelore, um em animais da raça Gir e os 21 restantes ocorreram em animais das raças Holandês, Pardo Suiço e mestiços das mesmas com zebuínos. Conclui-se que no sertão da Paraíba há áreas de instabilidade enzoótica, ocorrendo surtos de tristeza no final da época de chuvas, principalmente nas áreas de planaltos e serras da região da Borborema e em áreas úmidas como a Bacia do Rio do Peixe, Rio Piranhas e Rio Espinharas em que há a formação de microclimas favoráveis à sobrevivência do carrapato.

  8. Serotonin (5-HT) transport in human platelets is modulated by Src-catalysed Tyr-phosphorylation of the plasma membrane transporter SERT.

    Science.gov (United States)

    Zarpellon, Alessandro; Donella-Deana, Arianna; Folda, Alessandra; Turetta, Loris; Pavanetto, Martina; Deana, Renzo

    2008-01-01

    platelets possess tightly regulated systems for serotonin (5-HT) transport. This study analysed whether the 5-HT transport mediated by the plasma-membrane transporter SERT is regulated by its Tyr-phosphorylation. 5-HT transport was determined by filtration techniques, while immunoblotting procedures were adopted for detecting the Tyr-phosphorylation of SERT in human platelet fractions. 5-HT accumulation in platelets pre-treated with reserpine, which prevents the neurotransmitter transport into the dense granules, decreased upon cellular exposure to PP2 and SU6656, two structurally unrelated inhibitors of Src-kinases. By contrast, the protein Tyr-phosphatase inhibitor pervanadate increased the 5-HT accumulation. Anti-SERT immunostaining of the platelet fractions showed a major band displaying an apparent molecular mass of 50 kappaDa, indicating that, during the analytical procedure, SERT underwent proteolysis, which was counteracted by addition of 4 M urea in the cellular disrupting medium. The Tyr-phosphorylation degree of SERT immunoprecipitated from membrane extracts decreased by platelet treatment with SU6656 or PP2, and enhanced upon pervanadate treatment. The anti-SERT immunoprecipitates displayed anti-Src immunostaining and in vitro kinase activity towards a Src-specific peptide-substrate. Platelet treatment with PP2 or SU6656 also caused a decrease in the imipramine binding to platelets. It was concluded that the Src-mediated SERT Tyr-phosphorylation regulates the 5-HT transport by affecting the neurotransmitter binding sites.

  9. Tramadol and another atypical opioid meperidine have exaggerated serotonin syndrome behavioural effects, but decreased analgesic effects, in genetically deficient serotonin transporter (SERT) mice.

    Science.gov (United States)

    Fox, Meredith A; Jensen, Catherine L; Murphy, Dennis L

    2009-09-01

    The serotonin syndrome is a potential side-effect of serotonin-enhancing drugs, including antidepressants such as selective serotonin reuptake inhibitors (SSRIs) and monoamine oxidase inhibitors (MAOIs). We recently reported a genetic mouse model for the serotonin syndrome, as serotonin transporter (SERT)-deficient mice have exaggerated serotonin syndrome behavioural responses to the MAOI tranylcypromine and the serotonin precursor 5-hydroxy-l-tryptophan (5-HTP). As numerous case reports implicate the atypical opioids tramadol and meperidine in the development of the human serotonin syndrome, we examined tramadol and meperidine as possible causative drugs in the rodent model of the serotonin syndrome in SERT wild-type (+/+), heterozygous (+/-) and knockout (-/-) mice. Comparisons were made with SERT mice treated with either vehicle or morphine, an opioid not implicated in the serotonin syndrome in humans. Here we show that tramadol and meperidine, but not morphine, induce serotonin syndrome-like behaviours in mice, and we show that this response is exaggerated in mice lacking one or two copies of SERT. The exaggerated response to tramadol in SERT-/- mice was blocked by pretreatment with the 5-HT1A antagonist WAY 100635. Further, we show that morphine-, meperidine- and tramadol-induced analgesia is markedly decreased in SERT-/- mice. These studies suggest that caution seems warranted in prescribing or not warning patients receiving SSRIs or MAOIs that dangerous side-effects may occur during concurrent use of tramadol and similar agents. These findings suggest that it is conceivable that there might be increased vulnerability in individuals with SERT polymorphisms that may reduce SERT by more than 50%, the level in SERT+/- mice.

  10. O sertão dilacerado: outras histórias de Deus e o Diabo na terra do sol The Brazilian hinterland in Glauber Rocha's cinema

    Directory of Open Access Journals (Sweden)

    Pedro Paulo Gomes Pereira

    2008-01-01

    Full Text Available A busca deste texto será a de compreender como uma das mais importantes narrativas do cinema nacional - Deus e o Diabo na terra do sol, de Glauber Rocha (1963 - construiu o sertão, quais as imagens e as figuras utilizadas, ecomo esse sertão delineia e projeta o Brasil.This article tries to understand how one of the most important narratives of the national cinema - Glauber Rocha's Black God, white devil (1963 - has constructed the sertão (hinterland, which images and figures he has employed, and how that hinterland delineates and projects the country.

  11. Messianismos em conflito: interpretação teológico-política de os sertões Messianisms in conflict: teological-political interpretation of os sertões

    Directory of Open Access Journals (Sweden)

    Pablo Sanges Ghetti

    2010-01-01

    Full Text Available O ensaio investiga os fundamentos teológico-políticos da obra seminal de Euclides da Cunha, Os sertões, dando especial ênfase à relação entre messianismo e potencial construção da nação. Nele, não se aplica simplesmente o modelo "teológico-político" à leitura da obra, para comprovar, uma vez mais, a tese da equivalência estrutural entre conceitos teológicos e políticos. Mais do que isso, analisa os conflitos da época a partir das exigências teológico-políticas e, assim, compreende as oportunidades e as consequências de suas ruínas (no sentido duplo de destruição causada e de ruína da própria estrutura teológico-política. O ensaio contribui para uma nova percepção crítica do papel de Os sertões, no que diz respeito à complexa tradição messiânica brasileira.The essay investigates the theological-political grounds of Euclides da Cunha's seminal work, Os sertões, with special emphasis put on the relation between messianism and potential construction of the nation. This paper does not simply apply the "theological-political" model to the reading of the work, in order to prove once more the structural equivalence between theological and political concepts. More than that, it analyses the conflicts of the period on the basis of theological-political exigencies. It thus understands opportunities and consequences of its ruins (in the double sense of caused destruction and of the ruin of the theological-political structure itself. With regard to the complex Brazilian messianic tradition, this essay contributes to a new critical perception of the Os sertões role.

  12. A Synopsis of Ion Propulsion Development Projects in the United States: SERT 1 to Deep Space I

    Science.gov (United States)

    Sovey, James S.; Rawlin, Vincent K.; Patterson, Michael J.

    1999-01-01

    The historical background and characteristics of the experimental flights of ion propulsion systems and the major ground-based technology demonstrations were reviewed. The results of the first successful ion engine flight in 1964, SERT I which demonstrated ion beam neutralization, are discussed along with the extended operation of SERT II starting in 1970. These results together with the technology employed on the early cesium engine flights. the Applications Technology Satellite (ATS) series, and the ground-test demonstrations, have provided the evolutionary path for the development of xenon ion thruster component technologies, control systems, and power circuit implementations. In the 1997-1999 period, the communication satellite flights using ion engine systems and the Deep Space I flight confirmed that these auxiliary and primary propulsion systems have advanced to a high-level of flight-readiness.

  13. Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV

    Energy Technology Data Exchange (ETDEWEB)

    Endres, Christopher J; Pomper, Martin G [Russell H Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21231 (United States); Hammoud, Dima A, E-mail: endres@jhmi.edu [Radiology and Imaging Sciences, National Institutes of Health/Clinical Center, Bethesda, MD (United States)

    2011-04-21

    When applicable, it is generally preferred to evaluate positron emission tomography (PET) studies using a reference tissue-based approach as that avoids the need for invasive arterial blood sampling. However, most reference tissue methods have been shown to have a bias that is dependent on the level of tracer binding, and the variability of parameter estimates may be substantially affected by noise level. In a study of serotonin transporter (SERT) binding in HIV dementia, it was determined that applying parameter coupling to the simplified reference tissue model (SRTM) reduced the variability of parameter estimates and yielded the strongest between-group significant differences in SERT binding. The use of parameter coupling makes the application of SRTM more consistent with conventional blood input models and reduces the total number of fitted parameters, thus should yield more robust parameter estimates. Here, we provide a detailed evaluation of the application of parameter constraint and parameter coupling to [{sup 11}C]DASB PET studies. Five quantitative methods, including three methods that constrain the reference tissue clearance (k{sup r}{sub 2}) to a common value across regions were applied to the clinical and simulated data to compare measurement of the tracer binding potential (BP{sub ND}). Compared with standard SRTM, either coupling of k{sup r}{sub 2} across regions or constraining k{sup r}{sub 2} to a first-pass estimate improved the sensitivity of SRTM to measuring a significant difference in BP{sub ND} between patients and controls. Parameter coupling was particularly effective in reducing the variance of parameter estimates, which was less than 50% of the variance obtained with standard SRTM. A linear approach was also improved when constraining k{sup r}{sub 2} to a first-pass estimate, although the SRTM-based methods yielded stronger significant differences when applied to the clinical study. This work shows that parameter coupling reduces the

  14. Grande sertão: veredas: alguns neologismos semânticos

    Directory of Open Access Journals (Sweden)

    Maria Célia de Moraes Leonel

    2001-02-01

    Full Text Available

    A criação neológica estilística enfeixa a criatividade lexical e a neologia semântica. A neologia de sentido consiste no emprego de um significante já existente na língua c om um conteúdo que ele não possuía, ou porque o conteúdo é novo ou porque, até aquele momento, era expresso por outro significante. No texto literário, uma criação resultante desse tipo de procedimento tende a não se repetir. É o que chamamos de neologia semântica estilística. Nessa operação, a estrutura da frase tem função básica, pois, no mínimo, é necessário um sintagma para que surja novo sentido. A partir de algumas relações sintagmáticas, estudamos certos modos de manifestação da neologia semântica em Grande sertão: veredas.

  15. Vulnerability and Productivity Impacts of Farm-Level Interventions in the Brazilian Sertão

    Science.gov (United States)

    Burney, J. A.

    2014-12-01

    The Brazilian Sertão exemplifies the complex dynamics between climate, land use, agricultural production, and food security presently playing out across the world's semi-arid tropics. Regional climate change in the past half-century is some of the most dramatic in the world -- +2 degrees average warming in many districts and -300mm rainfall. Crop yields have improved weakly or remained stagnant, in stark contrast with the rest of Brazil. As a result many smallholder farmers have increasingly turned to milk production, but they remain dependent on rainfall for forage growth. During droughts they thus face a choice between overgrazing and letting their cattle die. As a result, deforestation of the native Caatinga biome has been rampant, with estimates of 85% loss. We present the results of controlled tests, conducted with over one hundred farmers, of several on-farm interventions meant to boost on-farm productivity, reduce vulnerability to rainfall shocks, and lessen the incentives for deforestation. These interventions -- water cisterns, smallholder irrigation systems, balancing of animal feed ratios, and cultivation and use of palma forrageira as cattle feed -- are described and presented with results of their impact on productivity and vulnerability/resilience metrics. Estimates of larger-scale social benefits and future land-use change impacts are also discussed.

  16. Grande sertão: veredas - as artimanhas da enunciação

    Directory of Open Access Journals (Sweden)

    Jeane Mari Sant'Ana Spera

    2005-10-01

    Full Text Available Responsável pela arquitetura narrativa de Grande sertão: veredas, o narrador Riobaldo conduz o  jogo dialógico de modo a criar  um vai­vém discursivo que  possibilita a detecção pontual de segmentos pertencentes à ordem do discurso e à ordem da história (respectivamente, mundo comentado e mundo narrado, segundo Harald Weinrich. Permeando um e outro mundo, estão as obsessões fundamentais do narrador, das quais destacamos aquela relativa à existência ou não do diabo. As ambiguidades derivadas desse  movimento oscilante entre o ser e o não-ser provocam ainda  o deslizamento entre o real e o irreal, o dito e o não-dito, o aparente e o oculto, o dado  e o suposto. A coerência, no entanto, é reconstituída no alinhavado constante de vários recursos argumentativos que busca m a adesão do  interlocutor, cuja voz só é entre ou vida pela voz do narrador. Nesses casos,  verificamos a presença do recurso ao argumento de autoridade, seja pela competência,  seja  pela  experiência,  seja, ainda,  pelo  testemunho. É, pois, nesses momentos de interlocução semiexplícita, na instância  da enunciação, que se apresentam, com  maior  nitidez, elementos linguísticos denunciadores das estratégias argumentativas que  provocam e incitam o interlocutor/leitor a acompanhar esse "narrar dificultoso” e a finalmente concordar que “O diabo não há!... Existe é homem  humano”.

  17. Entre Clio e Calíope: a construção da narrativa histórica em Os sertões Between Clio and Calliope: construction of the historical narrative in Os sertões

    Directory of Open Access Journals (Sweden)

    Luiz Fernando Valente

    1998-07-01

    Full Text Available Este artigo focaliza a complexa aliança entre a história e a ficção em Os sertões a partir de novas teorias sobre a textualidade da história e de novas metodologias de abordagem do texto literário, como o ‘novo historicismo’. Após uma sinopse dessas teorias e metodologias, examina os processos de construção da narrativa de Os sertões, demonstrando como o texto é marcado pela interpenetração do sistema que informa o cientista com o que rege o artista. À medida que o arcabouço intelectual e científico importado da Europa se mostra insuficiente para registrar a realidade brasileira, o texto euclidiano começa a deslizar entre a história e a ficção. A conclusão: apenas interstícios entre história e ficção Euclides consegue localizar aquela verdade que, desde a ‘Nota preliminar’, afirmava ser seu objetivo principal.The complex alliance between history and fiction found in Os sertões is examined from the perspective of new theories on the textuality of history and new methodologies in the study of literary texts, such as the so-called new historicism. After presenting a synthesis of these tools, the essay examines the construction of the narrative in Os sertões and shows how Cunha’s text is characterized by an inter-penetration of the system that informed the scientist with the system that governed the artist. As the intellectual and scientific framework imported from Europe proves inadequate in recording the Brazilian reality, Cunhas’ text begins slipping back and forth between history and fiction. In conclusion, it is argued that only in the interstices between history and fiction does Cunha manage to situate that truth which, starting right in his ‘Preliminary note’, he claimed as his prime objective.

  18. A personagem dostoievskiana e a relação autor/herói em Grande sertão: veredas / The Dostoevskian character and the relationship author/hero in Grande sertão: veredas

    Directory of Open Access Journals (Sweden)

    Sandra Mara Moraes Lima

    2011-11-01

    Full Text Available RESUMO: O trabalho tece considerações sobre o enfoque da personagem pelo autor no romance de Dostoiévski a partir da obra Problemas da poética de Dostoiévski de Bakhtin, estabelecendo uma analogia entre a relação autor/herói na obra de Dostoiévski e a relação autor/herói no romance Grande sertão: veredas, de Guimarães Rosa. Segundo Bakhtin, Dostoiévski inaugura o romance polifônico, dialógico, apresentando um herói cuja voz está equiparada à voz do autor. É nesse mesmo contexto que se analisa, no romance rosiano, o narrador Riobaldo. ABSTRACT: This work makes considerations about the focus of the character by the author on Dostoevsky romance from the work Problems of Dostoevsky’s Poetics of Bakhtin, establishing an analogy between author/hero in Dostoevsky work and the relationship author/hero in the romance Grande sertão: veredas from Guimarães Rosa. According toBakhtin Dostoevsky inaugurates the polyphonic, dialogical, presenting a hero whose voice is equalized to the author voice. In this context we presented the narrator Riobaldo.

  19. Differential expression of neuronal dopamine and serotonin transporters DAT and SERT in megakaryocytes and platelets generated from human MEG-01 megakaryoblasts.

    Science.gov (United States)

    Hohmann, Sarah; Schweinfurth, Nina; Lau, Thorsten; Deuschle, Michael; Lederbogen, Florian; Banaschewski, Tobias; Schloss, Patrick

    2011-11-01

    In the central nervous system, serotonergic and dopaminergic signaling is terminated by the activity of specialized transporter proteins for serotonin (SERT) and dopamine (DAT). These transporter proteins are found both on the cell surface and in intracellular transport vesicles. Trafficking between these subcellular domains regulates the efficiency of removal of extracellular neurotransmitters and hence the efficacy of neuronal signaling. Therefore, it is of high interest to gain more insight into the regulatory mechanisms of the human DAT and SERT cell surface expression in their natural surroundings, i.e., in human cells. Because it is not possible to cultivate human neuronal cells expressing these transporter proteins, there is a need to find other human cells expressing these neuronal proteins. Here, we have investigated the expression of human SERT and DAT on developing megakaryocytes and platelet-like particles derived from the megakaryocyte progenitor cell line MEG-01 upon differentiation by valproic acid (VPA) and all-trans retinoic acid (ATRA). Our results show that MEG-01 cells express SERT and DAT and that VPA and ATRA induce a significant increase of transporter expression on developing megakaryocytes and platelets. As compared to ATRA, VPA more efficiently induced SERT expression but not DAT expression. Comparable to naïve platelets and neurons, SERT was localized to both the cell surface and intracellular compartments. Hence, VPA and ATRA-treated MEG-01 cells provide a model well-suited to studying neuronal monoamine transporter expression, not only during transcription and translation but also with respect to protein trafficking to and from the cell surface.

  20. Uso e conhecimento tradicional de plantas medicinais no Sertão do Ribeirão, Florianópolis, SC, Brasil

    OpenAIRE

    Giraldi,Mariana; Hanazaki,Natalia

    2010-01-01

    O objetivo desta pesquisa foi realizar um estudo etnobotânico sobre o uso e o conhecimento tradicional de plantas medicinais no Sertão do Ribeirão, uma comunidade de origem açoriana, inserida no domínio da Mata Atlântica e localizada dentro dos limites do Parque Municipal da Lagoa do Peri. Foram realizadas 13 entrevistas com moradores do Sertão do Ribeirão, sendo identificadas 114 espécies de plantas medicinais, distribuídas em 48 famílias botânicas. A diversidade de plantas medicinais conhec...

  1. Necdin shapes serotonergic development and SERT activity modulating breathing in a mouse model for Prader-Willi syndrome.

    Science.gov (United States)

    Matarazzo, Valéry; Caccialupi, Laura; Schaller, Fabienne; Shvarev, Yuri; Kourdougli, Nazim; Bertoni, Alessandra; Menuet, Clément; Voituron, Nicolas; Deneris, Evan; Gaspar, Patricia; Bezin, Laurent; Durbec, Pascale; Hilaire, Gérard; Muscatelli, Françoise

    2017-10-31

    Prader-Willi syndrome (PWS) is a genetic neurodevelopmental disorder that presents with hypotonia and respiratory distress in neonates. The Necdin-deficient mouse is the only model that reproduces the respiratory phenotype of PWS (central apnea and blunted response to respiratory challenges). Here, we report that Necdin deletion disturbs the migration of serotonin (5-HT) neuronal precursors, leading to altered global serotonergic neuroarchitecture and increased spontaneous firing of 5-HT neurons. We show an increased expression and activity of 5-HT Transporter (SERT/Slc6a4) in 5-HT neurons leading to an increase of 5-HT uptake. In Necdin-KO pups, the genetic deletion of Slc6a4 or treatment with Fluoxetine, a 5-HT reuptake inhibitor, restored normal breathing. Unexpectedly, Fluoxetine administration was associated with respiratory side effects in wild-type animals. Overall, our results demonstrate that an increase of SERT activity is sufficient to cause the apneas in Necdin-KO pups, and that fluoxetine may offer therapeutic benefits to PWS patients with respiratory complications.

  2. Population differentiation and behavioural association of the two 'personality' genes DRD4 and SERT in dunnocks (Prunella modularis).

    Science.gov (United States)

    Holtmann, B; Grosser, S; Lagisz, M; Johnson, S L; Santos, E S A; Lara, C E; Robertson, B C; Nakagawa, S

    2016-02-01

    Quantifying the variation in behaviour-related genes within and between populations provides insight into how evolutionary processes shape consistent behavioural traits (i.e. personality). Deliberate introductions of non-native species offer opportunities to investigate how such genes differ between native and introduced populations and how polymorphisms in the genes are related to variation in behaviour. Here, we compared the genetic variation of the two 'personality' genes, DRD4 and SERT, between a native (United Kingdom, UK) and an introduced (New Zealand, NZ) population of dunnocks, Prunella modularis. The NZ population showed a significantly lower number of single nucleotide polymorphisms (SNPs) compared to the UK population. Standardized F'st estimates of the personality genes and neutral microsatellites indicate that selection (anthropogenic and natural) probably occurred during and post the introduction event. Notably, the largest genetic differentiation was found in the intronic regions of the genes. In the NZ population, we also examined the association between polymorphisms in DRD4 and SERT and two highly repeatable behavioural traits: flight-initiation distance and mating status (promiscuous females and cobreeding males). We found 38 significant associations (for different allele effect models) between the two behavioural traits and the studied genes. Further, 22 of the tested associations showed antagonistic allele effects for males and females. Our findings illustrate how introduction events and accompanying ecological changes could influence the genetic diversity of behaviour-related genes. © 2015 John Wiley & Sons Ltd.

  3. Figurações do "mal" e do "maligno" no Grande sertão: veredas

    Directory of Open Access Journals (Sweden)

    Marcus V. Mazzari

    2008-12-01

    Full Text Available Este texto constitui o segundo capítulo de um estudo sobre a trajetória de Riobaldo em sua oscilação entre o pacto fáustico e a tradição do chamado "romance de formação e desenvolvimento" (Bildungs- und Entwicklungsroman. Partindo de um trecho do romance O homem sem qualidades em que Musil discute os obstáculos que se colocam à arte da narrativa no século XX (antecipando reflexões teóricas de Adorno, Auerbach, Rosenfeld etc., o estudo enfoca, no primeiro capítulo, traços do Grande sertão que o vinculariam a um épico mais primitivo. Também se estabelecem aqui algumas relações com o Doutor Fausto de Thomas Mann, romance que tem igualmente no pacto demoníaco o seu motivo nuclear. Quanto ao presente texto, está voltado às formas e imagens que o relato de Riobaldo dispensa aos conceitos de "mal" e de "maligno" (assim como ao seu entrelaçamento. Em seguida, enfoca a personagem de Hermógenes, que encarna uma espécie de principium maleficum que dificilmente encontra paralelo na literatura ocidental. Para expor essa especificidade da personagem rosiana, o estudo procede por fim a uma comparação com a representação do Mal (e sua correspondente personagem no romance barroco Simplicissimus, de Grimmelshausen.This text represents the second chapter of a study on Robaldo's trajectory during his oscilation between the faustian bargain and the tradition of the so-called "Bildungsroman" (Bildungs - und Entwicklungsroman. Taking an excerpt of the novel The Man Without Qualities, in which Musil discusses the obstacles imposed on 20th century narrative art, as a starting point (and putting forth theorethical reflections by Adorno, Auerbach, Rosenfeld etc., the essay focuses, in the first chapter, on the features of Guimarães Rosa's novel The Devil to Pay in the Backlands that would connect it to a more primitive epic. Here, some relationships with Thomas Mann's Doctor Faustus, which also has the diabolic pact as a central motif, are

  4. O sertão na obra de dois cronistas coloniais: a construção de uma imagem barroca (séculos XVI-XVII

    Directory of Open Access Journals (Sweden)

    Silva, Kalina Vanderlei

    2006-01-01

    Full Text Available Este artigo aborda as representações do sertão no imaginário barroco das vilas canavieiras das capitanias do norte do Estado do Brasil, a partir da obra de dois cronistas coloniais, Gabriel Soares de Souza e Ambrosio Fernandes Brandão

  5. Vida de agricultoras e histórias de documentos no Sertão Central de Pernambuco Lives of peasant and worker women and stories of documents in the South Central Sertão of Pernambuco

    Directory of Open Access Journals (Sweden)

    Rosineide de L. Meira Cordeiro

    2007-08-01

    Full Text Available O artigo enfoca como as mulheres agricultoras, ao terem acesso a direitos sociais, especialmente à Previdência Social, lidam com a normatização e a regulamentação dos processos de nascimento, envelhecimento e morte. O objetivo é analisar as dificuldades e as estratégias que as mulheres utilizam para cumprirem as exigências legais de comprovação do trabalho na agricultura familiar através de documentos civis e profissionais. A pesquisa foi realizada nos municípios de Santa Cruz da Baixa Verde e Triunfo, situados no Sertão de Pernambuco, Nordeste do Brasil. A ausência de documentos é reveladora dos parâmetros de modernidade instaurados no país e deve ser entendida à luz das intersecções de gênero, classe, raça, etnia e critérios geopolíticos.The article focuses on how peasant and worker women deal with norms and rules about birth, ageing and death, in the process of getting access to social rights, especially to Social Security. The aim is to analyze difficulties and strategies used by women in order to comply with the legal demands of proof of work experience in family farming by way of civil and professional documents. Research was undertaken in the municipalities of Santa Cruz da Baixa Verde and Triunfo, in the Pernambuco Sertão in Northeast Brazil. The absence of documents reveals how parameters of modernity are installed in the nation, understanding them as necessarily related to gender, class, race, ethnicity and geopolitical criteria.

  6. Propostas de mudanças ao basquete no sertão cearense: dando voz aos praticantes

    Directory of Open Access Journals (Sweden)

    Bérgson Nogueira de Oliveira

    2017-06-01

    Full Text Available Objetivo: o presente artigo tem como objetivo compreender as percepções de mudanças sociais atribuídas pelos praticantes de basquete em um município do sertão cearense, destacando neste contexto, as suas representações sociais acerca do papel social desta prática esportiva. Método: foram entrevistados cinco sujeitos do sexo masculino que praticam a modalidade há mais de dez anos no contexto do sertão cearense e que estudaram em escolas públicas. Para a construção das informações, utilizamos a entrevista semi-estruturada, seguida por um roteiro composto por temas, que foi adaptado de um estudo realizado por Santos (2004. As análises dos dados se deu a partir da Análise de Conteúdo do tipo Análise Temática, em que foram elaboradas categorias, a partir do material das entrevistas. Resultados: as representações de mudança dos sujeitos indicam o incentivo do basquete nas escolas; criação de projetos sociais; investimento na infraestrutura esportiva; bem como o fomento à criação de competições. Conclusão: conclui-se que a falta de apoio, de forma geral, dificulta a inserção de novos praticantes para essa modalidade. Nesse sentido, entende-se que são necessários mais incentivos ao esporte, pois se trata de um pilar na formação humana e possibilita o seu trabalho, não apenas no alto rendimento, mas também em dimensões de lazer, participação, educação, inclusão social entre outros aspectos.

  7. Imaging of the brain serotonin transporters (SERT) with {sup 18}F-labelled fluoromethyl-McN5652 and PET in humans

    Energy Technology Data Exchange (ETDEWEB)

    Hesse, Swen [University of Leipzig, Department of Nuclear Medicine, Leipzig (Germany); Leipzig University Medical Center, AdiposityDiseases, Leipzig (Germany); Brust, Peter [Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmacy, Research Site Leipzig, Leipzig (Germany); Maeding, Peter; Zessin, Joerg; Fuechtner, Frank [Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmacy, Dresden (Germany); Becker, Georg-Alexander; Patt, Marianne; Seese, Anita; Sorger, Dietlind; Meyer, Philipp M.; Habermann, Bernd; Luthardt, Julia; Bresch, Anke; Sabri, Osama [University of Leipzig, Department of Nuclear Medicine, Leipzig (Germany); Lobsien, Donald [University of Leipzig, Department of Neuroradiology, Leipzig (Germany); Laudi, Sven [University of Leipzig, Department of Anaesthesiology and Intensive Care, Leipzig (Germany); Steinbach, Joerg [Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmacy, Dresden (Germany); Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmacy, Research Site Leipzig, Leipzig (Germany)

    2012-06-15

    [{sup 11}C]DASB is currently the most frequently used highly selective radiotracer for visualization and quantification of central SERT. Its use, however, is hampered by the short half-life of {sup 11}C, the moderate cortical test-retest reliability, and the lack of quantifying endogenous serotonin. Labelling with {sup 18}F allows in principle longer acquisition times for kinetic analysis in brain tissue and may provide higher sensitivity. The aim of our study was to firstly use the new highly SERT-selective {sup 18}F-labelled fluoromethyl analogue of (+)-McN5652 ((+)-[{sup 18}F]FMe-McN5652) in humans and to evaluate its potential for SERT quantification. The PET data from five healthy volunteers (three men, two women, age 39 {+-} 10 years) coregistered with individual MRI scans were semiquantitatively assessed by volume-of-interest analysis using the software package PMOD. Rate constants and total distribution volumes (V{sub T}) were calculated using a two-tissue compartment model and arterial input function measurements were corrected for metabolite/plasma data. Standardized uptake region-to-cerebellum ratios as a measure of specific radiotracer accumulation were compared with those of a [{sup 11}C]DASB PET dataset from 21 healthy subjects (10 men, 11 women, age 38 {+-} 8 years). The two-tissue compartment model provided adequate fits to the data. Estimates of total distribution volume (V{sub T}) demonstrated good identifiability based on the coefficients of variation (COV) for the volumes of interest in SERT-rich and cortical areas (COV V{sub T} <10%). Compared with [{sup 11}C]DASB PET, there was a tendency to lower mean uptake values in (+)-[{sup 18}F]FMe-McN5652 PET; however, the standard deviation was also somewhat lower. Altogether, cerebral (+)-[{sup 18}F]FMe-McN5652 uptake corresponded well with the known SERT distribution in humans. The results showed that (+)-[{sup 18}F]FMe-McN5652 is also suitable for in vivo quantification of SERT with PET. Because of

  8. Intoxicações por plantas em ruminantes e equídeos no Sertão Paraibano Plant poisonings in ruminants and equidae in the Sertão of Paraiba, Brazil

    Directory of Open Access Journals (Sweden)

    Tales S. Assis

    2009-11-01

    Full Text Available Foi realizado um levantamento das intoxicações por plantas em 20 municípios do Sertão Paraibano, onde foram entrevistados 50 produtores e 11 médicos veterinários. De acordo com o levantamento realizado, Ipomoea asarifolia e Mascagnia rigida são as intoxicações mais importantes. Indigofera suffruticosa, as plantas cianogênicas (Sorghum vulgare, Piptadenia macrocarpa e Manihot spp., Mimosa tenuiflora, Aspidosperma pyrifolium e Crotalaria retusa são plantas importantes como causa de intoxicações na região. Os entrevistados relataram casos esporádicos de intoxicação por Ricinus communis, Enterolobium contortisiliquum, Prosopis juliflorae Brachiaria decumbens. Ziziphus joazeiro, Passiflora sp., Caesalpina ferrea e Crescentia cujete foram mencionadas como causa de abortos em ruminantes. Frutos de Crescentia cujete foram administrados a duas cabras prenhes causando mortalidade perinatal e abortos. As cascas de feijão (Phaseolus vulgaris e Vigna unguiculata e as folhas de Licania rigida (oiticica são associadas à sobrecarga ruminal em bovinos. As frutas de Mangifera indica (mangae Anacardium occidentale (cajú são responsabilizadas por causarem intoxicação etílica. Dalechampia sp. e Croton sp. foram citadas pelos entrevistados como possíveis plantas tóxicas, que ainda não tiveram sua toxicidade comprovada.A survey of plant poisoning in ruminants and equidae was conducted in 20 municipalities of the semiarid region of the Sertão Paraibano. Fifty farmers and 11 veterinary practitioners were interviewed. Ipomoea asarifolia and Mascagnia rigida are the most important poisonous plants in the region. Indigofera suffruticosa, the cianogenic plants (Sorghum vulgare, Piptadenia macrocarpa, and Manihot spp., Mimosa tenuiflora, Aspidosperma pyrifolium and Crotalaria retusa cause also important intoxications in the area. Sporadic outbreaks of poisonings by Ricinus communis, Enterolobium contortisiliquum, Prosopis juliflora and Brachiaria

  9. serts alimentaires à Winnipeg (Canada : une nouvelle méthodologie de mesure d'un concept complexe et controversé

    Directory of Open Access Journals (Sweden)

    Joyce Slater

    2017-01-01

    Full Text Available Introduction : Les « déserts alimentaires » ont vu le jour dans les 20 dernières années et forment des secteurs préoccupants pour les collectivités, les autorités en santé publique et les chercheurs en raison de leur effet négatif possible sur la qualité de l’alimentation et en raison de leurs conséquences sur la santé. Ce sont des espaces résidentiels, habituellement en milieu urbain, où les résidents à faible revenu n’ont que peu ou pas accès à des établissements de vente au détail d'aliments qui offrent suffisamment de variété à un prix abordable. La recherche sur les déserts alimentaires présente des défis méthodologiques, notamment la façon de repérer et de classer les magasins d’alimentation au détail, la définition de la population à faible revenu ainsi que les paramètres concernant le transport et la proximité. De plus, les méthodes complexes qui sont souvent employées dans la recherche sur les déserts alimentaires peuvent être difficiles à reproduire et à communiquer aux principaux intervenants. Pour surmonter ces difficultés, nous avons voulu montrer qu’on pouvait concevoir une méthode simple et reproductible pour repérer les déserts alimentaires, à l’aide de données facilement accessibles en contexte canadien. Méthodologie : Cette étude a été menée à Winnipeg (Canada en 2014. Les établissements de vente au détail des aliments ont été trouvés à l’aide des Pages Jaunes et vérifiés par des diététistes en santé publique. Nous avons créé deux scénarios sur les déserts alimentaires en fonction de l’emplacement de la population à quintile de revenu le plus faible : a celle qui habitait à 500 m ou plus d’une épicerie appartenant à une chaîne nationale et b celle qui habitait à 500 m ou plus d’une épicerie appartenant à une chaîne nationale ou d’une épicerie à service complet. Résultats : En fonction du scénario utilisé, 64 574 ou 104 335 r

  10. Mixed World, World in Rebellion: on Violence in Grande Sertão: Veredas (Rural Settlements, by Guimarães Rosa

    Directory of Open Access Journals (Sweden)

    Carmello, Patricia

    2012-01-01

    Full Text Available The analysis of violence in Guimarães Rosa’s novel Grande Sertão: veredas reveals references to the Brazilian historical conflicts of that time, situated between town and country, the government and people of the country, the Winners and the Forgotten people of history. Furthermore, the theme of violence comes at a tension between a memory not forgotten, related to the repression, and the poverty of experience that’s not worth remembering.

  11. Drought in the sertão as a natural or social phenomenon: establishing the Inspetoria Federal de Obras Contra as Secas, 1909-1923

    Directory of Open Access Journals (Sweden)

    Eve Elizabeth Buckley

    2010-01-01

    Full Text Available This paper examines interpretations of the drought problem in Brazil's northeast sertão during the First Republic. It compares analysis of drought as primarily a natural or climatic phenomenon – embraced by civil engineers working for the Inspetoria [Federal] de Obras Contra as Secas (IFOCS – with analyses emphasizing social and political conditions that made drought a crisis for the sertanejo poor. The latter are evident in the report of doctors Belisário Penna and Artur Neiva describing their expedition through the sertão sponsored by IFOCS in 1912. This comparison allows for consideration of the intersection between natural (geographic, climatic and social (political, cultural factors that produced the region's periodic crisis. The analysis is informed by the work of social scientists who highlight the multi-dimensional causes underlying natural disasters in politically marginal communities. Technocrats' faith in the context-independent utility of their expertise lay at the heart of IFOCS's ultimate failure to rescue sertanejos from famine, migration and poverty. Because the drought agency's technical personnel never had the political will or muscle to confront the social organization underlying the sertão's recurrent calamity, their ability to alleviate the human suffering that droughts precipitated was severely limited.

  12. Drought in the sertão as a natural or social phenomenon: establishing the Inspetoria Federal de Obras Contra as Secas, 1909-1923

    Directory of Open Access Journals (Sweden)

    Eve Elizabeth Buckley

    Full Text Available This paper examines interpretations of the drought problem in Brazil's northeast sertão during the First Republic. It compares analysis of drought as primarily a natural or climatic phenomenon - embraced by civil engineers working for the Inspetoria [Federal] de Obras Contra as Secas (IFOCS - with analyses emphasizing social and political conditions that made drought a crisis for the sertanejo poor. The latter are evident in the report of doctors Belisário Penna and Artur Neiva describing their expedition through the sertão sponsored by IFOCS in 1912. This comparison allows for consideration of the intersection between natural (geographic, climatic and social (political, cultural factors that produced the region's periodic crisis. The analysis is informed by the work of social scientists who highlight the multi-dimensional causes underlying natural disasters in politically marginal communities. Technocrats' faith in the context-independent utility of their expertise lay at the heart of IFOCS's ultimate failure to rescue sertanejos from famine, migration and poverty. Because the drought agency's technical personnel never had the political will or muscle to confront the social organization underlying the sertão's recurrent calamity, their ability to alleviate the human suffering that droughts precipitated was severely limited.

  13. A tradução de Samuel Putnam de Os Sertões - Rebellion in the Backlands, de Euclides da Cunha

    Directory of Open Access Journals (Sweden)

    John Milton

    1997-11-01

    Full Text Available Der vorliegende Aufsatz untersucht Samuel Putnams Übersetzung des Romans Os Sertões von Euclides da Cunha (Rebellion in the Backlands unter verschiedenen Gesichtspunkten. Von großer Wichtigkeit ist die Tatsache, daß Os Sertões in Brasilien gewöhnlich als literarisches Werk betrachtet wird, während das Buch auf Englisch mehr als historischer Bericht gilt und vom Verlag, der University of Chicago Press, in der Sparte Literature/History geführt wird. Außerdem fügt Putnam eine große Zahl von Fußnoten zu denen von Euclides da Cunha hinzu.Von Interesse ist auch die Tatsache, daß Putnam, der seine Übersetzung gerade zu der Zeit anfertigte, als die USA in den Zweiten Weltkrieg eintraten, in seinem Vorwort ausführlich darauf eingeht, wie nah Os Sertões den Meinungsgegensätzen steht, die die amerikanische Erfahrung sowohl des Bürgerkrieges als auch des Eintritts in den Zweiten Weltkrieg kennzeichneten.

  14. Ser-estar no sertão: capítulos da vida como filosofia visceral

    Directory of Open Access Journals (Sweden)

    Renzo Taddei

    2014-09-01

    Full Text Available Uma pesquisa etnográfica no sertão cearense, o conceito de mimese corpórea em produção teatral e um filme documentário sobre rastejadores de cangaceiros na caatinga do Ceará, Brasil, são pontos de partida, neste texto, para uma discussão sobre a natureza do processo de “leitura de sinais” no mundo. As reflexões apresentadas sugerem que tais processos sejam entendidos menos como interpretação ou decodificação, e mais como um saber mover-se, no qual o compartilhamento existencial – em especial, a ingestão de substâncias – é elemento fundamental. Os materiais analisados apontam, ainda, para o fato de que a direcionalidade implicada em tal saber mover-se é recorrentemente entendida como dimensão visceral. As vísceras, desse modo, transformam-se em locus privilegiado da experiência e ação no mundo, sendo superfície de contato e equipamento transformador ao mesmo tempo. Tal perspectiva traz novas e instigantes oportunidades à teoria social.

  15. Genotype adaptability and stability

    Directory of Open Access Journals (Sweden)

    Dimitrijević Miodrag

    2000-01-01

    Full Text Available One of the primary concerns in breeding programs is a small genotype reaction to environmental factor variation for better usage of yield genetic potential. Particularly if one takes in consideration that yield could van greatly because of more and more variable meteorological conditions. Studies conducted to observe genotype and environmental relations relay on numerous mathematical models, but genotype behavior in various ecological conditions is not, still, precisely defined Major sources of variation influencing genotype behavior in different environments are genotype/environment interaction, genetic background and environmental conditions. These factors could play an important role in establishing growth regions for maximal realization of genotype genetic potential, as well as in selection of genotypes having better response to complex requirements of particular growth region. Stability, the genotype ability to perform high, uniform yield no meter of different environmental conditions, and adaptability, genotype ability to give uniform yield in a different environmental conditions, are two common terms used to define genotype reaction in a consequence of environmental changes. Most of the models dealing with stability and adaptability are based on variation sources appearing under the influence of treatment, multivariate effects and residue. No meter which statistical model is used for GE interaction estimation, there is an opinion that no solid proof for the existence of stable genotypes obtained in breeding programs, which make some space for further investigations. There are still questions to answer dealing with definitions, sources of variation, usage value of existent models and interpretation of the results. .

  16. PET imaging of the brain serotonin transporters (SERT) with N,N-dimethyl-2-(2-amino-4-[{sup 18}F]fluorophenylthio)benzylamine (4-[{sup 18}F]-ADAM) in humans: a preliminary study

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Wen-Sheng [PET Center, Tri-Service General Hospital, Department of Nuclear Medicine, Neihu, Taipei (China); Changhua Christian Hospital, Department of Nuclear Medicine, Changhua (China); Huang, San-Yuan; Ho, Pei-Shen; Yeh, Chin-Bin [Tri-Service General Hospital, Department of Psychiatry, Taipei (China); Ma, Kuo-Hsing [National Defense Medical Center, Department of Biology and Anatomy, Taipei (China); Huang, Ya-Yao; Shiue, Chyng-Yann [PET Center, Tri-Service General Hospital, Department of Nuclear Medicine, Neihu, Taipei (China); PET Center, National Taiwan University Hospital, Department of Nuclear Medicine, Taipei (China); Liu, Ren-Syuan [Taipei Veterans General Hospital, Department of Nuclear Medicine, Taipei (China); Cheng, Cheng-Yi [PET Center, Tri-Service General Hospital, Department of Nuclear Medicine, Neihu, Taipei (China)

    2013-01-15

    The aim of this study was to assess the feasibility of using 4-[{sup 18}F]-ADAM as a brain SERT imaging agent in humans. Enrolled in the study were 19 healthy Taiwanese subjects (11 men, 8 women; age 33 {+-} 9 years). The PET data were semiquantitatively analyzed and expressed as specific uptake ratios (SUR) and distribution volume ratios (DVR) using the software package PMOD. The SUR and DVR of 4-[{sup 18}F]-ADAM in the raphe nucleus (RN), midbrain (MB), thalamus (TH), striatum (STR) and prefrontal cortex (PFC) were determined using the cerebellum (CB) as the reference region. 4-[{sup 18}F]-ADAM bound to known SERT-rich regions in human brain. The order of the regional brain uptake was MB (RN) > TH > STR > PFC > CB. The DVR (n = 4, t* = 60 min) in the RN, TH, STR and PFC were 3.00 {+-} 0.50, 2.25 {+-} 0.45, 2.05 {+-} 0.31 and 1.40 {+-} 0.13, respectively. The optimal time for imaging brain SERT with 4-[{sup 18}F]-ADAM was 120-140 min after injection. At the optimal imaging time, the SURs (n = 15) in the MB, TH, STR, and PFC were 2.25 {+-} 0.20, 2.28 {+-} 0.20, 2.12 {+-} 0.18 and 1.47 {+-} 0.14, respectively. There were no significant differences in SERT availability between men and women (p < 0.05). The results of this study showed that 4-[{sup 18}F]-ADAM was safe for human studies and its distribution in human brain appeared to correlate well with the known distribution of SERT in the human brain. In addition, it had high specific binding and a reasonable optimal time for imaging brain SERT in humans. Thus, 4-[{sup 18}F]-ADAM may be feasible for assessing the status of brain SERT in humans. (orig.)

  17. O SABER CAMPONÊS: apropriação dos Recursos no Sertão dos Inhamuns - CE

    Directory of Open Access Journals (Sweden)

    José Levi Furtado Sampaio

    2007-01-01

    Full Text Available Aunque posee orígenes remotos, la cuestión agraria se materializa como un debate persistente en el inicio del siglo XXI. Aun delante de considerables transformaciones económicas, sociales y políticas, lo que se percibe en Brasil y en el mundo es la vitalidad de la lucha por tierra y de la demanda por reforma agraria, vía resistencia y superación de las adversidades puestas a los campesinos. Luego, resultantes tanto de la historia de vida, como de las costumbres, los campesinos expresan sus formas de apropiación por medio de las tradiciones culturales o costumbres campesinas. Ellos lanzan una mirada orientada por las necesidades, sus conocimientos y su saber hacer, para conseguir la soberanía alimentar, superación de los problemas campesinos y resistencia al sistema capitalista. La discusión sobre ese tema en el presente artículo envuelve la comprensión del contexto histórico en el que el campesino está inserido, bien como sus prácticas culturales. Esas reflexiones fueron poco a poco instigando la discusión sobre cómo las costumbres campesinas se reflejan en la apropiación de los recursos en el espacio agrario del asentamiento Ingá/Facundo, ubicado en el municipio de Parambu, Microrregión del Sertón de los Inhamuns, a 371 km de la ciudad de Fortaleza, en Ceará, puesto que tal hecho es elemento fundamental para comprender como se da la resistencia y superación de la cultura campesina delante de las condiciones, por veces, adversas del semiárido cearense.

  18. Fluoxetine protects against methamphetamine‑induced lung inflammation by suppressing oxidative stress through the SERT/p38 MAPK/Nrf2 pathway in rats.

    Science.gov (United States)

    Wang, Yun; Gu, Yu-Han; Liu, Ming; Bai, Yang; Wang, Huai-Liang

    2017-02-01

    Methamphetamine (MA) abuse is a major public health and safety concern throughout the world and a growing burden on healthcare costs. The purpose of the present study was to investigate the protective effect of fluoxetine against MA‑induced chronic pulmonary inflammation and to evaluate the potential role of nuclear factor erythroid 2-related factor 2 (Nrf2)-mediated antioxidative stress. Wistar rats were divided into control, MA and two fluoxetine‑treated groups. Rats in the MA and the two fluoxetine‑treated groups were treated daily with intraperitoneal injection of 10 mg/kg MA twice daily. Rats in the two fluoxetine‑treated groups were injected intragastrically with fluoxetine (2 and 10 mg/kg) once daily, respectively. After 5 weeks, the rats were euthanized and hematoxylin and eosin staining, immunohistochemistry, western blot analysis and redox assay were performed. It was demonstrated that chronic exposure to MA can induce pulmonary inflammation in rats, with the symptoms of inflammatory cell infiltration, crowded lung parenchyma, thickened septum and a reduced number of alveolar sacs. Fluoxetine attenuated pulmonary inflammation and the expression of interleukin‑6 and tumor necrosis factor‑α in rat lungs. Fluoxetine inhibited MA‑induced increases in the expression levels of serotonin transporter (SERT) and p‑p38 mitogen‑activated protein kinase (MAPK), and reversed the MA‑induced decrease in nuclear Nrf2 and human heme oxygenase‑1 in lungs. Fluoxetine at 10 mg/kg significantly reversed the reduced glutathione (GSH) level, the ratio of GSH/oxidized glutathione, and the reactive oxygen species level in rat lungs from the MA group. These findings suggested that fluoxetine, a SERT inhibitor, has a protective effect against MA‑induced lung inflammation by suppressing oxidative stress through the SERT/p38 MAPK/Nrf2 pathway in rats.

  19. Genotype to phenotype

    National Research Council Canada - National Science Library

    Malcolm, Sue; Goodship, Timothy H. J

    2001-01-01

    ... Disorders Molecular Genetics of Hypertension Human Gene EvolutionAnalysis of Multifactorial Disease Transcription Factors Molecular Genetics of Cancer, Second edition Genotype to Phenotype, second e...

  20. Características clínico-comportamentais de professores . universitários no sertão paraibano

    OpenAIRE

    Coêlho, Raimunda de Fátima Neves

    2013-01-01

    p. 1-153 comprometer a saúde física e mental dos indivíduos é necessária, para respaldar programas de suporte ao docente. O estudo objetivou descrever características clínico-comportamentais de professores universitários no sertão paraibano, tendo como objetivos secundários: avaliar correlação entre Resiliência, História de Trauma, Transtorno do Estresse Pós-traumático - TEPT, Impulsividade, Religiosidade, e Qualidade de Vida na população estudada; determinar a frequência de...

