Gene-environment correlations in the cross-generational transmission of parenting: Grandparenting moderates the effect of child 5-HTTLPR genotype on mothers' parenting.

Science.gov (United States)

Kopala-Sibley, Daniel C; Hayden, Elizabeth P; Singh, Shiva M; Sheikh, Haroon I; Kryski, Katie R; Klein, Daniel N

2017-11-01

Evidence suggests that parenting is associated cross-generationally and that children's genes may elicit specific parenting styles (evocative gene-environment correlation). This study examined whether the effect of children's genotype, specifically 5-HTTLPR, on mothers' parenting behaviors was moderated by her own parenting experiences from her mother. Two independent samples of three-year-olds (N = 476 and 405) were genotyped for the serotonin transporter gene, and observational measures of parenting were collected. Mothers completed measures of the parenting they received as children. The child having a short allele on 5-HTTLPR was associated with more maternal hostility (sample 1 and 2) and with less maternal support (sample 1), but only if the mother reported lower quality grandmothers' parenting (abuse and indifference in Sample 1 and lower levels of grandmother care in Sample 2). Results support the possibility of a moderated evocative gene-environment correlation.

Gene-environment correlations in the cross-generational transmission of parenting: Grandparenting moderates the effect of child 5-HTTLPR genotype on mothers’ parenting

Science.gov (United States)

Kopala-Sibley, Daniel C.; Hayden, Elizabeth P.; Singh, Shiva M.; Sheikh, Haroon I.; Kryski, Katie R.; Klein, Daniel N.

2017-01-01

Evidence suggests that parenting is associated cross-generationally and that children’s genes may elicit specific parenting styles (evocative gene-environment correlation). This study examined whether the effect of children’s genotype, specifically 5-HTTLPR, on mothers’ parenting behaviors was moderated by her own parenting experiences from her mother. Two independent samples of three-year-olds (N = 476 and 405) were genotyped for the serotonin transporter gene, and observational measures of parenting were collected. Mothers completed measures of the parenting they received as children. The child having a short allele on 5-HTTLPR was associated with more maternal hostility (sample 1 and 2) and with less maternal support (sample 1), but only if the mother reported lower quality grandmothers’ parenting (abuse and indifference in Sample 1 and lower levels of grandmother care in Sample 2). Results support the possibility of a moderated evocative gene-environment correlation. PMID:29628626

“When the going gets tough, who keeps going?” Depletion sensitivity moderates the ego-depletion effect

Science.gov (United States)

Salmon, Stefanie J.; Adriaanse, Marieke A.; De Vet, Emely; Fennis, Bob M.; De Ridder, Denise T. D.

2014-01-01

Self-control relies on a limited resource that can get depleted, a phenomenon that has been labeled ego-depletion. We argue that individuals may differ in their sensitivity to depleting tasks, and that consequently some people deplete their self-control resource at a faster rate than others. In three studies, we assessed individual differences in depletion sensitivity, and demonstrate that depletion sensitivity moderates ego-depletion effects. The Depletion Sensitivity Scale (DSS) was employed to assess depletion sensitivity. Study 1 employs the DSS to demonstrate that individual differences in sensitivity to ego-depletion exist. Study 2 shows moderate correlations of depletion sensitivity with related self-control concepts, indicating that these scales measure conceptually distinct constructs. Study 3 demonstrates that depletion sensitivity moderates the ego-depletion effect. Specifically, participants who are sensitive to depletion performed worse on a second self-control task, indicating a stronger ego-depletion effect, compared to participants less sensitive to depletion. PMID:25009523

Assessment of salinity tolerance in bell pepper (capsicum annuum l.) genotypes on the basis of germination, emergence and growth attributes

International Nuclear Information System (INIS)

Tehseen, S.; Ayyub, C.M.; Amjad, M.

2016-01-01

Abiotic stresses are principal threat to crop growth and productivity all over the world. The most devastating one is soil salinity which adversely affects the plants, so a comprehensive study was conducted to categorize different available bell pepper (Capsicum annuum L.) genotypes into salt tolerant, moderately tolerant and sensitive ones on the basis of germination and emergence parameters. Genotypes were exposed to different saline treatments (2, 4, 6 and 8 dS m-1) along with control (0 dS m-1). Germination test, conducted in petri dishes in incubator, revealed that salinity stress significantly decreased final germination percentage, germination index and embryo axis length of tested genotypes. On the other hand, mean germination time and time to 50% seeds germination were increased with the increasing salinity level from 2 to 8 dS m-1. Emergence test of bell pepper genotypes conducted in pots under greenhouse conditions, shown that salinity decreased the seedlings fresh and dry biomass, number of leaves, leaf area and root and shoot length. On the basis of overall percent decrease ranking table, genotypes were grouped into comparatively salt tolerant (Zard, Tasty, Super shimla, Aristotle), moderately tolerant (Capistrano, CW-03, Kaka-01, Orable, Yolo wonder, Crusadar) and sensitive ones (PEP-311, Admiral, Lafayette, Colossol). From these results, it can be extracted that germination and emergence tests are reliable screening tools for evaluating pepper genotypes for salt stress at seedling stage. Moreover, results of this study can be useful for local farmers to utilize their marginal soils by growing relatively salt tolerant bell pepper genotypes. (author)

Phenotypic, Genotypic, and Antibiotic Sensitivity Patterns of Strains Isolated from the Cholera Epidemic in Zimbabwe

NARCIS (Netherlands)

Islam, Mohammad S.; Mahmud, Zahid H.; Ansaruzzaman, Mohammad; Faruque, Shah M.; Talukder, Kaisar A.; Qadri, Firdausi; Alam, Munirul; Islam, Shafiqul; Bardhan, Pradip K.; Mazumder, Ramendra N.; Khan, Azharul I.; Ahmed, Sirajuddin; Iqbal, Anwarul; Chitsatso, Owen; Mudzori, James; Patel, Sheetal; Midzi, Stanley M.; Charimari, Lincoln; Endtz, Hubert P.; Cravioto, Alejandro

This paper details the phenotypic, genotypic, and antibiotic sensitivity patterns of 88 Vibrio cholerae strains from Zimbabwe. Of the 88 strains, 83 were classified as "altered El Tor" and 5 as "hybrid El Tor" strains. All of the strains were susceptible to tetracycline, doxycycline, ciprofloxacin,

Organizational strategy and diversity management: diversity-sensitive orientation as a moderating influence.

Science.gov (United States)

Dansky, Kathryn H; Weech-Maldonado, Robert; De Souza, Gita; Dreachslin, Janice L

2003-01-01

Empirical studies on diversity suggest that health care organizations have been slow to embrace diversity management. We propose that sensitivity to diversity, at the corporate level, moderates strategic decision making, which influences human resource management practices such as diversity initiatives. This study of 203 hospitals explored the relationships among organizational strategy, organizational sensitivity to diversity, and diversity management practices.

Metabolite Profiling of Low-P Tolerant and Low-P Sensitive Maize Genotypes under Phosphorus Starvation and Restoration Conditions.

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Arshid Hussain Ganie

Full Text Available Maize (Zea mays L. is one of the most widely cultivated crop plants. Unavoidable economic and environmental problems associated with the excessive use of phosphatic fertilizers demands its better management. The solution lies in improving the phosphorus (P use efficiency to sustain productivity even at low P levels. Untargeted metabolomic profiling of contrasting genotypes provides a snap shot of whole metabolome which differs under specific conditions. This information provides an understanding of the mechanisms underlying tolerance to P stress and the approach for increasing P-use-efficiency.A comparative metabolite-profiling approach based on gas chromatography-mass spectrometry (GC/MS was applied to investigate the effect of P starvation and its restoration in low-P sensitive (HM-4 and low-P tolerant (PEHM-2 maize genotypes. A comparison of the metabolite profiles of contrasting genotypes in response to P-deficiency revealed distinct differences among low-P sensitive and tolerant genotypes. Another set of these genotypes were grown under P-restoration condition and sampled at different time intervals (3, 5 and 10 days to investigate if the changes in metabolite profile under P-deficiency was restored. Significant variations in the metabolite pools of these genotypes were observed under P-deficiency which were genotype specific. Out of 180 distinct analytes, 91 were identified. Phosphorus-starvation resulted in accumulation of di- and trisaccharides and metabolites of ammonium metabolism, specifically in leaves, but decreased the levels of phosphate-containing metabolites and organic acids. A sharp increase in the concentrations of glutamine, asparagine, serine and glycine was observed in both shoots and roots under low-P condition.The new insights generated on the maize metabolome in response to P-starvation and restoration would be useful towards improvement of the P-use efficiency in maize.

AMMI and GGE biplot analysis for yield stability of promising bread wheat genotypes in bangladesh

International Nuclear Information System (INIS)

Ashrafulalam, M.; Li, M.; Farhad, M.; Hakim, M. A.

2017-01-01

Identification of stable and high yielding varieties under different environmental conditions prior to release as a variety is the major steps for plant breeding. Eight promising wheat genotypes were evaluated against two standard checks across five locations under terminal heat stress condition. The experimental design was an RCBD with three replications in over one year. AMMI analyses exhibited significant (p<0.01) variation in genotype, location and genotype by location interaction with respect to grain yield. The ASV value revealed that GEN4, GEN9, and GEN8 were stable, while GEN5, GEN1, and GEN6 were the most sensitive genotypes. The GGE results also confirmed GEN3, GEN7, GEN8, GEN9 and GEN4 were the most stable cultivars. Five distant mega-environments were identified including Dinajpur and Jamalpur with GEN3, GEN7 and GEN8 as the most favorable, Joydebpur, Rajshahi and Jessore with GEN4 and GEN9 as the most favorable. Genotype GEN7 and GEN8 showed highly resistant to BpLB, GEN3 and GEN4 showed moderately resistance to BpLB, and GEN9 showed moderate susceptible to BpLB. On the other hand, these five genotypes performed resistance to leaf rust. The genotype GEN7 (BAW 1202) was released as BARI Gom 32. Considering all analysis, GEN3 (BAW 1194), GEN7 (BAW 1202) and GEN8 (BAW 1203) demonstrated more stable genotypes with high mean yield, resistant to BpLB and leaf rust. Thus it is indicated that these genotypes can be used as suitable plant material for future breeding programs. (author)

Comparative analysis of DNA methylation polymorphism in drought sensitive (HPKC2) and tolerant (HPK4) genotypes of horse Gram (Macrotyloma uniflorum).

Science.gov (United States)

Bhardwaj, Jyoti; Mahajan, Monika; Yadav, Sudesh Kumar

2013-08-01

DNA methylation is known as an epigenetic modification that affects gene expression in plants. Variation in CpG methylation behavior was studied in two natural horse gram (Macrotyloma uniflorum [Lam.] Verdc.) genotypes, HPKC2 (drought-sensitive) and HPK4 (drought-tolerant). The methylation pattern in both genotypes was studied through methylation-sensitive amplified polymorphism. The results revealed that methylation was higher in HPKC2 (10.1%) than in HPK4 (8.6%). Sequencing demonstrated sequence homology with the DRE binding factor (cbf1), the POZ/BTB protein, and the Ty1-copia retrotransposon among some of the polymorphic fragments showing alteration in methylation behavior. Differences in DNA methylation patterns could explain the differential drought tolerance and the epigenetic signature of these two horse gram genotypes.

Diagnostic reproducibility of hydatidiform moles: ancillary techniques (p57 immunohistochemistry and molecular genotyping) improve morphologic diagnosis.

Science.gov (United States)

Vang, Russell; Gupta, Mamta; Wu, Lee-Shu-Fune; Yemelyanova, Anna V; Kurman, Robert J; Murphy, Kathleen M; Descipio, Cheryl; Ronnett, Brigitte M

2012-03-01

Distinction of hydatidiform moles (HMs) from nonmolar specimens (NMs) and subclassification of HMs as complete hydatidiform moles (CHMs) and partial hydatidiform moles (PHMs) are important for clinical practice and investigational studies; yet, diagnosis based solely on morphology is affected by interobserver variability. Molecular genotyping can distinguish these entities by discerning androgenetic diploidy, diandric triploidy, and biparental diploidy to diagnose CHMs, PHMs, and NMs, respectively. Eighty genotyped cases (27 CHMs, 27 PHMs, and 26 NMs) were selected from a series of 200 potentially molar specimens previously diagnosed using p57 immunostaining and genotyping. Cases were classified by 3 gynecologic pathologists on the basis of H&E slides (masked to p57 immunostaining and genotyping results) into 1 of 3 categories (CHM, PHM, or NM) during 2 diagnostic rounds; a third round incorporating p57 immunostaining results was also conducted. Consensus diagnoses (those rendered by 2 of 3 pathologists) were determined. Genotyping results were used as the gold standard for assessing diagnostic performance. Sensitivity of a diagnosis of CHM ranged from 59% to 100% for individual pathologists and from 70% to 81% by consensus; specificity ranged from 91% to 96% for individuals and from 94% to 98% by consensus. Sensitivity of a diagnosis of PHM ranged from 56% to 93% for individual pathologists and from 70% to 78% by consensus; specificity ranged from 58% to 92% for individuals and from 74% to 85% by consensus. The percentage of correct classification of all cases by morphology ranged from 55% to 75% for individual pathologists and from 70% to 75% by consensus. The κ values for interobserver agreement ranged from 0.59 to 0.73 (moderate to good) for a diagnosis of CHM, from 0.15 to 0.43 (poor to moderate) for PHM, and from 0.13 to 0.42 (poor to moderate) for NM. The κ values for intraobserver agreement ranged from 0.44 to 0.67 (moderate to good). Addition of the p57

Impact of variation in the BDNF gene on social stress sensitivity and the buffering impact of positive emotions: replication and extension of a gene-environment interaction.

Science.gov (United States)

van Winkel, Mark; Peeters, Frenk; van Winkel, Ruud; Kenis, Gunter; Collip, Dina; Geschwind, Nicole; Jacobs, Nele; Derom, Catherine; Thiery, Evert; van Os, Jim; Myin-Germeys, Inez; Wichers, Marieke

2014-06-01

A previous study reported that social stress sensitivity is moderated by the brain-derived-neurotrophic-factor(Val66Met) (BDNF rs6265) genotype. Additionally, positive emotions partially neutralize this moderating effect. The current study aimed to: (i) replicate in a new independent sample of subjects with residual depressive symptoms the moderating effect of BDNF(Val66Met) genotype on social stress sensitivity, (ii) replicate the neutralizing impact of positive emotions, (iii) extend these analyses to other variations in the BDNF gene in the new independent sample and the original sample of non-depressed individuals. Previous findings were replicated in an experience sampling method (ESM) study. Negative Affect (NA) responses to social stress were stronger in "Val/Met" carriers of BDNF(Val66Met) compared to "Val/Val" carriers. Positive emotions neutralized the moderating effect of BDNF(Val66Met) genotype on social stress sensitivity in a dose-response fashion. Finally, two of four additional BDNF SNPs (rs11030101, rs2049046) showed similar moderating effects on social stress-sensitivity across both samples. The neutralizing effect of positive emotions on the moderating effects of these two additional SNPs was found in one sample. In conclusion, ESM has important advantages in gene-environment (GxE) research and may attribute to more consistent findings in future GxE research. This study shows how the impact of BDNF genetic variation on depressive symptoms may be explained by its impact on subtle daily life responses to social stress. Further, it shows that the generation of positive affect (PA) can buffer social stress sensitivity and partially undo the genetic susceptibility. Copyright © 2014 Elsevier B.V. and ECNP. All rights reserved.

Early trauma and increased risk for physical aggression during adulthood: the moderating role of MAOA genotype.

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Giovanni Frazzetto

Full Text Available Previous research has reported that a functional polymorphism in the monoamine oxidase A (MAOA gene promoter can moderate the association between early life adversity and increased risk for violence and antisocial behavior. In this study of a combined population of psychiatric outpatients and healthy volunteers (N = 235, we tested the hypothesis that MAOA genotype moderates the association between early traumatic life events (ETLE experienced during the first 15 years of life and the display of physical aggression during adulthood, as assessed by the Aggression Questionnaire. An ANOVA model including gender, exposure to early trauma, and MAOA genotype as between-subjects factors showed significant MAOAxETLE (F(1,227 = 8.20, P = 0.005 and genderxMAOAxETLE (F(1,227 = 7.04, P = 0.009 interaction effects. Physical aggression scores were higher in men who had experienced early traumatic life events and who carried the low MAOA activity allele (MAOA-L. We repeated the analysis in the subgroup of healthy volunteers (N = 145 to exclude that the observed GxE interactions were due to the inclusion of psychiatric patients in our sample and were not generalizable to the population at large. The results for the subgroup of healthy volunteers were identical to those for the entire sample. The cumulative variance in the physical aggression score explained by the ANOVA effects involving the MAOA polymorphism was 6.6% in the entire sample and 12.1% in the sub-sample of healthy volunteers. Our results support the hypothesis that, when combined with exposure to early traumatic life events, low MAOA activity is a significant risk factor for aggressive behavior during adulthood and suggest that the use of dimensional measures focusing on behavioral aspects of aggression may increase the likelihood of detecting significant gene-by-environment interactions in studies of MAOA-related aggression.

Genetic moderation of effects of maternal sensitivity on girl's age of menarche: Replication of the Manuck et al. study.

Science.gov (United States)

Hartman, Sarah; Widaman, Keith F; Belsky, Jay

2015-08-01

Manuck, Craig, Flory, Halder, and Ferrell (2011) reported that a theoretically anticipated effect of family rearing on girls' menarcheal age was genetically moderated by two single nucleotide polymorphisms (SNPs) of the estrogen receptor-α gene. We sought to replicate and extend these findings, studying 210 White females followed from birth. The replication was general because a different measure of the rearing environment was used in this inquiry (i.e., maternal sensitivity) than in the prior one (i.e., family cohesion). Extensions of the work included prospective rather than retrospective measurements of the rearing environment, reports of first menstruation within a year of its occurrence rather than decades later, accounting for some heritability of menarcheal age by controlling for maternal age of menarche, and using a new model-fitting approach to competitively compare diathesis-stress versus differential-susceptibility models of Gene × Environment interaction. The replication/extension effort proved successful in the case of both estrogen receptor-α SNPs, with the Gene × Environment interactions principally reflecting diathesis-stress: lower levels of maternal sensitivity predicted earlier age of menarche for girls homozygous for the minor alleles of either SNP but not for girls carrying other genotypes. Results are discussed in light of the new analytic methods adopted.

Impact of osmotic stress on seedling growth observations, membrane characteristics and antioxidant defense system of different wheat genotypes

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Bardees M. Mickky

2017-03-01

Full Text Available The objective of the present study was to find out a straightforward technique for screening the tolerance of ten wheat genotypes to two levels of osmotic stress at early seedling stage. Data revealed that polyethylene glycol-induced drought had general negative effect on seedling morphological characters indicated by plumule and radicle length, number of adventitious roots as well as seedling biomass and water content. Water deficit could also suppress membrane integrity by stimulating lipid peroxidation with marked increase in membrane leakage and subsequent decrease in its stability index. For all the addressed germination parameters and seedling membrane features, the impact of severe drought was more pronounced than that of moderate drought. Simultaneously, moderate stress could activate peroxidase, polyphenol oxidase and ascorbic peroxidase of the studied genotypes; but these enzymes were inhibited by severe stress. The activity of catalase, superoxide dismutase and glutathione reductase was conversely retarded by drought whether at moderate or severe level. More interestingly, a novel function “Stress Impact Index; SII” was introduced to rank the estimated morpho-physiological traits (SIItrait as well as the considered genotypes (SIIgenotype according to their sensitivity to stress. Values of SIItrait implied that germination parameters were generally affected by drought more intensively than membrane characteristics and finally came the antioxidant enzymes with the least degree of suppression when applying stress. Based on the magnitudes of SIIgenotype, Sids 13 seemed to be the most drought-tolerant wheat cultivar while Shandawel 1 could be the most sensitive one at their juvenile growth stage.

5-HTTLPR Genotype Moderates the Effects of Past Ecstasy Use on Verbal Memory Performance in Adolescent and Emerging Adults: A Pilot Study.

Science.gov (United States)

Wright, Natasha E; Strong, Judith A; Gilbart, Erika R; Shollenbarger, Skyler G; Lisdahl, Krista M

2015-01-01

Ecstasy use is associated with memory deficits. Serotonin transporter gene (5-HTTLPR) polymorphisms have been linked with memory function in healthy samples. The present pilot study investigated the influence of 5-HTTLPR polymorphisms on memory performance in ecstasy users, marijuana-using controls, and non-drug-using controls, after a minimum of 7 days of abstinence. Data were collected from 116 young adults (18-25 years-old), including 45 controls, 42 marijuana users, and 29 ecstasy users, and were balanced for 5-HTTLPR genotype. Participants were abstinent seven days prior to completing memory testing. Three MANCOVAs and one ANCOVA were run to examine whether drug group, 5-HTTLPR genotype, and their interactions predicted verbal and visual memory after controlling for gender, past year alcohol use, other drug use, and nicotine cotinine levels. MANCOVA and ANCOVA analysis revealed a significant interaction between drug group and genotype (p = .03) such that ecstasy users with the L/L genotype performed significantly worse on CVLT-2 total recall (p = .05), short (p = .008) and long delay free recall (p = .01), and recognition (p = .006), with the reverse pattern found in controls. Ecstasy did not significantly predict visual memory. 5-HTTLPR genotype significantly predicted memory for faces (p = .02); short allele carriers performed better than those with L/L genotype. 5-HTTLPR genotype moderated the effects of ecstasy on verbal memory, with L/L carriers performing worse compared to controls. Future research should continue to examine individual differences in ecstasy's impact on neurocognitive performance as well as relationships with neuronal structure. Additional screening and prevention efforts focused on adolescents and emerging adults are necessary to prevent ecstasy consumption.

5-HTTLPR Genotype Moderates the Effects of Past Ecstasy Use on Verbal Memory Performance in Adolescent and Emerging Adults: A Pilot Study.

Directory of Open Access Journals (Sweden)

Natasha E Wright

Full Text Available Ecstasy use is associated with memory deficits. Serotonin transporter gene (5-HTTLPR polymorphisms have been linked with memory function in healthy samples. The present pilot study investigated the influence of 5-HTTLPR polymorphisms on memory performance in ecstasy users, marijuana-using controls, and non-drug-using controls, after a minimum of 7 days of abstinence.Data were collected from 116 young adults (18-25 years-old, including 45 controls, 42 marijuana users, and 29 ecstasy users, and were balanced for 5-HTTLPR genotype. Participants were abstinent seven days prior to completing memory testing. Three MANCOVAs and one ANCOVA were run to examine whether drug group, 5-HTTLPR genotype, and their interactions predicted verbal and visual memory after controlling for gender, past year alcohol use, other drug use, and nicotine cotinine levels.MANCOVA and ANCOVA analysis revealed a significant interaction between drug group and genotype (p = .03 such that ecstasy users with the L/L genotype performed significantly worse on CVLT-2 total recall (p = .05, short (p = .008 and long delay free recall (p = .01, and recognition (p = .006, with the reverse pattern found in controls. Ecstasy did not significantly predict visual memory. 5-HTTLPR genotype significantly predicted memory for faces (p = .02; short allele carriers performed better than those with L/L genotype.5-HTTLPR genotype moderated the effects of ecstasy on verbal memory, with L/L carriers performing worse compared to controls. Future research should continue to examine individual differences in ecstasy's impact on neurocognitive performance as well as relationships with neuronal structure. Additional screening and prevention efforts focused on adolescents and emerging adults are necessary to prevent ecstasy consumption.

Quantifying Wheat Sensitivities to Environmental Constraints to Dissect Genotype × Environment Interactions in the Field.

Science.gov (United States)

Parent, Boris; Bonneau, Julien; Maphosa, Lance; Kovalchuk, Alex; Langridge, Peter; Fleury, Delphine

2017-07-01

Yield is subject to strong genotype-by-environment (G × E) interactions in the field, especially under abiotic constraints such as soil water deficit (drought [D]) and high temperature (heat [H]). Since environmental conditions show strong fluctuations during the whole crop cycle, geneticists usually do not consider environmental measures as quantitative variables but rather as factors in multienvironment analyses. Based on 11 experiments in a field platform with contrasting temperature and soil water deficit, we determined the periods of sensitivity to drought and heat constraints in wheat ( Triticum aestivum ) and determined the average sensitivities for major yield components. G × E interactions were separated into their underlying components, constitutive genotypic effect (G), G × D, G × H, and G × H × D, and were analyzed for two genotypes, highlighting contrasting responses to heat and drought constraints. We then tested the constitutive and responsive behaviors of two strong quantitative trait loci (QTLs) associated previously with yield components. This analysis confirmed the constitutive effect of the chromosome 1B QTL and explained the G × E interaction of the chromosome 3B QTL by a benefit of one allele when temperature rises. In addition to the method itself, which can be applied to other data sets and populations, this study will support the cloning of a major yield QTL on chromosome 3B that is highly dependent on environmental conditions and for which the climatic interaction is now quantified. © 2017 American Society of Plant Biologists. All Rights Reserved.

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

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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

Anxiety sensitivity class membership moderates the effects of pre-quit reduction in anxiety sensitivity on quit-day tobacco craving

NARCIS (Netherlands)

Bakhshaie, J.; Zvolensky, M.J.; Langdon, K.J.; Leventhal, A.M.; Smits, J.A.J.; Allan, N.; Schmidt, N.B.

2016-01-01

Background: Although anxiety sensitivity has been primarily conceptualized as a dimensional latent construct, empirical evidence suggests that it also maintains a latent class structure, reflecting low-, moderate-, and high-risk underlying classes. The present study sought to explore whether these

The Energy Variation of the Sensitivity of a Polyethylene Moderated BF{sub 3} Proportional Counter

Energy Technology Data Exchange (ETDEWEB)

Fraeki, R; Leimdoerfer, M; Malmskog, S

1962-11-15

The variation with neutron energy of the sensitivity of a polyethylene moderated boron counter has been investigated experimentally at 2.3 MeV, 550 keV, 210 keV, 110 keV, 340 eV and 5 eV, and theoretically by the multigroup diffusion method in the same range. Different moderator thicknesses up to 10 cm were considered Results show good agreement between experimental and theoretical sensitivities for the keV and MeV energies, while a discrepancy of the order of a factor 2 at the most is obtained in the eV region.

Response of Different Genotypes of Faba Bean Plant to Drought Stress

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Manzer H. Siddiqui

2015-05-01

Full Text Available Drought stress is one of the major abiotic stresses that are a threat to crop production worldwide. Drought stress impairs the plants growth and yield. Therefore, the aim of the present experiment was to select the tolerant genotype/s on the basis of moprpho-physiological and biochemical characteristics of 10 Vicia faba genotypes (Zafar 1, Zafar 2, Shebam, Makamora, Espan, Giza Blanka, Giza 3, C4, C5 and G853 under drought stress. We studied the effect of different levels of drought stress i.e., (i normal irrigation (ii mild stress (iii moderate stress, and (iv severe stress on plant height (PH plant−1, fresh weight (FW and dry weight (DW plant−1, area leaf−1, leaf relative water content (RWC, proline (Pro content, total chlorophyll (Total Chl content, electrolyte leakage (EL, malondialdehyde (MDA, hydrogen peroxide (H2O2 content, and activities of catalase (CAT, peroxidase (POD and superoxide dismutase (SOD of genotypes of faba bean. Drought stress reduced all growth parameters and Total Chl content of all genotypes. However, the deteriorating effect of drought stress on the growth performance of genotypes “C5” and “Zafar 1” were relatively low due to its better antioxidant enzymes activities (CAT, POD and SOD, and accumulation of Pro and Total Chl, and leaf RWC. In the study, genotype “C5” and “Zafar 1” were found to be relatively tolerant to drought stress and genotypes “G853” and “C4” were sensitive to drought stress.

Noise sensitivity and diminished health: Testing moderators and mediators of the relationship

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Erin M Hill

2014-01-01

Full Text Available The concept of noise sensitivity emerged in public health and psychoacoustic research to help explain individual differences in reactions to noise. Noise sensitivity has been associated with health problems, but the mechanisms underlying this relationship have yet to be fully examined. Participants (n = 1102 were residents of Auckland, New Zealand, who completed questionnaires and returned them through the post. Models of noise sensitivity and health were tested in the analyses using bootstrapping methods to examine indirect effects. Results indicated that gender and noise exposure were not significant moderators in the model. Perceived stress and sleep problems were significant mediators of the relationship between noise sensitivity and subjective health complaints, even after controlling for the influence of neuroticism. However, the relationship between noise sensitivity and mental health complaints (anxiety and depression was accounted for by the variance explained by neuroticism. Overall, this study provides considerable understanding of the relationship between noise sensitivity and health problems and identifies areas for further research in the field.

The multi-year effects of repeatedly growing cotton with moderate resistance to Meloidogyne incognita

Science.gov (United States)

Kemerait, Robert C.

2009-01-01

Meloidogyne incognita causes more damage to cotton in the US than any other pathogen. The objective of this study was to document the cumulative effect of moderate resistance on M. incognita population density, root galling, and yield suppression in the southern United States on a moderately resistant cotton genotype grown continuously for three years. Cotton genotypes were Phytogen PH98-3196 (77% suppression of M. incognita), Acala NemX (85% suppression of M. incognita), and Delta and Pine Land DP458 B/R (susceptible standard, 0% suppression). Cotton was grown in fumigated and non-fumigated plots to measure yield loss. Each genotype and nematicide combination was planted in the same place for three years at two sites to document cumulative effects. In 2006, following three years of the different genotypes, all plots at one site were planted with susceptible cotton to document residual effects of planting resistant genotypes. Root galling and nematode population densities in the soil were significantly lower, and percentage yield suppression was numerically lower, when moderately resistant cotton was grown compared to the susceptible standard in both fields in all three years. Differences between susceptible and moderately resistant genotypes are established quickly (after only one season) and then either maintained at similar levels or slightly increased in subsequent years depending on initial nematode levels. However, when susceptible cotton was grown following three years of the moderately resistant genotypes, the nematode suppression provided by moderate resistance was undetectable by the end of the first season. Moderately resistant cotton genotypes are more beneficial than previously reported and should be pursued for nematode management. Rotation of moderately resistant and susceptible cotton could be used along with nematicides to manage root-knot nematodes in a continuous cotton cropping system and reduce selection pressure on the nematodes. PMID:22661787

The impact of short-term UV irradiation on grains of sensitive and tolerant cereal genotypes studied by EPR.

Science.gov (United States)

Kurdziel, Magdalena; Filek, Maria; Łabanowska, Maria

2018-05-01

UV irradiation has ionisation character and leads to the generation of reactive oxygen species (ROS). The destructive character of ROS was observed among others during interaction of cereal grains with ozone and was caused by changes in structures of biomolecules leading to the formation of stable organic radicals. That effect was more evident for stress sensitive genotypes. In this study we investigated the influence of UV irradiation on cereal grains originating from genotypes with different tolerance to oxidative stress. Grains and their parts (endosperm, embryo and seed coat) of barley, wheat and oat were subjected to short-term UV irradiation. It was found that UV caused the appearance of various kinds of reactive species (O 2 -• , H 2 O 2 ) and stable radicals (semiquinone, phenoxyl and carbon-centred). Simultaneously, lipid peroxidation occurred and the organic structure of Mn(II) and Fe(III) complexes become disturbed. UV irradiation causes damage of main biochemical structures of plant tissues, the effect is more significant in sensitive genotypes. In comparison with ozone treatment, UV irradiation leads to stronger destruction of biomolecules in grains and their parts. It is caused by the high energy of UV light, facilitating easier breakage of molecular bonds in biochemical compounds. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Salt sensitivity in chickpea (Cicer arietinum L.): ions in reproductive tissues and yield components in contrasting genotypes.

Science.gov (United States)

Kotula, Lukasz; Khan, Hammad A; Quealy, John; Turner, Neil C; Vadez, Vincent; Siddique, Kadambot H M; Clode, Peta L; Colmer, Timothy D

2015-08-01

The reproductive phase in chickpea (Cicer arietinum L.) is affected by salinity, but little is known about the underlying cause. We investigated whether high concentrations of Na(+) and Cl(-) in the reproductive structures influence reproductive processes. Chickpea genotypes contrasting in tolerance were subjected to 0, 35 or 50 mm NaCl applied to soil in pots. Flower production and abortion, pod number, percentage of empty pods, seed number and size were evaluated. The concentrations of Na(+) , K(+) and Cl(-) were measured in various plant tissues and, using X-ray microanalysis, in specific cells of developing reproductive structures. Genotypic variation in reproductive success measured as seed yield in saline conditions was associated with better maintenance of flower production and higher numbers of filled pods (and thus seed number), whereas seed size decreased in all genotypes. Despite the variation in reproductive success, the accumulation of Na(+) and Cl(-) in the early reproductive tissues of developing pods did not differ between a tolerant (Genesis836) and a sensitive (Rupali) genotype. Similarly, salinity tolerance was not associated with the accumulation of salt ions in leaves at the time of reproduction or in seeds at maturity. © 2015 John Wiley & Sons Ltd.

Sensitivity Analysis of RCW Temperature on the Moderator Subcooling Margin for the LBLOCA of Wolsong NPP Unit 1

International Nuclear Information System (INIS)

Seo, Si Won; Kim, Jong Hyun; Choi, Sung Soo; Kim, Sung Min

2016-01-01

Moderator subcooling margin has been analyzed using the MODTURC_CLAS code in the Large LOCA FSAR PARTs C and F. Performance of moderator heat exchangers depends on RCW (Raw reCirculated Water) temperature. And also the temperature is affected by sea water temperature. Unfortunately, sea water temperature is gradually increasing by global warming. So it will cause increase of RCW temperature inevitably. There is no assessment result of moderator subcooling with increasing RCW temperature even if it is important problem. Therefore, sensitivity analysis is performed to give information about the relation between RCW temperature and moderator subcooling in the present study. The moderator subcooling margin has to be ensured to establish the moderator heat removal when Large LOCA with LOECI and Loss of Class IV Power occurs. However, sea water temperature is increasing gradually due to global warming. So it is necessary that sensitivity analysis of RCW temperature on the moderator subcooling margin to estimate the availability of the moderator heat removal. In the present paper, the moderator subcooling analysis is performed using the same methodology and assumptions except for RCW temperature used in FSAR Large LOCA PART F.

Sensitivity Analysis of RCW Temperature on the Moderator Subcooling Margin for the LBLOCA of Wolsong NPP Unit 1

Energy Technology Data Exchange (ETDEWEB)

Seo, Si Won; Kim, Jong Hyun; Choi, Sung Soo [Atomic Creative Technology Co., Daejeon (Korea, Republic of); Kim, Sung Min [Central Research Institute, Korea Hydro and Nuclear Power Co., Daejeon (Korea, Republic of)

2016-05-15

Moderator subcooling margin has been analyzed using the MODTURC{sub C}LAS code in the Large LOCA FSAR PARTs C and F. Performance of moderator heat exchangers depends on RCW (Raw reCirculated Water) temperature. And also the temperature is affected by sea water temperature. Unfortunately, sea water temperature is gradually increasing by global warming. So it will cause increase of RCW temperature inevitably. There is no assessment result of moderator subcooling with increasing RCW temperature even if it is important problem. Therefore, sensitivity analysis is performed to give information about the relation between RCW temperature and moderator subcooling in the present study. The moderator subcooling margin has to be ensured to establish the moderator heat removal when Large LOCA with LOECI and Loss of Class IV Power occurs. However, sea water temperature is increasing gradually due to global warming. So it is necessary that sensitivity analysis of RCW temperature on the moderator subcooling margin to estimate the availability of the moderator heat removal. In the present paper, the moderator subcooling analysis is performed using the same methodology and assumptions except for RCW temperature used in FSAR Large LOCA PART F.

Genetic moderation of transactional relations between parenting practices and child self-regulation.

Science.gov (United States)

Cho, Junhan; Kogan, Steven M; Brody, Gene H

2016-10-01

The present study addressed the ways in which parent and child dopamine D4 receptor (DRD4) genotypes jointly moderate the transactional relations between parenting practices and child self-regulation. African American children (N = 309) and their parents provided longitudinal data spanning child ages 11 to 15 years and a saliva sample from which variation at DRD4 was genotyped. Based on the differential susceptibility perspective, this study examined moderation effects of DRD4 status on (a) the extent to which parenting practices affect child self-regulation and (b) the extent to which child self-regulation, as an environmental influence on the parent, affects parenting behavior. Results indicated that responsive-supportive parenting interacted with children's DRD4 status to influence increases in child self-regulation. Also, child self-regulation interacted with parent's DRD4 status to predict changes in parenting practices. Both Gene × Environment effects conformed to a differential susceptibility model in which parents' and children's DRD4 genes operated to increase environmental sensitivity "for better and for worse." (PsycINFO Database Record (c) 2016 APA, all rights reserved).

IgE Sensitization Profiles Differ between Adult Patients with Severe and Moderate Atopic Dermatitis.

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Irene Mittermann

Full Text Available Atopic dermatitis (AD is a complex chronic inflammatory disease where allergens can act as specific triggering factors.To characterize the specificities of IgE-reactivity in patients with AD to a broad panel of exogenous allergens including microbial and human antigens.Adult patients with AD were grouped according to the SCORAD index, into severe (n = 53 and moderate AD (n = 126. As controls 43 patients were included with seborrhoeic eczema and 97 individuals without history of allergy or skin diseases. Specific IgE reactivity was assessed in plasma using Phadiatop®, ImmunoCap™, micro-arrayed allergens, dot-blotted recombinant Malassezia sympodialis allergens, and immune-blotted microbial and human proteins.IgE reactivity was detected in 92% of patients with severe and 83% of patients with moderate AD. Sensitization to cat allergens occurred most frequently, followed by sensitization to birch pollen, grass pollen, and to the skin commensal yeast M. sympodialis. Patients with severe AD showed a significantly higher frequency of IgE reactivity to allergens like cat (rFel d 1 and house dust mite (rDer p 4 and 10, to Staphylococcus aureus, M. sympodialis, and to human antigens. In contrast, there were no significant differences in the frequencies of IgE reactivity to the grass pollen allergens rPhl p 1, 2, 5b, and 6 between the two AD groups. Furthermore the IgE reactivity profile of patients with severe AD was more spread towards several different allergen molecules as compared to patients with moderate AD.We have revealed a hitherto unknown difference regarding the molecular sensitization profile in patients with severe and moderate AD. Molecular profiling towards allergen components may provide a basis for future investigations aiming to explore the environmental, genetic and epigenetic factors which could be responsible for the different appearance and severity of disease phenotypes in AD.

IgE Sensitization Profiles Differ between Adult Patients with Severe and Moderate Atopic Dermatitis.

Science.gov (United States)

Mittermann, Irene; Wikberg, Gustav; Johansson, Catharina; Lupinek, Christian; Lundeberg, Lena; Crameri, Reto; Valenta, Rudolf; Scheynius, Annika

2016-01-01

Atopic dermatitis (AD) is a complex chronic inflammatory disease where allergens can act as specific triggering factors. To characterize the specificities of IgE-reactivity in patients with AD to a broad panel of exogenous allergens including microbial and human antigens. Adult patients with AD were grouped according to the SCORAD index, into severe (n = 53) and moderate AD (n = 126). As controls 43 patients were included with seborrhoeic eczema and 97 individuals without history of allergy or skin diseases. Specific IgE reactivity was assessed in plasma using Phadiatop®, ImmunoCap™, micro-arrayed allergens, dot-blotted recombinant Malassezia sympodialis allergens, and immune-blotted microbial and human proteins. IgE reactivity was detected in 92% of patients with severe and 83% of patients with moderate AD. Sensitization to cat allergens occurred most frequently, followed by sensitization to birch pollen, grass pollen, and to the skin commensal yeast M. sympodialis. Patients with severe AD showed a significantly higher frequency of IgE reactivity to allergens like cat (rFel d 1) and house dust mite (rDer p 4 and 10), to Staphylococcus aureus, M. sympodialis, and to human antigens. In contrast, there were no significant differences in the frequencies of IgE reactivity to the grass pollen allergens rPhl p 1, 2, 5b, and 6 between the two AD groups. Furthermore the IgE reactivity profile of patients with severe AD was more spread towards several different allergen molecules as compared to patients with moderate AD. We have revealed a hitherto unknown difference regarding the molecular sensitization profile in patients with severe and moderate AD. Molecular profiling towards allergen components may provide a basis for future investigations aiming to explore the environmental, genetic and epigenetic factors which could be responsible for the different appearance and severity of disease phenotypes in AD.

Comprehensive Screening of Some West and Central African Sesame Genotypes for Drought Resistance Probing by Agromorphological, Physiological, Biochemical and Seed Quality Traits

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Komivi Dossa

2017-12-01

Full Text Available Sesame is an important crop in West and Central Africa playing a role of an alternative cash crop for smallholders. However, sesame productivity is highly impaired by drought. This study aimed at identifying some drought-resistant genotypes and efficient screening traits in large sesame germplasm. Ten genotypes were examined based on 21 biochemical, physiological, agromorphological and seed quality traits under three weeks of water stress. A high variability for drought resistance was observed among the genotypes. The genotypes WC17, WC18 and WC14 were drought resistant, WC12, WC13, WC06 and WC03 were moderately drought resistant while, WC02, WC10 and WC08 were drought sensitive, based on principal component analysis. The resistant genotypes exhibited both avoidance and tolerance features including increase of the root system, reduced water loss, highest activity of antioxidative enzymes and accumulation of proline. They produced higher biomass and had higher ability to maintain seed quality under drought stress compared with the sensitive genotypes. Strong accumulation (~200% ratio stress/control of biochemical markers including superoxide dismutase, ascorbate peroxidase, catalase and proline could be regarded as an important indicator for selecting drought resistant genotypes. This study represents a reference for future research towards developing new varieties with improved drought resistance in West and Central Africa.

Effect of Moderate Alcohol Consumption on Adiponectin, Tumor Necrosis Factor-α, and Insulin Sensitivity

NARCIS (Netherlands)

Sierksma, A.; Patel, H.; Ouchi, N.; Kihara, S.; Funahashi, T.; Heine, R.J.; Grobbee, D.E.; Kluft, C.; Hendriks, H.F.J.

2004-01-01

OBJECTIVE - Epidemiological studies suggest that moderate alcohol consumers have enhanced insulin sensitivity and a reduced risk of type 2 diabetes. Adiponectin, an adipocyte-derived plasma protein, has been found to be negatively associated with adiposity and positively associated with insulin

[Evaluation of hepatitis B virus genotyping EIA kit].

Science.gov (United States)

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

2009-01-01

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

DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress.

Science.gov (United States)

Wang, Wensheng; Zhao, Xiuqin; Pan, Yajiao; Zhu, Linghua; Fu, Binying; Li, Zhikang

2011-09-20

DNA methylation, one of the most important epigenetic phenomena, plays a vital role in tuning gene expression during plant development as well as in response to environmental stimuli. In the present study, a methylation-sensitive amplified polymorphism (MSAP) analysis was performed to profile DNA methylation changes in two contrasting rice genotypes under salt stress. Consistent with visibly different phenotypes in response to salt stress, epigenetic markers classified as stable inter-cultivar DNA methylation differences were determined between salt-tolerant FL478 and salt-sensitive IR29. In addition, most tissue-specific DNA methylation loci were conserved, while many of the growth stage-dependent DNA methylation loci were dynamic between the two genotypes. Strikingly, salt stress induced a decrease in DNA methylation specifically in roots at the seedling stage that was more profound in IR29 than in the FL478. This result may indicate that demethylation of genes is an active epigenetic response to salt stress in roots at the seedling stage, and helps to further elucidate the implications of DNA methylation in crop growth and development. Copyright © 2011. Published by Elsevier Ltd.

Hypervariable Region 1 Shielding of Hepatitis C Virus Is a Main Contributor to Genotypic Differences in Neutralization Sensitivity

DEFF Research Database (Denmark)

Prentoe, Jannick; Velazquez-Moctezuma, Rodrigo; Foung, Steven K. H.

2016-01-01

protective HCV vaccines. Using cultured viruses expressing the E1/E2 complex of isolates H77 (genotype 1a), J6 (2a), or S52 (3a), with and without HVR1, we tested HVR1-mediated neutralization occlusion in vitro against a panel of 12 well-characterized human monoclonal antibodies (HMAbs) targeting diverse E1...... correlation for HVR1-deleted viruses but not for parental viruses retaining HVR1. The intergenotype neutralization sensitivity of the parental viruses to HMAb antigenic region (AR) 2A, AR3A, AR4A, AR5A, HC84.26, and HC33.4 varied greatly (>24-fold to >130-fold differences in 50% inhibitory concentration...... values). However, except for AR5A, these differences decreased to less than 6.0-fold when comparing the corresponding HVR1-deleted viruses. Importantly, this simplified pattern of neutralization sensitivity in the absence of HVR1 was also demonstrated in a panel of HVR1-deleted viruses of genotypes 1a, 2...

Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.

Science.gov (United States)

Manrubia, Susanna; Cuesta, José A

2017-04-01

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

Moderate Secularism, Difference Sensitivity and Contextualism

DEFF Research Database (Denmark)

Lægaard, Sune

2009-01-01

The article is a rejoinder to Tariq Modood's reply (Politics, Vol. 29, No. 1, 2009) to my article 'Moderate Secularism and Multicultural Equality' (Politics, Vol 28, No. 3, 2008).......The article is a rejoinder to Tariq Modood's reply (Politics, Vol. 29, No. 1, 2009) to my article 'Moderate Secularism and Multicultural Equality' (Politics, Vol 28, No. 3, 2008)....

Moderate and severe perinatal asphyxia induces differential effects on cocaine sensitization in adult rats.

Science.gov (United States)

Galeano, Pablo; Romero, Juan Ignacio; Luque-Rojas, María Jesús; Suárez, Juan; Holubiec, Mariana Inés; Bisagno, Verónica; Santín, Luis Javier; De Fonseca, Fernando Rodríguez; Capani, Francisco; Blanco, Eduardo

2013-09-01

Perinatal asphyxia (PA) increases the likelihood of suffering from dopamine-related disorders, such as ADHD and schizophrenia. Since dopaminergic transmission plays a major role in cocaine sensitization, the purpose of this study was to determine whether PA could be associated with altered behavioral sensitization to cocaine. To this end, adult rats born vaginally (CTL), by caesarean section (C+), or by C+ with 15 min (PA15, moderate PA) or 19 min (PA19, severe PA) of global anoxia were repeatedly administered with cocaine (i.p., 15 mg/kg) and then challenged with cocaine (i.p., 15 mg/kg) after a 5-day withdrawal period. In addition, c-Fos, FosB/ΔFosB, DAT, and TH expression were assessed in dorsal (CPu) and ventral (NAcc) striatum. Results indicated that PA15 rats exhibited an increased locomotor sensitization to cocaine, while PA19 rats displayed an abnormal acquisition of locomotor sensitization and did not express a sensitized response to cocaine. c-Fos expression in NAcc, but not in CPu, was associated with these alterations in cocaine sensitization. FosB/ΔFosB expression was increased in all groups and regions after repeated cocaine administration, although it reached lower expression levels in PA19 rats. In CTL, C+, and PA15, but not in PA19 rats, the expression of TH in NAcc was reduced in groups repeatedly treated with cocaine, independently of the challenge test. Furthermore, this reduction was more pronounced in PA15 rats. DAT expression remained unaltered in all groups and regions studied. These results suggest that moderate PA may increase the vulnerability to drug abuse and in particular to cocaine addiction. Copyright © 2013 Wiley Periodicals, Inc.

Exercise Self-Efficacy Moderates the Relation between Anxiety Sensitivity and Body Mass Index and Exercise Tolerance in Treatment-Seeking Smokers

Science.gov (United States)

Farris, Samantha G.; Davis, Michelle L.; Rosenfield, David; Kauffman, Brooke Y.; Baird, Scarlett O.; Powers, Mark B.; Otto, Michael W.; Marcus, Bess H.; Church, Timothy S.; Smits, Jasper A. J.; Zvolensky, Michael J.

2016-01-01

There is little known about factors that contribute to the comorbidity of cigarette smoking and obesity. The current study sought to test whether exercise self-efficacy moderated the relation between anxiety sensitivity (fear of internal sensations) and BMI and exercise tolerance among cigarette smokers. Smokers (n = 72; 50% female; Mcpd = 19.3, SD = 10.65) were recruited to participate in a smoking cessation treatment trial. During medical screen, we measured weight, height, and exercise tolerance (functional capacity) employing a standardized maximal exercise testing protocol. After adjusting for participant sex and cigarettes per day, exercise self-efficacy moderated the association between anxiety sensitivity and BMI, such that the positive association between anxiety sensitivity and BMI was significantly stronger when exercise self-efficacy was low. The same pattern of results emerged for exercise tolerance. Exercise self-efficacy moderated the association between anxiety sensitivity and exercise tolerance, such that the negative association between anxiety sensitivity and exercise tolerance was significantly stronger when exercise self-efficacy was low. Among smokers, anxiety sensitivity may be a risk variable that, directly and indirectly in the context of low self-efficacy for exercise, causes or maintains higher body weight and lower exercise tolerance. PMID:27725844

Sensitization to Gliadin Induces Moderate Enteropathy and Insulitis in Nonobese Diabetic-DQ8 Mice

Science.gov (United States)

Galipeau, Heather J.; Rulli, Nestor E.; Jury, Jennifer; Huang, Xianxi; Araya, Romina; Murray, Joseph A.; David, Chella S.; Chirdo, Fernando G.; McCoy, Kathy D.; Verdu, Elena F.

2012-01-01

Celiac disease (CD) is frequently diagnosed in patients with type 1 diabetes (T1D), and T1D patients can exhibit Abs against tissue transglutaminase, the auto-antigen in CD. Thus, gliadin, the trigger in CD, has been suggested to have a role in T1D pathogenesis. The objective of this study was to investigate whether gliadin contributes to enteropathy and insulitis in NOD-DQ8 mice, an animal model that does not spontaneously develop T1D. Gliadin-sensitized NOD-DQ8 mice developed moderate enteropathy, intraepithelial lymphocytosis, and barrier dysfunction, but not insulitis. Administration of anti-CD25 mAbs before gliadin-sensitization induced partial depletion of CD25+Foxp3+ T cells and led to severe insulitis, but did not exacerbate mucosal dysfunction. CD4+ T cells isolated from pancreatic lymph nodes of mice that developed insulitis showed increased proliferation and proinflammatory cytokines after incubation with gliadin but not with BSA. CD4+ T cells isolated from nonsensitized controls did not response to gliadin or BSA. In conclusion, gliadin sensitization induced moderate enteropathy in NOD-DQ8 mice. However, insulitis development required gliadin-sensitization and partial systemic depletion of CD25+Foxp3+ T cells. This humanized murine model provides a mechanistic link to explain how the mucosal intolerance to a dietary protein can lead to insulitis in the presence of partial regulatory T cell deficiency. PMID:21911598

Solar cycle predicts folate-sensitive neonatal genotypes at discrete phases of the first trimester of pregnancy: a novel folate-related human embryo loss hypothesis.

Science.gov (United States)

Lucock, Mark; Glanville, Tracey; Yates, Zoë; Walker, James; Furst, John; Simpson, Nigel

2012-08-01

Folate, a key periconceptional nutrient, is ultraviolet light (UV-R) sensitive. We therefore hypothesise that a relationship exists between sunspot activity, a proxy for total solar irradiance (particularly UV-R) reaching Earth, and the occurrence of folate-sensitive, epigenomic-related neonatal genotypes during the first trimester of pregnancy. Limited data is provided to support the hypothesis that the solar cycle predicts folate-related human embryo loss: 379 neonates born at latitude 54°N between 1998 and 2000 were examined for three folate-sensitive, epigenome-related polymorphisms, with solar activity for trimester one accessed via the Royal Greenwich Observatory-US Air force/National Oceanic and Atmospheric Administration Sunspot Database (34,110 total observation days). Logistic regression showed solar activity predicts C677T-methylenetetrahydrofolate reductase (C677T-MTHFR) and A66G-methionine synthase reductase (A66G-MSR) genotype at discrete phases of trimester one. Total and maximal sunspot activity predicts C677T-MTHFR genotype for days 31-60 of trimester one (p=0.0181 and 0.0366, respectively) and A66G-MSR genotype for days 61-90 of trimester one (p=0.0072 and 0.0105, respectively). Loss of UV-R sensitive folate associated with the sunspot cycle might therefore interact with variant folate genes to perturb DNA methylation and/or elaboration of the primary base sequence (thymidylate synthesis), as well as increase embryo-toxic homocysteine. We hypothesise that this may influence embryo viability leading to 677CC-MTHFR and 66GG-MSR embryo loss at times of increased solar activity. This provides an interesting and plausible link between well recognised 'folate gene originated developmental disorders' and 'solar activity/seasonality modulated developmental disorders'. Copyright © 2012 Elsevier Ltd. All rights reserved.