  1. Vestígios indígenas na cartografia do sertão da América portuguesa

    Directory of Open Access Journals (Sweden)

    Gl\\u00F3ria Kok

    2009-01-01

    Full Text Available During the first three centuries of colonization of Portuguese America, indigenous cartography helped the outlanders to decipher the space that they conventionally named sertão (backcountry. The colonizers in the Captaincy of São Paulo (expeditions, soldiers, settlers, bureaucrats, merchants, and adventurers mapped out the hinterland with utmost care. However, because the territory was a colony, such agents reorganized that space and classified the ethnic groups into distinct, fixed and homogenous categories. As the Portuguese Crown moved ahead with its conquest, the indigenous groups were gradually wiped out from the maps and their territories expropriated.

  2. Quantitative structure-activity relationship of phenoxyphenyl-methanamine compounds with 5HT2A, SERT, and hERG activities.

    Science.gov (United States)

    Mente, Scot; Gallaschun, Randall; Schmidt, Anne; Lebel, Lorrie; Vanase-Frawley, Michelle; Fliri, Anton

    2008-12-01

    QSAR models have been used to evaluate activities for compounds in the phenoxyphenyl-methanamine (PPMA) class of compounds. These models utilize Hammett-type donating-withdrawing substituent values as well as simple parameters to describe substituent size and elucidate the SAR of the 'A' and 'B' rings. Using this methodology, intuitive QSAR relationships were found for the three biological activities with R(2) values of 0.73, 0.45, and 0.58 for 5HT(2A), SerT, and hERG activities.

  3. Classificação de solos planossólicos do Sertão do Araripe (PE Classification of planossolic soils from the Sertão do Araripe region, of State Pernambuco, Brazil

    Directory of Open Access Journals (Sweden)

    L. B. Oliveira

    2003-08-01

    Full Text Available Neste trabalho objetivou-se caracterizar e classificar solos com horizonte B plânico subjacente a um horizonte B textural e, portanto, em posição não-diagnóstica para a classe dos Planossolos do Sistema Brasileiro de Classificação de Solos (SIBCS. Foram selecionados três perfis representativos destes solos no município de Ouricuri, microrregião de Araripina, no Sertão de Pernambuco, área de ocorrência expressiva de solos planossólicos. Os perfis foram descritos e amostras deformadas foram coletadas de todos os horizontes para realização das análises físicas e químicas. Amostras indeformadas foram coletadas para determinação da densidade do solo. Os resultados mostram que os solos, formados de uma dupla contribuição de material de origem (cobertura sedimentar e rochas cristalinas do Pré-Cambriano, apresentam duas seções distintas, que refletem a contribuição dos materiais originários. A seção superior é formada pelos horizontes A, BA, Bt e, ou, Btf, e a inferior é formada pelos horizontes 2Btbn e 2BCn. Os horizontes da seção superior apresentam cores cromadas, textura mais arenosa, densidade mais baixa, maior condutividade hidráulica e menor atividade da fração argila do que os horizontes da seção inferior dos perfis, que se apresentam muito densos, pouco cromados e constituem uma barreira à percolação da água. Propõe-se a seguinte classificação para os perfis estudados: Plintossolo Argilúvico eutrófico planossólico sódico (perfil 1; Argissolo Amarelo eutrófico planossólico solódico (perfil 2 e Argissolo Amarelo eutrófico plíntico planossólico sódico (perfil 3. Os resultados indicam a necessidade de modificações na conceituação do horizonte B plânico do SIBCS, para permitir o enquadramento dos solos estudados. Sugere-se a eliminação da obrigatoriedade de ser o horizonte B plânico imediatamente subjacente a um horizonte A ou E, bem como da necessidade de mudança textural abrupta

  4. Pengaruh stresor fisik terhadap distribusi SERT dan indeks apoptosis neuron hipokampus, serta distribusi TNF-± gaster tikus dengan mediasi kortisol dan IL-6

    Directory of Open Access Journals (Sweden)

    Suparno Suparno

    2012-02-01

    Full Text Available Generally, distres which followed by psychiatric disorders still more medicinal practice controversial especially physically stressor roles on holistic health condition. Therefore, researches still more needed to explain and clarify the infl uences and the role of physically stressors on psychiatric disorders. This study used an psychoneuroimmunologic paradigm, which used posttest-only true experiment design for the research. About 24 female Rattus norvegicus strain Wistar had been used, they were devided into six groups. To investigate functional changes, we had been used hippocampus SERT distribution changes as mirror of central serotonergic malfunction changes. While, to investigate structural changes we had been inspected apoptosis index of hippocampus CA3 regions (hippocampus slicing. We also took the blood from the rats heart to examinate IL – 6 and cortisol level, and gastric tissues for TNF-α level examination. Physical stressors lead to arise functional and structural changes include hippocampus SERT distribution, increases hippocampus apoptotic index, and increases TNF-α level, that fi nally arise the distress. These results of statistical analyses demonstrate that physical stressors tend to be mediated by serotonergic neurotransmission pathway. This study also support assumptions that psychological stressors caused and or related with gastrical changes.

  5. Reappraisal of spontaneous stereotypy in the deer mouse as an animal model of obsessive-compulsive disorder (OCD): response to escitalopram treatment and basal serotonin transporter (SERT) density.

    Science.gov (United States)

    Wolmarans, De Wet; Brand, Linda; Stein, Dan J; Harvey, Brian H

    2013-11-01

    Obsessive-compulsive disorder (OCD) is characterized by recurrent thoughts and repetitive motor actions. Hyposerotonergic signalling in the cortico-striatal circuitry is believed to be central to the pathology of OCD, while many patients only respond to chronic treatment with high dose selective serotonin (5HT) reuptake inhibitors (SSRIs). Confined deer mice spontaneously develop two forms of stereotypy, namely vertical jumping and pattern running. The purpose of this investigation was to reappraise these behaviours and strengthen the validity of deer mouse stereotypy as an animal model of OCD within a framework of three study questions: (1) can the time spent executing stereotypical behaviours be employed as a measure of extent of stereotypy, (2) does deer mouse stereotypy only respond to chronic, but not sub-chronic treatment with a high-dose SSRI, and (3) is deer mouse stereotypy associated with altered cortico-striatal 5HT transporter (SERT) binding? The current study demonstrates that treatment naïve high stereotypical (HS) deer mice spend significantly more time executing stereotypical behaviours while significantly less time is spent indulging in stereotypy following chronic, but not sub-chronic, treatment with escitalopram. Furthermore, HS deer mice present with a significant decrease in striatal SERT density compared to non-stereotypical (NS) controls. Building on previous validation studies, we conclude that deer mouse stereotypy is a valid naturalistic animal model of OCD with robust face, construct and predictive validity. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. APOE Genotyping, Cardiovascular Disease

    Science.gov (United States)

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

  7. HIV Genotypic Resistance Testing

    Science.gov (United States)

    ... High-sensitivity C-reactive Protein (hs-CRP) Histamine Histone Antibody HIV Antibody and HIV Antigen (p24) HIV ... antiretroviral drugs. With genotypic resistance testing, the genetic code of the HIV a person has been infected ...

  8. Beneficiamento do cultivo do Meloeiro pela apicultura no sertão do Moxotó representado por Modelo Digital do Terreno | Processing of Melon crops for beekeeping in the backwoods of Moxotó represented by Digital Terrain Model

    Directory of Open Access Journals (Sweden)

    Raphael Miller de Souza Caldas

    2016-04-01

    Full Text Available A região Nordeste é a principal produtora de melão do Brasil. O Semiárido brasileiro é uma região caracterizada por apresentar fatores climáticos favoráveis ao desenvolvimento da cultura do meloeiro. No presente estudo foi realizada a modelagem digital do terreno (MDT da microrregião Sertão do Moxotó para os parâmetros de precipitação, temperatura, PIB e IDH, afim de verificar a relação entre a cultura do meloeiro e a apicultura. Os municípios analisados foram Arcoverde, Betânia, Custódia, Ibimirim, Inajá, Sertânia e Manari. O cultivo do meloeiro tem potencial para ser implantado nos municípios do Sertão do Moxotó e está diretamente ligado a apicultura, pois a Apis mellifera é seu principal polinizador. Seu cultivo pode desempenhar papel vital no aumento ou manutenção da produção apícola. The Northeast region is the main melon producer of Brazil. The Brazilian semiarid region is characterized by climatic conditions favorable to the development of melon crop. In the present study, the digital terrain modeling (DTM of Sertão do Moxotó was performed to precipitation parameters, temperature, GDP, HDI and population in order to verifythe relationship between melon crop and apiculture. The districts analyzed were Arcoverde, Betânia, Custódia, Ibimirim, Inajá, Sertânia and Manari. Apis mellifera is the main pollinator of melon crop. Melon crop can support the bees during the shortage of bee flora and increase in bee production.

  9. Violência doméstica contra as mulheres: relações de gênero e de poder no sertão pernambucano

    OpenAIRE

    Lira, Kalline Flávia Silva de

    2015-01-01

    A presente pesquisa investiga a violação dos direitos humanos existentes na violência doméstica contra as mulheres, através de um recorte das relações de gênero e de poder no Sertão do Araripe de Pernambuco. Este estudo apresenta algumas considerações sobre a rede de enfrentamento da violência contra as mulheres na região, mapeando os serviços e apontando os números da violência, de 2010 a 2013, coletados em alguns dispositivos, além de realizar uma análise da violência a partir de entrevista...

  10. “Diadorim, meu amor” ou o Narciso Afogado: O mito do andrógino e ritos de passagem em Grande Sertão: Veredas

    Directory of Open Access Journals (Sweden)

    Cláudia Falluh Balduino Ferreira

    2012-04-01

    Full Text Available The present article studies the way that Diadorim - character from Sertão: Veredas, from João Guimarães Rosa -, vivifies and represents the archetype of totality represented by the Androgynous: emblematic entity, contradictory and also harmonic, double and unique, at the same time coincident and opposite. For this we will use the concepts and developments of this myth, passing first by an elucidation given both by the literary of psychological, such as the history of religions. Conscious of the breadth and depth that this issue involves the study of character will make it relating to 'themes of ritual initiation' at the light of the metaphysical, esoteric and symbolic contained in the text will be considered especially the specific episodes of death and funeral of the hero, after bloody battle.      

  11. Cauvin-Verner Corinne, Au désert. Une anthropologie du tourisme dans le Sud marocain, Paris, L’Harmattan, 2007, 317 p.

    Directory of Open Access Journals (Sweden)

    Isabelle Rivoal

    2008-04-01

    Full Text Available Il y a quelques années encore, la majorité des enquêtes sociologiques ou économiques portant sur les sociétés pastorales nomades des confins sahariens aux steppes du Proche-Orient en passant par le Sinaï égyptien s’appliquaient à décrire la fin du mode de vie nomade et les processus de sédentarisation de ces populations du désert. S’il s’agit encore d’évaluer une dynamique de changement, les travaux les plus récents portant sur les sociétés pastorales tribales tendent à remettre en perspectiv...

  12. Registro de ocorrência de vetores da esquistossomose mansônica em açude do Sertão de Pernambuco

    Directory of Open Access Journals (Sweden)

    Gazin Pierre

    2000-01-01

    Full Text Available O Sertão de Pernambuco não é área endêmica nem focal para esquistossomose mansônica. O presente trabalho registra a ocorrência de Biomphalaria straminea em açude da região, constatando que suas águas têm características físico-químicas favoráveis à proliferação destes moluscos. Chama a atenção para a possibilidade da introdução da doença no semi-árido, diante da crescente multiplicação de barragens.

  13. Rosa em policromia: cores, eros e íris (um arco de sexualidade entre Magma e Grande sertão: veredas

    Directory of Open Access Journals (Sweden)

    Wilberth Clayton Ferreira Salgueiro

    2005-10-01

    Full Text Available Numa  passagem de Grande sertão: veredas,  Riobaldo fala de uma "sonhice" que teve: "Diadorim  passando por debaixo do a rco-íris". Vinte anos antes,  em Magma,  Rosa esc reveu  um con junto de sete poemas, cujos  títu los  denunciam  a presen ça do arco-íris  e ativam sentidos que tal fenômeno carrega. Entender alguns destes sentidos, mostrando como as cores funcionam  na vida e na lite ratura, é o que quer o prese nte artigo. Para isso, analisam-se o poema "Ve rmelho" e a referida passagem-sonho como indicadores de um pensamento sobre a sexualidade.

  14. A universalidade em grande sertão: veredas e a noção de gramatica universaL

    Directory of Open Access Journals (Sweden)

    Lorenzo VITRAL

    2009-07-01

    Full Text Available Este artigo propõe uma reflexão sobre a sintaxe criada por Guimarães Rosa na sua obra-prima Grande sertão: veredas, Admite-se normalmente que sua linguagem utiliza volteios e estruturas provenientes de línguas estrangeiras, de certos dialetos falados do português do Brasil e de estágios históricos do português, Propomos que esses recursos são tão-somente elementos que incitam mecanismos da Gramática Universal, isto é, a entidade teórica proposta na teoria da Gramática Gerativa.

  15. A universalidade em grande sertão: veredas e a noção de gramatica universaL

    Directory of Open Access Journals (Sweden)

    Lorenzo VITRAL

    2013-11-01

    Full Text Available Este artigo propõe uma reflexão sobre a sintaxe criada por Guimarães Rosa na sua obra-prima Grande sertão: veredas, Admite-se normalmente que sua linguagem utiliza volteios e estruturas provenientes de línguas estrangeiras, de certos dialetos falados do português do Brasil e de estágios históricos do português, Propomos que esses recursos são tão-somente elementos que incitam mecanismos da Gramática Universal, isto é, a entidade teórica proposta na teoria da Gramática Gerativa.

  16. A comparison of theoretical CIV emission line strengths with active region observations obtained with the solar EUV rocket telescope and spectrograph (SERTS)

    Science.gov (United States)

    Keenan, F. P.; Thomas, R. J.; Neupert, W. M.; Conlon, E. S.; Burke, V. M.

    1993-01-01

    Theoretical line ratios involving 2s 2S - 3p 2P, 2p 2p - 3s 2S, and 2p 2S - 3d 2D transitions in C IV between 312 and 420 A are presented. A comparison of these with solar active region observational data obtained during a rocket flight by the Solar EUV Rocket Telescope and Spectrograph (SERTS) reveals good agreement between theory and experiment, with discrepancies that average only 22 percent. This provides experimental support for the accuracy of the atomic data adopted in the line ratio calculations, and also resolves discrepancies found previously when the theoretical results were compared with solar data from the S082A instrument on board Skylab. The potential usefulness of the C IV line ratios as electron temperature diagnostics for the solar transition region is briefly discussed.

  17. Guimarães Rosa, colecionador de palavras – uma leitura da poética das listas, em Grande sertão: veredas

    Directory of Open Access Journals (Sweden)

    Ivana Ferrante Rebello

    2017-05-01

    Full Text Available A escrita de Grande sertão: veredas, de Guimarães Rosa, apresenta uma série de listas, superpostas, que contribuem para conferir ao romance movimento e musicalidade. A partir das reflexões de Umberto Eco, em A vertigem das listas (2010, este artigo analisa o efeito poético das listas que compõem a escrita do romance. Enumerações de palavras, ditos populares, nomes de plantas e animais compõem as listas que estão presentes nas cadernetas do autor. Essas listas, que serviram de suporte à escrita inventiva do autor, também aparecem de forma abundante em sua ficção. Propomos, no presente estudo, uma reflexão acerca das imagens, da musicalidade e do ritmo que as listas superpostas conferem ao romance.

  18. Prevalence and genotyping of

    Directory of Open Access Journals (Sweden)

    Jawahir Alghamdi

    2016-11-01

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

  19. Socioeconomic indicators associated with the desertification process in “Microrregião do Sertão” of Pernambuco state, Brazil | Indicadores socioeconômicos associados ao processo de desertificação em "Microrregião do Sertão" do estado de Pernambuco, Brasil

    Directory of Open Access Journals (Sweden)

    Danielle de Fátima Gomes

    2017-06-01

    Full Text Available In all of humankind's history, there has never been as much concern about environmental issues as it has today. Within this theme, it is worth highlighting some issues such as: the climate change process and desertification. There are several indicators used to evaluate studies on this process. In order to do so, this study intends to compare the socioeconomic indicators in the Microregions of the “Sertão do Moxotó” and “Sertão do Pajeú”, State of Pernambuco, considered to be low susceptibility to desertification and with severe risk as described in the Map of Areas Susceptible to Desertification and Areas Affected by Desertification, Quoted by the Ministry of Environment. The data show that the absolute population manifests a greater control over natural resources, which ends up intervening in other factors, such as social ones. In this way, this research is expected to help in the elaboration of public policies aimed at adapting the population to future climatic scenarios.

  20. Axiom turkey genotyping array

    Science.gov (United States)

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

  1. Soroprevalência e fatores de risco para a língua azul em carneiros das mesorregiões do Sertão e da Borborema, semi-árido do Estado da Paraíba, Brasil Seroprevalence and risk factors for Bluetongue in rams of the Sertão and Borborema mesoregions, semi-arid of Paraíba state, Northeastern Brazil

    Directory of Open Access Journals (Sweden)

    Francisco de Assis Leandro Alves

    2009-04-01

    Full Text Available Neste estudo foi determinada a prevalência de anticorpos contra o vírus da língua azul em carneiros das mesorregiões do Sertão e da Borborema, semi-árido do Estado da Paraíba, bem como foram identificados os fatores de risco associados à infecção. A amostragem foi delineada para a determinação da prevalência de propriedades positivas (focos e de animais soropositivos por mesorregião. Foi realizada uma seleção aleatória de unidades primárias, composta por 189 propriedades no Sertão e 100 propriedades na Borborema. Dentro das unidades primárias, foram amostrados todos os carneiros (unidades secundárias, resultando em 321 animais no Sertão e 185 na Borborema. Na ocasião da coleta, foi aplicado um questionário epidemiológico por propriedade. Para o diagnóstico sorológico, foi utilizada a prova de imunodifusão em gel de ágar (IDGA, com antígeno produzido na Escola de Veterinária da Universidade Federal de Minas Gerais. Uma propriedade foi considerada foco quando apresentou pelo menos um animal soropositivo. Na mesorregião do Sertão, as prevalências de focos e de animais soropositivos foram de 11,6% [7,8% - 17,1%] e 8,4% [5,7% - 12,3%], respectivamente. Na mesorregião da Borborema, a prevalência de focos foi de 0,0% [0,0% - 3,6%] e a prevalência de animais soropositivos foi de 0,0% [0,0% - 2,0%]. Os fatores de risco associados à língua azul foram a não realização de higiene das instalações (OR = 5,51 e a vermifugação dos animais duas a quatro vezes ao ano (OR = 4,44.The prevalence of antibodies against Bluetongue virus in rams of the Sertão and Borborema mesoregions, semi-arid of the Paraíba state, Northeastern Brazil, was determined, and risk factors for the infection were identified. The sampling was delineated for the determination of the prevalence of positive herds and seropositive animals for each mesoregion. Herds (primary units were randomly selected in the Sertão mesoregion (n = 189 and in the

  2. Topofobia e topofilia em “A Terra”, de “Os Sertões”: uma análise ecocrítica do espaço sertanejo euclidiano / Topophobia and topophilia in”The Land” of “Os Sertões”: Analysis ecocriticism of space Sertanejo Euclideano

    Directory of Open Access Journals (Sweden)

    Edilane Ferreira da Silva

    2014-08-01

    Full Text Available In 1902, the journalist Euclides da Cunha published the work Os Sertões which, starting Pre-Brazilian Modernism and enhance Bahia´s backlands from the Canudos War. We analyze the chapter “The Earth” of the Euclidean book, in order to examine the discourse method analysis and the ecocriticism perspective - which concerns the interactions between literature and ecology - the author approaches between the backwoods and wilderness, and his own feelings regarding this space, considering topophobia concepts - aversion to physical environment and topophilia - familiarity or attachment, proposed by the chinese geographer Yi-Fu Tuan and related humanistic geography. Thus, the present discourse in the narrative demonstrate predominance of dislikes and horror feelings for the caatinga, regarding the subjectivity of the writer and oikos referenced by him.

  3. Gestão interfederativa do SUS: a experiência gerencial do Consórcio Intermunicipal do Sertão do Araripe de Pernambuco

    Directory of Open Access Journals (Sweden)

    Jadson Mendonça Galindo

    2014-12-01

    Full Text Available O objetivo deste artigo foi analisar a experiência gerencial do Consórcio Intermunicipal de Saúde do Sertão do Araripe de Pernambuco (Cisape. Para isso, utilizou-se uma pesquisa qualitativa do tipo análise documental. Os documentos analisados foram relatórios produzidos por consultoria especializada, envolvida na implantação da gestão regionalizada e consorciada do Sistema Único de Saúde (SUS em Pernambuco, no período de 2009 e 2010. Os resultados apontam que o Cisape adotou o modelo de gestão gerencialista, ou seja, orientado pela gestão pública pós-burocrática. A estrutura organizacional do Cisape foi definida como de direito público de natureza autárquica. A pesquisa identificou que em Pernambuco o Cisape se configurou como uma ferramenta importante para estimular a regionalização do SUS, porém com incipiente participação social.

  4. Analysis of social and environmental practices related to conscious consumption of students from public education of Sertão Pernambucano, Brazil

    Directory of Open Access Journals (Sweden)

    Anna Fernanda Beatriz Amorim Cavalcante

    2017-11-01

    Full Text Available This research aimed to analyze socio-environmental practices related to the conscious consumption of students of Sertão Pernambucano. A total of 174 high school students from two public schools were interviewed through a 29-item Likert-type measurement scale with five response levels. Among the students, 62.4% were female and 37.6% were male, aged between 15 and 20 years. It was found that 5.8% of the students were careful to take into account if the product residues were recyclable, 40.0% showed indifference or little commitment to use as few shopping bags as possible and the minority (8.3% of the students used to separate the waste by categories. 47.9% of the students affirmed to reuse draft paper and 55.9% save gift paper for future packaging. Few have the habit of watching (24.8%, talking to friends (12.9% or alerting people (23.2% about environmental problems or news. Therefore, Environmental Education, particularly, habits related to conscious consumption, needs to be inserted in the school context so that socio-educational actions become a daily practice, improving the expectations of future generations.

  5. MEDIAÇÕES CULTURAIS NO ALÉM-MAR: o padre Mamiani e os usos da língua kiriri nas brenhas dos sertões

    Directory of Open Access Journals (Sweden)

    Ane Luíse Silva Mecenas Santos

    2014-06-01

    Full Text Available Desde os primeiros anos do processo de conversão, os padres da Companhia de Jesus sistematizaram textos que possibilitariam a comunicação com os gentios. À medida que a catequese foi realizada com povos que não falavam a língua geral, novos instrumentos foram produzidos. Por isso, ao final do século XVII, fez-se necessário organizar para publicação uma gramática e um catecismo Kiriri. Esses dois documentos apresentam os indícios e os rastros do processo de mediação cultural ocorrido no sertão da América portuguesa. Em meio à normatização da língua oral, pelo filtro da gramaticalização latina, é possível perceber também o mundo indígena, em especial os costumes que causavam estranheza aos padres durante seu período de observação. O presente artigo busca analisar esses dois documentos, identificando os métodos de normatização da língua Kiriri.

  6. GENOTYPE X ENVIRONMENT INTERACTION AND STABILITY ...

    African Journals Online (AJOL)

    GENOTYPE X ENVIRONMENT INTERACTION AND STABILITY ANALYSIS OF SEED YIELD IN NAVY BEAN GENOTYPES. ... Abstract. Genotype x environment interactions, genotype response to environments and stability for seed yield of navy bean genotypes (Phaseolus vulgaris L.) were studied. Sixteen genotypes were ...

  7. Genotyping sleep disorders patients.

    Science.gov (United States)

    Kripke, Daniel F; Shadan, Farhad F; Dawson, Arthur; Cronin, John W; Jamil, Shazia M; Grizas, Alexandra P; Koziol, James A; Kline, Lawrence E

    2010-03-01

    The genetic susceptibility factors underlying sleep disorders might help us predict prognoses and responses to treatment. Several candidate polymorphisms for sleep disorders have been proposed, but there has as yet inadequate replication or validation that the candidates may be useful in the clinical setting. To assess the validity of several candidate associations, we obtained saliva deoxyribonucleic acid (DNA) samples and clinical information from 360 consenting research participants who were undergoing clinical polysomnograms. Ten single nucleotide polymorphisms (SNPs) were genotyped. These were thought to be related to depression, circadian sleep disorders, sleep apnea, restless legs syndrome (RLS), excessive sleepiness, or to slow waves in sleep. With multivariate generalized linear models, the association of TEF rs738499 with depressive symptoms was confirmed. Equivocal statistical evidence of association of rs1801260 (the C3111T SNP in the CLOCK gene) with morningness/eveningness and an association of Apolipoprotein E (APOE) rs429358 with the Epworth Sleepiness Scale (ESS) were obtained, but these associations were not strong enough to be of clinical value by themselves. Predicted association of SNPs with sleep apnea, RLS, and slow wave sleep were not confirmed. The SNPs tested would not, by themselves, be of use for clinical genotyping in a sleep clinic.

  8. SNP genotyping technologies

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland

    2013-01-01

    In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons for this is the availabil......In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons...... for this is the availability of high-throughput platforms for multiplexed SNP genotyping. Advancements in these technologies have enabled increased flexibility and throughput, allowing for the generation of adequate SNP marker data at very competitive cost per data point....

  9. Hepatitis C virus genotype 4: Genotype 1's little brother.

    Science.gov (United States)

    Llaneras, J; Riveiro-Barciela, M; Buti, M; Esteban, R

    2017-01-01

    Treatment for hepatitis C virus genotype 4 infection has undergone a major advance over the past 5 years with the emergence of direct-acting antiviral agents. Previously, genotype 4 treatment had been limited to the combination of pegylated interferon and ribavirin, with low rates of sustained virological response. The combinations of new direct-acting agents have resulted in a radical improvement in hepatitis C therapy. Much of the currently available efficacy and safety information in the treatment of genotype 4 has been extrapolated through the results of genotype 1. In this report, we review the efficacy and safety data obtained in recent studies focusing on genotype 4 patients, including special populations, such as those with decompensated cirrhosis. © 2016 John Wiley & Sons Ltd.

  10. Antes das Minas Gerais: conquista e ocupação dos sertões mineiros Before Minas Gerais: conquest and occupation of the captaincy's hinterland

    Directory of Open Access Journals (Sweden)

    Angelo Alves Carrara

    2007-12-01

    Full Text Available Neste artigo passa-se em revista a história da conquista e ocupação das terras do vale do São Francisco, cuja trama há quase um século adquiriu sua versão definitiva na historiografia tradicional, em vários capítulos a respeito a da "expansão geográfica", como em Basílio de Magalhães; ou b da "história territorial", por Felisbelo Freire; ou c dos "caminhos antigos e povoamento do Brasil", como em Capistrano de Abreu, autor que, se não o primeiro, sem dúvida foi o que mais influiu na tessitura do enredo. Aqui, contudo, os objetivos são distintos, apesar de suas fontes arquivísticas permanecerem inescapavelmente as mesmas. Parte-se do pressuposto de que, na segunda metade do século XVII, encerrou-se o processo de conquista do território às tribos indígenas estabelecidas na margem direita do alto-médio São Francisco. Sob esta perspectiva, ao invés de repetir, mais uma vez, a história das expedições ao interior do Brasil, o que aqui se busca é encontrar o lugar que estas expedições ocuparam nesse processo de conquista e ocupação territorial, que logo em seguida tornaram possível a articulação, tanto da costa com os sertões, quanto dos diferentes sertões entre si.This article aims at reviewing the history of the conquest and occupation of the San Francisco river valley, in Minas Gerais. The definite version of which was established more than a century ago, in several chapters concerning a the geographical expansion, as named by Basílio de Magalhaes; or b the territorial history, by Felisbelo Freire; or c the ancient routes and settlement of Brazil, as in Capistrano de Abreu. Here, meanwhile, the objectives are quite different, despite their archival sources be inescapably the same. It is assumed that in the second half of the sixteenth century the process of conquest of the territories occupied by indian tribes settled in the right bank of the San Francisco river had come to an end. Under this prospect, in spite

  11. Comportamento higiênico em colmeias de Apis mellifera L. africanizadas no Sertão da Paraíba

    Directory of Open Access Journals (Sweden)

    F. A. Olinto

    2015-12-01

    Full Text Available A apicultura é uma das poucas atividades agropecuárias que atende aos três requisitos da sustentabilidade: o econômico, o social e o ecológico. Sendo assim, fornece renda para o apicultor, ocupa mão de obra familiar ou contratada e contribui para a preservação da flora nativa. A sanidade pode afetar o desenvolvimento da apicultura, pois a Apis mellifera como qualquer outro organismo vivo, é susceptível a doenças causadas por bactérias, vírus, fungos e outros parasitas e as desordens metabólicas, nutricionais e hormonais, além de intoxicações diversas. Assim, em virtude da necessidade de estudos a respeito da sanidade apícola, objetiva-se estudar o comportamento higiênico em colônias de abelhas Apis mellifera em apiários localizados no Sertão do Estado da Paraíba. A pesquisa foi realizada no período de março, abril e maio de 2014, em cinco apiários localizados nos municípios de Condado, Pombal, Jericó, São Bentinho e São Domingos, ambos situados na Mesorregião do Sertão do Estado da Paraíba, com um total de 25 colmeias avaliadas. O teste de comportamento higiênico foi realizado com base no método de perfuração das células de crias. O percentual de comportamento higiênico foi semelhante em ambos os apiários, principalmente em Condado (93,96%, Pombal (94,30%, Jericó (87,63% e São Domingos (95,20%, ocorrendo apenas uma ligeira diferença no apiário de São Bentinho com uma média de 76,31%. O apiário localizado no município de Pombal obteve o melhor resultado, apresentando índice elevado de comportamento higiênico. Hygienic behavior in Apis mellifera L. africanized hives in the Backlands of ParaibaAbstract: Beekeeping is one of the few agricultural activities that meets the three requirements of sustainability: economic, social and ecological. Therefore, provides income for the beekeeper, occupies family labor or hired and contributes to the preservation of native flora. Sanity may affect the

  12. Imagens cruzadas: exército e sertão na Primeira República Intersecting images: the army and the hinterlands in the First Republic

    Directory of Open Access Journals (Sweden)

    Rogério Rosa Rodrigues

    2012-12-01

    Full Text Available Analisa a proposta político-social do Exército para a nação brasileira na década de 1910. Articula o momento de modernização do Exército com o contexto de avaliação crítica do regime republicano e valorização da corporação militar nos jogos de poder. O método de análise consistiu no cruzamento das fotografias da Guerra do Contestado com os discursos militaristas presentes nos livros escritos por oficiais do Exército, nos artigos publicados na imprensa carioca e nos discursos proferidos por Olavo Bilac em prol do sorteio militar. Foi identificado o desejo do Exército de ligar sertão e litoral, e de adotar a caserna como espaço privilegiado para a formação de cidadãos.The article analyzes the Army's political and social proposal for the Brazilian nation in the 1910s. It considers the Army's climate of modernization in conjunction with the prevailing context of critical evaluation of the republican regime and greater recognition of the role of the armed forces in power games. The analytical method was to cross-reference photographs from the Contestado campaign with militarist discourses found in books authored by Army officers, in articles published in the Rio de Janeiro press, and in Olavo Bilac's speeches in favor of a draft lottery. It was found that the Army wanted to link the hinterlands to the coast and to adopt the barracks as a prime space for forming citizens.

  13. Ocorrência de patógenos em cultivos de melancia e abóbora no sertão da Paraíba

    Directory of Open Access Journals (Sweden)

    M. G. F. O. Soares

    2016-01-01

    Full Text Available Por constituírem uma importante fonte de alimento, plantações de melancia e abóbora são comumente cultivadas no sertão paraibano, porém pouco se sabe sobre a ocorrência de patógenos causadores de doenças, os quais limitam a sua produtividade e renda aos produtores. Visando obter informações sobre a ocorrência dos patógenos virais e fúngicos em cultivos de abóbora e melancia situados em municípios produtores no sertão da Paraíba, amostras coletadas com sintomas de mosaico e deformação foliar, típicos de doenças virais foram analisadas pela técnica sorológica “enzime linked immuno sorbentassay” (Elisa indireto para Papaya ring spot virus, type watermelon (PRSV-W, Watermelon mosaic virus (WMV, Zucchini yellow mosaic virus (ZYMV e Cucumber mosaic virus (CMV. O teste de dupla difusão em Agar foi utilizado para verificar a presença de Squash mosaic virus (SqMV. Em contrapartida, amostras coletadas com sintomas de doenças fúngicas foram analisadas pelo isolamento do patógeno e visualização de suas características morfológicas em microscópio óptico. Em abóbora, houve prevalência dos vírus ZYMV e PRSV-W em infecções simples e mistas, e maior incidência dos fungos Cladosporium spp., e Alternaria spp. Em melancia detectou-se infecção simples e mistas das espécies PRSV-W, WMV e ZYMV, e maior freqüência de Fusarium spp. e Alternaria spp.. Não foram detectados os vírus CMV e SqMV. Os resultados obtidos revelam a ocorrência de vários patógenos fúngicos e viróticos em cultivos de abóbora e melancia situados no sertão da Paraíba e ressaltam a importância da utilização de estratégias de manejo que reduzem os danos ocasionados por esses patógenos.Occurrence of pathogens in watermelon and pumpkin crops in the State of ParaibaAbstract: By constitute an important food source, watermelon and pumpkin plantations are commonly grown on Paraíba backlands, but little is known about the occurrence of disease

  14. HBV Genotypic Variability in Cuba

    Science.gov (United States)

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

    2015-01-01

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

  15. Indução, caracterização bioquímica e ultra-estrutural de calos de aroeira-do-sertão (Myracrodruon urundeuva Fr. All. Induction, biochemical and ultrastructural characterization of the callus of "aroeira-do-sertão" (Myracrodruon urundeuva Fr. All.

    Directory of Open Access Journals (Sweden)

    J.N.C. Vasconcelos

    2012-01-01

    Full Text Available A aroeira-do-sertão (Myracrodruon urundeuva Fr. All. é espécie arbórea que apresenta grande valor econômico devido às propriedades químicas da casca com elevado teor de taninos. Em decorrência da exploração predatória encontra-se inserida na lista oficial de espécies da flora brasileira ameaçadas de extinção na categoria vulnerável. A micropropagação vem sendo colocada como importante forma de multiplicação dessa espécie, na busca de alternativa para a exploração sustentável. Este trabalho foi realizado com o objetivo de induzir calos a partir de segmentos foliares usando 2,4-D e caracterizá-los quanto aos aspectos morfológicos e bioquímicos. Os resultados obtidos indicam que é possível induzir calos a partir de segmentos foliares de aroeira-do-sertão utilizando-se 2,4-diclorofenoxiacético (2,4-D. Os calos obtidos foram compactos e não-embriogênicos, apresentando valores médios de 43,32 mg g-1 de açúcares solúveis totais; 23,62 mg g-1 de açúcares redutores; 3,157 mg g-1 de proteína total; 3,147 mg g-1 de aminoácidos livres e 0,914 mg g-1 de compostos fenólicos totais na matéria fresca."Aroeira-do-sertão" (Myracrodruon urundeuva Fr. All. is a tree species that has great economic value due to the chemical properties of its bark, which has high tannin content. On account of the predatory exploitation it has been placed in the official list of threatened species of the Brazilian flora, in the vulnerable category. Micropropagation has been considered an important form of multiplication of this species in the search for an alternative for its sustainable exploitation. This study was conducted with the aim of inducing callus from leaf segments using 2,4-D and characterizing them according to their morphological and biochemical aspects. The obtained results indicate that it is possible to induce callus from leaf segments of M. urundeuva using 2,4-dichlorophenoxyacetic (2,4-D. The obtained calluses were compact

  16. Genotype Specification Language.

    Science.gov (United States)

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

    2016-06-17

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

  17. Flapjack--graphical genotype visualization.

    Science.gov (United States)

    Milne, Iain; Shaw, Paul; Stephen, Gordon; Bayer, Micha; Cardle, Linda; Thomas, William T B; Flavell, Andrew J; Marshall, David

    2010-12-15

    New software tools for graphical genotyping are required that can routinely handle the large data volumes generated by the high-throughput single-nucleotide polymorphism (SNP) platforms, genotyping-by-sequencing and other comparable genotyping technologies. Flapjack has been developed to facilitate analysis of these data, providing real time rendering with rapid navigation and comparisons between lines, markers and chromosomes, with visualization, sorting and querying based on associated data, such as phenotypes, quantitative trait loci or other mappable features. Flapjack is freely available for Microsoft Windows, Mac OS X, Linux and Solaris, and can be downloaded from http://bioinf.scri.ac.uk/flapjack .

  18. Os Sert?es: un retrato de la locura colectiva

    National Research Council Canada - National Science Library

    Juan Manuel Fernández

    2013-01-01

    ... otros textos de la teoría psiquiátrica o de la literatura nos permitirán sondear la particularidad de las lecturas de Euclides da Cunha sobre la modernidad y su resto, sobre el crimen y la locura...

  19. Subúrbios e veredas - apontamentos para uma leitura comparada dos narradores em Dom Casmurro e Grande sertão: veredas

    Directory of Open Access Journals (Sweden)

    Wilson Madeira Filho

    2000-03-01

    Full Text Available Dois grandes autores, verdadeira unanimidade da crítica literária nacional, Machado de Assis e Guimarães Rosa representam a elaboração de uma escrita repleta de sutilezas, cuja metalinguagem permite desdobramentos na própria interação entre as esferas do autor e a do leitor. A questão da autoria, apresentada com picardia na abertura do Dom Casmurro, refrata-se em jogos interpretativos. No capítulo inicial, o narrador sugere uma bifurcação: de um lado, a biografia possível, de outro lado, a crônica histórico-social com a redação de uma Históriados subúrbios. No fundo, trata-se de um mesmo projeto, posto que ambos, o cidadão e a cidade, projetam-se em suas face tas ocultas; no centro urbano, as vias de acesso via trem da Central do Brasil, articulandoas a rtérias da polis; no homem, os recônditos da alma, a irromper no fluxo de uma memória que se quer centralizadora. Por sua vez, herdandoa perplexidade e tentativa de "atar as pontas da vida", a ascese de Riobaldo confunde-se com a de um grande sertão cujas trilhas compõema trajetória hermética de desvendamento dos contrários, da revelação do Tudo no Nada. A obra de Machado é permeada pelo pessimismode Schopenhauer, narrando-se o desespero de uma vida onde tudo tornou-se vão. A de Rosa, enlaça a admiração inicial de Nietzsche por Schopenhauer para, contudo, reverter esse pessimismo através da teoria do eterno retorno e dos aforismos de Zarathustra, com a alternânciada alegria e do desespero, da criação e da destru ição, do bem e do mal.

  20. Photography as anthropological record of leader females in inland central CearáA fotografia como registro antropológico das mulheres líderes no Sertão Central do Ceará

    Directory of Open Access Journals (Sweden)

    Cristiana Parente

    2007-01-01

    Full Text Available In the last few years, in the inland of Ceará state, changes have occurred in gender relations. Women who find themselves leaders are producing modifications in the history of their communities and contributing to the development of a new culture. Recording the lives of these women through photography as anthropological resource is the objective of this work. It covers the experiences of leader women in the landless settlements of PDHC – Projeto Dom Helder Câmara in the city of Quixeramobim, in central inland Ceará.Nos últimos anos, no sertão do estado do Ceará, tem ocorrido mudanças nas relações de gênero. Mulheres que se descobrem líderes têm transformado a história de suas comunidades e contribuído para o despertar de uma nova cultura. Documentar a realidade destas mulheres, usando a fotografia como registro antropológico, é o objetivo deste trabalho. Ele documenta experiências de mulheres líderes nos assentamentos do PDHC – Projeto Dom Hélder Câmara na cidade de Quixeramobim, no Sertão Central do Ceará.

  1. The equipment supply industry to sugar mills, ethanol and energy in Brazil: an analysis based in leading companies and key-organizations of sector and of LPA of Sertãozinho

    Directory of Open Access Journals (Sweden)

    Michelle Castro Carrijo

    2015-12-01

    Full Text Available This study aims to analyze the profile, organization, efficiency and innovation in the supply industry equipment for sugar mills, ethanol and energy in Brazil, contributing to an important discussion on the competitiveness of this industry. Therefore, the study was based on analysis of information obtained from two surveys: the first held with representative organizations and two industry-leading companies located in the cities of Sertãozinho and Piracicaba; and the second, through interviews with companies in the Local Productive Arrangement (LPA of Sertãozinho, known as the Silicon Valley Ethanol. The results suggest that the increasing modernization of the sector will require greater efforts from equipment industry to provide plants with the necessary technological innovations and potential efficiency gains and that the constituent companies of this industry, few invest in technology and professional training, in other words, are lacking in management training, which leads to loss of valuable opportunities, international market share is tiny, most companies turn to private sources of financing, and companies seem unaware of the real benefits of cooperation, although they appear in most companies in this industry.

  2. Considerações acerca do fracasso escolar em uma escola pública no Alto Sertão da Paraíba

    Directory of Open Access Journals (Sweden)

    Byanca Eugênia Duarte Silva

    2016-10-01

    Full Text Available O estudo realizado a luz das pesquisas dos autores Pio, Dias, Matos e Silva (2009, destaca o fenômeno do fracasso escolar e suas prováveis causas: evasão escolar, repetência e distorção idade-série. Para que a educação seja um direito de todos, como atesta a Constituição Federal (1988, faz-se necessário condições de acesso igualitário e permanência no espaço educacional. Este trabalho tem como objetivo apresentar as causas e consequências a respeito da evasão, repetência e distorção idade-série na escola Maria Guimarães Coêlho, situada no município de Cajazeiras no alto sertão Paraibano. A escolha desta escola se deu em função de ser uma das instituições de ensino com maior índice de distorção idade-série na cidade, segundo informações do Instituto Nacional de Ensino e Pesquisa (INEP. Este estudo trata-se de uma pesquisa descritiva de caráter qualitativo, de modo que para o desenvolvimento da mesma foi utilizado como instrumento para coleta de dados uma entrevista semiestruturada composta por 06 questões subjetivas. Através da análise dos dados, percebe-se que as causas dos fatores que caracterizam o fracasso escolar, voltam-se, principalmente ao fator socioeconômico, levando os alunos a evadirem em busca de trabalho para auxiliar na renda familiar. Conclui-se que há a necessidade de intervenção do governo competente, não apenas em criar estratégias compensatórias, amenizadoras, paliativas, pois para a problemática da evasão e da distorção idade/série, faz-se necessária a implantação de políticas públicas que previnam e reduzam ao máximo este fenômeno que assola parte da atual educação pública do país.Considerations About The School Failure In A Public High School Of Sertão ParaíbaAbstract: The study performed from Pio, Dias, Matos and Silva (2009 researches’ stresses the school failure phenomena and its possible causes: school dropout, retention and age-grade distortion. In

  3. À quoi sert une carte…

    Directory of Open Access Journals (Sweden)

    Baptiste Coulmont

    2006-05-01

    Full Text Available Dans un ouvrage devenu un « classique », Manuel Castells (Castells, 1983 s’aperçoit de la possibilité de matérialiser assez précisément, sur une carte de San Francisco, ce qu’il appelle la « communauté gay », qui a fait de sa visibilité spatiale un marqueur de sa cristallisation politique et sociale. À partir d’éléments tels que la proportion des votes que reçut un candidat gay par bureau de vote, les emplacements des bars homosexuels et des adhérents à la chambre ...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    O'Farrell, Brian; Haase, Jana K; Velayudhan, Vimalkumar; Murphy, Ronan A; Achtman, Mark

    2012-01-01

    Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of 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.

  6. Análise histológica da cicatrização da anastomose colônica, em ratos, sob ação de enema de Aroeira-do-sertão (Myracrodruon urundeuva fr. all. a 10% Histologic analysis of colonic anastomotic healing, in rats, under the action of 10% Aroeira-do-sertão (Myracrodruon urundeuva fr. all. enema

    Directory of Open Access Journals (Sweden)

    Annya Costa Araújo de Macedo Goes

    2005-04-01

    Full Text Available OBJETIVO: Avaliar, do ponto de vista histológico, a ação do extrato aquoso da aroeira-do-sertão na cicatrização da anastomose colônica, em ratos Wistar. MÉTODOS: Foram utilizados 48 ratos da linhagem Wistar, machos, com peso médio de 320g, distribuídos em dois grupos, com 24 animais, cada. Todos os animais foram submetidos à secção transversa completa do cólon descendente, seguida de anastomose colônica. Os ratos do grupo A receberam diariamente no pós-operatório enemas de veículo à base de carboximetilcelulose (CMC. Os animais do grupo B receberam no pós-operatório enemas de extrato aquoso de aroeira-do-sertão a 10% em veículo à base de CMC, até a data da eutanásia. Nas datas 3, 7, 14 e 21 do experimento, seis ratos de cada grupo foram submetidos à remoção de segmento colônico, incluindo a anastomose, destinado à apreciação histológica e análise qualitativa da resposta celular inflamatória e cicatricial. RESULTADOS: A análise morfológica revela diferença significante entre os grupos, no dia 7 (ñ PURPOSE: Evaluate, from a histologic view point, the action of the aqueous extract of aroeira-do-sertão on the healing of colonic anastomosis, in Wistar rats. METHODS: There were used 48 Wistar rats, males, with average weight of 320g, distributed in two groups, with 24 animals, each. All animals were subjected to a complete transverse section of the descending colon, followed by colonic anastomosis. The rats on group A received daily post-operative enemas of carboxymethylcellulose (CMC based vehicle. The animals on group B received post-operative enemas of 10% aqueous extract of aroeira-do-sertão in CMC based vehicle, until the date of euthanasia. On days 3, 7, 14 and 21 of the experiment, six rats in each group were subjected to removal of a colonic segment, including the anastomosis, destined to histological evaluation and qualitative analysis of inflammatory and healing cell response. RESULTS: The

  7. Água de Coco comercializadas no Sertão do Ceará e Paraíba: Imprópria ao consumo

    Directory of Open Access Journals (Sweden)

    Suziane Alves Josino Lima

    2014-10-01

    Full Text Available A água de coco é considerada um isotônico natural, rica em nutrientes e altamente atrativa devido a seu valor nutricional e sabor, com a busca por alimentos saudáveis nos tempos atuais seu consumo tem aumentado consideravelmente principalmente na forma industrializada no Nordeste do Brasil onde se concentram os maiores plantios do coqueiro anão verde, tornando assim indispensável a avaliação da qualidade da água de coco comercializada nesta região. Neste sentido, este trabalho objetivou avaliar a qualidade microbiológica de amostras de água de coco, industrializada e comercializada por duas empresas no sertão paraibano e cearense. Como parâmetros da qualidade microbiológica foram realizadas as seguintes análises: Coliformes Termotolerantes,Salmonella spp/25g, Bolores e Leveduras e contagem de Microrganismos Aeróbios Psicrotróficos nas amostras. A água de coco anão verde comercializada pela indústria A, apresentou resultados de coliformes totais variando de 7 NMP/mL a 1,5 x 102 NMP/mL e < 3 NMP/mL a 7 NMP/mL para coliformes termotolerantes, estes valores oscilaram durante os trintas dias de armazenamento tempo este de validade do produto industrializado. Também foram detectados nas amostras analisadas uma alta contagem de bactérias, nas amostras da água de coco da indústria A armazenada sob-refrigeração, indicando assim possivelmente o uso de matéria prima contaminada, falhas no processamento distribuição e ou armazenamento, estas diretamente relacionadas ao binômio tempo/temperatura insatisfatórios. Os valores encontrados para Bolores e Leveduras variaram de 5,05x102 UFC/mL a 7,6x105 UFC/mL, valores estes considerados elevados, caracterizando a água de coco como imprópria para o consumo quando comparadas á legislação vigente. De acordo com os resultados sugere-se que esta contaminação tenha ocorrido durante a manipulação e ou processamento, uma vez que esta apresenta-se estéril dentro do seu próprio inv

  8. Phenotypic and genotypic screening of rice genotypes at seedling ...

    African Journals Online (AJOL)

    of 11 genotypes was done in hydroponic system using salinized (EC 12 dS/m) nutrient solution. IRRI standard protocol was followed to evaluate salinity tolerance. Large variation in salinity tolerance among the rice germplasms was detected. Plant height and total dry matter of tolerant lines were reduced by 19.0 and 40.6%, ...