SALINITY TOLERANCE OF SEVERAL RICE GENOTYPES AT SEEDLING STAGE

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Heni Safitri

2018-01-01

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

Infestation of the banana root borer among different banana plant genotypes

Directory of Open Access Journals (Sweden)

Fernando Teixeira de Oliveira

Full Text Available ABSTRACT: In this study, we aimed to investigate Cosmopolites sordidus (Coleoptera: Dryophthoridae infestation among different banana genotypes in a commercial banana orchard over the course of 30 months. Banana root borer infestation was compared in 20 banana genotypes, including five varieties and 15 hybrids. Overall, we observed that 94.17% of pest infestation cases occurred in the cortex region, and only 5.83% occurred in the central cylinder. Genotypes least sensitive to infestation were the Prata Anã (AAB and Pacovan (AAB varieties, where no damage was recorded. Among the hybrid genotypes, PV 9401 and BRS Fhia 18 showed intermediate levels of sensitivity, while BRS Tropical hybrids (AAAB, PA 9401 (AAAB, BRS Vitoria (AAAB, YB 4203 (AAAB, and Bucaneiro (AAAA were the most sensitive to attack by banana root borer. This study demonstrated that the infestation of the banana root borer varies according banana plant genotype, and the utilization of less susceptible genotypes could reduce infestation rates of C. sordidus.

Oxytocin and Social Sensitivity: Gene Polymorphisms in Relation to Depressive Symptoms and Suicidal Ideation

Directory of Open Access Journals (Sweden)

Robyn Jane McQuaid

2016-07-01

Full Text Available Although the neuropeptide oxytocin has been associated with enhanced prosocial behaviors, it has also been linked to aggression and mental health disorders. Thus, it was suggested that oxytocin might act by increasing the salience of social stimuli, irrespective of whether these are positive or negative, thus increasing vulnerability to negative mental health outcomes. The current study (N = 243, conducted among White university students, examined the relation of trauma, depressive symptoms including suicidal ideation in relation to a single nucleotide polymorphism (SNP within the oxytocin receptor gene (OXTR, rs53576, and a SNP on the CD38 gene that controls oxytocin release, rs3796863. Individuals with the polymorphism on both alleles (AA genotype of the CD38 SNP had previously been linked to elevated plasma oxytocin levels. Consistent with the social sensitivity perspective, however, in the current study, individuals carrying the AA genotype displayed elevated feelings of alienation from parents and peers as well as increased levels of suicidal ideation. Moreover, they tended to report elevated depressive symptoms compared to CC homozygotes. It was also observed that the CD38 genotype moderated the relation between trauma and suicidal ideation scores, such that high levels of trauma were associated with elevated suicidal ideation among all CD38 genotypes, but this relationship was stronger among individuals with the AA genotype. In contrast, there was no relationship between the OXTR SNP, rs53576, depression or suicidal ideation. These findings support a social sensitivity hypothesis of oxytocin, wherein the AA genotype of the CD38 SNP, which has been considered the ‘protective allele’ was associated with increased sensitivity and susceptibility to disturbed social relations and suicidal ideation.

Sensitivity study and functionalization of cross section to fuel and moderator temperature

International Nuclear Information System (INIS)

Zee, Sung Quun; Song, Jae Seung; Cho, Young Chul

1995-11-01

A reactor core neutronics code MASTER is under development as a part of Korean Core Design System ADONIS. MASTER solves two-group three-dimensional; neutron diffusion equation which requires fuel assembly-wise group constants, to calculate the neutron flux distribution in the core. The group constants are obtained from the fuel assembly multi-group neutron transport calculation, and inputted as functions of the core operating condition. The functionalization of the group constant requires sensitivity analysis to various core operating conditions. In this report, the sensitivity of group constant to fuel and moderator temperature were analyzed. Lumped higher order macroscopic cross section derivative method was developed to reduce the computer memory and the number of floating point operations to treat group constants in MASTER. 1 fig., 6 tabs., 2 refs. (Author) .new

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

Science.gov (United States)

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

2014-11-01

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

Child Maltreatment, Impulsivity, and Antisocial Behavior in African-American Children: Moderation Effects from a Cumulative Dopaminergic Gene Index

Science.gov (United States)

Thibodeau, Eric L.; Cicchetti, Dante; Rogosch, Fred A.

2015-01-01

A model examining the effects of an increasing number of maltreatment subtypes experienced on antisocial behavior, as mediated by impulsivity and moderated by a polygenic index of dopaminergic genotypes, was investigated. An African American sample of children (N = 1012, M age = 10.07) with and without maltreatment histories participated. Indicators of aggression, delinquency, and disruptive peer behavior were obtained from peer and counselor rated measures to form a latent variable of antisocial behavior; impulsivity was assessed by counselor report. Five genotypes in four dopaminergic genes (DRD4, DRD2, DAT1, and COMT) conferring heightened environmental sensitivity were combined into one polygenic index. Using SEM, a first-stage, moderated-mediation model was evaluated. Age and sex were entered as covariates, both as main effects and in interaction with maltreatment and the gene index. The model had excellent fit: χ2(32, N =1012) = 86..51, pmaltreatment subtypes on antisocial behavior was partially mediated by impulsivity (β= 0.173, pmaltreatment and impulsivity was stronger as children evinced more differentiating genotypes, thereby strengthening the mediational effect of impulsivity on antisocial behavior. These findings elucidate the manner by which maltreated children develop early signs of antisocial behavior, and the genetic mechanisms involved in greater vulnerability for maladaptation in impulse-control within context of child maltreatment. PMID:26535948

Alpha 2B adrenoceptor genotype moderates effect of reboxetine on negative emotional memory bias in healthy volunteers.

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Gibbs, Ayana A; Bautista, Carla E; Mowlem, Florence D; Naudts, Kris H; Duka, Theodora

2013-10-23

Evidence suggests that emotional memory plays a role in the pathophysiology of depression/anxiety disorders. Noradrenaline crucially modulates emotional memory. Genetic variants involved in noradrenergic signaling contribute to individual differences in emotional memory and vulnerability to psychopathology. A functional deletion polymorphism in the α-2B adrenoceptor gene (ADRA2B) has been linked to emotional memory and post-traumatic stress disorder. The noradrenaline reuptake inhibitor reboxetine attenuates enhanced memory for negative stimuli in healthy and depressed individuals. We examined whether the effect of reboxetine on emotional memory in healthy individuals would be moderated by ADRA2B genotype. ADRA2B deletion carriers demonstrated enhanced emotional memory for negative stimuli compared with deletion noncarriers, consistent with prior studies. Reboxetine attenuated enhanced memory for negative stimuli in deletion noncarriers but had no significant effect in deletion carriers. This is the first demonstration of genetic variation influencing antidepressant drug effects on emotional processing in healthy humans.

Moderate alcohol consumption increases insulin sensitivity and ADIPOQ expression in postmenopausal women: A randomised, crossover trial

NARCIS (Netherlands)

Joosten, M.M.; Beulens, J.W.J.; Kersten, S.; Hendriks, H.F.J.

2008-01-01

Aims/hypothesis: To determine whether 6 weeks of daily, moderate alcohol consumption increases expression of the gene encoding adiponectin (ADIPOQ) and plasma levels of the protein, and improves insulin sensitivity in postmenopausal women. Methods: In a randomised, open-label, crossover trial

Is the Prediction of Adolescent Outcomes From Early Child Care Moderated by Later Maternal Sensitivity? Results From the NICHD Study of Early Child Care and Youth Development

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Burchinal, Margaret R.; Vandell, Deborah Lowe; Belsky, Jay

2016-01-01

Longitudinal data are used to examine whether effects of early child care are amplified and/or attenuated by later parenting. Analyses tested these interactions using parenting as both a categorical and continuous variable to balance power and flexibility in testing moderation. The most consistent finding was that maternal sensitivity during adolescence accentuated the association between child care quality and adolescent academic-cognitive skills at age 15 years when maternal sensitivity during adolescence was high. This interaction was obtained in analyses with maternal sensitivity as both a categorical and continuous variable. Relations between early child care hours and adolescent behavioral outcomes also were moderated by maternal sensitivity, with longer child care hours predicting more impulsivity and externalizing at age 15 when maternal sensitivity during middle childhood, scored as a categorical variable, was low to moderate and when maternal sensitivity during adolescence, scored as a continuous variable, was lower. These findings suggest that some child care effects are moderated by subsequent parenting and that this moderation may take both linear and nonlinear forms. PMID:23937381

Molecular Diagnosis of Brettanomyces bruxellensis’ Sulfur Dioxide Sensitivity Through Genotype Specific Method

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Marta Avramova

2018-06-01

Full Text Available The yeast species Brettanomyces bruxellensis is associated with important economic losses due to red wine spoilage. The most common method to prevent and/or control B. bruxellensis spoilage in winemaking is the addition of sulfur dioxide into must and wine. However, recently, it was reported that some B. bruxellensis strains could be tolerant to commonly used doses of SO2. In this work, B. bruxellensis response to SO2 was assessed in order to explore the relationship between SO2 tolerance and genotype. We selected 145 isolates representative of the genetic diversity of the species, and from different fermentation niches (roughly 70% from grape wine fermentation environment, and 30% from beer, ethanol, tequila, kombucha, etc.. These isolates were grown in media harboring increasing sulfite concentrations, from 0 to 0.6 mg.L-1 of molecular SO2. Three behaviors were defined: sensitive strains showed longer lag phase and slower growth rate and/or lower maximum population size in presence of increasing concentrations of SO2. Tolerant strains displayed increased lag phase, but maximal growth rate and maximal population size remained unchanged. Finally, resistant strains showed no growth variation whatever the SO2 concentrations. 36% (52/145 of B. bruxellensis isolates were resistant or tolerant to sulfite, and up to 43% (46/107 when considering only wine isolates. Moreover, most of the resistant/tolerant strains belonged to two specific genetic groups, allowing the use of microsatellite genotyping to predict the risk of sulfur dioxide resistance/tolerance with high reliability (>90%. Such molecular diagnosis could help the winemakers to adjust antimicrobial techniques and efficient spoilage prevention with minimal intervention.

Refractive Outcomes, Contrast Sensitivity, HOAs, and Patient Satisfaction in Moderate Myopia: Wavefront-Optimized Versus Tissue-Saving PRK.

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Nassiri, Nader; Sheibani, Kourosh; Azimi, Abbas; Khosravi, Farinaz Mahmoodi; Heravian, Javad; Yekta, Abasali; Moghaddam, Hadi Ostadi; Nassiri, Saman; Yasseri, Mehdi; Nassiri, Nariman

2015-10-01

To compare refractive outcomes, contrast sensitivity, higher-order aberrations (HOAs), and patient satisfaction after photorefractive keratectomy for correction of moderate myopia with two methods: tissue saving versus wavefront optimized. In this prospective, comparative study, 152 eyes (80 patients) with moderate myopia with and without astigmatism were randomly divided into two groups: the tissue-saving group (Technolas 217z Zyoptix laser; Bausch & Lomb, Rochester, NY) (76 eyes of 39 patients) or the wavefront-optimized group (WaveLight Allegretto Wave Eye-Q laser; Alcon Laboratories, Inc., Fort Worth, TX) (76 eyes of 41 patients). Preoperative and 3-month postoperative refractive outcomes, contrast sensitivity, HOAs, and patient satisfaction were compared between the two groups. The mean spherical equivalent was -4.50 ± 1.02 diopters. No statistically significant differences were detected between the groups in terms of uncorrected and corrected distance visual acuity and spherical equivalent preoperatively and 3 months postoperatively. No statistically significant differences were seen in the amount of preoperative to postoperative contrast sensitivity changes between the two groups in photopic and mesopic conditions. HOAs and Q factor increased in both groups postoperatively (P = .001), with the tissue-saving method causing more increases in HOAs (P = .007) and Q factor (P = .039). Patient satisfaction was comparable between both groups. Both platforms were effective in correcting moderate myopia with or without astigmatism. No difference in refractive outcome, contrast sensitivity changes, and patient satisfaction between the groups was observed. Postoperatively, the tissue-saving method caused a higher increase in HOAs and Q factor compared to the wavefront-optimized method, which could be due to larger optical zone sizes in the tissue-saving group. Copyright 2015, SLACK Incorporated.

Antioxidant Defense Mechanisms of Salinity Tolerance in Rice Genotypes

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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.

Introduction to a special issue on genotype by environment interaction

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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...

Identifying Moderators of the Link Between Parent and Child Anxiety Sensitivity: The Roles of Gender, Positive Parenting, and Corporal Punishment.

Science.gov (United States)

Graham, Rebecca A; Weems, Carl F

2015-07-01

A substantial body of literature suggests that anxiety sensitivity is a risk factor for the development of anxiety problems and research has now begun to examine the links between parenting, parent anxiety sensitivity and their child's anxiety sensitivity. However, the extant literature has provided mixed findings as to whether parent anxiety sensitivity is associated with child anxiety sensitivity, with some evidence suggesting that other factors may influence the association. Theoretically, specific parenting behaviors may be important to the development of child anxiety sensitivity and also in understanding the association between parent and child anxiety sensitivity. In this study, 191 families (n = 255 children and adolescents aged 6-17 and their parents) completed measures of child anxiety sensitivity (CASI) and parenting (APQ-C), and parents completed measures of their own anxiety sensitivity (ASI) and their parenting (APQ-P). Corporal punishment was associated with child anxiety sensitivity and the child's report of their parent's positive parenting behaviors moderated the association between parent and child anxiety sensitivity. The child's gender was also found to moderate the association between parent and child anxiety sensitivity, such that there was a positive association between girls' and their parents anxiety sensitivity and a negative association in boys. The findings advance the understanding of child anxiety sensitivity by establishing a link with corporal punishment and by showing that the association between parent and child anxiety sensitivity may depend upon the parenting context and child's gender.

Temporal stability of growth and yield among Hevea genotypes introduced to a non-traditional rubber growing region of peninsular India

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K.K. Vinod

2013-12-01

Full Text Available Extensive cultivation of Hevea brasiliensis in India now focus on non-traditional regions for rubber cultivation. As a prelude for selection of genotypes for commercial cultivation, many introduced genotypes are being tested in genotype adaptation experiments in these regions. Present study, reports for the first time, growth and yield adaptation of 28 genotypes in a non-traditional rubber growing region of peninsular India viz., the coastal Karnataka region. Agroclimate of this region was found favoring growth and establishment of all the genotypes evaluated. However, not all the genotypes grew and yielded well. Only four genotypes, RRII 203, KRS 25, PB 260 and PB 235 showed good growth and yield. On grouping, the genotypes fell into categories of moderate high yielders, moderate low yielders and low yielders. The most popular variety of the traditional region, RRII 105 did not perform well in this region. Biological stability in growth and yield of RRII 203 and PB 260 was identified as stable and these genotypes were the best adapted. KRS 25 and PB 235 had unstable yielding pattern. The best identified genotypes can be considered for extensive culture as single clone plantations or as major constituent of clone blends as well as parents in future breeding programmes. Other moderate stable yielders may be used for clone blending in smaller proportions and may be subjected to yield improvement.

Differential sensitivity of 5'UTR-NS5A recombinants of hepatitis C virus genotypes 1-6 to protease and NS5A inhibitors

DEFF Research Database (Denmark)

Li, Yi-Ping; Ramirez, Santseharay; Humes, Daryl

2014-01-01

BACKGROUND & AIMS: Hepatitis C virus (HCV) therapy will benefit from the preclinical evaluation of direct-acting antiviral (DAA) agents in infectious culture systems that test the effects on different virus genotypes. We developed HCV recombinants comprising the 5' untranslated region-NS5A (5-5A...... daclatasvir. The 1a(TN) 5-5A and JFH1-independent full-length viruses had similar levels of sensitivity to the DAA agents, validating the 5-5A recombinants as surrogates for full-length viruses in DAA testing. Compared with the 1a(TN) full-length virus, the 3a(S52) 5-5A recombinant was highly resistant to all...... protease inhibitors, and the 4a(ED43) recombinant was highly resistant to telaprevir and boceprevir, but most sensitive to other protease inhibitors. Compared with other protease inhibitors, MK-5172 had exceptional potency against all HCV genotypes. The NS5A inhibitor daclatasvir had the highest potency...

Comparison of performance of three commercial platforms for warfarin sensitivity genotyping.

Science.gov (United States)

Babic, Nikolina; Haverfield, Eden V; Burrus, Julie A; Lozada, Anthony; Das, Soma; Yeo, Kiang-Teck J

2009-08-01

We performed a 3-way comparison on the Osmetech eSensor, AutoGenomics INFINITI, and a real-time PCR method (Paragonx reagents/Stratagene RT-PCR platform) for their FDA-cleared warfarin panels, and additional polymorphisms (CYP2C9*5, *6, and 11 and extended VKORC1 panels) where available. One hundred de-identified DNA samples were used in this IRB-approved study. Accuracy was determined by comparison of genotyping results across three platforms. Any discrepancy was resolved by bi-directional sequencing. The CYP4F2 on Osmetech was validated by bi-directional sequencing. Accuracies for CYP2C9*2 and *3 were 100% for all 3 platforms. VKORC1 3673 genotyping accuracies were 100% on eSensor and 97% on Infiniti. CYP2C9*5, *6 and *11 showed 100% concordance between eSensor and Infiniti. VKORC1 6484 and 9041 variants compared between ParagonDx and Infiniti analyzer were 100% (6484) and 99% (9041) concordant. CYP4F2 was 100% concordant with sequencing results. The time required to generate the results from automated DNA extraction-to-result was approximately 8h on Infiniti, and 4h on eSensor and ParagonDx, respectively. Overall, we observed excellent CYP2C9*2 and *3 genotyping accuracy for all three platforms. For VKORC1 3673 genotyping, eSensor demonstrated a slightly higher accuracy than the Infiniti, and CYP4F2 on Osmetech was 100% accurate.

Response of soybean genotypes against armyworm, Spodoptera litura based on no-choice test

Science.gov (United States)

Bayu, M. S. Y. I.; Krisnawati, A.; Adie, M. M.

2018-01-01

Armyworm is important polyphagous pest causing economic losses in many agricultural crops including soybean. In Indonesia, there are no soybean varieties which indicated had a resistance against armyworm. The experiment was conducted in Laboratory of Entomology and Green House of Indonesian Legumes and Tuber Crops Research Institute from March to April 2016. The experiment was arranged using randomized block design with a total of 18 soybean genotypes as a treatment in three replicates. The results showed that the difference of soybean genotypes had a significant effect on the leaf damaged intensity. Based on no-choice test and the leaves damaged intensity compared with resistant check genotypes, there was no genotype indicated resistant against S. litura. Most of the tested genotype showed moderately resistant and others showed susceptible to highly susceptible. Genotypes that indicated as moderately resistant are G 511 H/Anjs-1-1, G 511 H/Arg//Arg///Arg-30-7, G 511 H/Kaba//Kaba///-4-4, G 511 H/Kaba//Kaba///Kaba////Kaba-16-2, G 511 H/Anjs/Anjs///Anjs-3-3, G 511 H/Anjs/Anjs-1-2, G 511 H/Anjs/Anjs-5-5, G 511 H/Anjs/Anjs///Anjs-6-11, and Argomulyo. In conclusion, those nine genotypes indicated have antixenosis resistance against armyworm and can be considered as a source of gene for improving the soybean resistance to armyworm.

Identifying the Genotypes of Hepatitis B Virus (HBV) with DNA Origami Label.

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Liu, Ke; Pan, Dun; Wen, Yanqin; Zhang, Honglu; Chao, Jie; Wang, Lihua; Song, Shiping; Fan, Chunhai; Shi, Yongyong

2018-02-01

The hepatitis B virus (HBV) genotyping may profoundly affect the accurate diagnosis and antiviral treatment of viral hepatitis. Existing genotyping methods such as serological, immunological, or molecular testing are still suffered from substandard specificity and low sensitivity in laboratory or clinical application. In a previous study, a set of high-efficiency hybridizable DNA origami-based shape ID probes to target the templates through which genetic variation could be determined in an ultrahigh resolution of atomic force microscopy (AFM) nanomechanical imaging are established. Here, as a further confirmatory research to explore the sensitivity and applicability of this assay, differentially predesigned DNA origami shape ID probes are also developed for precisely HBV genotyping. Through the specific identification of visualized DNA origami nanostructure with clinical HBV DNA samples, the genetic variation information of genotypes can be directly identified under AFM. As a proof-of-concept, five genotype B and six genotype C are detected in 11 HBV-infected patients' blood DNA samples of Han Chinese population in the single-blinded test. The AFM image-based DNA origami shape ID genotyping approach shows high specificity and sensitivity, which could be promising for virus infection diagnosis and precision medicine in the future. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Temporal stability of growth and yield among Hevea genotypes introduced to a non-traditional rubber growing region of peninsular India

Directory of Open Access Journals (Sweden)

K.K. Vinod

2010-09-01

Full Text Available Extensive cultivation of Hevea brasiliensis in India now focus onnon-traditional regions for rubber cultivation. As a prelude for selection of genotypes for commercial cultivation, many introduced genotypes are being tested in genotype adaptation experiments in these regions. Present study,reports for the first time, growth and yield adaptation of 28 genotypes in a non-traditional rubber growing region of peninsular India viz., the coastal Karnataka region. Agroclimate of this region was found favoring growth andestablishment of all the genotypes evaluated. However, not all the genotypes grew and yielded well. Only four genotypes, RRII 203, KRS 25, PB 260 and PB 235 showed good growth and yield. On grouping, the genotypes fell into categories of moderate high yielders, moderate low yielders and low yielders. The most popular variety of the traditional region, RRII 105 did not perform well in this region. Biological stability in growth and yield of RRII 203 and PB 260 was identified as stable and these genotypes were the best adapted. KRS 25 and PB 235 had unstable yielding pattern. The best identifiedgenotypes can be considered for extensive culture as single clone plantations or as major constituent of clone blends as well as parents in future breeding programmes. Other moderate stable yielders may be used for clone blending in smaller proportions and may be subjected to yield improvement.

Porphyromonas gingivalis Fim-A genotype distribution among Colombians

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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

Assessment of biochemical mechanisms of tolerance to chlorpyrifos in ancient and contemporary Daphnia pulicaria genotypes.

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Simpson, Adam M; Jeyasingh, Punidan D; Belden, Jason B

2017-12-01

The evolution of tolerance to environmental contaminants in non-target taxa has been largely studied by comparing extant populations experiencing contrasting exposure. Previous research has demonstrated that "resurrected" genotypes from a population of Daphnia pulicaria express temporal variation in sensitivity to the insecticide chlorpyrifos. Ancient genotypes (1301-1646AD.) were on average more sensitive to this chemical compared to the contemporary genotypes (1967-1977AD.). To determine the physiological mechanisms of tolerance, a series of biochemical assays was performed on three ancient and three contemporary genotypes; these six genotypes exhibited the most sensitive and most tolerant phenotypes within the population, respectively. Metabolic tolerance mechanisms were evaluated using acute toxicity testing, while target-site tolerance was assessed via in vitro acetylcholinesterase (AChE) assays. Acute toxicity tests were conducted using i) the toxic metabolite chlorpyrifos-oxon (CPF-oxon) and ii) CPF-oxon co-applied with piperonyl butoxide (PBO), a known Phase-I metabolic inhibitor. Both series of toxicity tests reduced the mean variation in sensitivity between tolerant and sensitive genotypes. Exposure to CPF-O reduced the disparity from a 4.7-fold to 1.6-fold difference in sensitivity. The addition of PBO further reduced the variation to a 1.2-fold difference in sensitivity. In vitro acetylcholinesterase assays yielded no significant differences in constitutive activity or target-site sensitivity. These findings suggest that pathways involving Phase-I detoxification and/or bioactivation of chlorpyrifos play a significant role in dictating the microevolutionary trajectories of tolerance in this population. Copyright © 2017 Elsevier B.V. All rights reserved.

Inhibition of Fungal Pathogens across Genotypes and Temperatures by Amphibian Skin Bacteria

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Carly R. Muletz-Wolz

2017-08-01

Full Text Available Symbiotic bacteria may dampen the impacts of infectious diseases on hosts by inhibiting pathogen growth. However, our understanding of the generality of pathogen inhibition by different bacterial taxa across pathogen genotypes and environmental conditions is limited. Bacterial inhibitory properties are of particular interest for the amphibian-killing fungal pathogens (Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans, for which probiotic applications as conservation strategies have been proposed. We quantified the inhibition strength of five putatively B. dendrobatidis-inhibitory bacteria isolated from woodland salamander skin against six Batrachochytrium genotypes at two temperatures (12 and 18°C. We selected six genotypes from across the Batrachochytrium phylogeny: B. salamandrivorans, B. dendrobatidis-Brazil and four genotypes of the B. dendrobatidis Global Panzootic Lineage (GPL1: JEL647, JEL404; GPL2: SRS810, JEL423. We performed 96-well plate challenge assays in a full factorial design. We detected a Batrachochytrium genotype by temperature interaction on bacterial inhibition score for all bacteria, indicating that bacteria vary in ability to inhibit Batrachochytrium depending on pathogen genotype and temperature. Acinetobacter rhizosphaerae moderately inhibited B. salamandrivorans at both temperatures (μ = 46–53%, but not any B. dendrobatidis genotypes. Chryseobacterium sp. inhibited three Batrachochytrium genotypes at both temperatures (μ = 5–71%. Pseudomonas sp. strain 1 inhibited all Batrachochytrium genotypes at 12°C and four Batrachochytrium genotypes at 18°C (μ = 5–100%. Pseudomonas sp. strain 2 and Stenotrophomonas sp. moderately to strongly inhibited all six Batrachochytrium genotypes at both temperatures (μ = 57–100%. All bacteria consistently inhibited B. salamandrivorans. Using cluster analysis of inhibition scores, we found that more closely related Batrachochytrium genotypes grouped together

Rejection Sensitivity as a Moderator of Psychosocial Outcomes Following Pediatric Traumatic Brain Injury.

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Meadows, Emily A; Owen Yeates, Keith; Rubin, Kenneth H; Taylor, H Gerry; Bigler, Erin D; Dennis, Maureen; Gerhardt, Cynthia A; Vannatta, Kathryn; Stancin, Terry; Hoskinson, Kristen R

2017-07-01

The current study examines whether psychosocial outcomes following pediatric traumatic brain injury (TBI) vary as a function of children's rejection sensitivity (RS), defined as their disposition to be hypersensitive to cues of rejection from peers. Children ages 8-13 with a history of severe TBI (STBI, n=16), complicated mild/moderate TBI (n=35), or orthopedic injury (OI, n=49) completed measures assessing self-esteem and RS on average 3.28 years post-injury (SD=1.33, range=1.25-6.34). Parents reported on their child's emotional and behavioral functioning and social participation. Regression analyses found moderation of group differences by RS for three outcomes: social participation, self-perceptions of social acceptance, and externalizing behavior problems. Conditional effects at varying levels of RS indicated that externalizing problems and social participation were significantly worse for children with STBI at high levels of RS, compared to children with OI. Social participation for the STBI group remained significantly lower than the OI group at mean levels of RS, but not at low levels of RS. At high levels of RS, self-perceptions of social acceptance were lower for children with moderate TBI compared to OI, but group differences were not significant at mean or low levels of RS. No evidence of moderation was found for global self-worth, self-perceptions of physical appearance or athletic ability, or internalizing problems. The findings highlight the salient nature of social outcomes in the context of varying levels of RS. These findings may have implications for the design of interventions to improve social outcomes following TBI. (JINS, 2017, 23, 451-459).

5-HTTLPR genotype potentiates the effects of war zone stressors on the emergence of PTSD, depressive and anxiety symptoms in soldiers deployed to iraq.

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Telch, Michael J; Beevers, Christopher G; Rosenfield, David; Lee, Han-Joo; Reijntjes, Albert; Ferrell, Robert E; Hariri, Ahmad R

2015-06-01

Exposure to war zone stressors is common, yet only a minority of soldiers experience clinically meaningful disturbance in psychological function. Identification of biomarkers that predict vulnerability to war zone stressors is critical for developing more effective treatment and prevention strategies not only in soldiers but also in civilians who are exposed to trauma. We investigated the role of the serotonin transporter linked polymorphic region (5-HTTLPR) genotype in predicting the emergence of post-traumatic stress disorder (PTSD), depressive and anxiety symptoms as a function of war zone stressors. A prospective cohort of 133 U.S. Army soldiers with no prior history of deployment to a war zone, who were scheduled to deploy to Iraq, was recruited. Multilevel regression models were used to investigate associations between 5-HTTLPR genotype, level of war zone stressors, and reported symptoms of PTSD, depression and anxiety while deployed to Iraq. Level of war zone stressors was associated with symptoms of PTSD, depression and anxiety. Consistent with its effects on stress responsiveness, 5-HTTLPR genotype moderated the relationship between level of war zone stressors and symptoms of emotional disturbance. Specifically, soldiers carrying one or two low functioning alleles (S or LG ) reported heightened symptoms of PTSD, depression and anxiety in response to increased levels of exposure to war zone stressors, relative to soldiers homozygous for the high functioning allele (LA ). These data suggest that 5-HTTLPR genotype moderates individual sensitivity to war zone stressors and the expression of emotional disturbance including PTSD symptoms. Replication of this association along with identification of other genetic moderators of risk can inform the development of biomarkers that can predict relative resilience vs. vulnerability to stress. © 2015 World Psychiatric Association.

Anxiety Sensitivity as a Mediator of the Relationship between Moderate-Intensity Exercise and Coping-Oriented Marijuana Use Motives

NARCIS (Netherlands)

Smits, J.A.J.; Bonn-Miller, M.O.; Tart, C.D.; Irons, J.G.; Zvolensky, M.J.

2011-01-01

he present study examined the working hypothesis that moderate-intensity exercise is associated with coping-oriented marijuana use motives through its association with the fear of somatic arousal (ie, anxiety sensitivity). Using data from 146 young adult current marijuana users, we found evidence

Moderation of antidepressant response by the serotonin transporter gene

DEFF Research Database (Denmark)

Huezo-Diaz, Patricia; Uher, Rudolf; Smith, Rebecca

2009-01-01

Background: There have been conflicting reports on whether the length polymorphism in the promoter of the serotonin transporter gene (5-HTTLPR) moderates the antidepressant effects of selective serotonin reuptake inhibitors (SSRIs). We hypothesised that the pharmacogenetic effect of 5-HTTLPR...... the serotonin transporter gene were genotyped in 795 adults with moderate-to-severe depression treated with escitalopram or nortriptyline in the Genome Based Therapeutic Drugs for Depression (GENDEP) project. Results: The 5-HTTLPR moderated the response to escitalopram, with long-allele carriers improving more...

Threat-related amygdala functional connectivity is associated with 5-HTTLPR genotype and neuroticism

DEFF Research Database (Denmark)

Madsen, Martin Korsbak; Mc Mahon, Brenda; Andersen, Sofie Bech

2016-01-01

between right amygdala and mPFC and visual cortex, and between both amygdalae and left lateral orbitofrontal (lOFC) and ventrolateral prefrontal cortex (vlPFC). Notably, 5-HTTLPR moderated the association between neuroticism and functional connectivity between both amygdalae and left l...... is not fully understood. Using functional magnetic resonance imaging, we evaluated independent and interactive effects of the 5-HTTLPR genotype and neuroticism on amygdala functional connectivity during an emotional faces paradigm in 76 healthy individuals. Functional connectivity between left amygdala......Communication between the amygdala and other brain regions critically regulates sensitivity to threat, which has been associated with risk for mood and affective disorders. The extent to which these neural pathways are genetically determined or correlate with risk-related personality measures...

Comparative salinity responses among tomato genotypes and rootstocks

International Nuclear Information System (INIS)

Oztekin, G.B.; Tuzel, Y.

2011-01-01

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

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.

Hepatitis C Virus: Viral Quasispecies and Genotypes.

Science.gov (United States)

Tsukiyama-Kohara, Kyoko; Kohara, Michinori

2017-12-22

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

Temperament trait of sensory processing sensitivity moderates cultural differences in neural response.

Science.gov (United States)

Aron, Arthur; Ketay, Sarah; Hedden, Trey; Aron, Elaine N; Rose Markus, Hazel; Gabrieli, John D E

2010-06-01

This study focused on a possible temperament-by-culture interaction. Specifically, it explored whether a basic temperament/personality trait (sensory processing sensitivity; SPS), perhaps having a genetic component, might moderate a previously established cultural difference in neural responses when making context-dependent vs context-independent judgments of simple visual stimuli. SPS has been hypothesized to underlie what has been called inhibitedness or reactivity in infants, introversion in adults, and reactivity or responsivness in diverse animal species. Some biologists view the trait as one of two innate strategies-observing carefully before acting vs being first to act. Thus the central characteristic of SPS is hypothesized to be a deep processing of information. Here, 10 European-Americans and 10 East Asians underwent functional magnetic resonance imaging while performing simple visuospatial tasks emphasizing judgments that were either context independent (typically easier for Americans) or context dependent (typically easier for Asians). As reported elsewhere, each group exhibited greater activation for the culturally non-preferred task in frontal and parietal regions associated with greater effort in attention and working memory. However, further analyses, reported here for the first time, provided preliminary support for moderation by SPS. Consistent with the careful-processing theory, high-SPS individuals showed little cultural difference; low-SPS, strong culture differences.

Interpersonal Sensitivity and Sexual Functioning in Young Men with Testicular Cancer: the Moderating Role of Coping.

Science.gov (United States)

Hoyt, Michael A; McCann, Connor; Savone, Mirko; Saigal, Christopher S; Stanton, Annette L

2015-12-01

Interpersonal sensitivity is characterized by the predisposition to perceive and elicit criticism, rejection, and negative social evaluation. It may be linked to poorer physical or functional health outcomes, particularly in the interpersonal context (cancer-related sexual dysfunction). This study tested the association of interpersonal sensitivity with sexual functioning following testicular cancer in young men and whether this association is moderated by coping processes. Men ages 18 to 29 (N = 171; M age = 25.2, SD = 3.32) with a history of testicular cancer were recruited via the California State Cancer Registry and completed questionnaire measures including assessments of interpersonal sensitivity, sexual functioning, and approach and avoidance coping. Regression analysis controlling for education, age, partner status, ethnic status, and time since diagnosis revealed that higher interpersonal sensitivity was significantly related to lower sexual functioning (β = -0.18, p related approach-oriented coping was associated with better sexual functioning (β = 0.19, p interpersonal sensitivity was more strongly associated with lower functioning among men with relatively low use of approach coping. Interpersonal sensitivity may be an important individual difference in vulnerability to sexual dysfunction after testicular cancer. Enhancement of coping skills may be a useful direction for intervention development for interpersonally sensitive young men with cancer.

Self-efficacy mediates the effects of topiramate and GRIK1 genotype on drinking.

Science.gov (United States)

Kranzler, Henry R; Armeli, Stephen; Wetherill, Reagan; Feinn, Richard; Tennen, Howard; Gelernter, Joel; Covault, Jonathan; Pond, Timothy

2016-03-01

Previous studies indicate that topiramate reduces alcohol use among problem drinkers, with one study showing that the effect was moderated by a polymorphism (rs2832407) in GRIK1, the gene encoding the GluK1 kainate subunit. We examined whether the interactive effect of medication and genotype (1) altered the association between daily self-efficacy and later-day drinking; and (2) had an indirect effect on drinking via self-efficacy. In a 12-week, placebo-controlled trial of topiramate, we used daily interactive voice response technology to measure self-efficacy (i.e. confidence in avoiding heavy drinking later in the day) and drinking behavior in 122 European-American heavy drinkers. Topiramate's effects on both self-efficacy and drinking level were moderated by rs2832407. C-allele homozygotes treated with topiramate showed higher levels of self-efficacy and lower levels of nighttime drinking across the 12-week trial. Further, the interactive effect of topiramate and genotype on mean nighttime drinking levels was mediated by mean levels of self-efficacy. By modeling topiramate's effects on nighttime drinking across multiple levels of analysis, we found that self-efficacy, a key psychologic construct, mediated the effect of topiramate, which was moderated by rs2832407 genotype. Thus, it may be possible to use an individualized assessment (i.e. genotype) to select treatment to optimize the reduction in heavy drinking and thereby provide a personalized treatment approach. © 2014 Society for the Study of Addiction.

Self-Efficacy Mediates the Effects of Topiramate and GRIK1 Genotype on Drinking

Science.gov (United States)

Kranzler, Henry R.; Armeli, Stephen; Wetherill, Reagan; Feinn, Richard; Tennen, Howard; Gelernter, Joel; Covault, Jonathan; Pond, Timothy

2014-01-01

Previous studies indicate that topiramate reduces alcohol use among problem drinkers, with one study showing that the effect was moderated by a polymorphism (rs2832407) in GRIK1, the gene encoding the GluK1 kainate subunit. We examined whether the interactive effect of medication and genotype (a) altered the association between daily self-efficacy and later day drinking and (b) had an indirect effect on drinking via self-efficacy. Methods In a 12-week, placebo-controlled trial of topiramate, we used daily interactive voice response technology to measure self-efficacy (i.e., confidence in avoiding heavy drinking later in the day) and drinking behavior in 122 European-American heavy drinkers. Results Topiramate’s effects on both self-efficacy and drinking level were moderated by rs2832407. C-allele homozygotes treated with topiramate showed higher levels of self-efficacy and lower levels of nighttime drinking across the 12-week trial. Further, the interactive effect of topiramate and genotype on mean nighttime drinking levels was mediated by mean levels of self-efficacy. Conclusion By modeling topiramate’s effects on nighttime drinking across multiple levels of analysis, we found that self-efficacy, a key psychological construct, mediated the effect of topiramate, which was moderated by rs2832407 genotype. Thus, it may be possible to use an individualized assessment (i.e., genotype) to select treatment (i.e., topiramate or psychotherapy aimed at enhancing self-efficacy) to optimize the reduction in heavy drinking to provide a personalized treatment approach. PMID:25496338

RT-PCR for detection of all seven genotypes of Lyssavirus genus.

Science.gov (United States)

Vázquez-Morón, S; Avellón, A; Echevarría, J E

2006-08-01

The Lyssavirus genus includes seven species or genotypes named 1-7. Rabies genotypes correlate with geographical distribution and specific hosts. Co-circulation of different lyssaviruses, imported cases, and the presence of unknown viruses, such as Aravan, Khujand, Irkut and West Caucasian Bat Virus, make it necessary to use generic methods able to detect all lyssaviruses. Primer sequences were chosen from conserved regions in all genotypes in order to optimise a generic RT-PCR. Serial dilutions of 12 RNA extracts from all seven Lyssavirus genotypes were examined to compare the sensitivity of the RT-PCR standardised in this study with a published RT-PCR optimised for EBLV1 detection and capable of amplifying RNA from all seven lyssaviruses. All seven genotypes were detected by both RT-PCRs, however, the sensitivity was higher with the new version of the test. Twenty samples submitted for rabies diagnosis were tested by the new RT-PCR. Eight out of 20 samples from six dogs, one horse and one bat were found positive, in agreement with immunofluorescence results. Seven samples from terrestrial mammals were genotype 1 and one from a bat was genotype 5. In conclusion, this method can be used to complement immunofluorescence for the diagnosis of rabies, enabling the detection of unexpected lyssaviruses during rabies surveillance.

Family dissolution and offspring depression and depressive symptoms: A systematic review of moderation effects.

Science.gov (United States)

Di Manno, Laura; Macdonald, Jacqui A; Knight, Tess

2015-12-01

Parental separation is associated with increased risk for offspring depression; however, depression outcomes are divergent. Knowledge of moderators could assist in understanding idiosyncratic outcomes and developing appropriately targeted prevention programs for those at heightened risk of depression following parental separation. Therefore, the objective of the review was to identify and evaluate studies that examined moderators of the relationship between parental separation and offspring depression A search of scientific, medical and psychological databases was conducted in April 2015 for longitudinal research that had evaluated any moderator/s of the relationship between parental separation or divorce and offspring depression or depressive symptoms. Papers were assessed for quality by evaluating the study's sample, attrition rates, methodology and measurement characteristics. Fourteen quantitative studies from five countries assessed sixteen moderating factors of the relationship between parental separation and offspring depression or depressive symptoms. A number of factors were found to moderate this relationship, including offspring gender, age (at assessment and at depression onset), genotype, preadolescent temperament, IQ, emotional problems in childhood and maternal sensitivity. While robust longitudinal research was selected for inclusion, common issues with longitudinal studies such as low rates of participation and attrition were among the methodological concerns evident in some of the reviewed papers. The current review is the first to assess interaction effects of the relationship between parental separation and offspring depression or depressive symptoms. While further research is recommended, this assessment is critical in understanding variation in heterogeneous populations and can inform targeted policy and prevention.

Assessment of antibiotic susceptibilities, genotypic characteristics ...

African Journals Online (AJOL)

Jane

2011-09-28

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

Hepatitis C Virus: Viral Quasispecies and Genotypes

Directory of Open Access Journals (Sweden)

Kyoko Tsukiyama-Kohara

2017-12-01

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

Understanding salt tolerance mechanisms in wheat genotypes by exploring antioxidant enzymes

DEFF Research Database (Denmark)

Amjad, M.; Akhtar, J.; Haq, M.A.

2014-01-01

The activities of antioxidant enzymes were analyzed in six wheat genotypes under different concentrations of NaCl (0, 100 and 200 mM). Plants were harvested after either 15 or 30 days of salt stress. The most salt tolerant genotype (SARC-1) maintained lower Na+ and higher relative growth rate (RGR......), shoot fresh weight (SFW), shoot-root ratio, and K+:Na+ ratio, compared to the most salt sensitive genotypes (S-9189 and S-9476). Superoxide dismutase (SOD) and catalase (CAT) increased significantly in SARC-1 and SARC-2 with increasing salt stress, while there was no difference in S-9189 and S- 9476....... Additionally, glutathione reductase (GR) activity was decreased in salt sensitive (S-9189 and S-9476) than salt tolerant (SARC-1) genotypes. Under salt stress conditions a negative relationship between SOD and leaf Na+, and a positive between SOD and shoot fresh weight (SFW), were observed. The higher...

Similar predictions of etravirine sensitivity regardless of genotypic testing method used: comparison of available scoring systems.

Science.gov (United States)

Vingerhoets, Johan; Nijs, Steven; Tambuyzer, Lotke; Hoogstoel, Annemie; Anderson, David; Picchio, Gaston

2012-01-01

The aims of this study were to compare various genotypic scoring systems commonly used to predict virological outcome to etravirine, and examine their concordance with etravirine phenotypic susceptibility. Six etravirine genotypic scoring systems were assessed: Tibotec 2010 (based on 20 mutations; TBT 20), Monogram, Stanford HIVdb, ANRS, Rega (based on 37, 30, 27 and 49 mutations, respectively) and virco(®)TYPE HIV-1 (predicted fold change based on genotype). Samples from treatment-experienced patients who participated in the DUET trials and with both genotypic and phenotypic data (n=403) were assessed using each scoring system. Results were retrospectively correlated with virological response in DUET. κ coefficients were calculated to estimate the degree of correlation between the different scoring systems. Correlation between the five scoring systems and the TBT 20 system was approximately 90%. Virological response by etravirine susceptibility was comparable regardless of which scoring system was utilized, with 70-74% of DUET patients determined as susceptible to etravirine by the different scoring systems achieving plasma viral load <50 HIV-1 RNA copies/ml. In samples classed as phenotypically susceptible to etravirine (fold change in 50% effective concentration ≤3), correlations with genotypic score were consistently high across scoring systems (≥70%). In general, the etravirine genotypic scoring systems produced similar results, and genotype-phenotype concordance was high. As such, phenotypic interpretations, and in their absence all genotypic scoring systems investigated, may be used to reliably predict the activity of etravirine.

Biochemical indicators of root damage in rice (Oryza sativa) genotypes under zinc deficiency stress.

Science.gov (United States)

Lee, Jae-Sung; Wissuwa, Matthias; Zamora, Oscar B; Ismail, Abdelbagi M

2017-11-01

Zn deficiency is one of the major soil constraints currently limiting rice production. Although recent studies demonstrated that higher antioxidant activity in leaf tissue effectively protects against Zn deficiency stress, little is known about whether similar tolerance mechanisms operate in root tissue. In this study we explored root-specific responses of different rice genotypes to Zn deficiency. Root solute leakage and biomass reduction, antioxidant activity, and metabolic changes were measured using plants grown in Zn-deficient soil and hydroponics. Solute leakage from roots was higher in sensitive genotypes and linked to membrane damage caused by Zn deficiency-induced oxidative stress. However, total root antioxidant activity was four-fold lower than in leaves and did not differ between sensitive and tolerant genotypes. Root metabolite analysis using gas chromatography-mass spectrometry and high performance liquid chromatography indicated that Zn deficiency triggered the accumulation of glycerol-3-phosphate and acetate in sensitive genotypes, while less or no accumulation was seen in tolerant genotypes. We suggest that these metabolites may serve as biochemical indicators of root damage under Zn deficiency.

Evaluation of maize genotypes for Turcicum leaf blight (Exserohilum turcicum in Terai and inner terai of Nepal

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Tirtha Raj Rijal

2016-12-01

Full Text Available Thirty maize genotypes in 2014-2015 at Dumarwana, Nijgadh, Keureni and Rampur and ten genotypes in 2015-2016 at Anandpur, Shitalnagar, Dumarwana, Nijgadh and Rampur were evaluated for resistance to Turcicum leaf blight (Exserohilum turcicum under farmers field conditions. The scale used for disease severity ranged from 1-5 scale based on the proportionate leaf area affected by the disease. The combined analysis over locations in 2014-2015 showed that among the 30 genotypes 25 genotypes were resistant (1.0-2.0 scale, and 5 genotypes were moderately resistant (2.1-3.0 scale. Similarly the pooled analysis over locations in 2015-2016 showed that 7 genotypes were resistant (1.0-2.0 scale and 3 genotypes were moderately resistant (2.1-3.0 scale. The maize genotypes namely Z376-26, Z478-3, Z433-99, Z464-5, Z478-2, Z466-1, CAH1513, RML-95/RML-96, CAH1515, CAH1521, CAH1515, CAH151, CAH153, ZH114228 , Z376-9, Z466-3, Z376-5, RML-32/RML-17, RML-86/RML-96 and 900MGold were resistant with disease severity scale of 1.5 and with higher grain yield in both the years. Thus above genotypes were identified as promising sources of resistance against E. turcicum and they can be used to develop disease resistant and high yielding varieties to enhance maize productivity in terai and inner terai of Nepal.

Feeding non-preference by Spodoptera frugiperda and Spodoptera eridania on tomato genotypes

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Bruno Henrique Sardinha de Souza

2013-02-01

Full Text Available Larvae of the genus Spodoptera spp. are highly polyphagous and can cause economical losses in several agricultural crops. Given their growing importance in the tomato crop, especially for industry, this work aimed to evaluate the feeding non-preference by larvae of Spodoptera frugiperda (J. E. Smith, 1797 and Spodoptera eridania (Cramer, 1782 on tomato genotypes and classify them by the levels of resistance. The commercial cultivar Santa Clara was set as the susceptible standard and line PI 134417 as the resistant standard to evaluate the lines PI 134418, PI 126931, LA 462 and LA 716. Feeding non-preference tests were performed under non-choice and free-choice conditions to evaluate the genotype attractiveness to larvae at predetermined times after their release, as well as the leaf area consumed. Overall, the genotypes LA 716 and PI 126931 were the least attractive to S. frugiperda, whereas Santa Clara was the most attractive and consumed. For S. eridania, the genotypes PI 126931, LA 462, LA 716 and PI 134418 were the least preferred for feeding, and Santa Clara and PI 134417 were the most attractive and consumed. The genotypes LA 716 and PI 126931 are moderately resistant to S. frugiperda and S. eridania; PI 134418 and LA 462 are moderately resistant to S. eridania; PI 134417 is susceptible to S. frugiperda and S. eridania; and Santa Clara is highly susceptible to both S. frugiperda and S. eridania.

Sensitivity to psychosocial chronic stressors and adolescents’ externalizing problems : Combined moderator effects of resting heart rate and parental psychiatric history

NARCIS (Netherlands)

Zandstra, A.R.E.; Ormel, J.; Dietrich, A.; van den Heuvel, E.R.; Hoekstra, P.J.; Hartman, C.A.

2018-01-01

From the literature it is not clear whether low resting heart rate (HR) reflects low or high sensitivity to the detrimental effects of adverse environments on externalizing problems. We studied parental psychiatric history (PH), reflecting general vulnerability, as possible moderator explaining

Molecular, physiological and biochemical responses of Theobroma cacao L. genotypes to soil water deficit.

Science.gov (United States)

Santos, Ivanildes C Dos; Almeida, Alex-Alan Furtado de; Anhert, Dário; Conceição, Alessandro S da; Pirovani, Carlos P; Pires, José L; Valle, Raúl René; Baligar, Virupax C

2014-01-01

Six months-old seminal plants of 36 cacao genotypes grown under greenhouse conditions were subjected to two soil water regimes (control and drought) to assess, the effects of water deficit on growth, chemical composition and oxidative stress. In the control, soil moisture was maintained near field capacity with leaf water potentials (ΨWL) ranging from -0.1 to -0.5 MPa. In the drought treatment, the soil moisture was reduced gradually by withholding additional water until ΨWL reached values of between -2.0 to -2.5 MPa. The tolerant genotypes PS-1319, MO-20 and MA-15 recorded significant increases in guaiacol peroxidase activity reflecting a more efficient antioxidant metabolism. In relation to drought tolerance, the most important variables in the distinguishing contrasting groups were: total leaf area per plant; leaf, stem and total dry biomass; relative growth rate; plant shoot biomass and leaf content of N, Ca, and Mg. From the results of these analyses, six genotypes were selected with contrasting characteristics for tolerance to soil water deficit [CC-40, C. SUL-4 and SIC-2 (non-tolerant) and MA-15, MO-20, and PA-13 (tolerant)] for further assessment of the expression of genes NCED5, PP2C, psbA and psbO to water deficit. Increased expression of NCED5, PP2C, psbA and psbO genes were found for non-tolerant genotypes, while in the majority of tolerant genotypes there was repression of these genes, with the exception of PA-13 that showed an increased expression of psbA. Mutivariate analysis showed that growth variables, leaf and total dry biomass, relative growth rate as well as Mg content of the leaves were the most important factor in the classification of the genotypes as tolerant, moderately tolerant and sensitive to water deficit. Therefore these variables are reliable plant traits in the selection of plants tolerant to drought.

DRD4 genotype predicts longevity in mouse and human.

Science.gov (United States)

Grady, Deborah L; Thanos, Panayotis K; Corrada, Maria M; Barnett, Jeffrey C; Ciobanu, Valentina; Shustarovich, Diana; Napoli, Anthony; Moyzis, Alexandra G; Grandy, David; Rubinstein, Marcelo; Wang, Gene-Jack; Kawas, Claudia H; Chen, Chuansheng; Dong, Qi; Wang, Eric; Volkow, Nora D; Moyzis, Robert K

2013-01-02

Longevity is influenced by genetic and environmental factors. The brain's dopamine system may be particularly relevant, since it modulates traits (e.g., sensitivity to reward, incentive motivation, sustained effort) that impact behavioral responses to the environment. In particular, the dopamine D4 receptor (DRD4) has been shown to moderate the impact of environments on behavior and health. We tested the hypothesis that the DRD4 gene influences longevity and that its impact is mediated through environmental effects. Surviving participants of a 30-year-old population-based health survey (N = 310; age range, 90-109 years; the 90+ Study) were genotyped/resequenced at the DRD4 gene and compared with a European ancestry-matched younger population (N = 2902; age range, 7-45 years). We found that the oldest-old population had a 66% increase in individuals carrying the DRD4 7R allele relative to the younger sample (p = 3.5 × 10(-9)), and that this genotype was strongly correlated with increased levels of physical activity. Consistent with these results, DRD4 knock-out mice, when compared with wild-type and heterozygous mice, displayed a 7-9.7% decrease in lifespan, reduced spontaneous locomotor activity, and no lifespan increase when reared in an enriched environment. These results support the hypothesis that DRD4 gene variants contribute to longevity in humans and in mice, and suggest that this effect is mediated by shaping behavioral responses to the environment.

Exercise self-efficacy moderates the relation between anxiety sensitivity and body mass index and exercise tolerance in treatment-seeking smokers

NARCIS (Netherlands)

Farris, S.G.; Davis, M.L.; Rosenfield, D.; Kauffman, B.Y.; Baird, S.O.; Powers, M.B.; Otto, M.W.; Marcus, B.H.; Church, T.S.; Smits, J.A.J.; Zvolensky, M.J.