  9. In vivo studies of the SERT-selective [{sup 18}F]FPBM and VMAT2-selective [{sup 18}F]AV-133 radiotracers in a rat model of Parkinson's disease

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Julie L. [Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 (United States); Oya, Shunichi; Parhi, Ajit K.; Lieberman, Brian P.; Ploessl, Karl; Hou, Catherine [Department of Radiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 (United States); Kung, Hank F. [Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 (United States); Department of Radiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 (United States)], E-mail: kunghf@sunmac.spect.upenn.edu

    2010-05-15

    Introduction: The utility of [{sup 18}F]FPBM [2-(2'-((dimethylamino)methyl)-4'-(3-[{sup 18}F] -fluoropropoxy)phenylthio)benzenamine], a selective serotonin transporter (SERT) tracer, and [{sup 18}F]AV-133 [(+)-2-Hydroxy-3-isobutyl-9-(3-fluoropropoxy)-10-methoxy-1,2,3,4,6, 7-hexahydro-11bH-benzo[a]quinolizine], a selective vesicular monoamine transporter 2 (VMAT2) tracer, were tested in the 6-hydroxydopamine (6-OHDA) unilateral lesioned rat model. Methods: Positron emission tomography (PET) imaging of three 6-OHDA unilateral lesioned male Sprague Dawley rats (Rats 1-3) were performed with [{sup 18}F]FPBM and [{sup 18}F]AV-133 to examine whether changes in SERT and VMAT2 binding, respectively, could be detected in the brain. The brains of the three rats were then removed and examined by in vitro autoradiography with [{sup 18}F]FPBM and the dopamine transporter ligand, [{sup 125}I]IPT [N-(3'-[{sup 125}I]-iodopropen-2'-yl)-2-beta-carbomethoxy-3-beta-(4-chloro phenyl) tropane, for confirmation. Biodistribution of [{sup 18}F]FPBM in a separate group of p-chloroamphetamine (PCA) treated rats were also performed. Results: PET image analysis showed varying levels of SERT binding reduction (Rat 1=-11%, Rat 2=-4%, Rat 3=-43%; n=2) and a clear and definitive loss of VMAT2 binding (Rat 1=-87%, Rat 2=-72%, and Rat 3=-91%; n=1) in the left striatum when compared to the right (non-lesioned side) striatum. The results from PET imaging were corroborated with quantitative in vitro autoradiography. Rats treated with a selective serotonin toxin (p-chloroamphetamine) showed a significant reduction of [{sup 18}F]FPBM uptake in the cortex and hypothalamus regions of the brain. Conclusion: The preliminary data suggest that [{sup 18}F]FPBM and [{sup 18}F]AV-133 may be useful for the examination of serotonergic and dopaminergic neuron integrity, respectively, in the living brain.

  10. Genotype networks in metabolic reaction spaces

    Science.gov (United States)

    2010-01-01

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

  11. Pooled DNA genotyping on Affymetrix SNP genotyping arrays

    Directory of Open Access Journals (Sweden)

    Owen Michael J

    2006-02-01

    Full Text Available Abstract Background Genotyping technology has advanced such that genome-wide association studies of complex diseases based upon dense marker maps are now technically feasible. However, the cost of such projects remains high. Pooled DNA genotyping offers the possibility of applying the same technologies at a fraction of the cost, and there is some evidence that certain ultra-high throughput platforms also perform with an acceptable accuracy. However, thus far, this conclusion is based upon published data concerning only a small number of SNPs. Results In the current study we prepared DNA pools from the parents and from the offspring of 30 parent-child trios that have been extensively genotyped by the HapMap project. We analysed the two pools with Affymetrix 10 K Xba 142 2.0 Arrays. The availability of the HapMap data allowed us to validate the performance of 6843 SNPs for which we had both complete individual and pooled genotyping data. Pooled analyses averaged over 5–6 microarrays resulted in highly reproducible results. Moreover, the accuracy of estimating differences in allele frequency between pools using this ultra-high throughput system was comparable with previous reports of pooling based upon lower throughput platforms, with an average error for the predicted allelic frequencies differences between the two pools of 1.37% and with 95% of SNPs showing an error of Conclusion Genotyping thousands of SNPs with DNA pooling using Affymetrix microarrays produces highly accurate results and can be used for genome-wide association studies.

  12. SCREENING SOYBEAN GENOTYPES FOR PROMISCUOUS ...

    African Journals Online (AJOL)

    ACSS

    2016-02-25

    Feb 25, 2016 ... symbiotic association with Bradyrhizobium sp. in order to identify genotypes with potential to be used as parents to initiate a breeding ... 5N as potential parental materials for subsequent breeding work. Key Words: Glycine max, nodules, ..... Journal of Systematic and Evolutionary. Microbiology50: 225-234.

  13. (Nigella sativa L.) genotypes from

    African Journals Online (AJOL)

    ajl yemi

    2011-10-26

    Oct 26, 2011 ... nutritional characteristics revealed five distinct clusters with genotypes which were markedly different. Thus, all clusters were ... Key words: Biodiversity, black seed, cluster analyses, kalonji, physico-chemical traits, principal components' analysis. ...... industry and thus may enhance farmers' productivity.

  14. Microsatellite genotyping of carnation varieties

    NARCIS (Netherlands)

    Smulders, M.J.M.; Noordijk, Y.; Rus-Kortekaas, W.; Bredemeijer, G.M.M.; Vosman, B.

    2003-01-01

    A set of 11 sequence-tagged microsatellite markers for carnation (Dianthus caryophyllus) was developed using a DNA library enriched for microsatellites. Supplemented with three markers derived from sequence database entries, these were used to genotype carnation varieties using a semi-automated

  15. FTO genotype and weight loss

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...

  16. SCREENING SOYBEAN GENOTYPES FOR PROMISCUOUS ...

    African Journals Online (AJOL)

    ACSS

    2016-02-25

    Feb 25, 2016 ... The current low soybean (Glycine max L. Merrill) yields in Sub-Saharan Africa can be alleviated by developing promiscuous genotypes. The research trend in Africa is towards developing promiscuous varieties for less labour and high yields in soybean production. A greenhouse experiment was conducted ...

  17. A obra de Euclides da Cunha e os debates sobre mestiçagem no Brasil no início do século xx: Os sertões e a medicina- antropologia do Museu Nacional The work of Euclides da Cunha and debates on racial admixture in Brazil in the early 20th century: Os sertões and the field of medicine- anthropology at the Museu Nacional

    Directory of Open Access Journals (Sweden)

    Ricardo Ventura Santos

    1998-07-01

    Full Text Available Este trabalho aborda certas interfaces entre a obra de Euclides da Cunha, e Os sertões em particular, e a medicina-antropologia no Brasil no início do século XX. Aponta-se que à obra euclidiana podem ser vinculadas duas vertentes médico-antropológicas que construíram explicações divergentes acerca das conseqüências da composição racial brasileira, em especial quanto à viabilidade de uma nação mestiça. Uma primeira, cujo expoente foi Raimundo Nina Rodrigues, esteve alinhada com uma perspectiva mais próxima de um fatalismo racial. Uma outra, representada por Edgard Roquette-Pinto, ligado ao Museu Nacional, argumentava que os mestiços não seriam orgânica ou racialmente inviáveis. No texto é analisada sobretudo a interpretação que a medicina-antropologia do Museu Nacional realizou da obra euclidiana.The article addresses certain interfaces between Euclides da Cunha’s work - particularly Os sertões - and medicine-anthropology in Brazil in the early 20th century. Cunha’s work can be tied in with two lines of thought in the field of medicine-anthropology, each of which constructed its own view of the consequences of Brazil’s racial make-up, especially regarding the viability of a mestizo nation. One of these lines, supported by Raimundo Nina Rodrigues, among others, leaned more towards racial fatalism. The other, represented by Edgard Roquette-Pinto of the Museu Nacional, argued that mestizos were neither organically nor racially inviable. The text is concerned above all with the interpretation of Cunha’s work proposed by those in the field of medicine- anthropology at the Museu Nacional.

  18. Univariate stability analysis methods for determining genotype ...

    African Journals Online (AJOL)

    However, superior genotypes are recommended for use by farmers in semi-arid areas. Finally, based on most statistics, mean yield and dynamic concept of stability genotype G13 was stable and favorable and is recommended for national release in rain-fed lands of Iran. Regression method's slopes, genotypic stability (D2) ...

  19. Genetic relationships among Ethiopian mustard genotypes based ...

    African Journals Online (AJOL)

    Genetic relationships among Ethiopian mustard genotypes based on oil content and fatty acid composition. ... Quantification and classification of genetic diversity among genotypes is essential for parental selection in breeding programs. The objective of this study was to classify and cluster Ethiopian mustard genotypes ...

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

    African Journals Online (AJOL)

    Dry yield and yield components from 6 multilocational trials of cassava genotypes conducted for 3 years in Nigeria were used to study the nature and magnitude of genotype x environment (G x E) interaction and to determine the optimum resource allocation for cassava yield trials. The effects of environment, genotype and G ...

  1. Compensatory and Susceptive Responses of Cowpea Genotypes...

    African Journals Online (AJOL)

    User

    turing genotypes of cowpea. Control of aphid's infestation in early maturing cowpea genotypes should not be delayed up to two weeks after infestation (28 days after planting) to avoid yield loss. Aphid infestation period for studies in susceptive response in medium to late matur- ing genotypes should go beyond 28 days after.

  2. Compensatory and Susceptive Responses of Cowpea Genotypes...

    African Journals Online (AJOL)

    User

    the seedlings of cowpea and causes direct dam- age on the crop by sucking ... Description of the 10 genotypes of cowpea by parentage or source. Genotype. Description. APAGBAALA. Prima/TVu. 4552/California. Blackeye. No.5//7977. Cultivar, released in ... genotypes started showing symptoms of dam- age. When the ...

  3. FTO genotype and weight loss

    DEFF Research Database (Denmark)

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

    2016-01-01

    : 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...... well to dietary, physical activity, or drug based weight loss interventions and thus genetic predisposition to obesity associated with the FTO minor allele can be at least partly counteracted through such interventions. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42015015969.......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 SOURCES...

  4. Two-mode clustering of genotype by trait and genotype by environment data

    NARCIS (Netherlands)

    Hageman, J.A.; Malosetti, M.; Eeuwijk, van F.A.

    2012-01-01

    In this paper, we demonstrate the use of two-mode clustering for genotype by trait and genotype by environment data. In contrast to two separate (one mode) clusterings on genotypes or traits/environments, two-mode clustering simultaneously produces homogeneous groups of genotypes and

  5. Quantifying uncertainty in genotype calls.

    Science.gov (United States)

    Carvalho, Benilton S; Louis, Thomas A; Irizarry, Rafael A

    2010-01-15

    Genome-wide association studies (GWAS) are used to discover genes underlying complex, heritable disorders for which less powerful study designs have failed in the past. The number of GWAS has skyrocketed recently with findings reported in top journals and the mainstream media. Microarrays are the genotype calling technology of choice in GWAS as they permit exploration of more than a million single nucleotide polymorphisms (SNPs) simultaneously. The starting point for the statistical analyses used by GWAS to determine association between loci and disease is making genotype calls (AA, AB or BB). However, the raw data, microarray probe intensities, are heavily processed before arriving at these calls. Various sophisticated statistical procedures have been proposed for transforming raw data into genotype calls. We find that variability in microarray output quality across different SNPs, different arrays and different sample batches have substantial influence on the accuracy of genotype calls made by existing algorithms. Failure to account for these sources of variability can adversely affect the quality of findings reported by the GWAS. We developed a method based on an enhanced version of the multi-level model used by CRLMM version 1. Two key differences are that we now account for variability across batches and improve the call-specific assessment of each call. The new model permits the development of quality metrics for SNPs, samples and batches of samples. Using three independent datasets, we demonstrate that the CRLMM version 2 outperforms CRLMM version 1 and the algorithm provided by Affymetrix, Birdseed. The main advantage of the new approach is that it enables the identification of low-quality SNPs, samples and batches. Software implementing of the method described in this article is available as free and open source code in the crlmm R/BioConductor package. Supplementary data are available at Bioinformatics online.

  6. [Molecular genotyping: development and limits].

    Science.gov (United States)

    Delpech, M

    2003-06-01

    Kits dedicated to molecular genotyping are now commercially available and are routinely used for diagnosis purpose. In the future these kits that use the classical reverse dot-blot approach will be replaced by micro-arrays, DNA chips and Labs on a chip. Some systems and DNA chips designed for medical diagnosis are already available. The present main problem is their very high cost.

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

    Science.gov (United States)

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

    2016-08-05

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

  8. Development of genotype-specific primers for differentiation of genotypes A and B of Aichi viruses.

    Science.gov (United States)

    Pham, Ngan Thi Kim; Trinh, Quang Duy; Nguyen, Tuan Anh; Dey, Shuvra Kanti; Phan, Tung Gia; Hoang, Le Phuc; Khamrin, Pattara; Maneekarn, Niwat; Okitsu, Shoko; Mizuguchi, Masashi; Ushijima, Hiroshi

    2009-03-01

    A nested polymerase chain reaction method using genotype-specific primers based on the capsid gene was developed to differentiate between genotypes A and B of Aichi viruses. Results of the study showed that the PCR using newly designed genotype-specific primers could generate appropriate PCR products from all 17 samples tested, the newly developed primers could differentiate genotype A from genotype B, and all matched those obtained by nucleotide sequencing of the capsid regions. The nested PCR method using genotype-specific primers is useful and can be used for genotyping of Aichi viruses isolated from epidemiological studies.

  9. Estimativas de tendências e parâmetros genéticos do peso padronizado aos 378 dias de idade, medidas corporais e perímetro escrotal de machos Nelore de Sertãozinho, SP Estimates of genetic parameters and trends for body weight at 378 days, body measurements and scrotal circumference of Sertãozinho Nellore males

    Directory of Open Access Journals (Sweden)

    Joslaine Noely dos Santos Gonçalves Cyrillo

    2001-02-01

    Full Text Available Os objetivos deste estudo foram estimar as tendências e os parâmetros genéticos e fenotípicos do peso padronizado aos 378 dias de idade (P378, medidas corporais e perímetro escrotal de machos Nelore, pertencentes às populações selecionadas e controle da Estação Experimental de Zootecnia de Sertãozinho. As herdabilidades, estimadas considerando-se modelo de touro e modelo animal, foram, respectivamente, 0,53±0,12 e 0,36 para P378; 0,38±0,11 e 0,58 para altura na garupa; 0,31±0,10 e 0,10 para perímetro torácico; 0,40± 0,11 e 0,13 para comprimento do corpo; 0,39±0,11 e 0,30 para comprimento do dorso; 0,33±0,10 e 0,12 para comprimento da garupa; 0,08± 0,07 e 0,14 para distância de ísquios; 0,23±0,09 e 0,08 para distância de íleos e 0,57±0,13 e 0,44 para perímetro escrotal. A correlação genética mais alta entre P378 e medidas corporais foi encontrada para perímetro torácico (0,86 ± 0,08; as demais variaram de 0,46 a 0,72. Os resultados deste estudo mostraram que, em função dos valores médios a altos das herdabilidades estimadas para P378 e da maioria das características de medidas do corpo dos animais, houve considerável variação genética aditiva nesses atributos. Além disso, devido às altas correlações genéticas de P378 com a maioria das características, pode-se concluir ser bastante provável que grande parte dos genes que controlam o peso pós-desmame também seja responsável pelo desenvolvimento das diferentes regiões do corpo de machos Nelore. A magnitude desses parâmetros justifica a tendência genética positiva nas características de seleção direta e nas secundárias.The objectives of this study were to estimate the genetic trends and also the genetic and phenotypic parameters for body weight at 378 days (W378, body measurements and scrotal circumferences of Nellore males from selected and control populations of the Estação Experimental de Zootecnia de Sertãozinho (SP, Brazil. The

  10. Mineralogia, micromorfologia e gênese de solos planossólicos do Sertão do Araripe, estado de Pernambuco Mineralogy, micromorphology and genesis of soils with stagnic properties from Sertão of Araripe, Pernambuco State, Brazil

    Directory of Open Access Journals (Sweden)

    L. B. Oliveira

    2004-08-01

    Full Text Available Neste trabalho, objetivou-se realizar a caracterização mineralógica e micromorfológica de solos planossólicos do Sertão do Araripe, estado de Pernambuco, visando proporcionar melhor entendimento de suas propriedades e dos processos envolvidos em sua gênese. Tais solos foram, até então, pouco estudados e se caracterizam pela ocorrência de um horizonte B plânico subjacente a um horizonte B textural, plíntico ou não. No município de Ouricuri, foram selecionados três perfis representativos destes solos, classificados como: Plintossolo Argilúvico eutrófico planossólico sódico (perfil 1; Argissolo Amarelo eutrófico planossólico solódico (perfil 2 e Argissolo Amarelo eutrófico plíntico planossólico sódico (perfil 3. A mineralogia das frações calhau e cascalho foi determinada macroscopicamente, enquanto a da areia, por lupa binocular. As frações silte e argila foram analisadas por difratometria de raios X. As descrições micromorfológicas foram realizadas em seções delgadas de amostras de horizontes selecionados. A fração areia destes solos é essencialmente composta por quartzo, mas feldspatos e mica também ocorrem a partir do horizonte 2Btbn. O silte é basicamente constituído por quartzo, feldspatos e mica. A argila é composta por caulinita, mica, interestratificados irregulares, esmectita e quartzo, ocorrendo as maiores quantidades de esmectita e interestratificados nos horizontes 2Btbn e 2BCn. O horizonte B plânico (2Btbn apresenta microestrutura em blocos angulares e expressivos argilãs (de iluviação e intemperização, enquanto o horizonte Bt sobrejacente apresenta microestrutura granular e ausência de qualquer tipo de argilã. A disparidade observada na mineralogia da fração argila e as distintas feições micromorfológicas corroboram a identificação de uma mudança de material de origem entre os horizontes Bt e B plânico dos solos estudados. A posição do horizonte B plânico, que apresenta

  11. Decoding noises in HIV computational genotyping.

    Science.gov (United States)

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

    2017-11-01

    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.

  12. O desafio da formação de auxiliares de biblioteca no Brasil: relato de uma experiência pioneira de educação profissional no sertão paraibano

    Directory of Open Access Journals (Sweden)

    Jobson Louis Santos de Almeida

    2015-04-01

    Full Text Available http://dx.doi.org/10.5007/1518-2924.2015v20n42p132 Relata uma experiência inédita de interiorização da educação profissional no sertão paraibano voltada para o contexto da formação de trabalhadores para bibliotecas, ocorrida no âmbito do Programa de Acesso ao Ensino Técnico e Emprego (PRONATEC ofertado pelo Instituto Federal da Paraíba – Campus Sousa. Descreve-se o perfil e as características particulares do curso Auxiliar de Biblioteca no supracitado contexto social e geográfico. Trata-se de uma pesquisa participante comunicada na forma de relato de experiência. Utilizou-se da pesquisa documental tanto para descrever com rigor e detalhes o perfil do curso analisado, quanto para elucidar as oportunidades de emprego no serviço público para tal segmento. A pesquisa bibliográfica possibilitou a contextualização e fundamentação teórica da abordagem. E a partir dos dados coletados, descritos e analisados foi possível refletir criticamente acerca do potencial dos cursos de formação inicial e continuada para a geração de oportunidades de emprego, transformação cultural e inclusão social. O estudo aponta para novos cenários e novas perspectivas de atuação do bibliotecário como agente socialmente responsável por projetos educativos. Conclui-se que a oferta de cursos de formação de auxiliares de biblioteca em regiões longínquas dos centros urbanos financeiros do país, tal como é o sertão paraibano, além de formar profissionais qualificados para atuarem em bibliotecas, possibilita a disseminação da cultura do livro, da leitura e das bibliotecas, inerente à responsabilidade social da Biblioteconomia e da Ciência da Informação.

  13. Morbidade da doença de Chagas em áreas do Sertão da Paraíba e da Caatinga do Piauí

    Directory of Open Access Journals (Sweden)

    José Rodrigues Coura

    1996-04-01

    Full Text Available Foram estudados 186 pares de indivíduos sorologicamente positivos e negativos para infecção chagásica, da mesma idade e sexo, do Sertão da Paraíba e 200 indivíduos também sorologicamente positivos nos municípios de Oeiras e Colônia do Piauí. Depois de confirmados por pelo menos dois outros testes sorológicos: imunofluorescência indireta quantitativa, ELISA, hemaglutinação ou fixação do complemento,foi feito o exame clínico, eletrocardiográfico e radiológico nos indivíduos selecionados para o estudo exenodiagnóstico, hemocultura e PCR em amostras representativas dos casos soropositivos. As manifestações clínicas predominantes entre os soropositivos em ambas as áreas foram palpitações, dispnéia aos esforços, disfagia, odinofagia, pirose e obstipação. As freqüências das alterações eletrocardiográficas sugestivas da doença de Chagas foram, respectivamente, na Paraíba e no Piauí: BAV = 3,8 % e 2 %, BRD III = 6,4 % e 7 %, BRD III + HBAE = 10,7 % e 10,5 % e extra-sístoles ventriculares complexas = 2,7 % e 3,% . O xenodiagnóstico foi positivo em 13 % dos casos soropositivos da Paraíba e em 34 % dos casos do Piauí, enquanto que o PCR foi positivo, respectivamente, em 44,6 e 59,5 %. A hemocultura realizada apenas no Piauí foi positiva em 25,7 % dos casos estudados. Foram realizados inquéritos triatomínicos em 132 domicílios e peridomicílios no Sertão da Paraíba e em 159 na Caatinga do Piauí, sendo capturados 16 exemplares de T. brasiliensis não infectados no peridomicílio na Paraíba e 750 exemplares no Piauí, dos quais 625 foram examinados: 49 de T. pseudomaculata não infectados com T. cruzi (19 no intradomicílio e 30 no peridomicílio e 576 de T. brasiliensis (371 no intradomicílio e 205 no peridomicílio entre os quais 32 (5,5% estavam infectados com T. cruzi (31 no intradomicílio e um no peridomicílio.

  14. Heterogeneous recombination among Hepatitis B virus genotypes.

    Science.gov (United States)

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

    2017-10-01

    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.

  15. Coxiella burnetii Genotypes in Iberian Wildlife.

    Science.gov (United States)

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

    2016-11-01

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

  16. Additional novel Cryptosporidium genotypes in ornamental fishes.

    Science.gov (United States)

    Morine, M; Yang, R; Ng, J; Kueh, S; Lymbery, A J; Ryan, U M

    2012-12-21

    Current knowledge on the prevalence and genotypes of Cryptosporidium in fishes is still limited. This study investigated the prevalence of Cryptosporidium species in 171 ornamental fishes, belonging to 33 species, collected from 8 commercial aquariums around Perth, Western Australia. All samples were screened by nested PCR targeting the 18S rRNA locus. A total of 6 positives were identified by PCR at the 18S locus from 4 different species of fishes (red eye tetra, Moenkhausia sanctaefilomenae; gold gourami, Trichogaster trichopterus; neon tetra, Paracheirodon innesi; goldfish, Carassius auratus auratus), giving an overall prevalence of 3.5% (6/171). Four different genotypes were identified, only one of which has been previously reported in fish; piscine genotype 4 in a neon tetra isolate, a rat genotype III-like isolate in a goldfish, a novel genotype in three isolates from red eye (piscine genotype 7) which exhibited a 3.5% genetic distance from piscine genotype 1 and a piscine genotype 6-like from a gold gourami (1% genetic distance). Further biological and genetic characterisation is required to determine the relationship of these genotypes to established species and strains of Cryptosporidium. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Avaliação da composição físico-química de polpas de frutas comercializadas em cinco cidades do Alto Sertão paraibano

    Directory of Open Access Journals (Sweden)

    Thamirys L. S. Lima

    2015-06-01

    Full Text Available O crescimento da indústria de frutas tem se baseado, em grande parte, à produção de polpas de frutas congeladas, a qual surge como uma alternativa de baixo custo para viabilizar a oferta de frutos nos períodos de safra e entressafra. O desenvolvimento desse mercado é resultado da produção de polpas congeladas por micro e pequenas empresas, muitas vezes implantadas com o intuito de melhorar a renda familiar de pequenos produtores rurais. A polpa de fruta comercializada deve apresentar características físicas, químicas e sensoriais similares da fruta in natura, bem como apresentar-se microbiológica mente segura e ainda deve atender aos padrões exigidos pela legislação brasileira vigente. Neste contexto, este trabalho tem como objetivo avaliar parâmetros físico-químicos (umidade, cinzas, acidez titulável, pH, sólidos solúveis em °Brix, determinação da relação SS/AT, açúcares redutores e ácido ascórbico em quinze polpas de frutas de diferentes sabores comercializadas em cinco cidades do sertão paraibano. Os resultados obtidos nesta pesquisa mostraram que 70% das polpas de frutas analisadas encontram-se de acordo com a legislação brasileira vigente.

  18. Quando morre a flor do sertão: figuração da morte em “Buriti” de João Guimarães Rosa

    Directory of Open Access Journals (Sweden)

    Sarah Maria Forte Diogo

    2008-12-01

    Full Text Available Este artigo tem por objetivo estudar de que modo é figurada a morte da personagem Maria Behú, de “Buriti”, Noites do sertão (1956, de João Guimarães Rosa e os símbolos que a ela se agregam. Para tanto, investigamos as focalizações narrativas que incidem sobre Behú, construindo sua imagem como beata, assexuada, atuante na esfera da metafísica, sendo a sua morte o início da intensa vivência da sexualidade pelos demais personagens. “Buriti” narra a estória dos habitantes da fazenda Buriti Bom e daqueles que por lá transitam e as mudanças que ocasionam na vida uns dos outros. Behú é a personagem que mais contrasta com o ambiente, pois dele difere por não apresentar marcas de erotismo ou vida plena. Behú funciona na novela como guardiã da tradição e da cultura, seus usos e seus costumes, estilizados pela linguagem roseana.Palavras-chave: João Guimarães Rosa; Cultura; Linguagem; Morte; Tradição.

  19. Anticorpos contra vírus do grupo da língua azul em caprinos e ovinos do sertão de Pernambuco e inferências sobre sua epidemiologia em regiões semiáridas

    Directory of Open Access Journals (Sweden)

    I.O. Mota

    2011-12-01

    Full Text Available The prevalence of antibodies against bluetongue virus was investigated in 41 dairy goats and 40 sheep herds in the semi-arid region of Pernambuco state and the conditions for insect Culicoides maintenance, considering climate dynamics and vector competence, were evaluated. The percents of seropositive herds in agar gel immunodiffusion test for bluetongue virus group were 24 for goats and 27.5 for sheep. The estimated prevalences of seropositive animals were 3.9% for goats (n = 410 and 4.3% for sheep (n = 400. The prevalences of seropositive animals were low in the mesoregion of Sertão Pernambucano (4.8% for goats and 4.1% for sheep and São Francisco Pernambucano (1.0% for goats and 4.5% for sheep. There were no significant differences between species and regions. Considering the social and economic importance of goats and sheep raising in the semi-arid region, it is essential to establish preventive measures to control imports of ruminants from these areas.

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

    African Journals Online (AJOL)

    enoh

    2012-03-29

    Mar 29, 2012 ... Selangor, Malaysia. Accepted 4 March, 2011. A banana germplasm was established containing 44 Musa genotypes collected from various locations in Malaysia. To detect ... number of new species in Malaysia has increased recently. ..... markers where nine primers allowed discrimination of all genotypes.

  1. AFLP analysis among Ethiopian arabica coffee genotypes ...

    African Journals Online (AJOL)

    African Journal of Biotechnology ... The genetic relationship of 28 Coffea arabica genotypes from Ethiopia was assessed using 10 Amplified ... All genotypes were independently distinguished and did not cluster according to collection region, demonstrating the presence of coffee genetic resource diversity within each region ...

  2. Phenotype and genotype differentiation between flathead grey ...

    African Journals Online (AJOL)

    This study aimed to study the phenotype and genotype differentiation and to compare the amount of differences in phenotype based on morphometric character indices and meristic counts with the amount of differences in genotype based on random amplified polymorphic DNA (RAPD) fingerprinting between two Mugilidae, ...

  3. Disentangling pooled triad genotypes for association studies.

    Science.gov (United States)

    Shi, Min; Umbach, David M; Weinberg, Clarice R

    2014-09-01

    Association studies that genotype affected offspring and their parents (triads) offer robustness to genetic population structure while enabling assessments of maternal effects, parent-of-origin effects, and gene-by-environment interaction. We propose case-parents designs that use pooled DNA specimens to make economical use of limited available specimens. One can markedly reduce the number of genotyping assays required by randomly partitioning the case-parent triads into pooling sets of h triads each and creating three pools from every pooling set, one pool each for mothers, fathers, and offspring. Maximum-likelihood estimation of relative risk parameters proceeds via log-linear modeling using the expectation-maximization algorithm. The approach can assess offspring and maternal genetic effects and accommodate genotyping errors and missing genotypes. We compare the power of our proposed analysis for testing offspring and maternal genetic effects to that based on a difference approach and that of the gold standard based on individual genotypes, under a range of allele frequencies, missing parent proportions, and genotyping error rates. Power calculations show that the pooling strategies cause only modest reductions in power if genotyping errors are low, while reducing genotyping costs and conserving limited specimens. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

  4. genotype by environment interaction of advanced generation

    African Journals Online (AJOL)

    facilitating a rapid response to selection. This multi-environment trial (MET) used. Additive Main effects and Multiplicative. Interactions (AMMI) and Genotype main effects plus genotype-by-environment interaction (GGE) to (i) determine the adaptability and stability of advanced generation soybean breeding lines in different ...

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

    African Journals Online (AJOL)

    Genetic relationship among Musa genotypes revealed by microsatellite markers. NAP Abdullah, GB Saleh, ETS Putra, ZB Wahab. Abstract. 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 ...

  6. Genomic evaluations with many more genotypes

    Directory of Open Access Journals (Sweden)

    Wiggans George R

    2011-03-01

    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

  7. Hepatitis C virus genotypes in Tirana, Albania.

    Science.gov (United States)

    Haldeda, Migena; Baume, Julien; Tamalet, Catherine; Bizhga, Melpomeni; Colson, Philippe

    2014-01-01

    Hepatitis C virus (HCV) infection is a worldwide concern. Knowledge of the HCV genotype is clinically important because it predicts the rate of response to therapy and guides the treatment duration. Moreover, it allows molecular epidemiology to be performed. To our knowledge, the prevalence of HCV genotypes has been assessed only once in Albania, using a line probe genotyping assay. We determined HCV genotypes by population sequencing of HCV-infected patients in Tirana, Albania. HCV genotype and sequence analyses were performed for serum samples collected from January 2011 through May 2012 from 61 HCV-seropositive patients using population sequencing of the NS3 protease gene and alternatively the NS5b gene and the 5' untranslated region (UTR). HCV RNA was retrieved from the blood samples of 50 patients. The HCV NS3 protease gene was sequenced for 28 patients and NS5b and/or 5'UTR fragments were sequenced for an additional 22 patients. The predominant genotype was 1b in 25 patients (50%), followed by genotypes 2c, 4a, 3a, and 1a in 18%, 14%, 8%, and 6% of cases, respectively. Best matches for these HCV RNAs in GenBank were obtained in different countries worldwide. One NS3 protease naturally harbored an amino acid conferring minor drug resistance to newly available HCV protease inhibitors. In conclusion, HCV-1b was predominant in the present Albanian population, as in southeastern Europe. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

  8. Structural properties of genotype-phenotype maps.

    Science.gov (United States)

    Ahnert, S E

    2017-07-01

    The map between genotype and phenotype is fundamental to biology. Biological information is stored and passed on in the form of genotypes, and expressed in the form of phenotypes. A growing body of literature has examined a wide range of genotype-phenotype (GP) maps and has established a number of properties that appear to be shared by many GP maps. These properties are 'structural' in the sense that they are properties of the distribution of phenotypes across the point-mutation network of genotypes. They include: a redundancy of genotypes, meaning that many genotypes map to the same phenotypes, a highly non-uniform distribution of the number of genotypes per phenotype, a high robustness of phenotypes and the ability to reach a large number of new phenotypes within a small number of mutational steps. A further important property is that the robustness and evolvability of phenotypes are positively correlated. In this review, I give an overview of the study of GP maps with particular emphasis on these structural properties, and discuss a model that attempts to explain why these properties arise, as well as some of the fundamental ways in which the structure of GP maps can affect evolutionary outcomes. © 2017 The Author(s).

  9. Helicobacter pylori Genotypes May Determine Gastric Histopathology

    Science.gov (United States)

    Nogueira, Cristina; Figueiredo, Céu; Carneiro, Fátima; Taveira Gomes, António; Barreira, Raul; Figueira, Paulo; Salgado, Céu; Belo, Luis; Peixoto, António; Bravo, Juan C.; Bravo, Luis E.; Realpe, Jose L.; Plaisier, Anton P.; Quint, Wim G. V.; Ruiz, Bernardo; Correa, Pelayo; van Doorn, Leen-Jan

    2001-01-01

    The outcome of Helicobacter pylori infection has been associated with specific virulence-associated bacterial genotypes. The present study aimed to investigate the gastric histopathology in Portuguese and Colombian patients infected with H. pylori and to assess its relationship with bacterial virulence-associated vacA, cagA, and iceA genotypes. A total of 370 patients from Portugal (n = 192) and Colombia (n = 178) were studied. Corpus and antrum biopsy specimens were collected from each individual. Histopathological features were recorded and graded according to the updated Sydney system. H. pylori vacA, cagA, and iceA genes were directly genotyped in the gastric biopsy specimens by polymerase chain reaction and reverse hybridization. Despite the significant differences between the Portuguese and Colombian patient groups, highly similar results were observed with respect to the relation between H. pylori genotypes and histopathology. H. pylori vacA s1, vacA m1, cagA+ genotypes were significantly associated with a higher H. pylori density, higher degrees of lymphocytic and neutrophilic infiltrates, atrophy, the type of intestinal metaplasia, and presence of epithelial damage. The iceA1 genotype was only associated with epithelial damage in Portuguese patients. These findings show that distinct H. pylori genotypes are strongly associated with histopathological findings in the stomach, confirming their relevance for the development of H. pylori-associated gastric pathology. PMID:11159201

  10. Entre reses e almas: questões sobre urbanização, arquitetura e arte das missões jesuíticas dos sertões das capitanias do norte

    Directory of Open Access Journals (Sweden)

    Esdras Arraes

    2015-02-01

    Full Text Available O povoamento e a instituição da rede urbana dos sertões das capitanias do Norte surgiram com o apoio régio ao duplo movimento realizado por criadores de gado e missionários, a partir de meados do século 17. Sendo assim, este ensaio busca interpretar, por meio de evidências materiais, como os encontros - simbióticos e/ou conflituosos - entre pecuária e catequese jesuítica estruturaram os fenômenos urbano, arquitetônico e artístico, em uma região considerada pela historiografia clássica como “periférica” aos interesses políticos da Coroa Portuguesa. Interpretaremos, no território, como as estratégias de conversão do indígena criaram uma malha de aldeamentos missioneiros precisamente locados na área. Ainda apontaremos, em linhas gerais, como as edificações jesuíticas seguiram modelos formais encontrados nos principais centros de irradiação cultural da colônia e da Europa. Sem esquecer, portanto, a consideração que tiveram os padres em “dialogar” tais arquiteturas com os condicionantes geográficos, naturais e sociais daquelas vastidões.

  11. Análise da Relação Entre Produção Agroecológica, Resiliência e Reprodução Social da Agricultura Familiar no Sertão do Araripe

    Directory of Open Access Journals (Sweden)

    Cecilia Tayse Muniz Teixeira

    Full Text Available Resumo: Este trabalho analisa os sistemas de produção de base agroecológica familiar frente à situação de estiagem prolongada, considerando a sua capacidade de promover resiliência como requisito essencial para a manutenção do sistema produtivo e para a reprodução social da agricultura familiar. A questão da segurança alimentar, tomando como referência a capacidade de armazenamento e de diversificação da produção nos sistemas agroecológicos, também constitui fonte de interesse dessa pesquisa. Para isso, estabeleceu-se, como referência empírica, a análise de dois sistemas agroflorestais, um quintal produtivo e um roçado agroecológico, situados no território do sertão do Araripe e assessorados pelo Caatinga. Os casos foram ilustrativos para a compreensão da importância da assessoria técnica em bases agroecológicas para amenizar os impactos da região semiárida sobre quem nela vive e trabalha. O armazenamento de água, sementes e forragens, a diversificação da produção, o acesso a uma dieta balanceada e a ampliação dos canais de comercialização vêm favorecendo a reprodução social da agricultura familiar dentro do que se discute como política de convivência com o semiárido. Esse debate ganha particular relevância num momento em que o semiárido nordestino vivencia a maior estiagem dos últimos 40 anos.

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

    Science.gov (United States)

    Mello, Francisco C A; Souto, Francisco J D; Nabuco, Leticia C; Villela-Nogueira, Cristiane A; Coelho, Henrique Sergio M; Franz, Helena Cristina F; Saraiva, Joao Carlos P; Virgolino, Helaine A; Motta-Castro, Ana Rita C; Melo, Mabel M M; Martins, Regina M B; Gomes, Selma A

    2007-11-23

    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. 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. 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 isolates belonged to cluster II, the presence of some

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

    Directory of Open Access Journals (Sweden)

    Virgolino Helaine A

    2007-11-01

    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

  14. Counsel the genotype, treat the phenotype

    NARCIS (Netherlands)

    van der Zwaag, Paul A.; van Tintelen, J. Peter

    2011-01-01

    This editorial refers to 'Novel correlations between the genotype and the phenotype of hypertrophic and dilated cardiomyopathy: results from the German Competence Network Heart Failure' by S. Waldmuller et al., published in this issue on pages 1185-1192.

  15. in common bean ( Phaseolus Vulgaris L.) genotypes

    African Journals Online (AJOL)

    Bako, Boshe and Gute) and years (2004 – 2005) with the objective of identifying high yielding, stable and adaptable varieties for western parts of Ethiopia. Regression and AMMI analysis were computed to identify stable genotypes across ...

  16. (AMMI) and genotype by environment interaction

    African Journals Online (AJOL)

    SARAH

    2014-04-30

    , stable and high yielding genotypes under varying environmental conditions prior to release as a cultivar is the first and foremost steps for plant breedingr and this has direct bearing on the adoption of the variety, ...

  17. ApoE (Apolipoprotein E) Genotyping

    Science.gov (United States)

    ... Questions Related Content View Sources Formal Name Apolipoprotein E Genotyping This article was last reviewed on March ... They Mean . What is being tested? Apolipoprotein (Apo) E is produced under the direction of the APOE ...

  18. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C

    2017-01-01

    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...... 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...... 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...

  19. HMSRP Hawaiian Monk Seal Microsatellite Genotypes

    Data.gov (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,...

  20. Micropropagation of Jatropha curcas superior genotypes and ...

    African Journals Online (AJOL)

    Micropropagation of Jatropha curcas superior genotypes and evaluation of clonal fidelity by target region amplification polymorphism (TRAP) molecular marker and flow cytometry. MC Franco, DA Marques, WJ Siqueira, RR Latado ...

  1. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie

    2008-01-01

    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...

  2. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie

    2008-01-01

    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....

  3. Selection of Gossypium hirsutum genotypes for interspecific ...

    African Journals Online (AJOL)

    FORRESTER

    hybridization. INTRODUCTION. Tetraploid upland cotton, Gossypium hirsutum L., is comprised of over 90% of global cotton production (Zhao et al., 2015). Cultivated G. hirsutum genotypes are considered to have a narrow genetic base, due in part to.

  4. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie

    2008-01-01

    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.......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....

  5. Pancreaticobiliary cancers with deficient methylenetetrahydrofolate reductase genotypes.

    Science.gov (United States)

    Matsubayashi, Hiroyuki; Skinner, Halcyon G; Iacobuzio-Donahue, Christine; Abe, Tadayoshi; Sato, Norihiro; Riall, Taylor Sohn; Yeo, Charles J; Kern, Scott E; Goggins, Michael

    2005-08-01

    Methyl group deficiency might promote carcinogenesis by inducing DNA breaks and DNA hypomethylation. We hypothesized that deficient methylenetetrahydrofolate reductase (MTHFR) genotypes could promote pancreatic cancer development. First, we performed a case-control study of germline MTHFR polymorphisms (C677T, A1298C) in 303 patients with pancreatic cancer and 305 matched control subjects. Pancreatic neoplasms frequently lose an MTHFR allele during tumorigenesis; we hypothesized that such loss could promote carcinogenesis. We therefore evaluated the cancer MTHFR genotypes of 82 patients with pancreaticobiliary cancers and correlated them to genome-wide measures of chromosomal deletion by using 386 microsatellite markers. Finally, MTHFR genotypes were correlated with global DNA methylation in 68 cancer cell lines. Germline MTHFR polymorphisms were not associated with an increased likelihood of having pancreatic cancer. Fractional allelic loss (a measure of chromosomal loss) trended higher in cancers with 677T genotypes than in cancers with other genotypes (P = .055). Among cancers with loss of an MTHFR allele, cancers with 677T MTHFR alleles had more deletions at folate-sensitive fragile sites (36.9%) and at tumor suppressor gene loci (68.5%) than 677C cancers (28.7% and 47.8%, P = .079 and .014, respectively). LINE1 methylation was lower in cancers with less functional 677T/TT genotypes (24.4%) than in those with 677CT (26.0%) and CC/C genotypes (32.5%) (P = .014). Cancers with defective MTHFR genotypes have more DNA hypomethylation and more chromosomal losses. Deficient MTHFR function due to loss of an MTHFR allele by an evolving neoplasm might, by promoting chromosomal losses, accelerate cancer development.

  6. Genotype-specific interactions between parasitic arthropods.

    Science.gov (United States)

    Orsucci, M; Navajas, M; Fellous, S

    2017-03-01

    Despite the ubiquity of coinfection, we know little of the effects of intra-specific genetic variability on coinfection by distinct parasite species. Here we test the hypothesis that parasite multiplication depends on the combination of parasite genotypes that coinfect the host (that is Genotype.parasite × Genotype.parasite interaction). To that aim, we infected tomato leaves with the ecto-parasitic mites Tetranychus urticae and Tetranychus evansi. We tested all possible combinations between four T. urticae and two T. evansi populations sampled on different hosts or localities. There was no universal (that is genotype-independent) effect of coinfection on mite multiplication; in many cases the two species had no effect on each other. However, several combinations of T. evansi and T. urticae populations led to elevated T. evansi numbers. Similarly, T. urticae reproduction largely depended on the interaction between T. urticae and T. evansi populations. This evidence for genotype-by-genotype interaction between coinfecting parasites indicates that the effect of coinfection on parasite epidemiology and evolution may vary in space according to the genetic composition of local parasite populations; it further suggests the possibility of coevolution between parasites species that share the same hosts.

  7. Monitoring coyote population dynamics by genotyping faeces.

    Science.gov (United States)

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

    2005-04-01

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

  8. Lactose intolerance: lactose tolerance test versus genotyping.

    Science.gov (United States)

    Ridefelt, Peter; Håkansson, Lena D

    2005-07-01

    Adult lactose intolerance, which affects the majority of the population in the world, has been associated with a single nucleotide polymorphism, C-13910T, located upstream of the lactase gene. Adult patients undergoing lactose tolerance tests with lactose challenge and plasma glucose measurements were included in the study comprising 44 Swedes and 7 non-Swedish individuals. A real-time PCR method was established for the genotyping. Out of 51 patients 48 had concordant results on genotyping and lactose tolerance tests, e.g. -13910T/T and -13910C/T genotypes had high glucose elevations. All patients with the heterozygous genotype, -13910C/T, had high glucose elevations, and no gene-dose relationship was observed when comparing maximal glucose increases for cases with -13910C/T and -13910T/T genotypes. Genotyping could replace lactose challenge as a first-stage screening test in adults of European descent, but should be used together with tolerance tests in children and patients where secondary lactose intolerance is suspected.

  9. Hepatitis C viral evolution in genotype 1 treatment-naïve and treatment-experienced patients receiving telaprevir-based therapy in clinical trials.

    Directory of Open Access Journals (Sweden)

    Tara L Kieffer

    Full Text Available In patients with genotype 1 chronic hepatitis C infection, telaprevir (TVR in combination with peginterferon and ribavirin (PR significantly increased sustained virologic response (SVR rates compared with PR alone. However, genotypic changes could be observed in TVR-treated patients who did not achieve an SVR.Population sequence analysis of the NS3•4A region was performed in patients who did not achieve SVR with TVR-based treatment.Resistant variants were observed after treatment with a telaprevir-based regimen in 12% of treatment-naïve patients (ADVANCE; T12PR arm, 6% of prior relapsers, 24% of prior partial responders, and 51% of prior null responder patients (REALIZE, T12PR48 arms. NS3 protease variants V36M, R155K, and V36M+R155K emerged frequently in patients with genotype 1a and V36A, T54A, and A156S/T in patients with genotype 1b. Lower-level resistance to telaprevir was conferred by V36A/M, T54A/S, R155K/T, and A156S variants; and higher-level resistance to telaprevir was conferred by A156T and V36M+R155K variants. Virologic failure during telaprevir treatment was more common in patients with genotype 1a and in prior PR nonresponder patients and was associated with higher-level telaprevir-resistant variants. Relapse was usually associated with wild-type or lower-level resistant variants. After treatment, viral populations were wild-type with a median time of 10 months for genotype 1a and 3 weeks for genotype 1b patients.A consistent, subtype-dependent resistance profile was observed in patients who did not achieve an SVR with telaprevir-based treatment. The primary role of TVR is to inhibit wild-type virus and variants with lower-levels of resistance to telaprevir. The complementary role of PR is to clear any remaining telaprevir-resistant variants, especially higher-level telaprevir-resistant variants. Resistant variants are detectable in most patients who fail to achieve SVR, but their levels decline over time after treatment.

  10. Análise tensional e morfológica da anastomose colônica na colite induzida por ácido acético a 10%, em ratos Wistar, tratados com extrato aquoso de aroeira-do-sertão a 10% (Myracrodruon urundeuva fr. all. Tensional and morphologic analysis of the colonic anastomosis on 10% acetic acid induced colitis, in Wistar rats, treated with 10% aroeira-do-sertão (Myracrodruon urundeuva fr. all. aqueous extract

    Directory of Open Access Journals (Sweden)

    Antonio Rubens Soares Martins Cavalcante

    2005-04-01

    Full Text Available OBJETIVO: Verificar, do ponto de vista tensional e morfológico, o efeito do extrato aquoso de aroeira-do-sertão a 10% na anastomose colônica, na vigência de colite induzida por ácido acético a 10%, em ratos Wistar. MÉTODOS: Foram utilizados 48 ratos da linhagem Wistar, distribuídos em dois grupos. Todos os animais foram submetidos à indução da colite por solução aquosa de ácido acético a 10%. Vinte e quatro horas após, os animais foram submetidos à laparotomia, colotomia transversa total e anastomose término-terminal com fio de polipropileno 5-0. Grupo A (veículo, animais tratados com veículo à base de carboximetilcelulose. Grupo B (aroeira, animais tratados com extrato aquoso de aroeira a 10%. Ambos tratamentos foram sob a forma de enema. Os grupos A e B foram distribuídos em subgrupos A3, A7, A14 e A21; B3, B7, B14 e B21, respectivamente, conforme a data prevista para a eutanásia (3, 7, 14 e 21 dias. Nas respectivas datas, os animais foram relaparotomizados, o segmento colônico contendo a anastomose foi ressecado, submetido ao teste de pressão e em seguida à análise histológica. Para o estudo morfológico, as lâminas foram coradas com hematoxilina-eosina e avaliou-se a condição de cicatrização baseado numa tabela de escores que variava de 0 a 16. Quanto maior o escore melhor o grau de cicatrização. RESULTADOS: Na avaliação do estudo morfológico, que quantifica a evolução e o grau de cicatrização, como resultado final do processo cicatricial, o grupo aroeira foi superior ao grupo veículo (pPURPOSE: Verify, from a morphologic and tensional view point, the effect of the 10% aqueous extract of aroeira-do-sertão on the colonic anastomosis, during the occurrence of 10% acetic acid induced colitis, in Wistar rats. METHODS: There were used 48 Wistar rats, distributed in two groups. All animals were subjected to induction of colitis by aqueous solution of 10% acetic acid. Twenty-four hours later, the animals

  11. Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP Genotyping Assays and the SNPlex Genotyping System.

    Science.gov (United States)

    De la Vega, Francisco M; Lazaruk, Katherine D; Rhodes, Michael D; Wenz, Michael H

    2005-06-03

    In this review we describe the principles, protocols, and applications of two commercially available SNP genotyping platforms, the TaqMan SNP Genotyping Assays and the SNPlex Genotyping System. Combined, these two technologies meet the requirements of multiple SNP applications in genetics research and pharmacogenetics. We also describe a set of SNP selection tools and validated assay resources which we developed to accelerate the cycle of experimentation on these platforms. Criteria for selecting the more appropriate of these two genotyping technologies are presented: the genetic architecture of the trait of interest, the throughput required, and the number of SNPs and samples needed for a successful study. Overall, the TaqMan assay format is suitable for low- to mid-throughput applications in which a high assay conversion rate, simple assay workflow, and low cost of automation are desirable. The SNPlex Genotyping System, on the other hand, is well suited for SNP applications in which throughput and cost-efficiency are essential, e.g., applications requiring either the testing of large numbers of SNPs and samples, or the flexibility to select various SNP subsets.

  12. Chlorophyll a fluorescence to phenotype wheat genotypes for heat tolerance

    DEFF Research Database (Denmark)

    Sharma, Dew Kumari; Andersen, Sven Bode; Ottosen, Carl-Otto

    for 72h was appropriate to induce genotype dependent variation in Fv/Fm. This standardized protocol was used to phenotype wheat genotypes until the variation in the genotypes was consistently high with increased heritability for the trait, Fv/Fm. Mass screening of 1273 wheat genotypes in a milder stress...

  13. Genotype x environment interactions and yield stability of stress ...

    African Journals Online (AJOL)

    Genotype x environment interactions are inherent in multilocational trials and complicate identification of superior genotypes. The aim of the study was to determine yield performance and stability of 13 maize genotypes in five locations of the Eastern Cape province, South Africa. The genotypes assessed were: ZM305, ...

  14. Effect of phosphorus nutrition on growth of potato genotypes with ...

    African Journals Online (AJOL)

    Effect of phosphorus nutrition on growth of potato genotypes with contrasting phosphorus effeciency. ... and inefficient genotypes. P-efficient genotype CGN 17903 allocated more dry matter yield to the leaf which might have enabled higher light harvesting, hence contributing to high biomass accumulation of this genotype.

  15. The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping.

    Science.gov (United States)

    Tobler, Andreas R; Short, Sabine; Andersen, Mark R; Paner, Teodoro M; Briggs, Jason C; Lambert, Stephen M; Wu, Priscilla P; Wang, Yiwen; Spoonde, Alexander Y; Koehler, Ryan T; Peyret, Nicolas; Chen, Caifu; Broomer, Adam J; Ridzon, Dana A; Zhou, Hui; Hoo, Bradley S; Hayashibara, Kathleen C; Leong, Lilley N; Ma, Congcong N; Rosenblum, Barnet B; Day, Joseph P; Ziegle, Janet S; De La Vega, Francisco M; Rhodes, Michael D; Hennessy, Kevin M; Wenz, H Michael

    2005-12-01

    We developed the SNPlex Genotyping System to address the need for accurate genotyping data, high sample throughput, study design flexibility, and cost efficiency. The system uses oligonucleotide ligation/polymerase chain reaction and capillary electrophoresis to analyze bi-allelic single nucleotide polymorphism genotypes. It is well suited for single nucleotide polymorphism genotyping efforts in which throughput and cost efficiency are essential. The SNPlex Genotyping System offers a high degree of flexibility and scalability, allowing the selection of custom-defined sets of SNPs for medium- to high-throughput genotyping projects. It is therefore suitable for a broad range of study designs. In this article we describe the principle and applications of the SNPlex Genotyping System, as well as a set of single nucleotide polymorphism selection tools and validated assay resources that accelerate the assay design process. We developed the control pool, an oligonucleotide ligation probe set for training and quality-control purposes, which interrogates 48 SNPs simultaneously. We present performance data from this control pool obtained by testing genomic DNA samples from 44 individuals. in addition, we present data from a study that analyzed 521 SNPs in 92 individuals. Combined, both studies show the SNPlex Genotyping system to have a 99.32% overall call rate, 99.95% precision, and 99.84% concordance with genotypes analyzed by TaqMan probe-based assays. The SNPlex Genotyping System is an efficient and reliable tool for a broad range of genotyping applications, supported by applications for study design, data analysis, and data management.

  16. Cotton genotypes selection through artificial neural networks.

    Science.gov (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

    2017-09-27

    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.

  17. Improved haplotype assembly using Xor genotypes.

    Science.gov (United States)

    Mousavi, Sayyed R

    2012-04-07

    Given a set of aligned fragments, haplotype assembly is the problem of finding the haplotypes from which the fragments have been read. The problem is important because haplotypes contain SNP information, which is essential to many genomic analyses such as the analysis of potential association between certain diseases and genetic variations. The current state-of-the-art haplotype assembly algorithm, HapSAT, does not exploit genotype information and only receives a read matrix as input. However, the imminent importance of haplotypes and inexpensiveness of genotype information motivate for exploiting genotype information to obtain more accurate haplotypes. In this paper, an improved haplotype assembly method, xGenHapSAT, is proposed, which exploits xor genotype information for more accurate haplotype assembly. Xor genotype information is even less expensive than full genotype information, e.g., using the Denaturing High-Performance Liquid Chromatography (DHPLC) technique. It is shown that using this inexpensively obtainable information significantly improves the accuracy of the assembled haplotypes. In addition, a new, more efficient, Max-2-SAT formulation is adopted in xGenHapSAT, which, on average, increases the speed of the algorithm. Moreover, the proposed xGenHapSAT method replaces the current state-of-the-art haplotype assembly method based on genotype information. Finally, our state-of-the-art haplotype assembly software, HapSoft, which includes both xGenHapSAT and HapSAT, is made freely available for research purposes. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. Genotyping Reveals the Presence of a Predominant Genotype of Coxiella burnetii in Consumer Milk Products

    NARCIS (Netherlands)

    Tilburg, J.J.H.C.; Roest, H.I.J.; Nabuurs-Fransen, M.H.; Horrevorts, A.M.; Klaassen, C.H.W.

    2012-01-01

    Real-time PCR shows the widespread presence of Coxiella burnetii DNA in a broad range of commercially available milk and milk products. MLVA genotyping shows that this is the result of the presence of a predominant C. burnetii genotype in the dairy cattle population.

  19. Rapid and precise genotyping of porcine microsatellites.

    Science.gov (United States)

    Yue, G H; Beeckmann, P; Bartenschlager, H; Moser, G; Geldermann, H

    1999-11-01

    Microsatellites are useful markers for genetic mapping and linkage analysis because they are highly polymorphic, abundant in genomes and relatively easily scored with polymerase chain reaction (PCR). A rapid genotyping system for microsatellites was developed, which included multiplex PCRs, multiple use of Hydrolink gels, automated fluorescent detection of fragments on an A.L.F. DNA sequencer, automatic assignment of alleles to each locus and verification of genotypes with a self-developed computer program "Fragtest". Eight multiplex PCRs have been developed to genotype 29 microsatellites for genetic and quantitative trait loci (QTL) mapping on pig chromosomes 6, 7, 12 and 13. Three to six microsatellites could be amplified in one multiplex PCR. Each multiplex reaction required only different concentrations of each pair of primers and a low concentration of dNTP (100 microM). A dNTP concentration of 100 microM proved to be optimal for the coamplification of microsatellites under the concentration of 1.5 mM MgCl2. Using four internal size standards added in each sample, the 5% Hydrolink gel could subsequently be used up to five times (total running time of 500 min) on the A.L.F. automated sequencer without significant loss of resolution and precision of fragment length analysis. Automatic assignment of alleles on each locus using "Fragtest" significantly increased the efficiency and precision of the genotyping. This system is thus a rapid, cheap, and highly discriminating genotyping system.

  20. Phenotypic and genotypic variation in Iranian Pistachios

    Directory of Open Access Journals (Sweden)

    Somayeh Tayefeh Aliakbarkhani

    2015-12-01

    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.

  1. Identification of Mislabeled Samples and Sample Mix-ups in Genotype Data using Barcode Genotypes

    DEFF Research Database (Denmark)

    Have, Christian Theil; Appel, Emil Vincent Rosenbaum; Grarup, Niels

    2014-01-01

    of identical genotypes between sample x and sample y by chance. Based on this we calculate a mix-up confidence score with penalization for introducing mismatches in the proposed new label and adjustment for independency among the genotypes. This confidence score is used to identify probable mix-ups.......Abstract—Undetected mislabeled samples may affect the results of genotype studies, particular when rare genetic variants are investigated. Mislabeled samples are often not detected during quality control and if they are detected, they are normally discarded due to a lack of a reliable method...... to recover the correct labels. Here we describe a statistical method which given a few extra independent genotypes (barcode genotypes) detects mislabeled samples and recovers the correct labels for sample mix-ups. We have implemented the method in a program (named Wunderbar) and we evaluate the reliability...

  2. Determinação de cobre e outros minerais em caprinos e ovinos criados no sertão do vale do rio São Francisco, Pernambuco

    Directory of Open Access Journals (Sweden)

    Salvador S. Silva Júnior

    2015-09-01

    Full Text Available Resumo: Para a determinação dos teores de cobre e de seus antagonistas, foram utilizadas 160 amostras de soro e de fígados, de caprinos e ovinos enviados ao matadouro municipal de Petrolina. As amostras de fígado e soro foram correlacionadas para o mesmo animal, a fim de evitar erros na obtenção dos dados. No soro a atividade da ceruloplasmina foi determinada por método colorimétrico. Para a determinação dos minerais, as amostras foram diluídas de seis a vinte vezes com água Milli-Q. Para determinação das concentrações dos elementos minerais no fígado, as amostras foram digeridas até que se obtivesse uma solução que mantivesse os minerais da amostra inicial e que fosse totalmente liquida, sem a presença de partículas sólidas que pudessem obstruir os capilares de sucção do espectrômetro e assim impedir as leituras das amostras. As concentrações de cobre, molibdênio, ferro e zinco foram determinadas através de espectrometria óptica por emissão de plasma (ICP. Desta forma, foi conduzido o experimento objetivando determinar a ocorrência e distribuição da carência de cobre no território do sertão do vale do rio São Francisco em Pernambuco. Foi observado que não houve carência de cobre nesta região do estado de Pernambuco, quando se avaliou os níveis médios de cobre hepático,. Os níveis de zinco estavam dentro de um padrão de normalidade, enquanto que os níveis de ferro foram mais elevados em ovinos, e os níveis de molibdênio mais reduzidos em caprinos. Verificou-se também que a atividade de ceruloplasmina foi um indicador dos níveis séricos de cobre.

  3. Produção de mudas de aroeira-do-sertão (Myracrodruon urundeuva Allemão em resíduos orgânicos

    Directory of Open Access Journals (Sweden)

    Lucas Kennedy Silva Lima

    Full Text Available RESUMO A aroeira é uma espécie de grande importância devido às diversas utilidades de sua madeira. Entretanto, encontra-se na lista de espécies ameaçadas de extinção, em virtude da exploração predatória. Diante da baixa tecnologia empregada na produção de mudas, este trabalho teve por objetivo avaliar o desenvolvimento de mudas de aroeira-do-sertão (Myracrodruon urundeuva Allemão, utilizando diferentes resíduos orgânicos em diferentes concentrações. Foram usados, como substratos, esterco bovino, esterco ovino, húmus de minhoca, resíduo oriundo do processo de torrefação do café e solo. O delineamento experimental utilizado foi o inteiramente casualizado, em esquema fatorial 4 x 4 (resíduos orgânicos x níveis de resíduo, constituído por 16 tratamentos e cinco repetições. Resultados superiores foram alcançados quando utilizado o esterco ovino, para o índice de qualidade de Dickson, massa seca da raiz e massa seca total, com máxima eficiência na concentração de 66%. Para as demais variáveis, não foi observada variação na comparação com o húmus de minhoca. O resíduo de café provocou efeito alelopático, mesmo nas menores concentrações, não sendo recomendado para formulação de substrato. Na maioria das variáveis, o esterco bovino comportou-se de forma intermediária, com decréscimo das variáveis, decorrentes das concentrações. O esterco de ovino e o húmus de minhoca são recomendados para produção de mudas de aroeira nas concentrações de 66 e 33%, respectivamente.

  4. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

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

    2015-01-01

    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...... samples for genotyping COMT val158met (rs4680). All subjects underwent clinical evaluations and neurocognitive assessment of decision-making, working memory, and impulsivity. The Val/Val COMT genotype was associated with the largest percentage of subjects with gambling disorder (31.8%), a rate...

  5. An Application of Molecular Genotyping in Mice

    Directory of Open Access Journals (Sweden)

    Underkoffler Lara A.

    2003-01-01

    Full Text Available Microsatellite markers are simple sequence repeats within the mammalian genome that can be used for identifying disease loci, mapping genes of interest as well as studying segregation patterns related to meiotic nondisjunction. Different strains of mice have variable CA repeat lengths and PCR based methods can be used to identify them, thus allowing for specific genotypes to be assigned. Molecular genotyping offers such identification at any developmental stage, which allows for a broad range of anomalies to be studied. We studied chromosomal segregation in relation to nondisjunction in early-gestation mouse embryos using molecular genotyping. Information on the parental origin as well as the number of chromosomes a given progeny carried was obtained in our analysis.

  6. Oilseed rape genotypes response to boron toxicity

    Directory of Open Access Journals (Sweden)

    Savić Jasna

    2013-01-01

    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

  7. Prevalence of hepatitis C virus genotypes in mashhad, northeast iran.

    Science.gov (United States)

    Vossughinia, H; Goshayeshi, LA; Bayegi, H Rafatpanah; Sima, H; Kazemi, A; Erfani, S; Abedini, S; Goshayeshi, LE; Ghaffarzadegan, K; Nomani, H; Jamehdar, S Amel

    2012-01-01

    Hepatitis C is a disease with significant global impact. The distribution of hepatitis C virus (HCV) genotypes in Mashhad (the Northeast and the biggest city after the capital of Iran) is unknown. The purpose of this study was to determine the prevalence of HCV genotypes among HCV seropositive patients, and to study the relationship between types, virologic and demographic features of patients in Mashhad. Three hundred and eighty-two clinical specimens obtained from HCV-infected patients referred to Ghaem Hospital in Mashhad during a period of 2009 to 2010 were selected. HCV genotype was determined by Nested PCR amplification of HCV core gene using genotype specific primers. Totally, 299 patients were male (79.9%). The most common HCV genotype was genotype 3a, with 150 (40%) of subjects. Genotype 1a was the other frequent genotype, with 147(39.2%) subjects. Frequency of genotypes for 1b, 5 and 2 was 41(10.9%), 13(3.4%) and 9(2.4%), respectively. Mix genotype including 1a+1b in 4 (1.04%), 1a+3a in 3 (0.8%) was found in 7 patients. Four percent out of these samples had an undetermined genotype. Among the hemophilia patient, there were 13(48.1%) genotypes as 1a, 3(11.1%) 1b and 10(37%) 3a, respectively. The dominant HCV genotype among patients living in Mashhad was 3a. This study gives added evidence of the predominant HCV genotypes in Iran.

  8. Sertão translated into Danish

    Directory of Open Access Journals (Sweden)

    Peter Poulsen

    2012-09-01

    Full Text Available This text is a transcription of a lecture given by Peter Poulsen, Danish writer and translator, during the event Discovering Brazilian Northeast with the Music by Luiz Gonzaga, which took place at Aarhus University on 26th and 27th of April, 2012. The aim of this event , promoted by the Brazilian Studies at Aarhus University, was to introduce Luiz Gonzaga and his music, showing how this singer-songwriter has shaped a vision of the people and landscape of northeast Brazil.

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

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2015-01-01

    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...

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

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Stuefer, Josef F.

    2011-01-01

    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...... for WClMV to provoke differential selection on T. repens genotypes, which may lead to negative frequency-dependent selection in host populations. †Conclusions The apparent G × E interaction and evident repercussions for relative fitness reported in this study stress the importance of viruses...

  11. GENOTYPES IN THE CENTRAL HIGHLANDS OF ETHIOPIA

    African Journals Online (AJOL)

    Eight promising bread wheat lines and one standard check cultivar were evaluated for grain yield performance, stability and adaptation across nine environments of the central highlands of Ethiopia. Results of the combined analysis of variance for grain yield showed highly significant effects of genotypes, environments, and ...

  12. Genotypic identification and technological characterization of lactic ...

    African Journals Online (AJOL)

    enoh

    African Journal of Biotechnology Vol. 11(28), pp. 7218-7226, 5 April, 2012 ... Key words: Lactic acid bacteria, genotypic characterization, technological characterization, tulum cheese. INTRODUCTION. Kargi tulum ... traditional production method of Kargi tulum cheese begins with fresh raw milk that is coagulated by adding.

  13. Genetic diversity evaluation of rapeseed genotypes ( Brassica ...

    African Journals Online (AJOL)

    Path analysis showed that number of pods per main branch had the highest direct effect on seed yield. Stepwise regressing showed numbers of pods per main branch was entered as the first variable in the model and explained 79% of seed yield variation. Phenotypic cluster showed that genotypes were divided into 4 ...

  14. genotype by environment interaction of advanced generation ...

    African Journals Online (AJOL)

    recommended as primary testing centres for new soybean genotypes. ACKNOWLEDGEMENT. This research was supported by Alliance for a. Green Revolution in Africa (AGRA) and Vegetable. Oil Development Project, of the Ministry of. Agriculture Animal Industry and Fisheries,. Uganda. We thank Makerere University and.

  15. genotyping methods in routine clinical practice

    African Journals Online (AJOL)

    milcah

    2013-05-08

    May 8, 2013 ... Pharmacogenetics requires robust and affordable tests to determine genetic variability. This study compares three genotyping methods: gene re-sequencing, real time polymerase chain reaction (PCR) allelic discrimination and PCR-RFLP for the detection of a genetic variation (516G>T) in the gene which.

  16. AFLP analysis among Ethiopian arabica coffee genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2008-09-17

    Sep 17, 2008 ... AFLP analysis among Ethiopian arabica coffee genotypes. Yigzaw Dessalegn1*, L. Herselman2 and M. T. Labuschagne2. 1IPMS Project, Bure PLW, P.O. Box 03, Bure, Ethiopia. 2University of the Free State, Department of Plant Sciences, P.O. Box 339, Bloemfontein 9300, Republic of South Africa.

  17. (Saccharum officinarum L) genotypes to callus induction ...

    African Journals Online (AJOL)

    Jane

    2010-12-20

    Dec 20, 2010 ... Cultivar CSSG-668 was found to be the best genotype yielding maximum embryogenic callus and regeneration whereas cultivar CPF-. 245 exhibited lowest callus induction frequency. Five different concentrations (0 ..... Planta, 89: 299-302. Bower R, Birch RG (1992). Transgenic sugarcane plants via micro-.

  18. Camelina: Adaptation and performance of genotypes

    Science.gov (United States)

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

  19. Phenotypic and Genotypic Characterization of Nosocomial Isolates ...

    African Journals Online (AJOL)

    Phenotypic and Genotypic Characterization of Nosocomial. Isolates of Staphylococcus aureus with Reference to. Methicillin Resistance. Mounir M Salem-Bekhit1,2. 1Kayyali Chair for Pharmaceutical Industries, Department of Pharmaceutics, College of Pharmacy, King Saud University, PO. Box 2457, Riyadh 11451, Saudi ...

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

    Indian Academy of Sciences (India)

    Cervical cancer is a leading cause of cancer-related deaths among women in India. Human papillomavirus (HPV) infection is the causative agent of cervical cancer; and infection with the high-risk genotypes, predominantly HPV16 and 18, is the biggest risk factor. Vaccines targeting HPV16 and 18 have been found to confer ...

  1. Probabilistic Transcriptome Assembly and Variant Graph Genotyping

    DEFF Research Database (Denmark)

    Sibbesen, Jonas Andreas

    that this approach outperforms existing state-of-the-art methods measured using sensitivity and precision on both simulated and real data. The second is a novel probabilistic method that uses exact alignment of k-mers to a set of variants graphs to provide unbiased estimates of genotypes in a population...

  2. 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 ...

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

    African Journals Online (AJOL)

    This study was designed to evaluate the antibiotic susceptibilities, genotypic characteristics and biofilm formation abilities of antibiotic-sensitive Staphylococcus aureus KACC 13236 (SAS), multiple antibiotic-resistant S. aureus CCARM 3080 (SAR), antibiotic-sensitive Salmonella Typhimurium KCCM 40253 (STS) and ...

  4. Heritability Studies of Some Cassava Genotypes

    African Journals Online (AJOL)

    komla

    82/00058, 82/00661, 82/00942 and 900942. These genotypes were grown under rainfed conditions in a randomized complete design with four replicates (Fig. 1). No fertilizers or any other agrochemicals were applied to the experimental plots. Plants were planted. 50 , West AfricanJournal of Applied Ecology, vol. 3, 2002 ...

  5. EFFECT OF TEMPERATURE AND HOST GENOTYPE ON ...

    African Journals Online (AJOL)

    Disease development in plants involves various inter-related processes each of which may be. influenced by environmental factors as well as host and pathogen genotypes Temperature in the range of 20~25°C was reported to be optimum for urediniospore germination of groundnut rust. (Subrahmanyam and McDonald ...

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

    Indian Academy of Sciences (India)

    PRAKASH KUMAR G

    known, together accounting for about 90% of all cervical cancer cases worldwide. HPV 31, 33 and 45 account for a high proportion of HPV16/18-negative cervical cancer cases. (Pretet et al 2007a, b) and to complete the representative spectrum of HPV genotypes, two low-risk HPV types, namely HPV6 and 11, known to be ...

  7. Fruit characteristics of the selected fig genotypes

    African Journals Online (AJOL)

    GREGORY

    2010-09-13

    Sep 13, 2010 ... Key words: Ficus carica L., genotype, fruit characteristics, quality, selection. INTRODUCTION. Turkey is the world's largest fig producing country. According to FAO statistics, world fig production is. 1.056,820 tonnes. Turkey's production of 285.000 tonnes is 27% of the world's total production and its 177.900.

  8. Morphometric characteristics of Lotus corniculatus L. genotypes

    African Journals Online (AJOL)

    LAB-89 sjemenarstvo

    2013-08-28

    Aug 28, 2013 ... Variability of productive characteristics and fodder quality of selected Birdsfoot Trefoil (Lotus corniculatus L.) genotypes. A. Periodical of Scientific Research on Field and Vegetable Crops, Novi. Sad, Serbia. 44 (1):45-50. Rumbaugh MD, Caddel JL, Rowe DE(1988). Breeding and Quantitative. Genetics.

  9. Participatory selection of mungbean genotypes in Uganda ...

    African Journals Online (AJOL)

    We captured twenty five traits during farmer interviews out of which six traits were identified (through group discussions) as the most often used by farmers when selecting the best mungbean genotypes. The traits were; yield, overall performance, seed size, seed colour, marketability and early maturity. Nine out of eleven ...

  10. Screening soybean genotypes for promiscuous symbiotic ...

    African Journals Online (AJOL)

    The current low soybean (Glycine max L. Merrill) yields in Sub-Saharan Africa can be alleviated by developing promiscuous genotypes. The research trend in Africa is towards developing promiscuous varieties for less labour and high yields in soybean production. A greenhouse experiment was conducted at Makerere ...

  11. Carbon isotope fractionation for cotton genotype selection

    Directory of Open Access Journals (Sweden)

    Giovani Greigh de Brito

    2014-09-01

    Full Text Available The objective of this work was to evaluate the carbon isotope fractionation as a phenomic facility for cotton selection in contrasting environments and to assess its relationship with yield components. The experiments were carried out in a randomized block design, with four replicates, in the municipalities of Santa Helena de Goiás (SHGO and Montividiu (MONT, in the state of Goiás, Brazil. The analysis of carbon isotope discrimination (Δ was performed in 15 breeding lines and three cultivars. Subsequently, the root growth kinetic and root system architecture from the selected genotypes were determined. In both locations, Δ analyses were suitable to discriminate cotton genotypes. There was a positive correlation between Δ and seed-cotton yield in SHGO, where water deficit was more severe. In this site, the negative correlations found between Δ and fiber percentage indicate an integrative effect of gas exchange on Δ and its association with yield components. As for root robustness and growth kinetic, the GO 05 809 genotype performance contributes to sustain the highest values of Δ found in MONT, where edaphoclimatic conditions were more suitable for cotton. The use of Δ analysis as a phenomic facility can help to select cotton genotypes, in order to obtain plants with higher efficiency for gas exchange and water use.

  12. Genotype 3 is the predominant hepatitis C genotype in a multi-ethnic Asian population in Malaysia.

    Science.gov (United States)

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

    2015-06-01

    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.

  13. HPV genotypes in invasive cervical cancer in Danish women

    DEFF Research Database (Denmark)

    Kirschner, Benny; Junge, Jette; Holl, Katsiaryna

    2013-01-01

    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....

  14. Experiência bem-sucedida no controle do Aedes aegypti sem uso de venenos no sertão cearense | Successful experience in the control of Aedes aegypti without the use of poisons in Ceará backcountry

    Directory of Open Access Journals (Sweden)

    Fernando Ferreira Carneiro

    2016-05-01

    Full Text Available O Brasil passa por uma emergência de saúde pública e por uma tríplice epidemia de dengue, zika e chikungunya, transmitidas pelo mosquito Aedes aegypti. Estudos atestam a ineficácia do modelo convencional de controle do vetor adotado há mais de 30 anos. Apresentamos a experiência do município de Pedra Branca no sertão do Ceará, que rompeu com o paradigma de combate ao vetor centrado no controle químico hegemônico no Brasil. O município obteve êxito nas suas ações de controle vetorial, apresentando ausência de transmissão local de dengue há mais de dez anos, alcançando no ano de 2016 por seis meses 0,09% de índice de infestação predial por Aedes aegypti. Esse resultado é fruto de um trabalho de cerca de 15 anos que vem sendo mantido pelas sucessivas gestões municipais, as quais destacamos: visitas mensais dos agentes de combate de endemias; ovitrampas; monitoramento ambiental; vedação de reservatórios; controle biológico; delimitação de focos; educação em saúde; integração da Estratégia Saúde da Família com agentes de combate de endemias e a Secretaria de Educação; e apoio da gestão municipal como um todo. A experiência desse município aponta para formas mais efetivas e sustentáveis, podendo subsidiar ações de enfrentamento da tríplice epidemia a serem implementadas em outros sistemas municipais de saúde. -------------------------------------------------------------------------------------------- Brazil is going through a public health emergency and a triple epidemic of Dengue, Chikungunya and Zika, transmitted by the Aedes aegypti mosquito. Studies attested the inefficacy of conventional model of vector control used for over 30 years. The experience of the city of Pedra Branca in the backcountry of the state of Ceará, which broke with the hegemonic paradigm of chemical control for the vector-centered combat in Brazil, is presented. The council was successful in its vector control activities

  15. Um Padre-Professor no sertão Educação e conquista dos índios do Rio Doce na Capitania de Minas Gerais (1758-1801

    Directory of Open Access Journals (Sweden)

    Bruno Duarte Guimarães Silva

    2012-10-01

    Full Text Available RESUMO: O presente artigo é resultado de um trabalho de investigação da trajetória do Padre e Professor Régio de Primeiras Letras, João Pedro de Almeida, que atuou em aldeias indígenas nas últimas décadas do século XVIII na região do Sertão Leste da Capitania de Minas Gerais. Nesse período a fronteira colonial da Capitania passava por um processo de expansão em direção à mesma região povoada por grupos indígenas, entre eles os botocudos. Tal processo foi marcado por um conjunto de estratégias de conquista dos índios e seu território, efetivadas em duas frentes: a violência e a educação. Aos índios que resistiam à colonização, a reação foi a guerra; já junto aos índios aldeados, práticas educativas dirigidas por um ideal civilizador foram experimentadas. Apresento o trabalho de João Pedro de Almeida como representativo da frente da educação e analiso sua atuação à luz das legislações indigenistas coloniais, procurando destacar do discurso civilizador a dinâmica da alteridade do europeu em relação ao índio.  PALAVRAS-CHAVES: Educação; Índios; Conquista. ABSTRACT: This article is the result of a Father of the trajectory of research work and Professor of First Letters Regal, João Pedro de Almeida, who served in Indian villages in the last decades of the eighteenth century in Eastern Hinterland region of Minas Gerais Captaincy. During this period the colonial frontier of the Province went through a process of expansion towards the same region populated by indigenous groups, including the botocudos. This process was marked by a set of winning strategies of the Indians and their territory, carried out on two fronts: the violence and education. The Indians who resisted colonization, the reaction was war; already close to the settled Indians, educational practices run by a civilizing ideal have been tried. Present the work of João Pedro de Almeida as representative for the front of education and

  16. Desempenho em Pastagens e Características de Carcaça da 16a Progênie dos Rebanhos Nelore, Guzerá e Caracu de Sertãozinho (SP

    Directory of Open Access Journals (Sweden)

    Razook Alexander George

    2002-01-01

    Full Text Available Quarenta e um machos inteiros dos rebanhos selecionados para peso aos 378 dias (P378, nascidos em 1996, foram terminados em pastagens de Panicum Maximum (Jacq., Panicum Maximum (Jaq cv. Tanzania 1 e Brachiaria brizantha (Hoschst Stapf cv. Marandu na Estação Experimental de Zootecnia de Sertãozinho (SP. As amostras, representando a média de P378 em cada rebanho, foram: 11 animais Nelore Seleção (NeS e 10 para cada um dos grupos Nelore Controle (NeC, Guzerá Seleção (GuS e Caracu (Ca. O abate ocorreu aos 824 dias de idade e condição corporal 7,6, em uma escala de 1 a 9. As médias mínimas e máximas ajustadas, para as principais características, considerando-se todos os grupos, foram: ganho de peso médio diário, 406 (NeC e 501 g (NeS; peso de abate (PAB, 446,8 (NeC e 544,3 kg (NeS ; peso de carcaça (PCAR, 249,8 (NeC e 309,7 kg (NeS; rendimento de carcaça (REND, 54,0 (GuS e 56,3% (NeC e NeS. No corte entre a 9feminine e 11feminine costelas : músculo 59,6 (NeC e 65,2% (Ca; gordura, 15,6 (Ca e 21,4% (NeC; osso, 18,9 (NeC e 20,2% (GuS; espessura de gordura (ESPGOR, 2,0 (Ca e 4,2 mm (NeC; área de olho de lombo (AOL, 65,6 (NeC e 71,1 cmsuperscript two (NeS e Ca; força de cisalhamento (FC, 4,5 (Ca e 6,6 kg (GuS e perdas totais no cozimento (PERDAS, 22,5 (NeC e 24,9% (GuS. A seleção para peso provocou, em NeS, maiores PAB e PCAR, sem interferir no REND, na composição da costela, FC e PERDAS na carne. Houve, porém, menor ESPGOR em relação à NeC. Os animais GuS apresentaram PAB e PCAR intermediários, entre NeS e Ca, e menor REND e os Ca maior proporção de músculo na costela e carne com maior maciez em relação ao Zebu.

  17. Comparison of the digene HPV genotyping LQ test and the PANArray HPV genotyping chip for detection of high-risk or probable high-risk human papillomavirus genotypes.

    Science.gov (United States)

    Park, Kyung Sun; Kim, Ji-Youn; Ki, Chang-Seok; Lee, Nam Yong

    2014-07-01

    We evaluated the performance of two different array-based techniques, a bead-based multiplex genotyping method (LQ; digene HPV Genotyping LQ Test, QIAGEN, Germany) and a DNA chip-based method using peptide nucleic acid probes (PANArray; PANArray HPV Genotyping Chip, Panagene, Korea), for detection of human papillomavirus (HPV) and genotyping of high-risk (HR) or probable high-risk (PHR) HPVs in healthy patients who visited a health-promotion center. We obtained 508 unselected, consecutive cervicovaginal swab specimens. All specimens were examined by using the PANArray and LQ tests. All HPV-positive samples were then analyzed by multiplex PCR and direct sequencing. The LQ test detected 47 HPV-positive cases (9.3%) with HR or PHR genotypes and the PANArray test identified 36 cases (7.1%). When the results of LQ and PANArray were compared by using comprehensive genotyping (integrated interpretation of the results of LQ, PANArray, multiplex PCR, and direct sequencing) for the detection of HR or PHR genotypes, the kappa values were 0.44 and 0.30 for LQ and PANArray, respectively. In comparison to comprehensive genotyping, the LQ test yielded 53 (60.0%) concordant and 12 (13.5%) compatible results, and the PANArray yielded 36 (40.4%) concordant and three (3.4%) compatible results. The results of the LQ test had higher concordance and/or greater compatibility with those of comprehensive genotyping for the detection of HR or PHR genotypes than those of the PANArray test.

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

    Science.gov (United States)

    Didion, John P; Yang, Hyuna; Sheppard, Keith; Fu, Chen-Ping; McMillan, Leonard; de Villena, Fernando Pardo-Manuel; Churchill, Gary A

    2012-01-19

    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. 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. The problems of ascertainment bias and missing information due to genotyping errors are widely recognized as

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

    Directory of Open Access Journals (Sweden)

    Didion John P

    2012-01-01

    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

  20. 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 ...

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

    African Journals Online (AJOL)

    GREGORY

    2011-06-01

    Jun 1, 2011 ... 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 ...

  2. Grain yield assessment of six pigeonpea genotypes in production ...

    African Journals Online (AJOL)

    Five improved pigeonpea genotypes obtained from ICRISAT of short- and medium-duration and a Nsukka local long-duration genotype were assessed for their grain yield in mixtures with two maize genotypes (hybrid and open pollinated types) and as sole crops in 2006 at Nsukka, Nigeria. The 2006 pigeonpea plants were ...

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

    Directory of Open Access Journals (Sweden)

    Mohammad Hasan Khadem Ansari

    2017-12-01

    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.

  4. Characterization of Kenyan sweet potato genotypes for SPVD ...

    African Journals Online (AJOL)

    had an average polymorphic information content (PIC) of 0.47. The average number of alleles within the 89 genotypes across the 6 loci was 13.52. Cluster analyses revealed a 50% variation among the 89 genotypes. The dendrogram did not reveal any unique clustering of the genotypes according to dry matter content and ...

  5. 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 ...

  6. 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 ...

  7. Introduction to a special issue on genotype by environment interaction

    Science.gov (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...

  8. 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 ...

  9. 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 ...

  10. Genotype identification and inference of genetic relatedness among ...

    African Journals Online (AJOL)

    The unweighted Neighbour-Joining tree generated using DARwin 5.0 software classified the germplasm into three different clusters. The grouping of the different genotypes in the tree had distinct order. Genotypes derived from the same species were in one group, while the genotypes having both or one parents common in ...

  11. Distribution of hepatitis delta virus genotypes in mashhad, northeast iran.

    Science.gov (United States)

    Sadeghian, Hamid; Varasteh, Naiemeh; Esmaeelzadeh, Abbas; Nomani, Hosein; Alimardani, Maliheh; Davoodnejad, Mahdieh; Meshkat, Mojtaba; Ahadi, Mitra; Sepahi, Samaneh; Rostami, Sina; Meshkat, Zahra

    2015-02-01

    Hepatitis delta virus (HDV) is dependent on the hepatitis B virus for transmission and propagation. Based on isolated HDV sequences from different parts of the world, at least three major different genotypes with different geographic distributions are suggested. Studies have shown that genotype 1 is the predominant genotype of HDV in different parts of Iran; however, the genotype distribution of this virus has not been identified in Mashhad, northeast Iran. This current study determines the frequency of HDV major genotypes in Mashhad, Iran. Twenty-five participants were enrolled in this study. All samples were positive for HBsAg (determined by Enzyme-linked immunosorbent assay (ELISA)) and anti-HDV. RNA extraction and cDNA synthesis was performed. Then, PCR was performed and HDV genotypes were determined by restriction fragment length polymorphism (RFLP). Of 25 patients, 12 (48%) were positive for HDV RNA. Genotype analysis of HDV RNA revealed that the prevalence of HDV genotypes I and II was 83.3% (n = 10) and 16.7% (n = 2), respectively. This study showed that the most prevalent genotype of HDV in Mashhad was genotype I. It was of interest that in contrast to other provinces of Iran, HDV genotype 2 was observed in Mashhad. Similar studies with larger sample sizes could provide valuable information regarding the molecular epidemiology and geographical distribution. It may also help control and prevent the spread of hepatitis D virus infections. In addition, the genotyping of HDV may predict the severity of the disease.

  12. 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 ...

  13. Assessment of rice genotypes for salt tolerance using microsatellite ...

    African Journals Online (AJOL)

    The results of phenotypic response of rice genotypes to salinity stress at the seedling stage indicated the varied genotypic responses. The genotypes were classified into five groups from highly tolerant (score 1) to highly sensitive (score 9). Number of alleles of the SSR markers ranged from 3 for RM10702 to 14 for RM8094.

  14. relationship of status of polymorphic rapd bands with genotypic

    African Journals Online (AJOL)

    jen

    Department of Plant Breeding and Genetics, College of Agriculture, Orissa University of Agriculture and. Technology ... millet may give some indication about specific adaptability of genotypes to poor environments. ... ments. These findings may help to predict the genotypic adaptation of different genotypes before going for.

  15. genotype by environment interaction and grain yield stability

    African Journals Online (AJOL)

    Preferred Customer

    IPCA, γgn is the genotype eigenvector for axis n, and δen is the environment eigenvector; εger is error term and ρge is PCA residual. Accordingly, genotypes with low magnitude regardless of the sign of interaction principal component analysis scores have general or wider adaptability while genotypes with high magnitude ...

  16. Genotype x row spacing and environment interaction of cowpea in ...

    African Journals Online (AJOL)

    Genotype x within row spacing interaction effects were not significant, suggesting that selection at low densities would be effective in identifying superior and productive genotypes for further testing in either within row spacing. Because of significant genotype x environment and WRS interaction effects, this effectiveness ...

  17. Strongyloides stercoralis genotypes in humans in Cambodia.

    Science.gov (United States)

    Schär, Fabian; Guo, Li; Streit, Adrian; Khieu, Virak; Muth, Sinuon; Marti, Hanspeter; Odermatt, Peter

    2014-06-01

    Little is known about the genetic variability of the soil-transmitted nematode, Strongyloides stercoralis, in humans. We sequenced portions of the small subunit rDNA (SSU), including the hyper variable regions (HVR) I and IV from S. stercoralis larvae derived from individuals living in a rural setting in Cambodia. We identified three polymorphic positions, including a previously reported one within the HVR I. HVR IV was invariable. Six different SSU alleles existed in our sample. Although different genotypes of S. stercoralis were found in the same individuals, no heterozygous larvae were found. This indicates that there is no or very little interbreeding between the different genotypes. Further studies are needed to examine if this is because sexual reproduction, which is facultative, is rare in our study area's S. stercoralis population or because what is considered to be S. stercoralis today is actually a complex of closely related species or subspecies. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  18. Learning monotonic genotype-phenotype maps.

    Science.gov (United States)

    Beerenwinkel, Niko; Knupfer, Patrick; Tresch, Achim

    2011-01-01

    Evolutionary escape of pathogens from the selective pressure of immune responses and from medical interventions is driven by the accumulation of mutations. We introduce a statistical model for jointly estimating the dynamics and dependencies among genetic alterations and the associated phenotypic changes. The model integrates conjunctive Bayesian networks, which define a partial order on the occurrences of genetic events, with isotonic regression. The resulting genotype-phenotype map is non-decreasing in the lattice of genotypes. It describes evolutionary escape as a directed process following a phenotypic gradient, such as a monotonic fitness landscape. We present efficient algorithms for parameter estimation and model selection. The model is validated using simulated data and applied to HIV drug resistance data. We find that the effect of many resistance mutations is non-linear and depends on the genetic background in which they occur.

  19. Identification of Zoonotic Genotypes of Giardia duodenalis

    DEFF Research Database (Denmark)

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

    2009-01-01

    . 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......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...... explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the zoonotic potential of G. duodenalis is evident, evidence on the contribution and frequency is (still) lacking. This newly developed molecular database has...

  20. 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)

    2017-06-15

    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

  1. Genome structural variation discovery and genotyping

    OpenAIRE

    Alkan, Can; Coe, Bradley P.; Eichler, Evan E.

    2011-01-01

    Comparisons of human genomes show that more base pairs are altered as a result of structural variation — including copy number variation — than as a result of point mutations. Here we review advances and challenges in the discovery and genotyping of structural variation. The recent application of massively parallel sequencing methods has complemented microarray-based methods and has led to an exponential increase in the discovery of smaller structural-variation events. Some glo...

  2. Genotype and phenotype data analysis and visualization

    Directory of Open Access Journals (Sweden)

    Alma Molytė

    2013-09-01

    Full Text Available In this paper, we present a comparative analysis of hierarchical clustering and multidimensional scaling methods for genotype and phenotype data analysis. Fisher's exact test was applied to determinate dependencies between congenital anomalies. In order to determine the relationship between the dependences of congenital anomalies, deformations, these systems’ micro anomalies and congenital anomalies associated with orofacial clefs, the Spearman and Kendall correlation coefficients were applied. It has been detected which methods are better for genetic data visualization.

  3. Canine hip dysplasia is predictable by genotyping.

    Science.gov (United States)

    Guo, G; Zhou, Z; Wang, Y; Zhao, K; Zhu, L; Lust, G; Hunter, L; Friedenberg, S; Li, J; Zhang, Y; Harris, S; Jones, P; Sandler, J; Krotscheck, U; Todhunter, R; Zhang, Z

    2011-04-01

    To establish a predictive method using whole genome genotyping for early intervention in canine hip dysplasia (CHD) risk management, for the prevention of the progression of secondary osteoarthritis (OA), and for selective breeding. Two sets of dogs (six breeds) were genotyped with dense SNPs covering the entire canine genome. The first set contained 359 dogs upon which a predictive formula for genomic breeding value (GBV) was derived by using their estimated breeding value (EBV) of the Norberg angle (a measure of CHD) and their genotypes. To investigate how well the formula would work for an individual dog with genotype only (without using EBV), a cross validation was performed by masking the EBV of one dog at a time. The genomic data and the EBV of the remaining dogs were used to predict the GBV for the single dog that was left out. The second set of dogs included 38 new Labrador retriever dogs, which had no pedigree relationship to the dogs in the first set. The cross validation showed a strong correlation (R>0.7) between the EBV and the GBV. The independent validation showed a moderate correlation (R=0.5) between GBV for the Norberg angle and the observed Norberg angle (no EBV was available for the new 38 dogs). Sensitivity, specificity, positive and negative predictive values of the genomic data were all above 70%. Prediction of CHD from genomic data is feasible, and can be applied for risk management of CHD and early selection for genetic improvement to reduce the prevalence of CHD in breeding programs. The prediction can be implemented before maturity, at which age current radiographic screening programs are traditionally applied, and as soon as DNA is available. Copyright © 2010 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

  4. Canine Hip Dysplasia is Predictable by Genotyping

    Science.gov (United States)

    Guo, Gang; Zhou, Zhengkui; Wang, Yachun; Zhao, Keyan; Zhu, Lan; Lust, George; Hunter, Linda; Friedenberg, Steven; Li, Junya; Zhang, Yuan; Harris, Stephen; Jones, Paul; Sandler, Jody; Krotscheck, Ursula; Todhunter, Rory; Zhang, Zhiwu

    2011-01-01

    Summary Objective To establish a predictive method using whole genome genotyping for early intervention in canine hip dysplasia (CHD) risk management, for the prevention of the progression of secondary osteoarthritis (OA), and for selective breeding. Design Two sets of dogs (6 breeds) were genotyped with dense SNPs covering the entire canine genome. The first set contained 359 dogs upon which a predictive formula for genomic breeding value (GBV) was derived by using their estimated breeding value (EBV) of the Norberg angle (a measure of CHD) and their genotypes. To investigate how well the formula would work for an individual dog with genotype only (without using EBV or phenotype), a cross validation was performed by masking the EBV of one dog at a time. The genomic data and the EBV of the remaining dogs were used to predict the GBV for the single dog that was left out. The second set of dogs included 38 new Labrador retriever dogs, which had no pedigree relationship to the dogs in the first set. Results The cross validation showed a strong correlation (r>0.7) between the EBV and the GBV. The independent validation showed a strong correlation (r=0.5) between GBV for the Norberg angle and the observed Norberg angle (no EBV was available for the new 38 dogs). Sensitivity, specificity, positive, and negative predictive value of the genomic data were all above 70%. Conclusions Prediction of CHD from genomic data is feasible, and can be applied for risk management of CHD and early selection for genetic improvement to reduce the prevalence of CHD in breeding programs. The prediction can be implemented before maturity, at which age current radiographic screening programs are traditionally applied, and as soon as DNA is available. PMID:21215318

  5. Intraspecies genotypic heterogeneity among Mycoplasma gallisepticum strains.

    OpenAIRE

    Santha, M; Lukacs, K; Burg, K; Bernath, S; Rasko, I; Stipkovits, L.

    1988-01-01

    The DNA cleavage patterns and protein profiles of six Mycoplasma gallisepticum strains from various parts of the world were compared. Obvious differences among the strains were obtained by DNA restriction analysis. Reflection of genotypic variations in the polypeptide patterns was less pronounced; slight differences in the protein profiles of the strains were found. The data presented here indicate that some intraspecies polymorphism exists among M. gallisepticum strains.