2016-01-01

There is little known about factors that contribute to the comorbidity of cigarette smoking and obesity. The current study sought to test whether exercise self-efficacy moderated the relation between anxiety sensitivity (fear of internal sensations) and BMI and exercise tolerance among cigarette

BDNF Val 66 Met and 5-HTTLPR genotype moderate the impact of early psychosocial adversity on plasma brain-derived neurotrophic factor and depressive symptoms: a prospective study.

Science.gov (United States)

Buchmann, Arlette F; Hellweg, Rainer; Rietschel, Marcella; Treutlein, Jens; Witt, Stephanie H; Zimmermann, Ulrich S; Schmidt, Martin H; Esser, Günter; Banaschewski, Tobias; Laucht, Manfred; Deuschle, Michael

2013-08-01

Recent studies have emphasized an important role for neurotrophins, such as brain-derived neurotrophic factor (BDNF), in regulating the plasticity of neural circuits involved in the pathophysiology of stress-related diseases. The aim of the present study was to examine the interplay of the BDNF Val⁶⁶Met and the serotonin transporter promoter (5-HTTLPR) polymorphisms in moderating the impact of early-life adversity on BDNF plasma concentration and depressive symptoms. Participants were taken from an epidemiological cohort study following the long-term outcome of early risk factors from birth into young adulthood. In 259 individuals (119 males, 140 females), genotyped for the BDNF Val⁶⁶Met and the 5-HTTLPR polymorphisms, plasma BDNF was assessed at the age of 19 years. In addition, participants completed the Beck Depression Inventory (BDI). Early adversity was determined according to a family adversity index assessed at 3 months of age. Results indicated that individuals homozygous for both the BDNF Val and the 5-HTTLPR L allele showed significantly reduced BDNF levels following exposure to high adversity. In contrast, BDNF levels appeared to be unaffected by early psychosocial adversity in carriers of the BDNF Met or the 5-HTTLPR S allele. While the former group appeared to be most susceptible to depressive symptoms, the impact of early adversity was less pronounced in the latter group. This is the first preliminary evidence indicating that early-life adverse experiences may have lasting sequelae for plasma BDNF levels in humans, highlighting that the susceptibility to this effect is moderated by BDNF Val⁶⁶Met and 5-HTTLPR genotype. Copyright © 2013. Published by Elsevier B.V.

Mudanças bioquímicas em genótipos de amendoim submetidos a déficit hídrico moderado Biochemical changes in peanut genotypes submitted to moderate water stress

Directory of Open Access Journals (Sweden)

Jacqueline Wanessa de Lima Pereira

2012-12-01

Full Text Available Cinco genótipos de amendoim de diferentes hábitos de crescimento foram submetidos a estresse hídrico moderado durante 7 dias em casa de vegetação. O plantio foi feito em vasos de 15 litros contendo solo e substrato (Plantmax®, otimizados para a cultura. O delineamento experimental adotado foi inteiramente casualizado, com esquema bi-fatorial 5 × 2 (5 genótipos × 2 tratamentos hídricos, com cinco repetições. As atividades enzimáticas da SOD, CAT, APX e GPX foram analisadas, além do acúmulo de carboidratos, amido e prolina. Em função do déficit hídrico submetido, verificou-se aumento nas atividades da SOD e da CAT em todos os genótipos, tanto nas folhas quanto na raiz, destacando-se as cv. 55 437 e BR 1 e a linhagem LBM Branco. O acúmulo de prolina e redução do teor de amido foram verificados em todos os genótipos, em resposta ao déficit hídrico, porém o teor de carboidratos foi elevado só nos materiais mais tolerantes. Em função das respostas obtidas, destacam-se como materiais mais tolerantes as cultivares 55 437 e BR 1, seguidas por LBM Branco. LBR Branco tem comportamento intermediário e LViPE 06 é o material mais sensível.Five peanut genotypes, with different growth habits were submitted to moderate water stress in a greenhouse for seven days. Seeds were planted in 15-litre pots containing soil and a substrate (Plantmax®, both optimized for the crop. The adopted experimental design was completely randomized, using a 5 x 2 bi-factorial scheme(5 genotypes × 2 water treatments with five replications. The enzymatic activities of SOD, CAT, APX and GPX were analyzed, as well as the carbohydrate, starch and proline. An increased activity was shown in SOD and CAT enzymes for all genotypes submitted to water stress, in both leaf and root, especially in the 55 437 and BR1 cultivars and also in LBM Branco line. Proline accumulation and reduced starch were verified in all stressed genotypes, but carbohydrate content was

Get even and feel good? Moderating effects of justice sensitivity and counterproductive work behavior on the relationship between illegitimate tasks and self-esteem.

Science.gov (United States)

Schulte-Braucks, Julia; Baethge, Anja; Dormann, Christian; Vahle-Hinz, Tim

2018-04-23

We proposed that effects of illegitimate tasks, which comprise unreasonable and unnecessary tasks, on self-esteem and counterproductive work behavior (CWB) are enhanced among employees who are highly sensitive to injustice. CWB was further proposed to be a moderating coping strategy, which restores justice and buffers the detrimental effects of illegitimate tasks on self-esteem. In this study, 241 employees participated in a diary study over five workdays and a follow-up questionnaire one week later. Daily effects were determined in multilevel analyses: Unreasonable tasks decreased self-esteem and increased CWB the same day, especially among employees high in trait justice sensitivity. Unnecessary tasks only related to more CWB the same day, regardless of one's justice sensitivity. Weekly effects were determined in cross-lagged panel analyses: Unreasonable and unnecessary tasks increased CWB, and justice sensitivity moderated the effect of unreasonable tasks on CWB and of unnecessary tasks on self-esteem. Moderating effects of CWB were split: In daily analyses, CWB buffered the negative effects of illegitimate tasks. In weekly analyses, CWB enhanced the negative effects of illegitimate tasks. Overall, illegitimate tasks rather affected CWB than self-esteem, with more consistent effects for unreasonable than for unnecessary tasks. Thus, we confirm illegitimate tasks as a relevant work stressor with issues of injustice being central to this concept and personality having an influence on what is perceived as (il)legitimate. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Salt and genotype impact on plant physiology and root proteome variations in tomato.

Science.gov (United States)

Manaa, Arafet; Ben Ahmed, Hela; Valot, Benoît; Bouchet, Jean-Paul; Aschi-Smiti, Samira; Causse, Mathilde; Faurobert, Mireille

2011-05-01

To evaluate the genotypic variation of salt stress response in tomato, physiological analyses and a proteomic approach have been conducted in parallel on four contrasting tomato genotypes. After a 14 d period of salt stress in hydroponic conditions, the genotypes exhibited different responses in terms of plant growth, particularly root growth, foliar accumulation of Na(+), and foliar K/Na ratio. As a whole, Levovil appeared to be the most tolerant genotype while Cervil was the most sensitive one. Roma and Supermarmande exhibited intermediary behaviours. Among the 1300 protein spots reproducibly detected by two-dimensional electrophoresis, 90 exhibited significant abundance variations between samples and were submitted to mass spectrometry for identification. A common set of proteins (nine spots), up- or down-regulated by salt-stress whatever the genotype, was detected. But the impact of the tomato genotype on the proteome variations was much higher than the salt effect: 33 spots that were not variable with salt stress varied with the genotype. The remaining number of variable spots (48) exhibited combined effects of the genotype and the salt factors, putatively linked to the degrees of genotype tolerance. The carbon metabolism and energy-related proteins were mainly up-regulated by salt stress and exhibited most-tolerant versus most-sensitive abundance variations. Unexpectedly, some antioxidant and defence proteins were also down-regulated, while some proteins putatively involved in osmoprotectant synthesis and cell wall reinforcement were up-regulated by salt stress mainly in tolerant genotypes. The results showed the effect of 14 d stress on the tomato root proteome and underlined significant genotype differences, suggesting the importance of making use of genetic variability.

Accurate genotyping across variant classes and lengths using variant graphs

DEFF Research Database (Denmark)

Sibbesen, Jonas Andreas; Maretty, Lasse; Jensen, Jacob Malte

2018-01-01

of read k-mers to a graph representation of the reference and variants to efficiently perform unbiased, probabilistic genotyping across the variation spectrum. We demonstrate that BayesTyper generally provides superior variant sensitivity and genotyping accuracy relative to existing methods when used...... collecting a set of candidate variants across discovery methods, individuals and databases, and then realigning the reads to the variants and reference simultaneously. However, this realignment problem has proved computationally difficult. Here, we present a new method (BayesTyper) that uses exact alignment...... to integrate variants across discovery approaches and individuals. Finally, we demonstrate that including a ‘variation-prior’ database containing already known variants significantly improves sensitivity....

Direct maximum parsimony phylogeny reconstruction from genotype data.

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

2007-12-05

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

Direct maximum parsimony phylogeny reconstruction from genotype data

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Ravi R

2007-12-01

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

SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays

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Stephen W. Erickson

2016-07-01

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

Temporal dynamic responses of roots in contrasting tomato genotypes to cadmium tolerance.

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Borges, Karina Lima Reis; Salvato, Fernanda; Alcântara, Berenice Kussumoto; Nalin, Rafael Storto; Piotto, Fernando Ângelo; Azevedo, Ricardo Antunes

2018-04-01

Despite numerous studies on cadmium (Cd) uptake and accumulation in crops, relatively little is available considering the temporal dynamic of Cd uptake and responses to stress focused on the root system. Here we highlighted the responses to Cd-induced stress in roots of two tomato genotypes contrasting in Cd-tolerance: the tolerant Pusa Ruby and the sensitive Calabash Rouge. Tomato genotypes growing in the presence of 35 μM CdCl 2 exhibited a similar trend of Cd accumulation in tissues, mainly in the root system and overall plants exhibited reduction in the dry matter weight. Both genotypes showed similar trends for malondialdehyde and hydrogen peroxide accumulation with increases when exposed to Cd, being this response more pronounced in the sensitive genotype. When the antioxidant machinery is concerned, in the presence of Cd the reduced glutathione content was decreased in roots while ascorbate peroxidase (APX), glutathione reductase (GR) and glutathione S-transferase (GST) activities were increased in the presence of Cd in the tolerant genotype. Altogether these results suggest APX, GR and GST as the main players of the antioxidant machinery against Cd-induced oxidative stress.

Moderate sensitivity and high specificity of emergency department administrative data for transient ischemic attacks.

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Yu, Amy Y X; Quan, Hude; McRae, Andrew; Wagner, Gabrielle O; Hill, Michael D; Coutts, Shelagh B

2017-09-18

Validation of administrative data case definitions is key for accurate passive surveillance of disease. Transient ischemic attack (TIA) is a condition primarily managed in the emergency department. However, prior validation studies have focused on data after inpatient hospitalization. We aimed to determine the validity of the Canadian 10th International Classification of Diseases (ICD-10-CA) codes for TIA in the national ambulatory administrative database. We performed a diagnostic accuracy study of four ICD-10-CA case definition algorithms for TIA in the emergency department setting. The study population was obtained from two ongoing studies on the diagnosis of TIA and minor stroke versus stroke mimic using serum biomarkers and neuroimaging. Two reference standards were used 1) the emergency department clinical diagnosis determined by chart abstractors and 2) the 90-day final diagnosis, both obtained by stroke neurologists, to calculate the sensitivity, specificity, positive and negative predictive values (PPV and NPV) of the ICD-10-CA algorithms for TIA. Among 417 patients, emergency department adjudication showed 163 (39.1%) TIA, 155 (37.2%) ischemic strokes, and 99 (23.7%) stroke mimics. The most restrictive algorithm, defined as a TIA code in the main position had the lowest sensitivity (36.8%), but highest specificity (92.5%) and PPV (76.0%). The most inclusive algorithm, defined as a TIA code in any position with and without query prefix had the highest sensitivity (63.8%), but lowest specificity (81.5%) and PPV (68.9%). Sensitivity, specificity, PPV, and NPV were overall lower when using the 90-day diagnosis as reference standard. Emergency department administrative data reflect diagnosis of suspected TIA with high specificity, but underestimate the burden of disease. Future studies are necessary to understand the reasons for the low to moderate sensitivity.

Bound volatile precursors in genotypes in the pedigree of 'Marion' blackberry (Rubus sp.).

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Du, Xiaofen; Finn, Chad E; Qian, Michael C

2010-03-24

Glycosidically bound volatiles and precursors in genotypes representing the pedigree for 'Marion' blackberry were investigated over two growing seasons. The volatile precursors were isolated using a C18 solid-phase extraction column. After enzymatic hydrolysis, the released volatiles were analyzed using stir bar sorptive extraction gas chromatography-mass spectrometry (GC-MS) and direct microvial insert thermal desorption GC-MS. The most abundant volatile precursors in the genotypes were alcohols, followed by shikimic acid derivatives. High amounts of furanone glycosides were also detected, while norisoprenoids only existed in a small amount in blackberries. The volatile precursor composition in the genotypes in the 'Marion' pedigree was very similar to their free volatile distribution. 'Logan' and 'Olallie' predominantly had bound norisoprenoids. Wild 'Himalaya' predominated with terpene alcohol and furaneol glycosides, whereas 'Santiam' and 'Chehalem' contained a high level of terpene alcohol glycosides. A similar inheritance pattern was also observed for some volatile precursors in the genotypes in the 'Marion' pedigree. A high content of linalool, hydroxylinalool, and alpha-ionol glycosides in 'Olallie' and a low content in 'Chehalem' resulted in a moderate level in their offspring 'Marion', while a low content of (E)-linalool oxide precursor in 'Olallie' and a high content in 'Chehalem' also resulted in a moderate level in 'Marion'. However, the concentration of furaneol glycosides in 'Marion' exceeded that of its two parents.

[The HVR genotypes and their relationship with the resistance of methicillin-resistant staphylococci].

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Liao, F; Fan, X; Lü, X; Feng, P

2001-06-01

To investigate the HVR-PCR genotype of methicillin-resistant Staphylococci in local hospitals and compare it with the antibiograms, with aview to selecting effective antibacterial agents, moreover, to discuss preliminarily its role in molecular epidemiology. The minimal inhibitory concentrations(MICs) of 86 MRSA, 10 MRSE(Mc'S. epidemidis), 5 MSSE(Mc'S. epidemidis), 8 MRSH(Mc'S. haemolyticus) and 5 MSSH(Mc'S. haemolyticus) clinical isolates collected from 4 local hospitals were tested by serial two-fold agar dilution method; their DNA were extracted by moved basic lytic method, whose polymerase chain reaction(PCR) products amplified, based on the size of mec-associated hypervariable region(HVR) were analyzed by PAG vertical and agarose gel electrophoresis. MRSA, MRSE and MRSH were grouped into 4, 3 and 2 HVR genotypes respectively according to the size of the PCR products. The PCR products amplified from 9 of 10 MRSE isolates were the same as the products amplified from MRSA isolates. MRSA strains in this study were mainly HVR genotypes A and D, which accounted for 52.32% and 39.53%; Genotypes B and C were the most multi-drug resistant, but genotype D was multi-sensitive. The I genotype of MRSE was multi-drug resistant, but its genotype III was multi-drug sensitive. The genotype a of MRSH was more resistant than genotype b. These results suggest that HVR-PCR genotype method is an easy and fast method for epidemiological investigation of nosocomial infections caused by MRSA, and it is helpful for clinical selection of antibacterial agents. This method can compare the mec determinants of MRSA and Mc'CNSt isolates and hence to search for the origin of the mec determinant.

Genotyping panel for assessing response to cancer chemotherapy

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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.

A influência do genótipo da ECA sobre a aptidão cardiovascular de jovens do sexo masculino moderadamente ativos The influence of ACE genotype on cardiovascular fitness of moderately active young men

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Jeeser Alves Almeida

2012-04-01

Full Text Available FUNDAMENTO: O gene da enzima conversora de angiotensina (gene ECA tem sido amplamente estudado em relação a fenótipos de aptidão cardiorrespiratória, contudo a associação do genótipo da ECA com corridas de meia-distância tem sido pouco investigada. OBJETIVO: O presente estudo investigou a possível influência da enzima conversora de angiotensina (ECA (I/D sobre a aptidão cardiovascular e o desempenho em corridas de meia-distância por parte de brasileiros jovens do sexo masculino. A validade da previsão de VO2max em relação ao genótipo da ECA também foi analisada. MÉTODOS: Um grupo homogêneo de homens jovens moderadamente ativos foi avaliado em um teste de corrida (V1600 m; m.min-1 e em um teste adicional em esteira ergométrica para a determinação de VO2max. Posteriormente, o [(0,177*V1600m + 8.101] VO2max real e previsto foi comparado com os genótipos da ECA. RESULTADOS: O VO2max e V1600m registrados para os genótipos DD, ID e II foram 45,6 (1,8; 51,9 (0,8 e 54,4 (1,0 mL.kg-1.min-1 e 211,2 (8,3; 249,1 (4,3 e 258,6 (5,4 m.min-1, respectivamente e foram significativamente mais baixos para os genótipos DD (p BACKGROUND: The angiotensin I-converting enzyme gene (ACE gene has been broadly studied as for cardiorespiratory fitness phenotypes, but the association of the ACE genotype to middle-distance running has been poorly investigated. OBJECTIVE: This study investigated the possible influence of Angiotensin-Converting Enzyme (ACE genotype (I/D on cardiovascular fitness and middle-distance running performance of Brazilian young males. The validity of VO2max to predict the ACE genotype was also analyzed. METHODS: A homogeneous group of moderately active young males were evaluated in a 1,600 m running track test (V1600m; m.min-1 and in an incremental treadmill test for VO2max determination. Subsequently, the actual and the predicted [(0.177*V1600m + 8.101] VO2max were compared to ACE genotypes. RESULTS: The VO2max and V1600m

Junk food advertising moderates the indirect effect of reward sensitivity and food consumption via the urge to eat.

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Kidd, Chloe; Loxton, Natalie J

2018-05-01

The current study aimed to identify how underlying individual differences increases vulnerability to television food advertising. In particular, this study examined how reward sensitivity, a biologically-based predisposition to approach rewards (such as appetitive foods) in the environment, influenced participants' vulnerability to television food advertising and subsequent food consumption. Ninety-eight participants were randomly assigned to a cue condition (food cues versus non-food cues) and then viewed a 30 min documentary interrupted by advertising featuring a mix of food and neutral advertising (food cue condition) or only neutral advertising (non-food cue condition). Participants' reward sensitivity, approach motivation measured as urge to eat, and food consumption were recorded. Moderated mediation regression analyses revealed the positive association between reward sensitivity and food consumption was mediated by an increase in urge to eat, but only when participants were exposed to food advertising. These findings suggest heightened reward sensitivity, exposure to appetitive food cues, and approach motivation are key interacting mechanisms that may lead to maladaptive eating behaviours. Copyright © 2018 Elsevier Inc. All rights reserved.

[Methicillin-sensitive Staphylococcus aureus isolates related to USA300 clone: Origin of community-genotype MRSA in Colombia?].

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Escobar-Pérez, Javier Antonio; Castro, Betsy Esperanza; Márquez-Ortiz, Ricaurte Alejandro; Gaines, Sebastián; Chavarro, Bibiana; Moreno, Jaime; Leal, Aura Lucía; Vanegas, Natasha

2014-04-01

USA300 is a genetic lineage found both in methicillin-resistant (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA) isolates. In Colombia, hospital and community MRSA infections are caused by a USA300-related community genotype MRSA (CG-MRSA) clone. The genetic origin of this clone is unknown yet. To identify and characterize methicillin-resistant (MRSA) and methicillin-sensitive S. aureus (MSSA) isolates in order to improve the information about the origin of the CG-MRSA isolates in Colombia. USA300-related MSSA isolates were detected and characterized from a study of 184 S. aureus isolates (90 MRSA and 94 MSSA) recovered from infections. The genetic relatedness of the isolates was established by means of pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and protein A gene typification ( spa typing). Among 184 isolates, 27 (14.7%) showed molecular characteristics and genetic relationship with the USA300 clone, of which 18 were MRSA and nine were MSSA. All USA300-related MRSA harbored Staphylococcal cassette chromosome mec (SCC mec ) IVc (3.1.2). In the MSSA isolates, SCC mec remnants or att B duplicate sites were not detected. In Colombia, the CG-MRSA isolates probably originated in the dissemination of an USA300-related MSSA clone which later acquired SCC mec IVc.

Why Have Tobacco Control Policies Stalled? Using Genetic Moderation to Examine Policy Impacts

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Fletcher, Jason M.

2012-01-01

Background Research has shown that tobacco control policies have helped produce the dramatic decline in use over the decades following the 1964 surgeon general’s report. However, prevalence rates have stagnated during the past two decades in the US, even with large tobacco taxes and expansions of clean air laws. The observed differences in tobacco control policy effectiveness and why policies do not help all smokers are largely unexplained. Objective The aim of this study was to determine the importance of genetics in explaining response to tobacco taxation policy by testing the potential of gene-policy interaction in determining adult tobacco use. Methods A moderated regression analysis framework was used to test interactive effects between genotype and tobacco policy in predicting tobacco use. Cross sectional data of US adults from the National Health and Nutrition Examination Survey (NHANES) linked with genotype and geocodes were used to identify tobacco use phenotypes, state-level taxation rates, and variation in the nicotinic acetylcholine receptor (CHRNA6) genotype. Tobacco use phenotypes included current use, number of cigarettes smoked per day, and blood serum cotinine measurements. Results Variation in the nicotinic acetylcholine receptor was found to moderate the influence of tobacco taxation on multiple measures of tobacco use. Individuals with the protective G/G polymorphism (51% of the sample) responded to taxation while others had no response. The estimated differences in response by genotype were C/C genotype: b = −0.016 se  = 0.018; G/C genotype: b = 0.014 se  = 0.017; G/G genotype: b = −0.071 se 0.029. Conclusions This study provides novel evidence of “gene-policy” interaction and suggests a genetic mechanism for the large differences in response to tobacco policies. The inability for these policies to reduce use for individuals with specific genotypes suggests alternative methods may be needed to further reduce use

Comparison of Four Human Papillomavirus Genotyping Methods: Next-generation Sequencing, INNO-LiPA, Electrochemical DNA Chip, and Nested-PCR.

Science.gov (United States)

Nilyanimit, Pornjarim; Chansaenroj, Jira; Poomipak, Witthaya; Praianantathavorn, Kesmanee; Payungporn, Sunchai; Poovorawan, Yong

2018-03-01

Human papillomavirus (HPV) infection causes cervical cancer, thus necessitating early detection by screening. Rapid and accurate HPV genotyping is crucial both for the assessment of patients with HPV infection and for surveillance studies. Fifty-eight cervicovaginal samples were tested for HPV genotypes using four methods in parallel: nested-PCR followed by conventional sequencing, INNO-LiPA, electrochemical DNA chip, and next-generation sequencing (NGS). Seven HPV genotypes (16, 18, 31, 33, 45, 56, and 58) were identified by all four methods. Nineteen HPV genotypes were detected by NGS, but not by nested-PCR, INNO-LiPA, or electrochemical DNA chip. Although NGS is relatively expensive and complex, it may serve as a sensitive HPV genotyping method. Because of its highly sensitive detection of multiple HPV genotypes, NGS may serve as an alternative for diagnostic HPV genotyping in certain situations. © The Korean Society for Laboratory Medicine

Characterization of some bread wheat genotypes using molecular markers for drought tolerance.

Science.gov (United States)

Ateş Sönmezoğlu, Özlem; Terzi, Begüm

2018-02-01

Because of its wide geographical adaptation and importance in human nutrition, wheat is one of the most important crops in the world. However, wheat yield has reduced due to drought stress posing threat to sustainability and world food security in agricultural production. The first stage of drought tolerant variety breeding occurs on the molecular and biochemical characterization and classification of wheat genotypes. The aim of the present study is characterization of widely grown bread wheat cultivars and breeding lines for drought tolerance so as to be adapted to different regions in Turkey. The genotypes were screened with molecular markers for the presence of QTLs mapped to different chromosomes. Results of the molecular studies identified and detected 15 polymorphic SSR markers which gave the clearest PCR bands among the control genotypes. At the end of the research, bread wheat genotypes which were classified for tolerance or sensitivity to drought and the genetic similarity within control varieties were determined by molecular markers. According to SSR based dendrogram, two main groups were obtained for drought tolerance. At end of the molecular screening with SSR primers, genetic similarity coefficients were obtained that ranged from 0.14 to 0.71. The ones numbered 8 and 11 were the closest genotypes to drought tolerant cultivar Gerek 79 and the furthest genotypes from this cultivar were number 16 and to drought sensitive cultivar Sultan 95. The genotypes as drought tolerance due to their SSR markers scores are expected to provide useful information for drought related molecular breeding studies.

Rapid and sensitive method to identify Mycobacterium avium subsp. paratuberculosis in cow's milk by DNA methylase genotyping.

Science.gov (United States)

Mundo, Silvia Leonor; Gilardoni, Liliana Rosa; Hoffman, Federico José; Lopez, Osvaldo Jorge

2013-03-01

Paratuberculosis is an infectious, chronic, and incurable disease that affects ruminants, caused by Mycobacterium avium subsp. paratuberculosis. This bacterium is shed primarily through feces of infected cows but can be also excreted in colostrum and milk and might survive pasteurization. Since an association of genomic sequences of M. avium subsp. paratuberculosis in patients with Crohn's disease has been described; it is of interest to rapidly detect M. avium subsp. paratuberculosis in milk for human consumption. IS900 insertion is used as a target for PCR amplification to identify the presence of M. avium subsp. paratuberculosis in biological samples. Two target sequences were selected: IS1 (155 bp) and IS2 (94 bp). These fragments have a 100% identity among all M. avium subsp. paratuberculosis strains sequenced. M. avium subsp. paratuberculosis was specifically concentrated from milk samples by immunomagnetic separation prior to performing PCR. The amplicons were characterized using DNA methylase Genotyping, i.e., the amplicons were methylated with 6-methyl-adenine and digested with restriction enzymes to confirm their identity. The methylated amplicons from 100 CFU of M. avium subsp. paratuberculosis can be visualized in a Western blot format using an anti-6-methyl-adenine monoclonal antibody. The use of DNA methyltransferase genotyping coupled to a scintillation proximity assay allows for the detection of up to 10 CFU of M. avium subsp. paratuberculosis per ml of milk. This test is rapid and sensitive and allows for automation and thus multiple samples can be tested at the same time.

Expression of Hepatitis B virus surface antigen (HBsAg from genotypes A, D and F and influence of amino acid variations related or not to genotypes on HBsAg detection

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Natalia M. Araujo

Full Text Available The impact of hepatitis B virus (HBV genotypes on the sensitivity of surface antigen (HBsAg detection assays has been poorly investigated. Here, plasmids carrying consensus or variant coding sequences for HBV surface proteins from genotypes A, D and F, were constructed. HBsAg levels were evaluated in medium and extracts of transfected CHO cells by a commercial polyclonal-based assay. We show that HBsAg detection values of consensus forms from genotypes D and F were, respectively, 37% and 30% lower than those obtained by genotype A. However, the presence of two single variations, T143M in genotype A, and T125M in genotype D, produced a decrease of 44% and an increase of 34%, respectively, on HBsAg mean values in comparison with their consensus forms. In conclusion, HBsAg detection levels varied among HBV genotypes. However, unique amino acid substitutions not linked to genotypes, such as T125M and T143M described here, should have more implications in HBV immunological diagnostics than the set of variations characteristic of each HBV genotype.

Screening for Terminal Drought Tolerance in Iranian and Exotic Safflower Genotypes Using Drought Tolerance and Susceptibility Indices

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R. Maleki Nejad

2015-06-01

Full Text Available This research was conducted to evaluate drought tolerance of safflower genotypes (Carthamus tinctorius L. at the research farm of Isfahan University of Technology, Isfahan, Iran during growing season of 2012. One hundred genotypes including 81 foreign genotypes along with 19 Iranian genotypes were evaluated under normal and moisture stress conditions according to a simple lattice design with two replications. Drought tolerance and sensitivity indices including mean productivity (MP, geometric mean productivity (GMP, stress tolerance index (STI, tolerance (TOL and stress susceptibility index (SSI were studied. Results of this study indicated that genotypes were significantly different for grain yield in both moisture conditions. Among all indices, MP, GMP and STI were identified as the best indices that can be used to determine tolerant genotypes. Based on MP, GMP and STI and also principal component analysis PI 369847 (Tajikistan, CART 56 (USA, PI 657820 (Jordan, PI 305527 (Soudan were determined as the most tolerant genotypes and PI 537652 (Mexico, CART 131 (Prague, PI 470942 (Bangladesh, PI 209286 (Romania and CART 32 (German as the most sensitive ones. Results also indicated that the biplot of principal component analysis is a powerful technique to discriminate genotypes based on the measured indices. The superior safflower genotypes can be used in future breeding programs.

Alternation of cowpea genotypes affects the biology of Callosobruchus maculatus (fabr. (Coleoptera: Bruchidae

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Lima Marcileyne Pessôa Leite de

2004-01-01

Full Text Available Callosobruchus maculatus (Fabr. is an important pest in stored cowpea, Vigna unguiculata (L. Walp., with ample distribution in tropical and subtropical regions. The effect of alternation of cowpea genotypes, susceptible (S and resistant (R, on the biology of (C. maculatus was studied after four generations. A no-choice test was carried out in a completely randomized design, factorial scheme, with five treatments, four host combinations (RR, RS, SR and SS and five replications. Each replication consisted of 30 grains of each genotype infested by two insect couples. The number of eggs per female was not different within or between combinations, evidencing that the genotypes and their alternation did not affect C. maculatus fecundity. Egg viability, however, varied between genotypes and between combinations. In combination RR, the longest duration of the immature stage was verified for genotype IT89KD-245; in addition, all genotypes presented the smallest survival for the same stage, resulting in a higher mortality of the pest. The resistance index categorized combination RR as moderately resistant for genotypes IT89KD-245, BR14-Mulato and BR17-Gurguéia, and as susceptible (S only for IT89KD-260, demonstrating that these combinations were not very adequate for the development of C. maculatus, a fact that was confirmed by the better performance of the pest on the genotype from combination SS, and because of a reduction in its performance when it returned to resistant genotypes.

Effect of Salt Stress on Morphological Traits of Lettuce Genotypes (Lactuca Sativa L.

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maryam zare

2017-02-01

Romaine lettuce long green Teresa genotype, respectivly. Increasing salinity led to significant reduction (p≤0.01 in the plant length lettuce in all genotypes. Root and plant fresh weight lettuce genotypes were significantly (p≤0.01 influenced by different levels of salinity. The greatest amount in root and plant fresh weight lettuce genotypes were obtained in the control treatment and the lowest amount at the level of 4 dS/m. Root and plant dry weight lettuce genotypes were significantly (p≤0.01 influenced by the salinity. Root and plant dry weight decreased with increasing salinity. So that the greatest amount of root and plant dry weight lettuce genotypes were obtained in control treatment and the lowest amount at the level of 4 dS/m.. The results showed that root and plant length ,root fresh and dry weight, plant fresh and dry weight and leaf length and width reduced with increasing salinity. The clustering pattern the genotypes were grouped into 3 clusters based on their charachters at 4 dS/m salinity. The first cluster were placed in salt tolerant groups, while the other genotypes were clustered into moderately tolerant cluster. Romaine lettuce long green Teresa genotype was placed in salt-tolerant group and Lettuce Everest, Lettuce May Queen, Curly endive hair angel, Cabbage Milan Aubervilliers and Romaine lettuce long blonde Galaica were placed in salt-sensitive group.

Effect of Salt Stress on Morphological Traits of Lettuce Genotypes (Lactuca Sativa L.

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maryam zare

2017-09-01

Romaine lettuce long green Teresa genotype, respectivly. Increasing salinity led to significant reduction (p≤0.01 in the plant length lettuce in all genotypes. Root and plant fresh weight lettuce genotypes were significantly (p≤0.01 influenced by different levels of salinity. The greatest amount in root and plant fresh weight lettuce genotypes were obtained in the control treatment and the lowest amount at the level of 4 dS/m. Root and plant dry weight lettuce genotypes were significantly (p≤0.01 influenced by the salinity. Root and plant dry weight decreased with increasing salinity. So that the greatest amount of root and plant dry weight lettuce genotypes were obtained in control treatment and the lowest amount at the level of 4 dS/m.. The results showed that root and plant length ,root fresh and dry weight, plant fresh and dry weight and leaf length and width reduced with increasing salinity. The clustering pattern the genotypes were grouped into 3 clusters based on their charachters at 4 dS/m salinity. The first cluster were placed in salt tolerant groups, while the other genotypes were clustered into moderately tolerant cluster. Romaine lettuce long green Teresa genotype was placed in salt-tolerant group and Lettuce Everest, Lettuce May Queen, Curly endive hair angel, Cabbage Milan Aubervilliers and Romaine lettuce long blonde Galaica were placed in salt-sensitive group.

High sensitivity C reactive protein as a prognostic marker in patients with mild to moderate aortic valve stenosis during lipid-lowering treatment

DEFF Research Database (Denmark)

Blyme, Adam; Asferg, Camilla; Nielsen, Olav W

2015-01-01

AIMS: To assess the prognostic importance of high-sensitive C reactive protein (hsCRP) in patients with mild to moderate aortic valve stenosis during placebo or simvastatin/ezetimibe treatment in Simvastatin and Ezetimibe in Aortic Stenosis (SEAS). METHODS AND RESULTS: In 1620 SEAS patients, we m...

Evaluation of Soybean and Cowpea Genotypes for Phosphorus Use Efficiency

Energy Technology Data Exchange (ETDEWEB)

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

2013-11-15

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

Genotypic differences in architectural and physiological responses to water restriction in rose bush

Science.gov (United States)

Li-Marchetti, Camille; Le Bras, Camille; Relion, Daniel; Citerne, Sylvie; Huché-Thélier, Lydie; Sakr, Soulaiman; Morel, Philippe; Crespel, Laurent

2015-01-01

The shape and, therefore, the architecture of the plant are dependent on genetic and environmental factors such as water supply. The architecture determines the visual quality, a key criterion underlying the decision to purchase an ornamental potted plant. The aim of this study was to analyze genotypic responses of eight rose bush cultivars to alternation of water restriction and re-watering periods, with soil water potential of -20 and -10 kPa respectively. Responses were evaluated at the architectural level through 3D digitalization using six architectural variables and at the physiological level by measuring stomatal conductance, water content, hormones [abscisic acid (ABA), auxin, cytokinins, jasmonic acid, and salicylic acid (SA)], sugars (sucrose, fructose, and glucose), and proline. Highly significant genotype and watering effects were revealed for all the architectural variables measured, as well as genotype × watering interaction, with three distinct genotypic architectural responses to water restriction – weak, moderate and strong – represented by Hw336, ‘Baipome’ and ‘The Fairy,’ respectively. The physiological analysis explained, at least in part, the more moderate architectural response of ‘Baipome’ compared to ‘The Fairy,’ but not that of Hw336 which is an interspecific hybrid. Such physiological responses in ‘Baipome’ could be related to: (i) the maintenance of the stimulation of budbreak and photosynthetic activity during water restriction periods due to a higher concentration in conjugated cytokinins (cCK) and to a lower concentration in SA; (ii) a better resumption of budbreak during the re-watering periods due to a lower concentration in ABA during this period. When associated with the six architectural descriptors, cCK, SA and ABA, which explained the genotypic differences in this study, could be used as selection criteria for breeding programs aimed at improving plant shape and tolerance to water restriction. PMID

Sensitivity to psychosocial chronic stressors and adolescents' externalizing problems: Combined moderator effects of resting heart rate and parental psychiatric history.

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Zandstra, Anna Roos E; Ormel, Johan; Dietrich, Andrea; van den Heuvel, Edwin R; Hoekstra, Pieter J; Hartman, Catharina A

2018-04-01

From the literature it is not clear whether low resting heart rate (HR) reflects low or high sensitivity to the detrimental effects of adverse environments on externalizing problems. We studied parental psychiatric history (PH), reflecting general vulnerability, as possible moderator explaining these inconsistencies. Using Linear Mixed Models, we analyzed data from 1914 subjects, obtained in three measurement waves (mean age 11, 13.5, and 16 years) from the TRacking Adolescents' Individual Lives Survey population-based cohort and the parallel clinic-referred cohort. As hypothesized, more chronic stressors predicted more externalizing problems in vulnerable individuals with high resting HR but not in those with low resting HR, suggesting high vs. low sensitivity, respectively, to adverse environmental influences. Low sensitivity to adverse environmental influences in vulnerable individuals exposed to high stressor levels was additionally confirmed by high heart rate variability (Root Mean Squared Successive Difference; RMSSD). In adolescents with low vulnerability, in contrast, the association between chronic stressors and externalizing problems did not substantially differ by resting HR and RMSSD. Future research may demonstrate whether our findings extend to other adverse, or beneficial, influences. Notwithstanding their theoretical interest, the effects were small, only pertained to parent-reported externalizing problems, refer to a small subset of respondents in our sample, and are in need of replication. We conclude that HR and RMSSD are unlikely to be strong moderators of the association between stressors and externalizing problems. Copyright © 2018 Elsevier B.V. All rights reserved.

Parenting and adolescent antisocial behavior and depression: evidence of genotype x parenting environment interaction.

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Feinberg, Mark E; Button, Tanya M M; Neiderhiser, Jenae M; Reiss, David; Hetherington, E Mavis

2007-04-01

Little is known about the interplay of genotypes and malleable risk factors in influencing adolescent psychiatric symptoms and disorders. Information on these processes is crucial in designing programs for the prevention of psychiatric disorders. To assess whether latent genetic factors and measured parent-child relationships interact (G x E) in predicting adolescent antisocial behavior and depression. We characterized risk of antisocial behavior and depression in adolescents by means of a genetically informed design. We used in-home questionnaire and observational measures of adolescent outcomes and environmental moderators (parenting), and a latent variable behavior genetic analytic model. A nationally distributed sample recruited from random-digit dialing and national market panels. A total of 720 families with at least 2 children, 9 through 18 years old, stratified by genetic relatedness (monozygotic and dizygotic twins, full biological siblings in nondivorced and stepfamilies, and half-siblings and biologically unrelated siblings in stepfamilies). Antisocial behavior and depressive symptoms. There was an interaction of genotype and both parental negativity and low warmth predicting overall antisocial behavior, as well as aggressive and nonaggressive forms of antisocial behavior, but not depression. Genetic influence was greater for adolescent antisocial behavior when parenting was more negative or less warm. Genotype-environment correlation was partialled out in the analysis and thus did not account for the results. This study demonstrates, on the basis of careful measurement and appropriate analytic methods, that a continuous measure of parenting in the normative range moderates the influence of genotype on antisocial behavior.

Evaluation of rice genotypes under salt stress at the seedling and reproductive stages using phenotypic and molecular markers

International Nuclear Information System (INIS)

Rubel, M.H.; Hassan, L.

2014-01-01

Salinity screening for 27 rice genotypes was performed at the seedling and reproductive stages respectively, in the hydroponic system and in sustained water bath. Three selected SSR markers were used to determine salinity tolerance in rice genotypes. Phenotyping of the germplasm was done at EC 12dS/m and 6dS/m at seedling and reproductive stages, respectively. Based on modified standard evaluation score for visual salt injury at seedling stage, eight genotypes were salt tolerant, four were moderately tolerant and the rest fifteen were susceptible. At the reproductive stage, six genotypes were tolerant to EC 6dS/m whereas eleven of them were susceptible. SSR based marker identified seven genotypes as tolerant but ten of them were susceptible for all three markers compared to two checks. Six genotypes were tolerant in both phenotypic and SSR screening. The indentified salt tolerant genotypes can be potential germplasm sources for future breeding program. (author)

Who does Red Bull give wings to? Sensation seeking moderates sensitivity to subliminal advertisement.

Science.gov (United States)

Bustin, Gaëlle M; Jones, Daniel N; Hansenne, Michel; Quoidbach, Jordi

2015-01-01

This study assessed whether subliminal priming of a brand name of a drink can affect people's choices for the primed brand, and whether this effect is moderated by personality traits. Participants with different levels of sensation seeking were presented subliminally with the words Red Bull or Lde Ublr. Results revealed that being exposed to Red Bull lead on average to small increases in participants' preferences for the primed brand. However, this effect was twice as strong for participants high in sensation seeking and did not occur for participants low in sensation seeking. Going beyond previous research showing that situational factors (e.g., thirst, fatigue…) can increase people's sensitivity to subliminal advertisement, our results suggest that some dispositional factors could have the same potentiating effect. These findings highlight the necessity of taking personality into account in non-conscious persuasion research.

Sensitivity of the ViroSeq HIV-1 Genotyping System for Detection of the K103N Resistance Mutation in HIV-1 Subtypes A, C, and D

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Church, Jessica D.; Jones, Dana; Flys, Tamara; Hoover, Donald; Marlowe, Natalia; Chen, Shu; Shi, Chanjuan; Eshleman, James R.; Guay, Laura A.; Jackson, J. Brooks; Kumwenda, Newton; Taha, Taha E.; Eshleman, Susan H.

2006-01-01

The US Food and Drug Administration-cleared ViroSeq HIV-1 Genotyping System (ViroSeq) and other population sequencing-based human immunodeficiency virus type 1 (HIV-1) genotyping methods detect antiretroviral drug resistance mutations present in the major viral population of a test sample. These assays also detect some mutations in viral variants that are present as mixtures. We compared detection of the K103N nevirapine resistance mutation using ViroSeq and a sensitive, quantitative point mutation assay, LigAmp. The LigAmp assay measured the percentage of K103N-containing variants in the viral population (percentage of K103N). We analyzed 305 samples with HIV-1 subtypes A, C, and D collected from African women after nevirapine administration. ViroSeq detected K103N in 100% of samples with >20% K103N, 77.8% of samples with 10 to 20% K103N, 71.4% of samples with 5 to 10% K103N, and 16.9% of samples with 1 to 5% K103N. The sensitivity of ViroSeq for detection of K103N was similar for subtypes A, C, and D. These data indicate that the ViroSeq system reliably detects the K103N mutation at levels above 20% and frequently detects the mutation at lower levels. Further studies are needed to compare the sensitivity of different assays for detection of HIV-1 drug resistance mutations and to determine the clinical relevance of HIV-1 minority variants. PMID:16931582

Precise genotyping and recombination detection of Enterovirus

Science.gov (United States)

2015-01-01

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

Comparison of inhibition of N2 fixation and ureide accumulation under water deficit in four common bean genotypes of contrasting drought tolerance.

Science.gov (United States)

Coleto, I; Pineda, M; Rodiño, A P; De Ron, A M; Alamillo, J M

2014-05-01

Drought is the principal constraint on world production of legume crops. There is considerable variability among genotypes in sensitivity of nitrogen fixation to drought, which has been related to accumulation of ureides in soybean. The aim of this study was to search for genotypic differences in drought sensitivity and ureide accumulation in common bean (Phaseolus vulgaris) germplasm that may be useful in the improvement of tolerance to water deficit in common bean. Changes in response to water deficit of nitrogen fixation rates, ureide content and the expression and activity of key enzymes for ureide metabolism were measured in four P. vulgaris genotypes differing in drought tolerance. A variable degree of drought-induced nitrogen fixation inhibition was found among the bean genotypes. In addition to inhibition of nitrogen fixation, there was accumulation of ureides in stems and leaves of sensitive and tolerant genotypes, although this was higher in the leaves of the most sensitive ones. In contrast, there was no accumulation of ureides in the nodules or roots of stressed plants. In addition, the level of ureides in the most sensitive genotype increased after inhibition of nitrogen fixation, suggesting that ureides originate in vegetative tissues as a response to water stress, probably mediated by the induction of allantoinase. Variability of drought-induced inhibition of nitrogen fixation among the P. vulgaris genotypes was accompanied by subsequent accumulation of ureides in stems and leaves, but not in nodules. The results indicate that shoot ureide accumulation after prolonged exposure to drought could not be the cause of inhibition of nitrogen fixation, as has been suggested in soybean. Instead, ureides seem to be produced as part of a general response to stress, and therefore higher accumulation might correspond to higher sensitivity to the stressful conditions.

Male Gametophytic Screening of Citrus Genotypes for Salt Stress Tolerance

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A. Barandan

2016-07-01

Full Text Available Citrus species are classified as a sensitive group of trees to salt stress, but the levels of their sensitivity or tolerance to salt are different among cultivars. In order to evaluate the effects of salinity stress on pollen germination of some citrus cultivars, an experiment was performed in factorial, based on completely randomized design in three replications with Cleopatra mandarin (Citrus reshni and Poncirus trifoliata as tolerant and sensitive controls along with 13 genotypes. Pollen grains of these genotypes were cultured in media containing different levels of sodium chloride (0, 0.87, 1.6, 2.4, 3.1 dS/m along with 15% sucrose, 0.7% agar and 100 mg/L boric acid. In order to understand the biochemical responses of pollen grains to salt stress, they were cultured in liquid media with three levels of salinity (i.e. 0, 0.87 and 1.6 dS/m and then the amounts of total protein and enzyme activities of superoxide dismutase (SOD and ascorbate peroxidase (APX were evaluated. Significant differences of pollen germination (P ≤ 0.01 were observed in different salinity levels, but there were no significant differences in pollen tube growth. Pollen germination in Cleopatra was greater in comparison to Poncirus trifoliate, indicating that Cleopatra is a tolerant cultivar. The amounts of total protein and enzyme activities of SOD and APX were influenced by genotypes, salinity levels and their interactions (P ≤ 0.01. Considering the fastness and accuracy of this type of experiment, the evaluation of citrus pollen responses may, potentially, be hired as an initial screening criteria for detecting salt-sensitive varieties from the tolerant citrus ones.

Gel versus capillary electrophoresis genotyping for categorizing treatment outcomes in two anti-malarial trials in Uganda

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Hubbard Alan E

2010-01-01

Full Text Available Abstract Background Molecular genotyping is performed in anti-malarial trials to determine whether recurrent parasitaemia after therapy represents a recrudescence (treatment failure or new infection. The use of capillary instead of agarose gel electrophoresis for genotyping offers technical advantages, but it is unclear whether capillary electrophoresis will result in improved classification of anti-malarial treatment outcomes. Methods Samples were genotyped using both gel and capillary electrophoresis from randomized trials of artemether-lumefantrine (AL vs. dihydroartemisinin-piperaquine (DP performed in two areas of Uganda: Kanungu, where transmission is moderate, and Apac, where transmission is very high. Both gel and capillary methods evaluated polymorphic regions of the merozoite surface protein 1 and 2 and glutamine rich protein genes. Results Capillary electrophoresis detected more alleles and provided higher discriminatory power than agarose gel electrophoresis at both study sites. There was only moderate agreement between classification of outcomes with the two methods in Kanungu (kappa = 0.66 and poor agreement in Apac (kappa = 0.24. Overall efficacy results were similar when using gel vs. capillary methods in Kanungu (42-day risk of treatment failure for AL: 6.9% vs. 5.5%, p = 0.4; DP 2.4% vs. 2.9%, p = 0.5. However, the measured risk of recrudescence was significantly higher when using gel vs. capillary electrophoresis in Apac (risk of treatment failure for AL: 17.0% vs. 10.7%, p = 0.02; DP: 8.5% vs. 3.4%, p = 0.03. Risk differences between AL and DP were not significantly different whether gel or capillary methods were used. Conclusions Genotyping with gel electrophoresis overestimates the risk of recrudescence in anti-malarial trials performed in areas of high transmission intensity. Capillary electrophoresis provides more accurate outcomes for such trials and should be performed when possible. In areas of moderate transmission

Gel versus capillary electrophoresis genotyping for categorizing treatment outcomes in two anti-malarial trials in Uganda.

Science.gov (United States)

Gupta, Vinay; Dorsey, Grant; Hubbard, Alan E; Rosenthal, Philip J; Greenhouse, Bryan

2010-01-15

Molecular genotyping is performed in anti-malarial trials to determine whether recurrent parasitaemia after therapy represents a recrudescence (treatment failure) or new infection. The use of capillary instead of agarose gel electrophoresis for genotyping offers technical advantages, but it is unclear whether capillary electrophoresis will result in improved classification of anti-malarial treatment outcomes. Samples were genotyped using both gel and capillary electrophoresis from randomized trials of artemether-lumefantrine (AL) vs. dihydroartemisinin-piperaquine (DP) performed in two areas of Uganda: Kanungu, where transmission is moderate, and Apac, where transmission is very high. Both gel and capillary methods evaluated polymorphic regions of the merozoite surface protein 1 and 2 and glutamine rich protein genes. Capillary electrophoresis detected more alleles and provided higher discriminatory power than agarose gel electrophoresis at both study sites. There was only moderate agreement between classification of outcomes with the two methods in Kanungu (kappa = 0.66) and poor agreement in Apac (kappa = 0.24). Overall efficacy results were similar when using gel vs. capillary methods in Kanungu (42-day risk of treatment failure for AL: 6.9% vs. 5.5%, p = 0.4; DP 2.4% vs. 2.9%, p = 0.5). However, the measured risk of recrudescence was significantly higher when using gel vs. capillary electrophoresis in Apac (risk of treatment failure for AL: 17.0% vs. 10.7%, p = 0.02; DP: 8.5% vs. 3.4%, p = 0.03). Risk differences between AL and DP were not significantly different whether gel or capillary methods were used. Genotyping with gel electrophoresis overestimates the risk of recrudescence in anti-malarial trials performed in areas of high transmission intensity. Capillary electrophoresis provides more accurate outcomes for such trials and should be performed when possible. In areas of moderate transmission, gel electrophoresis appears adequate to estimate comparative

Validation of the DNATyper™15 PCR Genotyping System for Forensic Application

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Jian Ye

2015-01-01

Full Text Available We describe the optimization and validation of the DNATyper™15 multiplex polymerase chain reaction (PCR genotyping system for autosomal short tandem repeat (STR amplification at 14 autosomal loci (D6S1043, D21S11, D7S820, CSF1PO, D2S1338, D3S1358, D13S317, D8S1179, D16S539, Penta E, D5S818, vWA, D18S51, and FGA and  amelogenin, a sex-determining locus. Several DNATyper™15 assay variables were optimized, including hot start Taq polymerase concentration, Taq polymerase activation time, magnesium concentration, primer concentration, annealing temperature, reaction volume, and cycle number. The performance of the assay was validated with respect to species specificity, sensitivity to template concentration, stability, accuracy, influence of the DNA extraction methods, and the ability to genotype the mixture samples. The performance of the DNATyper™15 system on casework samples was compared with that of two widely used STR amplification kits, Identifiler™ (Applied Biosystems, Carlsbad, CA, USA and PowerPlex 16 ® (Promega, Madison, WI, USA. The conditions for PCR-based DNATyper™15 genotyping were optimized. Contamination from forensically relevant nonhuman DNA was not found to impact genotyping results, and full profiles were generated for all the reactions containing ≥ 0.125 ng of DNA template. No significant difference in performance was observed even after the DNATyper™15 assay components were subjected to 20 freeze-thaw cycles. The performances of DNATyper™15, Identifiler™, and PowerPlex 16 ® were comparable in terms of sensitivity and the ability to genotype the mixed samples and case-type samples, with the assays giving the same genotyping results for all the shared loci. The DNA extraction methods did not affect the performance of any of the systems. Our results demonstrate that the DNATyper™15 system is suitable for genotyping in both forensic DNA database work and case-type samples.

Who does Red Bull give wings to? Sensation seeking moderates sensitivity to subliminal advertisement

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Gaëlle Marie Bustin

2015-06-01

Full Text Available This study assessed whether subliminal priming of a brand name of a drink can affect people’s choices for the primed brand, and whether this effect is moderated by personality traits. Participants with different levels of sensation seeking were presented subliminally with the words Red Bull or Lde Ublr. Results revealed that being exposed to Red Bull lead on average to small increases in participants’ preferences for the primed brand. However, this effect was twice as strong for participants high in sensation seeking and did not occur for participants low in sensation seeking. Going beyond previous research showing that situational factors (e.g., thirst, fatigue… can increase people’s sensitivity to subliminal advertisement, our results suggest that some dispositional factors could have the same potentiating effect. These findings highlight the necessity of taking personality into account in non-conscious persuasion research.

Rapid and Sensitive Detection of BLAD in Cattle Population

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Daniela Elena Ilie

2014-05-01

Full Text Available Bovine leukocyte adhesion deficiency (BLAD is an autosomal recessive disorder with negative impact on dairy cattle breeding. The molecular basis of BLAD is a single point mutation (A→G, resulting in a single amino acid substitution (aspartic acid → glycine at amino acid 128 in the adhesion molecule CD18. The object of this study was to establish a fast and sensitive molecular genotyping assay to detect BLAD carriers using high-resolution melting (HRM curve analysis. We tested animals with known genotypes for BLAD that were previously confirmed by PCR-RFLP method, and then examined the sensitivity of mutation detection using PCR followed by HRM curve analysis. BLAD carriers were readily detectable using HRM assay. Thus, the PCR-HRM genotyping method is a rapid, easily interpretable, reliable and cost-effective assay for BLAD mutant allele detection. This assay can be useful in cattle genotyping and genetic selection.

Physiological responses of genotypes soybean to simulated drought stress

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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.

Stress and skin disease quality of life: the moderating role of anxiety sensitivity social concerns.

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Dixon, L J; Witcraft, S M; McCowan, N K; Brodell, R T

2018-04-01

Stress is an important factor in the onset, exacerbation and reoccurrence of many skin diseases. Little is known about psychological risk factors that affect the association between stress and dermatological conditions. One relevant factor that may modulate this link is anxiety sensitivity (AS) social concerns - the propensity to respond fearfully to anxiety-related sensations (e.g. sweating, flushing) owing to perceived social consequences (e.g. rejection or humiliation). To gain insight into psychological factors affecting skin disease, we examined the moderating role of AS social concerns in the relationship between stress and skin disease quality of life (QoL). Participants [n = 237 (161 female), mean ± SD age 34·18 ± 9·57 years] with active skin disease symptoms were recruited online and completed questionnaires assessing stress, AS social concerns, skin disease QoL and global skin disease symptom severity. AS social concerns moderated the association between stress and skin-related emotional and social functioning in adults with skin disease. Stress was a significant predictor of the impairment associated with skin disease. Stress was linked to skin disease-related emotional and functional impairment associated with skin disease among individuals with high AS social concerns. These results highlight the potential for AS reduction interventions to break the vicious cycle of stress and skin disease symptoms and to improve psychosocial well-being in dermatology patients. © 2017 British Association of Dermatologists.

In vitro evaluation of boron tolerance in wheat (Triticum aestivum L. genotypes

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Kondić-Špika Ankica

2010-01-01

Full Text Available Wheat tolerance to high boron concentrations was determined using mature embryo culture. The testing was performed on a modified MS nutrient medium to which boric acid was added in two concentrations: 15 mM and 30 mM. The control medium contained no excess boric acid. The experiment involved 14 Serbian varieties. After one month of cultivation callus fresh weight (CFW was measured and reductions of fresh callus weight (RFCW at boron (B concentration of 15 mM in relation to the control were calculated. The genotypes differed significantly according to their reaction to different B concentrations. Six genotypes had RFCWs below 50.0 %, while eight genotypes had RFCWs above 50.1 %. Cultivars Nevesinjka and Pesma were considered the most tolerant genotypes, while cultivars Balada and Vila were the most sensitive. The results confirmed that differences in genotype reactions to excess B are visible at the cellular level and that they may serve as a selection criterion. .

Comparative analysis of miRNAs of two rapeseed genotypes in response to acetohydroxyacid synthase-inhibiting herbicides by high-throughput sequencing.

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Maolong Hu

Full Text Available Acetohydroxyacid synthase (AHAS, also called acetolactate synthase, is a key enzyme involved in the first step of the biosynthesis of the branched-chain amino acids valine, isoleucine and leucine. Acetohydroxyacid synthase-inhibiting herbicides (AHAS herbicides are five chemical families of herbicides that inhibit AHAS enzymes, including imidazolinones (IMI, sulfonylureas (SU, pyrimidinylthiobenzoates, triazolinones and triazolopyrimidines. Five AHAS genes have been identified in rapeseed, but little information is available regarding the role of miRNAs in response to AHAS herbicides. In this study, an AHAS herbicides tolerant genotype and a sensitive genotype were used for miRNA comparative analysis. A total of 20 small RNA libraries were obtained of these two genotypes at three time points (0h, 24 h and 48 h after spraying SU and IMI herbicides with two replicates. We identified 940 conserved miRNAs and 1515 novel candidate miRNAs in Brassica napus using high-throughput sequencing methods combined with computing analysis. A total of 3284 genes were predicted to be targets of these miRNAs, and their functions were shown using GO, KOG and KEGG annotations. The differentiation expression results of miRNAs showed almost twice as many differentiated miRNAs were found in tolerant genotype M342 (309 miRNAs after SU herbicide application than in sensitive genotype N131 (164 miRNAs. In additiond 177 and 296 miRNAs defined as differentiated in sensitive genotype and tolerant genotype in response to SU herbicides. The miR398 family was observed to be associated with AHAS herbicide tolerance because their expression increased in the tolerant genotype but decreased in the sensitive genotype. Moreover, 50 novel miRNAs from 39 precursors were predicted. There were 8 conserved miRNAs, 4 novel miRNAs and 3 target genes were validated by quantitative real-time PCR experiment. This study not only provides novel insights into the miRNA content of AHAS herbicides

Human papillomavirus testing and genotyping in cervical screening

DEFF Research Database (Denmark)

Rebolj, Matejka; Lynge, Elsebeth; Bonde, Jesper

2011-01-01

the incidence of cervical cancer, but has a low sensitivity for high-grade cervical intraepithelial neoplasia (CIN) and requires frequent testing. Several HPV tests have become available commercially. They appear to be more sensitive for high-grade CIN, and may further reduce the incidence of cervical cancer......Mass vaccination against human papillomavirus (HPV) genotypes 16 and 18 will, in the long term, reduce the incidence of cervical cancer, but screening will remain an important cancer control measure in both vaccinated and unvaccinated women. Since the 1960s, cytology screening has helped to reduce...

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

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Raquel Santiago Barro

2012-07-01

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

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

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Yuwei Wang

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

Association of the TYMS 3G/3G genotype with poor response and GGH 354GG genotype with the bone marrow toxicity of the methotrexate in RA patients.

Science.gov (United States)

Jekic, Biljana; Lukovic, Ljiljana; Bunjevacki, Vera; Milic, Vera; Novakovic, Ivana; Damnjanovic, Tatjana; Milasin, Jelena; Popovic, Branka; Maksimovic, Nela; Damjanov, Nemanja; Radunovic, Goran; Kovacevic, Ljiljana; Krajinovic, Maja

2013-03-01

Gamma-glutamyl hydrolase (GGH), cyclin D1 (CCND1) and thymidylate synthase (TS) genes encode enzymes that are involved in methotrexate (MTX) action. In a group of 184 RA patients treated with MTX, we have investigated whether selected polymorphisms in these genes modulate MTX efficacy and/or have impact on adverse drug effects (ADEs). The efficacy of the MTX therapy has been estimated using the disease activity score in 28 joints (DAS28-ESR) based on EULAR criteria and relative DAS28 values (rDAS28). All adverse drug events were recorded. Patients were genotyped for selected polymorphisms of the GGH (-354 G > T and 452 C > T), CCND1 (870 A > G) and TYMS (variable number of tandem repeats, VNTR, and G to C substitution of triple repeat, 3R allele) gene. Association studies have been performed between obtained genotypes and the efficacy and toxicity of MTX. According to the EULAR response criteria, 146 RA patients (79.3 %) were classified as responders (good/moderate response) and 38 (20.7 %) as non-responders (poor response). Higher frequency of the TYMS 3 G/3 G genotype has been found among non-responders as compared to individuals with remaining genotypes (p = 0.02). ADEs were recorded in 53 patients. Among those patients eight experienced bone marrow toxicity, all of them carried GGH -354GG genotype (p = 0.003). No other significant association were observed. The 3 G/3 G genotype of the TYMS gene may indicate predisposition of poor response to MTX and GG genotype of GGH -354 T > G polymorphism may have high predictive value for myelosuppression in RA patients.

[Effectiveness of human papillomavirus genotyping for detection of high-grade anal intraepithelial neoplasia compared to anal cytology].

Science.gov (United States)

Padilla-España, Laura; Repiso-Jiménez, Juan Bosco; Fernández-Sánchez, Fernando; Pereda, Teresa; Rivas-Ruiz, Francisco; Fernández-Morano, Teresa; de la Torre-Lima, Javier; Palma, Fermín; Redondo, Maximino; de Troya-Martín, Magdalena

2016-01-01

The incidence of high-grade anal intraepithelial neoplasia (HGAIN) -with an aetiological based on high-risk types of human papillomavirus- is increasing in some high-risk groups. Screening for HGAIN includes routine anal cytology and, more recently, HPV genotyping. The main objective of this study was to determine the sensitivity and specificity of anal cytology and HPV genotyping for the detection of HGAIN. This is a study to determine the correlation of cytological and microbiological findings with anal biopsy findings in a cohort of patients at high risk of developing AIN referred to the department of sexually transmitted infections of the Hospital Costa del Sol, Spain, between January 2008 and December 2014. Of the 151 patients subjected to screening, a total of 92 patients, all of them with the result of three screening test (anal cytology, genotyping and biopsy) were included in the study. Just under two-thirds (62%) of them were HIV-positive. The sensitivity and specificity of anal cytology to detect HGAIN were 52.8 and 85.7%, respectively (k: 0.328), and 78 and 62.8% to detect two or more HPV oncogenic genotypes (k: 0.417). The detection of oncogenic HPV genotypes allowed the identification of 23 new cases of HGAIN that had been underdiagnosed with anal cytology, with 14 cases containing at least three high-risk genotypes. Anal cytology did not show enough sensitivity in HGAIN screening. HPV genotyping has shown to be a useful tool to detect HGAIN cases, although it could lead to an over-diagnosis as a solitary screening procedure. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Detection and genotyping of enteroviruses in cerebrospinal fluid in patients in Victoria, Australia, 2007-2013.

Science.gov (United States)

Papadakis, Georgina; Chibo, Doris; Druce, Julian; Catton, Michael; Birch, Chris

2014-09-01

Genotyping by VP1 fragment polymerase chain reaction (PCR) and nucleic acid sequencing to detect enterovirus (EV) genotypes was performed directly on 729 EV PCR positive cerebrospinal fluid (CSF) samples collected between 2007 and 2012 from Victorian hospital inpatients. The overall genotype identification rate from CSF-positive material was 43%. The four most common genotypes identified were Echovirus 6 (24%), Echovirus 30 (17%), Echovirus 25 (10%), and Coxsackievirus A9 (10%), together comprising 61% of all EVs typed. The seasonal distribution of all EVs identified followed the recognized pattern of mainly summer epidemics. Three of the four predominant genotypes were present in each of the 6 years in which the study was conducted, with 20 other EV genotypes also detected, often in only a single year. Genotyping of EVs directly in CSF is faster, simpler and more sensitive than traditional virus neutralization assays performed on EV positive samples. © 2014 Wiley Periodicals, Inc.

Preschoolers’ Genetic, Physiological, and Behavioral Sensitivity Factors Moderate Links Between Parenting Stress and Child Internalizing, Externalizing, and Sleep Problems

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Davis, Molly; Thomassin, Kristel; Bilms, Joanie; Suveg, Cynthia; Shaffer, Anne; Beach, Steven R. H.

2017-01-01

This study examined three potential moderators of the relations between maternal parenting stress and preschoolers’ adjustment problems: a genetic polymorphism - the short allele of the serotonin transporter (5-HTTLPR, ss/sl allele) gene, a physiological indicator - children’s baseline respiratory sinus arrhythmia (RSA), and a behavioral indicator - mothers’ reports of children’s negative emotionality. A total of 108 mothers (Mage = 30.68 years, SDage = 6.06) reported on their parenting stress as well as their preschoolers’ (Mage = 3.50 years, SDage = .51, 61% boys) negative emotionality and internalizing, externalizing, and sleep problems. Results indicated that the genetic sensitivity variable functioned according to a differential susceptibility model; however, the results involving physiological and behavioral sensitivity factors were most consistent with a diathesis-stress framework. Implications for prevention and intervention efforts to counter the effects of parenting stress are discussed. PMID:28295263

Simultaneous selection for cowpea (Vigna unguiculata L.) genotypes with adaptability and yield stability using mixed models.

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Torres, F E; Teodoro, P E; Rodrigues, E V; Santos, A; Corrêa, A M; Ceccon, G

2016-04-29

The aim of this study was to select erect cowpea (Vigna unguiculata L.) genotypes simultaneously for high adaptability, stability, and yield grain in Mato Grosso do Sul, Brazil using mixed models. We conducted six trials of different cowpea genotypes in 2005 and 2006 in Aquidauana, Chapadão do Sul, Dourados, and Primavera do Leste. The experimental design was randomized complete blocks with four replications and 20 genotypes. Genetic parameters were estimated by restricted maximum likelihood/best linear unbiased prediction, and selection was based on the harmonic mean of the relative performance of genetic values method using three strategies: selection based on the predicted breeding value, having considered the performance mean of the genotypes in all environments (no interaction effect); the performance in each environment (with an interaction effect); and the simultaneous selection for grain yield, stability, and adaptability. The MNC99542F-5 and MNC99-537F-4 genotypes could be grown in various environments, as they exhibited high grain yield, adaptability, and stability. The average heritability of the genotypes was moderate to high and the selective accuracy was 82%, indicating an excellent potential for selection.

MMP-8 genotypes influence the inflammatory response in human endotoxemia.

Science.gov (United States)

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

2014-04-01

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

Genotype-Dependent Effect of Exogenous Nitric Oxide on Cd-induced Changes in Antioxidative Metabolism, Ultrastructure, and Photosynthetic Performance in Barley Seedlings (Hordeum vulgare)

DEFF Research Database (Denmark)

Chen, Fei; Wang, Fang; Sun, Hongyan

2010-01-01

M Cd increased the accumulation of O2•-, H2O2, and malondialdehyde (MDA) but reduced plant height, chlorophyll content, net photosynthetic rate (P n), and biomass, with a much more severe response in the Cd-sensitive genotype. Antioxidant enzyme activities increased significantly under Cd stress......A greenhouse hydroponic experiment was performed using Cd-sensitive (cv. Dong 17) and Cd-tolerant (Weisuobuzhi) barley seedlings to evaluate how different genotypes responded to cadmium (Cd) toxicity in the presence of sodium nitroprusside (SNP), a nitric oxide (NO) donor. Results showed that 5 μ...... in the roots of the tolerant genotype, whereas in leaves of the sensitive genotype, superoxide dismutase (SOD) and ascorbate peroxide (APX), especially cytosol ascorbate peroxidase (cAPX), decreased after 5-15 days Cd exposure. Moreover, Cd induces NO synthesis by stimulating nitrate reductase and nitric oxide...

Effects of sulphur dioxide (SO2) on growth and flowering of SO2-tolerant and non-tolerant genotypes of Phleum pratense.

Science.gov (United States)

Clapperton, M J; Reid, D M

1994-01-01

The objective of this study was to compare the growth and interaction of clipping and sulphur dioxide (SO(2)) exposure on SO(2)-tolerant and non-tolerant genotypes of Phleum pratense at two field sites along an SO(2)-concentration gradient. Sulphur-dioxide-tolerant and non-tolerant genotypes of Phleum pratense were identified from indigenous populations that had been collected along the same SO(2)-concentration gradient in southern Alberta, Canada. Physiological differences between the two genotypes were confirmed by supplying leaves with (14)CO(2) and examining the assimilate partitioning between the genotypes. For the field experiment, clones of each genotype and seedlings grown from commercial seed were planted at two different field sites along an SO(2)-emission gradient. There were no differences in growth between the genotypes at the two field sites after the first year except that the SO(2)-tolerant clones had a greater percentage of root length colonised by vesicular-arbuscular (VA) mycorrhizal fungi. After the second growing season, there was a significant decrease in the number of inflorescences produced by plants exposed to SO(2), particularly by the non-tolerant genotype. The added stress of defoliation appeared to increase the sensitivity of flowering to SO(2), again particularly in the non-tolerant genotype. The results of the field study showed that flowering as opposed to vegetative plant growth was more sensitive to long-term low-concentration SO(2) exposure and that this sensitivity was compounded by the stress interaction of defoliation.

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

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Motamedi Marzieh

2016-12-01

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

Moderating the Covariance Between Family Member’s Substance Use Behavior

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Eaves, Lindon J.; Neale, Michael C.

2014-01-01

Twin and family studies implicitly assume that the covariation between family members remains constant across differences in age between the members of the family. However, age-specificity in gene expression for shared environmental factors could generate higher correlations between family members who are more similar in age. Cohort effects (cohort × genotype or cohort × common environment) could have the same effects, and both potentially reduce effect sizes estimated in genome-wide association studies where the subjects are heterogeneous in age. In this paper we describe a model in which the covariance between twins and non-twin siblings is moderated as a function of age difference. We describe the details of the model and simulate data using a variety of different parameter values to demonstrate that model fitting returns unbiased parameter estimates. Power analyses are then conducted to estimate the sample sizes required to detect the effects of moderation in a design of twins and siblings. Finally, the model is applied to data on cigarette smoking. We find that (1) the model effectively recovers the simulated parameters, (2) the power is relatively low and therefore requires large sample sizes before small to moderate effect sizes can be found reliably, and (3) the genetic covariance between siblings for smoking behavior decays very rapidly. Result 3 implies that, e.g., genome-wide studies of smoking behavior that use individuals assessed at different ages, or belonging to different birth-year cohorts may have had substantially reduced power to detect effects of genotype on cigarette use. It also implies that significant special twin environmental effects can be explained by age-moderation in some cases. This effect likely contributes to the missing heritability paradox. PMID:24647834

In vitro screening of potato genotypes for osmotic stress tolerance

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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

Aerobic Fitness Linked to Cortical Brain Development in Adolescent Males: Preliminary Findings Suggest a Possible Role of BDNF Genotype.

Science.gov (United States)

Herting, Megan M; Keenan, Madison F; Nagel, Bonnie J

2016-01-01

Aerobic exercise has been shown to impact brain structure and cognition in children and adults. Exercise-induced activation of a growth protein known as brain derived neurotrophic factor (BDNF) is thought to contribute to such relationships. To date, however, no study has examined how aerobic fitness relates to cortical brain structure during development and if BDNF genotype moderates these relationships. Using structural magnetic resonance imaging (MRI) and FreeSurfer, the current study examined how aerobic fitness relates to volume, thickness, and surface area in 34 male adolescents, 15 to 18 years old. Moreover, we examined if the val66met BDNF genotype moderated these relationships. We hypothesized that aerobic fitness would relate to greater thickness and volumes in frontal, parietal, and motor regions, and that these relationships would be less robust in individuals carrying a Met allele, since this genotype leads to lower BDNF expression. We found that aerobic fitness positively related to right rostral middle frontal cortical volume in all adolescents. However, results also showed BDNF genotype moderated the relationship between aerobic fitness and bilateral medial precuneus surface area, with a positive relationship seen in individuals with the Val/Val allele, but no relationship detected in those adolescents carrying a Met allele. Lastly, using self-reported levels of aerobic activity, we found that higher-fit adolescents showed larger right medial pericalcarine, right cuneus and left precuneus surface areas as compared to their low-fit peers. Our findings suggest that aerobic fitness is linked to cortical brain development in male adolescents, and that more research is warranted to determine how an individual's genes may influence these relationships.

Aerobic Fitness Linked to Cortical Brain Development in Adolescent Males: Preliminary Findings Suggest a Possible Role of BDNF Genotype

Science.gov (United States)

Herting, Megan M.; Keenan, Madison F.; Nagel, Bonnie J.

2016-01-01

Aerobic exercise has been shown to impact brain structure and cognition in children and adults. Exercise-induced activation of a growth protein known as brain derived neurotrophic factor (BDNF) is thought to contribute to such relationships. To date, however, no study has examined how aerobic fitness relates to cortical brain structure during development and if BDNF genotype moderates these relationships. Using structural magnetic resonance imaging (MRI) and FreeSurfer, the current study examined how aerobic fitness relates to volume, thickness, and surface area in 34 male adolescents, 15 to 18 years old. Moreover, we examined if the val66met BDNF genotype moderated these relationships. We hypothesized that aerobic fitness would relate to greater thickness and volumes in frontal, parietal, and motor regions, and that these relationships would be less robust in individuals carrying a Met allele, since this genotype leads to lower BDNF expression. We found that aerobic fitness positively related to right rostral middle frontal cortical volume in all adolescents. However, results also showed BDNF genotype moderated the relationship between aerobic fitness and bilateral medial precuneus surface area, with a positive relationship seen in individuals with the Val/Val allele, but no relationship detected in those adolescents carrying a Met allele. Lastly, using self-reported levels of aerobic activity, we found that higher-fit adolescents showed larger right medial pericalcarine, right cuneus and left precuneus surface areas as compared to their low-fit peers. Our findings suggest that aerobic fitness is linked to cortical brain development in male adolescents, and that more research is warranted to determine how an individual’s genes may influence these relationships. PMID:27445764

Interpreting genotype × environment interactions for grain yield of rainfed durum wheat in Iran

Directory of Open Access Journals (Sweden)

Reza Mohammadi

2015-12-01

Full Text Available Clustering genotype × environment (GE interactions and understanding the causes of GE interactions are among the most important tasks in crop breeding programs. Pattern analysis (cluster and ordination techniques was applied to analyze GE interactions for grain yield of 24 durum wheat (Triticum turgidum L. var. durum genotypes (breeding lines and old and new cultivars along with a popular bread wheat (Triticum aestivum cultivar grown in 21 different rainfed environments during the 2010–2013 cropping seasons. To investigate the causes of GE interaction, several genotypic and environmental covariables were used. In a combined ANOVA, environment was the predominant source of variation, accounting for 81.2% of the total sum of squares (TSS, and the remaining TSS due to the GE interaction effect was almost seven times that of the genetic effect. Cluster analysis separated the environments into four groups with similar discriminating ability among genotypes, and genotypes into five groups with similar patterns in yield performance. Pattern analysis confirmed two major environmental clusters (cold and warm, and allowed the discrimination and characterization of genotype adaptation. Within the cold-environment cluster, several subclusters were identified. The breeding lines were most adapted to moderate and warm environments, whereas the old varieties were adapted to cold environments. The results indicated that winter rainfall and plant height were among the environmental and genotypic covariables, respectively, that contributed most to GE interaction for grain yield in rainfed durum wheat.

GenoType HelicoDR test in the determination of antimicrobial resistance of Helicobacter pylori in Korea.

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Lee, Jung Won; Kim, Nayoung; Nam, Ryoung Hee; Park, Ji Hyun; Choi, Yoon Jin; Kim, Jung Mogg; Kim, Joo Sung; Jung, Hyun Chae

2014-09-01

Antimicrobial resistance of Helicobacter pylori is most important factor in eradication success. GenoType HelicoDR test has been developed for rapid detection of antimicrobial resistance. The present study evaluated the clinical usefulness of GenoType HelicoDR test in Korea. To detect 23S rRNA for clarithromycin resistance and gyrA mutations for fluoroquinolone resistance, both DNA sequencing after minimal inhibitory test (MIC) and GenoType HelicoDR test were performed in H. pylori isolates from the gastric mucosa of 101 patients. The eradication results of clarithromycin and moxifloxacin-containing triple therapy were evaluated by the 23S rRNA and gyrA mutations. For 42 isolates with A2143G mutation by GenoType HelicoDR, 83.3% (35/42) of concordance rate was estimated with DNA sequencing method and 85.7% (36/42) for MIC test. For 43 isolates with N87K mutation by GenoType HelicoDR, 71.1% (31/43) of concordance rate was estimated with DNA sequencing and 88.4% (38/43) for MIC test. The sensitivity and specificity of GenoType HelicoDR test in determination of 23S rRNA mutation were 94.9% and 87.1%, and those of gyrA 98.2% and 80.0%. The sensitivity and specificity of GenoType HelicoDR test in determination of clarithromycin resistance based on MIC test were 55.0% and 80.0%, for fluoroquinolone 74.4% and 70.0%. GenoType HelicoDR test is useful to determine mutations responsible for clarithromycin or fluoroquinolone-containing eradication failure but has a limitation for the clinical applicability in determination of resistance.

Characterization of Rubisco activase from thermally contrasting genotypes of Acer rubrum (Aceraceae).

Science.gov (United States)

Weston, David J; Bauerle, William L; Swire-Clark, Ginger A; Moore, Brandon D; Baird, Wm Vance

2007-06-01

The lability of Rubisco activase function is thought to have a major role in the decline of leaf photosynthesis under moderate heat (RCA1 and RCA2 proteins increased modestly in FL plants under warmer temperature, while only RCA2 protein increased in MN plants. Rubisco large subunit (RbsL) protein abundance was relatively unaffected in either genotype by temperature. These results support the idea that Rubisco activase, particularly the ratio of Rubisco activase to Rubisco, may play a role in the photosynthetic heat acclimation in A. rubrum and may have adaptive significance. This mechanism alone is not likely to entirely explain the thermotolerance in the FL genotype, and future research on adaptive mechanisms to high temperatures should consider activase function in a multipathway framework.

Glutathione S-transferase M1-null genotype as risk factor for SOS in oxaliplatin-treated patients with metastatic colorectal cancer.

Science.gov (United States)

Vreuls, C P H; Olde Damink, S W M; Koek, G H; Winstanley, A; Wisse, E; Cloots, R H E; van den Broek, M A J; Dejong, C H C; Bosman, F T; Driessen, A

2013-02-19

Oxaliplatin is used as a neo-adjuvant therapy in hepatic colorectal carcinoma metastasis. This treatment has significant side effects, as oxaliplatin is toxic to the sinusoidal endothelial cells and can induce sinusoidal obstruction syndrome (SOS), which is related to decreased overall survival. Glutathione has an important role in the defence system, catalysed by glutathione S-transferase (GST), including two non-enzyme producing polymorphisms (GSTM1-null and GSTT1-null). We hypothesise that patients with a non-enzyme producing polymorphism have a higher risk of developing toxic injury owing to oxaliplatin. In the nontumour-bearing liver, the presence of SOS was studied histopathologically. The genotype was determined by a semi-nested PCR. Thirty-two of the 55 (58%) patients showed SOS lesions, consisting of 27% mild, 22% moderate and 9% severe lesions. The GSTM1-null genotype was present in 25 of the 55 (46%). Multivariate analysis showed that the GSTM1-null genotype significantly correlated with the presence of (moderate-severe) SOS (P=0.026). The GSTM1-null genotype is an independent risk factor for SOS. This finding allows us, in association with other risk factors, to conceive a potential risk profile predicting whether the patient is at risk of developing SOS, before starting oxaliplatin, and subsequently might result in adjustment of treatment.

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

Science.gov (United States)

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

2010-08-01

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

Genetic moderation of interpersonal psychotherapy efficacy for low-income mothers with major depressive disorder: implications for differential susceptibility.

Science.gov (United States)

Cicchetti, Dante; Toth, Sheree L; Handley, Elizabeth D

2015-02-01

Genetic moderation of interpersonal psychotherapy (IPT) efficacy for economically disadvantaged women with major depressive disorder was examined. Specifically, we investigated whether genotypic variation in corticotropin releasing hormone receptor 1 (CRHR1) and the linked polymorphic region of the serotonin transporter gene (5-HTTLPR) moderated effects of IPT on depressive symptoms over time. We also tested genotype moderation of IPT mechanisms on social adjustment and perceived stress. Non-treatment-seeking urban women at or below the poverty level with infants were recruited from the community (N = 126; M age = 25.33 years, SD = 4.99; 54.0% African American, 22.2% Caucasian, and 23.8% Hispanic/biracial) and randomized to individual IPT or Enhanced Community Standard groups. The results revealed that changes in depressive symptoms over time depended on both intervention group and genotypes (5-HTTLPR and CRHR1). Moreover, multiple-group path analysis indicated that IPT improved depressive symptoms, increased social adjustment, and decreased perceived stress at posttreatment among women with the 0 copies of the CRHR1 TAT haplotype only. Finally, improved social adjustment at postintervention significantly mediated the effect of IPT on reduced depressive symptoms at 8 months postintervention for women with 0 copies of the TAT haplotype only. Post hoc analyses of 5-HTTLPR were indicative of differential susceptibility, albeit among African American women only.

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

Science.gov (United States)

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

2016-09-17

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

Rationality and emotionality: serotonin transporter genotype influences reasoning bias.

Science.gov (United States)

Stollstorff, Melanie; Bean, Stephanie E; Anderson, Lindsay M; Devaney, Joseph M; Vaidya, Chandan J

2013-04-01

Reasoning often occurs under emotionally charged, opinion-laden circumstances. The belief-bias effect indexes the extent to which reasoning is based upon beliefs rather than logical structure. We examined whether emotional content increases this effect, particularly for adults genetically predisposed to be more emotionally reactive. SS/SL(G) carriers of the serotonin transporter genotype (5-HTTLPR) were less accurate selectively for evaluating emotional relational reasoning problems with belief-logic conflict relative to L(A)L(A) carriers. Trait anxiety was positively associated with emotional belief-bias, and the 5-HTTLPR genotype significantly accounted for the variance in this association. Thus, deductive reasoning, a higher cognitive ability, is sensitive to differences in emotionality rooted in serotonin neurotransmitter function.

Profile and functional properties of seed proteins from six pea (Pisum sativum) genotypes.

Science.gov (United States)

Barac, Miroljub; Cabrilo, Slavica; Pesic, Mirjana; Stanojevic, Sladjana; Zilic, Sladjana; Macej, Ognjen; Ristic, Nikola

2010-01-01

Extractability, extractable protein compositions, technological-functional properties of pea (Pisum sativum) proteins from six genotypes grown in Serbia were investigated. Also, the relationship between these characteristics was presented. Investigated genotypes showed significant differences in storage protein content, composition and extractability. The ratio of vicilin:legumin concentrations, as well as the ratio of vicilin + convicilin: Legumin concentrations were positively correlated with extractability. Our data suggest that the higher level of vicilin and/or a lower level of legumin have a positive influence on protein extractability. The emulsion activity index (EAI) was strongly and positively correlated with the solubility, while no significant correlation was found between emulsion stability (ESI) and solubility, nor between foaming properties and solubility. No association was evident between ESI and EAI. A moderate positive correlation between emulsion stability and foam capacity was observed. Proteins from the investigated genotypes expressed significantly different emulsifying properties and foam capacity at different pH values, whereas low foam stability was detected. It appears that genotype has considerable influence on content, composition and technological-functional properties of pea bean proteins. This fact can be very useful for food scientists in efforts to improve the quality of peas and pea protein products.

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

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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

Antibiosis in Soybean Genotypes and the Resistance Levels to Spodoptera eridania (Cramer) (Lepidoptera: Noctuidae).

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Souza, B H S; Silva, A G; Janini, J C; Boica Júnior, A L

2014-12-01

The southern armyworm (SAW) Spodoptera eridania (Cramer) is one of the most common armyworm species defoliating soybeans. Preliminary screening trials have indicated that some soybean genotypes exhibit resistance to SAW. Therefore, in this study, we evaluated the development of SAW larvae fed on ten soybean genotypes in order to identify genotypes with antibiosis-type resistance. Neonate SAW larvae were daily fed with young leaves collected from plants at the vegetative growth stages V4-V5. Larval development and survival were recorded. Genotypes PI 227687 and PI 227682 delayed larval, pupal, and larva-adult development and yielded larvae with the lowest weight and survival and pupae with the lowest weight. Genotypes IAC 100 and DM 339 also negatively affected larval and pupal development and larval survival but at a lower level. Based on our results, the soybean lines PI 227687 and PI 227682 could be used as sources of genes for soybean breeding programs aiming to develop high yield, SAW-resistant cultivars. Moreover, further trials must be carried out under field conditions to validate if the commercial cultivars IAC 100 and DM 339, which expressed moderate levels of antibiosis-type resistance in the laboratory, are effective in suppressing SAW larvae populations.

Phenotypes in defined genotypes including siblings with Usher syndrome.

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Malm, Eva; Ponjavic, Vesna; Möller, Claes; Kimberling, William J; Andréasson, Sten

2011-06-01

To characterize visual function in defined genotypes including siblings with Usher syndrome. Thirteen patients with phenotypically different subtypes of Usher syndrome, including 3 families with affected siblings, were selected. Genetic analysis and ophthalmological examinations including visual fields, full-field electroretinography (ERG), multifocal electroretinography (mf ERG), and optical coherence tomography (OCT) were assessed. The patients' degree of visual handicap was evaluated by a questionnaire (ADL). Twelve of thirteen patients were genotyped as Usher 1B, 1D, 1F, 2A, 2C or 3A. In 12 of 13 patients examined with ERG the 30 Hz flickering light response revealed remaining cone function. In 3 of the patients with Usher type 1 mf ERG demonstrated a specific pattern, with a sharp distinction between the area with reduced function and the central area with remaining macular function and normal peak time. OCT demonstrated loss of foveal depression with distortion of the foveal architecture in the macula in all patients. The foveal thickness ranged from 159 to 384 µm and was not correlated to retinal function. Three siblings shared the same mutation for Usher 2C but in contrast to previous reports regarding this genotype, 1 of them diverged in phenotype with substantially normal visual fields, almost normal OCT and mf ERG findings, and only moderately reduced rod and cone function according to ERG. Evaluation of visual function comprising both the severity of the rod cone degeneration and the function in the macular region confirm phenotypical heterogeneity within siblings and between different genotypes of Usher syndrome.

A Multiplex PCR for the Simultaneous Detection and Genotyping of the Echinococcus granulosus Complex

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Boubaker, Ghalia; Macchiaroli, Natalia; Prada, Laura; Cucher, Marcela A.; Rosenzvit, Mara C.; Ziadinov, Iskender; Deplazes, Peter; Saarma, Urmas; Babba, Hamouda; Gottstein, Bruno; Spiliotis, Markus

2013-01-01

Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1–G10) and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1–G3), E. equinus (G4), E. ortleppi (G5), and E. canadensis (G6–G10). The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR) allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex in common, and (iii) the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20) and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13). The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (Echinococcus genus. PMID:23350011

A multiplex PCR for the simultaneous detection and genotyping of the Echinococcus granulosus complex.

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Boubaker, Ghalia; Macchiaroli, Natalia; Prada, Laura; Cucher, Marcela A; Rosenzvit, Mara C; Ziadinov, Iskender; Deplazes, Peter; Saarma, Urmas; Babba, Hamouda; Gottstein, Bruno; Spiliotis, Markus

2013-01-01

Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1-G10) and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1-G3), E. equinus (G4), E. ortleppi (G5), and E. canadensis (G6-G10). The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR) allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex in common, and (iii) the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20) and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13). The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (Echinococcus genus.

Evaluation of High Resolution Melting for MTHFR C677T Genotyping in Congenital Heart Disease.

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Ying Wang

Full Text Available High resolution melting (HRM is a simple, flexible and low-cost mutation screening technique. The methylenetetrahydrofolate reductase (MTHFR gene encoding a critical enzyme, potentially affects susceptibility to some congenital defects like congenital heart disease (CHD. We evaluate the performance of HRM for genotyping of the MTHFR gene C677T locus in CHD cases and healthy controls of Chinese Han population.A total of 315 blood samples from 147 CHD patients (male72, female 75 and 168 healthy controls (male 92, female 76 were enrolled in the study. HRM was utilized to genotype MTHFR C677T locus of all the samples. The results were compared to that of PCR-RFLP and Sanger sequencing. The association of the MTHFR C677T genotypes and the risk of CHD was analyzed using odds ratio with their 95% confidence interval (CIs from unconditional logistic regression.All the samples were successfully genotyped by HRM within 1 hour and 30 minutes while at least 6 hours were needed for PCR-RFLP and sequencing. The genotypes of MTHFR C677T CC, CT, and TT were 9.52%, 49.66%, and 40.82% in CHD group but 29.17%, 50% and 20.83% in control group, which were identical using both methods of HRM and PCR-RFLP, demonstrating the sensitivity and specificity of HRM were all 100%.MTHFR C677T is a potential risk factor for CHD in our local residents of Shandong province in China. HRM is a fast, sensitive, specific and reliable method for clinical application of genotyping.

Physiological, Biochemical, Epigenetic and Molecular Analyses of Wheat (Triticum aestivum Genotypes with Contrasting Salt Tolerance

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Suresh Kumar

2017-06-01

Full Text Available Abiotic stress exerts significant impact on plant’s growth, development, and productivity. Productivity of crop plants under salt stress is lagging behind because of our limited knowledge about physiological, biochemical, epigenetic, and molecular mechanisms of salt tolerance in plants. This study aimed to investigate physio-biochemical, molecular indices and defense responses of selected wheat cultivars to identify the most contrasting salt-responsive genotypes and the mechanisms associated with their differential responses. Physio-biochemical traits specifically membrane stability index, antioxidant potential, osmoprotectants and chlorophyll contents, measured at vegetative stage, were used for multivariate analysis to identify the most contrasting genotypes. Genetic and epigenetic analyses indicated the possible mechanisms associated with differential response of the wheat genotypes under salt stress. Better antioxidant potential, membrane stability, increased accumulation of osmolytes/phytophenolics, and higher K+/Na+ ratio under 200 mM NaCl stress identified Kharchia-65 to be the most salt-tolerant cultivar. By contrast, increased MDA level, reduced soluble sugar, proline, total chlorophyll, total phenolics contents, and lower antioxidant potential in HD-2329 marked it to be sensitive to the stress. Genetic and bioinformatics analyses of HKT1;4 of contrasting genotypes (Kharchia-65 and HD-2329 revealed deletions, transitions, and transversions resulting into altered structure, loss of conserved motifs (Ser-Gly-Gly-Gly and Gly-Arg and function in salt-sensitive (HD-2329 genotype. Expression analysis of HKTs rationalized the observed responses. Epigenetic variations in cytosine methylation explained tissue- and genotype-specific differential expression of HKT2;1 and HKT2;3.

A two-step real-time PCR assay for quantitation and genotyping of human parvovirus 4.

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Väisänen, E; Lahtinen, A; Eis-Hübinger, A M; Lappalainen, M; Hedman, K; Söderlund-Venermo, M

2014-01-01

Human parvovirus 4 (PARV4) of the family Parvoviridae was discovered in a plasma sample of a patient with an undiagnosed acute infection in 2005. Currently, three PARV4 genotypes have been identified, however, with an unknown clinical significance. Interestingly, these genotypes seem to differ in epidemiology. In Northern Europe, USA and Asia, genotypes 1 and 2 have been found to occur mainly in persons with a history of injecting drug use or other parenteral exposure. In contrast, genotype 3 appears to be endemic in sub-Saharan Africa, where it infects children and adults without such risk behaviour. In this study, a novel straightforward and cost-efficient molecular assay for both quantitation and genotyping of PARV4 DNA was developed. The two-step method first applies a single-probe pan-PARV4 qPCR for screening and quantitation of this relatively rare virus, and subsequently, only the positive samples undergo a real-time PCR-based multi-probe genotyping. The new qPCR-GT method is highly sensitive and specific regardless of the genotype, and thus being suitable for studying the clinical impact and occurrence of the different PARV4 genotypes. Copyright © 2013 Elsevier B.V. All rights reserved.

Only minor additional metabolic health benefits of high as opposed to moderate dose physical exercise in young, moderately overweight men.

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Reichkendler, M H; Rosenkilde, M; Auerbach, P L; Agerschou, J; Nielsen, M B; Kjaer, A; Hoejgaard, L; Sjödin, A; Ploug, T; Stallknecht, B

2014-05-01

The dose-response effects of exercise training on insulin sensitivity, metabolic risk, and quality of life were examined. Sixty-one healthy, sedentary (VO₂max: 35 ± 5 ml/kg/min), moderately overweight (BMI: 27.9 ± 1.8), young (age: 29 ± 6 years) men were randomized to sedentary living (sedentary control group; n = 18), moderate (moderate dose training group [MOD]: 300 kcal/day, n = 21), or high (high dose training group [HIGH]: 600 kcal/day, n = 22) dose physical exercise for 11 weeks. The return rate for post-intervention testing was 82-94% across groups. Weekly exercise amounted to 2,004 ± 24 and 3,774 ± 68 kcal, respectively, in MOD and HIGH. Cardiorespiratory fitness increased (P exercise groups (MOD: 32 ± 1 to 29 ± 1%; HIGH: 30 ± 1 to 27 ± 1%). Peripheral insulin sensitivity increased (P benefits were found when exercising ∼3,800 as opposed to ∼2,000 kcal/week in young moderately overweight men. This finding may have important public health implications. Copyright © 2012 The Obesity Society.

Performance of faba bean genotypes with Orobanche foetida Poir. and Orobanche crenata Forsk. infestation in Tunisia

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Imen Trabelsi

2015-03-01

Full Text Available Orobanche foetida Poir. and O. crenata Forsk. are major constraints to faba bean (Vicia faba L. cultivation in Tunisia. To evalúate the different levels of resistance of seven small-seeded faba bean genotypes to these parasitic weed species, three trials were conducted in fields infested and non-infested with O. foetida in the Oued Beja Agricultural Experimental Unit and O. crenata in an experimental field at Ariana of the National Institute of Agricultural Research during three cropping seasons. Compared to the susceptible cv. Bad'i, the seven genotypes showed moderate to high levels of resistance to both Orobanche species. The number and dry weight of emerged broomrapes and underground tubercles recorded on the new improved genotypes were lower than those recorded on released and resistant 'Najeh' and 'Baraca'. The parasitism index on the new genotypes varied from 2-6 times less than susceptible 'Bad'i' in both Oued-Beja and Ariana. Yield reduction due to O.foetida infection varied from 13.5% on genotype XAR-VF00.13-89-2-1-1-1-1 to 59.7% on 'Baraca', whereas the yield loss was about 92% on the susceptible control. Parasitic infection did not affect dry grain protein accumulation in the tested genotypes.

Preschoolers' genetic, physiological, and behavioral sensitivity factors moderate links between parenting stress and child internalizing, externalizing, and sleep problems.

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Davis, Molly; Thomassin, Kristel; Bilms, Joanie; Suveg, Cynthia; Shaffer, Anne; Beach, Steven R H

2017-05-01

This study examined three potential moderators of the relations between maternal parenting stress and preschoolers' adjustment problems: a genetic polymorphism-the short allele of the serotonin transporter (5-HTTLPR, ss/sl allele) gene, a physiological indicator-children's baseline respiratory sinus arrhythmia (RSA), and a behavioral indicator-mothers' reports of children's negative emotionality. A total of 108 mothers (M age  = 30.68 years, SD age  = 6.06) reported on their parenting stress as well as their preschoolers' (M age  = 3.50 years, SD age  = 0.51, 61% boys) negative emotionality and internalizing, externalizing, and sleep problems. Results indicated that the genetic sensitivity variable functioned according to a differential susceptibility model; however, the results involving physiological and behavioral sensitivity factors were most consistent with a diathesis-stress framework. Implications for prevention and intervention efforts to counter the effects of parenting stress are discussed. © 2017 Wiley Periodicals, Inc.

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

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

2017-01-01

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

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

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Alejandra Mendoza-Cantú

2017-01-01

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

Evaluation of common bean (Phaseolus vulgaris L. genotypes for drought stress adaptation in Ethiopia

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Kwabena Darkwa

2016-10-01

Full Text Available Drought stress linked with climate change is one of the major constraints faced by common bean farmers in Africa and elsewhere. Mitigating this constraint requires the selection of resilient varieties that withstand drought threats to common bean production. This study assessed the drought response of 64 small red-seeded genotypes of common bean grown in a lattice design replicated twice under contrasting moisture regimes, terminal drought stress and non-stress, in Ethiopia during the dry season from November 2014 to March 2015. Multiple plant traits associated with drought were assessed for their contribution to drought adaptation of the genotypes. Drought stress determined by a drought intensity index was moderate (0.3. All the assessed traits showed significantly different genotypic responses under drought stress and non-stress conditions. Eleven genotypes significantly (P ≤ 0.05 outperformed the drought check cultivar under both drought stress and non-stress conditions in seed yielding potential. Seed yield showed positive and significant correlations with chlorophyll meter reading, vertical root pulling resistance force, number of pods per plant, and seeds per pod under both soil moisture regimes, indicating their potential use in selection of genotypes yielding well under drought stress and non-stress conditions. Clustering analysis using Mahalanobis distance grouped the genotypes into four groups showing high and significant inter-cluster distance, suggesting that hybridization between drought-adapted parents from the groups will provide the maximum genetic recombination for drought tolerance in subsequent generations.

Screening of salinity tolerant jute (corchorus capsularis and c. olitorius) genotypes via phenotypic and phsiology-assisted procedures

International Nuclear Information System (INIS)

Hongyu, M.A.; Wang, Z.; Wang, X.

2011-01-01

To obtain salt tolerant genotypes, salt tolerance of 10 jute genotypes of different origins was evaluated by relative salt harm rate at germination stage and by index of salt harm at seedling stage, respectively. The results indicated that salt tolerance of germination stage of jute was consistent with that of seedling stage, with a markedly significant (P < 0.01) correlation of 0.8432 (n =10). Two high salt tolerant genotypes (Huang No.1 and 9511) and two salt sensitive genotypes (Mengyuan and 07-21) were screened out by these methods. Further activity analysis of POD, SOD and CAT and determination of MDA content at seedling stage validated that genotypes Huang No.1 and 9511 were more salt tolerant than genotypes Mengyuan and 07-21. Our results indicated that the combination of relative salt harm rate at germination stage and index of salt harm at seedling stage can be used to evaluate salt tolerance of jute genotypes. (author)

High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification

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Sun Zhenyu

2001-08-01

Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the foundation of powerful complex trait and pharmacogenomic analyses. The availability of large SNP databases, however, has emphasized a need for inexpensive SNP genotyping methods of commensurate simplicity, robustness, and scalability. We describe a solution-based, microtiter plate method for SNP genotyping of human genomic DNA. The method is based upon allele discrimination by ligation of open circle probes followed by rolling circle amplification of the signal using fluorescent primers. Only the probe with a 3' base complementary to the SNP is circularized by ligation. Results SNP scoring by ligation was optimized to a 100,000 fold discrimination against probe mismatched to the SNP. The assay was used to genotype 10 SNPs from a set of 192 genomic DNA samples in a high-throughput format. Assay directly from genomic DNA eliminates the need to preamplify the target as done for many other genotyping methods. The sensitivity of the assay was demonstrated by genotyping from 1 ng of genomic DNA. We demonstrate that the assay can detect a single molecule of the circularized probe. Conclusions Compatibility with homogeneous formats and the ability to assay small amounts of genomic DNA meets the exacting requirements of automated, high-throughput SNP scoring.

Contrast sensitivity to spatial gratings in moderate and dim light conditions in patients with diabetes in the absence of diabetic retinopathy.

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Safi, Sare; Rahimi, Anoushiravan; Raeesi, Afsaneh; Safi, Hamid; Aghazadeh Amiri, Mohammad; Malek, Mojtaba; Yaseri, Mehdi; Haeri, Mohammad; Middleton, Frank A; Solessio, Eduardo; Ahmadieh, Hamid

2017-01-01

To evaluate the ability of contrast sensitivity (CS) to discriminate loss of visual function in diabetic subjects with no clinical signs of retinopathy relative to that of normal subjects. In this prospective cross-sectional study, we measured CS in 46 diabetic subjects with a mean age of 48±6 years, a best-corrected visual acuity of 20/20 and no signs of diabetic retinopathy. The CS in these subjects was compared with CS measurements in 46 normal control subjects at four spatial frequencies (3, 6, 12, 18 cycles per degree) under moderate (500 lux) and dim (less than 2 lux) background light conditions. CS was approximately 0.16 log units lower in patients with diabetes relative to controls both in moderate and in dim background light conditions. Logistic regression classification and receiver operating characteristic curve analysis indicated that CS analysis using two light conditions was more accurate (0.78) overall compared with CS analysis using only a single illumination condition (accuracy values were 0.67 and 0.70 in moderate and dim light conditions, respectively). Our results showed that patients with diabetes without clinical signs of retinopathy exhibit a uniform loss in CS at all spatial frequencies tested. Measuring the loss in CS at two spatial frequencies (3 and 6 cycles per degree) and two light conditions (moderate and dim) is sufficiently robust to classify diabetic subjects with no retinopathy versus control subjects.

Common genotypes of hepatitis B virus

International Nuclear Information System (INIS)

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

2004-01-01

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

Substantial advantage of a combined Bayesian and genotyping approach in testosterone doping tests.

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Schulze, Jenny Jakobsson; Lundmark, Jonas; Garle, Mats; Ekström, Lena; Sottas, Pierre-Edouard; Rane, Anders

2009-03-01

Testosterone abuse is conventionally assessed by the urinary testosterone/epitestosterone (T/E) ratio, levels above 4.0 being considered suspicious. A deletion polymorphism in the gene coding for UGT2B17 is strongly associated with reduced testosterone glucuronide (TG) levels in urine. Many of the individuals devoid of the gene would not reach a T/E ratio of 4.0 after testosterone intake. Future test programs will most likely shift from population based- to individual-based T/E cut-off ratios using Bayesian inference. A longitudinal analysis is dependent on an individual's true negative baseline T/E ratio. The aim was to investigate whether it is possible to increase the sensitivity and specificity of the T/E test by addition of UGT2B17 genotype information in a Bayesian framework. A single intramuscular dose of 500mg testosterone enanthate was given to 55 healthy male volunteers with either two, one or no allele (ins/ins, ins/del or del/del) of the UGT2B17 gene. Urinary excretion of TG and the T/E ratio was measured during 15 days. The Bayesian analysis was conducted to calculate the individual T/E cut-off ratio. When adding the genotype information, the program returned lower individual cut-off ratios in all del/del subjects increasing the sensitivity of the test considerably. It will be difficult, if not impossible, to discriminate between a true negative baseline T/E value and a false negative one without knowledge of the UGT2B17 genotype. UGT2B17 genotype information is crucial, both to decide which initial cut-off ratio to use for an individual, and for increasing the sensitivity of the Bayesian analysis.

Moderate alcohol use and cardiovascular disease from Mendelian randomization.

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Shiu Lun Au Yeung

Full Text Available BACKGROUND: Observational studies show moderate alcohol use negatively associated with ischemic heart disease (IHD and cardiovascular disease (CVD. However, healthier attributes among moderate users compared to never users may confound the apparent association. A potentially less biased way to examine the association is Mendelian randomization, using alcohol metabolizing genes which influence alcohol use. METHODS: We used instrumental variable analysis with aldehyde dehydrogenase 2 (ALDH2 genotypes (AA/GA/GG as instrumental variables for alcohol use to examine the association of alcohol use (10 g ethanol/day with CVD risk factors (blood pressure, lipids and glucose and morbidity (self-reported IHD and CVD among men in the Guangzhou Biobank Cohort Study. RESULTS: ALDH2 genotypes were a credible instrument for alcohol use (F-statistic 74.6. Alcohol was positively associated with HDL-cholesterol (0.05 mmol/L per alcohol unit, 95% confidence interval (CI 0.02 to 0.08 and diastolic blood pressure (1.15 mmHg, 95% CI 0.23 to 2.07 but not with systolic blood pressure (1.00 mmHg, 95% CI -0.74 to 2.74, LDL-cholesterol (0.03 mmol/L, 95% CI -0.03 to 0.08, log transformed triglycerides (0.03 mmol/L, 95% CI -0.01 to 0.08 or log transformed fasting glucose (0.01 mmol/L, 95% CI -0.006 to 0.03, self-reported CVD (odds ratio (OR 0.98, 95% CI 0.76 to 1.27 or self-reported IHD (OR 1.10, 95% CI 0.83 to 1.45. CONCLUSION: Low to moderate alcohol use among men had the expected effects on most CVD risk factors but not fasting glucose. Larger studies are needed to confirm the null associations with IHD, CVD and fasting glucose.

Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana.

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Ibañez, Carla; Poeschl, Yvonne; Peterson, Tom; Bellstädt, Julia; Denk, Kathrin; Gogol-Döring, Andreas; Quint, Marcel; Delker, Carolin

2017-07-06

Global increase in ambient temperatures constitute a significant challenge to wild and cultivated plant species. Forward genetic analyses of individual temperature-responsive traits have resulted in the identification of several signaling and response components. However, a comprehensive knowledge about temperature sensitivity of different developmental stages and the contribution of natural variation is still scarce and fragmented at best. Here, we systematically analyze thermomorphogenesis throughout a complete life cycle in ten natural Arabidopsis thaliana accessions grown under long day conditions in four different temperatures ranging from 16 to 28 °C. We used Q 10 , GxE, phenotypic divergence and correlation analyses to assess temperature sensitivity and genotype effects of more than 30 morphometric and developmental traits representing five phenotype classes. We found that genotype and temperature differentially affected plant growth and development with variing strengths. Furthermore, overall correlations among phenotypic temperature responses was relatively low which seems to be caused by differential capacities for temperature adaptations of individual accessions. Genotype-specific temperature responses may be attractive targets for future forward genetic approaches and accession-specific thermomorphogenesis maps may aid the assessment of functional relevance of known and novel regulatory components.

Real-Time Polymerase Chain Reaction Quantification of Phytophthora capsici in Different Pepper Genotypes.