  6. Intraspecies genotypic heterogeneity among Mycoplasma gallisepticum strains.

    Science.gov (United States)

    Santha, M; Lukacs, K; Burg, K; Bernath, S; Rasko, I; Stipkovits, L

    1988-01-01

    The DNA cleavage patterns and protein profiles of six Mycoplasma gallisepticum strains from various parts of the world were compared. Obvious differences among the strains were obtained by DNA restriction analysis. Reflection of genotypic variations in the polypeptide patterns was less pronounced; slight differences in the protein profiles of the strains were found. The data presented here indicate that some intraspecies polymorphism exists among M. gallisepticum strains. PMID:2895605

  7. Wheat genotypes under different seeding rates

    Directory of Open Access Journals (Sweden)

    Luís César Vieira Tavares

    2014-06-01

    Full Text Available The wheat tillering capacity defines yield and yield components, being affected by seeding rate. This study aimed at evaluating wheat genotypes under different seeding rates, in Londrina and Ponta Grossa, Paraná State, Brazil, in 2009 and 2010. A completely randomized blocks design, in a factorial scheme, with four replications, was used. The agronomic traits of three wheat genotypes (PF 014384, BRS Tangará and BRS Pardela were evaluated under the seeding rates of 150 pl m-2, 250 pl m-2, 350 pl m-2 and 450 pl m-2. In Londrina, the maximum yield was observed at densities close to 270 pl m-2, while in Ponta Grossa (2009 there was a linear fit. There was no adjustment for plant height, concerning seeding rate. The number of ears per area (ears m-2 was higher in Ponta Grossa (2009 and did not differ between the locations, in 2010. In Ponta Grossa (2010, the highest one thousand seeds weight was estimated at the density of 341 pl m-2, while in Londrina (2010 it was estimated at 150 pl m-2 and 450 pl m-2. The seeding rate affected grain yield, depending on place and year. In Londrina, there was a limit for yield, concerning seeding rate. The one thousand seeds weight was influenced by seeding rate, depending on year and location. Plant height was affected by genotype and growing area.

  8. Screening cotton genotypes for seedling drought tolerance

    Directory of Open Access Journals (Sweden)

    Penna Julio C. Viglioni

    1998-01-01

    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.

  9. The genotype role in maize competitive ability

    Directory of Open Access Journals (Sweden)

    Simić Milena

    2009-01-01

    Full Text Available Growing competitive crops is an important component of the integrated weed management system, although selection of genotypes with the increased competitive ability is rather difficult. The possibility of reducing weed infestation by increasing the competitive activity of crops by growing genotypes, i.e. hybrids that better 'endure' a greater density, depends on the FAO maturity group and morphological properties of a genotype, environmental conditions and the growing regions. The competition between maize and weeds varies over the modified crop arrangement pattern. The greatest weed infestation is recorded in the crops of the sparse-spaced plants, while the height and the weight of weeds are significantly lower in closely-spaced plants. The height, growth intensity in the initial stages, embryo vigour and leaf area of the plant are important for a greater competitive ability, as they are components of competitive effects of crops on weeds. Weed infestation and maize hybrids yielding were studied in dependence on the hybrids arrangement pattern and the application of herbicides. Obtained results show statistically significant differences in the weed fresh weight, but only in certain years and in accordance with differences in the height and the leaf area of ZP maize hybrids.

  10. Morpho-physiological characterization of soybean genotypes under subtropical environment

    Directory of Open Access Journals (Sweden)

    Al-Hadi Gaffar M.A.

    2017-01-01

    Full Text Available Soybean is a promising oilseed crop in rice-based cropping systems in South and Southeast Asia. In spite of immense scope of its expansion, the crop is not being popular to the farmers because of poor yield of the existing cultivars. Therefore, this study evaluated eighty-soybean genotypes of diverse growth habits with a view to searching genotype(s of desirable morpho-physiological characters and high yield potential. Sixteen quantitative plant traits were evaluated to classify the genotypes into different groups using various multivariate methods. A wide range of variation was found in almost all qualitative plant traits. The study reveals that plants tend to become taller as the phenological cycle is longer. Seed yield was the product of the number of pods per plant, pod weight and seeds per pod. The first three components of principal component analysis explained 75% of the total variations of the soybean genotypes. Using Dendrogram from cluster analysis, the genotypes were grouped into six clusters. The maximum number of genotypes was concentrated in cluster 5 followed by clusters 4. The phenology, plant height, the number of pods and seed yield were the important discriminating variables in grouping the genotypes. The number of pods per plant displayed the principal role in explaining the maximum variance in the genotypes. The clustering pattern of the genotypes revealed that the genotypes under cluster 2 and cluster 6 were long statures, late maturing and produced higher seed yield. The genotype G00003 under cluster 2 is the best entry giving the highest seed yield. From cluster 6, the genotype G00209 could be the better choice for much better seed yield. The cluster 3 genotypes were comparatively early maturing and gave reasonable yield. It is concluded that the genotypes under clusters 2 and 6 and 3 can be important resources for developing a high yielding variety and sustainability of growing soybean in the subtropical conditions.

  11. THE EFFECT OF GENOTYPE AND SEX ON PORK QUALITY

    Directory of Open Access Journals (Sweden)

    Marjeta Furman

    2007-06-01

    Full Text Available The effects of genotype and sex on the most important factors for technological meat quality were analyzed. In the experiment 63 gilts and 57 barrows of three different boar genotypes (44, 54 and 74 were included. Slaughter was carried out in two groups, the first was about 100 kg and the second group was about 125 kg of live weight. After the slaughter colour of meat, pH value, drip loss and conductivity were measured and intramuscular fat was defined in laboratory. Statistical analysis of data was done with statistical package SAS/STAT with last square method where procedure for general linear models (GLM was used. The effects were genotype, sex and carcass weight as regression. The results showed that barrows had significant higher content of intramuscular fat than gilts at 100 kg (p=0.0019 and 125 kg (p<0.0001 of live weight, respectively. In other traits sex did not have an influence. Genotype had no effect on intramuscular fat content. Genotype 74 had darker meat (lower value L* in both groups. Genotype 44 had significant higher value a* and value b*. There were no differences between genotype in pH and conductivity in the first group. In the second group genotype 44 had lower pH value as genotype 54 (p=0.0345 and genotype 74 (p=0.0188 and higher conductivity (p=0.0004 and p=0.0001 on m. longissimus dorsi. On m. semimembranossus genotype 54 had higher pH than genotype 44 (p=0.0160 and lower than genotype 74 (p=0.0148. Drip loss on both muscles was higher in genotype 44 in the first group and higher than genotype 74 in the second group.

  12. Identification of polymorphic inversions from genotypes

    Directory of Open Access Journals (Sweden)

    Cáceres Alejandro

    2012-02-01

    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

  13. 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

  14. Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch

    Directory of Open Access Journals (Sweden)

    Mitui Marcelo

    2012-08-01

    Full Text Available Abstract Reverse transcription (RT-PCR is now the standard method for typing group A rotaviruses (RVA to monitor the circulating genotypes in a population. Selection of primers that can accurately type the circulating genotypes is crucial in the context of vaccine introduction and correctly interpreting the impact of vaccination on strain distribution. To our knowledge this study is the first report from Asia of misidentification of genotype G9 as G3 due to a primer-template mismatch. We tested two published G-genotype specific primers sets, designed by Gouvea and colleagues (Set A and Iturriza‐Gomara and colleagues (Set B on RVA from Hong Kong and Sri Lanka. Among 52 rotaviruses typed as G3 by set A primers, 36 (69.2% were identified as G9 by nucleotide sequencing and set B primers. Moreover, of 300 rotaviruses tested, 28.3% were untypable by set A primers whereas only 12.3% were untypable by set B primers. Our findings reinforce the need to periodically monitor the primers used for RVA genotyping.

  15. Genotyping of HCV RNA Reveals That 3a Is the Most Prevalent Genotype in Mardan, Pakistan

    Directory of Open Access Journals (Sweden)

    Sajid Ali

    2014-01-01

    Full Text Available The clinical outcomes of patients infected with hepatitis C virus (HCV range from acute resolving hepatitis to chronic liver diseases such as liver cirrhosis or hepatocellular carcinoma. Identification of the infecting virus genotype is indispensable for the exploration of many aspects of HCV infection, including epidemiology, pathogenesis, and response to antiviral therapy. 1419 individuals were screened for anti-HCV in this study, of which 166 (11.7% were found reactive by ICT (Immunochromatographic test. These 166 anti-HCV positive and 26 normal individuals were further analyzed. RNA was extracted from serum and reverse-transcribed to cDNA and the core region of HCV genome was targeted and amplified by multiplex PCR. HCV RNA was detected in 121 individuals, of which 87 were male and 34 were female. Genotype 3a was the most prevalent among all the genotypes observed followed by 3b. Genotypes 1a, 2a, and 2b were found in 10.89%, 13.22%, and 6.61% patients, respectively. 25.41% of the HCV RNA positive samples were not typed. 6.05% of patients were found having mixed genotypes. These findings will not only help the physicians to prescribe more appropriate treatment for the HCV infection but will also draw the attention of health-related policy makers to devise strategies to curb the disease more effectively.

  16. Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch.

    Science.gov (United States)

    Mitui, Marcelo Takahiro; Chandrasena, Tga Nilmini; Chan, Paul Ks; Rajindrajith, Shaman; Nelson, E Anthony S; Leung, Ting Fan; Nishizono, Akira; Ahmed, Kamruddin

    2012-08-03

    Reverse transcription (RT)-PCR is now the standard method for typing group A rotaviruses (RVA) to monitor the circulating genotypes in a population. Selection of primers that can accurately type the circulating genotypes is crucial in the context of vaccine introduction and correctly interpreting the impact of vaccination on strain distribution. To our knowledge this study is the first report from Asia of misidentification of genotype G9 as G3 due to a primer-template mismatch. We tested two published G-genotype specific primers sets, designed by Gouvea and colleagues (Set A) and Iturriza-Gomara and colleagues (Set B) on RVA from Hong Kong and Sri Lanka. Among 52 rotaviruses typed as G3 by set A primers, 36 (69.2%) were identified as G9 by nucleotide sequencing and set B primers. Moreover, of 300 rotaviruses tested, 28.3% were untypable by set A primers whereas only 12.3% were untypable by set B primers. Our findings reinforce the need to periodically monitor the primers used for RVA genotyping.

  17. Citrus tristeza virus: Evolution of complex and varied genotypic groups

    Directory of Open Access Journals (Sweden)

    Scott J Harper

    2013-04-01

    Full Text Available Amongst the Closteroviridae, Citrus tristeza virus (CTV is almost unique in possessing a number of distinct and characterized strains, isolates of which produce a wide range of phenotype combinations among its different hosts. There is little understanding to connect genotypes to phenotypes, and to complicate matters more, these genotypes are found throughout the world as members of mixed populations within a single host plant. There is essentially no understanding of how combinations of genotypes affect symptom expression and disease severity. We know little about the evolution of the genotypes that have been characterized to date, little about the biological role of their diversity and particularly, about the effects of recombination. Additionally, genotype grouping has not been standardized. In this study we utilized an extensive array of CTV genomic information to classify the major genotypes, and to determine the major evolutionary processes that led to their formation and subsequent retention. Our analyses suggest that three major processes act on these genotypes: 1. ancestral diversification of the major CTV lineages, followed by 2. conservation and co-evolution of the major functional domains within, though not between CTV genotypes, and 3. extensive recombination between lineages that have given rise to new genotypes that have subsequently been retained within the global population. The effects of genotype diversity and host interaction are discussed, as is a proposal for standardizing the classification of existing and novel CTV genotypes.

  18. Citrus tristeza virus: Evolution of Complex and Varied Genotypic Groups.

    Science.gov (United States)

    Harper, S J

    2013-01-01

    Amongst the Closteroviridae, Citrus tristeza virus (CTV) is almost unique in possessing a number of distinct and characterized strains, isolates of which produce a wide range of phenotype combinations among its different hosts. There is little understanding to connect genotypes to phenotypes, and to complicate matters more, these genotypes are found throughout the world as members of mixed populations within a single host plant. There is essentially no understanding of how combinations of genotypes affect symptom expression and disease severity. We know little about the evolution of the genotypes that have been characterized to date, little about the biological role of their diversity and particularly, about the effects of recombination. Additionally, genotype grouping has not been standardized. In this study we utilized an extensive array of CTV genomic information to classify the major genotypes, and to determine the major evolutionary processes that led to their formation and subsequent retention. Our analyses suggest that three major processes act on these genotypes: (1) ancestral diversification of the major CTV lineages, followed by (2) conservation and co-evolution of the major functional domains within, though not between CTV genotypes, and (3) extensive recombination between lineages that have given rise to new genotypes that have subsequently been retained within the global population. The effects of genotype diversity and host-interaction are discussed, as is a proposal for standardizing the classification of existing and novel CTV genotypes.

  19. Genotypic diversity of root and shoot characteristics of

    Directory of Open Access Journals (Sweden)

    ali ganjali

    2009-06-01

    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

  20. Hepatitis B virus genotype E variability in Africa.

    Science.gov (United States)

    Hübschen, Judith M; Andernach, Iris E; Muller, Claude P

    2008-12-01

    In sub-Saharan Africa, genotype E is the predominant genotype throughout a vast region spanning from Senegal to Namibia and extending to the Central African Republic in the East. Despite its wide geographic distribution and the high prevalence throughout this genotype E crescent, this genotype has a very low genetic diversity. Here we review our current understanding of genotype E reanalysing all currently available sequences of the S gene and the complete genome. Phylogenetic analysis of the complete genome sequences confirmed a previously suggested South-West/Central African cluster and several lineages of West African sequences. The overall mean genetic distance was 1.71%, with the more Southern countries of the genotype E crescent exhibiting lower distances than the Northern countries. Genotype E seems to have a longer natural history in the Northern part of the genotype E crescent than in the Southern countries. As genotype E is essentially absent from the Americas despite the Afro-American slave trade until at least the beginning of the 19th century, genotype E strains may have been introduced into the general African population only within the past 200 years. How the virus may have spread throughout the genotype E crescent warrants further investigation.

  1. Citrus tristeza virus: Evolution of Complex and Varied Genotypic Groups

    Science.gov (United States)

    Harper, S. J.

    2013-01-01

    Amongst the Closteroviridae, Citrus tristeza virus (CTV) is almost unique in possessing a number of distinct and characterized strains, isolates of which produce a wide range of phenotype combinations among its different hosts. There is little understanding to connect genotypes to phenotypes, and to complicate matters more, these genotypes are found throughout the world as members of mixed populations within a single host plant. There is essentially no understanding of how combinations of genotypes affect symptom expression and disease severity. We know little about the evolution of the genotypes that have been characterized to date, little about the biological role of their diversity and particularly, about the effects of recombination. Additionally, genotype grouping has not been standardized. In this study we utilized an extensive array of CTV genomic information to classify the major genotypes, and to determine the major evolutionary processes that led to their formation and subsequent retention. Our analyses suggest that three major processes act on these genotypes: (1) ancestral diversification of the major CTV lineages, followed by (2) conservation and co-evolution of the major functional domains within, though not between CTV genotypes, and (3) extensive recombination between lineages that have given rise to new genotypes that have subsequently been retained within the global population. The effects of genotype diversity and host-interaction are discussed, as is a proposal for standardizing the classification of existing and novel CTV genotypes. PMID:23630519

  2. Genotyping by genome reducing and sequencing for outbred animals.

    Directory of Open Access Journals (Sweden)

    Qiang Chen

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

  3. Performance Comparison of the Versant HCV Genotype 2.0 Assay (LiPA) and the Abbott Realtime HCV Genotype II Assay for Detecting Hepatitis C Virus Genotype 6

    Science.gov (United States)

    Yang, Ruifeng; Cong, Xu; Du, Shaocai; Fei, Ran; Rao, Huiying

    2014-01-01

    The Versant HCV genotype 2.0 assay (line probe assay [LiPA] 2.0), based on reverse hybridization, and the Abbott Realtime HCV genotype II assay (Realtime II), based on genotype-specific real-time PCR, have been widely used to analyze hepatitis C virus (HCV) genotypes. However, their performances for detecting HCV genotype 6 infections have not been well studied. Here, we analyzed genotype 6 in 63 samples from the China HCV Genotyping Study that were originally identified as genotype 6 using the LiPA 2.0. The genotyping results were confirmed by nonstructural 5B (NS5B) or core sequence phylogenetic analysis. A total of 57 samples were confirmed to be genotype 6 (51 genotype 6a, 5 genotype 6n, and 1 genotype 6e). Four samples identified as a mixture of genotypes 6 and 4 by the LiPA 2.0 were confirmed to be genotype 3b. The remaining two samples classified as genotype 6 by the LiPA 2.0 were confirmed to be genotype 1b, which were intergenotypic recombinants and excluded from further comparison. In 57 genotype 6 samples detected using the Realtime II version 2.00 assay, 47 genotype 6a samples were identified as genotype 6, one 6e sample was misclassified as genotype 1, and four 6a and five 6n samples yielded indeterminate results. Nine nucleotide profiles in the 5′ untranslated region affected the performances of both assays. Therefore, our analysis shows that both assays have limitations in identifying HCV genotype 6. The LiPA 2.0 cannot distinguish some 3b samples from genotype 6 samples. The Realtime II assay fails to identify some 6a and all non-6a subtypes, and it misclassifies genotype 6e as genotype 1. PMID:25100817

  4. Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing.

    Directory of Open Access Journals (Sweden)

    Niloofar Vaghefi

    Full Text Available Genotyping-by-sequencing (GBS was conducted on 333 Cercospora isolates collected from Beta vulgaris (sugar beet, table beet and swiss chard in the USA and Europe. Cercospora beticola was confirmed as the species predominantly isolated from leaves with Cercospora leaf spot (CLS symptoms. However, C. cf. flagellaris also was detected at a frequency of 3% in two table beet fields in New York. Resolution of the spatial structure and identification of clonal lineages in C. beticola populations using genome-wide single nucleotide polymorphisms (SNPs obtained from GBS was compared to genotyping using microsatellites. Varying distance thresholds (bitwise distance = 0, 1.854599 × 10-4, and 1.298 × 10-3 were used for delineation of clonal lineages in C. beticola populations. Results supported previous reports of long distance dispersal of C. beticola through genotype flow. The GBS-SNP data set provided higher resolution in discriminating clonal lineages; however, genotype identification was impacted by filtering parameters and the distance threshold at which the multi-locus genotypes (MLGs were contracted to multi-locus lineages. The type of marker or different filtering strategies did not impact estimates of population differentiation and structure. Results emphasize the importance of robust filtering strategies and designation of distance thresholds for delineating clonal lineages in population genomics analyses that depend on individual assignment and identification of clonal lineages. Detection of recurrent clonal lineages shared between the USA and Europe, even in the relaxed-filtered SNP data set and with a conservative distance threshold for contraction of MLGs, provided strong evidence for global genotype flow in C. beticola populations. The implications of intercontinental migration in C. beticola populations for CLS management are discussed.

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

    Directory of Open Access Journals (Sweden)

    Prasanth VP

    2006-08-01

    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

  6. Estruturação de um programa de qualificação em gestão da qualidade, segurança e saúde ocupacional: apresentação dos resultados de uma aplicação piloto realizada no aglomerado metal-mecânico de Sertãozinho - São Paulo Structuring a qualification program on quality, occupational health and safety management: presenting the results of a pilot application in the metal-mechanic cluster in Sertõzinho, São Paulo state, Brazil

    Directory of Open Access Journals (Sweden)

    Gislaine Aparecida Vitoreli

    2012-12-01

    Full Text Available Este artigo apresenta e discute a estruturação de um programa de qualificação para pequenas e médias empresas em gestão de qualidade, segurança e saúde ocupacional. O programa de qualificação proposto inclui a estruturação de um modelo de sistema de gestão integrado bem como a estruturação dos processos de implementação e auditoria deste sistema. O método de pesquisa-ação foi adotado para a condução da aplicação piloto desta proposta que foi realizada no aglomerado metal-mecânico de Sertãozinho, São Paulo. Os resultados preliminares da aplicação piloto apontam para possibilidade de operacionalização da proposta que pode contribuir em dois aspectos importantes: maior competitividade para as empresas do aglomerado e melhoria na competência da governança local em coordenar ações conjuntas. Ressalta-se ainda a existência de desafios para a continuidade do programa de qualificação, sendo a sua manutenção pela agência de coordenação local um dos mais críticos.This article aims to present and discuss the framework of a qualification program on quality, occupational health and safety management for small and medium sized enterprises. The proposed qualification program includes an integrated management system model, as well as a process for conducting periodic audits. Action research was the methodological approach chosen to conduct the pilot application of the proposed qualification program. The pilot application was performed with a group of small and medium enterprises of the Sertãozinho's metal-mechanic cluster, located in the state of São Paulo Preliminary results indicate the possibility of operationalization of the proposal as well as its contributions to two key aspects: increase competitiveness of the companies in the cluster and increase competence of the cluster governance team to coordinate joint actions. Nevertheless, there are great challenges to maintain the qualification program, and its

  7. NUTRITIONAL AND ROTI QUALITY OF SORGHUM GENOTYPES

    Directory of Open Access Journals (Sweden)

    U.D. Chavan

    2016-10-01

    Full Text Available Sorghum grains are mostly used for the roti preparation. The M 35-1 (Maldhandi a sorghum cultivar is known for its good quality of roti due to having pearly white grain color, its flour having higher water holding capacity, and good organoleptic taste. However, this cultivar is low yielder. To evolve sorghum high yielding genotype coupled with this good roti qualities, systematic breeding program was planned and executed to overcome this problem. Twenty local land races, 92 genotypes, and seven improved cultivars of sorghum along with check M 35-1 were studied for various nutritional quality parameters, with special reference to the roti quality. Considering nutritional quality and organoleptic evaluation parameters studied for roti quality, the local land races viz., RSLG 428-1, RSLG 1238, RSLG 1275 and the genotypes viz., RSV 290, RSV 292, RSV 858, RSV 859, RSV 861, RSV 868, RSV 894, RSV 985, RSV 992, RSV 995, RSV 999 were found to be promising for protein, sugar, water absorption, and soluble protein content. Therefore, they can be used for further improvement in nutritional quality through breeding program. Among the improved cultivars, Phule Vasudha (RSV 423, CSV 22, and Phule Chitra (SPV 1546 werefound to be most promising for roti quality. The maximum score for overall acceptability was found for Phule Vasudha followed by Phule Anuradha (RSV 458, Phule Yeshoda (RSLG 262, and Phule Maulee (CSV 216.

  8. SBE primer : multiplexing minisequencing-based genotyping

    Energy Technology Data Exchange (ETDEWEB)

    Kaderali, L. (Lars); Deshpande, A. (Alina); Uribe-Romeo, F. J. (Francisco J.); Schliep, A.; Torney, D. C. (David C.)

    2002-01-01

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

  9. Multilocus genotyping of Giardia duodenalis in Malaysia.

    Science.gov (United States)

    Huey, Choy Seow; Mahdy, Mohammed A K; Al-Mekhlafi, Hesham M; Nasr, Nabil A; Lim, Yvonne A L; Mahmud, Rohela; Surin, Johari

    2013-07-01

    Giardia duodenalis is considered the most common intestinal parasite in humans worldwide. In Malaysia, many studies have been conducted on the epidemiology of giardiasis. However, there is a scarcity of information on the genetic diversity and the dynamics of transmission of G. duodenalis. The present study was conducted to identify G. duodenalis assemblages and sub-assemblages based on multilocus analysis of the glutamate dehydrogenase (gdh), beta-giardin (bg) and triose phosphate isomerase (tpi) genes. Faecal specimens were collected from 484 Orang Asli children with a mean age of 7 years and examined using light microscopy. Specimens positive for Giardia were subjected to PCR analysis of the three genes and subsequent sequencing in both directions. Sequences were edited and analysed by phylogenetic analysis. G. duodenalis was detected in 17% (84 of 484) of the examined specimens. Among them, 71 were successfully sequenced using at least one locus. Genotyping results showed that 30 (42%) of the isolates belonged to assemblage A, 32 (45%) belonged to assemblage B, while discordant genotype results were observed in 9 specimens. Mixed infections were detected in 43 specimens using a tpi-based assemblage specific protocol. At the sub-assemblages level, isolates belonged to assemblage A were AII. High nucleotide variation found in isolates of assemblage B made subtyping difficult to achieve. The finding of assemblage B and the anthroponotic genotype AII implicates human-to-human transmission as the most possible mode of transmission among Malaysian aborigines. The high polymorphism found in isolates of assemblage B warrants a more defining tool to discriminate assemblage B at the sub-assemblage level. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Audioprofiles and antioxidant enzyme genotypes in presbycusis.

    Science.gov (United States)

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

    2012-11-01

    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.

  11. Celer: an Efficient Program for Genotype Elimination

    Directory of Open Access Journals (Sweden)

    Nicoletta De Francesco

    2010-08-01

    Full Text Available This paper presents an efficient program for checking Mendelian consistency in a pedigree. Since pedigrees may contain incomplete and/or erroneous information, geneticists need to pre-process them before performing linkage analysis. Removing superfluous genotypes that do not respect the Mendelian inheritance laws can speed up the linkage analysis. We have described in a formal way the Mendelian consistency problem and algorithms known in literature. The formalization helped to polish the algorithms and to find efficient data structures. The performance of the tool has been tested on a wide range of benchmarks. The results are promising if compared to other programs that treat Mendelian consistency.

  12. Coffee Berry Borer Resistance in Coffee Genotypes

    Directory of Open Access Journals (Sweden)

    Gustavo Hiroshi Sera

    2010-04-01

    Full Text Available The aim of this study was to evaluate the coffee germplasm of the Paraná Agronomic Institute (IAPAR for resistance to the coffee-berry-borer. Preliminary field evaluation was performed in August 2004 and the fruits of less damaged genotypes in the field were evaluated under controlled condition with obligated and free choice experiments established in a randomized complete design with three replications. The genotypes were evaluated fifteen days after infestation with one borer per fruit in Petri dishes. The data were analyzed by the Scott-Knott means test at 1 % and by the χ2 test. Statistical analysis indicated that Coffea kapakata, Psilanthus bengalensis, C. eugenioides and genotypes with C. eugenioides genes were resistant. These genotypes presented low frequency of bored grains. C. eugenioides and C. kapakata could present resistance at epicarp level but not in the grain. P. bengalensis could present resistance also in the grains.O objetivo deste trabalho foi identificar fontes de resistência genética a H. hampei em diferentes espécies de café do banco de germoplasma do Instituto Agronômico do Paraná (IAPAR, Londrina, PR. Foram realizadas avaliações preliminares de campo, para posterior testes de confinamento e de livre escolha, em laboratório, instalados em delineamento inteiramente casualizado com três repetições. Os genótipos foram avaliados quinze dias após a infestação com uma broca por fruto em placas de petri. Os dados foram analisados pelo teste de médias Scott-Knott a 1 % e pelo teste de χ2. Foi observado que C. eugenioides, C. kapakata e P. bengalensis constituem importantes fontes de resistência à broca, pois apresentaram menor freqüência de grãos brocados. Os dois primeiros podem apresentar substâncias voláteis antagônicas à broca na casca e a resistência de P. bengalensis pode estar também no grão.

  13. Single molecule genotyping by TIRF microscopy.

    Science.gov (United States)

    Rüttinger, Steffen; Lamarre, Baptiste; Knight, Alex E

    2008-09-01

    As part of a programme to develop a metrological framework for single molecule measurements in biology, we have investigated the applications of single molecule imaging to genomics. Specifically, we have developed a technique for measuring the frequencies of single nucleotide polymorphisms (SNPs) in complex or pooled samples of DNA. We believe that this technique has applications to statistical genotyping-the identification of correlations between SNP frequencies and particular phenotypes-and other areas where it is desirable to track the frequencies of SNPs in complex DNA populations.

  14. Prevalence of hepatitis C virus genotypes in Mexican patients.

    Science.gov (United States)

    Dehesa-Violante, Margarita; Bosques-Padilla, Francisco; Kershenobich-Stalnikowitz, David

    2007-01-01

    Worldwide HCV studies have documented its large genetic variability; HCV has major genetic groups called genotypes that are designated from 1 to 6, as well as > 50 subtypes. This is very important considering that treatment response varies according to genotype. The purpose of this trial was to ascertain prevalence of HCV genotypes in a group of patients from 10 states in Mexico. This study enrolled patients from 22 hospitals throughout the country. Patients tested positive to hepatitis C antibody and genotyping was preformed by Lipa method. To carry out a comparison, two regions were arbitrarily defined, the northern region embodied the cities of Culiacan, Torreón, Monterrey, Ciudad Obregón, and Tijuana, while the central-southern region embodied Mexico City, Guadalajara, León, Puebla, and Veracruz. The test was performed on a total of 421 patients. The most frequently found genotype was genotype 1, present in 70.55% of cases. The majority (40.1%) corresponded to genotype 1b, 17.81% to 1a, and genotype 2a/2c (11.64%). A total of 29.4% of samples corresponded to genotypes non-1. Genotype 1 was found in 72.34 (northern region) and 70.03% (central-southern) of the two regions, and genotypes non-1 in 27.66 and 29.97%, respectively. We conclude that the most frequent genotype in Mexico is 1b, followed by 1a, and, in third place 1b1a, for a total of 70.55%; the remaining 29.45% had genotypes other than 1.

  15. Geographic distribution of hepatitis C virus genotypes in Brazil

    Directory of Open Access Journals (Sweden)

    Campiotto S.

    2005-01-01

    Full Text Available Brazil is a country of continental dimension with a population of different ethnic backgrounds. Thus, a wide variation in the frequencies of hepatitis C virus (HCV genotypes is expected to occur. To address this point, 1,688 sequential samples from chronic HCV patients were analyzed. HCV-RNA was amplified by the RT-PCR from blood samples collected from 1995 to 2000 at different laboratories located in different cities from all Brazilian States. Samples were collected in tubes containing a gel separator, centrifuged in the site of collection and sent by express mail in a refrigerated container to Laboratório Bioquímico Jardim Paulista, São Paulo, SP, Brazil. HCV- RNA was extracted from serum and submitted to RT and nested PCR using standard procedures. Nested PCR products were submitted to cycle sequencing reactions without prior purification. Sequences were analyzed for genotype determination and the following frequencies were found: 64.9% (1,095 for genotype 1, 4.6% (78 for genotype 2, 30.2% (510 for genotype 3, 0.2% (3 for genotype 4, and 0.1% (2 for genotype 5. The frequencies of HCV genotypes were statistically different among Brazilian regions (P = 0.00017. In all regions, genotype 1 was the most frequent (51.7 to 74.1%, reaching the highest value in the North; genotype 2 was more prevalent in the Center-West region (11.4%, especially in Mato Grosso State (25.8%, while genotype 3 was more common in the South (43.2%. Genotypes 4 and 5 were rarely found and only in the Southeast, in São Paulo State. The present data indicate the need for careful epidemiological surveys throughout Brazil since knowing the frequency and distribution of the genotypes would provide key information for understanding the spread of HCV.

  16. HPV genotypes co-infections associated with cervical carcinoma: Special focus on phylogenetically related and non-vaccine targeted genotypes.

    Science.gov (United States)

    Senapati, Rashmirani; Nayak, Bhagyalaxmi; Kar, Shantanu Kumar; Dwibedi, Bhagirathi

    2017-01-01

    HPV is the major causative agent for cervical cancer. Study on the risk of cervical cancer associated with different hr-HPV genotypes would be useful for disease management and new vaccine strategy. With limited reports available, the present study aimed to investigate the pattern of HPV genotypes coinfections and risk of cervical carcinoma associated with them in Indian population. 15 HPV genotypes were detected by E6/E7 multiplex nested type-specific PCR in the HPV-positive cervical samples of 172 cervical cancer cases and 174 subjects with normal cytology. Association between the genotypes and cervical cancer was estimated by calculating the Odds ratio and 95% confidence interval. Risk of cervical carcinoma was associated with multiple genotypes excluding HPV16 (OR:5.87; 95% CI-1.28-26-29; p = .02), multiple genotypes excluding HPV18 (OR = 2.5; 95% CI = 1.09-6.05; p = .03), multiple genotypes of α9 species(OR = 5.3 95% CI = 1.14-24.03; p = .007), and multiple genotypes of α7 species (OR = 2.5; 95% CI = .49-13.45; p = .2). Genotypes not targeted by quadrivalent vaccine types (OR = 2.94 95% CI = 1.48-5.80; p = .001) conferred 2.94 fold higher risk of cervical carcinoma. Cases those coinfected with phylogenetically related genotypes (OR = 2.29; 95% CI(.69-7.59) p = .17) were at 2.9 fold higher risk of invasive cervical carcinoma than those infected with other genotypes although it is not statistically significant. Whereas phylogenetically unrelated genotypes coinfection is negatively associated with cervical carcinoma (OR = .44 95% CI (.244-.8) p = .007) and it is statistically significant.Genotypes not targeted by 9-valent vaccines (OR = .40; 95% CI = .19-.85; p = .017) associated with lesser risk of cervical carcinoma as compared to other genotypes. Subjects infected with any HPV genotype/genotypes excluding HPV16 in association with HPV 18 (OR = 4.1; 95% CI = 1.81-9.25 P = < .001) were at 4.1 fold higher risk of developing invasive cervical carcinoma

  17. Genotype harmonizer : automatic strand alignment and format conversion for genotype data integration

    NARCIS (Netherlands)

    Deelen, Patrick; Bonder, Marc Jan; van der Velde, K Joeri; Westra, Harm-Jan; Winder, Erwin; Hendriksen, Dennis; Franke, Lude; Swertz, Morris A

    2014-01-01

    BACKGROUND: To gain statistical power or to allow fine mapping, researchers typically want to pool data before meta-analyses or genotype imputation. However, the necessary harmonization of genetic datasets is currently error-prone because of many different file formats and lack of clarity about

  18. Advantages of continuous genotype values over genotype classes for GWAS in higher polyploids

    NARCIS (Netherlands)

    Grandke, Fabian; Singh, Priyanka; Heuven, Henri C.M.; Haan, de Jorn R.; Metzler, Dirk

    2016-01-01

    Background: Association studies are an essential part of modern plant breeding, but are limited for polyploid crops. The increased number of possible genotype classes complicates the differentiation between them. Available methods are limited with respect to the ploidy level or data producing

  19. Genotypic correlation and path analysis in early and super-early maize genotypes.

    Science.gov (United States)

    Alves, B M; Cargnelutti Filho, A

    2017-05-25

    The aims of this study were to assess the linear relationships between agronomic and nutritional traits and to identify promising traits for indirect selection in early and super-early maturing maize genotypes. Two trials were run in the 2009/2010 agricultural year, each consisting of a randomized block design with three replications. One trial was run on 36 early maturing maize genotypes and the other on 22 super-early maturing genotypes. Six agronomic traits, 11 protein-nutritional traits, and four energetic-nutritional traits were measured. Error normality assumptions were verified using the Kolmogorov-Smirnov test and residual variance homogeneity assumptions using the Levene test. Analysis of variance and the F-test were run for each of the 21 traits. Next, the genotype correlation coefficient matrix was estimated for the 21 traits and each trial. Ridge path analysis was based on values of k = 0.00 and k = 0.10 on the diagonal of X'X correlation matrix, taking the nutritional traits as principal variables and agronomic traits as explanatory variables. The number of days from sowing to male flowering, the number of days from sowing to female flowering, plant height, ear insertion height, ear weight and grain yield can be used in indirect selection as indicators of grain nutritional quality.

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

    Science.gov (United States)

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

    2016-11-01

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

  1. Associating Symptom Phenotype and Genotype in Preeclampsia.

    Science.gov (United States)

    Founds, Sandra A; Tsigas, Eleni; Ren, Dianxu; Barmada, M Michael

    2018-03-01

    Preeclampsia is a complex genetic disorder with an incompletely understood pathogenesis. Its phenotype may be better elucidated by integrating symptoms. This study aimed to identify symptoms by gestational age and associations with novel preeclampsia candidate genes. Women with a history of preeclampsia recruited from The Preeclampsia Registry completed clinical/demographic, symptom surveys and provided medical records. DNA extracted from saliva was processed with multiplexed assays for eight single-nucleotide polymorphisms (SNPs) selected to tag candidate genes and/or located in symptom susceptibility regions. Groups with versus without symptoms were compared using χ 2 . Associations between SNPs and symptoms were analyzed as genotype categories and presence/absence of the variant allele. Logistic regression modeling was conducted with exploratory p = .05. In 114 participants, 113 reported at least 1 of the 18 symptoms. Symptoms varied by trimester. Nine symptoms were associated with seven SNPs. Visual disturbances were associated with three SNPs and nausea/vomiting with two SNPs. Modeling adjustment for maternal age and parity resulted in 15 associations between 9 symptoms and 8 SNPs. Medical records demonstrated 100% concordance with self-reported diagnosis and 48% concordance with reported severity. Findings indicated novel symptom-genotype associations in preeclampsia. The small sample was self-selected, but results support future studies including medical records review. When validated, these results may lead to holistic phenotyping of women to characterize subsets of preeclampsia. This approach may optimize health in pregnancy and later life for mothers and offspring through prediction, prevention, and precision nursing care.

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

    Directory of Open Access Journals (Sweden)

    Suzanna M. Evans

    2016-02-01

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

  3. Genotype-Specific Evolution of Hepatitis E Virus

    Science.gov (United States)

    Brayne, Adam B.; Dearlove, Bethany L.; Lester, James S.; Kosakovsky Pond, Sergei L.

    2017-01-01

    ABSTRACT Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis globally. HEV comprises four genotypes with different geographic distributions and host ranges. We utilize this natural case-control study for investigating the evolution of zoonotic viruses compared to single-host viruses, using 244 near-full-length HEV genomes. Genome-wide estimates of the ratio of nonsynonymous to synonymous evolutionary changes (dN/dS ratio) located a region of overlapping reading frames, which is subject to positive selection in genotypes 3 and 4. The open reading frames (ORFs) involved have functions related to host-pathogen interaction, so genotype-specific evolution of these regions may reflect their fitness. Bayesian inference of evolutionary rates shows that genotypes 3 and 4 have significantly higher rates than genotype 1 across all ORFs. Reconstruction of the phylogenies of zoonotic genotypes demonstrates significant intermingling of isolates between hosts. We speculate that the genotype-specific differences may result from cyclical adaptation to different hosts in genotypes 3 and 4. IMPORTANCE Hepatitis E virus (HEV) is increasingly recognized as a pathogen that affects both the developing and the developed world. While most often clinically mild, HEV can be severe or fatal in certain demographics, such as expectant mothers. Like many other viral pathogens, HEV has been classified into several distinct genotypes. We show that most of the HEV genome is evolutionarily constrained. One locus of positive selection is unusual in that it encodes two distinct protein products. We are the first to detect positive selection in this overlap region. Genotype 1, which infects humans only, appears to be evolving differently from genotypes 3 and 4, which infect multiple species, possibly because genotypes 3 and 4 are unable to achieve the same fitness due to repeated host jumps. PMID:28202767

  4. Genotype-Specific Evolution of Hepatitis E Virus.

    Science.gov (United States)

    Brayne, Adam B; Dearlove, Bethany L; Lester, James S; Kosakovsky Pond, Sergei L; Frost, Simon D W

    2017-05-01

    Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis globally. HEV comprises four genotypes with different geographic distributions and host ranges. We utilize this natural case-control study for investigating the evolution of zoonotic viruses compared to single-host viruses, using 244 near-full-length HEV genomes. Genome-wide estimates of the ratio of nonsynonymous to synonymous evolutionary changes (dN/dS ratio) located a region of overlapping reading frames, which is subject to positive selection in genotypes 3 and 4. The open reading frames (ORFs) involved have functions related to host-pathogen interaction, so genotype-specific evolution of these regions may reflect their fitness. Bayesian inference of evolutionary rates shows that genotypes 3 and 4 have significantly higher rates than genotype 1 across all ORFs. Reconstruction of the phylogenies of zoonotic genotypes demonstrates significant intermingling of isolates between hosts. We speculate that the genotype-specific differences may result from cyclical adaptation to different hosts in genotypes 3 and 4.IMPORTANCE Hepatitis E virus (HEV) is increasingly recognized as a pathogen that affects both the developing and the developed world. While most often clinically mild, HEV can be severe or fatal in certain demographics, such as expectant mothers. Like many other viral pathogens, HEV has been classified into several distinct genotypes. We show that most of the HEV genome is evolutionarily constrained. One locus of positive selection is unusual in that it encodes two distinct protein products. We are the first to detect positive selection in this overlap region. Genotype 1, which infects humans only, appears to be evolving differently from genotypes 3 and 4, which infect multiple species, possibly because genotypes 3 and 4 are unable to achieve the same fitness due to repeated host jumps. Copyright © 2017 American Society for Microbiology.

  5. Hepatitis B virus genotypes A and D in Uganda.

    Science.gov (United States)

    Zirabamuzale, Jackie T; Opio, Christopher K; Bwanga, Freddie; Seremba, Emmanuel; Apica, Betty S; Colebunders, Robert; Ocama, Ponsiano

    2016-01-01

    The prevalence of hepatitis B virus (HBV) infection in Uganda is 10%. Hepatitis B virus genotypes impact on treatment response, rate of spontaneous recovery and progression of chronic HBV infection and hepatocellular carcinoma. There is little information on the HBV genotypic distribution in Uganda. To determine HBV genotypes in Uganda. The MBN clinical laboratory performs HBV viral load and genotype testing in Uganda. It receives hepatitis B surface antigen (HBsAg)-positive samples from all over the country for additional HBV testing. Samples are stored for 6 months before being discarded. Our study used delinked stored samples. PCR-positive samples had DNA extracted and used as template for HBV genome amplification by nested PCR. Reverse hybridisation was performed and genotypes were determined by the line probe assay method (INNO-LiPA). One hundred stored HBsAg-positive plasma samples with detectable viral loads were analysed. Of these, 93 samples showed PCR amplification products and gave genotype-specific probe lines on the INNO-LiPA assay. Of the patients, where gender was recorded, 60.9% were female, and the overall median age (IQR) was 25 (2-60) years. There was a predominance of HBV genotype D (47 patients; 50.5%), followed by genotype A, (16 patients; 17.2%). One patient (1.1%) had genotype E. In 28% of the samples mixed infections were detected with genotypes A/E (9.7%) and A/D (6.5%) being most common. Genotypes B, C, E and H only occurred as part of mixed infections. Hepatitis B genotypes D and A were predominant in our study population.

  6. Deep Sequencing Analysis of HBV Genotype Shift and Correlation with Antiviral Efficiency during Adefovir Dipivoxil Therapy

    Science.gov (United States)

    Shan, Youlan; Huang, Wenxiang; Zhang, Dazhi; Zen, Aizhong; Zhou, Xin; Zhao, Yao; Gong, Xuyang; Xu, Ge; Zhang, Xiuyu; Chen, Juan; Huang, Ailong

    2015-01-01

    Background Viral genotype shift in chronic hepatitis B (CHB) patients during antiviral therapy has been reported, but the underlying mechanism remains elusive. Methods 38 CHB patients treated with ADV for one year were selected for studying genotype shift by both deep sequencing and Sanger sequencing method. Results 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. Conclusions 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. PMID:26110616

  7. Cryptosporidium parvum: infectivity and pathogenicity of the 'porcine' genotype

    DEFF Research Database (Denmark)

    Enemark, Heidi L.; Ahrens, Peter; Bille-Hansen, Vivi

    2003-01-01

    Genetic studies have demonstrated profound differences between the 'porcine' genotype of Cryptosporidium parvum, versus 'human' and 'bovine' genotypes. The study analysed infectivity and pathogenicity of the 'porcine' genotype (CPP-13 isolate) of C. parvum, and compared the results with published...... data on the 'bovine' genotype (CPB-0 isolate). This was investigated in calves and piglets from commercial herds. Piglets were mildly affected by the CPP-13 isolate, contrary to piglets infected with the CPB-0 isolate, which caused diarrhoea of a mean duration of 3.5 days. CPP-13 produced no or very...

  8. Genotype and Phenotype Analysis in Pediatric Patients with Cystinuria.

    Science.gov (United States)

    Kim, Ji Hyun; Park, Eujin; Hyun, Hye Sun; Lee, Beom Hee; Kim, Gu Hwan; Lee, Joo Hoon; Park, Young Seo; Kang, Hee Gyung; Ha, Il Soo; Cheong, Hae Il

    2017-02-01

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

  9. Genotype Calling from Population-Genomic Sequencing Data

    Science.gov (United States)

    Maruki, Takahiro; Lynch, Michael

    2017-01-01

    Genotype calling plays important roles in population-genomic studies, which have been greatly accelerated by sequencing technologies. To take full advantage of the resultant information, we have developed maximum-likelihood (ML) methods for calling genotypes from high-throughput sequencing data. As the statistical uncertainties associated with sequencing data depend on depths of coverage, we have developed two types of genotype callers. One approach is appropriate for low-coverage sequencing data, and incorporates population-level information on genotype frequencies and error rates pre-estimated by an ML method. Performance evaluation using computer simulations and human data shows that the proposed framework yields less biased estimates of allele frequencies and more accurate genotype calls than current widely used methods. Another type of genotype caller applies to high-coverage sequencing data, requires no prior genotype-frequency estimates, and makes no assumption on the number of alleles at a polymorphic site. Using computer simulations, we determine the depth of coverage necessary to accurately characterize polymorphisms using this second method. We applied the proposed method to high-coverage (mean 18×) sequencing data of 83 clones from a population of Daphnia pulex. The results show that the proposed method enables conservative and reasonably powerful detection of polymorphisms with arbitrary numbers of alleles. We have extended the proposed method to the analysis of genomic data for polyploid organisms, showing that calling accurate polyploid genotypes requires much higher coverage than diploid genotypes. PMID:28108551

  10. Temperature alters host genotype-specific susceptibility to chytrid infection

    National Research Council Canada - National Science Library

    Gsell, A.S; De Senerpont Domis, L.N; Van Donk, E; Ibelings, B.W

    2013-01-01

    .... We exposed seven genetically different but concurrent strains of the diatom Asterionella formosa to one genotype of its naturally co-occurring chytrid parasite Zygorhizidium planktonicum across five...

  11. The metabolomic profile of red non-V. vinifera genotypes.

    Science.gov (United States)

    Ruocco, Silvia; Stefanini, Marco; Stanstrup, Jan; Perenzoni, Daniele; Mattivi, Fulvio; Vrhovsek, Urska

    2017-08-01

    Wild American genotypes represent an important part of the Vitis germplasm in relation to grape improvement. Today, these genotypes are currently involved in breeding programmes in order to introgress traits resistant to pests and diseases in V. vinifera cultivars. Nevertheless, the metabolic composition of their grapes has not been widely investigated. This study aimed to explore in detail the metabolomic profile in terms of simple phenolic, proanthocyanidin, anthocyanin and lipid compounds in two hybrids and five American genotypes. The results were compared with those of two V. vinifera cultivars. A multi-targeted metabolomics approach using a combination of LC-MS and LC-DAD methods was used to identify and quantify 124 selected metabolites. The genotypes studied showed considerable variability in the metabolomic profile according to the grape composition of V. vinifera and other Vitis genotypes. As regards the composition of anthocyanins, not all wild genotypes contained both mono- and di-glucoside derivatives. Wild genotype 41B and V. vinifera cultivars contained only monoglucoside anthocyanins. The proanthocyanidins of non-V. vinifera genotypes were mainly rich in oligomers and short-chain polymers. The analysis of lipids in wild Vitis genotypes, here reported for the first time, showed the existence of a certain diversity in their composition suggesting a strong influence of the environmental conditions on the general lipid pattern. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Variability of acorn anatomical characteristics in Quercus robur L. genotypes

    Directory of Open Access Journals (Sweden)

    Nikolić Nataša P.

    2010-01-01

    Full Text Available The aim of this study was to examine variability of acorn anatomical characteristics in seventeen Quercus robur L. genotypes. Acorns were collected in clonal seed orchard Banov Brod (Srem, Vojvodina, Serbia. Microscopic measurements were done for pericarp (total thickness, thickness of exocarp and mesocarp, seed coat (total thickness, thickness of outer epidermis, parenchyma, and inner epidermis, and embryo axis (diameter, thickness of cortical region, and diameter of stellar zone. Obtained results revealed certain divergence between genotypes. The thickness of pericarp varied from 418 to 559 mm (genotypes 20 and 22, respectively. On average, the participation of exocarp in the total thickness of pericarp was 36.3%, of mesocarp 61.0%, while of endocarp 2.6%. The thickness of seed coat for individual genotypes ranged from 71 mm (genotype 28 to 157 mm (genotype 38. In addition, anatomic parameters of embryo axis varied among studied genotypes. The lowest cortical zone thickness and stellar zone diameter were measured in genotype 40, while the highest values in genotype 33.