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Silvar, C; Díaz, J; Merino, F

2005-12-01

ABSTRACT Reliable and sensitive quantification of Phytophthora capsici in pepper plants is of crucial importance in managing the multiple syndromes caused by this pathogen. A real-time polymerase chain reaction (PCR) assay was developed for the determination of P. capsici in pepper tissues. DNA levels of a highly virulent and a less virulent isolate were measured in different pepper genotypes with varying degrees of resistance. Using SYBR Green and specific primers for P. capsici, the minimal amount of pathogen DNA quantified was 10 pg. Pathogen DNA was recorded as early as 8 h postinoculation. Thereafter, the increase was rapid in susceptible cultivars and slower in resistant ones. The amount of pathogen DNA quantified in each pepper genotype correlated with susceptibility to Phytophthora root rot. Likewise, there was a relationship between the virulence of the pathogen and the degree of colonization. Differences also were found in oomycete amount among pepper tissues, with maximal pathogen biomass occurring in stems. The real-time PCR technique developed in this study was sensitive and robust enough to assess both pathogen development and resistance to Phytophthora root rot in different pepper genotypes.

Catechol-O-methyltransferase Val158Met genotype in healthy and personality disorder individuals: Preliminary results from an examination of cognitive tests hypothetically differentially sensitive to dopamine functions

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Winnie W Leung

2007-01-01

Full Text Available Winnie W Leung1, Margaret M McClure1, Larry J Siever1,2, Deanna M Barch3, Philip D Harvey1,21Department of Veterans Affairs, VISN 3 Mental Illness Research, Education, and Clinical Center (MIRECC, Bronx, NY, USA; 2Department of Psychiatry, Mt. Sinai School of Medicine, New York, NY, USA; 3Departments of Psychology and Psychiatry, Washington University, St. Louis, MO, USAAbstract: A functional polymorphism of the gene coding for Catechol-O-methyltrasferase (COMT, an enzyme responsible for the degradation of the catecholamine dopamine (DA, epinephrine, and norepinephrine, is associated with cognitive deficits. However, previous studies have not examined the effects of COMT on context processing, as measured by the AX-CPT, a task hypothesized to be maximally relevant to DA function. 32 individuals who were either healthy, with schizotypal personality disorder, or non-cluster A, personality disorder (OPD were genotyped at the COMT Val158Met locus. Met/Met (n = 6, Val/Met (n = 10, Val/Val (n = 16 individuals were administered a neuropsychological battery, including the AX-CPT and the N-back working memory test. For the AX-CPT, Met/Met demonstrated more AY errors (reflecting good maintenance of context than the other genotypes, who showed equivalent error rates. Val/Val demonstrated disproportionately greater deterioration with increased task difficulty from 0-back to 1-back working memory demands as compared to Met/Met, while Val/Met did not differ from either genotypes. No differences were found on processing speed or verbal working memory. Both context processing and working memory appear related to COMT genotype and the AX-CPT and N-back may be most sensitive to the effects of COMT variation.Keywords: COMT, dopamine, context processing, working memory, schizotypal personality disorder

Genetic moderation of the association between adolescent romantic involvement and depression: Contributions of serotonin transporter gene polymorphism, chronic stress, and family discord.

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Starr, Lisa R; Hammen, Constance

2016-05-01

Studies support a link between adolescent romantic involvement and depression. Adolescent romantic relationships may increase depression risk by introducing chronic stress, and genetic vulnerability to stress reactivity/emotion dysregulation may moderate these associations. We tested genetic moderation of longitudinal associations between adolescent romantic involvement and later depressive symptoms by a polymorphism in the serotonin transporter linked polymorphic region gene (5-HTTLPR) and examined contributory roles of chronic stress and family discord. Three hundred eighty-one youth participated at ages 15 and 20. The results indicated that 5-HTTLPR moderated the association between age 15 romantic involvement and age 20 depressive symptoms, with strongest effects for short homozygotes. Conditional process analysis revealed that chronic stress functioned as a moderated mediator of this association, fully accounting for the romantic involvement-depression link among short/short genotypes. Also, romantic involvement predicted later depressive symptoms most strongly among short-allele carriers with high family discord. The results have important implications for understanding the romantic involvement-depression link and the behavioral and emotional correlates of the 5-HTTLPR genotype.

A multiplex PCR for the simultaneous detection and genotyping of the Echinococcus granulosus complex.

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Ghalia Boubaker

Full Text Available Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1-G10 and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1-G3, E. equinus (G4, E. ortleppi (G5, and E. canadensis (G6-G10. The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR allowing three levels of discrimination: (i Echinococcus genus, (ii E. granulosus complex in common, and (iii the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20 and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13. The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (<40%. Thus, except for copro analysis, the mPCR described here has a high potential for a worldwide application in large-scale molecular epidemiological studies on the Echinococcus genus.

Varietals resistance and susceptibility in mustard (brassica campestris l.) genotypes against aphid myzus persicae (sulzer) (homoptera: aphididae)

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Sarwar, M.; Ahmad, N.; Khan, G.Z.; Tofique, M.

2009-01-01

The exploitation of resistant cultivars is an imperative, simple, practical and flexible way to cope with insect pests incidence. Thirty genotypes of mustard (Brassica campestris L.) were tested for their resistance and susceptibility to aphid Myzus persicae (Sulzer) exposed under natural field conditions. Data on pest tolerance of genotypes were judged by quantitative traits such as number of aphids on each infested plant and mean dry weight of seeds per genotype. Studies observed the discrepancy in overall rates of pest invasion and seed yield contained by trailed mustard genotypes. Agati sarson (P), S-9-S-97-100/45 and S-9-S-97-100/45 were the least damaged genotypes showing their moderate resistance. Amongst other genotypes, MM-I/01-5, MM-I285 and MM-I/01-6 were the most damaged showing oversensitive response. Although the majority of genotypes were found vulnerable to pest, Agati sarson (P) and S-9-S-97-100/45 due to their lowest hypersensitive response toward aphid contamination and increased pods yield could be used for the development of essential resistance in mustard plant. A marked mode of damage inflicted by aphid on the crop was noticed and the abiotic factors contributing variations in aphid infestation levels during both growing seasons were determined. Knowledge about the host plant resistance investigated can facilitate growers to choose the most appropriate cultivars as pest control strategy. (author)

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

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Jie Liu

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

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

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

2018-05-01

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

Evaluation of the Abbott Real Time HCV genotype II assay for Hepatitis C virus genotyping.

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

2015-01-01

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

Differential accumulation of dehydrins in response to water stress for hybrid and common bermudagrass genotypes differing in drought tolerance.

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Hu, Longxing; Wang, Zhaolong; Du, Hongmei; Huang, Bingru

2010-01-15

Expression of dehydrin proteins may be induced or enhanced by environmental stresses that lead to cell dehydration. The objective of the this study was to investigate genetic variation in dehydrin protein accumulation in response to drought stress of whole-plants or dehydration of detached leaves and to identify dehydrins differentially expressed in bermudagrass (Cynodon spp.) genotypes differing in drought tolerance. Plants of four hybrid bermudagrass (Cynodondactylon L. xCynodontransvaalensis L.) ('Tifway', 'Tifdwarf', 'Tifeagle', 'Kan1') and four common bermudagrass (Cynodon dactylon) ('C299', 'Sportbermuda', 'H10', and 'H19') genotypes were subjected to 14d of drought stress and detached leaves of two genotypes were exposed to dehydration in growth chambers. Turf quality and leaf relative water content (RWC) decreased while electrolyte leakage (EL) increased during whole-plant drought stress for all genotypes, with more pronounced changes in each parameter for 'C299' and 'Tifeagle' than those for other genotypes ('Tifway', 'Kan 1', 'Sportbermuda', 'H10', and H19'), suggesting that the former two genotypes were more sensitive to drought stress than the other genotypes. During dehydration of detached leaves, relative water loss rate (RWL) was significantly lower in drought-tolerant 'Tifway' than in drought-sensitive 'C299'. Immunoblotting analysis indicated that no dehydrin polypeptides were detected in all genotypes under well-watered conditions. A 24-kDa polypeptide was detected in 'C299' at 6 d of drought, but not in the other genotypes. The dehydrin polypeptides of about 14-74kDa accumulated at 10d of drought stress and in a range of RWL for detached leaves, and two dehydrins (31 and 40kDa) exhibited differential accumulation in the drought-sensitive 'C299' and tolerant 'Tifway', as demonstrated by the whole-plant drought responses. The 31-kDa dehydrin polypeptide was present only in 'Tifway' and 'H19' at 10d of drought stress, and accumulated with the

Molecular epidemiology, genotype-phenotype correlation and BH4 responsiveness in Spanish patients with phenylketonuria.

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Aldámiz-Echevarría, Luis; Llarena, Marta; Bueno, María A; Dalmau, Jaime; Vitoria, Isidro; Fernández-Marmiesse, Ana; Andrade, Fernando; Blasco, Javier; Alcalde, Carlos; Gil, David; García, María C; González-Lamuño, Domingo; Ruiz, Mónica; Ruiz, María A; Peña-Quintana, Luis; González, David; Sánchez-Valverde, Felix; Desviat, Lourdes R; Pérez, Belen; Couce, María L

2016-08-01

Phenylketonuria (PKU), the most common inborn error of amino acid metabolism, is caused by mutations in the phenylalanine-4-hydroxylase (PAH) gene. This study aimed to assess the genotype-phenotype correlation in the PKU Spanish population and the usefulness in establishing genotype-based predictions of BH4 responsiveness in our population. It involved the molecular characterization of 411 Spanish PKU patients: mild hyperphenylalaninemia non-treated (mild HPA-NT) (34%), mild HPA (8.8%), mild-moderate (20.7%) and classic (36.5%) PKU. BH4 responsiveness was evaluated using a 6R-BH4 loading test. We assessed genotype-phenotype associations and genotype-BH4 responsiveness in our population according to literature and classification of the mutations. The mutational spectrum analysis showed 116 distinct mutations, most missense (70.7%) and located in the catalytic domain (62.9%). The most prevalent mutations were c.1066-11G>A (9.7%), p.Val388Met (6.6%) and p.Arg261Gln (6.3%). Three novel mutations (c.61-13del9, p.Ile283Val and p.Gly148Val) were reported. Although good genotype-phenotype correlation was observed, there was no exact correlation for some genotypes. Among the patients monitored for the 6R-BH4 loading test: 102 were responders (87, carried either one or two BH4-responsive alleles) and 194 non-responders (50, had two non-responsive mutations). More discrepancies were observed in non-responders. Our data reveal a great genetic heterogeneity in our population. Genotype is quite a good predictor of phenotype and BH4 responsiveness, which is relevant for patient management, treatment and follow-up.

Comparative DNA microarray analysis of human monocyte derived dendritic cells and MUTZ-3 cells exposed to the moderate skin sensitizer cinnamaldehyde

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Python, Francois; Goebel, Carsten; Aeby, Pierre

2009-01-01

The number of studies involved in the development of in vitro skin sensitization tests has increased since the adoption of the EU 7th amendment to the cosmetics directive proposing to ban animal testing for cosmetic ingredients by 2013. Several studies have recently demonstrated that sensitizers induce a relevant up-regulation of activation markers such as CD86, CD54, IL-8 or IL-1β in human myeloid cell lines (e.g., U937, MUTZ-3, THP-1) or in human peripheral blood monocyte-derived dendritic cells (PBMDCs). The present study aimed at the identification of new dendritic cell activation markers in order to further improve the in vitro evaluation of the sensitizing potential of chemicals. We have compared the gene expression profiles of PBMDCs and the human cell line MUTZ-3 after a 24-h exposure to the moderate sensitizer cinnamaldehyde. A list of 80 genes modulated in both cell types was obtained and a set of candidate marker genes was selected for further analysis. Cells were exposed to selected sensitizers and non-sensitizers for 24 h and gene expression was analyzed by quantitative real-time reverse transcriptase-polymerase chain reaction. Results indicated that PIR, TRIM16 and two Nrf2-regulated genes, CES1 and NQO1, are modulated by most sensitizers. Up-regulation of these genes could also be observed in our recently published DC-activation test with U937 cells. Due to their role in DC activation, these new genes may help to further refine the in vitro approaches for the screening of the sensitizing properties of a chemical.

Association of interleukin-1 gene variations with moderate to severe chronic periodontitis in multiple ethnicities

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Wu, X; Offenbacher, S; Lόpez, N J; Chen, D; Wang, H-Y; Rogus, J; Zhou, J; Beck, J; Jiang, S; Bao, X; Wilkins, L; Doucette-Stamm, L; Kornman, K

2015-01-01

Background and Objective Genetic markers associated with disease are often non-functional and generally tag one or more functional “causative” variants in linkage disequilibrium. Markers may not show tight linkage to the causative variants across multiple ethnicities due to evolutionary divergence, and therefore may not be informative across different population groups. Validated markers of disease suggest causative variants exist in the gene and, if the causative variants can be identified, it is reasonable to hypothesize that such variants will be informative across diverse populations. The aim of this study was to test that hypothesis using functional Interleukin-1 (IL-1) gene variations across multiple ethnic populations to replace the non-functional markers originally associated with chronic adult periodontitis in Caucasians. Material and Methods Adult chronic periodontitis cases and controls from four ethnic groups (Caucasians, African Americans, Hispanics and Asians) were recruited in the USA, Chile and China. Genotypes of IL1B gene single nucleotide polymorphisms (SNPs), including three functional SNPs (rs16944, rs1143623, rs4848306) in the promoter and one intronic SNP (rs1143633), were determined using a single base extension method or TaqMan 5′ nuclease assay. Logistic regression and other statistical analyses were used to examine the association between moderate to severe periodontitis and IL1B gene variations, including SNPs, haplotypes and composite genotypes. Genotype patterns associated with disease in the discovery study were then evaluated in independent validation studies. Results Significant associations were identified in the discovery study, consisting of Caucasians and African Americans, between moderate to severe adult chronic periodontitis and functional variations in the IL1B gene, including a pattern of four IL1B SNPs (OR = 1.87, p < 0.0001). The association between the disease and this IL1B composite genotype pattern was validated

Community phylogenetic analysis of moderately thermophilic cyanobacterial mats from China, the Philippines and Thailand.

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Hongmei, Jing; Aitchison, Jonathan C; Lacap, Donnabella C; Peerapornpisal, Yuwadee; Sompong, Udomluk; Pointing, Stephen B

2005-08-01

Most community molecular studies of thermophilic cyanobacterial mats to date have focused on Synechococcus occurring at temperatures of approximately 50-65 degrees C. These reveal that molecular diversity exceeds that indicated by morphology, and that phylogeographic lineages exist. The moderately thermophilic and generally filamentous cyanobacterial mat communities occurring at lower temperatures have not previously been investigated at the community molecular level. Here we report community diversity in mats of 42-53 degrees C recovered from previously unstudied geothermal locations. Separation of 16S rRNA gene-defined genotypes from community DNA was achieved by DGGE. Genotypic diversity was greater than morphotype diversity in all mats sampled, although genotypes generally corresponded to observed morphotypes. Thirty-six sequences were recovered from DGGE bands. Phylogenetic analyses revealed these to form novel thermophilic lineages distinct from their mesophilic counterparts, within Calothrix, Cyanothece, Fischerella, Phormidium, Pleurocapsa, Oscillatoria and Synechococcus. Where filamentous cyanobacterial sequences belonging to the same genus were recovered from the same site, these were generally closely affiliated. Location-specific sequences were observed for some genotypes recovered from geochemically similar yet spatially separated sites, thus providing evidence for phylogeographic lineages that evolve in isolation. Other genotypes were more closely affiliated to geographically remote counterparts from similar habitats suggesting that adaptation to certain niches is also important.

The Great Recession, genetic sensitivity, and maternal harsh parenting.

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Lee, Dohoon; Brooks-Gunn, Jeanne; McLanahan, Sara S; Notterman, Daniel; Garfinkel, Irwin

2013-08-20

Using data from the Fragile Families and Child Wellbeing Study, this study examined the effects of the Great Recession on maternal harsh parenting. We found that changes in macroeconomic conditions, rather than current conditions, affected harsh parenting, that declines in macroeconomic conditions had a stronger impact on harsh parenting than improvements in conditions, and that mothers' responses to adverse economic conditions were moderated by the DRD2 Taq1A genotype. We found no evidence of a moderating effect for two other, less well-studied SNPs from the DRD4 and DAT1 genes.

Effective salt criteria in callus-cultured tomato genotypes.

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Dogan, Mahmut; Tipirdamaz, Rukiye; Demir, Yavuz

2010-01-01

Na+, Cl-, K+, Ca2+, and proline contents, the rate of lipid peroxidation level in terms of malondialdehyde (MDA) and chlorophyll content, and the changes in the activity of antioxidant enzymes, such as superoxide dismutase (SOD: EC 1.15.1.1), catalase (CAT: EC 1.11.1.6), ascorbate peroxidase (APX: EC 1.11.1.11), and glutathione reductase (GR: EC 1.6.4.2), in tissues of five tomato cultivars in salt tolerance were investigated in a callus culture. The selection of effective parameters used in these tomato genotypes and to find out the use of in vitro tests in place of in vivo salt tolerance tests were investigated. As a material, five different tomato genotypes during a 10-day time period were used, and 150 mM NaCl was applied at callus plant tissue. The exposure to NaCl induced a significant increase in MDA content in both salt-resistant and salt-sensitive cultivars. But the MDA content was higher in salt-sensitive cultivars. The chlorophyll content was more decreased in salt-sensitive than in salt-resistant ones. The proline amount was more increased in salt-sensitive than in salt-resistant ones. It has been reported that salt-tolerant plants, besides being able to regulate the ion and water movements, also exhibit a strong antioxidative enzyme system for effective removal of ROS. The degree of damage depends on the balance between the formation of ROS and its removal by the antioxidative scavenging system that protects against them. Exclusion or inclusion of Na+, Cl-, K+, and Ca2+, antioxidant enzymes and MDA concentration play a key protective role against stress, and this feature at the callus plant tissue used as an identifier for tolerance to salt proved to be an effective criterion.

Tunisian Toxoplasma gondii strains genotyping by the use of AK69 marker

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Aoun Karim

2011-08-01

Full Text Available Abstract Background Clinical manifestation due to infection by Toxoplasma gondii is closely linked to the infecting strain of the parasite. Several genetic markers are available to determinate its genotype but few of them are able to discriminate between the three predominant lineages, namely types I, II and III. The number of markers decreases when atypical, recombinant/mixed genotypes need to be identified. Findings In our study, the contribution of sequence polymorphisms in the AK69 gene as typing markers for T. gondii was investigated for the first time in an epidemiological study. The coding region of the marker was amplified, sequenced and aligned for different Toxoplasma strains. The identified nucleotide polymorphism at 12 positions was able to highly discriminate between the different congenital toxoplasmosis Tunisian strains. Moreover the high detection sensitivity level of the marker enabled unambiguous identification of mixed/recombinant genotypes directly. Conclusion It can be, thus, very useful for direct typing in areas where such genotypes are frequently encountered, mainly in the African continent.

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

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Christine T Shiner

2016-05-01

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

Motivated Shield From Chronic Noise Environment: Moderation of the Relationship Between Noise Sensitivity and Work Wellbeing by Need for Closure

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Stefano Livi

2018-05-01

Full Text Available Several studies have underlined how chronic exposure to environmental noise may have negative effects on performance, wellbeing, and social relations. The present study (N = 90 employees of a motor factory who are chronically exposed to environmental noise investigated whether the negative effects of chronic exposure of noise-sensitive individuals to noise in the workplace may be moderated by the need for cognitive closure (i.e., an epistemic tendency to reduce uncertainty; NFCC, Kruglanski, 2004. As NFCC has been shown to enhance protection of the focal goal by reducing interference (Kossowska, 2007; Pica et al., 2013, we hypothesized that people with high NFCC should be able to manage the interference coming from environmental noise and concentrate on their tasks more than their low-NFCC counterparts. The results confirm that the negative effects of noise sensitivity on job satisfaction, state anxiety, and turnover intent were higher among low (vs. high-NFCC individuals.

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

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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.

Drought tolerance indices and their correlation with yield in exotic wheat genotypes

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Anwar, J.; Subhani, G.M.; Ahmad, J.; Hussain, M.; Munir, M.

2011-01-01

Performance of nineteen exotic genotypes along with local check variety was studied during 2009-10 at Wheat Research Institute, AARI, Faisalabad, Pakistan. The experiment was conducted under two field conditions i.e., stress and irrigated conditions. In case of water stress experiment, only soaking irrigation was applied for seed bed preparation and no further irrigation was applied up to maturity. While, four irrigations were applied at critical growth stages to the second experiment (irrigated). At maturity, grain yield was recorded in both experiments (stress Y/sub s/ and irrigated Y/sub p/). From grain yield data, some drought tolerance/resistance indices such as tolerance index (TOL), mean productivity (MP), harmonic mean (HM), stress susceptibility index (SSI), geometric mean productivity (GMP), stress tolerance index (STI), yield index (YI), yield stability index (YSI) and modified stress tolerance index (k/sub 1/STI and k/sub 2/STI) were calculated. Genotypic correlation, genetic components and heritability were also calculated for grain yield and all indices. Significant differences among genotypes were observed for Y/sub p/, Y/sub s/ and all other drought tolerance indices. Moderate to high heritability and genetic advance were observed for Y/sub p/, Y/sub s/ and all drought tolerance indices. Grain yield under irrigated environment (Y/sub p/) was positively and significantly correlated with MP, HM, GMP, STI and k/sub 1/STI. Similarly, positive and significant association has also been observed between grain yield under stress condition (Y/sub s/) and MP, HM, GMP, STI, YI and k/sub 2/STI so they were the better predictor of potential yield Y/sub p/ and Y/sub s/ than TOL, SSI and YSI. According to Fernandez model; genotypes No. 2, 4, 6, 7, 9 and 13 have uniform superiority under both conditions (stress and irrigated). Genotypes No. 1, 11, 15, 16, 17, 18 and 19 were recommended for irrigated conditions. Genotypes No. 3 and 5 were identified suitable for

Cost Effectiveness of Genotype-Guided Warfarin Dosing in Patients with Mechanical Heart Valve Replacement Under the Fee-for-Service System.

Science.gov (United States)

Kim, Dong-Jin; Kim, Ho-Sook; Oh, Minkyung; Kim, Eun-Young; Shin, Jae-Gook

2017-10-01

Although studies assessing the cost effectiveness of genotype-guided warfarin dosing for the management of atrial fibrillation, deep vein thrombosis, and pulmonary embolism have been reported, no publications have addressed genotype-guided warfarin therapy in mechanical heart valve replacement (MHVR) patients or genotype-guided warfarin therapy under the fee-for-service (FFS) insurance system. The aim of this study was to evaluate the cost effectiveness of genotype-guided warfarin dosing in patients with MHVR under the FFS system from the Korea healthcare sector perspective. A decision-analytic Markov model was developed to evaluate the cost effectiveness of genotype-guided warfarin dosing compared with standard dosing. Estimates of clinical adverse event rates and health state utilities were derived from the published literature. The outcome measure was the incremental cost-effectiveness ratio (ICER) per quality-adjusted life-year (QALY). One-way and probabilistic sensitivity analyses were performed to explore the range of plausible results. In a base-case analysis, genotype-guided warfarin dosing was associated with marginally higher QALYs than standard warfarin dosing (6.088 vs. 6.083, respectively), at a slightly higher cost (US$6.8) (year 2016 values). The ICER was US$1356.2 per QALY gained. In probabilistic sensitivity analysis, there was an 82.7% probability that genotype-guided dosing was dominant compared with standard dosing, and a 99.8% probability that it was cost effective at a willingness-to-pay threshold of US$50,000 per QALY gained. Compared with only standard warfarin therapy, genotype-guided warfarin dosing was cost effective in MHVR patients under the FFS insurance system.

Development of a rapid HRM genotyping method for detection of dog-derived Giardia lamblia.

Science.gov (United States)

Tan, Liping; Yu, Xingang; Abdullahi, Auwalu Yusuf; Wu, Sheng; Zheng, Guochao; Hu, Wei; Song, Meiran; Wang, Zhen; Jiang, Biao; Li, Guoqing

2015-11-01

Giardia lamblia is a zoonotic flagellate protozoan in the intestine of human and many mammals including dogs. To assess a threat of dog-derived G. lamblia to humans, the common dog-derived G. lamblia assemblages A, C, and D were genotyped by high-resolution melting (HRM) technology. According to β-giardin gene sequence, the qPCR-HRM primers BG5 and BG7 were designed. A series of experiments on the stability, sensitivity, and accuracy of the HRM method were also tested. Results showed that the primers BG5 and BG7 could distinguish among three assemblages A, C, and D, which Tm value differences were about 1 °C to each other. The melting curves of intra-assay reproducibility were almost coincided, and those of inter-assay reproducibility were much the same shape. The lowest detection concentration was about 5 × 10(-6)-ng/μL sample. The genotyping results from 21 G. lamblia samples by the HRM method were in complete accordance with sequencing results. It is concluded that the HRM genotyping method is rapid, stable, specific, highly sensitive, and suitable for clinical detection and molecular epidemiological survey of dog-derived G. lamblia.

Histo-blood group ABO antigen in oral potentially malignant lesions and squamous cell carcinoma--genotypic and phenotypic characterization

DEFF Research Database (Denmark)

Gao, Shan; Bennett, Erik Paul; Reibel, Jesper

2004-01-01

Loss of histo-blood group A/B antigens is frequent in oral cancer. It is unclear whether this alteration is due to loss of the chromosomal region encoding the genes. The aim was to investigate genotypic alterations in the ABO locus in oral potentially malignant lesions and carcinomas. Seventy...... to establish the ABO genotype. Total and patchy loss of A/B antigen expression was found in 24/32 carcinomas, 6/7 leukoplakias with severe dysplasia, 12/17 leukoplakias with mild and moderate dysplasia, and 6/17 leukoplakias without dysplasia. Specific A/B allele loss was found in 8/24 cases with carcinoma...

Evaluation of wheat genotypes originated from interspecific crossing and gamma radiation

International Nuclear Information System (INIS)

Camargo, C.E.O.; Ferreira Filho, A.W.P.; Freitas, J.G.; Tulmann Neto, A.; Pettinelli Junior, A.; Castro, J.L.

1995-01-01

Twenty three inbred HEXAPLOID wheat lines were evaluated. They were originated by selections made in populations submitted to gamma radiation (27.5 krad), in the F 4 generation, from the interspecific hybrid between BH-1146 (triticum aestivum L.) and Anhinga S x Winged S (Triticum durum L.) and the cultivars BH-1146 and Yavaros S (T. durum L.) Nine trials were carried out with irrigation and in upland conditions. Several agronomic characteristics were assessed. Under laboratory conditions the genotypes were evaluated with respect to Al toxicity using nutrient solutions. Semi dwarf line 11 and 19, with moderate lodging resistance, medium cycle from emergence to flowering, tolerance to aluminum toxicity, were the most productive. Seven lines showed resistance to the causal agent of mildew, but all genotypes were susceptible to the causal agents of leaf spots. Some of the genotypes could be used in cross breeding as genetic sources for short plant, long head, large number of spikelets per head, large number of grains per head and per spikelet and heavy grains. BH-1146 and seven from the 23 lines were considered the most tolerant to aluminium toxicity, presenting good regrowth after treatment in nutrient solutions with 10 mg/liter of Al +3 . (author). 15 refs., 7 tabs

Genotypic carriers of the obesity-associated FTO polymorphism exhibit different cardiometabolic profiles after an intervention

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GREICE G. MORAES

Full Text Available ABSTRACT Background: Children and adolescents with at-risk genotypes (AA/AT of the rs9939609 polymorphism in FTO, a fat mass and obesity-associated gene, may exhibit different cardiometabolic profile responses than subjects with the TT genotype after an interdisciplinary intervention. Methods: The sample consisted of 36 school children from southern Brazil. We used DNA quantitation and real-time polymerase chain reaction (PCR for polymorphism genotyping. We measured anthropometric parameters (body mass index (BMI, waist circumference, hip circumference, waist-hip ratio, body fat percentage and skinfold sum, biochemical parameters (glucose, lipid profile, ultra-sensitive C-reactive protein, uric acid, alanine aminotransferase, aspartate aminotransferase, insulin and adiponectin and blood pressure. The 4-month intervention consisted of physical education classes, nutritional counseling, and postural and oral health counseling. Results: We observed no significant differences among the groups (AA, AT and TT after the intervention. However, we observed improvements in three parameters (waist circumference, hip circumference and C-reactive protein in the AT/AA genotype group and in two parameters (hip circumference and uric acid in the TT genotype group. Conclusions: After an intervention program, carriers of at-risk genotypes for obesity (AA/AT do not exhibit differences in biochemical parameters, blood pressure and anthropometric parameters compared with carriers of the TT genotype.

Differential Susceptibility: The Genetic Moderation of Peer Pressure on Alcohol Use

OpenAIRE

Griffin, Amanda M.; Cleveland, H. Harrington; Schlomer, Gabriel L.; Vandenbergh, David J.; Feinberg, Mark E.

2015-01-01

Although peer pressure can influence adolescents’ alcohol use, individual susceptibility to these pressures varies across individuals. The dopamine receptor D4 gene (DRD4) is a potential candidate gene that may influence adolescents’ susceptibility to their peer environment due to the role dopamine plays in reward sensation during social interaction. We hypothesized that DRD4 genotype status would moderate the impact of 7th-grade antisocial peer pressure on 12th-grade lifetime alcohol use (n ...

Assessment of genetic diversity among moderately drought tolerant landraces of rice using RAPD markers

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Md. Shariful Islam

2013-01-01

Full Text Available Genetic diversity and relationships among six rice genotypes were investigated using five random amplified polymorphic DNA (RAPD markers. A total of 69 alleles were amplified, of which 66 were polymorphic. The size of the amplified alleles was between 0.25 and 2.35 kbp. The number of polymorphic alleles detected with each primer ranged from 7 to 24 with an average of 13.2 per primer and the polymorphism information content (PIC values varied from 0.8672 to 0.9471. Pair-wise similarity estimated the range of 0.308 to 0.718 among all the genotypes and the highest genetic similarity was found between Maloti and BRRI dhan53. Cluster analysis using UPGMA (unweighted pair group method with arithmetic averages revealed three clusters at genetic similarity of 46%. A moderately drought tolerant landrace, Boalia, formed a single cluster and the remaining genotypes grouped into distinct clusters based on their relatedness. The results showed a high level of genetic diversity among studied genotypes and this information will assist in conservation as well as selection of parents during breeding programs for the development of drought tolerant rice varieties in near future.

Probing Phosphorus Efficient Low Phytic Acid Content Soybean Genotypes with Phosphorus Starvation in Hydroponics Growth System.

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Kumar, Varun; Singh, Tiratha Raj; Hada, Alkesh; Jolly, Monica; Ganapathi, Andy; Sachdev, Archana

2015-10-01

Phosphorus is an essential nutrient required for soybean growth but is bound in phytic acid which causes negative effects on both the environment as well as the animal nutrition. Lowering of phytic acid levels is associated with reduced agronomic characteristics, and relatively little information is available on the response of soybean plants to phosphorus (P) starvation. In this study, we evaluated the effects of different P starvation concentrations on the phytic acid content, growth, and yield of seven mutant genotypes along with the unirradiated control, JS-335, in a hydroponics growth system. The low phytic acid containing mutant genotypes, IR-JS-101, IR-DS-118, and IR-V-101, showed a relatively high growth rate in low P concentration containing nutrient solution (2 μM), whereas the high P concentration (50 μM) favored the growth of IR-DS-111 and IR-DS-115 mutant genotypes containing moderate phytate levels. The mutant genotypes with high phytic acid content, IR-DS-122, IR-DS-114, and JS-335, responded well under P starvation and did not have any significant effect on the growth and yield of plants. Moreover, the reduction of P concentration in nutrient solution from 50 to 2 μM also reduced the phytic acid content in the seeds of all the soybean genotypes under study. The desirable agronomic performance of low phytic acid containing mutant genotype IR-DS-118 reported in this study suggested it to be a P-efficient genotype which could be considered for agricultural practices under P limiting soils.

Comparison of virulence of Francisella tularensis ssp. holarctica genotypes B.12 and B.FTNF002-00.

Science.gov (United States)

Kreizinger, Zsuzsa; Erdélyi, Károly; Felde, Orsolya; Fabbi, Massimo; Sulyok, Kinga M; Magyar, Tibor; Gyuranecz, Miklós

2017-02-10

Two main genetic groups (B.12 and B.FTNF002-00) of Francisella tularensis ssp. holarctica are endemic in Europe. The B.FTNF002-00 group proved to be dominant in Western European countries, while strains of the B.12 group were isolated mainly in Northern, Central and Eastern Europe. The clinical course of tularemia in the European brown hare (Lepus europaeus) also shows distinct patterns according to the geographical area. Acute course of the disease is observed in hares in Western European countries, while signs of sub-acute or chronic infection are more frequently detected in the eastern part of the continent. The aim of the present study was to examine whether there is any difference in the virulence of the strains belonging to the B.FTNF002-00 and B.12 genetic clades. Experimental infection of Fischer 344 rats was performed by intra-peritoneal injection of three dilutions of a Hungarian (B.12 genotype) and an Italian (B.FTNF002-00 genotype) F. tularensis ssp. holarctica strain. Moderate difference was observed in the virulence of the two genotypes. Significant differences were observed in total weight loss values and scores of clinical signs between the two genotypes with more rats succumbing to tularemia in groups infected with the B.FTNF002-00 genotype. Results of the experimental infection are consistent with previous clinical observations and pathological studies suggesting that F. tularensis ssp. holarctica genotype B.FTNF002-00 has higher pathogenic potential than the B.12 genotype.

A Review of Nutrition-Specific and Nutrition-Sensitive Approaches to Preventing Moderate Acute Malnutrition

International Nuclear Information System (INIS)

Mucha, Noreen; Jimenez, Michelle; Stone-Jimenez, Maryanne; Brown, Rebecca

2014-01-01

Full text: Recent literature reviews have demonstrated the limited efficacy of targeted supplementary feeding programmes aimed at both treating and preventing moderate acute malnutrition (MAM), with high rates of defaulting, low coverage and high associated costs. There is a growing interest in a) reviewing and improving protocols / tools for the management of acute malnutrition and b) increasing the quality and variety of products available for the treatment / prevention of moderate acute malnutrition. There is however, varying evidence on the impact of nutritional products aimed at preventing or treating acute malnutrition, or on the comparative efficacy of different products. Following several literature reviews and operational research with varying results, there is increasing consensus that MAM should be tackled not only through products, and that clearer guidance should be provided on broader preventive strategies, such as optimal infant and young child feeding (IYCF) and caregiving practices, optimal maternal nutrition, counselling, social protection, food security and livelihoods, and water, sanitation and hygiene (WASH). The CMAM Forum has commissioned Technical Briefs which aim to summarise current thinking and practice relating to preventive approaches to MAM, looking at the role of both nutrition-specific and nutrition-sensitive interventions. The work is being launched in January 2014 and results will be available for presentation at the IAEA MAM Symposium in May 2014. The briefs aim to provide: • An overview of approaches to preventing MAM across different sectors (e.g. agriculture, health, IYCF, social protection, water and sanitation) and in different contexts. • A review of current knowledge including: – Evidence from systematic and literature reviews. – Existing approaches and practice for prevention of MAM. – Current guidance on making programmatic choices relating to MAM prevention interventions and decision-making frameworks. �

Prenatal stress exposure, oxytocin receptor gene (OXTR) methylation, and child autistic traits: The moderating role of OXTR rs53576 genotype.

Science.gov (United States)

Rijlaarsdam, Jolien; van IJzendoorn, Marinus H; Verhulst, Frank C; Jaddoe, Vincent W V; Felix, Janine F; Tiemeier, Henning; Bakermans-Kranenburg, Marian J

2017-03-01

Findings of studies investigating OXTR SNP rs53576 (G-A) variation in social behavior have been inconsistent, possibly because DNA methylation after stress exposure was eliminated from consideration. Our goal was to examine OXTR rs53576 allele-specific sensitivity for neonatal OXTR DNA methylation in relation to (1) a prenatal maternal stress composite, and (2) child autistic traits. Prospective data from fetal life to age 6 years were collected in a total of 743 children participating in the Generation R Study. Prenatal maternal stress exposure was uniquely associated with child autistic traits but was unrelated to OXTR methylation across both OXTR rs53576 G-allele homozygous children and A-allele carriers. For child autistic traits in general and social communication problems in particular, we observed a significant OXTR rs53576 genotype by OXTR methylation interaction in the absence of main effects, suggesting that opposing effects cancelled each other out. Indeed, OXTR methylation levels were positively associated with social problems for OXTR rs53576 G-allele homozygous children but not for A-allele carriers. These results highlight the importance of incorporating epi-allelic information and support the role of OXTR methylation in child autistic traits. Autism Res 2017, 10: 430-438. © 2016 International Society for Autism Research, Wiley Periodicals, Inc. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.

Genetic divergence of bean genotypes to infestation of Zabrotes subfasciatus (Bohemann (Coleoptera: Bruchidae

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Eduardo Neves Costa

2013-12-01

Full Text Available The aim of this work was to evaluate the genetics divergence of bean genotypes in relation to the oviposition, feeding and development of Zabrotes subfasciatus, determining the degrees of resistance to the weevil. The genotypes used were: IAC Carioca-Tybatã, IAC Fortaleza, IAPAR 81, IAC Carioca-Eté, IAC Galante, IAC Harmonia, IAC Una, IAC Diplomata, BRS Supremo and RAZ 49. Tests were performed in laboratory under controlled humidity, temperature and photophase conditions. In free choice test, 10 g of bean genotypes seeds were distributed in circular openings placed equidistant from each other in aluminum trays, where 70 couples were released. The attractiveness was evaluated 24 hours and seven days after the experiment started, and then the number of eggs was evaluated. In non choice test, 10 g of seeds were used where seven couples of Z. subfasciatus, 24 hours-old, were released, remaining seven days, and after the adults retreat, the total number eggs, viable and unviable eggs, the number and percentage of emerged adults, weight, longevity and period from egg to adult of males and females, sex ratio, dry mass and dry mass consumed by insect were evaluated. In the genotype IAC Harmonia was observed the lower oviposition; RAZ 49 was the most non preference-type resistant for feeding and/or antibiosis-type resistant; BRS Supremo, IAC Carioca-Eté and IAPAR 81 are no preference for feeding and/or antibiosis-type moderate resistant; IAC Galante is susceptible and the other genotypes are highly susceptible to Z. subfasciatus

Is the Prediction of Adolescent Outcomes from Early Child Care Moderated by Later Maternal Sensitivity? Results from the NICHD Study of Early Child Care and Youth Development

Science.gov (United States)

Burchinal, Margaret R.; Lowe Vandell, Deborah; Belsky, Jay

2014-01-01

Longitudinal data are used to examine whether effects of early child care are amplified and/or attenuated by later parenting. Analyses tested these interactions using parenting as both a categorical and continuous variable to balance power and flexibility in testing moderation. The most consistent finding was that maternal sensitivity during…

Serotonin-related gene expression in female monkeys with individual sensitivity to stress.

Science.gov (United States)

Bethea, C L; Streicher, J M; Mirkes, S J; Sanchez, R L; Reddy, A P; Cameron, J L

2005-01-01

Female cynomolgus monkeys exhibit different degrees of reproductive dysfunction with moderate metabolic and psychosocial stress. In this study, the expression of four genes pivotal to serotonin neural function was assessed in monkeys previously categorized as highly stress resistant (n=3; normal menstrual cyclicity through two stress cycles), medium stress resistant (n=5; ovulatory in the first stress cycle but anovulatory in the second stress cycle), or low stress resistant (i.e. stress-sensitive; n=4; anovulatory as soon as stress is initiated). In situ hybridization and quantitative image analysis was used to measure mRNAs coding for SERT (serotonin transporter), 5HT1A autoreceptor, MAO-A and MAO-B (monoamine oxidases) at six levels of the dorsal raphe nucleus (DRN). Optical density (OD) and positive pixel area were measured with NIH Image software. In addition, serotonin neurons were immunostained and counted at three levels of the DRN. Finally, each animal was genotyped for the serotonin transporter long polymorphic region (5HTTLPR). Stress sensitive animals had lower expression of SERT mRNA in the caudal region of the DRN (PMAO-A mRNA signal in the stress-sensitive group (PMAO-A OD was positively correlated with progesterone from a pre-stress control cycle (PMAO-B mRNA exhibited a similar downward trend in the stress-sensitive group. MAO-B OD also correlated with control cycle progesterone (PMAO-A) or exhibited a lower trend (5HT1A, MAO-B) in the stress sensitive animals, which probably reflects the lower number of serotonin neurons present.

Morphological characterization and estimation of genotype * environment interaction of indigenous buckwheat germplasm collected from Gilgit Baltistan, Pakistan

International Nuclear Information System (INIS)

Facho, Z.H.; Tarhatullah, A.; Khalil, I.H.; Ali, S.

2016-01-01

A two-year study (2011 and 2012) was conducted at two locations (Skardu and Ghanche) of Gilgit Baltistan, Pakistan to characterize and estimate genotype by environment interaction (GEI) for 20 buckwheat genotypes collected from 18 locations of Gilgit - Baltistan, Pakistan. The GE interaction was studied using a set of six quantitative descriptors. Wide range of variations was recorded for flowering, maturity, plant height, 1000 grain weight, grains plant-1 and grain yield ha-1. Significant differences in locations for all traits were recorded. Years * locations interactions was also significant (p= 0.05) for all traits except grains plant-1 and grain yield ha-1. Similarly, genotype * location * year interaction existed for most of the traits except plant height, grains plant-1 and grain yield ha-1. The genotype Sh-914 (29.91 g) excelled in 1000-grain weight, followed by Rd-915 (27.04 g). Maximum grains plant-1 were produced by Sh-914 (323.62) followed by the genotype Gh-918 (229.16). Maximum grain yield of 2010.27 kg ha-1 was produced by genotype Sh-914, followed by the genotype Gh-918 (1910.40 kg ha-1). Days to flowering, days to maturity, and 1000 grain weight were the major contributors towards genetic divergence among the buckwheat genotypes. Moderate to high estimates of broad-sense heritability and selection response were observed for traits at two test locations. Cluster analysis based on morphological and yield related traits classified buckwheat genotypes of two species (Fagopyrum esculentum and F. tataricum) into three main groups. The clustering pattern revealed that genotypes collected from the same location were grouped into different clusters. Data obtained on the basis of Dendrogram showed differences for various phenological and yield traits among buckwheat genotypes. Buckwheat genotypes Sh-914 and Gh-918 performed well at Skardu and Sh-914 and Rd-915 at Ghanche. The information on the existing genetic variability for morphological and yield

Modelling of genotype by environment interaction and prediction of complex traits across multiple environments as a synthesis of crop growth modelling, genetics and statistics

OpenAIRE

Bustos-Korts, Daniela

2017-01-01

The main objective of plant breeders is to create and identify genotypes that are well-adapted to the target population of environments (TPE). The TPE corresponds to the future growing conditions in which the varieties produced by a breeding program will be grown. All possible genotypes that could be considered as selection candidates for a specific TPE are said to belong to the target population of genotypes, TPG. Genotypes commonly show different sensitivities to environmental gradients and...

Simultaneous detection and differentiation of three genotypes of Brassica yellows virus by multiplex reverse transcription-polymerase chain reaction.

Science.gov (United States)

Zhang, Xiaoyan; Peng, Yanmei; Wang, Ying; Zhang, Zongying; Li, Dawei; Yu, Jialin; Han, Chenggui

2016-11-22

Brassica yellows virus (BrYV), proposed to be a new polerovirus species, three distinct genotypes (BrYV-A, BrYV-B and BrYV-C) have been described. This study was to develop a simple, rapid, sensitive, cost-effective method for simultaneous detection and differentiation of three genotypes of BrYV. In this study, a multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for simultaneous detection and differentiation of the three genotypes of BrYV. The three genotypes of BrYV and Tunip yellows virus (TuYV) could be differentiated simultaneously using six optimized specific oligonucleotide primers, including one universal primer for detecting BrYV, three BrYV genotype-specific primers, and a pair of primers for specific detection of TuYV. Primers were designed from conserved regions of each virus and their specificity was confirmed by sequencing PCR products. The mRT-PCR products were 278 bp for BrYV-A, 674 bp for BrYV-B, 505 bp for BrYV-C, and 205 bp for TuYV. Amplification of three target genotypes was optimized by increasing the PCR annealing temperatures to 62 °C. One to three fragments specific for the virus genotypes were simultaneously amplified from infected samples and identified by their specific molecular sizes in agarose gel electrophoresis. No specific products could be amplified from cDNAs of other viruses which could infect crucifer crops. Detection limits of the plasmids for multiplex PCR were 100 fg for BrYV-A and BrYV-B, 10 pg for BrYV-C, and 1 pg for TuYV, respectively. The mRT-PCR was applied successfully for detection of three BrYV genotypes from field samples collected in China. The simple, rapid, sensitive, and cost-effective mRT-PCR was developed successfully for detection and differentiation of the three genotypes of BrYV.

Novel non-invasive biological predictive index for liver fibrosis in hepatitis C virus genotype 4 patients

Science.gov (United States)

Khattab, Mahmoud; Sakr, Mohamed Amin; Fattah, Mohamed Abdel; Mousa, Youssef; Soliman, Elwy; Breedy, Ashraf; Fathi, Mona; Gaber, Salwa; Altaweil, Ahmed; Osman, Ashraf; Hassouna, Ahmed; Motawea, Ibrahim

2016-01-01

AIM To investigate the diagnostic ability of a non-invasive biological marker to predict liver fibrosis in hepatitis C genotype 4 patients with high accuracy. METHODS A cohort of 332 patients infected with hepatitis C genotype 4 was included in this cross-sectional study. Fasting plasma glucose, insulin, C-peptide, and angiotensin-converting enzyme serum levels were measured. Insulin resistance was mathematically calculated using the homeostasis model of insulin resistance (HOMA-IR). RESULTS Fibrosis stages were distributed based on Metavir score as follows: F0 = 43, F1 = 136, F2 = 64, F3 = 45 and F4 = 44. Statistical analysis relied upon reclassification of fibrosis stages into mild fibrosis (F0-F) = 179, moderate fibrosis (F2) = 64, and advanced fibrosis (F3-F4) = 89. Univariate analysis indicated that age, log aspartate amino transaminase, log HOMA-IR and log platelet count were independent predictors of liver fibrosis stage (P < 0.0001). A stepwise multivariate discriminant functional analysis was used to drive a discriminative model for liver fibrosis. Our index used cut-off values of ≥ 0.86 and ≤ -0.31 to diagnose advanced and mild fibrosis, respectively, with receiving operating characteristics of 0.91 and 0.88, respectively. The sensitivity, specificity, positive predictive value, negative predictive value and positive likelihood ratio were: 73%, 91%, 75%, 90% and 8.0 respectively for advanced fibrosis, and 67%, 88%, 84%, 70% and 4.9, respectively, for mild fibrosis. CONCLUSION Our predictive model is easily available and reproducible, and predicted liver fibrosis with acceptable accuracy. PMID:27917265

Novel non-invasive biological predictive index for liver fibrosis in hepatitis C virus genotype 4 patients.

Science.gov (United States)

Khattab, Mahmoud; Sakr, Mohamed Amin; Fattah, Mohamed Abdel; Mousa, Youssef; Soliman, Elwy; Breedy, Ashraf; Fathi, Mona; Gaber, Salwa; Altaweil, Ahmed; Osman, Ashraf; Hassouna, Ahmed; Motawea, Ibrahim

2016-11-18

To investigate the diagnostic ability of a non-invasive biological marker to predict liver fibrosis in hepatitis C genotype 4 patients with high accuracy. A cohort of 332 patients infected with hepatitis C genotype 4 was included in this cross-sectional study. Fasting plasma glucose, insulin, C-peptide, and angiotensin-converting enzyme serum levels were measured. Insulin resistance was mathematically calculated using the homeostasis model of insulin resistance (HOMA-IR). Fibrosis stages were distributed based on Metavir score as follows: F0 = 43, F1 = 136, F2 = 64, F3 = 45 and F4 = 44. Statistical analysis relied upon reclassification of fibrosis stages into mild fibrosis (F0-F) = 179, moderate fibrosis (F2) = 64, and advanced fibrosis (F3-F4) = 89. Univariate analysis indicated that age, log aspartate amino transaminase, log HOMA-IR and log platelet count were independent predictors of liver fibrosis stage ( P < 0.0001). A stepwise multivariate discriminant functional analysis was used to drive a discriminative model for liver fibrosis. Our index used cut-off values of ≥ 0.86 and ≤ -0.31 to diagnose advanced and mild fibrosis, respectively, with receiving operating characteristics of 0.91 and 0.88, respectively. The sensitivity, specificity, positive predictive value, negative predictive value and positive likelihood ratio were: 73%, 91%, 75%, 90% and 8.0 respectively for advanced fibrosis, and 67%, 88%, 84%, 70% and 4.9, respectively, for mild fibrosis. Our predictive model is easily available and reproducible, and predicted liver fibrosis with acceptable accuracy.

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.

Effect of alcohol dehydrogenase-1B and -7 polymorphisms on blood ethanol and acetaldehyde concentrations in healthy subjects with a history of moderate alcohol consumption.

Science.gov (United States)

Pastorino, Roberta; Iuliano, Luigi; Vecchioni, Alessia; Arzani, Dario; Milic, Mirta; Annunziata, Francesca; Zerbinati, Chiara; Capoluongo, Ettore; Bonassi, Stefano; McKay, James D; Boccia, Stefania

2018-03-01

This study aims to evaluate the effect of ADH1B and ADH7 genotypes on blood acetaldehyde and ethanol levels after alcohol ingestion, and to measure the genotoxic effect of smoking and ethanol on the buccal cells, also controlling for ADH variants. We recruited healthy Italian subjects with at least a moderate history of alcohol consumption. All subjects were given an alcoholic drink of 0.4 g ethanol /kg of body weight. Blood venous samples were collected at baseline, and 30, 60, 90, and 120 minutes after ingestion. Buccal cells were collected before ethanol ingestion. Sixty subjects were enrolled in the study. Individuals with the ADH1B GG genotype had median ethanol levels of 5.0mM (IQR 3.4-7.2), and those with the ADH1B GT/TT genotype had 4.7mM (IQR 4.2-4.8). Corresponding acetaldehyde levels were 1.5μM (IQR 0.7-2.6) for ADH1B GG genotype and 1.6μM (IQR 1.5-1.7) for ADH1B CG/GG genotype. Individuals with the ADH7 CC genotype had median ethanol levels of 5.0mM (IQR 3.3-7.2), while 5.0mM (IQR 4.7-5.6) was in those with the ADH7 CG/GG genotype. Corresponding acetaldehyde levels were 1.5 μM (IQR 0.7-2.6) for ADH7 CC genotype and 1.5 μM (IQR 1.4-1.6) for ADH7 CG/GG genotypes. A non-significant increase in the frequency of karyolitic and pyknotic cells was found in the group of heavy drinkers and current smokers, when compared to the moderate drinkers and the non-smokers. Our study does not support the hypothesis that ADH1B and ADH7 genotypes affect blood ethanol and acetaldehyde concentration. Copyright © 2017 John Wiley & Sons, Ltd.

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

International Nuclear Information System (INIS)

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

2007-01-01

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

Chlorophyll a fluorescence to phenotype wheat genotypes for heat tolerance

DEFF Research Database (Denmark)

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

In prospects of global climate change, heat stress is a rising constraint for the productivity of wheat (Triticum aestivum L.). It is a heat-susceptible crop beyond 17-23oC temperature throughout its phenological stages, flowering phase being the most sensitive stage. Chlorophyll a fluorescence...... parameter, maximum quantum yield efficiency of PSII (Fv/Fm) is used as a physiological marker for early stress detection in PSII in plants. We established a reproducible protocol to measure response of wheat genotypes to high temperature based on Fv/Fm. The heat treatment of 40°C in 300 µmol m-2s-1 PAR...... enabled the identification of contrasting wheat genotypes that can be used to study the genetic and physiological nature of heat stress tolerance to dissect quantitative traits into simpler and more heritable traits....

Rapid ABO genotyping by high-speed droplet allele-specific PCR using crude samples.

Science.gov (United States)

Taira, Chiaki; Matsuda, Kazuyuki; Takeichi, Naoya; Furukawa, Satomi; Sugano, Mitsutoshi; Uehara, Takeshi; Okumura, Nobuo; Honda, Takayuki

2018-01-01

ABO genotyping has common tools for personal identification of forensic and transplantation field. We developed a new method based on a droplet allele-specific PCR (droplet-AS-PCR) that enabled rapid PCR amplification. We attempted rapid ABO genotyping using crude DNA isolated from dried blood and buccal cells. We designed allele-specific primers for three SNPs (at nucleotides 261, 526, and 803) in exons 6 and 7 of the ABO gene. We pretreated dried blood and buccal cells with proteinase K, and obtained crude DNAs without DNA purification. Droplet-AS-PCR allowed specific amplification of the SNPs at the three loci using crude DNA, with results similar to those for DNA extracted from fresh peripheral blood. The sensitivity of the methods was 5%-10%. The genotyping of extracted DNA and crude DNA were completed within 8 and 9 minutes, respectively. The genotypes determined by the droplet-AS-PCR method were always consistent with those obtained by direct sequencing. The droplet-AS-PCR method enabled rapid and specific amplification of three SNPs of the ABO gene from crude DNA treated with proteinase K. ABO genotyping by the droplet-AS-PCR has the potential to be applied to various fields including a forensic medicine and transplantation medical care. © 2017 Wiley Periodicals, Inc.