  13. Noninvasive fetal RhD genotyping

    DEFF Research Database (Denmark)

    Clausen, Frederik Banch; Damkjær, Merete Berthu; Dziegiel, Morten Hanefeld

    2014-01-01

    Immunization against RhD is the major cause of hemolytic disease of the fetus and newborn (HDFN), which causes fetal or neonatal death. The introduction of postnatal immune prophylaxis in the 1960s drastically reduced immunization incidents in pregnant, D-negative women. In several countries......, antenatal prophylaxis is combined with postnatal prophylaxis to further minimize the immunization risk. Due to lack of knowledge of the fetal RhD type, antenatal prophylaxis is given to all D-negative women. In the European population, approximately 40% of pregnant women carry a D-negative fetus...... and are thus at no risk of immunization. Noninvasive fetal RhD genotyping enables antenatal prophylaxis to be targeted to only those women carrying a D-positive fetus to avoid unnecessary treatment. Based on an analysis of cell-free fetal DNA from the plasma of pregnant women, this approach has recently...

  14. Genome structural variation discovery and genotyping.

    Science.gov (United States)

    Alkan, Can; Coe, Bradley P; Eichler, Evan E

    2011-05-01

    Comparisons of human genomes show that more base pairs are altered as a result of structural variation - including copy number variation - than as a result of point mutations. Here we review advances and challenges in the discovery and genotyping of structural variation. The recent application of massively parallel sequencing methods has complemented microarray-based methods and has led to an exponential increase in the discovery of smaller structural-variation events. Some global discovery biases remain, but the integration of experimental and computational approaches is proving fruitful for accurate characterization of the copy, content and structure of variable regions. We argue that the long-term goal should be routine, cost-effective and high quality de novo assembly of human genomes to comprehensively assess all classes of structural variation.

  15. Genotypic Variation in Wheat Flour Lysophospholipids

    Directory of Open Access Journals (Sweden)

    Lei Liu

    2017-05-01

    Full Text Available Lysophospholipids (LPLs are the most abundant polar lipids in wheat endosperm and naturally complex with amylose, affecting starch physicochemical properties. We analyzed LPLs in wheat flour from 58 cultivars which differ by grain hardness using liquid chromatography mass spectrometry (LCMS. There were significant differences in LPL content between cultivars, demonstrating that genotype rather than environment contributes most to the total variance in wheat endosperm LPLs. Polar lipids such as LPLs may play a role in grain hardness through their interaction with puroindoline proteins, however, no strong correlation between kernel hardness and LPLs was detected. This may reflect the location of LPLs within the starch granule as opposed to the puroindoline proteins outside starch granules. LPLs may have an indirect relationship with kernel hardness as they could share the same origin as polar lipids that interact with puroindoline on the starch granule surface.

  16. Medulloblastoma Genotype Dictates Blood Brain Barrier Phenotype.

    Science.gov (United States)

    Phoenix, Timothy N; Patmore, Deanna M; Boop, Scott; Boulos, Nidal; Jacus, Megan O; Patel, Yogesh T; Roussel, Martine F; Finkelstein, David; Goumnerova, Liliana; Perreault, Sebastien; Wadhwa, Elizabeth; Cho, Yoon-Jae; Stewart, Clinton F; Gilbertson, Richard J

    2016-04-11

    The childhood brain tumor, medulloblastoma, includes four subtypes with very different prognoses. Here, we show that paracrine signals driven by mutant β-catenin in WNT-medulloblastoma, an essentially curable form of the disease, induce an aberrant fenestrated vasculature that permits the accumulation of high levels of intra-tumoral chemotherapy and a robust therapeutic response. In contrast, SHH-medulloblastoma, a less curable disease subtype, contains an intact blood brain barrier, rendering this tumor impermeable and resistant to chemotherapy. The medulloblastoma-endothelial cell paracrine axis can be manipulated in vivo, altering chemotherapy permeability and clinical response. Thus, medulloblastoma genotype dictates tumor vessel phenotype, explaining in part the disparate prognoses among medulloblastoma subtypes and suggesting an approach to enhance the chemoresponsiveness of other brain tumors. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Sources of Wilhelm Johannsen's genotype theory.

    Science.gov (United States)

    Roll-Hansen, Nils

    2009-01-01

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

  18. Genotype Imputation with Thousands of Genomes

    Science.gov (United States)

    Howie, Bryan; Marchini, Jonathan; Stephens, Matthew

    2011-01-01

    Genotype imputation is a statistical technique that is often used to increase the power and resolution of genetic association studies. Imputation methods work by using haplotype patterns in a reference panel to predict unobserved genotypes in a study dataset, and a number of approaches have been proposed for choosing subsets of reference haplotypes that will maximize accuracy in a given study population. These panel selection strategies become harder to apply and interpret as sequencing efforts like the 1000 Genomes Project produce larger and more diverse reference sets, which led us to develop an alternative framework. Our approach is built around a new approximation that uses local sequence similarity to choose a custom reference panel for each study haplotype in each region of the genome. This approximation makes it computationally efficient to use all available reference haplotypes, which allows us to bypass the panel selection step and to improve accuracy at low-frequency variants by capturing unexpected allele sharing among populations. Using data from HapMap 3, we show that our framework produces accurate results in a wide range of human populations. We also use data from the Malaria Genetic Epidemiology Network (MalariaGEN) to provide recommendations for imputation-based studies in Africa. We demonstrate that our approximation improves efficiency in large, sequence-based reference panels, and we discuss general computational strategies for modern reference datasets. Genome-wide association studies will soon be able to harness the power of thousands of reference genomes, and our work provides a practical way for investigators to use this rich information. New methodology from this study is implemented in the IMPUTE2 software package. PMID:22384356

  19. 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)

    1994-09-01

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

  20. Hepatitis C virus genotypes in Cordoba, Argentina unexpected high prevalence of genotype 2

    Directory of Open Access Journals (Sweden)

    V. Re

    2003-06-01

    Full Text Available To determine hepatitis C virus (HCV genotypes circulating in the central region of Argentina, 96 consecutive anti-HCV positive subjects were studied. The presence of HCV RNA was detected in 60 samples by RT-nested PCR of the 5' noncoding region (5' NCR. Genotyping was performed by restriction fragment length polymorphism analysis of 5' NCR region combined with PCR using type-specific primers of the core region. The groups of individuals in this study included hemophilia and hemodialysis patients, injecting drug users, screened blood donors, and patients with acute or chronic liver disease, all from Córdoba, Argentina. Overall, genotype 2 was the most prevalent (55.0%, followed by genotypes 1 (38.3 %, and 3 (5.0%. Within genotype 1, subtype 1b was the most prevalent. An unexpected high prevalence of genotype 2 (61.9% was found among patients with acute or chronic HCV infection (without known risk factors. These figures differ from other cohorts from East-Argentina where genotype 1 has been found as the most prevalent. This indicates that regional differences of genotype distribution might exist between Central and East Argentina.A fin de determinar los genotipos del virus de la hepatitis C (HCV circulantes en la región central de Argentina, se estudiaron 96 individuos anti-HCV positivos. La presencia del ARN de HCV se detectó en 60 muestras mediante RT-nested PCR de la región 5' no codificante (5' NCR. La genotipificación se realizó mediante restricción enzimática y el análisis del polimorfismo de los fragmentos largos de la región 5' NCR combinada con PCR usando primers tipo específico de la región del core. El grupo de individuos estudiados incluyó pacientes hemofílicos y hemodializados, drogadictos intravenosos, donantes de sangre y pacientes con enfermedad hepática aguda y crónica, todos provenientes de Córdoba, Argentina. El genotipo 2 fue el más prevalente (55.0%, seguido por los genotipos 1 (38.3 %, con mayor prevalencia

  1. 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.

  2. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    For a number of important crop plants, SNP markers are now being used to design genotyping arrays containing thousands of markers spread over the entire genome and to analyse large numbers of samples. In this article, we discuss aspects that should be considered during the design of such large genotyping arrays and ...

  3. SURVIVAL OF NORTH AMERICAN GENOTYPES OF TRICHINELLA IN FROZEN PORK

    Science.gov (United States)

    North American genotypes of Trichinella (T. nativa (T-2), T. pseudospiralis (T-4), T. murrelli (T-5), and Trichinella (T-6)) were examined for susceptibility to freezing in pork using established parameters for control of T. spiralis. Pig infections with these Trichinella genotypes were established ...

  4. Effect of Genotypes and Seed Production Environments on Seed ...

    African Journals Online (AJOL)

    Seeds from each harvest were subjected to different seed quality tests and data generated were analyzed. Seed quality traits were considerably affected by the genotypes and growing conditions i.e. plant population and cropping seasons. Genotypes with superior seed quality were prevalent at 166.667 and 266.667 plants ...

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

    African Journals Online (AJOL)

    symbiotic fixation). A set of 52 random lines from a broad-based reference population was evaluated for 2 years with and without B.japonicum inoculation in a split-plot design. Inoculation increased ... Genotype x: Inoculation Interactions, Nitrogen fixation ..... genotype x N treatment interaction was non significant each year ...

  6. CYP2D6 genotype determination in the Danish population

    DEFF Research Database (Denmark)

    Brøsen, K; Nielsen, P N; Brusgaard, K

    1994-01-01

    CYP2D6 genotyping was carried out by XbaI restriction fragment length polymorphism analysis and polymerase chain reaction in 168 healthy Danish volunteers, 77 extensive metabolizers (EM) and 91 poor metabolizers (PM) of sparteine. All EM were genotyped correctly as heterozygous or homozygous...

  7. Microsatellite analysis of selected Lablab purpureus genotypes in ...

    African Journals Online (AJOL)

    cntaganda

    main branches using UPGMA clustering method based on Nei's (1978) genetic distance (Figure 3). The first branch had only one genotype 12158, a gene bank accession. The other 12 genotypes were found in the second branch which had four sub clusters. In the first sub cluster, Mbeere 1 and Mbeere 2 had the least.

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

    African Journals Online (AJOL)

    In the process of introducing cotton cultivars, it is essential to assess their productive behavior for different environments for which they will be recommended. Knowledge of the magnitude of the genotype interaction with environment allows the evaluation of the stability and adaptability of genotypes where one intends to ...

  9. Clusters of incompatible genotypes evolve with limited dispersal

    Science.gov (United States)

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

    2015-01-01

    Theoretical and empirical studies have shown heterogeneous selection to be the primary driver for the evolution of reproductively isolated genotypes in the absence of geographic barriers. Here, we ask whether limited dispersal alone can lead to the evolution of reproductively isolated genotypes despite the absence of any geographic barriers or heterogeneous...

  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. Distribution of HCV genotypes in the metropolitan area of Naples

    Directory of Open Access Journals (Sweden)

    Giuseppe Sodano

    2013-08-01

    Full Text Available The Hepatitis C virus is characterized by high genomic variability that leads to the identification of six different genotypes and many subtypes. In this work, we show the prevalence of genotypes in patients living in the metropolitan area of Naples collected in one year, analyzing differences in the distribution depending on sex and age groups.

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

    African Journals Online (AJOL)

    Lindomar

    2016-08-31

    Aug 31, 2016 ... 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 ...

  13. Screening of Wheat Genotypes for Boron Efficiency in Bangladesh

    Science.gov (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 ...

  14. Monotonicity is a key feature of genotype-phenotype maps

    Science.gov (United States)

    Gjuvsland, Arne B.; Wang, Yunpeng; Plahte, Erik; Omholt, Stig W.

    2013-01-01

    It was recently shown that monotone gene action, i.e., order-preservation between allele content and corresponding genotypic values in the mapping from genotypes to phenotypes, is a prerequisite for achieving a predictable parent-offspring relationship across the whole allele frequency spectrum. Here we test the consequential prediction that the design principles underlying gene regulatory networks are likely to generate highly monotone genotype-phenotype maps. To this end we present two measures of the monotonicity of a genotype-phenotype map, one based on allele substitution effects, and the other based on isotonic regression. We apply these measures to genotype-phenotype maps emerging from simulations of 1881 different 3-gene regulatory networks. We confirm that in general, genotype-phenotype maps are indeed highly monotonic across network types. However, regulatory motifs involving incoherent feedforward or positive feedback, as well as pleiotropy in the mapping between genotypes and gene regulatory parameters, are clearly predisposed for generating non-monotonicity. We present analytical results confirming these deep connections between molecular regulatory architecture and monotonicity properties of the genotype-phenotype map. These connections seem to be beyond reach by the classical distinction between additive and non-additive gene action. PMID:24223579

  15. Performance of Bemisia tabaci Biotype B on Soybean Genotypes.

    Science.gov (United States)

    Cruz, P L; Baldin, E L L

    2017-04-01

    Bemisia tabaci (Genn.) (Hemiptera: Aleyrodidae) has been recognized as an important pest of many agricultural systems including soybean [Glycine max (L.) Merrill] crops. As an alternative to chemical control, the use of resistant genotypes represents an important tool for integrated pest management (IPM). This study aimed to evaluate the biological development of Bemisia tabaci biotype B confined on 13 soybean genotypes under greenhouse conditions. Initially, the nymphal period, complete development period (egg-adult), and the viability of the silverleaf whitefly nymphs were evaluated in all genotypes. Then, four genotypes promising for resistance ('Jackson,' UX-2569-159, 'P98Y11,' and 'TMG132 RR') and a susceptible genotype (PI-227687) were selected for further assays, where two insect populations were compared: a first population from the initial rearing (cabbage plants) and another corresponding to insects previously reared out on the selected genotypes. In addition to the parameters evaluated in preliminary tests, we also determined the viability and incubation period of eggs. Moderate levels of resistance (antibiosis/antixenosis) to B. tabaci biotype B were found in three genotypes. 'P98Y11' and 'TMG132 RR' were less suitable for insect development, extending the development cycle, and UX-2569-159 caused high nymphal mortality. We did not observe a significant increase in the level of plant resistance by the use of previously stressed insects. This suggests that the evaluation of a single whitefly generation may be sufficient to make correct decisions on promising soybean genotypes.

  16. Molecular investigation of two contrasting genotypes of Medicago ...

    African Journals Online (AJOL)

    The EST-SSRs markers were polymorphic with an average of 1.33 alleles per primers and gave moderate values of polymorphic information content (PIC) that ranged from 0 to 0.267. The analysis of polymorphism loci for each genotype showed that the tolerant genotype (Tru 131) population had two alleles; genetic ...

  17. Influence of genotype and plant growth regulator on somatic ...

    African Journals Online (AJOL)

    USER

    2010-06-28

    Jun 28, 2010 ... Two genotypes of Brassica napus species (Talayeh and RGS003) and the explants segment (hypocotyls and cotyledon) were tested for their potential to produce somatic embryos in in vitro condition. The effect of genotype, different explants and also different concentrations of plant growth regulators.

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

    African Journals Online (AJOL)

    AJL

    2012-01-26

    Jan 26, 2012 ... genotypes. 3D graphs, Bi-plot and cluster analysis confirmed these results. Principal components analysis showed two components which explained 98.0% variation. Genotypes were grouped in cluster analysis (using Ward's method) based on Yp, Ys and quantitative indices of drought tolerance. Finally,.

  19. Screening upland rice ( Oryza sativa L. ssp. indica ) genotypes for ...

    African Journals Online (AJOL)

    Screening upland rice (Oryza sativa L. ssp. indica) genotypes for salt-tolerance using multivariate cluster analysis. S Cha-um, M Ashraf, C Kirdmanee. Abstract. Seedlings of thirteen genotypes of rice were photoautotrophically grown on MS medium and subsequently exposed to 0 (control) or 200 mM NaCl (salt stress) for 14 ...

  20. Genotype-dependent responses of wheat ( Triticum aestivum L ...

    African Journals Online (AJOL)

    Genotype-dependent responses of wheat ( Triticum aestivum L.) seedlings to drought, UV-B radiation and their combined stresses. ... and ascobate acid, AsA) exhibited differences under the tested stressful conditions in the two genotypes, indicating that they play significant roles in plant responses to these stresses.

  1. Assessment of rice genotypes for salt tolerance using microsatellite ...

    African Journals Online (AJOL)

    SERVER

    2008-03-18

    Mar 18, 2008 ... homeostasis in the rice shoots. To test the usefulness of microsatellite (SSR) markers associated with Saltol QTL, a collection of 36 diverse rice genotypes were used. Phenotypic response of the genotypes to salt stress with EC=12 was assessed under controlled environmental conditions at seedling stage ...

  2. Genetic analysis of some Egyptian rice genotypes using RAPD, SSR ...

    African Journals Online (AJOL)

    nformation of genetic similarities and diversity among superior Egyptian rice genotypes is necessary for future rice breeding programs and derivation of plant lines. Genetic variability and relationships among seven Egyptian rice genotypes namely Giza 178, Giza177, Giza 175, Giza171 Giza 172, Sakha 102, and Sakha 101 ...

  3. Influence of genotype and plant growth regulator on somatic ...

    African Journals Online (AJOL)

    Two genotypes of Brassica napus species (Talayeh and RGS003) and the explants segment (hypocotyls and cotyledon) were tested for their potential to produce somatic embryos in in vitro condition. The effect of genotype, different explants and also different concentrations of plant growth regulators (PGRs) including: ...

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

    African Journals Online (AJOL)

    Eighteen genotypes from the NationalSweetpotato Programme were evaluated for their fresh storage root yield and reaction to stem and leafbUght (Alternaria bataticola) at Kachwckano (2000 metres above sea level) in Southwest. Uganda. The trials were set up to identify sweetpotato genotypes with adaptation to highland ...

  5. Genetic evaluation of spring wheat (Triticum aestivum L.) genotypes ...

    African Journals Online (AJOL)

    SAM

    2014-04-30

    Apr 30, 2014 ... yield (g) was observed in genotypes WH1132 and WH 1131. Grain yield per plot (g) .... Genotype. Pedigree. Source. Amber 28. WG5669/2/MACS2496/BOW. KSPL,Jalna (M.H). WCW 2009-06. PBW 343/WH 147. SVBPUA&T, Merrut (U.P). HUW 660 .... cient analysis was accessed by Dewey and Lu (1959).

  6. The nutritive value of forage sorghum genotypes developed for the ...

    African Journals Online (AJOL)

    Jack Ouda

    for all genotypes after 24 h incubation but Lan-12 had the highest methane production after 72 h incubation. After 24 h and 72 h incubation all the genotypes produced a .... The rumen fluid used was collected from cannulated sheep kept on a maintenance diet with a 60:40 forage to concentrate composition. The forage was ...

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

    African Journals Online (AJOL)

    Prof Ezechukwu

    2011-10-23

    Oct 23, 2011 ... 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 informa- tion on the relationship between Hb genotype and level of ...

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

    African Journals Online (AJOL)

    Crossbreeding of large white and Nsukka local pigs: Genotype and age are related changes in haematological parameters. ... Nigerian Journal of Animal Science ... However, significant genotype x age interactions were found for RBC, MCH, WBC, lymphocytes, monicytes and eosinophils which limit the inferences made on ...

  9. Leveraging from genotype by environment interaction for bread ...

    African Journals Online (AJOL)

    Developing high yielding and stable genotypes for wide and specific adaptation is important in wheat (Triticum aestivum L.) production. The objective of this study was to exploit the gains from genotype by environment interaction for increased bread wheat production in eastern Africa. Thirty-three advanced bread wheat ...

  10. 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 ...

  11. Responses of some selected Malaysian rice genotypes to callus ...

    African Journals Online (AJOL)

    user

    2011-01-17

    Jan 17, 2011 ... genotype performance for in vitro salt stress responses in some selected Malaysian rice genotypes. Differences in culture conditions, ... stress, which prevents the crop from reaching its full genetic potential as well as .... hydrolysates did not respond to callus induction, but only resulted in seed germination.

  12. Comparison and suitability of genotype by environment analysis ...

    African Journals Online (AJOL)

    ACSS

    Genotype by environment analysis methods for yield-related traits of pearl millet probably no stand-alone method exists. (Kaya et al., 2006). ... percentage of productive tillers (PRO) at plot level. Data analysis was conducted using the ...... Haussmann, B.I.G. 2014. Patterns of pearl millet genotype-by-environment interaction ...

  13. 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 ...

  14. Identification of blast resistance expression in rice genotypes using ...

    African Journals Online (AJOL)

    Markers OPA-05, OPF-06, OPF-09, OPF-17, OPG-17, OPG-18, OPG-19, OPH-18, OPK-12, P-265-550 and P-286-350 found linked to blast resistance in most of the resistant genotypes could be considered as potent molecular markers in the selection of blast resistant genotypes. Amplification with RAPD and SCAR primers ...

  15. Genotype W environment interaction effects on some physiological ...

    African Journals Online (AJOL)

    A simple crop physiological model was employed to study the yield basis and environmental effects on 31cowpea genotypes of early, medium and late maturities. The tests were carried out at four sites in northern Ghana between 1992 and 1994. Genotypic variations observed for pod yields (Y), reproductive duration (RD), ...

  16. Genotype x Environment interaction for quality traits in durum wheat ...

    African Journals Online (AJOL)

    To evaluate the effects of genotype, environment and genotype x environment interaction on quality traits such as vitreousness, SDS sedimentation test, yellow pigment index, protein content and test weight, twelve Moroccan durum wheat cultivars representing a range of agronomic adaptation were tested in five locations ...

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

    African Journals Online (AJOL)

    SAM

    2014-05-07

    May 7, 2014 ... In the process of introducing cotton cultivars, it is essential to assess their productive behavior for different environments for which they will be recommended. Knowledge of the magnitude of the genotype interaction with environment allows the evaluation of the stability and adaptability of genotypes where ...

  18. Characteristics of Streptococcus mutans genotypes and dental caries in children.

    Science.gov (United States)

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

    2013-06-01

    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 as being at high caries risk, had plaque collected from baseline through 36 months for S. mutans isolation and genotyping using repetitive extragenic palindromic-PCR (4,392 total isolates). Decayed, missing, or filled surfaces (dmfs (primary teeth)/DMFS (secondary teeth)) 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 two 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 this was negatively associated with the 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 suggests that fewer decayed surfaces are significantly associated with lower diversity and higher stability of S. mutans genotypes. © 2013 Eur J Oral Sci.

  19. stability analysis of food barley genotypes in northern ethiopia ...

    African Journals Online (AJOL)

    ACSS

    interaction principal component axis, AMMI- additive main effect and multiplicative interaction. Figure 1. AMMI1 biplot for grain yield (t ha-1) and IPCA1of food barley genotypes grown in northern Ethiopia. Stability analysis for genotypic performance. AMMI Stability Value (ASV). Table 5 shows. AMMI stability values for ...

  20. Genotype x environment interactions for seed yield in sesame in ...

    African Journals Online (AJOL)

    As sesame is a short day plant and sensitive to light, heat, and moisture stress the yield is not stable. The selection of stable genotypes that interact less with the varying environment in which they are to be grown is required. The extent of genotype by environment interaction indicates the likelihood of adaptation of a given ...

  1. Screening ten genotypes of natural rubber seedlings ( Hevea ...

    African Journals Online (AJOL)

    A field study was conducted in 2012 and 2013 cropping season at the Research Farm of National Root Crops Research Institute, (NRCRI) Umudike, in Abia State, to screen 10 rubber genotypes collected from Rubber Research Institute of Nigeria for tolerant to drought conditions. The aim was to select tolerant genotypes for ...

  2. Variation of meat quality traits among five genotypes of chicken.

    Science.gov (United States)

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

    2009-10-01

    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.

  3. Magnitude of genotype x environment interaction for bacterial leaf ...

    African Journals Online (AJOL)

    Magnitude of genotype x environment interaction for bacterial leaf blight resistance in rice growing areas of Uganda. ... Low attack was observed on pyramided genotypes in all locations and two with single gene, i.e. IRBB8 and IRBB21, respectively. Interestingly, IR24 was as resistant as any of the pyramided combinations.

  4. Prevalence of heamoglobin genotype screening and awareness of ...

    African Journals Online (AJOL)

    Even though majority of the respondents (72.3%) had fair knowledge of the disease, only a quarter (28.2%) of them had ever done their genotype test prior to the study. Factors that positively influenced respondents' practice of premarital genotype screening included; age, being married, parental educational background ...

  5. Genotype X environment interactions and stability of soybean for ...

    African Journals Online (AJOL)

    Soybean Glycine max (L.) Merrill] is the world's leading source of oil and protein. It has the highest protein content of all food crops and is second only to groundnut in terms of oil content among food legumes. Study on genotype x enviroment interaction (GE) and stability of twenty soybean [Glycine max (L.) Merrill] genotypes ...

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

    African Journals Online (AJOL)

    Seventeen (17) genotypes were evaluated in randomized complete block design (RCBD) with four replications in five locations. Various stability indices were used to assess stability and genotype by environment performances. Combined analysis of variance (ANOVA) for yield and yield components revealed highly ...

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...

  8. Influence of cowpea genotype and sorghum-cropping system on ...

    African Journals Online (AJOL)

    Influence of cowpea genotype and sorghum-cropping system on cowpea infestation by some insect pests in the sudan savannah of Nigeria. ... seasons to investigate the influence of cowpea genotypes and sorghum cropping system on cowpea damage by legume pod borer, Maruca testulalis (Fabricius), bean flower thrips,

  9. (Prunus dulcis, Batch) genotypes as revealed by PCR analysis

    African Journals Online (AJOL)

    STORAGESEVER

    2010-06-07

    Jun 7, 2010 ... The identification of pollen-pistil compatibility relationships among almond cultivars and genotypes is very important for breeders and growers. In the present study, PCR based technique was used to identify S-alleles in 10 late blooming almond genotypes. In total, 19 alleles were amplified by five primer.

  10. 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 ...

  11. Genetic diversity among selected genotypes of almond Prunus ...

    African Journals Online (AJOL)

    Genetic relatedness and diversity in 32 almond genotypes were analysed using random amplified polymorphic DNA (RAPD) markers. All the genotypes maintained at Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, India comprised ten exotic introductions and 22 indigenous selections. Using 16 selected ...

  12. Genetic analysis of Ethiopian mustard genotypes using amplified ...

    African Journals Online (AJOL)

    Genetic diversity within Brassica carinata A. Braun has not been extensively examined with molecular markers. The objective of this study was to investigate the genetic relationships among 39 B. carinata genotypes using amplified fragment length polymorphisms (AFLPs). Thirty-nine genotypes of B. carinata were analyzed ...

  13. Genotypic character relationship and phenotypic path coefficient analysis in chili pepper genotypes grown under tropical condition.

    Science.gov (United States)

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

    2017-03-01

    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.

  14. Grouping genotypes and test environments by some cluster methods regarding genotype × environment interaction in multi-environment trials

    Directory of Open Access Journals (Sweden)

    Sabaghnia Naser

    2012-01-01

    Full Text Available Lentil (Lens culinaris Medik. is an important source of protein and carbohydrate food for people of developing countries and is popular in some developed countries where they are perceived as a healthy component of the diet. Ten lentil genotypes were tested for grain yield in five different environmental conditions, over two consecutive years to classify thes genotypes for yield stability. Seed yield of lentil genotypes ranged from 989.3 to 1.367 kg ha-1 and the linear regression coefficient ranged from 0.75 to 1.18. The combined analysis of variance showed that the effect of environment (E and genotype by environment (GE interaction were highly significant while the main effect of genotype (G was significant at 0.05 probability level. Four different cluster procedures were used for grouping genotypes and environments. According to dendograms of regression methods for lentil genotypes there were two different genotypic groups based on G plus GE or GE sources. Also, the dendograms of ANOVA methods indicated 5 groups based on G and GE sources and 4 groups based on GE sources. According to dendograms of regression methods for environments there were 5 different groups based on G plus GE sources while the dendograms of ANOVA methods indicated 9 groups based on G and GE sources and 3 groups based on GE sources. The mentioned groups were determined via F-test as an empirical stopping criterion for clustering. The most responsive genotypes with high mean yield genotypes are G2 (1145.3 kg ha-1, G8 (1200.2 kg ha-1 and G9 (1267.9 kg ha-1 and could be recommended as the most favorable genotypes for farmers.

  15. Distribution study of Chlamydia trachomatis genotypes in symptomatic patients in Buenos Aires, Argentina: association between genotype E and neonatal conjunctivitis

    Directory of Open Access Journals (Sweden)

    Corominas Ana I

    2010-02-01

    Full Text Available Abstract Background Chlamydia trachomatis infections are the most prevalent sexually transmitted bacterial infections in the world. There is scarce data available referring to the distribution of C. trachomatis genotypes in Argentina. The aim of this study was to identify the genotypes of C. trachomatis circulating in the metropolitan area of Buenos Aires (Argentina associated with ophthalmia neonatorum and genital infections. Findings From 2001 to 2006, 199 positive samples for C. trachomatis infection from symptomatic adult patients and neonates with ophthalmia neonatorum from two public hospitals were studied. C. trachomatis genotypes were determined by PCR-RFLP of an ompA fragment. Genotype E was the most prevalent regardless of the sample origin (46.3% 57/123 in adults and 72.4% 55/76 in neonates, followed by genotype D (19.5% 24/123 and F (14.6% 18/123 in adults, and G (9.2% 7/76 and D (7.9% 6/76 in neonates. We detected a significantly higher frequency of genotype E (p ophthalmia neonatorum than in genital specimens. Genotype D was associated with genital localization (p Conclusion We found a particularly increased frequency of C. trachomatis genotype E in neonatal conjunctivitis, which may indicate an epidemiological association between this genotype and the newborn population. The present study also contributed to increase the knowledge on genotype distribution of Chlamydia trachomatis in symptomatic adult patients in Buenos Aires, Argentina, in which genotypes E, D and F were the predominant ones.

  16. Genotypic diversity of european Phytophthora ramorum isolates based on SSR analysis

    Science.gov (United States)

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

    2013-01-01

    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...

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

    Science.gov (United States)

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

    2010-10-01

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

  18. Leber Congenital Amaurosis: Genotypes and Retinal Structure Phenotypes.

    Science.gov (United States)

    Jacobson, Samuel G; Cideciyan, Artur V; Huang, Wei Chieh; Sumaroka, Alexander; Nam, Hyun Ju; Sheplock, Rebecca; Schwartz, Sharon B

    2016-01-01

    Leber congenital amaurosis (LCA) patients of 10 known genotypes (n = 24; age range, 3-25 years) were studied clinically and by optical coherence tomography (OCT). Comparisons were made between OCT results across the horizontal meridian (central 60(o)) of the patients. Three patterns were identified. First, there were LCA genotypes with unusual and readily identifiable patterns, such as near normal outer nuclear layer (ONL) across the central retina or severely dysplastic retina. Second, there were genotypes with well-formed foveal architecture but only residual central islands of normal or reduced ONL thickness. Third, some genotypes showed central ONL losses or dysmorphology suggesting early macular disease or foveal maldevelopment. Objective in vivo morphological features could complement other phenotypic characteristics and help guide genetic testing of LCA patients or at least permit a differential diagnosis of genotypes to be made in the clinic.

  19. Genotyping of measles virus in Canada: 1979-2002.

    Science.gov (United States)

    Tipples, Graham A; Gray, Michael; Garbutt, Michael; Rota, Paul A

    2004-05-01

    Genotyping is an important component of measles surveillance. In this study, we report the genotypes of 30 measles viruses from cases in Canada; 6 of these were collected between 1979 and 1996 and 24 were collected from 1997 through 2002. Many measles virus genotypes were found (C1, C2, D3, D4, D5, D6, D7, D8, E, and H1). These data indicate that the predominant measles virus genotypes detected from 1979 to 1997 in Canada are no longer commonly found. Since the implementation of a routine second dose of measles vaccine and catch-up campaigns in 1996-1997, the wide variety of measles virus genotypes found supports epidemiological data showing that importation of measles is the source of current measles cases in Canada.

  20. Micropropagation of six Paulownia genotypes through tissue culture

    Directory of Open Access Journals (Sweden)

    Lydia Shtereva

    2014-12-01

    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.

  1. Sunflower 1000-seed weight as affected by year and genotype

    Directory of Open Access Journals (Sweden)

    Radić Velimir

    2013-01-01

    Full Text Available For a successful seed production, it is necessary to know the size, i.e. 1000-seed weight, since it affects the sowing rate, plant density over the vegetative period as well as the seed yield per unit area. The study was conducted in field conditions, on plots where seed production of sunflower hybrids parental components was organized. Seed production was based at three different localities. Observation was conducted during the course of three years. The study was performed on 18 different genotypes. Considering the total number of the observed genotypes, 10 genotypes represented lines based on CMS, while the remaining 8 genotypes represented restorer lines. The study showed that 1000-seed weight was higher with CMS based lines than with restorer lines, which was expected considering the branching of the restorer lines. Sunflower 1000-seed weight depended on the year of observation and the observed genotype. Year had a significant effect on 1000-seed weight.

  2. Evaluation of reference evapotranspiration by Penman-Monteith using minimum climatic data in the backcountry of Ceará = Avaliação da evapotranspiração de referência por Penman-Monteith usando dados climáticos mínimos no sertão do Ceará

    Directory of Open Access Journals (Sweden)

    Mairton Gomes da Silva

    2013-12-01

    Full Text Available In areas of semiarid climate, water resources are limited and seriously threatened by excessive exploitation. This study’s objective is to evaluate the performance of the method FAO 56 Penman-Monteith (PM-FAO 56 to estimate the reference evapotranspiration (ETo with minimum data (maximum and minimum air temperature in the backcountry of the state of Ceará. The work was developed based on maximum and minimum air temperatures, relative air humidity, wind speed, and insolation of the conventional stations of the backcountry of Ceará, obtained from the National Institute of Meteorology (INMET. To compare the values of ETo estimated by FAO PM-56 with complete data where the minimum was considered the ratio between the mean (ξ, the standard error of estimation (SEE, correlation coefficient (r, accuracy or concordance index (d and performance or confidence index (c. Maps of ETo by PM-FAO 56 were made with minimum data for the mesoregion of the backcountry of Ceara, by means of the inverse distance weighted (IDW. The following of estimates of ETo by PM-FAO 56 with maximum and minimum air temperatures worked satisfactorily and by means of spatialisation and generation of thematic maps, it was possible to visualize the ETo in the most remote areas of the region of the study. = Nas regiões de clima semiárido os recursos hídricos são limitados e seriamente ameaçados pela excessiva exploração. Objetivou-se com este estudo avaliar o desempenho do método Penman-Monteith FAO 56 (PM-FAO 56 para estimar a evapotranspiração de referência (ETo com dados mínimos (temperatura máxima e mínima do ar, no sertão do estado do Ceará. O trabalho foi desenvolvido a partir de dados de temperatura máxima e mínima do ar, umidade relativa do ar, velocidade do vento e insolação das estações convencionais da região do sertão cearense, obtidos com o Instituto Nacional de Meteorologia (INMET. Para comparar os valores de ETo estimados por PM-FAO 56 com

  3. Differential biocide susceptibility of the multiple genotypes of Mycobacterium immunogenum.

    Science.gov (United States)

    Selvaraju, Suresh B; Khan, Izhar U H; Yadav, Jagjit S

    2008-03-01

    The non-tuberculous mycobacterium Mycobacterium immunogenum colonizes industrial metalworking fluids (MWFs) presumably due to its relative resistance to the currently practiced biocides and has been implicated in occupational respiratory hazards, particularly hypersensitivity pneumonitis. With an aim to understand its inherent biocide susceptibility profile and survival potential in MWF, five different genotypes of this organism, including a reference genotype (700506) and four novel test genotypes (MJY-3, MJY-4, MJY-10 and MJY-12) isolated in our recent study from diverse MWF operations were evaluated. For this, two commercial biocide formulations, Grotan (Hexahydro-1,3,5-tris(2-hydroxyethyl)-s-triazine) and Kathon (5-chloro-2-methyl-4-isothiazolin-3-one) currently practiced for the control of microorganisms, including mycobacteria, in MWF operations were tested. Effect of the fluid matrix on the biocide susceptibility was investigated for the synthetic (S) and semi-synthetic (SS) MWF matrices. In general, the minimum inhibitory concentration values were higher for the HCHO-releasing biocide Grotan than the isothiazolone biocide Kathon. All genotypes (except the reference genotype) showed lower susceptibility in SS as compared to S fluid matrix for Grotan. However, in case of Kathon, a greater susceptibility was observed in SS fluid for majority of the test genotypes (MJY-3, 4 and 10). The test genotypes were more resistant than the reference genotype to either biocide in both fluid types. Furthermore, the individual genotypes showed differential biocidal susceptibility, with MJY-10 being the most resistant. These observations emphasize the importance of using the resistant genotypes of M. immunogenum as the test strains for formulation or development and evaluation of existing and novel biocides, for industrial applications.

  4. Genetic diversity of the genotype VII Newcastle disease virus: identification of a novel VIIj sub-genotype.

    Science.gov (United States)

    Xue, Cong; Cong, Yanlong; Yin, Renfu; Sun, Yixue; Ding, Chan; Yu, Shengqing; Liu, Xiufan; Hu, Shunlin; Qian, Jing; Yuan, Qianliang; Yang, Mingxi; Wang, Chunfeng; Ding, Zhuang

    2017-02-01

    Newcastle disease (ND) is a highly contagious disease of poultry caused by Newcastle disease virus (NDV). Multiple genotypes of NDV have been circulating worldwide and NDV is continuously evolving, resulting into more diversity. Of multiple viral genotypes, VII is particularly important given that it had been associated with most recent ND outbreaks worldwide. In this study, an epidemiological investigation performed in northeastern China during 2014-2015 showed that 11 genotype VII isolates amounted to 55 percent in a total number of NDV isolates. Therefore, to evaluate the genetic diversity worldwide and epidemiological distribution in China of genotype VII NDV, a phylogenetic analysis based on the 1255 complete F gene sequences showed that VII is the most predominant genotype worldwide. A further detailed characterization on genotype VII was conducted based on the 477 complete F gene sequences from 11 isolates and 466 reference viruses available in GenBank. The results demonstrated that VII can be further divided into 8 sub-genotypes (VIIb, VIId-VIIj), indicating its complex genetic diversity. It is worthy of note that the isolation rate of VIIj is increasing recently. It emphasizes the necessity to pay close attention to the epidemiological dynamic of genotype VII NDV and highlights the importance of vaccination program.

  5. Toxoplasma gondii isolates: multilocus RFLP-PCR genotyping from human patients in Sao Paulo State, Brazil identified distinct genotypes.

    Science.gov (United States)

    Ferreira, Isabelle Martins Ribeiro; Vidal, Jose Ernesto; de Mattos, Cinara de Cássia Brandão; de Mattos, Luiz Carlos; Qu, Daofeng; Su, Chunlei; Pereira-Chioccola, Vera Lucia

    2011-10-01

    This study investigated the genetic characteristics of Toxoplasma gondii samples collected from 62 patients with toxoplasmosis in Sao Paulo State, Brazil. DNA samples were isolated from blood, cerebrospinal fluid and amniotic fluids of 25 patients with cerebral toxoplasmosis and AIDS, two patients with acute toxoplasmosis, 12 patients with ocular toxoplasmosis, six newborns with congenital toxoplasmosis and 17 pregnant women with acute infection. Diagnosis of toxoplasmosis was based in clinical, radiological and laboratory features. Genotyping was performed using multilocus PCR-RFLP genetic markers including SAG1, SAG2, 5'- and 3'-SAG2, alt.SAG2, SAG3, BTUB, GRA6, C22-8, c29-2, L358, PK1 and Apico. Among the 62 clinical samples, 20 (32%) were successfully genotyped at eight or more genetic loci and were grouped to three distinct genotypes. Eighteen samples belonged to ToxoDB Genotype #65 and the other two samples were identified as ToxoDB Genotypes #6 and #71, respectively (http://toxodb.org/toxo/). Patients presenting Genotypes #6 and #71 had severe and atypical cerebral toxoplasmosis, characterized by diffuse encephalitis without extensive brain lesions. These results indicate that T. gondii Genotype #65 may have a high frequency in causing human toxoplasmosis in Sao Paulo State, Brazil. This unusual finding highlights the need to investigate the possible association of parasite genotypes with human toxoplasmosis. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. Combined use of phenotypic and genotypic information in sampling animalsfor genotyping in detection of quantitative trait loci

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P

    2008-01-01

    Conventional selective genotyping which is using the extreme phenotypes (EP) was compared with alternative criteria to find the most informative animals for genotyping with respects to mapping quantitative trait loci (QTL). Alternative sampling strategies were based on minimizing the sampling error...... of the estimated QTL effect (MinERR) and maximizing likelihood ratio test (MaxLRT) using both phenotypic and genotypic information. In comparison, animals were randomly genotyped either within or across families. One hundred data sets were simulated each with 30 half-sib families and 120 daughters per family....... The strategies were compared in these datasets with respect to estimated effect and position of a QTL within a previously defined genomic region at genotyping 10, 20 or 30% of the animals. Combined linkage disequilibrium linkage analysis (LDLA) was applied in a variance component approach. Power to detect QTL...

  7. Newcastle disease virus in Madagascar: identification of an original genotype possibly deriving from a died out ancestor of genotype IV.

    Directory of Open Access Journals (Sweden)

    Olivier F Maminiaina

    Full Text Available In Madagascar, Newcastle disease (ND has become enzootic after the first documented epizootics in 1946, with recurrent annual outbreaks causing mortality up to 40%. Four ND viruses recently isolated in Madagascar were genotypically and pathotypically characterised. By phylogenetic inference based on the F and HN genes, and also full-genome sequence analyses, the NDV Malagasy isolates form a cluster distant enough to constitute a new genotype hereby proposed as genotype XI. This new genotype is presumably deriving from an ancestor close to genotype IV introduced in the island probably more than 50 years ago. Our data show also that all the previously described neutralising epitopes are conserved between Malagasy and vaccine strains. However, the potential implication in vaccination failures of specific amino acid substitutions predominantly found on surface-exposed epitopes of F and HN proteins is discussed.

  8. Genotype � Environment Interaction and Stability Analysis of Seed Yield of Durum Wheat Genotypes in Dryland Conditions

    Directory of Open Access Journals (Sweden)

    Mohtasham MOHAMMADI

    2012-08-01

    Full Text Available The objective of this investigation was to evaluate seed yield of twenty durum wheat (Triticum turgidum spp. durum genotypes. Evaluation of genotype � environment interaction and stability were also carried out at five diverse locations during the 2007-2009 growing seasons. Significant differences were found among the genotypes for seed yield on individual years and combined over years, in all locations. Genotype � environment interaction showed significance (p>0.001 for seed yield. According to the coefficients of linear regression and deviations from the regression model, genotypes G2, G7 and G8 proved to be the most stable while based on ? and ? parameters, genotypes G7, G12 and G13 were identified the most stable. Clustering genotypes based on all stability methods and mean yield divided them into four major classes, which Class II had relatively high stability and high mean yield performance. To compare relationships among stability statistics, hierarchical clustering procedure showed that the ten stability statistics and mean yield could be categorized into three major groups, which methods of Group C indicated dynamic concept of yield stability. The genotypic stability, stability variance, superiority index and desirability index provide information for reaching definitive conclusions. Also, the best recommended genotypes, according to the present investigation, were G2 (2697.18 kg ha-1, G7 (2644.70 kg ha-1, G8 (2580.16 kg ha-1 and G10 (2637.43 kg ha-1, which had high mean yield and were the most stable genotypes based on the above mentioned stability statistics.

  9. Genotype-environment interaction in tomato.

    Science.gov (United States)

    Cuartero, J; Cubero, J I

    1982-09-01

    Twelve varieties of tomato of economic importance and their hybrids (including reciprocals) were studied in four environments: inside and outside of greenhouses and with and without plastic mulching. Seven characters were recorded per plant per environment: (1) total yield, (2) fruit weight, (3) locules/fruit, (4) fruits/cluster, (5) earliness in maturity, (6) earliness in harvesting and (7) leaves between clusters. There was an almost general tendency for hybrids to show higher values than the parentals for characters (1), (4) and (7); the opposite was true for (2) and (3), even when the differences were not statistically significant at the 5% level. Environments were always highly significant; the effect of the greenhouse explained most of the variation. Genotype-environment interaction by regression analysis showed that the performance of the hybrids was generally higher than that of the parents for characters (1), (4) and (7). Total yield was higher, in general, in the most protected environments. Locules per fruit was very constant but when interaction did exist, the number of locules was higher in the less protected environments. Hybrids interacted with environments more strongly than parent lines. Earliness was the most environmental dependent characteristic the choice of early harvesting being irrelevant. Some of the hybrids obtained seem promising from a commercial point of view.

  10. Dopamine transporter genotype predicts implicit sequence learning.

    Science.gov (United States)

    Simon, Jessica R; Stollstorff, Melanie; Westbay, Lauren C; Vaidya, Chandan J; Howard, James H; Howard, Darlene V

    2011-01-01

    Implicit learning, the non-conscious acquisition of sequential and spatial environmental regularities, underlies skills such as language, social intuition, or detecting a target in a complex scene. We examined relationships between a variation of the dopamine transporter (DAT1) gene (SLC6A3), which influences dopamine transporter expression in the striatum, and two forms of implicit learning that differ in the regularity to be learned and in striatal involvement. Participants, grouped as 9-repeat carriers or 10/10 homozygotes, completed the triplets learning task (TLT) and the spatial contextual cueing task (SCCT). The TLT assesses sequence learning, recruiting the striatal system, particularly as training continues. In contrast, the SCCT assesses spatial context learning, recruiting medial temporal brain networks. For both tasks, participants demonstrated learning in faster and/or more accurate responses to repeating patterns or spatial arrays. As predicted, TLT learning was greater for the 9-repeat carriers than the 10/10 group (despite equal overall accuracy and response speed) whereas there were no significant group differences in SCCT. Thus, presence of the DAT1 9-repeat allele was beneficial only for implicit sequence learning, indicating the influence of DAT1 genotype on one form of implicit learning and supporting evidence that implicit learning of sequential dependencies and spatial layouts recruit different neural systems. Copyright © 2010 Elsevier B.V. All rights reserved.

  11. Genotyping of Canine parvovirus in western Mexico.

    Science.gov (United States)

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

    2015-01-01

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

  12. Plant genotype, microbial recruitment and nutritional security

    Directory of Open Access Journals (Sweden)

    Jai Singh Patel

    2015-08-01

    Full Text Available Agricultural food products with high nutritive value are always preferred over food products with low nutritive value. Efforts are being made to increase the nutritive value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritive value of food is increased under natural conditions in the food products especially in the agricultural produces. Fragmented researches have led to the conclusion that it is possible to increase nutritive value of the agricultural products naturally in agricultural fields. The rhizosphere is of vital importance in this regard for not only health and nutritional status of plants but also for the microorganisms colonising the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of plant host in discriminating its colonisers. A large amount 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.

  13. A SNP Genotyping Array for Hexaploid Oat

    Directory of Open Access Journals (Sweden)

    Nicholas A. Tinker

    2014-11-01

    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.

  14. Homeostasis in defined genotypes of Matthiola incana.

    Science.gov (United States)

    Seyffert, W

    1983-02-01

    Based on 256 defined genotypes of the Brassicaceae Matthiola incana the influence of the alleles at four different loci and of their combinations on homeostasis was investigated against an isogenic background. The measured character was the anthocyanin content of the flowers. There are significant maternal and paternal influences on homeostasis. Moreover the extent of heterozygosity as well as the number of wildtype alleles, summarized over all loci, are positively correlated with the increase of homeostasis. The analysis of individual gene effects shows distinct graduations between the contributions of the particular loci. In principle, the wild-type allele proved to be more homeostatic when compared to the mutant; in some cases monogenic heterosis was indicated. Nonallelic interactions of first and second order do considerably modify the degree of expression of homeostasis; they are neither strongly correlated with the individual gene effects nor with the interactions of lower order, and hence they are not predictable. This means also that it is not possible to formulate a general hypothesis as to the causes of homeostasis. We have to assume rather that homeostasis depends on specific gene combinations which enable the organism to stabilize its phenotype by means of certain physiological conditions.