Parental acceptance, postpartum depression, and maternal sensitivity: mediating and moderating processes.

Science.gov (United States)

Crockenberg, Susan C; Leerkes, Esther M

2003-03-01

Mothers (n = 92), fathers (n = 84), and their infants (60% male) participated in a longitudinal study of postpartum depression and maternal sensitivity. Mothers completed questionnaire measures of remembered parental acceptance, depressive symptoms, and infant distress to novelty and limits. Mothers and partners reported on marital aggression and avoidance. Maternal sensitivity was observed in the laboratory at 6 months. Characteristics of mothers, partners, and infants combined to predict postpartum depression and maternal sensitivity. Remembered parental rejection predicted postpartum depressive symptoms with prenatal depression controlled; self-esteem mediated this effect. Paternal acceptance buffered against postpartum depression when infants were highly reactive and when partners were aggressive. Paternal acceptance reduced the impact of postpartum depression on maternal sensitivity; having an aggressive marital partner exacerbated the effect.

HBV genotypic variability in Cuba.

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Carmen L Loureiro

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

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

Assimilation and Translocation of Dry Matter and Phosphorus in Rice Genotypes Affected by Salt-Alkaline Stress

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Zhijie Tian

2016-06-01

Full Text Available Salt-alkaline stress generally leads to soil compaction and fertility decline. It also restricts rice growth and phosphorus acquisition. In this pot experiment, two relatively salt-alkaline tolerant (Dongdao-4 and Changbai-9 and sensitive (Changbai-25 and Tongyu-315 rice genotypes were planted in sandy (control and salt-alkaline soil to evaluate the characteristics of dry matter and phosphorus assimilation and translocation in rice. The results showed that dry matter and phosphorus assimilation in rice greatly decreased under salt-alkaline stress as the plants grew. The translocation and contribution of dry matter and phosphorus to the grains also increased markedly; different performances were observed between genotypes under salt-alkaline stress. D4 and C9 showed higher dry matter translocation, translocation efficiency and contribution of dry matter assimilation to panicles than those of C25 and T315. These changes in D4 and C9 indexes occurred at low levels of salt-alkaline treatment. Higher phosphorus acquisition efficiency of D4 and C9 were also found under salt-alkaline conditions. Additionally, the phosphorus translocation significantly decreased in C25 and T315 in the stress treatment. In conclusion, the results indicated that salt-alkaline-tolerant rice genotypes may have stronger abilities to assimilate and transfer biomass and phosphorus than sensitive genotypes, especially in salt-alkaline conditions.

Virulence of viral hemorrhagic septicemia virus (VHSV) genotypes Ia, IVa, IVb, and IVc in five fish species.

Science.gov (United States)

Emmenegger, Eveline J.; Moon, Chang Hoon; Hershberger, Paul K.; Kurath, Gael

2013-01-01

The susceptibility of yellow perch Perca flavescens, rainbow trout Oncorhynchus mykiss, Chinook salmon O. tshawytscha, koi Cyprinus carpio koi, and Pacific herring Clupea pallasii to 4 strains of viral hemorrhagic septicemia virus (VHSV) was assessed. Fish were challenged via intraperitoneal injection with high (1 × 106 plaque-forming units, PFU) and low (1 × 103 PFU) doses of a European strain (genotype Ia), and North American strains from the West coast (genotype IVa), Great Lakes (genotype IVb), and the East coast (genotype IVc). Pacific herring were exposed to the same VHSV strains, but at a single dose of 5 × 103 PFU ml-1 by immersion in static seawater. Overall, yellow perch were the most susceptible, with cumulative percent mortality (CPM) ranging from 84 to 100%, and 30 to 93% in fish injected with high or low doses of virus, respectively. Rainbow trout and Chinook salmon experienced higher mortalities (47 to 98% CPM) after exposure to strain Ia than to the other virus genotypes. Pacific herring were most susceptible to strain IVa with an average CPM of 80% and moderately susceptible (42 to 52% CPM) to the other genotypes. Koi had very low susceptibility (≤5.0% CPM) to all 4 VHSV strains. Fish tested at 7 d post challenge were positive for all virus strains, with yellow perch having the highest prevalence and concentrations of virus, and koi the lowest. While genotype Ia had higher virulence in salmonid species, there was little difference in virulence or host-specificity between isolates from subtypes IVa, IVb, and IVc.  

Design and validation of new genotypic tools for easy and reliable estimation of HIV tropism before using CCR5 antagonists.

Science.gov (United States)

Poveda, Eva; Seclén, Eduardo; González, María del Mar; García, Federico; Chueca, Natalia; Aguilera, Antonio; Rodríguez, Jose Javier; González-Lahoz, Juan; Soriano, Vincent

2009-05-01

Genotypic tools may allow easier and less expensive estimation of HIV tropism before prescription of CCR5 antagonists compared with the Trofile assay (Monogram Biosciences, South San Francisco, CA, USA). Paired genotypic and Trofile results were compared in plasma samples derived from the maraviroc expanded access programme (EAP) in Europe. A new genotypic approach was built to improve the sensitivity to detect X4 variants based on an optimization of the webPSSM algorithm. Then, the new tool was validated in specimens from patients included in the ALLEGRO trial, a multicentre study conducted in Spain to assess the prevalence of R5 variants in treatment-experienced HIV patients. A total of 266 specimens from the maraviroc EAP were tested. Overall geno/pheno concordance was above 72%. A high specificity was generally seen for the detection of X4 variants using genotypic tools (ranging from 58% to 95%), while sensitivity was low (ranging from 31% to 76%). The PSSM score was then optimized to enhance the sensitivity to detect X4 variants changing the original threshold for R5 categorization. The new PSSM algorithms, PSSM(X4R5-8) and PSSM(SINSI-6.4), considered as X4 all V3 scoring values above -8 or -6.4, respectively, increasing the sensitivity to detect X4 variants up to 80%. The new algorithms were then validated in 148 specimens derived from patients included in the ALLEGRO trial. The sensitivity/specificity to detect X4 variants was 93%/69% for PSSM(X4R5-8) and 93%/70% for PSSM(SINSI-6.4). PSSM(X4R5-8) and PSSM(SINSI-6.4) may confidently assist therapeutic decisions for using CCR5 antagonists in HIV patients, providing an easier and rapid estimation of tropism in clinical samples.

The Physiological Response of Soybean Genotypes to VAM Inoculation on Selected Drought Stress Levels

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HAPSOH

2006-06-01

Full Text Available Present research was aimed to study physiological changes of soybean which were inoculated with vesicular arbuscular mycorrhizal fungi (VAM. Glomus etunicatum was exposed to moderate and severe drought condition. Symbiotic association with VAM improved adaptability as it was shown by the increasing leaf proline content. The MLG 3474 and Sindoro are the more tolerant genotypes while the responses of plant to VAM on improving the adaptability to drought were larger on Lokon.

Effect of Planting Date on Cold Tolerance of Winter and Spring Barley Genotypes

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A. R. Eivazi

2015-01-01

Full Text Available In order to evaluate cold tolerance of twenty barley genotypes under field conditions, an experiment was carried out in a randomized complete block design at 3 sowing dates of October 5, November 5, and December 5 in Saatlu Agricultural Research Station, West Azarbaijan, Iran, during 2010-11 seasons. Also, another experiment was conducted on the same genotypes based on a completely randomized design under greenhouse conditions. in wich Cold stress was applied up to -25°C at two, four and six leaf development stages. LT50, ion leakage and dry matter were measured and apex photographed. Field experiment results showed the lowest significant differences at p≤0.05 between different levels of sowing date, genotype, and interaction between them for plant height, spike/m2, kernel per spike, 1000-kernel weight, grain yield and total dry matter. Genotypes of winter growth type had higher grain yield (4250kg/ha than those with spring growth type (4190kg/ha. There were significant differences for ion leakage and dry matter at 4 and 6 leaf development stages under greenhouse conditions. Genotype 1 (winter growth type with lowest values of range and standard deviation for grain yield, total dry matter and LT50 = -38 °C showed a relatively low ion leakage. In contrast, genotypes 5, 10 and 14 (spring growth type were identified sensitive to cold stress due to having more values of range, standard deviation for grain yield and total dry matter, LT50 = -18 to -27 °C and ion leakage from 25 to 33µS/m. Regression analysis showed 1000-kernel weight and total dry matter to remain at final model. Cluster analysis indicated that genotypes 2, 18, 1, 17 and 19 were superior genotypes. In principal component analysis, four components showed 80% of total variations, and the first component with 26% of variation was an important yield component for improving grain yield of barley genotypes. In conclusion, grain yields of winter and spring barley genotypes were

Desmanthus GENOTYPES

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JOSÉ HENRIQUE DE ALBUQUERQUE RANGEL

2015-01-01

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

Comparison of antioxidant enzyme activities and DNA damage in chickpea (Cicer arietinum L.) genotypes exposed to vanadium.

Science.gov (United States)

Imtiaz, Muhammad; Mushtaq, Muhammad Adnan; Rizwan, Muhammad Shahid; Arif, Muhammad Saleem; Yousaf, Balal; Ashraf, Muhammad; Shuanglian, Xiong; Rizwan, Muhammad; Mehmood, Sajid; Tu, Shuxin

2016-10-01

The present study was done to elucidate the effects of vanadium (V) on photosynthetic pigments, membrane damage, antioxidant enzymes, protein, and deoxyribonucleic acid (DNA) integrity in the following chickpea genotypes: C-44 (tolerant) and Balkasar (sensitive). Changes in these parameters were strikingly dependent on levels of V, at 60 and 120 mg V L(-1) induced DNA damage in Balkasar only, while photosynthetic pigments and protein were decreased from 15 to 120 mg V L(-1) and membrane was also damaged. It was shown that photosynthetic pigments and protein production declined from 15 to 120 mg V L(-1) and the membrane was also damaged, while DNA damage was not observed at any level of V stress in C-44. Moreover, the antioxidant enzyme activities such as superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) were increased in both genotypes of chickpea against V stress; however, more activities were observed in C-44 than Balkasar. The results suggest that DNA damage in sensitive genotypes can be triggered due to exposure of higher vanadium.

Genetic and DNA methylation changes in cotton (Gossypium genotypes and tissues.

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Kenji Osabe

Full Text Available In plants, epigenetic regulation is important in normal development and in modulating some agronomic traits. The potential contribution of DNA methylation mediated gene regulation to phenotypic diversity and development in cotton was investigated between cotton genotypes and various tissues. DNA methylation diversity, genetic diversity, and changes in methylation context were investigated using methylation-sensitive amplified polymorphism (MSAP assays including a methylation insensitive enzyme (BsiSI, and the total DNA methylation level was measured by high-performance liquid chromatography (HPLC. DNA methylation diversity was greater than the genetic diversity in the selected cotton genotypes and significantly different levels of DNA methylation were identified between tissues, including fibre. The higher DNA methylation diversity (CHG methylation being more diverse than CG methylation in cotton genotypes suggest epigenetic regulation may be important for cotton, and the change in DNA methylation between fibre and other tissues hints that some genes may be epigenetically regulated for fibre development. The novel approach using BsiSI allowed direct comparison between genetic and epigenetic diversity, and also measured CC methylation level that cannot be detected by conventional MSAP.

Genetic and DNA methylation changes in cotton (Gossypium) genotypes and tissues.

Science.gov (United States)

Osabe, Kenji; Clement, Jenny D; Bedon, Frank; Pettolino, Filomena A; Ziolkowski, Lisa; Llewellyn, Danny J; Finnegan, E Jean; Wilson, Iain W

2014-01-01

In plants, epigenetic regulation is important in normal development and in modulating some agronomic traits. The potential contribution of DNA methylation mediated gene regulation to phenotypic diversity and development in cotton was investigated between cotton genotypes and various tissues. DNA methylation diversity, genetic diversity, and changes in methylation context were investigated using methylation-sensitive amplified polymorphism (MSAP) assays including a methylation insensitive enzyme (BsiSI), and the total DNA methylation level was measured by high-performance liquid chromatography (HPLC). DNA methylation diversity was greater than the genetic diversity in the selected cotton genotypes and significantly different levels of DNA methylation were identified between tissues, including fibre. The higher DNA methylation diversity (CHG methylation being more diverse than CG methylation) in cotton genotypes suggest epigenetic regulation may be important for cotton, and the change in DNA methylation between fibre and other tissues hints that some genes may be epigenetically regulated for fibre development. The novel approach using BsiSI allowed direct comparison between genetic and epigenetic diversity, and also measured CC methylation level that cannot be detected by conventional MSAP.

Specific and straightforward molecular investigation of β-thalassemia mutations in the Malaysian Malays and Chinese using direct TaqMan genotyping assays.

Science.gov (United States)

Kho, S L; Chua, K H; George, E; Tan, J A M A

2013-07-15

Beta-thalassemia is a life-threatening inherited blood disorder. Rapid characterization of β-globin gene mutations is necessary because of the high frequency of Malaysian β-thalassemia carriers. A combination real-time polymerase chain reaction genotyping assay using TaqMan probes was developed to confirm β-globin gene mutations. In this study, primers and probes were designed to specifically identify 8 common β-thalassemia mutations in the Malaysian Malay and Chinese ethnic groups using the Primer Express software. "Blind tests" using DNA samples from healthy individuals and β-thalassemia patients with different genotypes were performed to determine the specificity and sensitivity of this newly designed assay. Our results showed 100% sensitivity and specificity for this novel assay. In conclusion, the TaqMan genotyping assay is a straightforward assay that allows detection of β-globin gene mutations in less than 40 min. The simplicity and reproducibility of the TaqMan genotyping assay permit its use in laboratories as a rapid and cost-effective diagnostic tool for confirmation of common β-thalassemia mutations in Malaysia.

Reaction of genotypes of lulo (Solanum quitoense Lam. to Meloidogyne spp. under field conditions

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Claudia Salazar-González

2017-05-01

Full Text Available In Colombia, root-knot nematodes Meloidog yne spp. are considered as one of the main constraints in lulo crop production . These nematodes can cause root damage resulting in low production. The aim of this study was to evaluate under field conditions the reaction of 16 genotypes of lulo, Solanum quitoense Lam. (Solanaceae, of the Castilla variety and the species S. hirtum Vahl., previously selected in a greenhouse experiment and categorized as moderately resistant and resistant to the attack by Meloidog yne sp. A chemical treatment and a control treatment, the latter based on the most susceptible genotype in greenhouse experiments were also included. The experiment was conducted in a lulo grove naturally infested with root-knot nematodes under a randomized complete block design with three replications and nine plants per experimental unit. The response variables were incidence, severity and yield. The incidence was higher than 80 % in all cases, but the severity varied because of their genetic condition; BR03 and BR01 being genotypes with lower rates of severity, with values of 1.0 % and 0.8 %, respectively. The yield analysis of variance showed significant differences, indicating that genotypes SQBR01 and SQLF04, reached the highest values with 4.77 and 4.74 t/ha in a total of three harvests.

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

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Brian O'Farrell

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

The 5-HTTLPR polymorphism moderates the effect of stressful life events on drinking behavior in college students of African descent.

Science.gov (United States)

Kranzler, Henry R; Scott, Denise; Tennen, Howard; Feinn, Richard; Williams, Carla; Armeli, Stephen; Taylor, Robert E; Briggs-Gowan, Margaret J; Covault, Jonathan

2012-07-01

Covault et al. [Covault et al. (2007); Biol Psychiatry 61(5): 609-616] reported that the common functional polymorphism, 5-HTTLPR, in the serotonin transporter gene moderated the association between past-year stressful events and daily reports of drinking in a sample of European-American (EA) college students. We examined this effect in college students of African descent. Students recruited at a Historically Black University (n = 564) completed web-based measures of past-year stressful life experiences and daily reports of drinking and heavy drinking over a 30-day period. Participants were genotyped for the tri-allelic 5-HTTLPR polymorphism and dichotomized as low-activity S' allele carriers or high-activity L' homozygotes. Generalized linear models were used to examine the effects of life stress, genotype, and their interaction on the two drinking measures. In students who completed 15 or more daily surveys (n = 393), there was a significant interaction of past-year stressful events, 5-HTTLPR genotype, and gender on the number of drinking days (P = 0.002). Similar findings were obtained in relation to heavy drinking days (P = 0.007). Men showed a main effect of past-year stressful events on both drinking outcomes (P's life stressors on the frequency of drinking and heavy drinking days (P's stressful events were associated with more frequent drinking and heavy drinking, an effect that was moderated by the 5-HTTLPR polymorphism. However, in contrast to the findings in EA students, in the current sample, 5-HTTLPR moderated the association only among women. Copyright © 2012 Wiley Periodicals, Inc.

Individual and Joint Associations of Methylenetetrahydrofolate Reductase C677T Genotype and Plasma Homocysteine With Dyslipidemia in a Chinese Population With Hypertension.

Science.gov (United States)

Liu, Yanhong; Li, Kang; Venners, Scott A; Hsu, Yi-Hsiang; Jiang, Shanqun; Weinstock, Justin; Wang, Binyan; Tang, Genfu; Xu, Xiping

2017-04-01

We aimed to examine the cross-sectional associations of plasma total homocysteine (tHcy) concentrations and methylenetetrahydrofolate reductase ( MTHFR) C677T genotype with dyslipidemia. A total of 231 patients with mild-to-moderate essential hypertension were enrolled from the Huoqiu and Yuexi communities in Anhui Province, China. Plasma tHcy levels were measured by high-performance liquid chromatography. Genotyping was performed by TaqMan allelic discrimination technique. Compared with MTHFR 677 CC + CT genotype carriers, TT genotype carriers had higher odds of hypercholesterolemia (adjusted odds ratio [OR] [95% confidence interval (CI)]: 2.7 [1.4-5.2]; P = .004) and higher odds of abnormal low-density lipoprotein cholesterol (adjusted OR [95% CI]: 2.3 [1.1-4.8]; P = .030). The individuals with the TT genotype had higher concentrations of log(tHcy) than those with the 677 CC + CT genotype (adjusted β [standard error]: .2 [0.03]; P dyslipidemia in Chinese patients with essential hypertension. Further studies are needed to confirm the role of tHcy and the MTHFR C677T mutation in the development of dyslipidemia in a larger sample.

Breed distribution of the ABCB1-1Delta (multidrug sensitivity) polymorphism among dogs undergoing ABCB1 genotyping.

Science.gov (United States)

Mealey, Katrina L; Meurs, Kathryn M

2008-09-15

To evaluate the breed distribution of the ABCB1-1Delta polymorphism in a large number of dogs in North America, including dogs of several herding breeds in which this polymorphism has been detected and other breeds in which this polymorphism has not yet been identified. Cross-sectional study. 5,368 dogs from which buccal swab samples were collected for purposes of ABCB1 genotyping. From May 1, 2004, to September 30, 2007, DNA specimens derived from buccal swab samples collected from 5,368 dogs underwent ABCB1 genotyping. These data were reviewed, and results for each dog were recorded in a spreadsheet, along with the dog's breed. The genotypes for each breed were tallied by use of a sorting function. The ABCB1-1Delta allele was identified in 9 breeds of dogs and in many mixed-breed dogs. Breeds that had the ABCB1-1Delta allele included Collie, Longhaired Whippet, Australian Shepherd (standard and miniature), Shetland Sheepdog, Old English Sheepdog, Border Collie, Silken Windhound, and German Shepherd Dog (a breed in which this mutation had not been detected previously). The ABCB1-1Delta polymorphism is associated with increased susceptibility to many adverse drug reactions and with suppression of the hypothalamic-pituitary-adrenal axis and is present in many herding breeds of dog. Veterinarians should be familiar with the breeds that have the ABCB1-1Delta polymorphism to make appropriate pharmacologic choices for these patients.

Comparison of physiological and genetic effects of gamma radiation and sodium azide on two rice (Oryza sativa, L.) genotypes

International Nuclear Information System (INIS)

Faracco, A.L.A.

1990-01-01

The sensitivity of both genotypes (Oryzica 1 and Strain 30036) to gamma rays and sodium azide is studied. Doses of gamma-rays and concentrations of sodium azide were chosen so as to produce around 20%-25% height reduction in these genotypes. Emergence, survival and fertility were the physiological effects on M 1 generation analysed after the final treatment. The number of chlorophyll mutations and the number of seedling mutants were counted in M 2 generation. Taking into consideration, specially M 1 generation sterility, it was concluded that for the two genotypes studied, sodium azide presented a greater mutagen effect. (M.A.C.)

Effect of Salinity on Germination and Its Relationship with Vegetative growth in Bromus danthoniae Genotypes from Saline and Non-Saline Areas of Iran

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M. Rezaei

2018-02-01

Full Text Available Bromus danthoniae Trin. is an annual grass species that is well adapted to harsh climates and could be considered as an important genetic resources for tolerance to environmental stresses such as salinity. In this study, 24 genotypes collected from Ilam, Kurdistan, Kermanshah (non-saline areas and West Azerbaijan (saline area: shores of Uremia Salt Lake provinces of Iran were investigated at the germination stage under salt treatments with concentrations of 0, 60, 120, 180, 240 and 300 mM sodium chloride. Germination percentage, germination rate index, seed vigor, root length, shoot length and seedling fresh and dry weights were measured. In addition, the relationship between the percentage of germination in 300 mM sodium chloride and the survival rate (% after four weeks in 350 mM sodium chloride at the vegetative stage was evaluated. The results of analysis of variance showed that salinity treatments caused significant reductions in all the studied traits. Genotypic variation and the interaction of genotype × salt treatments were also significant. Genotypes USLN3 and KER4 were found to be the most tolerant and sensitive genotypes to salinity stress, with 13% and 98% reduction in germination percentage at 300 mM NaCl, respectively. Cluster analysis divided the genotypes into three groups, with one group containing only tolerant genotypes from Uremia Salt Lake, another one comprising only sensitive genotypes from non-saline regions, and the third one containing genotypes from both regions. The correlation between the germination percentage and the survival rate at the vegetative stage was not significant, indicating that different mechanisms are, perhaps, responsible for salinity tolerance at the germination and vegetative stages in B. danthoniae.

Blood group genotyping: the power and limitations of the Hemo ID Panel and MassARRAY platform.

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McBean, Rhiannon S; Hyland, Catherine A; Flower, Robert L

2015-01-01

Matrix-assisted laser desorption/ionization, time-of-flight mass spectrometry (MALDI-TOF MS), is a sensitive analytical method capable of resolving DNA fragments varying in mass by a single nucleotide. MALDI-TOF MS is applicable to blood group genotyping, as the majority of blood group antigens are encoded by single nucleotide polymorphisms. Blood group genotyping by MALDI-TOF MS can be performed using a panel (Hemo ID Blood Group Genotyping Panel, Agena Bioscience Inc., San Diego, CA) that is a set of genotyping assays that predict the phenotype for 101 antigens from 16 blood group systems. These assays involve three fundamental stages: multiplex target-specific polymerase chain reaction amplification, allele-specific single base primer extension, and MALDI-TOFMS analysis using the MassARRAY system. MALDI-TOF MS-based genotyping has many advantages over alternative methods including high throughput, high multiplex capability, flexibility and adaptability, and the high level of accuracy based on the direct detection method. Currently available platforms for MALDI-TOF MS-based genotyping are not without limitations, including high upfront instrumentation costs and the number of non-automated steps. The Hemo ID Blood Group Genotyping Panel, developed and optimized in a collaboration between the vendor and the Blood Transfusion Service of the Swiss Red Cross in Zurich, Switzerland, is not yet widely utilized, although several laboratories are currently evaluating the MassARRAY system for blood group genotyping. Based on the accuracy and other advantages offered by MALDITOF MS analysis, in the future, this method is likely to become widely adopted for blood group genotyping, in particular, for population screening.

INVESTIGATIONS ON THE RESISTANCE OF SOME BULGARIAN COMMON BEAN GENOTYPES TOWARDS BEAN WEEVIL (ACANTHOSCELIDES OBTECTUS SAY

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Elena Dimitrova Apostolova

2013-12-01

Full Text Available The most effective, environmentally sound and safety way to fight pests with biological means is the use of resistant varieties to them. In the present study were indicated the reactions of 30 Bulgarian common bean genotypes to the most economically important enemy – bean weevil (Acanthoscelidis obtectus Say. For this purpose, the following indicators were traced – seed damages and young adult insects, which largely characterized the response of different common bean genotypes to that biological pest enemy. The results of this investigation present a sensitive response to the sustainability of different genotypes to the bean weevil. The Bulgarian common bean varieties Plovdiv 11M, Abritus, Crystal and Bulgari can be used in breeding programs as donors of resistance to the bean weevil.

The Effect of Low Temperature on some Physiological and Biochemical Trait of some Semi-orange Genotype in the North Iran

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saleh Mohammadi

2018-03-01

Full Text Available Introduction: Among citrus producing provinces in the country, Mazandaran province ranks first with 1.88 million tons yields. Orange is one of the horticulture crop which is sensitive to low temperature stress. Low temperature stress is one of the abiotic stresses that its negative effects is the disruption of the electron transfer process through the thylacoid membrane. Actived oxygen radicals can be reacted with methyl unsaturated fatty acid groups and produce active fatty acid radicals. Very reactive formed radicals are capable of initiating lipid peroxidation chain reactions, which leads to the accumulation of free oxygen radicals that can lead to degradation of plant chlorophylls and membrane peroxidation and disruption of photosynthesis, accumulation of ROS, damage to cell membranes, destruction of plant pigments and nucleic acids. Plants can resist against low temperature stress by water saving and utilization of antioxidant system. The amount of free proline in many plants increases in response to environmental stresses such as cold and drought stress, and this physiological response can affect the resistance of the herbal substance under stress. Due to the diversity of citrus native genotypes in the country, the aim of this study was to determine the tolerance of native genotypes against low temperature stress in north of the country. Materials and Methods: This experiment was conducted during the years 2015_2016 at the Citrus and Semi-Traditional Fruit Research Center in Ramsar with the aim of determining the low temperature tolerance of six native pseudo orange genotypes at 4 temperature levels (3, 0,- 3,- 6, compared to The test was carried out by Unsho and Sensitive Persian Lime (low temperature stress. Therefore, in this study, the vulnerability to low-stress conditions in controlled environmental conditions was compared with that of temperature treatments (3, 0, _3 and -6 degrees Celsius in six genotypes of native pseudo

Influence of COMT genotype and affective distractors on the processing of self-generated thought.

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Kilford, Emma J; Dumontheil, Iroise; Wood, Nicholas W; Blakemore, Sarah-Jayne

2015-06-01

The catechol-O-methyltransferase (COMT) enzyme is a major determinant of prefrontal dopamine levels. The Val(158)Met polymorphism affects COMT enzymatic activity and has been associated with variation in executive function and affective processing. This study investigated the effect of COMT genotype on the flexible modulation of the balance between processing self-generated and processing stimulus-oriented information, in the presence or absence of affective distractors. Analyses included 124 healthy adult participants, who were also assessed on standard working memory (WM) tasks. Relative to Val carriers, Met homozygotes made fewer errors when selecting and manipulating self-generated thoughts. This effect was partly accounted for by an association between COMT genotype and visuospatial WM performance. We also observed a complex interaction between the influence of affective distractors, COMT genotype and sex on task accuracy: male, but not female, participants showed a sensitivity to the affective distractors that was dependent on COMT genotype. This was not accounted for by WM performance. This study provides novel evidence of the role of dopaminergic genetic variation on the ability to select and manipulate self-generated thoughts. The results also suggest sexually dimorphic effects of COMT genotype on the influence of affective distractors on executive function. © The Author (2014). Published by Oxford University Press.

Genetic moderation of cocaine subjective effects by variation in the TPH1, TPH2, and SLC6A4 serotonin genes.

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Patriquin, Michelle A; Hamon, Sara C; Harding, Mark J; Nielsen, Ellen M; Newton, Thomas F; De La Garza, Richard; Nielsen, David A

2017-10-01

This study investigated variants of tryptophan hydroxylase (TPH)1, TPH2, and SLC6A4 in the moderation of the subjective effects of cocaine. Non-treatment-seeking cocaine-dependent individuals (N=66) were intravenously administered saline and cocaine (40 mg) in a randomized order. Participants self-reported subjective effects of cocaine using a visual analog scale starting before administration of saline or cocaine (-15 min) to up to 20 min after infusion. Self-report ratings on the visual analog scale ranged from 0 (no effect) to 100 (greatest effect). Participants were genotyped for the TPH1 rs1799913, TPH2 rs4290270, and SLC6A4 5-HTTLPR variants. Repeated-measures analysis of covariance was used to examine changes in subjective effect scores over time while controlling for population structure. Participants carrying the TPH1 rs1799913 A allele reported greater subjective response to cocaine for 'stimulated' and 'access' relative to the CC genotype group. Those carrying the TPH2 rs4290270 A allele reported higher 'good effect' and lower 'depressed' effect relative to the TT genotype group. Those carrying the SLC6A4 5-HTTLPR S' allele reported greater 'desire' and 'access' compared with the L'L' genotype group. These findings indicate that TPH1, TPH2, and SLC6A4 variants moderate the subjective effects of cocaine in non-treatment-seeking cocaine-dependent participants.

Rotavirus genotype shifts among Swedish children and adults-Application of a real-time PCR genotyping.

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Andersson, Maria; Lindh, Magnus

2017-11-01

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

An efficient genotyping method for genome-modified animals and human cells generated with CRISPR/Cas9 system.

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Zhu, Xiaoxiao; Xu, Yajie; Yu, Shanshan; Lu, Lu; Ding, Mingqin; Cheng, Jing; Song, Guoxu; Gao, Xing; Yao, Liangming; Fan, Dongdong; Meng, Shu; Zhang, Xuewen; Hu, Shengdi; Tian, Yong

2014-09-19

The rapid generation of various species and strains of laboratory animals using CRISPR/Cas9 technology has dramatically accelerated the interrogation of gene function in vivo. So far, the dominant approach for genotyping of genome-modified animals has been the T7E1 endonuclease cleavage assay. Here, we present a polyacrylamide gel electrophoresis-based (PAGE) method to genotype mice harboring different types of indel mutations. We developed 6 strains of genome-modified mice using CRISPR/Cas9 system, and utilized this approach to genotype mice from F0 to F2 generation, which included single and multiplexed genome-modified mice. We also determined the maximal detection sensitivity for detecting mosaic DNA using PAGE-based assay as 0.5%. We further applied PAGE-based genotyping approach to detect CRISPR/Cas9-mediated on- and off-target effect in human 293T and induced pluripotent stem cells (iPSCs). Thus, PAGE-based genotyping approach meets the rapidly increasing demand for genotyping of the fast-growing number of genome-modified animals and human cell lines created using CRISPR/Cas9 system or other nuclease systems such as TALEN or ZFN.

DRD4 polymorphism moderates the effect of alcohol consumption on social bonding.

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Kasey G Creswell

Full Text Available Development of interpersonal relationships is a fundamental human motivation, and behaviors facilitating social bonding are prized. Some individuals experience enhanced reward from alcohol in social contexts and may be at heightened risk for developing and maintaining problematic drinking. We employed a 3 (group beverage condition ×2 (genotype design (N = 422 to test the moderating influence of the dopamine D4 receptor gene (DRD4 VNTR polymorphism on the effects of alcohol on social bonding. A significant gene x environment interaction showed that carriers of at least one copy of the 7-repeat allele reported higher social bonding in the alcohol, relative to placebo or control conditions, whereas alcohol did not affect ratings of 7-absent allele carriers. Carriers of the 7-repeat allele were especially sensitive to alcohol's effects on social bonding. These data converge with other recent gene-environment interaction findings implicating the DRD4 polymorphism in the development of alcohol use disorders, and results suggest a specific pathway by which social factors may increase risk for problematic drinking among 7-repeat carriers. More generally, our findings highlight the potential utility of employing transdisciplinary methods that integrate genetic methodologies, social psychology, and addiction theory to improve theories of alcohol use and abuse.

DRD4 polymorphism moderates the effect of alcohol consumption on social bonding.

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Creswell, Kasey G; Sayette, Michael A; Manuck, Stephen B; Ferrell, Robert E; Hill, Shirley Y; Dimoff, John D

2012-01-01

Development of interpersonal relationships is a fundamental human motivation, and behaviors facilitating social bonding are prized. Some individuals experience enhanced reward from alcohol in social contexts and may be at heightened risk for developing and maintaining problematic drinking. We employed a 3 (group beverage condition) ×2 (genotype) design (N = 422) to test the moderating influence of the dopamine D4 receptor gene (DRD4 VNTR) polymorphism on the effects of alcohol on social bonding. A significant gene x environment interaction showed that carriers of at least one copy of the 7-repeat allele reported higher social bonding in the alcohol, relative to placebo or control conditions, whereas alcohol did not affect ratings of 7-absent allele carriers. Carriers of the 7-repeat allele were especially sensitive to alcohol's effects on social bonding. These data converge with other recent gene-environment interaction findings implicating the DRD4 polymorphism in the development of alcohol use disorders, and results suggest a specific pathway by which social factors may increase risk for problematic drinking among 7-repeat carriers. More generally, our findings highlight the potential utility of employing transdisciplinary methods that integrate genetic methodologies, social psychology, and addiction theory to improve theories of alcohol use and abuse.

The effect of angiotensin converting enzyme genotype on aerobic capacity following high intensity interval training

OpenAIRE

Goddard, N; Baker, M.D; Higgins, T; Cobbold, C

2014-01-01

Obesity increases the risk of developing type 2 diabetes mellitus (T2DM) and cardiovascular disease (CVD). Physical activity can reduce T2DM and CVD risk, and increase aerobic capacity, a significant predictor of all-cause mortality and morbidity. High intensity interval training (HIIT) produces similar improvements in aerobic capacity to continuous moderate exercise (CME). Different genotypes of angiotensin converting enzyme (ACE) have been implicated in improving aerobic capacity and theref...

High performance of a new PCR-based urine assay for HPV-DNA detection and genotyping.

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Tanzi, Elisabetta; Bianchi, Silvia; Fasolo, Maria Michela; Frati, Elena R; Mazza, Francesca; Martinelli, Marianna; Colzani, Daniela; Beretta, Rosangela; Zappa, Alessandra; Orlando, Giovanna

2013-01-01

Human papillomavirus (HPV) testing has been proposed as a means of replacing or supporting conventional cervical screening (Pap test). However, both methods require the collection of cervical samples. Urine sample is easier and more acceptable to collect and could be helpful in facilitating cervical cancer screening. The aim of this study was to evaluate the sensitivity and specificity of urine testing compared to conventional cervical smear testing using a PCR-based method with a new, designed specifically primer set. Paired cervical and first voided urine samples collected from 107 women infected with HIV were subjected to HPV-DNA detection and genotyping using a PCR-based assay and a restriction fragment length polymorphism method. Sensitivity, specificity, Positive Predictive Value (PPV), and Negative Predictive Value (NPV) were calculated using the McNemar's test for differences. Concordance between tests was assessed using the Cohen's unweighted Kappa (k). HPV DNA was detected in 64.5% (95% CI: 55.1-73.1%) of both cytobrush and urine samples. High concordance rates of HPV-DNA detection (k = 0.96; 95% CI: 0.90-1.0) and of high risk-clade and low-risk genotyping in paired samples (k = 0.80; 95% CI: 0.67-0.92 and k = 0.74; 95% CI: 0.60-0.88, respectively) were observed. HPV-DNA detection in urine versus cervix testing revealed a sensitivity of 98.6% (95% CI: 93.1-99.9%) and a specificity of 97.4% (95% CI: 87.7-99.9%), with a very high NPV (97.4%; 95% CI: 87.7-99.9%). The PCR-based assay utilized in this study proved highly sensitive and specific for HPV-DNA detection and genotyping in urine samples. These data suggest that a urine-based assay would be a suitable and effective tool for epidemiological surveillance and, most of all, screening programs. Copyright © 2012 Wiley Periodicals, Inc.

Toxoplasma gondii seroprevalence and genotype diversity in select wildlife species from the southeastern United States

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Richard W. Gerhold

2017-10-01

Full Text Available Abstract Background Toxoplasma gondii is a widespread protozoan parasite that infects humans and other animals. Previous studies indicate some genotypes of T. gondii are more frequently isolated in wildlife than agricultural animals, suggesting a wild/feral animal diversity model. To determine seroprevalence and genetic diversity of T. gondii in southeastern US wildlife, we collected sera from 471 wild animals, including 453 mammals and 18 birds, between 2011 and 2014. These serum samples were assayed for T. gondii infection using the modified agglutination test (MAT. Heart or tongue tissues from 66 seropositive animals were bioassayed in mice and 19 isolates were obtained. The isolated parasites were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP method employing 10 genetic markers. Results One hundred and ninety-six of 471 samples (41.6% had a titer ≥1:32 and were considered positive for T. gondii infection. Of 453 mammals, 195 (43% were seropositive, whereas only one (5.6% of 18 birds was seropositive. The seroprevalence in mammals was significantly higher than in the birds. Mammalian hosts with adequate samples size (≥ 20 comprised white-tailed deer (n = 241, feral hogs (n = 100, raccoons (n = 34 and coyotes (n = 22, with seroprevalences of 41.0%, 51.0%, 50.0% and 72.7%, respectively. Coyotes had significantly higher seroprevalence than the white-tailed deer. Genotyping revealed five distinct genotypes, including the ToxoDB PCR-RFLP genotype #5 (a.k.a type 12 for 15 isolates, genotype #3 (a.k.a. type II for 1 isolate, and genotypes #154, #167 and #216, each for 1 isolate. The results showed moderate to high infection rates of T. gondii in white-tailed deer, feral hogs, raccoons and coyotes. Genotyping results indicated limited genetic diversity and a dominance of genotype #5, which has been reported as a major type in wildlife in North America. Conclusions We conclude that T. gondii

Real-Time Determination of Photosynthesis, Transpiration, Water-Use Efficiency and Gene Expression of Two Sorghum bicolor (Moench Genotypes Subjected to Dry-Down

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Alessandra Fracasso

2017-05-01

Full Text Available Plant growth and productivity are strongly affected by limited water availability in drought prone environments. The current climate change scenario, characterized by long periods without precipitations followed by short but intense rainfall, forces plants to implement different strategies to cope with drought stress. Understanding how plants use water during periods of limited water availability is of primary importance to identify and select the best adapted genotypes to a certain environment. Two sorghum genotypes IS22330 and IS20351, previously characterized as drought tolerant and drought sensitive genotypes, were subjected to progressive drought stress through a dry-down experiment. A whole-canopy multi-chamber system was used to determine the in vivo water use efficiency (WUE. This system records whole-canopy net photosynthetic and transpiration rate of 12 chambers five times per hour allowing the calculation of whole-canopy instantaneous WUE daily trends. Daily net photosynthesis and transpiration rates were coupled with gene expression dynamics of five drought related genes. Under drought stress, the tolerant genotype increased expression level for all the genes analyzed, whilst the opposite trend was highlighted by the drought sensitive genotype. Correlation between gene expression dynamics and gas exchange measurements allowed to identify three genes as valuable candidate to assess drought tolerance in sorghum.

Real-Time Determination of Photosynthesis, Transpiration, Water-Use Efficiency and Gene Expression of Two Sorghum bicolor (Moench) Genotypes Subjected to Dry-Down.

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Fracasso, Alessandra; Magnanini, Eugenio; Marocco, Adriano; Amaducci, Stefano

2017-01-01

Plant growth and productivity are strongly affected by limited water availability in drought prone environments. The current climate change scenario, characterized by long periods without precipitations followed by short but intense rainfall, forces plants to implement different strategies to cope with drought stress. Understanding how plants use water during periods of limited water availability is of primary importance to identify and select the best adapted genotypes to a certain environment. Two sorghum genotypes IS22330 and IS20351, previously characterized as drought tolerant and drought sensitive genotypes, were subjected to progressive drought stress through a dry-down experiment. A whole-canopy multi-chamber system was used to determine the in vivo water use efficiency (WUE). This system records whole-canopy net photosynthetic and transpiration rate of 12 chambers five times per hour allowing the calculation of whole-canopy instantaneous WUE daily trends. Daily net photosynthesis and transpiration rates were coupled with gene expression dynamics of five drought related genes. Under drought stress, the tolerant genotype increased expression level for all the genes analyzed, whilst the opposite trend was highlighted by the drought sensitive genotype. Correlation between gene expression dynamics and gas exchange measurements allowed to identify three genes as valuable candidate to assess drought tolerance in sorghum.

Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates.

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Low, Andrew J; Dong, Winnie; Chan, Dennison; Sing, Tobias; Swanstrom, Ronald; Jensen, Mark; Pillai, Satish; Good, Benjamin; Harrigan, P Richard

2007-09-12

Integrating CCR5 antagonists into clinical practice would benefit from accurate assays of co-receptor usage (CCR5 versus CXCR4) with fast turnaround and low cost. Published HIV V3-loop based predictors of co-receptor usage were compared with actual phenotypic tropism results in a large cohort of antiretroviral naive individuals to determine accuracy on clinical samples and identify areas for improvement. Aligned HIV envelope V3 loop sequences (n = 977), derived by bulk sequencing were analyzed by six methods: the 11/25 rule; a neural network (NN), two support vector machines, and two subtype-B position specific scoring matrices (PSSM). Co-receptor phenotype results (Trofile Co-receptor Phenotype Assay; Monogram Biosciences) were stratified by CXCR4 relative light unit (RLU) readout and CD4 cell count. Co-receptor phenotype was available for 920 clinical samples with V3 genotypes having fewer than seven amino acid mixtures (n = 769 R5; n = 151 X4-capable). Sensitivity and specificity for predicting X4 capacity were evaluated for the 11/25 rule (30% sensitivity/93% specificity), NN (44%/88%), PSSM(sinsi) (34%/96%), PSSM(x4r5) (24%/97%), SVMgenomiac (22%/90%) and SVMgeno2pheno (50%/89%). Quantitative increases in sensitivity could be obtained by optimizing the cut-off for methods with continuous output (PSSM methods), and/or integrating clinical data (CD4%). Sensitivity was directly proportional to strength of X4 signal in the phenotype assay (P < 0.05). Current default implementations of co-receptor prediction algorithms are inadequate for predicting HIV X4 co-receptor usage in clinical samples, particularly those X4 phenotypes with low CXCR4 RLU signals. Significant improvements can be made to genotypic predictors, including training on clinical samples, using additional data to improve predictions and optimizing cutoffs and increasing genotype sensitivity.

A functional brain-derived neurotrophic factor (BDNF) gene variant increases the risk of moderate-to-severe allergic rhinitis.

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Jin, Peng; Andiappan, Anand Kumar; Quek, Jia Min; Lee, Bernett; Au, Bijin; Sio, Yang Yie; Irwanto, Astrid; Schurmann, Claudia; Grabe, Hans Jörgen; Suri, Bani Kaur; Matta, Sri Anusha; Westra, Harm-Jan; Franke, Lude; Esko, Tonu; Sun, Liangdan; Zhang, Xuejun; Liu, Hong; Zhang, Furen; Larbi, Anis; Xu, Xin; Poidinger, Michael; Liu, Jianjun; Chew, Fook Tim; Rotzschke, Olaf; Shi, Li; Wang, De Yun

2015-06-01

Brain-derived neurotrophic factor (BDNF) is a secretory protein that has been implicated in the pathogenesis of allergic rhinitis (AR), atopic asthma, and eczema, but it is currently unknown whether BDNF polymorphisms influence susceptibility to moderate-to-severe AR. We sought to identify disease associations and the functional effect of BDNF genetic variants in patients with moderate-to-severe AR. Tagging single nucleotide polymorphisms (SNPs) spanning the BDNF gene were selected from the human HapMap Han Chinese from Beijing (CHB) data set, and associations with moderate-to-severe AR were assessed in 2 independent cohorts of Chinese patients (2216 from Shandong province and 1239 living in Singapore). The functional effects of the BDNF genetic variants were determined by using both in vitro and ex vivo assays. The tagging SNP rs10767664 was significantly associated with the risk of moderate-to-severe AR in both Singapore Chinese (P = .0017; odds ratio, 1.324) and Shandong Chinese populations (P = .039; odds ratio, 1.180). The coding nonsynonymous SNP rs6265 was in perfect linkage with rs10767664 and conferred increased BDNF protein secretion by a human cell line in vitro. Subjects bearing the AA genotype of rs10767664 exhibited increased risk of moderate-to-severe AR and displayed increased BDNF protein and total IgE levels in plasma. Using a large-scale expression quantitative trait locus study, we demonstrated that BDNF SNPs are significantly associated with altered BDNF concentrations in peripheral blood. A common genetic variant of the BDNF gene is associated with increased risk of moderate-to-severe AR, and the AA genotype is associated with increased BDNF mRNA levels in peripheral blood. Together, these data indicate that functional BDNF gene variants increase the risk of moderate-to-severe AR. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis

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Thiele Bernhard

2011-05-01

Full Text Available Abstract Background Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4 variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Methods Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Results Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%, and defining a minority cutoff of 5%, the results were concordant in all but one isolate. Conclusions The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.

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Däumer, Martin; Kaiser, Rolf; Klein, Rolf; Lengauer, Thomas; Thiele, Bernhard; Thielen, Alexander

2011-05-13

Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4) variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS) detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%), and defining a minority cutoff of 5%, the results were concordant in all but one isolate. The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

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

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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

Studies on biological effects of nitrogen ion implantation in different genotype rice

International Nuclear Information System (INIS)

Xie Jiahua; Xia Yingwu; Shu Qingyao

1994-01-01

The biological effects of nitrogen ion implantation on different genotype rice (Oryza sativa L) were studied. The results showed that there were obvious differences in physiological damages for the M 1 generation, mutation frequencies and mutagenic efficiencies of chlorophyll, heading date and plant height for M 2 generation of different genotypes. Treated by nitrogen ions, the varieties with high mutation frequency and mutagenic efficiency of chlorophyll in the M 2 generation were not necessarily high in those of heading date and plant height. Moreover, the radiation sensitivity of Fu8530 and Fuxian No.6 which were bred by using early maturing and semidwarf mutants as maternal plant was low. The early maturing and high stature mutation were not induced with these two varieties

Genotype and environment effects on sensory, nutritional, and physical traits in chickpea (Cicer arietinum L.

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Maria J. Cobos

2016-12-01

Full Text Available The development of chickpea cultivars with high quality grains for human consumption is an important objective in breeding programs. Genotype and environment effects on seed quality traits (sensorial, nutritional and physical were studied in chickpea dry grain. Twenty genotypes were grown in winter and spring sowings over two campaigns in four different locations in southern Spain. Significant differences were observed in oil, acid detergent fiber (ADF and protein content between sowing times (S. In winter, oil and ADF content were higher, while protein content was lower. Although, in general, highly significant variation was detected for genotype (G, environment (E and single interactions (GE, GS and ES, the genotype effect was stronger for ADF, neutral detergent fiber (NDF, oil, starch and protein content, and for physical and sensory traits (r2>27%. In contrast, environment played an important role in variation in the content of amylose and amylopectin (r2=71.7%. No high relationships were found between the sensory and nutritional or physical characteristics studied. In general, our results suggest a high genetic gain for seed quality in nutritional, physical and sensory traits in chickpea. Genotypes with good seed sensory quality should be selected in the final stages of the breeding program, because it is not feasible to evaluate very large numbers of samples. However, in some cases, moderate correlations were found between sensory and either nutritional or physical traits. Therefore, indirect selection to increase the frequency of genes for sensory traits in an early stage should be considered.

Genotype and environment effects on sensory, nutritional, and physical traits in chickpea (Cicer arietinum L.)

International Nuclear Information System (INIS)

Cobos, M.J.; Izquierdo, M. A.; Sanz, A.T.; Gil, J.; Flores, F.; Rubio, J.

2016-01-01

The development of chickpea cultivars with high quality grains for human consumption is an important objective in breeding programs. Genotype and environment effects on seed quality traits (sensorial, nutritional and physical) were studied in chickpea dry grain. Twenty genotypes were grown in winter and spring sowings over two campaigns in four different locations in southern Spain. Significant differences were observed in oil, acid detergent fiber (ADF) and protein content between sowing times (S). In winter, oil and ADF content were higher, while protein content was lower. Although, in general, highly significant variation was detected for genotype (G), environment (E) and single interactions (GE, GS and ES), the genotype effect was stronger for ADF, neutral detergent fiber (NDF), oil, starch and protein content, and for physical and sensory traits (r2>27%). In contrast, environment played an important role in variation in the content of amylose and amylopectin (r2=71.7%). No high relationships were found between the sensory and nutritional or physical characteristics studied. In general, our results suggest a high genetic gain for seed quality in nutritional, physical and sensory traits in chickpea. Genotypes with good seed sensory quality should be selected in the final stages of the breeding program, because it is not feasible to evaluate very large numbers of samples. However, in some cases, moderate correlations were found between sensory and either nutritional or physical traits. Therefore, indirect selection to increase the frequency of genes for sensory traits in an early stage should be considered.

Genotype and environment effects on sensory, nutritional, and physical traits in chickpea (Cicer arietinum L.)

Energy Technology Data Exchange (ETDEWEB)

Cobos, M.J.; Izquierdo, M. A.; Sanz, A.T.; Gil, J.; Flores, F.; Rubio, J.

2016-07-01

The development of chickpea cultivars with high quality grains for human consumption is an important objective in breeding programs. Genotype and environment effects on seed quality traits (sensorial, nutritional and physical) were studied in chickpea dry grain. Twenty genotypes were grown in winter and spring sowings over two campaigns in four different locations in southern Spain. Significant differences were observed in oil, acid detergent fiber (ADF) and protein content between sowing times (S). In winter, oil and ADF content were higher, while protein content was lower. Although, in general, highly significant variation was detected for genotype (G), environment (E) and single interactions (GE, GS and ES), the genotype effect was stronger for ADF, neutral detergent fiber (NDF), oil, starch and protein content, and for physical and sensory traits (r2>27%). In contrast, environment played an important role in variation in the content of amylose and amylopectin (r2=71.7%). No high relationships were found between the sensory and nutritional or physical characteristics studied. In general, our results suggest a high genetic gain for seed quality in nutritional, physical and sensory traits in chickpea. Genotypes with good seed sensory quality should be selected in the final stages of the breeding program, because it is not feasible to evaluate very large numbers of samples. However, in some cases, moderate correlations were found between sensory and either nutritional or physical traits. Therefore, indirect selection to increase the frequency of genes for sensory traits in an early stage should be considered.

Hepatitis C virus genotypes in Myanmar.

Science.gov (United States)

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

2016-07-21

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

DRD4-exonIII-VNTR moderates the effect of childhood adversities on emotional resilience in young-adults.

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Debjani Das

Full Text Available Most individuals successfully maintain psychological well-being even when exposed to trauma or adversity. Emotional resilience or the ability to thrive in the face of adversity is determined by complex interactions between genetic makeup, previous exposure to stress, personality, coping style, availability of social support, etc. Recent studies have demonstrated that childhood trauma diminishes resilience in adults and affects mental health. The Dopamine receptor D4 (DRD4 exon III variable number tandem repeat (VNTR polymorphism was reported to moderate the impact of adverse childhood environment on behaviour, mood and other health-related outcomes. In this study we investigated whether DRD4-exIII-VNTR genotype moderates the effect of childhood adversities (CA on resilience. In a representative population sample (n = 1148 aged 30-34 years, we observed an interactive effect of DRD4 genotype and CA (β = 0.132; p = 0.003 on resilience despite no main effect of the genotype when effects of age, gender and education were controlled for. The 7-repeat allele appears to protect against the adverse effect of CA since the decline in resilience associated with increased adversity was evident only in individuals without the 7-repeat allele. Resilience was also significantly associated with approach-/avoidance-related personality measures (behavioural inhibition/activation system; BIS/BAS measures and an interactive effect of DRD4-exIII-VNTR genotype and CA on BAS was observed. Hence it is possible that approach-related personality traits could be mediating the effect of the DRD4 gene and childhood environment interaction on resilience such that when stressors are present, the 7-repeat allele influences the development of personality in a way that provides protection against adverse outcomes.

Field study of dried blood spot specimens for HIV-1 drug resistance genotyping.

Science.gov (United States)

Parry, C M; Parkin, N; Diallo, K; Mwebaza, S; Batamwita, R; DeVos, J; Bbosa, N; Lyagoba, F; Magambo, B; Jordan, M R; Downing, R; Zhang, G; Kaleebu, P; Yang, C; Bertagnolio, S

2014-08-01

Dried blood spots (DBS) are an alternative specimen type for HIV drug resistance genotyping in resource-limited settings. Data relating to the impact of DBS storage and shipment conditions on genotyping efficiency under field conditions are limited. We compared the genotyping efficiencies and resistance profiles of DBS stored and shipped at different temperatures to those of plasma specimens collected in parallel from patients receiving antiretroviral therapy in Uganda. Plasma and four DBS cards from anti-coagulated venous blood and a fifth card from finger-prick blood were prepared from 103 HIV patients with a median viral load (VL) of 57,062 copies/ml (range, 1,081 to 2,964,191). DBS were stored at ambient temperature for 2 or 4 weeks or frozen at -80 °C and shipped from Uganda to the United States at ambient temperature or frozen on dry ice for genotyping using a broadly sensitive in-house method. Plasma (97.1%) and DBS (98.1%) stored and shipped frozen had similar genotyping efficiencies. DBS stored frozen (97.1%) or at ambient temperature for 2 weeks (93.2%) and shipped at ambient temperature also had similar genotyping efficiencies. Genotyping efficiency was reduced for DBS stored at ambient temperature for 4 weeks (89.3%, P = 0.03) or prepared from finger-prick blood and stored at ambient temperature for 2 weeks (77.7%, P blood and handled similarly. Resistance profiles were similar between plasma and DBS specimens. This report delineates the optimal DBS collection, storage, and shipping conditions and opens a new avenue for cost-saving ambient-temperature DBS specimen shipments for HIV drug resistance (HIVDR) surveillances in resource-limited settings. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Effect of calcium on the salt tolerance of different wheat (triticum aestivum l.) genotypes

International Nuclear Information System (INIS)

Arshad, M.; Saqib, M.; Akhtar, J.

2012-01-01

In saline soil conditions the availability and uptake of Ca/sup 2+/ is reduced that results in the loss of membrane integrity and other disorders associated with Ca/sup 2+/ deficiency in plants. A wheat genotype efficient in uptake and utilization of calcium under saline conditions may be better able to withstand saline conditions in the field. Very little information is available on wheat response to salinity and low Ca/sup 2+/ as screening of wheat genotypes has usually been done against salinity alone. The present study was designed to evaluate the performance of different wheat genotypes against salinity at low and adequate calcium supply. The experiment was conducted in hydroponics with four treatments including T1: non-saline with adequate Ca/sup 2+/, T2: non-saline with low Ca/sup 2+/ (level of calcium was 1/4 of the adequate level), T3: saline (125 mM NaCl) with adequate Ca/sup 2+/ and T4: saline with low calcium. All the physical growth parameters including shoot length, root length, and shoot and root fresh weights were decreased significantly due to salinity and low calcium alone as well as in combination. Reduction was more pronounced under the combined stress of salinity and low calcium and different genotypes differed significantly in different stress treatments for shoot and root fresh weight production. In saline treatment (T3), the genotypes 25-SAWSN-39 and 25-SAWSN-31 showed better growth performance and accumulated lower Na+ and higher Ca/sup 2+/ where as the genotypes 25-SAWSN-35 and 25-SAWSN-47 showed less growth and had less accumulation of Ca/sup 2+/ and high accumulation of Na+. In salinity + low calcium treatment the genotype 25-SAWSN-39 behaved as a tolerant genotype where as 25-SAWSN-31 behaved similar to the sensitive genotype and these differences were due to high accumulation of Ca/sup 2+/ in 25-SAWSN-39 and vice versa. This study shows that the salt tolerance of wheat genotypes differs with the availability and accumulation of calcium

COMT ValMet moderation of cannabis-induced psychosis: a momentary assessment study of 'switching on' hallucinations in the flow of daily life.

Science.gov (United States)

Henquet, C; Rosa, A; Delespaul, P; Papiol, S; Fananás, L; van Os, J; Myin-Germeys, I

2009-02-01

A functional polymorphism in the catechol-o-methyltransferase gene (COMT Val(158)Met) may moderate the psychosis-inducing effects of cannabis. In order to extend this finding to dynamic effects in the flow of daily life, a momentary assessment study of psychotic symptoms in response to cannabis use was conducted. The experience sampling technique was used to collect data on cannabis use and occurrence of symptoms in daily life in patients with a psychotic disorder (n = 31) and healthy controls (n = 25). Carriers of the COMT Val(158)Met Val allele, but not subjects with the Met/Met genotype, showed an increase in hallucinations after cannabis exposure, conditional on prior evidence of psychometric psychosis liability. The findings confirm that in people with psychometric evidence of psychosis liability, COMT Val(158)Met genotype moderates the association between cannabis and psychotic phenomena in the flow of daily life.

Characterization and Selection of Phosphorus Deficiency Tolerant Rice Genotypes in Sri Lanka

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Y.C. Aluwihare

2016-07-01

Full Text Available Phosphorus (P deficiency in soil is a major constrain for rice production. An important set of rice genotypes (landraces, old improved and new improved varieties were screened for P deficiency tolerance in two major cropping seasons of Sri Lanka, in 2012. The Ultisol soil, which was collected from a plot cultivated with rice without fertilizer application for past 40 years (P0 at the Rice Research and Development Institute (RRDI, Bathalagoda, Sri Lanka, was used as the potting medium for greenhouse trials. Two field trials were conducted in the same plots at RRDI. Both P0 and P30 (30 mg/kg P2O5 conditions were used in the two greenhouse trials. At the early vegetative (three weeks after transplanting, late vegetative (six weeks after transplanting and flowering stages, plant height and number of tillers per plant were recorded. At the flowering stage, shoots were harvested and shoot dry weight, shoot P concentration, shoot P uptake and P utilization efficiency were measured. All data were statistically analyzed using analysis of variance, regression and cluster procedures. The measured parameters were significantly different between P0 and P30 conditions (P < 0.05. Higher shoot dry weight was reported by the rice genotypes H4 and Marss under P0 conditions. The regression analysis between shoot dry weight and P utilization efficiency revealed that the studied rice genotypes could be categorized to three P deficiency tolerance classes. A total of 13 genotypes could be considered as highly tolerant and 4 genotypes as sensitive for P deficiency. These results could be used to select parental genotypes for breeding and genetic studies and also to select interesting varieties or landraces for organic rice production.

Evaluation of multiplex polymerase chain reaction as an alternative to conventional antibiotic sensitivity test

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K. Rathore

2018-04-01

Full Text Available Aim: This study was designed to evaluate the potential of the use of multiplex polymerase chain reaction (PCR as an alternative to conventional antibiotic sensitivity test. Materials and Methods: Isolates of Staphylococcus aureus (total = 36 from clinical cases presented to Teaching Veterinary Clinical Complex of College of Veterinary and Animal Sciences (CVAS, Navania, Udaipur, were characterized by morphological, cultural, and biochemical methods. Then, the isolates were further subjected to molecular characterization by PCR targeting S. aureus-specific sequence (107 bp. Phenotypic antibiotic sensitivity pattern was analyzed by Kirby Bauer disc diffusion method against 11 commonly used antibiotics in veterinary medicine in and around Udaipur region. The genotypic antibiotic sensitivity pattern was studied against methicillin, aminoglycosides, and tetracycline targeting the gene mecA, aacA-aphD, and tetK by multiplex PCR. Results: There was 100% correlation between the phenotype and genotype of aminoglycoside resistance, more than 90% correlation for methicillin resistance, and 58.3% in the case tetracycline resistance. Conclusion: As there is a good correlation between phenotype and genotype of antibiotic resistance, multiplex PCR can be used as an alternative to the conventional antibiotic susceptibility testing, as it can give a rapid and true prediction of antibiotic sensitivity pattern.

Radio-sensitivity and mutability in lentil (Lens culinars Medik.) as related to seed size

International Nuclear Information System (INIS)

Malik, I.A.; Chaudhry, M.S.; Ashraf, M.; Erskine, W.

1998-01-01

Eight diverse genotypes of lentil (Lens culinaris Medikus) were irradiated with 0, 10, 20, 30 and 40 kR of gamma rays. The mean lethal dose (LD50) for survival was 25.0 kR, radiation sensitivity varying over genotypes from 51.6 to 16.2 kR. The optimum irradiation dose to produce chlorophyll mutants was 21.8 kR, and that for morphological mutants was 21.4 kR. Correlations were made between a group of traits measuring radio-sensitivity and mutability, and a range of other plant characters. Most correlation coefficients between the two character groups were non-significant [it

Development and evaluation of novel one-step TaqMan realtime RT-PCR assays for the detection and direct genotyping of genogroup I and II noroviruses

DEFF Research Database (Denmark)

Schultz, Anna Charlotte; Vega, Everado; Dalsgaard, Anders

2011-01-01

BackgroundCurrent detection and genotyping methods of genogroup (G) I and II noroviruses (NoVs) consist of a 2-step approach including detection of viral RNA by TaqMan realtime RT-PCR (RT-qPCR) followed by conventional RT-PCR and sequencing of partial regions of ORF1 or ORF2. ObjectiveTo develop ......Man RT-qPCR assays for the sensitive detection and direct genotyping of GI and GII NoVs from clinical and environmental matrices...... novel long-template one-step TaqMan assays (L-RT-qPCR) for the rapid detection and direct genotyping of GI and GII NoVs and to evaluate the sensitivity and specificity of the assays. Study designGI and GII-specific broadly reactive L-RT-qPCR assays were developed by combining existing NoV primers...... and probes targeting the open reading frame (ORF)1–ORF2 junction as well as region C at the 5′–ORF2. The assays were validated using GI and GII RNA transcripts and a coded panel of 75 stool samples containing NoV strains representing 9 GI genotypes and 12 GII genotypes, as well as sapoviruses, astroviruses...

Identification of Novel Source of Resistance and Differential Response of Allium Genotypes to Purple Blotch Pathogen, Alternaria porri (Ellis) Ciferri.

Science.gov (United States)

Nanda, Satyabrata; Chand, Subodh Kumar; Mandal, Purander; Tripathy, Pradyumna; Joshi, Raj Kumar

2016-12-01

Purple blotch, caused by Alternaria porri (Ellis) Cifferi, is a serious disease incurring heavy yield losses in the bulb and seed crop of onion and garlic worldwide. There is an immediate need for identification of effective resistance sources for use in host resistance breeding. A total of 43 Allium genotypes were screened for purple blotch resistance under field conditions. Allium cepa accession 'CBT-Ac77' and cultivar 'Arka Kalyan' were observed to be highly resistant. In vitro inoculation of a selected set of genotypes with A. porri , revealed that 7 days after inoculation was suitable to observe the disease severity. In vitro screening of 43 genotypes for resistance to A. porri revealed two resistant lines. An additional 14 genotypes showed consistent moderate resistance in the field as well as in vitro evaluations. Among the related Allium species, A. schoenoprasum and A. roylei showed the least disease index and can be used for interspecific hybridization with cultivated onion. Differential reaction analysis of three A. porri isolates ( Apo-Chiplima, Apn-Nasik, Apg-Guntur ) in 43 genotypes revealed significant variation among the evaluated Allium species ( P = 0.001). All together, the present study suggest that, the newly identified resistance sources can be used as potential donors for ongoing purple blotch resistance breeding program in India.

A Simple PCR Method for Rapid Genotype Analysis of Mycobacterium ulcerans

Science.gov (United States)

Stinear, Timothy; Davies, John K.; Jenkin, Grant A.; Portaels, Françoise; Ross, Bruce C.; OppEdIsano, Frances; Purcell, Maria; Hayman, John A.; Johnson, Paul D. R.

2000-01-01

Two high-copy-number insertion sequences, IS2404 and IS2606, were recently identified in Mycobacterium ulcerans and were shown by Southern hybridization to possess restriction fragment length polymorphism between strains from different geographic origins. We have designed a simple genotyping method that captures these differences by PCR amplification of the region between adjacent copies of IS2404 and IS2606. We have called this system 2426 PCR. The method is rapid, reproducible, sensitive, and specific for M. ulcerans, and it has confirmed previous studies suggesting a clonal population structure of M. ulcerans within a geographic region. M. ulcerans isolates from Australia, Papua New Guinea, Malaysia, Surinam, Mexico, Japan, China, and several countries in Africa were easily differentiated based on an array of 4 to 14 PCR products ranging in size from 200 to 900 bp. Numerical analysis of the banding patterns suggested a close evolutionary link between M. ulcerans isolates from Africa and southeast Asia. The application of 2426 PCR to total DNA, extracted directly from M. ulcerans-infected tissue specimens without culture, demonstrated the sensitivity and specificity of this method and confirmed for the first time that both animal and human isolates from areas of endemicity in southeast Australia have the same genotype. PMID:10747130

BDNF rs6265 methylation and genotype interact on risk for schizophrenia.

Science.gov (United States)

Ursini, Gianluca; Cavalleri, Tommaso; Fazio, Leonardo; Angrisano, Tiziana; Iacovelli, Luisa; Porcelli, Annamaria; Maddalena, Giancarlo; Punzi, Giovanna; Mancini, Marina; Gelao, Barbara; Romano, Raffaella; Masellis, Rita; Calabrese, Francesca; Rampino, Antonio; Taurisano, Paolo; Di Giorgio, Annabella; Keller, Simona; Tarantini, Letizia; Sinibaldi, Lorenzo; Quarto, Tiziana; Popolizio, Teresa; Caforio, Grazia; Blasi, Giuseppe; Riva, Marco A; De Blasi, Antonio; Chiariotti, Lorenzo; Bollati, Valentina; Bertolino, Alessandro

2016-01-01

Epigenetic mechanisms can mediate gene-environment interactions relevant for complex disorders. The BDNF gene is crucial for development and brain plasticity, is sensitive to environmental stressors, such as hypoxia, and harbors the functional SNP rs6265 (Val(66)Met), which creates or abolishes a CpG dinucleotide for DNA methylation. We found that methylation at the BDNF rs6265 Val allele in peripheral blood of healthy subjects is associated with hypoxia-related early life events (hOCs) and intermediate phenotypes for schizophrenia in a distinctive manner, depending on rs6265 genotype: in ValVal individuals increased methylation is associated with exposure to hOCs and impaired working memory (WM) accuracy, while the opposite is true for ValMet subjects. Also, rs6265 methylation and hOCs interact in modulating WM-related prefrontal activity, another intermediate phenotype for schizophrenia, with an analogous opposite direction in the 2 genotypes. Consistently, rs6265 methylation has a different association with schizophrenia risk in ValVals and ValMets. The relationships of methylation with BDNF levels and of genotype with BHLHB2 binding likely contribute to these opposite effects of methylation. We conclude that BDNF rs6265 methylation interacts with genotype to bridge early environmental exposures to adult phenotypes, relevant for schizophrenia. The study of epigenetic changes in regions containing genetic variation relevant for human diseases may have beneficial implications for the understanding of how genes are actually translated into phenotypes.

Does the Incredible Years reduce child externalizing problems through improved parenting? The role of child negative affectivity and serotonin transporter linked polymorphic region (5-HTTLPR) genotype.

Science.gov (United States)

Weeland, Joyce; Chhangur, Rabia R; Jaffee, Sara R; Van Der Giessen, Danielle; Matthys, Walter; Orobio De Castro, Bram; Overbeek, Geertjan

2018-02-01

In a randomized controlled trial, the Observational Randomized Controlled Trial of Childhood Differential Susceptibility (ORCHIDS study), we tested whether observed parental affect and observed and reported parenting behavior are mechanisms of change underlying the effects of the behavioral parent training program the Incredible Years (IY). Furthermore, we tested whether some children are more susceptible to these change mechanisms because of their temperamental negative affectivity and/or serotonin transporter linked polymorphic region (5-HTTLPR) genotype. Participants were 387 Dutch children between 4 and 8 years of age (M age = 6.31, SD = 1.33; 55.3% boys) and their parents. Results showed that although IY was successful in improving parenting behavior and increasing parental positive affect, these effects did not explain the significant decreases in child externalizing problems. We therefore found no evidence for changes in parenting behavior or parental affect being the putative mechanisms of IY effectiveness. Furthermore, intervention effects on child externalizing behavior were not moderated by child negative affectivity or 5-HTTLPR genotype. However, child 5-HTTLPR genotype did moderate intervention effects on negative parenting behavior. This suggests that in research on behavioral parent training programs, "what works for which parents" might also be an important question.

Sensitivity of Amoxicillin-Resistant Helicobacter pylori to Other Penicillins

Science.gov (United States)

Dore, Maria P.; Graham, David Y.; Sepulveda, Antonia R.; Realdi, Giuseppe; Osato, Michael S.

1999-01-01

The sensitivities to penicillins and to a penicillin and β-lactamase inhibitor combination agent were determined for Helicobacter pylori strains that were sensitive, moderately resistant, or highly resistant to amoxicillin. All strains were resistant to nafcillin and oxacillin. Moderately resistant strains showed an intermediate zone of inhibition to ticarcillin, mezlocillin, piperacillin, and amoxicillin-clavulanic acid. High-level resistance was associated with the smallest zone size for all penicillins tested. PMID:10390249

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

Science.gov (United States)

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

2010-12-15

Simulated pot experiments were conducted on four rice (Oryza sativa L.) genotypes (Triguna, IR-36, PNR-519, and IET-4786) to examine the effects of As(V) on amino acids and mineral nutrient status in grain along with antioxidant response to arsenic exposure. Rice genotypes responded differentially to As(V) exposure in terms of amino acids and antioxidant profiles. Total amino acid content in grains of all rice genotypes was positively correlated with arsenic accumulation. While, most of the essential amino acids increased in all cultivars except IR-36, glutamic acid and glycine increased in IET-4786 and PNR-519. The level of nonprotein thiols (NPTs) and the activities of superoxide dismutase (SOD; EC 1.15.1.1), glutathione reductase (GR; EC 1.6.4.2) and ascorbate peroxidase (APX; EC 1.11.1.11) increased in all rice cultivars except IET-4786. A significant genotypic variation was also observed in specific arsenic uptake (SAU; mg kg(-1)dw), which was in the order of Triguna (134) > IR-36 (71) > PNR-519 (53) > IET-4786 (29). Further, application of As(V) at lower doses (4 and 8 mg L(-1) As) enhanced the accumulation of selenium (Se) and other nutrients (Fe, P, Zn, and S), however, higher dose (12 mg L(-1) As) limits the nutrient uptake in rice. In conclusion, low As accumulating genotype, IET-4786, which also had significantly induced level of essential amino acids, seems suitable for cultivation in moderately As contaminated soil and would be safe for human consumption.

A Polyethylene Moderator Design for Auxiliary Ex-core Neutron Detector

International Nuclear Information System (INIS)

Lee, Hwan Soo; Shin, Ho Cheol; Bae, Seong Man

2012-01-01

The moderator of detector assembly in ENFMS (Excore Neutron Flux Monitoring System) plays a key role for slowing down from fast neutron to thermal neutron at outside of reactor vessel. Since neutron monitoring detector such as BF3, fission chamber detectors mostly responds to thermal neutron, moderator should be included to neutron detector assembly to detect more efficiently. Generally, resin has been used for moderator of detector in ENFMS of OPR1000 and APR1400, because resin has stable thermal resistance, availability and high neutron moderation characteristics due to the light atomic materials. In case of an auxiliary ex-core neutron detector, the polyethylene is suggested that polyethylene has a better moderator rather than resin, then, the amounts of moderator are reduced. This is important thing for auxiliary ex-core detector equipment at reactor, because the auxiliary equipment should affect minimally to another system. In this study, polyethylene moderator is designed for auxiliary ex-core neutron detector. To find out the optimal thickness of polyethylene moderator, preliminary simulation and experiments are performed. And sensitivity simulation for detector moderator at actual reactor is performed by DORT code

Genomic evaluations with many more genotypes

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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

Genotype-environment interaction in passive avoidance learning of the paradise fish (Macropodus opercularis).

Science.gov (United States)

Csányi, V; Gervai, J

1985-01-01

Passive dark avoidance conditioning and effects of the presence and absence of a fish-like dummy on the training process were studied in four inbred strains of paradise fish. Strain differences were found in the shuttle activity during habituation trials, and in the sensitivity to the mild electric shock punishment. The presence or absence of the dummy in the punished dark side of the shuttle box had a genotype-dependent effect on the measures taken during the conditioning process. The statistical analysis of the learning curves revealed differences in the way the strains varied in the different environments, i.e. genotype--environment interaction components of variances were identified. The results are discussed in the light of previous investigations and their implication in further genetic analysis.

The Clinical Course of Patients with Preschool Manifestation of Type 1 Diabetes Is Independent of the HLA DR-DQ Genotype

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Christina Reinauer

2017-05-01

Full Text Available Introduction: Major histocompatibility complex class II genes are considered major genetic risk factors for autoimmune diabetes. We analysed Human Leukocyte Antigen (HLA DR and DQ haplotypes in a cohort with early-onset (age < 5 years, long term type 1 diabetes (T1D and explored their influence on clinical and laboratory parameters. Methods: Intermediate resolution HLA-DRB1, DQA1 and DQB1 typing was performed in 233 samples from the German Paediatric Diabetes Biobank and compared with a local control cohort of 19,544 cases. Clinical follow-up data of 195 patients (diabetes duration 14.2 ± 2.9 years and residual C-peptide levels were compared between three HLA risk groups using multiple linear regression analysis. Results: Genetic variability was low, 44.6% (104/233 of early-onset T1D patients carried the highest-risk genotype HLA-DRB1*03:01-DQA1*05:01-DQB1*02:01/DRB1*04-DQA1*03:01-DQB1*03:02 (HLA-DRB1*04 denoting 04:01/02/04/05, and 231 of 233 individuals carried at least one of six risk haplotypes. Comparing clinical data between the highest (n = 83, moderate (n = 106 and low risk (n = 6 genotypes, we found no difference in age at diagnosis (mean age 2.8 ± 1.1 vs. 2.8 ± 1.2 vs. 3.2 ± 1.5 years, metabolic control, or frequency of associated autoimmune diseases between HLA risk groups (each p > 0.05. Residual C-peptide was detectable in 23.5% and C-peptide levels in the highest-risk group were comparable to levels in moderate to high risk genotypes. Conclusion: In this study, we saw no evidence for a different clinical course of early-onset T1D based on the HLA genotype within the first ten years after manifestation.

Comparative proteomic analysis reveals molecular mechanism of seedling roots of different salt tolerant soybean genotypes in responses to salinity stress

Directory of Open Access Journals (Sweden)

Hongyu Ma

2014-09-01

Full Text Available Salinity stress is one of the major abiotic stresses that limit agricultural yield. To understand salt-responsive protein networks in soybean seedling, the extracted proteins from seedling roots of two different genotypes (Lee 68 and Jackson were analyzed under salt stress by two-dimensional polyacrylamide gel electrophoresis. Sixty-eight differentially expressed proteins were detected and identified. The identified proteins were involved in 13 metabolic pathways and cellular processes. Proteins correlated to brassinosteroid and gilbberellin signalings were significantly increased only in the genotype Lee 68 under salt stress; abscisic acid content was positively correlated with this genotype; proteins that can be correlated to Ca2+ signaling were more strongly enhanced by salt stress in the seedling roots of genotype Lee 68 than in those of genotype Jackson; moreover, genotype Lee 68 had stronger capability of reactive oxygen species scavenging and cell K+/Na+ homeostasis maintaining in seedling roots than genotype Jackson under salt stress. Since the genotype Lee 68 has been described in literature as being tolerant and Jackson as sensitive, we hypothesize that these major differences in the genotype Lee 68 might contribute to salt tolerance. Combined with our previous comparative proteomics analysis on seedling leaves, the similarities and differences between the salt-responsive protein networks found in the seedling leaves and roots of both the genotypes were discussed. Such a result will be helpful in breeding of salt-tolerant soybean cultivars.

Heterogeneous recombination among Hepatitis B virus genotypes.

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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.

An automated quantitative DNA image cytometry system detects abnormal cells in cervical cytology with high sensitivity.

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Wong, O G; Ho, M W; Tsun, O K; Ng, A K; Tsui, E Y; Chow, J N; Ip, P P; Cheung, A N

2018-03-26

To evaluate the performance of an automated DNA-image-cytometry system as a tool to detect cervical carcinoma. Of 384 liquid-based cervical cytology samples with available biopsy follow-up were analyzed by both the Imager System and a high-risk HPV test (Cobas). The sensitivity and specificity of Imager System for detecting biopsy proven high-grade squamous intraepithelial lesion (HSIL, cervical intraepithelial neoplasia [CIN]2-3) and carcinoma were 89.58% and 56.25%, respectively, compared to 97.22% and 23.33% of HPV test but additional HPV 16/18 genotyping increased the specificity to 69.58%. The sensitivity and specificity of the Imager System for predicting HSIL+ (CIN2-3+) lesions among atypical squamous cells of undetermined significance samples were 80.00% and 70.53%, respectively, compared to 100% and 11.58% of HPV test whilst the HPV 16/18 genotyping increased the specificity to 77.89%. Among atypical squamous cells-cannot exclude HSIL, the sensitivity and specificity of Imager System for predicting HSIL+ (CIN2-3+) lesions upon follow up were 82.86% and 33.33%%, respectively, compared to 97.14% and 4.76% of HPV test and the HPV 16/18 genotyping increased the specificity to 19.05%. Among low-grade squamous intraepithelial lesion cases, the sensitivity and specificity of the Imager System for predicting HSIL+ (CIN2-3+) lesions were 66.67% and 35.71%%, respectively, compared to 66.67% and 29.76% of HPV test while HPV 16/18 genotyping increased the specificity to 79.76%. The overall results of imager and high-risk HPV test agreed in 69.43% (268) of all samples. The automated imager system and HPV 16/18 genotyping can enhance the specificity of detecting HSIL+ (CIN2-3+) lesions. © 2018 John Wiley & Sons Ltd.

Evaluation of the BACTEC MGIT 960 SL DST Kit and the GenoType MTBDRsl Test for Detecting Extensively Drug-resistant Tuberculosis Cases.

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Tekin, Kemal; Albay, Ali; Simsek, Hulya; Sig, Ali Korhan; Guney, Mustafa

2017-10-01

The present study aimed to evaluate the performances of the BACTEC MGIT 960 SL DST kit and the GenoType MTBDRsl test for detecting second-line antituberculosis drug resistance in Multidrug-resistant TB (MDR-TB) cases. Forty-six MDR-TB strains were studied. Second-line antituberculosis drug resistances were detected using the BACTEC MGIT 960 SL DST kit and the GenoType MTBDRsl test. The Middlebrook 7H10 agar proportion method was used as the reference test. The sensitivity and specificity values for the BACTEC MGIT 960 SL DST kit were both 100% for amikacin, kanamycin, capreomycin (4 µg/mL), and ofloxacin; 100% and 95.3%, respectively, for capreomycin (10 µg/mL); and 85.7% and 100%, respectively, for moxifloxacin (0.5 µg/mL). The sensitivity and specificity values for the GenoType MTBDRsl test to detect fluoroquinolone and aminoglycoside/cyclic peptide resistance were 88.9% and 100%, respectively, for ofloxacin and 85.7% and 94.9%, respectively, for moxifloxacin (0.5 µg/mL). The accuracy of the GenoType MTBDRsl assay for kanamycin, capreomycin, ofloxacin, and moxifloxacin was lower than that of the BACTEC MGIT 960 SL DST. The BACTEC MGIT 960 SL DST kit and the GenoType MTBDRsl were successful in detecting second-line antituberculosis drug resistance. Preliminary results of the GenoType MTBDRsl are very valuable for early treatment decisions, but we still recommend additional BACTEC MGIT 960 SL DST kit usage in the routine evaluation of drug-resistant tuberculosis.

Evaluation of the BACTEC MGIT 960 SL DST Kit and the GenoType MTBDRsl Test for Detecting Extensively Drug-resistant Tuberculosis Cases

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Tekin, Kemal; Albay, Ali; Simsek, Hulya; Sig, Ali Korhan; Guney, Mustafa

2017-01-01

Objective: The present study aimed to evaluate the performances of the BACTEC MGIT 960 SL DST kit and the GenoType MTBDRsl test for detecting second-line antituberculosis drug resistance in Multidrug-resistant TB (MDR-TB) cases. Materials and Methods: Forty-six MDR-TB strains were studied. Second-line antituberculosis drug resistances were detected using the BACTEC MGIT 960 SL DST kit and the GenoType MTBDRsl test. The Middlebrook 7H10 agar proportion method was used as the reference test. Results: The sensitivity and specificity values for the BACTEC MGIT 960 SL DST kit were both 100% for amikacin, kanamycin, capreomycin (4 µg/mL), and ofloxacin; 100% and 95.3%, respectively, for capreomycin (10 µg/mL); and 85.7% and 100%, respectively, for moxifloxacin (0.5 µg/mL). The sensitivity and specificity values for the GenoType MTBDRsl test to detect fluoroquinolone and aminoglycoside/cyclic peptide resistance were 88.9% and 100%, respectively, for ofloxacin and 85.7% and 94.9%, respectively, for moxifloxacin (0.5 µg/mL). The accuracy of the GenoType MTBDRsl assay for kanamycin, capreomycin, ofloxacin, and moxifloxacin was lower than that of the BACTEC MGIT 960 SL DST. Conclusion: The BACTEC MGIT 960 SL DST kit and the GenoType MTBDRsl were successful in detecting second-line antituberculosis drug resistance. Preliminary results of the GenoType MTBDRsl are very valuable for early treatment decisions, but we still recommend additional BACTEC MGIT 960 SL DST kit usage in the routine evaluation of drug-resistant tuberculosis. PMID:29123441

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

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Angela J. Hanson

2016-03-01

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

Extreme Thermal Sensitivity and Pain-Induced Sensitization in a Fibromyalgia Patient

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Fong Wong

2010-01-01

Full Text Available During the course of a psychophysical study of fibromyalgia syndrome (FMS, one of the subjects with a long history of headache and facial pain displayed an extraordinarily severe thermal allodynia. Her stimulus-response function for ratings of cutaneous heat pain revealed a sensitivity clearly beyond that of normal controls and most FMS subjects. Specially designed psychophysical methods showed that heat sensitivity sometimes increased dramatically within a series of stimuli. Prior exposure to moderate heat pain served as a trigger for allodynic ratings of series of normally neutral thermal stimulation. These observations document a case of breakthrough pain sensitivity with implications for mechanisms of FMS pain.

[Mexican phenotype and genotype Vibrio cholerae 01].

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

1995-01-01

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

HFE genotype affects exosome phenotype in cancer.

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

2017-08-01

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

Recurrent high level parvovirus B19/genotype 2 viremia in a renal transplant recipient analyzed by real-time PCR for simultaneous detection of genotypes 1 to 3.

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Liefeldt, Lutz; Plentz, Annelie; Klempa, Boris; Kershaw, Olivia; Endres, Anne-Sophie; Raab, Ulla; Neumayer, Hans-H; Meisel, Helga; Modrow, Susanne

2005-01-01

Organ transplant recipients infected with parvovirus B19 frequently develop persistent viremia associated with chronic anemia and pure red cell aplasia. In this study, a male renal transplant recipient who had been infected with parvovirus B19/genotype 2 after renal transplantation at the age of 34 years is described. The patient was repeatedly treated with high dose intravenous immunoglobulin (IVIG) that resulted in the resolvement of symptoms but not in virus eradication. During an observation period of 33 months after transplantation three phases associated with high parvovirus B19 viremia were observed. Both the first and the second viremic phases were combined with severe anemia. Parvovirus B19 specific IgM-antibodies were initially detected at the beginning of the second phase in continually rising concentrations. Initially eradication of the virus by immunoglobulin therapy was reported after the first viremic phase [Liefeldt et al. (2002): Nephrol Dial Transplant 17:1840-1842]. Retrospectively this statement has to be corrected. It was based on the use of a qualitative PCR assay specific for parvovirus B19 genotype 1 associated with reduced sensitivity for detection of genotype 2. After sequence analysis of the viral DNA and adjustment of a real-time PCR assay (TaqMan) for quantitative detection of all three B19 virus genotypes analysis of consecutive serum samples allowed the demonstration of long lasting phases with reduced viral loads following IVIG-treatment. These results demonstrate that IVIG treatment of parvovirus B19-triggered anemia in transplant recipients offers an opportunity to resolve symptoms, but does not guarantee eradication of the virus. Since reactivation of parvovirus B19 infection can result in high virus load associated with the recurrence of symptoms repeated screening for viral DNA is recommended using the TaqMan system established for quantitative detection of all three genotypes of parvovirus B19. Copyright 2005 Wiley-Liss, Inc.

Genetic moderation of the effects of cannabis: catechol-O-methyltransferase (COMT) affects the impact of Δ9-tetrahydrocannabinol (THC) on working memory performance but not on the occurrence of psychotic experiences.

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Tunbridge, Elizabeth M; Dunn, Graham; Murray, Robin M; Evans, Nicole; Lister, Rachel; Stumpenhorst, Katharina; Harrison, Paul J; Morrison, Paul D; Freeman, Daniel

2015-11-01

Cannabis use can induce cognitive impairments and psychotic experiences. A functional polymorphism in the catechol-O-methyltransferase (COMT) gene (Val(158)Met) appears to influence the immediate cognitive and psychotic effects of cannabis, or ∆(9)-tetrahydrocannabinol (THC), its primary psychoactive ingredient. This study investigated the moderation of the impact of experimentally administered THC by COMT. Cognitive performance and psychotic experiences were studied in participants without a psychiatric diagnosis, using a between-subjects design (THC vs. placebo). The effect of COMT Val(158)Met genotype on the cognitive and psychotic effects of THC, administered intravenously in a double-blind, placebo-controlled manner to 78 participants who were vulnerable to paranoia, was examined. The results showed interactive effects of genotype and drug group (THC or placebo) on working memory, assayed using the Digit Span Backwards task. Specifically, THC impaired performance in COMT Val/Val, but not Met, carriers. In contrast, the effect of THC on psychotic experiences, measured using the Community Assessment of Psychic Experiences (CAPE) positive dimension, was unaffected by COMT genotype. This study is the largest to date examining the impact of COMT genotype on response to experimentally administered THC, and the first using a purely non-clinical cohort. The data suggest that COMT genotype moderates the cognitive, but not the psychotic, effects of acutely administered THC. © The Author(s) 2015.

Positive alcohol use expectancies moderate the association between anxiety sensitivity and alcohol use across adolescence.

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Borges, Allison M; Lejuez, Carl W; Felton, Julia W

2018-06-01

Anxiety sensitivity (AS), or the fear of anxious symptoms and the belief that these symptoms may have negative physical, social, and cognitive consequences, is one personality trait that emerges in early adolescence and may be linked to alcohol use. However, findings are equivocal as to whether elevated AS during adolescence directly predicts alcohol use. Adolescents do report increases in positive alcohol use expectancies during this developmental period, and these expectancies have been found to be significantly associated with alcohol use. The current study examined whether positive alcohol use expectancies and AS in early adolescence predicted changes in alcohol use throughout adolescence. This aim was examined via secondary data analyses from a longitudinal study examining the development of risk behaviors in adolescents. Results of univariate latent growth curve modeling suggest that AS alone was not a significant predictor of baseline alcohol use or change in use over time after controlling for gender, age, and self-reported anxiety. However, AS in early adolescence was found to be a significant predictor of increases in alcohol use across adolescence for youth who reported greater positive alcohol use expectancies. These results indicate that beliefs regarding the positive effects of alcohol use are an important moderator in the relation between AS and change in alcohol use during adolescence. Copyright © 2018 Elsevier B.V. All rights reserved.

An accurate and efficient method for large-scale SSR genotyping and applications.

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Li, Lun; Fang, Zhiwei; Zhou, Junfei; Chen, Hong; Hu, Zhangfeng; Gao, Lifen; Chen, Lihong; Ren, Sheng; Ma, Hongyu; Lu, Long; Zhang, Weixiong; Peng, Hai

2017-06-02

Accurate and efficient genotyping of simple sequence repeats (SSRs) constitutes the basis of SSRs as an effective genetic marker with various applications. However, the existing methods for SSR genotyping suffer from low sensitivity, low accuracy, low efficiency and high cost. In order to fully exploit the potential of SSRs as genetic marker, we developed a novel method for SSR genotyping, named as AmpSeq-SSR, which combines multiplexing polymerase chain reaction (PCR), targeted deep sequencing and comprehensive analysis. AmpSeq-SSR is able to genotype potentially more than a million SSRs at once using the current sequencing techniques. In the current study, we simultaneously genotyped 3105 SSRs in eight rice varieties, which were further validated experimentally. The results showed that the accuracies of AmpSeq-SSR were nearly 100 and 94% with a single base resolution for homozygous and heterozygous samples, respectively. To demonstrate the power of AmpSeq-SSR, we adopted it in two applications. The first was to construct discriminative fingerprints of the rice varieties using 3105 SSRs, which offer much greater discriminative power than the 48 SSRs commonly used for rice. The second was to map Xa21, a gene that confers persistent resistance to rice bacterial blight. We demonstrated that genome-scale fingerprints of an organism can be efficiently constructed and candidate genes, such as Xa21 in rice, can be accurately and efficiently mapped using an innovative strategy consisting of multiplexing PCR, targeted sequencing and computational analysis. While the work we present focused on rice, AmpSeq-SSR can be readily extended to animals and micro-organisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Comparative Transcriptional Profiling of Two Contrasting Barley Genotypes under Salinity Stress during the Seedling Stage

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Runhong Gao

2013-01-01

Full Text Available Salinity is one of the major abiotic stresses that affect crop productivity. Identification of the potential novel genes responsible for salt tolerance in barley will contribute to understanding the molecular mechanism of barley responses to salt stress. We compared changes in transcriptome between Hua 11 (a salt-tolerant genotype and Hua 30 (a salt sensitive genotype in response to salt stress at the seedling stage using barley cDNA microarrays. In total, 557 and 247 salt-responsive genes were expressed exclusively in the shoot and root tissue of the salt-tolerant genotype, respectively. Among these genes, a number of signal-related genes, transcription factors and compatible solutes were identified and some of these genes were carefully discussed. Notably, a LysM RLK was firstly found involved in salt stress response. Moreover, key enzymes in the pathways of jasmonic acid biosynthesis, lipid metabolism and indole-3-acetic acid homeostasis were specifically affected by salt stress in salt tolerance genotype. These salt-responsive genes and biochemical pathways identified in this study could provide further information for understanding the mechanisms of salt tolerance in barley.

FKBP5 moderation of the relationship between childhood trauma and maladaptive emotion regulation strategies in adolescents.

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Halldorsdottir, Thorhildur; de Matos, Ana Paula Soares; Awaloff, Yvonne; Arnarson, Eiríkur Örn; Craighead, W Edward; Binder, Elisabeth B

2017-10-01

Maladaptive emotion regulation strategies, such as rumination and catastrophizing, are transdiagnostic risk factors for psychopathology. FK506-binding protein 51 (FKBP5) has been found to moderate the relationship between stressful life events and various psychiatric disorders. Given the cross-disorder moderation effect of FKBP5 at the diagnostic level, the aim of the current study was to examine whether the relationship between exposure to childhood trauma and transdiagnostic maladaptive emotion regulation processes would also be moderated by genetic FKBP5 variation in a community sample of adolescents. We hypothesized that adolescent carriers of the FKBP5 CATT haplotype composed of rs9296158, rs3800373, rs1360780, and rs9470080, that has been associated with increased risk for psychiatric disorders in adulthood, would also show higher levels of rumination and catastrophizing. Participants included 1345 genotyped adolescents (M age =13.95, 64.2% female; 100% European Caucasians of Portuguese descent) who completed self-report measures on exposure to childhood trauma and emotion regulation strategies. Genotypes of rs9296158, rs3800373, rs1360780, and rs9470080 were used to estimate the CATT haplotype (carriers versus non-carriers). Consistent with our hypotheses and previous findings, adolescent CATT haplotype carriers with higher levels of childhood trauma endorsed higher levels of both rumination and catastrophizing compared to non-carriers. Given the association of these maladaptive emotion regulation processes and psychiatric disorders, the findings suggest possible psychological mechanisms why FKBP5 haplotype carriers exposed to childhood trauma are more vulnerable to developing a psychiatric disorder later in life. Copyright © 2017. Published by Elsevier Ltd.

Response of Various Tomato Genotypes to Begomovirus Infection and Its Improved Diagnostic

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NOOR AIDAWATI

2007-09-01

Full Text Available Begomovirus infection was identified from tomato growing areas in West Java (Bogor, Central Java (Boyolali, and D.I. Yogyakarta (Kaliurang. Efforts to reduce the infection among others are planting resistance varieties. This research was undertaken to evaluate 14 tomato genotypes for their response to the infection. Dot blot hybridization using nonradioactive (digoxigenin DNA probe was employed to determine the presence of begomovirus in inoculated plants. Polymerase chain reaction-amplified product of DNA clone of tobacco leaf curl virus –Indonesia was used as a source of DNA probe. All of tomato genotypes evaluated in this study was infected separately by three strain of begomovirus (GVPSlm, GVABy, GVCBgr. Tomato genotypes Bonanza, Jelita, Safira, Permata, Presto, PSPT 8, PSPT 5B, Apel-Belgia, Karibia, Mitra, PSPT 9, Marta, and PSPT 2, showed susceptible or highly susceptible response to the three strains of begomovirus. Exception to those was shown by cv. Intan which resulted in moderate resistance when inoculated with GVCBgr although it resulted susceptible response with the other two strains. Dot-blot hybridization technique was proved to be a powerful tool to detect begomovirus infection in plants showing symptom as well as symptom-less plants. Accumulation of the virus in those plants was relatively high, except in cv. Bonanza and Apel-Belgia. Dot-blot hybridization technique using DIG-labeled DNA probe was able to detect begomovirus DNA in infected tissue up to 10−2 dilution factor.

Executive control in schizophrenia: a preliminary study on the moderating role of COMT Val158Met for comorbid alcohol and substance use disorders.

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Carrà, Giuseppe; Nicolini, Gabriella; Crocamo, Cristina; Lax, Annamaria; Amidani, Francesca; Bartoli, Francesco; Castellano, Filippo; Chiorazzi, Alessia; Gamba, Giulia; Papagno, Costanza; Clerici, Massimo

2017-07-01

A functional polymorphism in the catechol-O-methyltransferase (COMT) gene (Val158Met) appears to influence cognition in people with alcohol/substance use disorders (AUD/SUD) and in those with psychosis. To explore the potential moderating effect of these factors, a cross-sectional study was conducted, randomly recruiting subjects with DSM-IV diagnosis of schizophrenia. AUD/SUD was rigorously assessed, as well as COMT Val158Met polymorphism. Executive control functioning was measured using the Intra-Extra Dimensional Set Shift (IED). The effect of a possible interaction between comorbid AUD/SUD and COMT Val158Met polymorphism on IED scores was explored. Subjects with schizophrenia, comorbid AUD/SUD, and MetMet carriers for SNP rs4680 of the COMT gene showed worse performance on IED completed stages scores, as compared with individuals with ValVal genotype. However, among subjects without AUD/SUD, those with the MetMet variant performed better than people carrying ValVal genotype. This study is the first to date examining the impact of COMT on cognition in a highly representative sample of people with schizophrenia and comorbid AUD/SUD. Differential moderating effects of COMT Val/Met genotype variations may similarly influence executive functions in people with schizophrenia and comorbid AUD/SUD.

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

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Musa Sarıca

2014-01-01

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

Genotypic evaluation of etravirine sensitivity of clinical human immunodeficiency virus type 1 (HIV-1) isolates carrying resistance mutations to nevirapine and efavirenz.

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Oumar, A A; Jnaoui, K; Kabamba-Mukadi, B; Yombi, J C; Vandercam, B; Goubau, P; Ruelle, J

2010-01-01

Etravirine is a second-generation non-nucleoside reverse transcriptase inhibitor (NNRTI) with a pattern of resistance mutations quite distinct from the current NNRTIs. We collected all routine samples of HIV-1 patients followed in the AIDS reference laboratory of UCLouvain (in 2006 and 2007) carrying resistance-associated mutations to nevirapine (NVP) or efavirenz (EFV). The sensitivity to Etravirine was estimated using three different drug resistance algorithms: ANRS (July 2008), IAS (December 2008) and Stanford (November 2008). We also verified whether the mutations described as resistance mutations are not due to virus polymorphisms by the study of 58 genotypes of NNRTI-naive patients. Sixty one samples harboured resistance to NVP and EFV: 41/61 had at least one resistance mutation to Etravirine according to ANRS-IAS algorithms; 42/61 samples had at least one resistance mutation to Etravirine according to the Stanford algorithm. 48 and 53 cases were fully sensitive to Etravirine according to ANRS-IAS and Stanford algorithms, respectively. Three cases harboured more than three mutations and presented a pattern of high-degree resistance to Etravirine according to ANRS-IAS algorithm, while one case harboured more than three mutations and presented high degree resistance to Etravirine according to the Stanford algorithm. The V1061 and V179D mutations were more frequent in the ARV-naive group than in the NNRTI-experienced one. According to the currently available algorithms, Etravirine can still be used in the majority of patients with virus showing resistance to NVP and/or EFV, if a combination of other active drugs is included.

Reducing false-positive incidental findings with ensemble genotyping and logistic regression based variant filtering methods.

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Hwang, Kyu-Baek; Lee, In-Hee; Park, Jin-Ho; Hambuch, Tina; Choe, Yongjoon; Kim, MinHyeok; Lee, Kyungjoon; Song, Taemin; Neu, Matthew B; Gupta, Neha; Kohane, Isaac S; Green, Robert C; Kong, Sek Won

2014-08-01

As whole genome sequencing (WGS) uncovers variants associated with rare and common diseases, an immediate challenge is to minimize false-positive findings due to sequencing and variant calling errors. False positives can be reduced by combining results from orthogonal sequencing methods, but costly. Here, we present variant filtering approaches using logistic regression (LR) and ensemble genotyping to minimize false positives without sacrificing sensitivity. We evaluated the methods using paired WGS datasets of an extended family prepared using two sequencing platforms and a validated set of variants in NA12878. Using LR or ensemble genotyping based filtering, false-negative rates were significantly reduced by 1.1- to 17.8-fold at the same levels of false discovery rates (5.4% for heterozygous and 4.5% for homozygous single nucleotide variants (SNVs); 30.0% for heterozygous and 18.7% for homozygous insertions; 25.2% for heterozygous and 16.6% for homozygous deletions) compared to the filtering based on genotype quality scores. Moreover, ensemble genotyping excluded > 98% (105,080 of 107,167) of false positives while retaining > 95% (897 of 937) of true positives in de novo mutation (DNM) discovery in NA12878, and performed better than a consensus method using two sequencing platforms. Our proposed methods were effective in prioritizing phenotype-associated variants, and an ensemble genotyping would be essential to minimize false-positive DNM candidates. © 2014 WILEY PERIODICALS, INC.

Genotyping Applications for Transplantation and Transfusion Management: The Emory Experience.

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Fasano, Ross M; Sullivan, Harold Cliff; Bray, Robert A; Gebel, Howard M; Meyer, Erin K; Winkler, Annie M; Josephson, Cassandra D; Stowell, Sean R; Sandy Duncan, Alexander; Roback, John D

2017-03-01

Current genotyping methodologies for transplantation and transfusion management employ multiplex systems that allow for simultaneous detection of multiple HLA antigens, human platelet antigens, and red blood cell (RBC) antigens. The development of high-resolution, molecular HLA typing has led to improved outcomes in unrelated hematopoietic stem cell transplants by better identifying compatible alleles of the HLA-A, B, C, DRB1, and DQB1 antigens. In solid organ transplantation, the combination of high-resolution HLA typing with solid-phase antibody identification has proven of value for highly sensitized patients and has significantly reduced incompatible crossmatches at the time of organ allocation. This database-driven, combined HLA antigen/antibody testing has enabled routine implementation of "virtual crossmatching" and may even obviate the need for physical crossmatching. In addition, DNA-based testing for RBC antigens provides an alternative typing method that mitigates many of the limitations of hemagglutination-based phenotyping. Although RBC genotyping has utility in various transfusion settings, it has arguably been most useful for minimizing alloimmunization in the management of transfusion-dependent patients with sickle cell disease or thalassemia. The availability of high-throughput RBC genotyping for both individuals and large populations of donors, along with coordinated informatics systems to compare patients' antigen profiles with available antigen-negative and/or rare blood-typed donors, holds promise for improving the efficiency, reliability, and extent of RBC matching for this population.

Avaliação de genótipos de caupi sob salinidade Assessment of cowpea genotypes under salinity

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José P. Dantas

2002-12-01

Full Text Available Foram conduzidos ensaios em abrigo telado de vegetação com cobertura de telha de fibra de vidro com o objetivo de se avaliar a tolerância de 50 genótipos de caupi sob salinidade. Os tratamentos de salinidade aplicados no solo, em termos de condutividade elétrica do extrato de saturação (CE, foram: CE1 - 0,3, CE2 - 3,0, CE3 - 6,0, CE4 - 9,0 e CE5 - 12,0 dS m-1. Os genótipos foram classificados para tolerância à salinidade com base na redução percentual do peso de matéria seca da parte aérea. No tratamento CE2, 36 genótipos foram tolerantes (T, 12 moderadamente tolerantes (MT e 2 moderadamente sensíveis (MS; no tratamento CE3, 3 foram T, 14 MT, 30 MS e 3 sensíveis (S; no tratamento CE4, um foi MS e 49 S e, no tratamento CE5, todos foram S. O teor de proteína nos grãos foi influenciado pela salinidade e variou de genótipo para genótipo.To assess the tolerance of 50 cowpea genotypes under salinity, experiments were conducted in greenhouse covered with fiberglass sheets. The salinity treatments applied in terms of electrical conductivity of saturation extract of soil (EC were EC1 - 0.3; EC2 - 3.0; EC3 - 6.0; EC4 - 9.0 and EC5 - 12.0 dS m-1. The genotypes were classified for the salinity tolerance on the basis of the reduction in dry weight (% of shoot. Under EC2, 36 genotypes were tolerant (T, 12 moderately tolerant (MT and 2 moderately susceptible (MS; under EC3, 3 were T, 14 MT, 30 MS and 3 susceptible (S; under EC4, one was MS and 49 S and under EC5, all were S. The protein content of seed was influenced by salinity and varied with the genotype.

Comparative sensitizing potencies of fragrances, preservatives, and hair dyes

DEFF Research Database (Denmark)

Lidén, Carola; Yazar, Kerem; Johansen, Jeanne Duus

2016-01-01

the sensitizing potencies of fragrance substances, preservatives, and hair dye substances, which are skin sensitizers that frequently come into contact with the skin of consumers and workers, LLNA results and EC3 values for 72 fragrance substances, 25 preservatives and 107 hair dye substances were obtained from...... two published compilations of LLNA data and opinions by the Scientific Committee on Consumer Safety and its predecessors. The median EC3 values of fragrances (n = 61), preservatives (n = 19) and hair dyes (n = 59) were 5.9%, 0.9%, and 1.3%, respectively. The majority of sensitizing preservatives...... and hair dyes are thus strong or extreme sensitizers (EC3 value of ≤2%), and fragrances are mostly moderate sensitizers. Although fragrances are typically moderate sensitizers, they are among the most frequent causes of contact allergy. This indicates that factors other than potency need to be addressed...

Comparative Effects of Salt Stress and Extreme pH Stress Combined on Glycinebetaine Accumulation, Photosynthetic Abilities and Growth Characters of Two Rice Genotypes

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Suriyan CHA-UM

2009-12-01

Full Text Available Glycinebetaine (Glybet accumulation, photosynthetic efficiency and growth performance in indica rice cultivated under salt stress and extreme pH stress were investigated. Betaine aldehyde dehydrogenase (BADH activity and Glybet accumulation in the seedlings of salt-tolerant and salt-sensitive rice varieties grown under saline and acidic conditions peaked after treatment for 72 h and 96 h, respectively, and were higher than those grown under neutral pH and alkaline salt stress. A positive correlation was found between BADH activity and Glybet content in both salt-tolerant (r2 = 0.71 and salt-sensitive (r2 = 0.86 genotypes. The chlorophyll a, chlorophyll b, total chlorophyll and total carotenoids contents in the stressed seedlings significantly decreased under both acidic and alkaline stresses, especially in the salt-sensitive genotype. Similarly, the maximum quantum yield of PSII (Fv/Fm, photon yield of PSII (ΦPSII, non-photochemical quenching (NPQ and net photosynthetic rate (Pn in the stressed seedlings were inhibited, leading to overall growth reduction. The positive correlations between chlorophyll a content and Fv/Fm, total chlorophyll content and ΦPSII, ΦPSII and Pn as well as Pn and leaf area in both salt-tolerant and salt-sensitive genotypes were found. Saline acidic and saline alkaline soils may play a key role affecting vegetative growth prior to the reproductive stage in rice plants.

Production of infectious chimeric hepatitis C virus genotype 2b harboring minimal regions of JFH-1.