  15. Porphyromonas gingivalis Fim-A genotype distribution among Colombians.

    Science.gov (United States)

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

    2015-09-30

    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. To identify FimA genotypes of P. gingivalis in subjects from Cali-Colombia, including the co-infection with Aggregatibacter actinomycetemcomitans, Treponema denticola, and Tannerella forsythia. 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. 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. 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.

  16. Relationship among eastern cottonwood genotypes according to early rooting traits

    Directory of Open Access Journals (Sweden)

    Kovačević Branislav

    2011-01-01

    Full Text Available The relationship between twelve genotypes of eastern cottonwood (Populus deltoides Bartr. was analyzed according to sixteen early rooting traits and cutting survival. Principal component analysis (PCA and cluster analysis were used on data that were standardized by common and by one alternative way of standardization. Alternative way of standardization (standardization with within-genotype standard deviation instead of standard deviation of genotypes’ means was used in order to emphasize the contribution of genotype to the effect of differences among genotypes on total variation. After bought ways the first principal component had high correlation with the most of rooting traits and cutting survival, while the second was mainly related to the traits of root formation on the basal cut of cutting (wound roots. Three difficult-to-root genotypes (S6-7, S1-3, 129/81 were distinctly grouped against other examined genotypes, by bought principal component and cluster analysis. There was a slight difference in grouping of easy-to-root genotypes (B-229 and PE19/66 among examined ways of standardization.

  17. Porphyromonas gingivalis Fim-A genotype distribution among Colombians

    Science.gov (United States)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Rafaela Morando

    2015-06-01

    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.

  19. Morphological Characteristics, Genetic Diversity and Classification of Chrysanthemum Genotypes

    Directory of Open Access Journals (Sweden)

    Z. Roein

    2015-09-01

    Full Text Available Chrysanthemum is one of the most important ornamental plants. The genus chrysanthemum is a popular cut flower, medicinal and pot plant. Morphological traits such as cut rooting and leaf characteristics and genetic diversity among 50 genotypes of chrysanthemum morifolium were analyzed. Based on analysis of variance of data all traits in the studied genotypes showed significant differences at 1% level. The results of correlation coefficient indicated a positive and significant correlation between stem length, leaf length, leaf width and leaf serration number.The leaf length showed the highest correlation (r = +0.90** with leaf width. Results showed that stem length and petiole length had the highest (h2>80% heritability. Cluster analysis according to the morphological traits using the Ward method classified all the genotypes into six groups. In this classification, two genotypes (‘Takapo’ and ‘Poloneh’ were classified into one cluster that was characterized by tall stem and low branch number. In this study, canonical discriminant analysis of 20 morphological traits revealed that 3 canonical discriminant variables explained 89.6% of the total variation among genotypes. Results revealed that among the studied traits, number of cutting root, leaf size, petiol length, stem length, number of branches and number of offsets were the most important traits for discriminating among chrysanthemum genotypes. The results of this study indicate that these traits are useful for selecting and identify superior genotypes of chrysanthemum germplasm. Using some of the genotypes belonging to cluster A (with a small size of plant and genotypes belonging to cluster E (with a large size of plant as parents can be practiced as a criteria for breeding programs.

  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. Genotype networks, innovation, and robustness in sulfur metabolism

    Science.gov (United States)

    2011-01-01

    Background A metabolism is a complex network of chemical reactions. This network synthesizes multiple small precursor molecules of biomass from chemicals that occur in the environment. The metabolic network of any one organism is encoded by a metabolic genotype, defined as the set of enzyme-coding genes whose products catalyze the network's reactions. Each metabolic genotype has a metabolic phenotype. We define this metabolic phenotype as the spectrum of different sources of a chemical element that a metabolism can use to synthesize biomass. We here focus on the element sulfur. We study properties of the space of all possible metabolic genotypes in sulfur metabolism by analyzing random metabolic genotypes that are viable on different numbers of sulfur sources. Results We show that metabolic genotypes with the same phenotype form large connected genotype networks - networks of metabolic networks - that extend far through metabolic genotype space. How far they reach through this space depends linearly on the number of super-essential reactions. A super-essential reaction is an essential reaction that occurs in all networks viable in a given environment. Metabolic networks can differ in how robust their phenotype is to the removal of individual reactions. We find that this robustness depends on metabolic network size, and on other variables, such as the size of minimal metabolic networks whose reactions are all essential in a specific environment. We show that different neighborhoods of any genotype network harbor very different novel phenotypes, metabolic innovations that can sustain life on novel sulfur sources. We also analyze the ability of evolving populations of metabolic networks to explore novel metabolic phenotypes. This ability is facilitated by the existence of genotype networks, because different neighborhoods of these networks contain very different novel phenotypes. Conclusions We show that the space of metabolic genotypes involved in sulfur metabolism

  2. PAX6 mutations: genotype-phenotype correlations

    Directory of Open Access Journals (Sweden)

    Hanson Isabel M

    2005-05-01

    Full Text Available Abstract Background The PAX6 protein is a highly conserved transcriptional regulator that is important for normal ocular and neural development. In humans, heterozygous mutations of the PAX6 gene cause aniridia (absence of the iris and related developmental eye diseases. PAX6 mutations are archived in the Human PAX6 Allelic Variant Database, which currently contains 309 records, 286 of which are mutations in patients with eye malformations. Results We examined the records in the Human PAX6 Allelic Variant Database and documented the frequency of different mutation types, the phenotypes associated with different mutation types, the contribution of CpG transitions to the PAX6 mutation spectrum, and the distribution of chain-terminating mutations in the open reading frame. Mutations that introduce a premature termination codon into the open reading frame are predominantly associated with aniridia; in contrast, non-aniridia phenotypes are typically associated with missense mutations. Four CpG dinucleotides in exons 8, 9, 10 and 11 are major mutation hotspots, and transitions at these CpG's account for over half of all nonsense mutations in the database. Truncating mutations are distributed throughout the PAX6 coding region, except for the last half of exon 12 and the coding part of exon 13, where they are completely absent. The absence of truncating mutations in the 3' part of the coding region is statistically significant and is consistent with the idea that nonsense-mediated decay acts on PAX6 mutant alleles. Conclusion The PAX6 Allelic Variant Database is a valuable resource for studying genotype-phenotype correlations. The consistent association of truncating mutations with the aniridia phenotype, and the distribution of truncating mutations in the PAX6 open reading frame, suggests that nonsense-mediated decay acts on PAX6 mutant alleles.

  3. Genotypically defined lissencephalies show distinct pathologies.

    Science.gov (United States)

    Forman, Mark S; Squier, Waney; Dobyns, William B; Golden, Jeffrey A

    2005-10-01

    Lissencephaly is traditionally divided into 2 distinct pathologic forms: classic (type I) and cobblestone (type II). To date, mutations in 4 genes, LIS1, DCX, RELN, and ARX, have been associated with distinct type I lissencephaly syndromes. Each of these genes has been shown to play a role in normal cell migration, consistent with the presumed pathogenesis of type I lissencephaly. Based on these data, we hypothesized that all forms of radiographically defined type I lissencephaly independent of genotype would be pathologically similar. To test this hypothesis, we examined brains from 16 patients, including 15 lissencephalic patients and one patient with subcortical band heterotopia. Of these 16 patients, 6 had LIS1 deletions, 2 had DCX mutations, and 2 had ARX mutations. In addition, 6 patients had no defined genetic defect, although the patient with subcortical band heterotopia exhibited the same pattern of malformation expected with an XLIS mutation. In all cases, the cortex was thickened; however, the topographic distribution of the cortical pathology varied, ranging from frontal- to occipital-biased pathology to diffuse involvement of the neocortex. Although brains with LIS1 deletions exhibited the classic 4-layer lissencephalic architecture, patients with DCX and ARX mutations each had unique cytoarchitectural findings distinct from LIS1. Furthermore, 2 of the 5 patients with no known genetic defect showed a fourth type of histopathology characterized by a 2-layered cortex. Interestingly, the 2 brains with the fourth type of lissencephaly showed profound brainstem and cerebellar abnormalities. In summary, we identified at least 4 distinct histopathologic subtypes of lissencephaly that stratify with the underlying genetic defect. Based on these data, a new classification for lissencephaly is proposed that incorporates both pathologic and genetic findings.

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

    Directory of Open Access Journals (Sweden)

    Pingchuan Li

    2017-12-01

    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 (https://www.ncbi.nlm.nih.gov/sra?term=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. Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies

    Directory of Open Access Journals (Sweden)

    Katy Denise Heath

    2014-04-01

    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.

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

    African Journals Online (AJOL)

    1993, 1993-1994 and 1994-1995) in three agro-ecological zones in Nigeria to study their reaction to cassava anthracnose disease (CAD), caused by Colletotrichum gloeosporioides, investigate genotype x environment (G x E) interaction ...

  7. Characterization of cowpea genotype resistance to Callosobruchus maculatus

    Directory of Open Access Journals (Sweden)

    Maria de Jesus Passos de Castro

    2013-09-01

    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.

  8. Single nucleotide polymorphism genotyping and its application on ...

    African Journals Online (AJOL)

    ... and its application on mapping and marker-assisted plant breeding. ... is the basis for the development of molecular markers, an indispensable tool in genetic ... principles that underlie SNP-genotyping methods specifically for large panel ...

  9. Response of potato genotypes to different levels of nitrogen

    National Research Council Canada - National Science Library

    Bakht Amin; Abid Yaqub; Muhammad Ali; Misbah Ullah; Abid Khan; Tayeb Muhammad; Adil Khan; Muhammad Ayaz

    2016-01-01

      The present study was carried out to evaluate response of potato genotypes to different levels of nitrogen at fruit and vegetable nursery, Department of Horticulture, The University of Azad Jammu...

  10. New measles virus genotype associated with outbreak, China.

    Science.gov (United States)

    Zhang, Yan; Ding, Zhengrong; Wang, Huiling; Li, Liqun; Pang, Yankun; Brown, Kevin E; Xu, Songtao; Zhu, Zhen; Rota, Paul A; Featherstone, David; Xu, Wenbo

    2010-06-01

    To determine the origin of the virus associated with a measles outbreak in Menglian County, Yunnan Province, People's Republic of China, in 2009, we conducted genetic analyses. Phylogenetic analyses based on nucleoprotein (N) and hemagglutinin (H) gene sequences showed that these Menglian viruses were not closely related to sequences of any World Health Organization (WHO) reference strains representing the 23 currently recognized genotypes. The minimum nucleotide divergence between the Menglian viruses and the most closely related reference strain, genotype D7, was 3.3% for the N gene and 3.0% for the H gene. A search of the databases of GenBank, WHO, and the Health Protection Agency Measles Nucleotide Surveillance showed that the Menglian viruses, together with the 2 older non-Menglian viruses, could be members of a new proposed measles genotype, d11. The new genotype designation will allow for better description of measles transmission patterns, especially in the Southeast Asian and Western Pacific regions.

  11. Giardia and Cryptosporidium species and genotypes in coyotes (Canis latrans).

    Science.gov (United States)

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

    2006-06-01

    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.

  12. Development of somaclones in sugarcane genotype BF-162 and ...

    African Journals Online (AJOL)

    Development of somaclones in sugarcane genotype BF-162 and assessment of variability by random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) markers in selected red rot resistant somaclones.

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

    African Journals Online (AJOL)

    uvp

    2014-08-24

    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 when it is ignored. .... and phenotypic and genetic levels of health and fertility.

  14. Molecular methods for bacterial genotyping and analyzed gene regions

    Directory of Open Access Journals (Sweden)

    İbrahim Halil Yıldırım1, Seval Cing Yıldırım2, Nadir Koçak3

    2011-06-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Moysés Nascimento

    2015-02-01

    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.

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

    Science.gov (United States)

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

    2014-10-01

    Retrospective serologic screening of 1077 serum samples collected from the primitive tribe from north-eastern India in 1963 revealed high prevalence of HBV (15% HBsAg carrier rate) and HCV (7% anti-HCV positivity) and co-circulation of multiple HBV genotypes-A, C, D and G. Full genome sequencing classified all the G-genotype samples as genotype-I. Comparison of genotype-I-HBV full-genome sequences representing 1963 (n=5, this study) and 2005 (reported earlier) showed identical recombination break-points of genotypes-A/G/C. Genotype-C and genotype-C-fragment of I-genotype circulating in 1963 were distinctly different. The data demonstrates that the recombination events were not recent. Molecular clock analysis predicted existence of genotype-I in this tribe during 1920s. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Changing HCV genotypes distribution in Poland--relation to source and time of infection.

    Science.gov (United States)

    Chlabicz, Slawomir; Flisiak, Robert; Kowalczuk, Oksana; Grzeszczuk, Anna; Pytel-Krolczuk, Barbara; Prokopowicz, Danuta; Chyczewski, Lech

    2008-06-01

    Understanding the distribution of HCV genotypes has implications for prognosis and therapy of hepatitis C. To describe the distribution of HCV genotypes in Poland in relation to route of transmission and year of infection. Patients with chronic liver disease were evaluated at the Department of Infectious Diseases, Bialystok (Poland). HCV genotype was determined by means of 5'UTR sequencing and comparison with known sequences of particular genotypes. The genotypes mostly frequently detected were genotype 1 (57.5%); genotype 3 (31.3%); and genotype 4 (8.4%). Genotype 1 constituted the majority of HCV infections caused by blood transfusion (68.8%) and only 34.8% of HCV infections in the intravenous drug use (IVDU) group (prelative proportion of genotype 1b in Poland has decreased and that of genotype 3a has increased, especially among IVDU.

  18. Rotavirus genotype distribution in Kyrgyzstan and Kazakhstan, 2007-2009.

    Science.gov (United States)

    Vainio, Kirsti; Latipov, Renat; Utegenova, Elmira; Kasymbekova, Kaliya; Juraev, Rivojiddin; Asilova, Mukhayyo; Flem, Elmira

    2013-05-01

    This is the first study to present rotavirus genotype distribution in children admitted to a hospital with acute gastroenteritis in Kyrgyzstan and Kazakhstan from January 2007 through December 2009. In total, 858 rotavirus ELISA-positive samples were characterized by RT-PCR, with a considerable geographical and seasonal variation in genotype distribution observed during the study. The globally common genotypes (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8], G12P[8] and G12P[6]) accounted for 81.5-88.2% of the infections in Kyrgyzstan and 72.3-79.3% of the infections in Kazakhstan. The predominant genotypes were G1P[8], G2P[4] and G3P[8]. G1P[8] was the dominating genotype in Kyrgyzstan, detected in 51-64.7% of the samples. A similar predominance was not seen for G1P[8] in Kazakhstan, with a shift to G2P[4] predominance being seen in 2008. G9P[8] was a rare genotype in both countries, whereas G12 was detected in between 2.2% and 7.6% of the samples. The surveillance period was characterized by many co-circulating genotypes, and eight unusual combinations (G1P[4], G2P[8], G2P[6], G3P[4], G9P[4], G12P[4], G9P[9] and G10P[4]) were detected. This study provides important baseline data on rotavirus genotypes in Kyrgyzstan and Kazakhstan in the pre-vaccine era, and the results may indicate that the two licensed vaccines can be expected to prevent rotavirus disease in these countries. © 2012 The Authors APMIS © 2012 APMIS.

  19. Robust SNP genotyping by multiplex PCR and arrayed primer extension

    Directory of Open Access Journals (Sweden)

    Podder Mohua

    2008-01-01

    Full Text Available Abstract Background Arrayed primer extension (APEX is a microarray-based rapid minisequencing methodology that may have utility in 'personalized medicine' applications that involve genetic diagnostics of single nucleotide polymorphisms (SNPs. However, to date there have been few reports that objectively evaluate the assay completion rate, call rate and accuracy of APEX. We have further developed robust assay design, chemistry and analysis methodologies, and have sought to determine how effective APEX is in comparison to leading 'gold-standard' genotyping platforms. Our methods have been tested against industry-leading technologies in two blinded experiments based on Coriell DNA samples and SNP genotype data from the International HapMap Project. Results In the first experiment, we genotyped 50 SNPs across the entire 270 HapMap Coriell DNA sample set. For each Coriell sample, DNA template was amplified in a total of 7 multiplex PCRs prior to genotyping. We obtained good results for 41 of the SNPs, with 99.8% genotype concordance with HapMap data, at an automated call rate of 94.9% (not including the 9 failed SNPs. In the second experiment, involving modifications to the initial DNA amplification so that a single 50-plex PCR could be achieved, genotyping of the same 50 SNPs across each of 49 randomly chosen Coriell DNA samples allowed extremely robust 50-plex genotyping from as little as 5 ng of DNA, with 100% assay completion rate, 100% call rate and >99.9% accuracy. Conclusion We have shown our methods to be effective for robust multiplex SNP genotyping using APEX, with 100% call rate and >99.9% accuracy. We believe that such methodology may be useful in future point-of-care clinical diagnostic applications where accuracy and call rate are both paramount.

  20. Variability of traits quinoa introduced genotypes (Chenopodium quinoa Willd.)

    OpenAIRE

    Dražić Slobodan; Živanović Tomislav; Maletić Radojka; Glamočlija Đorđe; Žarković Branka; Dražić Milena

    2013-01-01

    We analyzed variability and influence of investigated factors on grain yield of quinoa during three year period (2009, 2010, 2011). The experiment was conducted at two locations (Nova Pazova and Surduk), using two introduced genotypes of quinoa: KVL 37 and KVL 52. We detected that location and genotype had important impact. Grain yield varied according to years of study (1224 kg/ha to 1671 kg/ha). Results of regression and correlation analysis indicate on variation of the impact of plant heig...

  1. The molecular biology of hepatitis C virus. Genotypes and quasispecies.

    Science.gov (United States)

    Forns, X; Bukh, J

    1999-11-01

    Hepatitis C virus (HCV) is an important cause of chronic liver disease worldwide. HCV is a positive-strand genotype RNA virus with extensive genetic heterogeneity; HCV isolates define 6 major genotypes, and HCV circulates within an infected individual as a number of closely related but distinct species, termed a quasispecies. This article reviews characteristic aspects of HCV molecular biology and their implications for treatment and vaccine development.

  2. Warfarin genotyping in a single PCR reaction for microchip electrophoresis.

    Science.gov (United States)

    Poe, Brian L; Haverstick, Doris M; Landers, James P

    2012-04-01

    Warfarin is the most commonly prescribed oral anticoagulant medication but also is the second leading cause of emergency room visits for adverse drug reactions. Genetic testing for warfarin sensitivity may reduce hospitalization rates, but prospective genotyping is impeded in part by the turnaround time and costs of genotyping. Microfluidics-based assays can reduce reagent consumption and analysis time; however, no current assay has integrated multiplexed allele-specific PCR for warfarin genotyping with electrophoretic microfluidics hardware. Ideally, such an assay would use a single PCR reaction and, without further processing, a single microchip electrophoresis (ME) run to determine the 3 single-nucleotide polymorphisms (SNPs) affecting warfarin sensitivity [i.e., CYP2C9 (cytochrome P450, family 2, subfamily C, polypeptide 9) *2, CYP2C9 *3, and the VKORC1 (vitamin K epoxide reductase complex 1) A/B haplotype]. We designed and optimized primers for a fully multiplexed assay to examine 3 biallelic SNPs with the tetraprimer amplification refractory mutation system (T-ARMS). The assay was developed with conventional PCR equipment and demonstrated for microfluidic infrared-mediated PCR. Genotypes were determined by ME on the basis of the pattern of PCR products. Thirty-five samples of human genomic DNA were analyzed with this multiplex T-ARMS assay, and 100% of the genotype determinations agreed with the results obtained by other validated methods. The sample population included several genotypes conferring warfarin sensitivity, with both homozygous and heterozygous genotypes for each SNP. Total analysis times for the PCR and ME were approximately 75 min (1-sample run) and 90 min (12-sample run). This multiplexed T-ARMS assay coupled with microfluidics hardware constitutes a promising avenue for an inexpensive and rapid platform for warfarin genotyping.

  3. Missing call bias in high-throughput genotyping

    Directory of Open Access Journals (Sweden)

    Lin Rong

    2009-03-01

    Full Text Available Abstract Background The advent of high-throughput and cost-effective genotyping platforms made genome-wide association (GWA studies a reality. While the primary focus has been invested upon the improvement of reducing genotyping error, the problems associated with missing calls are largely overlooked. Results To probe into the effect of missing calls on GWAs, we demonstrated experimentally the prevalence and severity of the problem of missing call bias (MCB in four genotyping technologies (Affymetrix 500 K SNP array, SNPstream, TaqMan, and Illumina Beadlab. Subsequently, we showed theoretically that MCB leads to biased conclusions in the subsequent analyses, including estimation of allele/genotype frequencies, the measurement of HWE and association tests under various modes of inheritance relationships. We showed that MCB usually leads to power loss in association tests, and such power change is greater than what could be achieved by equivalent reduction of sample size unbiasedly. We also compared the bias in allele frequency estimation and in association tests introduced by MCB with those by genotyping errors. Our results illustrated that in most cases, the bias can be greatly reduced by increasing the call-rate at the cost of genotyping error rate. Conclusion The commonly used 'no-call' procedure for the observations of borderline quality should be modified. If the objective is to minimize the bias, the cut-off for call-rate and that for genotyping error rate should be properly coupled in GWA. We suggested that the ongoing QC cut-off for call-rate should be increased, while the cut-off for genotyping error rate can be reduced properly.

  4. Ledipasvir and sofosbuvir for untreated HCV genotype 1 infection.

    OpenAIRE

    Afdhal, Nezam; Zeuzem, Stefan; Kwo, Paul Y.; Chojkier, Mario; Gitlin, Norman; Puoti, Massimo; Romero Gomez, Manuel; Zarski, Jean Pierre; Agarwal, Kosh; Buggisch, Peter; Foster, Graham R.; Bräu, Norbert; Buti, Maria; Jacobson, Ira M.; Subramanian, G.Mani

    2014-01-01

    BACKGROUND: In phase 2 studies, treatment with the all-oral combination of the nucleotide polymerase inhibitor sofosbuvir and the NS5A inhibitor ledipasvir resulted in high rates of sustained virologic response among previously untreated patients with hepatitis C virus (HCV) genotype 1 infection. METHODS: We conducted a phase 3, open-label study involving previously untreated patients with chronic HCV genotype 1 infection. Patients were randomly assigned in a 1:1:1:1 ratio to receive ledipasv...

  5. Genotype and SNP calling from next-generation sequencing data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Paul, Joshua S.; Albrechtsen, Anders

    2011-01-01

    Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated w...... with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies....

  6. Biofilm formation of Staphylococcus aureus dairy isolates representing different genotypes.

    Science.gov (United States)

    Thiran, E; Di Ciccio, P A; Graber, H U; Zanardi, E; Ianieri, A; Hummerjohann, J

    2017-11-15

    The objective of this study was to compare the biofilm-forming capabilities of different genotypes of Staphylococcus aureus dairy isolates from Switzerland and northern Italy, including Staph. aureus genotype B (GTB) and methicillin-resistant Staph. aureus (MRSA). We hypothesized that biofilm formation might be more pronounced in the contagious GTB isolates compared with other genotypes affecting individual animals. Twenty-four dairy isolates, including 9 MRSA, were further characterized by genotyping by using ribosomal spacer PCR, spa typing, biofilm formation under static and dynamic conditions, and scanning electron microscopy. The GTB isolates (n = 6) were more able to form biofilms than other genotypes at 37°C and at 20°C after 48 and 72 h of incubation in the static assay using polystyrene microtiter plates. This result was supported by scanning electron micrographs showing a GTB isolate producing strong biofilm with extracellular matrix in contrast to a genotype C isolate. Furthermore, none of the MRSA isolates formed strong biofilms in the static assay. However, some MRSA produced low or moderate amounts of biofilm depending on the applied conditions. Under dynamic conditions, a much more diverse situation was observed. The ability of GTB isolates to be strong biofilm formers was not observed in all cases, emphasizing the importance of growth conditions for the expression of biofilm-related genes. No specific genotype, spa type, or MRSA isolate could be categorized significantly into one level of biofilm formation. Nineteen percent of isolates behaved similarly under static and dynamic conditions. The results of this study expand our knowledge of different dairy-related Staph. aureus subtypes and indicate the benefit of genotyping when biofilms are studied. The Authors. Published by the Federation of Animal Science Societies and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY

  7. Antioxidant Defense Mechanisms of Salinity Tolerance in Rice Genotypes

    Directory of Open Access Journals (Sweden)

    Mohammad Golam Kibria

    2017-05-01

    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.

  8. Analysis of Phenotypic Stability in Ten Cassava Genotypes in Three ...

    African Journals Online (AJOL)

    komla

    CV% 30.78. LSD 2.99 sum of squares, respectively. The genotype and year interaction was not significant and this reflected in the low contribution to the total sums of squares. Genotype >< location interaction was significant and contributed. 4.83% to the total sums 'of squares. This is an indicati0n that both favourable and.

  9. The genetic diversity of hepatitis A genotype I in Bulgaria

    Science.gov (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

    2018-01-01

    Abstract 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.

  10. Genotyping panel for assessing response to cancer chemotherapy

    Directory of Open Access Journals (Sweden)

    Hampel Heather

    2008-06-01

    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.

  11. Independent prognostic role of human papillomavirus genotype in cervical cancer.

    Science.gov (United States)

    Hang, Dong; Jia, Meiqun; Ma, Hongxia; Zhou, Jing; Feng, Xiaoshuang; Lyu, Zhangyan; Yin, Jian; Cui, Hong; Yin, Yin; Jin, Guangfu; Hu, Zhibin; Shen, Hongbing; Zhang, Kai; Li, Ni; Dai, Min

    2017-06-05

    Although the correlation of HPV genotype with cervical precursor lesions and invasive cancer has been confirmed, the role of HPV genotype in cervical cancer prognosis is less conclusive. This study aims to systematically investigate the independent prognostic role of HPV genotype in cervical cancer. A total of 306 eligible patients provided cervical cell specimens for HPV genotyping before therapy and had a median follow-up time of 54 months after diagnosis. Survival times were measured from the date of diagnosis to the date of cervical cancer-related death (overall survival, OS) and from the date of diagnosis to the date of recurrence or metastasis (disease free survival, DFS). Log-rank tests and Cox proportional hazard models were performed to evaluate the association between HPV genotype and survival times. A total of 12 types of high-risk HPV were detected and the leading ten types belong to two species: alpha-9 and alpha-7. HPV16 and 18 were the two most common types, with the prevalence of 60.8% and 8.8%, respectively. In the univariate analysis, HPV16-positive cases were associated with better OS (P = 0.037) and HPV16-related species alpha-9 predicted better OS and DFS (both P genotype poses differential prognoses for cervical cancer patients. The presence of HPV16 and its related species alpha-9 indicates an improved survival.

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

    Directory of Open Access Journals (Sweden)

    M.J. Hasan

    2014-06-01

    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.

  13. SPATIAL ANALYSIS TO SUPPORT GEOGRAPHIC TARGETING OF GENOTYPES TO ENVIRONMENTS

    Directory of Open Access Journals (Sweden)

    Glenn eHyman

    2013-03-01

    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.

  14. Determination of Fe Deficiency Tolerance in Sunflower Genotypes

    Directory of Open Access Journals (Sweden)

    Ayfer Alkan Torun

    2017-10-01

    Full Text Available Iron deficiency (Fe is an important nutritional disorder of plants and humans worldwide including Turkey. Sunflower is known as a Fe sensitive crop and its deficiency leads to severe yield and quality losses. In this study, the sensitivity of different sunflower genotypes to Fe deficiency was determined. For this purpose, sunflower genotypes TR-6149-SA, TR-3080 and 6480 were grown either without Fe (0 µmol or with Fe (100 µmol hydroponically. At the end of experiment symptom grade, SPAD value, chlorophyll concentration, shoot dry matter yield, Fe-reductase activity, shoot Fe concentration and pH value of growth medium were measured. It was found out that Fe uptake and Fe reductase activity were the most important factors determining the Fe-deficiency tolerance of a genotype. In the deficiency of Fe conditions, the activity of Fe reductase enzyme in the roots was found higher in the genotype of TR-3080 compared to the other genotypes. The results revealed that the genotypic responses to the different Fe concentrations applied are significantly different and Fe reductase enzyme activity may play an important role in amelioration of iron deficiency.

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

    Directory of Open Access Journals (Sweden)

    S. Jafari Rad

    2015-12-01

    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.

  16. Analyzing genotype-by-environment interaction using curvilinear regression

    Directory of Open Access Journals (Sweden)

    Dulce Gamito Santinhos Pereira

    2012-12-01

    Full Text Available In the context of multi-environment trials, where a series of experiments is conducted across different environmental conditions, the analysis of the structure of genotype-by-environment interaction is an important topic. This paper presents a generalization of the joint regression analysis for the cases where the response (e.g. yield is not linear across environments and can be written as a second (or higher order polynomial or another non-linear function. After identifying the common form regression function for all genotypes, we propose a selection procedure based on the adaptation of two tests: (i a test for parallelism of regression curves; and (ii a test of coincidence for those regressions. When the hypothesis of parallelism is rejected, subgroups of genotypes where the responses are parallel (or coincident should be identified. The use of the Scheffé multiple comparison method for regression coefficients in second-order polynomials allows to group the genotypes in two types of groups: one with upward-facing concavity (i.e. potential yield growth, and the other with downward-facing concavity (i.e. the yield approaches saturation. Theoretical results for genotype comparison and genotype selection are illustrated with an example of yield from a non-orthogonal series of experiments with winter rye (Secalecereale L.. We have deleted 10 % of that data at random to show that our meteorology is fully applicable to incomplete data sets, often observed in multi-environment trials.

  17. [Genetic diversity of a rare hepatitis A virus genotype].

    Science.gov (United States)

    Desbois, D; Couturier, E; Graube, A; Letort, M-J; Dussaix, E; Roque-Afonso, A-M

    2011-02-01

    Very few is known on genotype II hepatitis A virus (HAV) since it is rarely isolated. From 2002 to 2007, the French observatory of HAV identified six sub-genotype IIA strains of which one from a patient having travelled to West Africa. To investigate the possible African origin of sub-genotype IIA, we determined its prevalence among French travellers in 2008 and characterised its genetic variability. The 2008 mandatory notification records were screened for travel to Africa. Viral genotype was determined on the nucleotide sequencing of the VP1/2A junction region. The P1 region coding for capsid proteins was used to compare the genetic diversity of IIA isolates to those of other genotypes. In 2008, five out of 54 patients returning from West Africa were infected by IIA strains and an additional "autochthonous" case was identified. Two more African cases were identified in 2009. A total of 14 IIA isolates (eight African and six "autochthonous") were analysed. Nucleotide and amino-acid variability of IIA sequences was lower than that of the other genotypes. Phylogenetic analysis revealed the clustering of two "autochthonous" cases with African isolates whereas the other ones belonged to a different lineage. Most IIA strains isolated in France are imported by travellers returning from West Africa. However, the unexplained contamination mode of some "autochthonous" cases suggests another geographical origin to discover or a French reservoir to explore. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

  18. HPV genotypes co-infections associated with cervical carcinoma: Special focus on phylogenetically related and non-vaccine targeted genotypes

    National Research Council Canada - National Science Library

    Rashmirani Senapati; Bhagyalaxmi Nayak; Shantanu Kumar Kar; Bhagirathi Dwibedi

    2017-01-01

    HPV is the major causative agent for cervical cancer. Study on the risk of cervical cancer associated with different hr-HPV genotypes would be useful for disease management and new vaccine strategy...

  19. Computational strategies for alternative single-step Bayesian regression models with large numbers of genotyped and non-genotyped animals.

    Science.gov (United States)

    Fernando, Rohan L; Cheng, Hao; Golden, Bruce L; Garrick, Dorian J

    2016-12-08

    Two types of models have been used for single-step genomic prediction and genome-wide association studies that include phenotypes from both genotyped animals and their non-genotyped relatives. The two types are breeding value models (BVM) that fit breeding values explicitly and marker effects models (MEM) that express the breeding values in terms of the effects of observed or imputed genotypes. MEM can accommodate a wider class of analyses, including variable selection or mixture model analyses. The order of the equations that need to be solved and the inverses required in their construction vary widely, and thus the computational effort required depends upon the size of the pedigree, the number of genotyped animals and the number of loci. We present computational strategies to avoid storing large, dense blocks of the MME that involve imputed genotypes. Furthermore, we present a hybrid model that fits a MEM for animals with observed genotypes and a BVM for those without genotypes. The hybrid model is computationally attractive for pedigree files containing millions of animals with a large proportion of those being genotyped. We demonstrate the practicality on both the original MEM and the hybrid model using real data with 6,179,960 animals in the pedigree with 4,934,101 phenotypes and 31,453 animals genotyped at 40,214 informative loci. To complete a single-trait analysis on a desk-top computer with four graphics cards required about 3 h using the hybrid model to obtain both preconditioned conjugate gradient solutions and 42,000 Markov chain Monte-Carlo (MCMC) samples of breeding values, which allowed making inferences from posterior means, variances and covariances. The MCMC sampling required one quarter of the effort when the hybrid model was used compared to the published MEM. We present a hybrid model that fits a MEM for animals with genotypes and a BVM for those without genotypes. Its practicality and considerable reduction in computing effort was

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

    Directory of Open Access Journals (Sweden)

    Gelmesa Dandena

    2017-02-01

    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

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

    Directory of Open Access Journals (Sweden)

    Salma Ghulam Nabi

    2013-01-01

    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.

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

    Science.gov (United States)

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

    2015-07-01

    Human respiratory syncytial virus (HRSV) is the most common viral pathogen causing lower respiratory infections in infants and young children worldwide. HRSV ON1 genotype in subgroup A with a characteristic of a 72 nucleotide duplication in the second highly variable region of attachment glycoprotein gene, has been reported in some countries since it was first detected in clinical samples collected in Canada in 2010. In this study, 557 HRSV antigen-positive nasopharyngeal aspirates were randomly selected during 2012/2013 to 2013/2014 HRSV seasons in Beijing for subgroup typing and for ON1 genotype screening by using a PCR based method developed for easily identifying genotype ON1 out of strains of subtype A. It was found that subgroup B was dominant in the 2012/2013 season and sudden shift of subgroup dominance from B to A and rapid replacement of previously prevailing NA1 genotype by ON1 genotype occurred in the 2013/2014 season. Reversible amino acid replacement in the G protein gene was found in a new branch of ON1 genotype. The evolutionary rate of the 351 global ON1 sequences was estimated to 7.34 × 10(-3) nucleotide substitutions per site per year (95% highest probability density intervals, HPD, 5.71 × 10(-3) to 9.04 × 10(-3)), with the time of most recent common ancestor dating back to June 2009. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. First report of gastroenteritis by genotype G12 rotavirus in Dakar, Senegal

    OpenAIRE

    Dia, M.L.; Diop, A.; Sonko, M.A.; Bâ, M.; Cissé, M.F.

    2015-01-01

    The genotype G12 rotavirus was isolated from the stool of children 5 years old or younger with acute gastroenteritis during 1 year in three Dakar hospitals. The G12 genotype was the most common (58.25%). VP4 genotyping revealed mixed genotypes (1.94%).

  4. RHD maternal-fetal genotype incompatibility increases schizophrenia susceptibility.

    Science.gov (United States)

    Palmer, Christina G S; Turunen, Joni A; Sinsheimer, Janet S; Minassian, Sonia; Paunio, Tiina; Lönnqvist, Jouko; Peltonen, Leena; Woodward, J Arthur

    2002-12-01

    Fetal events and obstetric complications are associated with schizophrenia. Here we report the results of a family-based candidate-gene study that assesses the role of maternal-fetal genotype incompatibility at the RHD locus in schizophrenia. We adapted the case-parent-trio log-linear modeling approach to test for RHD maternal-fetal genotype incompatibility and to distinguish this effect from a high-risk allele at or near the RHD locus and from a direct maternal effect alone. Eighty-eight patient-parent trios, 72 patient-mother pairs, and 21 patient-father pairs were genotyped at the RHD locus. Of the 181 patients, 62% were male and 81% were second born or later. Only three patients were born after prophylaxis against maternal isoimmunization had become common practice. There was significant evidence for an RHD maternal-fetal genotype incompatibility, and the incompatibility parameter was estimated at 2.6. There was no evidence to support linkage/association with schizophrenia at or near the RHD locus nor any evidence to support the role of maternal genotype effect alone. Our results replicate previous findings that implicate the RHD locus in schizophrenia, and the candidate-gene design of this study allows the elimination of alternative explanations for the role of this locus in disease. Thus, the present study provides increasing evidence that the RHD locus increases schizophrenia risk through a maternal-fetal genotype incompatibility mechanism that increases risk of an adverse prenatal environment (e.g., Rh incompatibility) rather than through linkage/association with the disorder, linkage disequilibrium with an unknown nearby susceptibility locus, or a direct maternal effect alone. This is the first candidate-gene study to explicitly test for and provide evidence of a maternal-fetal genotype incompatibility mechanism in schizophrenia.

  5. Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives.

    Science.gov (United States)

    Rasheed, Awais; Hao, Yuanfeng; Xia, Xianchun; Khan, Awais; Xu, Yunbi; Varshney, Rajeev K; He, Zhonghu

    2017-08-07

    There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2010-09-01

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

  7. Genetic variation in southern USA rice genotypes for salinity tolerance

    Directory of Open Access Journals (Sweden)

    Teresa B De Leon

    2015-05-01

    Full Text Available The success of a rice breeding program in developing salt tolerant varieties depends on genetic variation and the salt stress response of adapted and donor rice germplasm. In this study, we used a combination of morphological and physiological traits in multivariate analyses to elucidate the phenotypic and genetic variation in salinity tolerance of thirty Southern USA rice genotypes, along with nineteen donor genotypes with varying degrees of tolerance. Significant genotypic variation and correlations were found among the salt injury score (SIS, ion leakage, chlorophyll reduction, shoot length reduction, shoot K+ concentration, and shoot Na+/K+ ratio. Using these parameters, the combined methods of cluster analysis and discriminant analysis validated the salinity response of known genotypes and classified most of the USA varieties into sensitive groups, except for three and seven varieties placed in the tolerant and moderately tolerant groups, respectively. Discriminant function and MANOVA delineated the differences in tolerance and suggested no differences between sensitive and highly sensitive groups. DNA profiling using simple sequence repeat markers showed narrow genetic diversity among USA genotypes. However, the overall genetic clustering was mostly due to subspecies and grain type differentiation and not by varietal grouping based on salinity tolerance. Among the donor genotypes, Nona Bokra, Pokkali, and its derived breeding lines remained the donors of choice for improving salinity tolerance during the seedling stage. However, due to undesirable agronomic attributes and photosensitivity of these donors, alternative genotypes such as TCCP266, Geumgangbyeo, and R609 are recommended as useful and novel sources of salinity tolerance for USA rice breeding programs.

  8. Identification of a new porcine circovirus type 2 (PCV2) genotype in Danish archive pigsamples

    DEFF Research Database (Denmark)

    Dupont, Kitt; Larsen, Lars Erik

    PCV2 is the major causative agent of postweaning multisystemic wasting syndrome (PMWS) in pigs. Two genotypes of PCV2 have been identified: genotype 1 and 2 (Olvera et al., 2007). PCV2 genotype 2 was involved in the first cases of PMWS in Canada (Hamel et al.,. 1998). PCV2 genotype 1 may be more...... pathogenic than PCV2 genotype 2, as a recent study from Grau-Roma et al. (2007) showed that genotype 2 primary was found in non-PMWS affected herds in Spain, while genotype 1 was found in PMWS affected herds....

  9. Identification of Potato Genotypes Using Digital Image Analysis

    Directory of Open Access Journals (Sweden)

    Máté CSÁK

    2011-07-01

    Full Text Available Based on the fractal analysis of digital images, a new classifying system has been proposed at the Potato Research Centre of Keszthely. It is a qualifying system generating objective values to distinguish potato varieties or detect quality differences within the genotype in a relatively simple way. The goal of the research project was to investigate whether Spectral Fractal Dimension (SFD value of digital images is applicable to describe various quality characters of potato tubers and whether SFD values could be used for the identification of certain varieties – if so, which conditions were the most important to enable this process. Considering the above aims, we developed an evaluation computer program which determines the SFD values of the 4 conditions of potato tubers: skin colour; raw flesh-colour; boiled flesh-colour; greying of flesh-colour after 24 hours in RGB spectrum and in all of its sub-spectrums (R, G, B. In total 2080 digital images of 13 varieties from 4 examining periods were analysed. Based on our results we can conclude that SFD analysis can be used in potato breeding only when digital images were made under well-determined, standardized conditions. Detailed statistical analysis (hypothesis tests, principal component analysis and non-hierarchic cluster analysis showed that SFD was not suitable for qualifying tuber characters within a genotype. When images were examined for different years and the same genotype, it became evident, that there are significant deviations between years and within same genotypes. We could conclude that the identification of genotypes should be related not to one particular SFD value, but to the control of the given year with the known value. When analyzing the differences between genotypes on yearly basis, irrespective of characteristics or the studied spectrum, we could not significantly separate genotypes, although there were some that could be separated, even though genotypes and their

  10. Auto-interpreter for CYP2D6 SNaPshot genotyping.

    Science.gov (United States)

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

    2008-11-06

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

  11. Physiological responses of genotypes soybean to simulated drought stress

    Directory of Open Access Journals (Sweden)

    Eleonóra Krivosudská

    2016-12-01

    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.

  12. Nutrient uptake of soybean genotypes under aluminum toxicity

    Directory of Open Access Journals (Sweden)

    Heru Kuswantoro

    2014-09-01

    Full Text Available The objective of this research was to study the nutrient uptake of soybean exposed to aluminium (Al toxicity. The factorial design consisted of two treatments arranged in a randomized block design with three replications. Liming was the first factor which consisted of four levels, i.e. i without liming; ii liming with 0.5×Al(exchangeable/ec; iii liming with 1×Al(ec; and iv liming with 1.5×Al(ec. Five genotypes were used as second factor, i.e. three tolerant genotypes (W3898- 14-3, Wilis, and Kawi, and two sensitve genotypes (MLG 3209 and MLG 3083. It was found that two tolerant genotypes, W3898-14-3 and Kawi, had a higher potassium (K and sodium (Na uptake than susceptible genotypes. Liming affected significantly the ratio of Al/[calcium (Ca + magnesium (Mg] in roots and leaves, the content of Ca and Mg in the roots and the content of Mg in the leaves. The K content in the roots and the content of Ca, K, and Na in the leaves were unresponsive to the alteration of pH and Al saturation.

  13. Does sex trade with violence among genotypes in Drosophila melanogaster?

    Directory of Open Access Journals (Sweden)

    Larry G Cabral

    Full Text Available 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.

  14. The quality of silage of different sorghum genotypes

    Directory of Open Access Journals (Sweden)

    Daniella Cangussú Tolentino

    2016-05-01

    Full Text Available The objective was to select from among 24 sorghum genotypes the superior ones for silage production. The study was conducted in the experimental field of Embrapa Maize & Sorghum, in the municipality of Sete Lagoas, Minas Gerais State. It used 24 forage sorghum genotypes, 21 being hybrids from the crossing of grain sorghum females and forage males (12F38019, 12F38006, 12F40006, 12F40005, 12F40019, 12F37016, 12F37005, 12F37043, 12F39006, 12F39005, 12F39019, 12F38005, 12F38007, 12F37007, 12F39007, 12F40007, 12F38014, 12F37014, 12F39014, 12F40014 e 12F38009 and three witnesses: BRS 610, BRS 655 and Volumax. It estimated productivity per area, in vitro dry matter digestibility, and assessed the bromatological and fermentation characteristics of sorghum silage. In vitro dry matter digestibility, unavailable protein in neutral detergent, neutral detergent fiber corrected for ashes and protein, acid detergent fiber, hemicellulose and lignin differed as to the genotypes tested. The pH and the ammoniacal nitrogen of the silage also showed differences between genotypes. Most of the genotypes tested are favorable for silage production, except the hybrid with higher lignin content 12F370014, and the hybrids 12F37007 and 12F370014, which showed the highest NDFap values.

  15. Identification of novel Cryptosporidium genotypes in kangaroos from Western Australia.

    Science.gov (United States)

    Yang, Rongchang; Fenwick, Stanley; Potter, Abbey; Ng, Josephine; Ryan, Una

    2011-06-30

    A total of 763 faecal samples were collected from western grey kangaroos (Macropus fuliginosus) in Western Australia and screened for the presence of Cryptosporidium by PCR at the 18S ribosomal RNA (rRNA) locus. Samples that were positive at the 18S locus were also amplified at the actin locus. The overall prevalence was 9.3% (71/763). At the 18S rRNA locus, sequences were obtained for 28 of the 71 positives. Sequence analysis identified four species; Cryptosporidium fayeri in seven isolates, Cryptosporidium marcopodum in four isolates, Cryptosporidium xiaoi in six isolates and a novel genotype (kangaroo genotype I) in eleven isolates. Analysis at the actin locus confirmed the genetic distinctness of the novel genotype. The results of the present study indicate that in addition to C. fayeri and C. marcopodum, kangaroos may be capable of being infected with a wider range of Cryptosporidium species and genotypes including livestock species such as C. xiaoi. The novel genotype identified in the kangaroos most likely represents a cryptic species that requires further analyses to confirm its species status. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. Genotyping-by-Sequencing for Plant Breeding and Genetics

    Directory of Open Access Journals (Sweden)

    Jesse A. Poland

    2012-11-01

    Full Text Available Rapid advances in “next-generation” DNA sequencing technology have brought the US$1000 human ( genome within reach while providing the raw sequencing output for researchers to revolutionize the way populations are genotyped. To capitalize on these advancements, genotyping-by-sequencing (GBS has been developed as a rapid and robust approach for reduced-representation sequencing of multiplexed samples that combines genome-wide molecular marker discovery and genotyping. The flexibility and low cost of GBS makes this an excellent tool for many applications and research questions in plant genetics and breeding. Here we address some of the new research opportunities that are becoming more feasible with GBS. Furthermore, we highlight areas in which GBS will become more powerful with the continued increase of sequencing output, development of reference genomes, and improvement of bioinformatics. The ultimate goal of plant biology scientists is to connect phenotype to genotype. In plant breeding, the genotype can then be used to predict phenotypes and select improved cultivars. Furthering our understanding of the connection between heritable genetic factors and the resulting phenotypes will enable genomics-assisted breeding to exist on the scale needed to increase global food supplies in the face of decreasing arable land and climate change.

  17. Molecular genotyping of duck hepatitis A viruses (DHAV) in Vietnam.

    Science.gov (United States)

    Doan, Huong Thi Thanh; Le, Xuyen Thi Kim; Do, Roan Thi; Hoang, Chau Thi Minh; Nguyen, Khue Thi; Le, Thanh Hoa

    2016-09-30

    The aim of this study was to identify the genetic characteristics and molecular genotyping of duck hepatitis A virus (DHAV) isolated in Vietnam during 2009-2013. Thirty duckling livers from outbreaks between 2009 and 2013 in seven provinces were collected and identified by polymerase chain reaction (PCR). Then, VP1 genes of eleven positive samples and two attenuated vaccine strains were sequenced and analyzed. Genotypic and phylogenetic analyses indicated that the 13 Vietnamese isolates were classified into two genotypes, DHAV-1 and DHAV-3. The rate of identity and homology was 91%-100% between the 10 Vietnamese and 26 global strains of DHAV-3, and 92%-100% between 3 Vietnamese and 16 strains of DHAV-1. Between the DHAV-3 and DHAV-1 strains, the divergence reached 30%. At the C-terminal of VP1 for the different strains, a hypervariable region was observed, and notably, six of the Vietnamese DHAV-3 strains in this study showed four consistent differences (at positions T184M, Q200H, K207N, and K214R) within this group that were distinct from all other DHAV-3 strains. This is the first report of molecular characterization of DHAVs in Vietnam. At least two genotypes were identified, DHAV-1 and DHAV-3, with diversified clades within and between genotypes. DHAV-3 seemed to be dominant in Vietnam.

  18. Improved dry-fleshed sweetpotato genotypes resistant to insect pests.

    Science.gov (United States)

    Jackson, D Michael; Bohac, J R

    2006-10-01

    Thirty-five mostly dry-fleshed sweetpotato, Ipomoea batatas (L.) Lam. (Convolvulaceae), genotypes from the USDA-ARS/Clemson University sweetpotato breeding program were evaluated in nine field experiments at the U.S. Vegetable Laboratory, Charleston, SC, from 1998 to 2004. There were highly significant entry effects for percentage of uninjured roots; wireworm, Diabrotica, and Systena (WDS) index; percentage of roots damaged by sweetpotato weevil, Cylas formicarius elegantulus (Summers); percentage of roots damaged by sweetpotato flea beetle, Chaetocnema confinis Crotch); and percentage of roots damaged by white grub larvae (primarily Plectris aliena Chapin). The susceptible control, 'SC1149-19', had a significantly lower percentage of uninjured roots, a significantly higher WDS rating, and higher percentage infestations of flea beetle, grubs, and sweetpotato weevils than all other sweetpotato entries in this study. Twenty-seven genotypes had significantly less insect damage than 'Beauregard', the leading commercial orange-fleshed cultivar in the United States. In addition, 11 genotypes had significantly less insect injury than 'Picadito', a commercial boniato-type sweetpotato grown extensively in southern Florida. Overall, no genotypes were more resistant to soil insect pests than the resistant checks 'Sumor' and 'Regal'. Many of the advanced dry-flesh sweetpotato genotypes had high levels of resistance to soil insect pests, and they represent a useful source of advanced germplasm for use in sweetpotato breeding programs.

  19. Immunoglobulin G genotypes and the risk of schizophrenia.

    Science.gov (United States)

    Pandey, Janardan P; Namboodiri, Aryan M; Elston, Robert C

    2016-10-01

    Genes of the immune system are relevant to the etiology of schizophrenia. However, to our knowledge, no large-scale studies, using molecular methods, have been undertaken to investigate the role of highly polymorphic immunoglobulin GM (γ marker) genes in this disorder. In this investigation, we aimed to determine whether particular GM genotypes were associated with susceptibility to schizophrenia. Using a matched case-control study design, we analyzed DNA samples from 798 subjects-398 patients with schizophrenia and 400 controls-obtained from the U.S. National Institute of Mental Health Repository. GM alleles were determined by the TaqMan(®) genotyping assay. The GM 3/3; 23-/23- genotype was highly significantly associated with susceptibility to schizophrenia (p = 0.0002). Subjects with this genotype were over three times (OR 3.4; 95 % CI 1.7-6.7) as likely to develop schizophrenia as those without this genotype. Our results show that immunoglobulin GM genes are risk factors for the development of schizophrenia. Since GM alleles have been implicated in gluten sensitivity and in immunity to neurotropic viruses associated with cognitive impairment, the results presented here may help unify these two disparate areas of pathology affected in this disorder.

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

    Directory of Open Access Journals (Sweden)

    Marcelo Vivas

    2017-06-01

    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

  1. Evaluating Some Turkish Originated Oat Genotypes for Some Agronomic Traits

    Directory of Open Access Journals (Sweden)

    Ziya Dumlupınar

    2017-07-01

    Full Text Available In this study 384 Turkish originated oat genotypes obtained from different gene banks, were characterized and evaluated for agronomical traits with four commercial cultivars (Checota, Sebat, Faikbey and Seydişehir under augmented experiment design for 2012-2013 and 2013-2014 cropping years. Oat landraces were evaluated for stem diameter (SD, plant height (PH, panicle length (PL, vegetative period (VP, grain filling period (GFP, days to maturity (DM, grain number per panicle (GNP, grain weight per panicle (GWP, thousand kernel weight (TKW, lodging (LOD, barley yellow dwarf virus (BYDV and single row yield (SRY under Kahramanmaraş conditions. According to the results of field trail for two years, differences of genotypes were significant for SD, PH, PL, VP, DM, TKW and SRY. However, the components such as SD, PL, VP, GFP, DM, GNP, GWP, TKW and SRY were significantly changed for the years and year x genotype interactions were also significant for PL, VP, DM, TKW and SRY. The landraces performed better than the commercial ones for the most of the evaluated traits. The SRW ranged between 4.65 g (TL444 to 202.1 g (TL614. Moreover, the other genotypes with the higher SRY were TL708, TL714, TL734 and TL703 genotypes with 167.85, 160.25, 153.90 and 149.7 g SRY, respectively.

  2. FTO genotype and adiposity in children: physical activity levels influence the effect of the risk genotype in adolescent males.

    Science.gov (United States)

    Scott, Robert A; Bailey, Mark E S; Moran, Colin N; Wilson, Richard H; Fuku, Noriyuki; Tanaka, Masashi; Tsiokanos, Athanasios; Jamurtas, Athanasios Z; Grammatikaki, Evangelia; Moschonis, George; Manios, Yannis; Pitsiladis, Yannis P

    2010-12-01

    Studies of the fat mass and obesity-associated (FTO) gene provide compelling evidence of genetic variation in the general population that influences fat levels and obesity risk. Studies of the interaction between genetic and environmental factors such as physical activity (PA) will promote the understanding of how lifestyle can modulate genetic contributions to obesity. In this study, we investigated the effect of FTO genotype, and interactions with PA or energy intake, in young children and adolescents. In all, 1-5-year-old children from the Growth, Exercise and Nutrition Epidemiological Study in preSchoolers (GENESIS) study (N=1980) and 11-18-year-old Greek adolescents (N=949) were measured for adiposity-related phenotypes and genotyped at the FTO single-nucleotide polymorphism (SNP) marker, rs17817449. Adolescents were classified as physically active or inactive based on self-reported levels of PA. In adolescents, FTO genotype influenced weight (P=0.001) and BMI (P=0.007). There was also a significant SNP(*)PA(*)gender interaction (P=0.028) on BMI, which reflected the association between FTO genotype and BMI in males (P=0.016), but not females (P=0.15), and significant SNP(*)PA interaction in males (P=0.007), but not females (P=0.74). The FTO genotype effect was more pronounced in inactive than active males. Inactive males homozygous for the G allele had a mean BMI 3 kg/m(2) higher than T carriers (P=0.008). In the GENESIS study, no significant association between FTO genotype and adiposity was found. The present findings highlight PA as an important factor modifying the effect of FTO genotype.

  3. Vida em Santidade: modos de ser santo em uma comunidade messiânico-milenarista do sertão baiano (Pau de Colher, 1934-1938 - DOI: 10.5752/P.2175-5841.2010v8n18p170

    Directory of Open Access Journals (Sweden)

    Filipe Pinto Monteiro

    2010-11-01

    Full Text Available A proposta do artigo é analisar o fenômeno peculiar da honraria santoral na comunidade messiânico-milenarista de Pau de Colher (Casa Nova, sertão da Bahia, 1934-1938. A partir de um recorte histórico-cultural e teológico, a investigação será encaminhada no sentido de esclarecer a atuação de uma liderança religiosa, popular e carismática atada a modelos de santidade gestados durante o período medieval no ocidente cristão e transmigrados para o Novo Mundo após os descobrimentos. O texto apresenta documentação inédita e estabelece uma discussão - a partir de obras clássicas e outras referências garimpadas ao longo da pesquisa - em torno da manifestação de santos católicos no interior baiano na década de 30 do século XX. O movimento de Pau de Colher, através da pregação de seus líderes, instituiu um diálogo com uma tradição que remonta às origens do cristianismo; fez crer na ressurreição de personagens como São José, o Carpinteiro e Santa Maria, a Imaculada -, figuras privilegiadas em nosso estudo -; e re-atualizou um conjunto de credos e valores transmitidos pelas mãos de missionários itinerantes e de beatos errantes durante a história do Brasil, revelando um intenso hibridismo entre catolicismo popular e eclesiástico. Palavras-chave: Pau de Colher; santos; sertão; catolicismo; religiosidade popular.   Abstract The aim of this paper is to analyze the peculiar phenomenon of the honor saints in the messianic-millenarian community of Pau de Colher (Casa Nova, interior of Bahia, 1934-1938. From a cultural-historical and theological approach, the research will be directed towards clarifying the role of religious, popular and charismatic leadership tied to models of holiness gestated during the medieval period in the Christian West and transmigrated to the New World after the discoveries. The paper presents unpublished documentation and provides a discussion - from classical works and other references panned

  4. Apolipoprotein E genotypes in Parkinson's disease with and without dementia.

    Science.gov (United States)

    Koller, W C; Glatt, S L; Hubble, J P; Paolo, A; Tröster, A I; Handler, M S; Horvat, R T; Martin, C; Schmidt, K; Karst, A

    1995-02-01

    The apolipoprotein E gene (Apo E) type 4 allele is a genetic risk factor influencing the development and age of onset of Alzheimer's disease. Because Parkinson's disease shares many characteristics of Alzheimer's disease, we studied the frequencies of Apo E genotypes in a cohort of 52 Parkinson's disease patients with dementia and 61 patients without dementia. Dementia was determined per National Institute of Neurological and Communicative Disorders and Stroke criteria and Mattis Dementia Rating Scale (DRS) 132. Apo E genotype and allele frequencies did not differ between demented and nondemented parkinsonian patients. Neither group's genotype and allele frequencies differed from that of a nondemented population of 78 controls. We conclude that the Apo E epsilon 4 allele influences neither the development of Parkinson's disease nor the dementia associated with Parkinson's disease.

  5. Selection of cotton genotypes for greater length of fibers

    Directory of Open Access Journals (Sweden)

    Luiz Paulo de Carvalho

    2016-11-01

    Full Text Available In cotton breeding programs, it is necessary to identify genotypes with predictable behavior on the length of fibers, and which are responsive to environmental variations, in specific or broad conditions. The aim of this study was to employ the methodology of mixed models for simultaneous selection of cotton genotypes with greater length of fibers, adaptability and stability. It was evaluated 36 lines in three trials located in Apodi (2013 and 2014 and Santa Helena (2013, in a randomized block design with two replications. Genetic parameters were estimated by the restricted maximum likelihood/best linear unbiased predictor method (REML/BLUP and the selection was based on the method of harmonic mean of the relative performance of genetic values. The genotypes CNPA 2012-55, CNPA 2012-58, CNPA 2012-62 and CNPA 2012-64 can be grown in all tested environments, since they gather greater length of fibers, stability and adaptability.

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

    Directory of Open Access Journals (Sweden)

    Maria D'Agata

    2012-07-01

    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

  7. [AFLP marking of the genotypes of leek (Allium porrum) varieties].

    Science.gov (United States)

    Filiushin, M A; Kholda, O A; Kochieva, E Z; Ryzhova, N N

    2011-04-01

    The results of the AFLP analysis of 16 leek (Allium porrum) accessions and related species of the sections of the genus Allium are presented. Restriction enzymes and primer combinations for the identification of the genotypes of the A. porrum accessions were chosen. As a result, 265 polymorphic AFLP fragments were amplified for 25 analyzed genotypes, and specific spectra of DNA fragments were obtained for each accession. A total of 24 fragments specific for the A. porrum genome was detected, of which only two characterized the genotypes of individual accessions. A wide range of genetic diversity (0.11-0.32) was revealed for the A. porrum varieties and lines used in the analysis. The highest level of similarity in the analyzed set of accessions was found between A. porrum and sand leek (A. scorodoprasum).

  8. Bioactive compounds in Mexican genotypes of cocoa cotyledon and husk.

    Science.gov (United States)

    Hernández-Hernández, Carolina; Viera-Alcaide, Isabel; Morales-Sillero, Ana María; Fernández-Bolaños, Juan; Rodríguez-Gutiérrez, Guillermo

    2018-02-01

    A characterization of the phenolic profile of 25 cocoa genotypes established in a Mexican gene bank was carried out. From five different extraction methods commonly used for phenols, extraction with acidified methanol-water was chosen as the best to quantify the concentrations of theobromine and individual phenols in cocoa beans. High concentrations of individual and total phenols were found for genotypes native to Mexico (like RIM105, M031, and M033) or from Peru and Ecuador (INI10), but not the commercial mix (CAF), and were directly associated with their antioxidant activities. Despite the loss of some theobromine and phenols during fermentation, epicatechin remained in the fermented cotyledon in high concentrations. This study could help promote the commercialization of Mexican genotypes of cocoa and reports the possibility of upcycling fermented cocoa husks, which are rich in bioactive compounds and fiber, as novel functional extracts for use in food formulation or for nutraceutical purposes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. First genotype identification of Trichosporon asahii in Sfax, Tunisia.

    Science.gov (United States)

    Sellami, Hayet; Trabelsi, Houaida; Neji, Sourour; Amouri, Imen; Cheikhrouhou, Fatma; Makni, Fattouma; Ayadi, Ali

    2017-04-01

    The objectives of our study were species identification and genotyping of Trichosporon isolates collected at the Parasitology and Mycology Laboratory in Sfax, Tunisia. Molecular identification was carried out by analysing the IGS1 regions of the rDNA of 30 Trichosporon isolates. Trichosporon asahii was the most frequent species detected. Furthermore, four genotypes were identified in Tunisia: 1 (46.4 %), 4 (35.7 %), 7 (14.3 %) and 3 (3.6 %). In vitro antifungal susceptibility testing of the isolates showed that voriconazole exhibited the highest activity. This is the first reported study of genotype identification of T. asahii in Tunisia and even in the African continent.

  10. Genotypic variability for protoplast regeneration in Saintpaulia ionantha (H. Wendl.).

    Science.gov (United States)

    Winkelmann, T; Grunewaldt, J

    1995-08-01

    The behaviour of eleven Saintpaulia ionantha (H. Wendl.) genotypes in protoplast culture was compared. Isolation of protoplasts from young shootlets regenerated in vitro on leaf explants, yielded 0.7 to 1.8 × 10(6) protoplasts per gram fresh weight. In all cultivars and breeding lines tested, cell divisions were observed. The mean division frequencies varied between 1.0 and 5.0% after 14 days, and between 6.4 and 13.8% after 24 days of culture. In ten genotypes callussing and shoot regeneration were achieved. The difference between the genotypes in shoot regeneration rate, between 2 and 68%, was more pronounced. The comparison of four cytokinins indicated hat thidiazuron was most effective for shoot regeneration, but often resulted in poorer shoot quality than benzylaminopurine.

  11. Genotyping with CRISPR-Cas-derived RNA-guided endonucleases.

    Science.gov (United States)

    Kim, Jong Min; Kim, Daesik; Kim, Seokjoong; Kim, Jin-Soo

    2014-01-01

    Restriction fragment length polymorphism (RFLP) analysis is one of the oldest, most convenient and least expensive methods of genotyping, but is limited by the availability of restriction endonuclease sites. Here we present a novel method of employing CRISPR/Cas-derived RNA-guided engineered nucleases (RGENs) in RFLP analysis. We prepare RGENs by complexing recombinant Cas9 protein derived from Streptococcus pyogenes with in vitro transcribed guide RNAs that are complementary to the DNA sequences of interest. Then, we genotype recurrent mutations found in cancer and small insertions or deletions (indels) induced in cultured cells and animals by RGENs and other engineered nucleases such as transcription activator-like effector nucleases (TALENs). Unlike T7 endonuclease I or Surveyor assays that are widely used for genotyping engineered nuclease-induced mutations, RGEN-mediated RFLP analysis can detect homozygous mutant clones that contain identical biallelic indel sequences and is not limited by sequence polymorphisms near the nuclease target sites.

  12. ENVIRONMENTAL AND SOCIO-ECONOMIC ASPECT OF GROWING MISCANTHUS GENOTYPES

    Directory of Open Access Journals (Sweden)

    Marián KOTRLA

    2013-01-01

    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.

  13. Investigation of the genotype III to genotype I shift in Japanese encephalitis virus and the impact on human cases.

    Science.gov (United States)

    Han, Na; Adams, James; Fang, Wei; Liu, Si-Qing; Rayner, Simon

    2015-08-01

    Japanese encephalitis is a mosquito borne disease and is the leading cause of viral encephalitis in the Asia-Pacific area. The causative agent, Japanese encephalitis virus (JEV) can be phylogenetically classified into five genotypes based on nucleotide sequence. In recent years, genotype I (GI) has displaced genotype III (GIII) as the dominant lineage, but the mechanisms behind this displacement event requires elucidation. In an earlier study, we compared host variation over time between the two genotypes and observed that GI appears to have evolved to achieve more efficient infection in hosts in the replication cycle, with the tradeoff of reduced infectivity in secondary hosts such as humans. To further investigate this phenomenon, we collected JEV surveillance data on human cases and, together with sequence data, and generated genotype/case profiles from seven Asia-Pacific countries and regions to characterize the GI/GIII displacement event. We found that, when comprehensive and consistent vaccination and surveillance data was available, and the GIII to GI shift occurred within a well-defined time period, there was a statistically significant drop in JEV human cases. Our findings provide further support for the argument that GI is less effective in infecting humans, who represent a dead end host. However, experimental investigation is necessary to confirm this hypothesis. The study highlights the value of alternative approaches to investigation of epidemics, as well as the importance of effective data collection for disease surveillance and control.

  14. Human Genome Variation and the Concept of Genotype Networks

    Science.gov (United States)

    Dall'Olio, Giovanni Marco; Bertranpetit, Jaume; Wagner, Andreas; Laayouni, Hafid

    2014-01-01

    Genotype networks are a concept used in systems biology to study sets of genotypes having the same phenotype, and the ability of these to bring forth novel phenotypes. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of systems such as metabolic networks and RNA folds. Recently, they have been the base for reconciling the neutralist and selectionist views on evolution. Here, we adapted this concept to the study of population genetics data. Specifically, we applied genotype networks to the human 1000 genomes dataset, and analyzed networks composed of short haplotypes of Single Nucleotide Variants (SNV). The result is a scan of how properties related to genetic heterogeneity and stability to mutations are distributed along the human genome. We found that genes involved in acquired immunity, such as some HLA and MHC genes, tend to have the most heterogeneous and connected networks, and that coding regions tend to be more heterogeneous and stable to mutations than non-coding regions. We also found, using coalescent simulations, that regions under selection have more extended and connected networks. The application of the concept of genotype networks can provide a new opportunity to understand the evolutionary processes that shaped our genome. Learning how the genotype space of each region of our genome has been explored during the evolutionary history of the human species can lead to a better understanding on how selective pressures and neutral factors have shaped genetic diversity within populations and among individuals. Combined with the availability of larger datasets of sequencing data, genotype networks represent a new approach to the study of human genetic diversity that looks to the whole genome, and goes beyond the classical division between selection and neutrality methods. PMID:24911413

  15. Genomic prediction when some animals are not genotyped

    Directory of Open Access Journals (Sweden)

    Lund Mogens S

    2010-01-01

    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.

  16. Chimpanzee Personality and the Arginine Vasopressin Receptor 1A Genotype.

    Science.gov (United States)

    Wilson, V A D; Weiss, A; Humle, T; Morimura, N; Udono, T; Idani, G; Matsuzawa, T; Hirata, S; Inoue-Murayama, M

    2017-03-01

    Polymorphisms of the arginine vasopressin receptor 1a (AVPR1a) gene have been linked to various measures related to human social behavior, including sibling conflict and agreeableness. In chimpanzees, AVPR1a polymorphisms have been associated with traits important for social interactions, including sociability, joint attention, dominance, conscientiousness, and hierarchical personality dimensions named low alpha/stability, disinhibition, and negative emotionality/low dominance. We examined associations between AVPR1a and six personality domains and hierarchical personality dimensions in 129 chimpanzees (Pan troglodytes) living in Japan or in a sanctuary in Guinea. We fit three linear and three animal models. The first model included genotype, the second included sex and genotype, and the third included genotype, sex, and sex × genotype. All personality phenotypes were heritable. Chimpanzees possessing the long form of the allele were higher in conscientiousness, but only in models that did not include the other predictors; however, additional analyses suggested that this may have been a consequence of study design. In animal models that included sex and sex × genotype, chimpanzees homozygous for the short form of the allele were higher in extraversion. Taken with the findings of previous studies of chimpanzees and humans, the findings related to conscientiousness suggest that AVPR1a may be related to lower levels of impulsive aggression. The direction of the association between AVPR1a genotype and extraversion ran counter to what one would expect if AVPR1a was related to social behaviors. These results help us further understand the genetic basis of personality in chimpanzees.

  17. Genotyping of Brucella species using clade specific SNPs

    Directory of Open Access Journals (Sweden)

    Foster Jeffrey T

    2012-06-01

    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.

  18. Methylenetetrahydrofolate reductase genotype association with the risk of follicular lymphoma.

    Science.gov (United States)

    Ismail, Said I; Ababneh, Nida A; Khader, Yousef; Abu-Khader, Ahmad A; Awidi, Abdullah

    2009-12-01

    The metabolism of folate is essential in DNA synthesis, and polymorphisms of genes involved in such metabolism have been implicated in many types of cancer. Among these, the methylene tetrahydrofolate reductase gene (MTHFR) encodes an enzyme that converts folate to a methyl donor used for DNA methylation. We studied the association between the different genotypes of the two most common MTHFR polymorphisms, C677T and A1298C, and the risk of follicular lymphoma (FL). For this purpose, 55 previously diagnosed FL patients and 170 normal control subjects were examined using polymerase chain reaction followed by restriction fragment length polymorphism. The frequency of the A1298C CC homozygous mutant genotype was significantly higher in patients with FL than in control subjects (OR = 3.51, 95% CI = 1.39-8.86, P = 0.008). No such association was found for the heterozygous A1298C AC genotype (OR = 1.08, 95% CI = 0.55-2.12, P = 0.83). On the other hand, no significant association was found for either the C677T CT heterozygous genotype (OR = 0.79, 95% CI = 0.42-1.51, P = 0.49) or the C677T TT homozygous mutant genotype (OR = 0.55, 95% CI = 0.12-2.65, P = 0.46). The present findings add to the very few reports suggesting a link between the A1298C CC homozygous MTHFR genotype and a higher risk of developing FL, and the first such in a Jordanian population.

  19. Human papillomavirus genotyping and integration in ovarian cancer Saudi patients

    Science.gov (United States)

    2013-01-01

    Background Human papillomavirus (HPV) is associated with different malignancies but its role in the pathogenesis of ovarian cancer is controversial. This study investigated the prevalence, genotyping and physical state of HPV in ovarian cancer Saudi patients. Methods Hundred formalin fixed paraffin embedded (FFPE) ovarian carcinoma tissues and their normal adjacent tissues (NAT) were included in the study. HPV was detected by nested polymerase chain reaction (PCR) using degenerated HPVL1 consensus primer pairs MY09/MY11 and GP5+/GP6 + to amplify a broad spectrum of HPV genotypes in a single reaction. The HPV positive samples were further genotyped using DNA sequencing. The physical state of the virus was identified using Amplification of Papillomavirus Oncogene Transcripts (APOT) assay in the samples positive for HPV16 and/or HPV18. Results High percentage of HPV (42%) was observed in ovarian carcinoma compared to 8% in the NAT. The high-risk HPV types 16, 18 and 45 were highly associated with the advanced stages of tumor, while low-risk types 6 and 11 were present in NAT. In malignant tissues, HPV-16 was the most predominant genotype followed by HPV-18 and -45. The percentage of viral integration into the host genome was significantly high (61.1%) compared to 38.9% episomal in HPV positive tumors tissues. In HPV18 genotype the percentage of viral integration was 54.5% compared to 45.5% episomal. Conclusion The high risk HPV genotypes in ovarian cancer may indicate its role in ovarian carcinogenesis. The HPV vaccination is highly recommended to reduce this type of cancer. PMID:24252426

  20. Measles virus genotypes circulating in India, 2011-2015.

    Science.gov (United States)

    Vaidya, Sunil R; Chowdhury, Deepika T

    2017-05-01

    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.

  1. Human genome variation and the concept of genotype networks.

    Science.gov (United States)

    Dall'Olio, Giovanni Marco; Bertranpetit, Jaume; Wagner, Andreas; Laayouni, Hafid

    2014-01-01

    Genotype networks are a concept used in systems biology to study sets of genotypes having the same phenotype, and the ability of these to bring forth novel phenotypes. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of systems such as metabolic networks and RNA folds. Recently, they have been the base for reconciling the neutralist and selectionist views on evolution. Here, we adapted this concept to the study of population genetics data. Specifically, we applied genotype networks to the human 1000 genomes dataset, and analyzed networks composed of short haplotypes of Single Nucleotide Variants (SNV). The result is a scan of how properties related to genetic heterogeneity and stability to mutations are distributed along the human genome. We found that genes involved in acquired immunity, such as some HLA and MHC genes, tend to have the most heterogeneous and connected networks, and that coding regions tend to be more heterogeneous and stable to mutations than non-coding regions. We also found, using coalescent simulations, that regions under selection have more extended and connected networks. The application of the concept of genotype networks can provide a new opportunity to understand the evolutionary processes that shaped our genome. Learning how the genotype space of each region of our genome has been explored during the evolutionary history of the human species can lead to a better understanding on how selective pressures and neutral factors have shaped genetic diversity within populations and among individuals. Combined with the availability of larger datasets of sequencing data, genotype networks represent a new approach to the study of human genetic diversity that looks to the whole genome, and goes beyond the classical division between selection and neutrality methods.

  2. Rotavirus genotypes associated with acute diarrhea in Egyptian infants.

    Science.gov (United States)

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

    2014-01-01

    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.

  3. Chlorophyll a fluorescence to phenotype wheat genotypes for heat tolerance

    DEFF Research Database (Denmark)

    Sharma, Dew Kumari; Andersen, Sven Bode; Ottosen, Carl-Otto

    Wheat (Triticum aestivum L.) is a heat-susceptible crop throughout its phenological stages, flowering phase being the most sensitive stage. Early stress detection method with advanced physiological measurements may provide new dimensions to establish a high throughput phenotyping technique....... Initial phenotyping of 1300 wheat genotypes in a milder stress at 38oC for 2 h showed a heritability of 7% for Fv/Fm. However, a stronger stress at 40oC for 72 h in repeated experiments on 138 extreme performing lines resulted in a genotype dependent drop in Fv/Fm and an increased genetic component of 15...

  4. Neuregulin-1 genotypes and eye movements in schizophrenia

    DEFF Research Database (Denmark)

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

    2010-01-01

    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

  5. RHD Maternal-Fetal Genotype Incompatibility Increases Schizophrenia Susceptibility

    OpenAIRE

    Palmer, Christina G. S.; Turunen, Joni A.; Sinsheimer, Janet S.; Minassian, Sonia; Paunio, Tiina; Lönnqvist, Jouko; Peltonen, Leena; Woodward, J. Arthur

    2002-01-01

    Fetal events and obstetric complications are associated with schizophrenia. Here we report the results of a family-based candidate-gene study that assesses the role of maternal-fetal genotype incompatibility at the RHD locus in schizophrenia. We adapted the case-parent–trio log-linear modeling approach to test for RHD maternal-fetal genotype incompatibility and to distinguish this effect from a high-risk allele at or near the RHD locus and from a direct maternal effect alone. Eighty-eight pat...

  6. Nephele: genotyping via complete composition vectors and MapReduce

    Directory of Open Access Journals (Sweden)

    Mardis Scott

    2011-08-01

    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

  7. LASER server: ancestry tracing with genotypes or sequence reads.

    Science.gov (United States)

    Taliun, Daniel; Chothani, Sonia P; Schönherr, Sebastian; Forer, Lukas; Boehnke, Michael; Abecasis, Gonçalo R; Wang, Chaolong

    2017-07-01

    To enable direct comparison of ancestry background in different studies, we developed LASER to estimate individual ancestry by placing either sezquenced or genotyped samples in a common ancestry space, regardless of the sequencing strategy or genotyping array used to characterize each sample. Here we describe the LASER server to facilitate application of the method to a wide range of genetic studies. The server provides genetic ancestry estimation for different geographic regions and user-friendly interactive visualization of the results. The LASER server is freely accessible at http://laser.sph.umich.edu/. dtaliun@umich.edu or wangcl@gis.a-star.edu.sg. Supplementary data are available at Bioinformatics online.

  8. The microanalysis on resistance of new tomato genotypes

    Directory of Open Access Journals (Sweden)

    Tatiana Calalb

    2013-04-01

    Full Text Available Microscopic study on the leaf of the new tomato genotypes has shown that the most informative structural indicators of drought resistance of these plants are: a presence, level of development and the distribution of protective and glandulartrichomes on the leaves; b presence and occurrence of the cells with oxalate calcium sand in the leaf mesophyll. Statistical processing of the results determines that new tomato genotypes “Line 50” – ‚Prizor’ × (‚Prizor’ × Lycopersicon hirsutum and “Line 47” – ‘Friguşor’ × (Lycopersicon peruvianum × ‚Victoria’ are resistant to drought.

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

    Directory of Open Access Journals (Sweden)

    Sara Akhiani

    2017-05-01

    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.

  10. The Envelope Gene of Hepatitis B Virus Is Implicated in Both Differential Virion Secretion and Genome Replication Capacities between Genotype B and Genotype C Isolates.

    Science.gov (United States)

    Jia, Haodi; Qin, Yanli; Chen, Chaoyang; Zhang, Fei; Li, Cheng; Zong, Li; Wang, Yongxiang; Zhang, Jiming; Li, Jisu; Wen, Yumei; Tong, Shuping

    2017-03-28

    Chronic infection by hepatitis B virus (HBV) genotype C is associated with a prolonged replicative phase and an increased risk of liver cancer, compared with genotype B infection. We previously found lower replication capacity but more efficient virion secretion by genotype C than genotype B isolates. Virion secretion requires interaction between core particles and ENVELOPE proteins. In the present study, chimeric constructs between genotype B and genotype C clones were generated to identify the structural basis for differential virion secretion. In addition to dimeric constructs, we also employed 1.1mer constructs, where the cytomegalovirus (CMV) promoter drove pregenomic RNA transcription. Through transient transfection experiments in Huh7 cells, we found that exchanging the entire envelope gene or just its S region could enhance virion secretion by genotype B clones while diminishing virion secretion by genotype C. Site-directed mutagenesis established the contribution of genotype-specific divergence at codons 108 and 115 in the preS1 region, as well as codon 126 in the S region, to differential virion secretion. Surprisingly, exchanging the envelope gene or just its S region, but not the core gene or 3' S region, could markedly increase intracellular replicative DNA for genotype C clones but diminish that for genotype B, although the underlying mechanism remains to be clarified.

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

    Science.gov (United States)

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

    2012-04-01

    In India, systematic genotype replacement has been observed for serotype A foot-and-mouth disease virus. After a decade of co-circulation of genotypes VI and VII, genotype VII emerged as the single dominant genotype since 2001. To derive possible explanations for such epochal evolution dynamics, in vitro intergenotype growth competition experiments involving both co- and superinfection regimes were conducted. Coinfection of BHK-21 cells demonstrated abrupt loss in the genotype VI viral load with commensurate increase in the load of genotype VII as measured by the genotype differentiating ELISA, RT-PCR and real-time RT-PCR. The superinfection dynamics was shaped by temporal spacing of infection, where the invading genotype VII took more number of passages than coinfection to eventually overtake the resident genotype VI. It was speculated that such superior replicative fitness of genotype VII could have been a possible factor for the ultimate dominance of genotype VII in nature. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Distinct Distribution Pattern of Hepatitis B Virus Genotype C and D in Liver Tissue and Serum of Dual Genotype Infected Liver Cirrhosis and Hepatocellular Carcinoma Patients

    Science.gov (United States)

    Datta, Somenath; Roychoudhury, Shrabasti; Ghosh, Alip; Dasgupta, Debanjali; Ghosh, Amit; Chakraborty, Bidhan; Roy, Sukanta; Gupta, Subash; Santra, Amal Kumar; Datta, Simanti; Das, Kausik; Dhali, Gopal Krishna; Chowdhury, Abhijit; Banerjee, Soma

    2014-01-01

    Aims The impact of co-infection of several hepatitis B virus (HBV) genotypes on the clinical outcome remains controversial. This study has for the first time investigated the distribution of HBV genotypes in the serum and in the intrahepatic tissue of liver cirrhotic (LC) and hepatocellular carcinoma (HCC) patients from India. In addition, the genotype-genotype interplay and plausible mechanism of development of HCC has also been explored. Methods The assessment of HBV genotypes was performed by nested PCR using either surface or HBx specific primers from both the circulating virus in the serum and replicative virus that includes covalently closed circular DNA (cccDNA) and relaxed circular DNA (rcDNA) of HBV from the intrahepatic tissue. The integrated virus within the host chromosome was genotyped by Alu-PCR method. Each PCR products were cloned and sequences of five randomly selected clones were subsequently analysed. Results HBV/genotype D was detected in the serum of all LC and HCC patients whereas the sequences of the replicative HBV DNA (cccDNA and rcDNA) from the intrahepatic tissue of the same patients revealed the presence of both HBV/genotype C and D. The sequences of the integrated viruses exhibited the solo presence of HBV/genotype C in the majority of LC and HCC tissues while both HBV/genotype C and D clones were found in few patients in which HBV/genotype C was predominated. Moreover, compared to HBV/genotype D, genotype C had higher propensity to generate double strand breaks, ER stress and reactive oxygen species and it had also showed higher cellular homologous-recombination efficiency that engendered more chromosomal rearrangements, which ultimately led to development of HCC. Conclusions Our study highlights the necessity of routine analysis of HBV genotype from the liver tissue of each chronic HBV infected patient in clinical practice to understand the disease prognosis and also to select therapeutic strategy. PMID:25032957

  13. Hepatitis C virus genotype and subtype distribution in Chinese chronic hepatitis C patients: nationwide spread of HCV genotypes 3 and 6.

    Science.gov (United States)

    Ju, Wei; Yang, Song; Feng, Shenghu; Wang, Qi; Liu, Shunai; Xing, Huichun; Xie, Wen; Zhu, Liying; Cheng, Jun

    2015-07-25

    Hepatitis C virus (HCV) genotype and subtype are related to disease progression and response to antiviral therapy. Current HCV genotype and subtype distribution data, especially for genotypes 3 and 6, are limited in China. Our purpose was to investigate the current HCV genotype and subtype distributions in chronic hepatitis C patients in China. Chronic hepatitis C patients (n = 1012) were enrolled, and demographic information and possible transmission risk factors were collected. Serum samples were subjected to reverse-transcription polymerase chain reaction, followed by direct DNA sequencing and phylogenetic analysis of the NS5B and core/E1 regions to determine HCV genotypes/subtypes. The geographical distributions of HCV genotypes/subtypes were analyzed. Demographic information and transmission risk factors were compared between different HCV genotypes/subtypes. Four genotypes and seven subtypes of HCV were detected in 970 patients. Subtypes 1b, 2a, 3a, 6a, 3b, 6n, and 1a were detected at frequencies of 71.96%, 19.90%, 3.20%, 2.16%, 1.96%, 0.41%, and 0.41%, respectively. Genotypes 3 and 6 showed an increasingly wide geographic distribution over time. Patients with subtypes 1b and 2a were older than those with 3a, 3b, 6a, and 6n subtypes (p genotype 1 and 2 patients underwent blood transfusion than those with genotype 3 (all p genotype 3 and 6 patients had a history of intravenous drug use than those with genotypes 1 and 2 (all p genotype 3 and 6 HCV infections have already spread nationwide from southern and western China.

  14. A POWERFUL METHOD FOR INCLUDING GENOTYPE UNCERTAINTY IN TESTS OF HARDY-WEINBERG EQUILIBRIUM.

    Science.gov (United States)

    Beck, Andrew; Luedtke, Alexander; Liu, Keli; Tintle, Nathan

    2017-01-01

    The use of posterior probabilities to summarize genotype uncertainty is pervasive across genotype, sequencing and imputation platforms. Prior work in many contexts has shown the utility of incorporating genotype uncertainty (posterior probabilities) in downstream statistical tests. Typical approaches to incorporating genotype uncertainty when testing Hardy-Weinberg equilibrium tend to lack calibration in the type I error rate, especially as genotype uncertainty increases. We propose a new approach in the spirit of genomic control that properly calibrates the type I error rate, while yielding improved power to detect deviations from Hardy-Weinberg Equilibrium. We demonstrate the improved performance of our method on both simulated and real genotypes.

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

    African Journals Online (AJOL)

    Wheat breeders have to determine the new cultivars and lines responsive to the environmental changes for grain yield and yield components. Therefore, this study was conducted to evaluate 25 durum wheat (Triticum turgidum spp. durum) genotypes including 12 registered cultivars and 13 advanced breeding lines for their ...

  16. The nickel dose–response relationship by filaggrin genotype (FLG)

    DEFF Research Database (Denmark)

    Ross-Hansen, Katrine; Johansen, Jeanne D; Vølund, Aage

    2014-01-01

    -sensitized female patients, seven heterozygous mutation carriers and six non-mutation carriers (genotyped for R501X, 2282del4, or R2447X), were patch tested and performed a repeated open application test (ROAT) with a nickel sulfate dilution series. Logistic threshold dose-response analyses were used to test...

  17. Evaluation of selected fig genotypes from South east Turkey ...

    African Journals Online (AJOL)

    Turkey has great variations and distributions in wild fig forms as well as fig cultivars. This study was carried out in Mardin and anlýurfa provinces during 2004 - 2005. Nine fig genotypes were evaluated in this selection study for two years. In this study, some morphological characteristics investigated were tree growth habit, ...

  18. [STR genotyping from trace epithelial cells on fountain pen].

    Science.gov (United States)

    Yang, Fan; Mei, Shan-Zong; Li, Yong-Hong; Feng, Yan; Yu, Wei-Dong; Zhang, Yue

    2008-02-01

    To evaluate the feasibility of STR genotyping from trace epithelial cells on fountain pen and to discuss the impact of conservation time on DNA typing. Seven fountain pens were separately used by each of the 17 volunteers 20 minutes per day for a month and then were preserved on day 1, 3, 5, 7, 14, 21, and 28. DNA was extracted from the epithelial cells on fountain pen by silicon bead and was genotyped by Identifier kit. The corresponding control samples were buccal swabs of the above volunteers. The detectable numbers of loci were counted for assessment. There were statistically significant differences in the DNA genotyping by detectable numbers of gene loci between buccal swabs and epithelial cells on fountain pen of different conservation times (P fountain pen preserved on day 1, 3, 5, 7, 14, 21, 28 and the corresponding oral swabs were also statistically significant (P fountain pen if the tests were performed within 24 hours. The trace epithelial cells on fountain pen can be used as biological samples for personal identification, but the conservation time would have influence on the results of DNA genotyping.

  19. Contribution Paternelle De Genotypes Sauvages d\\'Hevea ( Hevea ...

    African Journals Online (AJOL)

    Thus, the reproduction system of the wild rubber tree collection is no panmictic. No Inter annual variation of the genotypes paternal contribution occured. Thus, paternal contribution appear to be a clonal characteristic of rubber tree species. Keywords: Hevea brasiliensis, système de reproduction, verger à graines, ...

  20. 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 ...

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

    African Journals Online (AJOL)

    AJL

    2012-01-26

    Jan 26, 2012 ... Drought is a major problem reducing agronomic crop production worldwide. Increasing the genetic potential of yield in water deficit condition is one of the major objectives of durum wheat breeding programs in Iran and other countries. This study was conducted to determine drought tolerant genotypes with ...

  2. Stability analysis in bread wheat ( Triticum aestivum L.) genotypes in ...

    African Journals Online (AJOL)

    The treatment consisted of twelve bread wheat genotypes, namely, Bolo (G8), Dand'a (G5), Gambo (G4), Gassay (G6), Hidase (G1), Huluka (G3), Kubsa (G12), Menze (G10), Ogolcho (G2), Shorima (G11), Tay (G7), and Tsehay (G9). The experiments were laid out as a randomized complete block design with three ...

  3. Genotype by Environment Interaction (G x E) and Grain Yield ...

    African Journals Online (AJOL)

    Genotype by Environment Interaction (G x E) and Grain Yield Stability Analysis of Ethiopian Linseed and Niger Seed Varieties. ... Among Niger seed varieties, Shambu-1 and Esete-1 had comparable seed yield with moderately stable for the tested environments whereas Kuyu and local variety were unstable and not ...

  4. 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 ...

  5. Halothane genotype and pork production. 2 Processed pork ...

    African Journals Online (AJOL)

    Halothane genotype and pork production. 2 Processed pork products. P. Fisher* and FD. Mellett. Department of Animal Sciences, University of Stellenbosch, 7600 Stellenbosch, South Africa. Received 19 July 1996; accepted 22 May 1997. The effect of the halothane gene on processed pork characteristics was investigated ...

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

    African Journals Online (AJOL)

    SERVER

    2007-07-04

    Jul 4, 2007 ... This study aims to observe the effect of genotype, hormone and culture conditions on sunflower. (Helianthus annuus L.) callus ... formation is controlled by growth regulating substances present in the medium (auxins ... the most important factors for callus induction like shoot regeneration in tissue culture ...

  7. Tissue Fractions of Cadmium in Two Hyperaccumulating Jerusalem Artichoke Genotypes

    Directory of Open Access Journals (Sweden)

    Xiaohua Long

    2014-01-01

    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.

  8. Responses of some selected Malaysian rice genotypes to callus ...

    African Journals Online (AJOL)

    Responses of some selected Malaysian rice genotypes to callus induction under in vitro salt stress. NN Htwe, M Maziah, HC Ling, FQ Zaman, AM Zain. Abstract. Tissue culture technique can be used as a source for genetic variability by means of genetic modifications through the process of in vitro cultures. This technique ...

  9. DNA Genotype of Human Papilloma Virus Infection among ...

    African Journals Online (AJOL)

    Objective: To determine DNA genotype of HPV infection among adolescent girls at KNH - Youth Clinic and use it as an advocacy tool for the introduction of the HPV vaccine provision in the clinic. Design: Cross-sectional study. Setting: Kenyatta National Hospital Youth clinic. Subjects: Adolescent (and youths) girls aged ...

  10. Coral host transcriptomic states are correlated with Symbiodinium genotypes

    KAUST Repository

    DeSalvo, Michael K.

    2010-03-01

    A mutualistic relationship between reef-building corals and endosymbiotic dinoflagellates (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. In this study, we monitored Symbiodinium physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered fragments of the coral Montastraea faveolata using a custom cDNA gene expression microarray. Interestingly, gene expression was more similar among samples with the same Symbiodinium content rather than the same experimental condition. In order to discount for host-genotypic effects, we sampled fragments from a single colony of M. faveolata containing different symbiont types, and found that the host transcriptomic states grouped according to Symbiodinium genotype rather than thermal stress. As the first study that links coral host transcriptomic patterns to the clade content of their Symbiodinium community, our results provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-Symbiodinium partnerships. © 2010 Blackwell Publishing Ltd.

  11. Murine models susceptibility to distinct Trypanosoma cruzi I genotypes infection.

    Science.gov (United States)

    León, Cielo M; Montilla, Marleny; Vanegas, Ricardo; Castillo, Maria; Parra, Edgar; Ramírez, Juan David

    2017-04-01

    Chagas disease is a complex zoonosis that affects around 8 million people worldwide. This pathology is caused by Trypanosoma cruzi, a kinetoplastid parasite that shows tremendous genetic diversity evinced in six distinct Discrete Typing Units (TcI-TcVI) including a recent genotype named as TcBat and associated with anthropogenic bats. TcI presents a broad geographical distribution and has been associated with chronic cardiomyopathy. Recent phylogenetic studies suggest the existence of two genotypes (Domestic (TcIDom) and sylvatic TcI) within TcI. The understanding of the course of the infection in different mouse models by these two genotypes is not yet known. Therefore, we infected 126 animals (ICR-CD1, National Institute of Health (NIH) and Balb/c) with two TcIDom strains and one sylvatic strain for a follow-up period of 60 days. We quantified the parasitaemia, immune response and histopathology observing that the maximum day of parasitaemia was achieved at day 21 post-infection. Domestic strains showed higher parasitaemia than the sylvatic strain in the three mouse models; however in the survival curves Balb/c mice were less susceptible to infection compared with NIH and ICR-CD1. Our results suggest that the genetic background plays a fundamental role in the natural history of the infection and the sympatric TcI genotypes have relevant implications in disease pathogenesis.

  12. The influence of root rot incidence on cassava genotype on ...

    African Journals Online (AJOL)

    28 panelists were asked to indicate their degree of preference for the colour, odour and taste of each gari sample by choosing the appropriate category in the hedonic scale. The results were compared with the tuberous root rot incidence and severity of genotypes in the field. All experiments were repeated and the data ...

  13. Breeding value of primary synthetic wheat genotypes for grain yield

    Science.gov (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...

  14. 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

    2009-01-01

    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

  15. Attitude Towards Marriage in the Face of Haemoglobin Genotype ...

    African Journals Online (AJOL)

    Background Sickle cell disease is the commonest genetic disease world over and predominantly affects Africans and the generality of the black race. The issue of genotype incompatibility among prospective couples and decisions on marriage under such circumstances can have significant implications on the control of this ...

  16. Effect of genotype on growth traits of rabbits | Oke | International ...

    African Journals Online (AJOL)

    Genotype effect on growth traits of rabbits were investigated in a randomised complete block design using one hundred and twenty - 10-week-old breeding rabbits. The breeds of rabbits used were New Zealand white, Dutch, chinchilla and were characterized using body weight (BW), heart girth (HG), shoulder to tail (ST), ...

  17. Genotype variation in grain yield response to basal N fertilizer ...

    African Journals Online (AJOL)

    user

    2012-07-24

    Jul 24, 2012 ... pollution. During the past decades, many investigations have been reported, related to nitrogen efficiency of different plant genotypes (Zhang et al., 1997; .... 274. 411. 548. Gr ai n yi el d wi t hout basal grain yield with basal fertilizer (g/8 plants). I. Ⅱ. (a). -20. -10. 0. 10. 20. -1. 99. 199. Rice variety number. A.

  18. Genetic evaluation of spring wheat ( Triticum aestivum L.) genotypes ...

    African Journals Online (AJOL)

    The breeding objective of the present experiment is to identify genetically diverse wheat genotypes for developing high yielding and disease resistant variety for Eastern Gangetic Plains of India. Keywords: AUDPC, cluster analysis, dendrogram, genetic advance, yield, PCA and PCV African Journal of Biotechnology, Vol ...

  19. LHRH and LHR genotypes and prostate cancer incidence and survival.

    Science.gov (United States)

    Ingles, Sue Ann; Liu, Stephen V; Pinski, Jacek

    2013-01-01

    Despite their crucial role in initiating steroid-hormone synthesis, the hypothalamic and pituitary hormones (LH, LHRH) and their receptors have received scant attention in genetic studies of hormone-related diseases. This study included 1,170 men diagnosed with prostate cancer (PC) in Los Angeles County between 1999 and 2003. LHRH and LH receptor genotypes were examined for association with PC survival. Additionally, associations with PC incidence were examined by comparing PC cases to control men of similar age and race/ethnicity. The LHR 312 G allele was found to be associated with increased PC mortality (p=0.01). Ten years after diagnosis, 16% of men carrying two copies of the G allele (genotype GG) had died of PC, compared to 11% of those with genotype AG and 9% of those with AA. In a case-control comparison, this same allele was significantly associated with decreased PC risk: OR=0.68 (95% CI: 0.49, 0.93) for genotype GG vs. AA. These results suggest that androgens may play opposing roles in PC initiation and progression, and highlight the need to include these important but overlooked genes in future studies of PC etiology, prognosis, and treatment.

  20. (Zea mays L.) GENOTYPES BY LEPIDOPTEROUS STEM BORERS ...

    African Journals Online (AJOL)

    Admin

    Two field experiments were conducted in July and August 2004 to determine the effect of date of planting and rate of application of carbofuran (Furadan 3G) on damage by stem borers to flint, sweet and pop maize (Zea mays L) genotypes. Each experiment was laid out in a randomized complete block design (RCBD), with a ...