Science.gov (United States)

Murayama, Asako; Kato, Takanobu; Akazawa, Daisuke; Sugiyama, Nao; Date, Tomoko; Masaki, Takahiro; Nakamoto, Shingo; Tanaka, Yasuhito; Mizokami, Masashi; Yokosuka, Osamu; Nomoto, Akio; Wakita, Takaji

2012-02-01

To establish a cell culture system for chimeric hepatitis C virus (HCV) genotype 2b, we prepared a chimeric construct harboring the 5' untranslated region (UTR) to the E2 region of the MA strain (genotype 2b) and the region of p7 to the 3' UTR of the JFH-1 strain (genotype 2a). This chimeric RNA (MA/JFH-1.1) replicated and produced infectious virus in Huh7.5.1 cells. Replacement of the 5' UTR of this chimera with that from JFH-1 (MA/JFH-1.2) enhanced virus production, but infectivity remained low. In a long-term follow-up study, we identified a cell culture-adaptive mutation in the core region (R167G) and found that it enhanced virus assembly. We previously reported that the NS3 helicase (N3H) and the region of NS5B to 3' X (N5BX) of JFH-1 enabled replication of the J6CF strain (genotype 2a), which could not replicate in cells. To reduce JFH-1 content in MA/JFH-1.2, we produced a chimeric viral genome for MA harboring the N3H and N5BX regions of JFH-1, combined with a JFH-1 5' UTR replacement and the R167G mutation (MA/N3H+N5BX-JFH1/R167G). This chimeric RNA replicated efficiently, but virus production was low. After the introduction of four additional cell culture-adaptive mutations, MA/N3H+N5BX-JFH1/5am produced infectious virus efficiently. Using this chimeric virus harboring minimal regions of JFH-1, we analyzed interferon sensitivity and found that this chimeric virus was more sensitive to interferon than JFH-1 and another chimeric virus containing more regions from JFH-1 (MA/JFH-1.2/R167G). In conclusion, we established an HCV genotype 2b cell culture system using a chimeric genome harboring minimal regions of JFH-1. This cell culture system may be useful for characterizing genotype 2b viruses and developing antiviral strategies.

Prevalence and genotyping of HPV, by cervical brushing, in Irpinia area of Campania region

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Pia Carmen Melillo

2012-03-01

Full Text Available Cervical cancer is due to persistent genital infection with Human Papillomavirus (HPV.The purpose of this study was to evaluate prevalence of HPV in Irpinia (Campania region, Italy, distribution of different viral genotypes, correlating cytological results and virological investigations. In the period 2006-2011, were made 1080 cervical samples of women aged 18-65 years for HPV identification and genotyping. Detection of the virus was performed by Multiplex-PCR System (Seegene,Arrow and typing with INNO-LiPA HPV Genotyping Extra test (Innogenetics. Out of the 1080 tested samples, 330 (30.6% samples were positive for HPV DNA. The most frequently occurring High Risk (HR-HPV genotype in single infections was HPV16 (16.6%, followed by HPV51 (10.7%, in multiple infections HPV16 (15.7% and 31 (14.6%. The prevalence of infection, correlated with age of patients studied, is greater in the group aged 26-30 years (42.5%. HR-HPV were detected in different percent in patients with Pap test scores: 22.5% in normal Pap smear (20% HPV16, 14.5% ASCUS (47.6% HPV16, 24% LSIL (20% HPV16, 79.3% HSIL (72.7% HPV16; 9.1% HPV18 detected only in this type of cellular alteration. The high prevalence of HR-HPV in patients with ASCUS or normal Pap test, suggesting the real advantage of HPV screening test, more sensitive in selecting the actual population at risk. Based on the findings of our epidemiological study, HR-HPV screening and HPV genotyping test should be strongly advised also to the vaccinated population for the high incidence of genotypes which are not included in vaccines (67%.

A window into the transcriptomic basis of genotype-by-genotype interactions in the legume-rhizobia mutualism.

Science.gov (United States)

Wood, Corlett W; Stinchcombe, John R

2017-11-01

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

COMT Val158Met polymorphism moderates the association between PTSD symptom severity and hippocampal volume.

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Hayes, Jasmeet P; Logue, Mark W; Reagan, Andrew; Salat, David; Wolf, Erika J; Sadeh, Naomi; Spielberg, Jeffrey M; Sperbeck, Emily; Hayes, Scott M; McGlinchey, Regina E; Milberg, William P; Verfaellie, Mieke; Stone, Annjanette; Schichman, Steven A; Miller, Mark W

2017-03-01

Memory-based alterations are among the hallmark symptoms of posttraumatic stress disorder (PTSD) and may be associated with the integrity of the hippocampus. However, neuroimaging studies of hippocampal volume in individuals with PTSD have yielded inconsistent results, raising the possibility that various moderators, such as genetic factors, may influence this association. We examined whether the catechol-O-methyltransferase (COMT) Val158Met polymorphism, which has previously been shown to be associated with hippocampal volume in healthy individuals, moderates the association between PTSD and hippocampal volume. Recent war veterans underwent structural MRI on a 3 T scanner. We extracted volumes of the right and left hippocampus using FreeSurfer and adjusted them for individual differences in intracranial volume. We assessed PTSD severity using the Clinician-Administered PTSD Scale. Hierarchical linear regression was used to model the genotype (Val158Met polymorphism) × PTSD severity interaction and its association with hippocampal volume. We included 146 white, non-Hispanic recent war veterans (90% male, 53% with diagnosed PTSD) in our analyses. A significant genotype × PTSD symptom severity interaction emerged such that individuals with greater current PTSD symptom severity who were homozygous for the Val allele showed significant reductions in left hippocampal volume. The direction of proposed effects is unknown, thus precluding definitive assessment of whether differences in hippocampal volume reflect a consequence of PTSD, a pre-existing characteristic, or both. Our findings suggest that the COMT polymorphism moderates the association between PTSD and hippocampal volume. These results highlight the role that the dopaminergic system has in brain structure and suggest a possible mechanism for memory disturbance in individuals with PTSD.

Different Roles of COMT and HTR2A Genotypes in Working Memory Subprocesses.

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Hirohito M Kondo

Full Text Available Working memory is linked to the functions of the frontal areas, in which neural activity is mediated by dopaminergic and serotonergic tones. However, there is no consensus regarding how the dopaminergic and serotonergic systems influence working memory subprocesses. The present study used an imaging genetics approach to examine the interaction between neurochemical functions and working memory performance. We focused on functional polymorphisms of the catechol-O-methyltransferase (COMT Val(158Met and serotonin 2A receptor (HTR2A -1438G/A genes, and devised a delayed recognition task to isolate the encoding, retention, and retrieval processes for visual information. The COMT genotypes affected recognition accuracy, whereas the HTR2A genotypes were associated with recognition response times. Activations specifically related to working memory were found in the right frontal and parietal areas, such as the middle frontal gyrus (MFG, inferior frontal gyrus (IFG, anterior cingulate cortex (ACC, and inferior parietal lobule (IPL. MFG and ACC/IPL activations were sensitive to differences between the COMT genotypes and between the HTR2A genotypes, respectively. Structural equation modeling demonstrated that stronger connectivity in the ACC-MFG and ACC-IFG networks is related to better task performance. The behavioral and fMRI results suggest that the dopaminergic and serotonergic systems play different roles in the working memory subprocesses and modulate closer cooperation between lateral and medial frontal activations.

Responses of meristematic callus cells of two Cynodon dactylon genotypes to aluminium.

Science.gov (United States)

Ramgareeb, Sumita; Cooke, John A; Watt, M Paula

2004-11-01

Responses to Al3+ of embryogenic callus cells of an Al-sensitive (Al-S) and Al-resistant (Al-R) Cynodon dactylon genotype were evaluated with regard to Al3+ toxicity and resistance. A chemical equilibrium speciation model (MINTEQA2) was used to ensure the availability of the Al3+ ion in culture media, which was supplied as 0.08-2.3 mM Al3+ for 2-8 weeks. Increasing Al3+ concentration and exposure time had a greater negative impact on the Al-S than on the Al-R genotype, in terms of callus growth rate and frequency of non-embryogenic cells. Exposure to 0.8 mM Al3+ for 2 weeks resulted in an 88% reduction in the Al-S meristematic cell number, whereas that of the Al-R genotype remained unaffected. In addition, the Al-S cells accumulated three times more Al in the nucleus than did the Al-R cells, suggesting that Al interfered with mitosis. The Al-R cells appeared to exclude Al3+ from its cells through an increase in extracellular pH (4.34 in Al-R and 4.08 in Al-S) and by the immobilisation of Al in the cell wall (33% more in Al-R). The results showed that by studying the cellular responses to Al3+ it is possible to discriminate between the Al-S and Al-R C. dactylon genotypes.

AKT1 moderation of cannabis-induced cognitive alterations in psychotic disorder.

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van Winkel, Ruud; van Beveren, Nico J M; Simons, Claudia

2011-11-01

Genetic variation in AKT1 may be associated with sensitivity to the psychotomimetic effects of cannabis as well as with increased risk for psychotic disorder following cannabis use. Investigation of the effect of this interaction on relevant intermediate phenotypes for psychosis, such as cognition, may help to clarify the underlying mechanism. Thus, verbal memory (visually presented Word Learning Task), sustained attention (Continuous Performance Test, CPT), AKT1 rs2494732 genotype, and cannabis use were examined in a large cohort of patients with psychotic disorder. No evidence was found for AKT1 × cannabis interaction on verbal memory. Cannabis use preceding onset of psychotic disorder did interact significantly with AKT1 rs2494732 genotype to affect CPT reaction time (β=8.0, SE 3.9, p=0.037) and CPT accuracy (β=-1.2, SE 0.4, p=0.003). Cannabis-using patients with the a priori vulnerability C/C genotype were slower and less accurate on the CPT, whereas cannabis-using patients with the T/T genotype had similar or better performance than non-using patients with psychotic disorder. The interaction was also apparent in patients with psychotic disorder who had not used cannabis in the 12 months preceding assessment, but was absent in the unaffected siblings of these patients and in healthy controls. In conclusion, cannabis use before onset of psychosis may have long-lasting effects on measures of sustained attention, even in the absence of current use, contingent on AKT1 rs2494732 genotype. The results suggest that long-term changes in cognition may mediate the risk-increasing effect of the AKT1 × cannabis interaction on psychotic disorder.

Identification of Novel Source of Resistance and Differential Response of Allium Genotypes to Purple Blotch Pathogen, Alternaria porri (Ellis Ciferri

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Satyabrata Nanda

2016-12-01

Full Text Available Purple blotch, caused by Alternaria porri (Ellis Cifferi, is a serious disease incurring heavy yield losses in the bulb and seed crop of onion and garlic worldwide. There is an immediate need for identification of effective resistance sources for use in host resistance breeding. A total of 43 Allium genotypes were screened for purple blotch resistance under field conditions. Allium cepa accession ‘CBT-Ac77’ and cultivar ‘Arka Kalyan’ were observed to be highly resistant. In vitro inoculation of a selected set of genotypes with A. porri, revealed that 7 days after inoculation was suitable to observe the disease severity. In vitro screening of 43 genotypes for resistance to A. porri revealed two resistant lines. An additional 14 genotypes showed consistent moderate resistance in the field as well as in vitro evaluations. Among the related Allium species, A. schoenoprasum and A. roylei showed the least disease index and can be used for interspecific hybridization with cultivated onion. Differential reaction analysis of three A. porri isolates (Apo-Chiplima, Apn-Nasik, Apg-Guntur in 43 genotypes revealed significant variation among the evaluated Allium species (P = 0.001. All together, the present study suggest that, the newly identified resistance sources can be used as potential donors for ongoing purple blotch resistance breeding program in India.

Variably Protease-Sensitive Prionopathy: A New Sporadic Disease of the Prion Protein

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Zou, Wen-Quan; Puoti, Gianfranco; Xiao, Xiangzhu; Yuan, Jue; Qing, Liuting; Cali, Ignazio; Shimoji, Miyuki; Langeveld, Jan P. M.; Castellani, Rudy; Notari, Silvio; Crain, Barbara; Schmidt, Robert E.; Geschwind, Michael; DeArmond, Stephen J.; Cairns, Nigel J.; Dickson, Dennis; Honig, Lawrence; Torres, Juan Maria; Mastrianni, James; Capellari, Sabina; Giaccone, Giorgio; Belay, Ermias D.; Schonberger, Lawrence B.; Cohen, Mark; Perry, George; Kong, Qingzhong; Parchi, Piero; Tagliavini, Fabrizio; Gambetti, Pierluigi

2011-01-01

Objective The objective of the study is to report 2 new genotypic forms of protease-sensitive prionopathy (PSPr), a novel prion disease described in 2008, in 11 subjects all homozygous for valine at codon 129 of the prion protein (PrP) gene (129VV). The 2 new PSPr forms affect individuals who are either homozygous for methionine (129MM) or heterozygous for methionine/valine (129MV). Methods Fifteen affected subjects with 129MM, 129MV, and 129VV underwent comparative evaluation at the National Prion Disease Pathology Surveillance Center for clinical, histopathologic, immunohistochemical, genotypical, and PrP characteristics. Results Disease duration (between 22 and 45 months) was significantly different in the 129VV and 129MV subjects. Most other phenotypic features along with the PrP electrophoretic profile were similar but distinguishable in the 3 129 genotypes. A major difference laid in the sensitivity to protease digestion of the disease-associated PrP, which was high in 129VV but much lower, or altogether lacking, in 129MV and 129MM. This difference prompted the substitution of the original designation with “variably protease-sensitive prionopathy” (VPSPr). None of the subjects had mutations in the PrP gene coding region. Interpretation Because all 3 129 genotypes are involved, and are associated with distinguishable phenotypes, VPSPr becomes the second sporadic prion protein disease with this feature after Creutzfeldt-Jakob disease, originally reported in 1920. However, the characteristics of the abnormal prion protein suggest that VPSPr is different from typical prion diseases, and perhaps more akin to subtypes of Gerstmann-Sträussler-Scheinker disease. PMID:20695009

Popcorn genotypes resistance to fall armyworm

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Nádia Cristina de Oliveira

2018-02-01

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

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

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

Identification of field caught Anopheles gambiae s.s. and Anopheles arabiensis by TaqMan single nucleotide polymorphism genotyping

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Bayoh Nabie M

2007-02-01

Full Text Available Abstract Background Identification of Anopheles gambiae s.s. and Anopheles arabiensis from field-collected Anopheles gambiae s.l. is often necessary in basic and applied research, and in operational control programmes. The currently accepted method involves use of standard polymerase chain reaction amplification of ribosomal DNA (rDNA from the 3' 28S to 5' intergenic spacer region of the genome, and visual confirmation of amplicons of predicted size on agarose gels, after electrophoresis. This report describes development and evaluation of an automated, quantitative PCR method based upon TaqMan™ single nucleotide polymorphism (SNP genotyping. Methods Standard PCR, and TaqMan SNP genotyping with newly designed primers and fluorophore-labeled probes hybridizing to sequences of complementary rDNA specific for either An. gambiae s.s. or An. arabiensis, were conducted in three experiments involving field-collected An. gambiae s.l. from western Kenya, and defined laboratory strains. DNA extraction was from a single leg, sonicated for five minutes in buffer in wells of 96-well PCR plates. Results TaqMan SNP genotyping showed a reaction success rate, sensitivity, and species specificity comparable to that of standard PCR. In an extensive field study, only 29 of 3,041 (0.95% were determined to be hybrids by TaqMan (i.e., having rDNA sequences from both species, however, all but one were An. arabiensis by standard PCR, suggesting an acceptably low (ca. 1% error rate for TaqMan genotyping in mistakenly identifying species hybrids. Conclusion TaqMan SNP genotyping proved to be a sensitive and rapid method for identification of An. gambiae s.l. and An. arabiensis, with a high success rate, specific results, and congruence with the standard PCR method.

Depression, anxiety and loss of resilience after multiple traumas: an illustration of a mediated moderation model of sensitization in a group of children who survived the Nazi Holocaust.

Science.gov (United States)

Fossion, Pierre; Leys, Christophe; Kempenaers, Chantal; Braun, Stephanie; Verbanck, Paul; Linkowski, Paul

2013-12-01

Depressive and anxiety disorders (DAD) have become a major public health problem. Multiple trauma is known to increase the risk of DAD through a sensitization mechanism. We investigate the hypothesis that resilience is a mediator of this mechanism. Former Hidden Children (FHC), the Jewish youths who spent World War II in various hideaway shelters across Nazi-occupied Europe, were compared with a control group. In each group, we measured the presence of multiple traumas, the resilience with the Resilience Scale for Adults, which has a six factors solution, and the DAD with the Hopkins Symptoms Checklist. We test a mediated moderation model with childhood trauma as the predictor; Later trauma as the moderator; Resilience as the mediator; and DAD as the outcome variable. Results are consistent with a sensitization model of DAD mediated by resilience: confrontation with a primary trauma during childhood followed by secondary trauma(s) after childhood damages resilience, which, in turn, results in higher level of DAD. We are unable to differentiate if the sensitization process is a consequence of the nature of the trauma endured by FHC (long-standing exposure to extreme external events) or a consequence of the fact that this first trauma occurred during childhood. Resilience construct is multi-factorial and a limited damaging of some of the factors is sufficient to lead to DAD even if other factors remain unaltered. Resilience can be altered by multiple traumas and, therefore, needs to be bolstered in therapy sessions. Copyright © 2013. Published by Elsevier B.V.

The sensitizing capacity of multifunctional acrylates in the guinea pig.

Science.gov (United States)

Björkner, B

1984-10-01

The multifunctional acrylates used in ultraviolet (UV) curable resins act as cross-linkers and "diluents". They are usually based on di(meth)acrylate esters of dialcohols or tri- and tetra-acrylate esters of polyalcohols. In UV-curable coatings, the most commonly used are pentaerythritol triacrylate (PETA), trimethylolpropane triacrylate (TMPTA) and 1,6-hexanediol diacrylate (HDDA). In other uses, such as dental composite resin materials, the dimethacrylic monomers based on n-ethylene glycol are the most useful. The sensitizing capacity of various multifunctional acrylates and their cross-reactivity pattern have been investigated with the guinea pig maximization test. The tests show that BUDA (1,4-butanediol diacrylate) and HDDA are moderate to strong sensitizers and that they probably cross-react with each other. The n-ethylene glycol diacrylates and methacrylates tested are weak or non-sensitizers. Tripropylene glycol diacrylate (TPGDA) is a moderate and neopentyl glycol diacrylate (NPGDA) a strong sensitizer, whereas neopentyl glycol dimethacrylate is a non-sensitizer. The commercial PETA is a mixture of pentaerythritol tri- and tetra-acrylate (PETA-3 and PETA-4). PETA-3 is a much stronger sensitizer than PETA-4. Simultaneous reactions were seen between PETA-3, PETA-4 and TMPTA. The oligotriacrylate OTA 480 is a moderate sensitizer, but no concomitant reactions were seen with PETA-3, PETA-4 or TMPTA. Of the multifunctional acrylates tested, the di- and triacrylic compounds should be regarded as potent sensitizers. The methacrylated multifunctional acrylic compounds are weak or non-sensitizers.

Hepatitis C Virus: Virology and Genotypes

KAUST Repository

Abdelaziz, Ahmed

2017-12-01

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

Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird.

Science.gov (United States)

Biedrzycka, Aleksandra; Sebastian, Alvaro; Migalska, Magdalena; Westerdahl, Helena; Radwan, Jacek

2017-07-01

Characterization of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here, we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated data set, to test the effect of amplicon coverage (range: 500-20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches. A third replicate employed unique barcoding to assess the extent of tag jumping, that is swapping of individual tag identifiers, which may confound genotyping. The reliability of MHC genotyping increased with coverage and approached or exceeded 90% within-method repeatability of allele calling at coverages of >5000 reads per amplicon. We found generally high agreement between genotyping methods, especially at high coverages. High reliability of the tested genotyping approaches was further supported by our analysis of the simulated data set, although the genotyping approach relying primarily on replication of variants in independent amplicons proved sensitive to repeatable errors. According to the most repeatable genotyping method, the number of co-amplifying variants per individual ranged from 19 to 42. Tag jumping was detectable, but at such low frequencies that it did not affect the reliability of genotyping. We thus demonstrate that gene families with many co-amplifying genes can be reliably genotyped using HTS, provided that there is sufficient per amplicon coverage. © 2016 John Wiley & Sons Ltd.

Developmental plasticity: re-conceiving the genotype.

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Sultan, Sonia E

2017-10-06

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

Performance of chickpea genotypes under Swat valley conditions

International Nuclear Information System (INIS)

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

2004-01-01

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

Helicobacter pylori genotypes and types of gastritis in first-degree relatives of gastric cancer patients.

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Siavoshi, F; Asgharzadeh, A; Ghadiri, H; Massarrat, S; Latifi-Navid, S; Zamani, M

2011-08-01

The frequency of Helicobacter pylori vacA alleles, cagA, and jhp0947 and their association with types and advanced forms of gastritis in 143 first-degree relatives of gastric cancer (GC) patients was assessed. The subjects included 64/143 with antral-predominant gastritis, 68/143 with pangastritis, and 11/143 with corpus-predominant gastritis, with or without atrophy or intestinal metaplasia (IM). Further classification included the severity of atrophy or IM. Group I (40/143) included the subjects with moderate-marked atrophy or IM, group II (58/143) those with no atrophy or IM, and group III (45/143) with mild atrophy or IM. The frequency of vacA s1 was 79.7%, vacA s2 20.3%, m1 49.7%, m2 50.3%, cagA 76.2%, and jhp0947 58%. The most prevalent combination was vacAs1 cagA (+) (65.7%) (P=0.001). Of the 143 subjects, 85 (59.4%) showed atrophy or IM, and 40/85 (47%) developed the moderate-marked atrophy or IM. No significant correlation was found between genotypes and the types of gastritis, non-atrophy, atrophy, or IM and severe forms of atrophy or IM (P>0.05). It is proposed that H. pylori genotype status might not be considered as an important determinant of the types and advanced forms of gastritis in the first-degree relatives of GC patients. Copyright © 2011 Elsevier GmbH. All rights reserved.

Hormone-sensitive lipase null mice exhibit signs of impaired insulin sensitivity whereas insulin secretion is intact

DEFF Research Database (Denmark)

Mulder, Hindrik; Sörhede-Winzell, Maria; Contreras, Juan Antonio

2003-01-01

of increased amounts of insulin. Impaired insulin sensitivity was further indicated by retarded glucose disposal during an insulin tolerance test. A euglycemic hyperinsulinemic clamp revealed that hepatic glucose production was insufficiently blocked by insulin in HSL null mice. In vitro, insulin......-stimulated glucose uptake into soleus muscle, and lipogenesis in adipocytes were moderately reduced, suggesting additional sites of insulin resistance. Morphometric analysis of pancreatic islets revealed a doubling of beta-cell mass in HSL null mice, which is consistent with an adaptation to insulin resistance....... Insulin secretion in vitro, examined by perifusion of isolated islets, was not impacted by HSL deficiency. Thus, HSL deficiency results in a moderate impairment of insulin sensitivity in multiple target tissues of the hormone but is compensated by hyperinsulinemia....

Disentangling the influence of parasite genotype, host genotype and maternal environment on different stages of bacterial infection in Daphnia magna.

Science.gov (United States)

Hall, Matthew D; Ebert, Dieter

2012-08-22

Individuals naturally vary in the severity of infectious disease when exposed to a parasite. Dissecting this variation into genetic and environmental components can reveal whether or not this variation depends on the host genotype, parasite genotype or a range of environmental conditions. Complicating this task, however, is that the symptoms of disease result from the combined effect of a series of events, from the initial encounter between a host and parasite, through to the activation of the host immune system and the exploitation of host resources. Here, we use the crustacean Daphnia magna and its parasite Pasteuria ramosa to show how disentangling genetic and environmental factors at different stages of infection improves our understanding of the processes shaping infectious disease. Using compatible host-parasite combinations, we experimentally exclude variation in the ability of a parasite to penetrate the host, from measures of parasite clearance, the reduction in host fecundity and the proliferation of the parasite. We show how parasite resistance consists of two components that vary in environmental sensitivity, how the maternal environment influences all measured aspects of the within-host infection process and how host-parasite interactions following the penetration of the parasite into the host have a distinct temporal component.

Moderation analysis with missing data in the predictors.

Science.gov (United States)

Zhang, Qian; Wang, Lijuan

2017-12-01

The most widely used statistical model for conducting moderation analysis is the moderated multiple regression (MMR) model. In MMR modeling, missing data could pose a challenge, mainly because the interaction term is a product of two or more variables and thus is a nonlinear function of the involved variables. In this study, we consider a simple MMR model, where the effect of the focal predictor X on the outcome Y is moderated by a moderator U. The primary interest is to find ways of estimating and testing the moderation effect with the existence of missing data in X. We mainly focus on cases when X is missing completely at random (MCAR) and missing at random (MAR). Three methods are compared: (a) Normal-distribution-based maximum likelihood estimation (NML); (b) Normal-distribution-based multiple imputation (NMI); and (c) Bayesian estimation (BE). Via simulations, we found that NML and NMI could lead to biased estimates of moderation effects under MAR missingness mechanism. The BE method outperformed NMI and NML for MMR modeling with missing data in the focal predictor, missingness depending on the moderator and/or auxiliary variables, and correctly specified distributions for the focal predictor. In addition, more robust BE methods are needed in terms of the distribution mis-specification problem of the focal predictor. An empirical example was used to illustrate the applications of the methods with a simple sensitivity analysis. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Heritability and Genetic Advance among Chili Pepper Genotypes for Heat Tolerance and Morphophysiological Characteristics

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Magaji G. Usman

2014-01-01

Full Text Available High temperature tolerance is an important component of adaptation to arid and semiarid cropping environment in chili pepper. Two experiments were carried out to study the genetic variability among chili pepper for heat tolerance and morphophysiological traits and to estimate heritability and genetic advance expected from selection. There was a highly significant variation among the genotypes in response to high temperature (CMT, photosynthesis rate, plant height, disease incidence, fruit length, fruit weight, number of fruits, and yield per plant. At 5% selection intensity, high genetic advance as percent of the mean (>20% was observed for CMT, photosynthesis rate, fruit length, fruit weight, number of fruits, and yield per plant. Similarly, high heritability (>60% was also observed indicating the substantial effect of additive gene more than the environmental effect. Yield per plant showed strong to moderately positive correlations (r=0.23–0.56 at phenotypic level while at genotypic level correlation coefficient ranged from 0.16 to 0.72 for CMT, plant height, fruit length, and number of fruits. Cluster analysis revealed eight groups and Group VIII recorded the highest CMT and yield. Group IV recorded 13 genotypes while Groups II, VII, and VIII recorded one each. The results showed that the availability of genetic variance could be useful for exploitation through selection for further breeding purposes.

Culture, distress, and oxytocin receptor polymorphism (OXTR) interact to influence emotional support seeking.

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Kim, Heejung S; Sherman, David K; Sasaki, Joni Y; Xu, Jun; Chu, Thai Q; Ryu, Chorong; Suh, Eunkook M; Graham, Kelsey; Taylor, Shelley E

2010-09-07

Research has demonstrated that certain genotypes are expressed in different forms, depending on input from the social environment. To examine sensitivity to cultural norms regarding emotional support seeking as a type of social environment, we explored the behavioral expression of oxytocin receptor polymorphism (OXTR) rs53576, a gene previously related to socio-emotional sensitivity. Seeking emotional support in times of distress is normative in American culture but not in Korean culture. Consequently, we predicted a three-way interaction of culture, distress, and OXTR genotype on emotional support seeking. Korean and American participants (n = 274) completed assessments of psychological distress and emotional support seeking and were genotyped for OXTR. We found the predicted three-way interaction: among distressed American participants, those with the GG/AG genotypes reported seeking more emotional social support, compared with those with the AA genotype, whereas Korean participants did not differ significantly by genotype; under conditions of low distress, OXTR groups did not differ significantly in either cultural group. These findings suggest that OXTR rs53576 is sensitive to input from the social environment, specifically cultural norms regarding emotional social support seeking. These findings also indicate that psychological distress and culture are important moderators that shape behavioral outcomes associated with OXTR genotypes.

Evaluation of the genotypic prediction of HIV-1 coreceptor use versus a phenotypic assay and correlation with the virological response to maraviroc: the ANRS GenoTropism study.

Science.gov (United States)

Recordon-Pinson, Patricia; Soulié, Cathia; Flandre, Philippe; Descamps, Diane; Lazrek, Mouna; Charpentier, Charlotte; Montes, Brigitte; Trabaud, Mary-Anne; Cottalorda, Jacqueline; Schneider, Véronique; Morand-Joubert, Laurence; Tamalet, Catherine; Desbois, Delphine; Macé, Muriel; Ferré, Virginie; Vabret, Astrid; Ruffault, Annick; Pallier, Coralie; Raymond, Stéphanie; Izopet, Jacques; Reynes, Jacques; Marcelin, Anne-Geneviève; Masquelier, Bernard

2010-08-01

Genotypic algorithms for prediction of HIV-1 coreceptor usage need to be evaluated in a clinical setting. We aimed at studying (i) the correlation of genotypic prediction of coreceptor use in comparison with a phenotypic assay and (ii) the relationship between genotypic prediction of coreceptor use at baseline and the virological response (VR) to a therapy including maraviroc (MVC). Antiretroviral-experienced patients were included in the MVC Expanded Access Program if they had an R5 screening result with Trofile (Monogram Biosciences). V3 loop sequences were determined at screening, and coreceptor use was predicted using 13 genotypic algorithms or combinations of algorithms. Genotypic predictions were compared to Trofile; dual or mixed (D/M) variants were considered as X4 variants. Both genotypic and phenotypic results were obtained for 189 patients at screening, with 54 isolates scored as X4 or D/M and 135 scored as R5 with Trofile. The highest sensitivity (59.3%) for detection of X4 was obtained with the Geno2pheno algorithm, with a false-positive rate set up at 10% (Geno2pheno10). In the 112 patients receiving MVC, a plasma viral RNA load of <50 copies/ml was obtained in 68% of cases at month 6. In multivariate analysis, the prediction of the X4 genotype at baseline with the Geno2pheno10 algorithm including baseline viral load and CD4 nadir was independently associated with a worse VR at months 1 and 3. The baseline weighted genotypic sensitivity score was associated with VR at month 6. There were strong arguments in favor of using genotypic coreceptor use assays for determining which patients would respond to CCR5 antagonist.

Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance.

Directory of Open Access Journals (Sweden)

Dawn M Dudley

Full Text Available Great efforts have been made to increase accessibility of HIV antiretroviral therapy (ART in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures the use of appropriate first-line regimens to maximize efficacy of ART programs where drug options are limited. However, traditional HIV genotyping is extremely expensive, providing a cost barrier to wide-scale and frequent HIV drug resistance surveillance.We have developed a low-cost laboratory-scale next-generation sequencing-based genotyping method to monitor drug resistance. We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. Using this approach, we characterized drug resistance from plasma in 81 HIV infected individuals collected in São Paulo, Brazil. We describe the complexities of analyzing next-generation sequencing data and present a simplified open-source workflow to analyze drug resistance data. From this data, we identified drug resistance mutations in 20% of treatment naïve individuals in our cohort, which is similar to frequencies identified using traditional genotyping in Brazilian patient samples.The developed ultra-wide sequencing approach described here allows multiplexing of at least 48 patient samples per sequencing run, 4 times more than the current genotyping method. This method is also 4-fold more sensitive (5% minimal detection frequency vs. 20% at a cost 3-5× less than the traditional Sanger-based genotyping method. Lastly, by using a benchtop next-generation sequencer (Roche/454 GS Junior, this approach can be more easily implemented in low-resource settings. This data provides proof-of-concept that next

Doping test results dependent on genotype of uridine diphospho-glucuronosyl transferase 2B17, the major enzyme for testosterone glucuronidation.

Science.gov (United States)

Schulze, Jenny Jakobsson; Lundmark, Jonas; Garle, Mats; Skilving, Ilona; Ekström, Lena; Rane, Anders

2008-07-01

Testosterone abuse is conventionally assessed by the urinary testosterone/epitestosterone (T/E) ratio, levels above 4.0 being considered suspicious. The large variation in testosterone glucuronide (TG) excretion and its strong association with a deletion polymorphism in the uridine diphospho-glucuronosyl transferase (UGT) 2B17 gene challenge the accuracy of the T/E ratio test. Our objective was to investigate whether genotype-based cutoff values will improve the sensitivity and specificity of the test. This was an open three-armed comparative study. A total of 55 healthy male volunteers with either two, one, or no allele [insertion/insertion, insertion/deletion, or deletion/deletion (del/del)] of the UGT2B17 gene was included in the study. A single im dose of 500 mg testosterone enanthate was administered. Urinary excretion of TG after dose and the T/E ratio during 15 d were calculated. The degree and rate of increase in the TG excretion rate were highly dependent on the UGT2B17 genotype with a 20-fold higher average maximum increase in the insertion/insertion group compared with the del/del group. Of the del/del subjects, 40% never reached the T/E ratio of 4.0 on any of the 15 d after the dose. When differentiated cutoff levels for the del/del (1.0) and the other genotypes (6.0) were applied, the sensitivity increased substantially for the del/del group, and false positives in the other genotypes were eliminated. Consideration of the genetic variation in disposition of androgens will improve the sensitivity and specificity of the testosterone doping test. This is of interest not only for combating androgen doping in sports, but also for detecting and preventing androgen abuse in society.

Hepatitis C virus genotypes in Bahawalpur

International Nuclear Information System (INIS)

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

2006-01-01

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

PROP sensitivity reflects sensory discrimination between custard desserts

NARCIS (Netherlands)

Wijk, R.A. de; Dijksterhuis, G.; Vereijken, P.; Prinz, J.F.; Weenen, H.

2007-01-01

Sensitivity to 6-n-propylthiouracil (PROP) for a group of 180 naïve consumers was related to their perception of 16 commercially available vanilla custard desserts. Rated intensities of taste and texture attributes varied moderately and inconsistently with PROP sensitivity. In contrast,

Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies.

Science.gov (United States)

McGovern, Rachel A; Thielen, Alexander; Mo, Theresa; Dong, Winnie; Woods, Conan K; Chapman, Douglass; Lewis, Marilyn; James, Ian; Heera, Jayvant; Valdez, Hernan; Harrigan, P Richard

2010-10-23

The MOTIVATE-1 and 2 studies compared maraviroc (MVC) along with optimized background therapy (OBT) vs. placebo along with OBT in treatment-experienced patients screened as having R5-HIV (original Monogram Trofile). A subset screened with non-R5 HIV were treated with MVC or placebo along with OBT in a sister safety trial, A4001029. This analysis retrospectively examined the performance of population-based sequence analysis of HIV-1 env V3-loop to predict coreceptor tropism. Triplicate V3-loop sequences were generated using stored screening plasma samples and data was processed using custom software ('ReCall'), blinded to clinical response. Tropism was inferred using geno2pheno ('g2p'; 5% false positive rate). Primary outcomes were viral load changes after starting maraviroc; and concordance with prior screening Trofile results. Genotype and Trofile results were available for 1164 individuals with virological outcome data (N = 169 non-R5 by Trofile). Compared with Trofile, V3 genotyping had a specificity of 92.6% and a sensitivity of 67.4% for detecting non-R5 virus. However, when compared with clinical outcome, virological responses were consistently similar between Trofile and V3 genotype at weeks 8 and 24 following the initiation of therapy for patients categorized as R5. Despite differences in sensitivity for predicting non-R5 HIV, week 8 and 24 week virological responses were similar in this treatment-experienced population. These findings suggest the potential utility of V3 genotyping as an accessible assay to select patients who may benefit from maraviroc treatment. Optimization of the predictive tropism algorithm may lead to further improvement in the clinical utility of HIV genotypic tropism assays.

Predictive factors for the severity of liver fibrosis in patients with chronic hepatitis C and moderate alcohol consumption.

Science.gov (United States)

Vădan, Roxana; Gheorghe, Liana; Becheanu, Gabriel; Iacob, Răzvan; Iacob, Speranţa; Gheorghe, Cristian

2003-09-01

Among the histological lesions seen in chronic hepatitis C (CHC), the presence of steatosis, bile duct lesions and lymphoid aggregates are characteristic. Recent reports suggest that steatosis is an independent risk factor for liver fibrosis in CHC. The aim of our study was to determine the relative contribution of steatosis and moderate alcohol consumption to the severity of liver fibrosis in patients infected with genotype 1 hepatitis C virus. We evaluated the patients with biopsy proven CHC and no or only moderate alcohol intake (<40 g/day). The demographical parameters of the study population, the indices of alcohol consumption: erythrocyte median corpuscular volume (MCV), gamma-glutamyl transpeptidase (GGT), the histological characteristics were noted and a statistical analysis was performed in order to determine the factors independently associated with severe fibrosis and with severe steatosis. From the 200 patients included in the study, 82 were males and 118 females, with a mean age of 47.75+/-10.42 years. At univariate analysis, advanced (grade 2, 3) fibrosis correlated with: the age at the time of biopsy, increased inflammatory activity (HAI), moderate/severe steatosis, alcohol intake, elevated GGT and MCV values. After multivariate logistic regression only age, HAI and steatosis were independently associated with advanced fibrosis stage. Regarding hepatic steatosis, from the factors found to correlate with severe steatosis at univariate analysis (alcohol intake, elevated GGT and MCV levels, severe fibrosis), after multivariate logistic regression only the elevated level of GGT was an independent prognostic factor for severe steatosis. Steatosis is an important risk factor for the severity of liver disease in CHC patients. Among patients with genotype 1 hepatitis C virus infection and moderate alcohol intake, those with serum levels of GGT over two times the normal value are at high risk for severe steatosis.

High Resolution Melting (HRM) for High-Throughput Genotyping-Limitations and Caveats in Practical Case Studies.

Science.gov (United States)

Słomka, Marcin; Sobalska-Kwapis, Marta; Wachulec, Monika; Bartosz, Grzegorz; Strapagiel, Dominik

2017-11-03

High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.

IDENTIFICATION OF TECHNOLOGICALLY IMPORTANT GENES AND THEIR PRODUCTS IN THE COLLECTION OF BREAD WHEAT GENOTYPES

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Milan Chňapek

2015-02-01

Full Text Available Wheat is the second most cultivated crop on the world and is very important plant for feed not only mankind but also animals. Because of this is necessary to develop new varieties with better properties. Bread making quality of wheat grain is one of the most important paramaters for quality evaluation. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE of wheat storage proteins and allelic specific polymerase chain reaction (AS-PCR are analysis suitable for identification, differentiation and characterization of bread wheat (Triticum aestivum L.. There were analysed 16 genotypes of new varieties of bread wheat in our work by SDS-PAGE and obtained results were verified by AS-PCR. Analysed genotypes of bread wheat genotypes were homogenous and single line with very good bread making quality. Our results confirmed hypothesis, that cultivated bread wheat genotypes are uniformed with high production and quality but there is a risk of sensitivity to environmental conditions. SDS-PAGE analyses of wheat grain proteins are fast and not very expensive technique, which provide us information of bread making quality of grains. However, there is possibility of environmental influence on protein synthesis and because of this is necessary to couple these analysis with analysis of DNA.

Grain yield stability of early maize genotypes

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Chitra Bahadur Kunwar

2016-12-01

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

Development and characterization of a high density SNP genotyping assay for cattle.

Directory of Open Access Journals (Sweden)

Lakshmi K Matukumalli

Full Text Available The success of genome-wide association (GWA studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP genotyping for the identification of quantitative trait loci (QTL and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF ranging from 0.24 to 0.27. The assay also identified 79 putative copy number variants in cattle. Utility for GWA was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. The combination of SNP selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. Aspects of the approach can be exploited in species which lack an available genome sequence. The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle.

Moral judgment modulation by disgust is bi-directionally moderated by individual sensitivity

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How Hwee eOng

2014-03-01

Full Text Available Modern theories of moral judgment predict that both conscious reasoning and unconscious emotional influences affect the way people decide about right and wrong. In a series of experiments, we tested the effect of subliminal and conscious priming of disgust facial expressions on moral dilemmas. Trolley-car-type scenarios were used, with subjects rating how acceptable they found the utilitarian course of action to be. On average, subliminal priming of disgust facial expressions resulted in higher rates of utilitarian judgments compared to neutral facial expressions. Further, in replication, we found that individual change in moral acceptability ratings due to disgust priming was modulated by individual sensitivity to disgust, revealing a bi-directional function. Our second replication extended this result to show that the function held for both subliminally and consciously presented stimuli. Combined across these experiments, we show a reliable bi-directional function, with presentation of disgust expression primes to individuals with higher disgust sensitivity resulting in more utilitarian judgments (i.e., number-based and presentations to individuals with lower sensitivity resulting in more deontological judgments (i.e., rules-based. Our results may reconcile previous conflicting reports of disgust modulation of moral judgment by modeling how individual sensitivity to disgust determines the direction and degree of this effect.

Moral judgment modulation by disgust is bi-directionally moderated by individual sensitivity

Science.gov (United States)

Ong, How Hwee; Mullette-Gillman, O’Dhaniel A.; Kwok, Kenneth; Lim, Julian

2014-01-01

Modern theories of moral judgment predict that both conscious reasoning and unconscious emotional influences affect the way people decide about right and wrong. In a series of experiments, we tested the effect of subliminal and conscious priming of disgust facial expressions on moral dilemmas. “Trolley-car”-type scenarios were used, with subjects rating how acceptable they found the utilitarian course of action to be. On average, subliminal priming of disgust facial expressions resulted in higher rates of utilitarian judgments compared to neutral facial expressions. Further, in replication, we found that individual change in moral acceptability ratings due to disgust priming was modulated by individual sensitivity to disgust, revealing a bi-directional function. Our second replication extended this result to show that the function held for both subliminally and consciously presented stimuli. Combined across these experiments, we show a reliable bi-directional function, with presentation of disgust expression primes to individuals with higher disgust sensitivity resulting in more utilitarian judgments (i.e., number-based) and presentations to individuals with lower sensitivity resulting in more deontological judgments (i.e., rules-based). Our results may reconcile previous conflicting reports of disgust modulation of moral judgment by modeling how individual sensitivity to disgust determines the direction and degree of this effect. PMID:24639665

Does selection in a challenging environment produce Nile tilapia genotypes that can thrive in a range of production systems?

Science.gov (United States)

Thoa, Ngo Phu; Ninh, Nguyen Huu; Knibb, Wayne; Nguyen, Nguyen Hong

2016-02-19

This study assessed whether selection for high growth in a challenging environment of medium salinity produces tilapia genotypes that perform well across different production environments. We estimated the genetic correlations between trait expressions in saline and freshwater using a strain of Nile tilapia selected for fast growth under salinity water of 15-20 ppt. We also estimated the heritability and genetic correlations for new traits of commercial importance (sexual maturity, feed conversion ratio, deformity and gill condition) in a full pedigree comprising 36,145 fish. The genetic correlations for the novel characters between the two environments were 0.78-0.99, suggesting that the effect of genotype by environment interaction was not biologically important. Across the environments, the heritability for body weight was moderate to high (0.32-0.62), indicating that this population will continue responding to future selection. The estimates of heritability for sexual maturity and survival were low but significant. The additive genetic components also exist for FCR, gill condition and deformity. Genetic correlations of harvest body weight with sexual maturity were positive and those between harvest body weight with FCR were negative. Our results indicate that the genetic line selected under a moderate saline water environment can be cultured successfully in freshwater systems.

The generation and development of the moderators for slow positron beam

International Nuclear Information System (INIS)

Yu Weizhong; Yuan Jiaping

2001-01-01

The positron annihilation technique is a sensitive tool for studying microdefects and phase transitions in various materials. Usually the energy of positrons is on the order of MeV and the implantation depth about 100 microns, so the bulk average defect density can be studied. In a slow positron beam the positron energy is about keV and the implantation depth a few microns, so surface defects can be detected. Positron moderator is the key device for obtaining a slow positron beam. The authors review the history and development of the positron moderator, including four methods that convert fast positrons into slow mono-energetic positrons and five array types. The tungsten moderator is the most widely used one while the inert gas solid moderator is the most efficient. Field-enhanced moderators with their high efficiency have great potential but need to be developed. The vane arrangement is the most commonly found

Evaluation of tomato genotypes against tomato mosaic virus (ToMV) and its effect on yield contributing parameters

International Nuclear Information System (INIS)

Ullah, N.; Ali, A.; Ahmad, M.; Din, N.; Ahmad, F.; Fahim, M.

2017-01-01

The use of resistant varieties is an effective, economic and environment friendly management of plant diseases particularly those caused by viruses. This paper reports, evaluation of 21 different tomato genotypes to find out resistance sources against Tomato mosaic virus (ToMV) and to study effect of the virus on yield contributing parameters. The virus identity was confirmed both by Direct Antibody Coating Enzyme Linked Immunoassay (DAC-ELISA) and differential host assay. Characteristic necrotic lesions were observed on differential hosts viz., Nicotiana tabacum var. White burly and Chenopodium amaranticolor after 10 and 3-4 days of inoculation, respectively. Upon ToMV inoculation, plants of accession No. 017902 developed no symptoms and were rated as highly resistant. Its resistance was further confirmed by both DAC-ELISA and indicator host assay, while the remaining genotypes displayed a range of symptoms. Plants of accession No. 017883 showed lowest percent disease index (PDI) and were rated as resistant, while plants of cultivar Red jumbo showed maximum PDI (44.97%) and were rated as susceptible. In susceptible genotypes average ELISA absorbance A405 value (2.19) was found higher than resistant one (1.05), while in control healthy plants ELISA absorbance A405 was 0.18. Maximum virus titre 2.73 and 0.91 were found in leaf and root tissues of cultivar Red jumbo, respectively. Among tested genotypes, one was highly resistant, one resistant, four moderately susceptible and 15 were susceptible. The virus significantly (p<=0.05) reduced the yield contributing parameters i.e. plant height, fresh shoot and root weight, dry shoot and root weight in susceptible genotypes. (author)

Inter-genotypic differences in drought tolerance of maritime pine are modified by elevated [CO2].

Science.gov (United States)

Sánchez-Gómez, David; Mancha, José A; Cervera, M Teresa; Aranda, Ismael

2017-10-17

Despite the importance of growth [CO 2 ] and water availability for tree growth and survival, little information is available on how the interplay of these two factors can shape intraspecific patterns of functional variation in tree species, particularly for conifers. The main objective of the study was to test whether the range of realized drought tolerance within the species can be affected by elevated [CO 2 ]. Intraspecific variability in leaf gas exchange, growth rate and other leaf functional traits were studied in clones of maritime pine. A factorial experiment including water availability, growth [CO 2 ] and four different genotypes was conducted in growth rooms. A 'water deficit' treatment was imposed by applying a cycle of progressive soil water depletion and recovery at two levels of growth [CO 2 ]: 'ambient [CO 2 ]' (aCO 2 400 μmol mol -1 ) and 'elevated [CO 2 ]' (eCO 2 800 μmol mol -1 ). eCO2 had a neutral effect on the impact of drought on growth and leaf gas exchange of the most drought-sensitive genotypes while it aggravated the impact of drought on the most drought-tolerant genotypes at aCO2. Thus, eCO2 attenuated genotypic differences in drought tolerance as compared with those observed at aCO2. Genotypic variation at both levels of growth [CO2] was found in specific leaf area and leaf nitrogen content but not in other physiological leaf traits such as intrinsic water use efficiency and leaf osmotic potential. eCO2 increased Δ 13 C but had no significant effect on δ 18 O. This effect did not interact with the impact of drought, which increased δ 18 O and decreased Δ 13 C. Nevertheless, correlations between Δ 13 C and δ 18 O indicated the non-stomatal component of water use efficiency in this species can be particularly sensitive to drought. Evidence from this study suggests elevated [CO 2 ] can modify current ranges of drought tolerance within tree species. © The Author 2017. Published by Oxford University Press on behalf of the Annals

Genotype by energy expenditure interaction with metabolic syndrome traits: the Portuguese healthy family study.

Science.gov (United States)

Santos, Daniel M V; Katzmarzyk, Peter T; Diego, Vincent P; Souza, Michele C; Chaves, Raquel N; Blangero, John; Maia, José A R

2013-01-01

Moderate-to-high levels of physical activity are established as preventive factors in metabolic syndrome development. However, there is variability in the phenotypic expression of metabolic syndrome under distinct physical activity conditions. In the present study we applied a Genotype X Environment interaction method to examine the presence of GxEE interaction in the phenotypic expression of metabolic syndrome. A total of 958 subjects, from 294 families of The Portuguese Healthy Family study, were included in the analysis. Total daily energy expenditure was assessed using a 3 day physical activity diary. Six metabolic syndrome related traits, including waist circumference, systolic blood pressure, glucose, HDL cholesterol, total cholesterol and triglycerides, were measured and adjusted for age and sex. GxEE examination was performed on SOLAR 4.3.1. All metabolic syndrome indicators were significantly heritable. The GxEE interaction model fitted the data better than the polygenic model (pmetabolic syndrome traits expression is significantly influenced by the interaction established between total daily energy expenditure and genotypes. Physical activity may be considered an environmental variable that promotes metabolic differences between individuals that are distinctively active.

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...

Identification of genetically diverse genotypes for photoperiod insensitivity in soybean using RAPD markers.

Science.gov (United States)

Singh, R K; Bhatia, V S; Yadav, Sanjeev; Athale, Rashmi; Lakshmi, N; Guruprasad, K N; Chauhan, G S

2008-10-01

Most of the Indian soybean varieties were found to be highly sensitive to photoperiod, which limits their cultivation in only localized area. Identification of genetically diverse source of photoperiod insensitive would help to broaden the genetic base for this trait. Present study was undertaken with RAPD markers for genetic diversity estimation in 44 accessions of soybean differing in response to photoperiod sensitivity. The selected twenty-five RAPD primers produced a total of 199 amplicons, which generated 89.9 % polymorphism. The number of amplification products ranged from 2 to 13 for different primers. The polymorphism information content ranged from 0.0 for monomorphic loci to 0.5 with an average of 0.289. Genetic diversity between pairs of genotypes was 37.7% with a range of 3.9 to 71.6%. UPGMA cluster analysis placed all the accessions of soybean into four major clusters. No discernable geographical patterns were observed in clustering however; the smaller groups corresponded well with pedigree. Mantel's test (r = 0.915) indicates very good fit for clustering pattern. Two genotypes, MACS 330 and 111/2/1939 made a very divergent group from other accessions of soybean and highly photoperiod insensitive that may be potential source for broadening the genetic base of soybean for this trait.

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

APOE moderates the association between lifestyle activities and cognitive performance: evidence of genetic plasticity in aging.

Science.gov (United States)

Runge, Shannon K; Small, Brent J; McFall, G Peggy; Dixon, Roger A

2014-05-01

The current study examined independent and interactive effects between Apolipoprotein E (APOE) genotype and two types of cognitively-stimulating lifestyle activities (CSLA)-integrated information processing (CSLA-II) and novel information processing (CSLA-NI)-on concurrent and longitudinal changes in cognition. Three-wave data across 6 years of follow-up from the Victoria Longitudinal Study (n=278; ages 55-94) and linear mixed model analyses were used to characterize the effects of APOE genotype and participation in CSLA-II and CSLA-NI in four cognitive domains. Significant CSLA effects on cognition were observed. More frequent participation in challenging activities (i.e., CSLA-NI) was associated with higher baseline scores on word recall, fact recall, vocabulary and verbal fluency. Conversely, higher participation in less cognitively-challenging activities (i.e., CSLA-II) was associated with lower scores on fact recall and verbal fluency. No longitudinal CSLA-cognition effects were found. Two significant genetic effects were observed. First, APOE moderated CSLA-II and CSLA-NI associations with baseline verbal fluency and fact recall scores. Second, APOE non-ɛ4 carriers' baseline performance were more likely to be moderated by CSLA participation, compared to APOE-ɛ4 carriers. Our findings suggest APOE may be a "plasticity" gene that makes individuals more or less amenable to the influence of protective factors such as CSLA.

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

Energy Technology Data Exchange (ETDEWEB)

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

2013-11-15

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

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

Science.gov (United States)

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

2012-01-01

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

Echinococcus granulosus genotypes in Iran

Science.gov (United States)

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

2014-01-01

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

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.

Effect of NaCl induced salinity on some physiological and agronomic traits of wheat

International Nuclear Information System (INIS)

Bilkis, A.; Islam, M.H.R.; Hasan, M.A.

2016-01-01

Wheat genotypes were evaluated for salt stress at early seedling stage (solution culture) and maturity (pot culture) at Crop Physiology and Ecology Laboratory, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh. Shoot length, root length, root to shoot length ratio and seedling dry weight of 15 days old seedlings were found to be reduced at 12 dS m-1 salinity level compared to control condition. Based on seedling dry weight Shatabdi, BARI Gom 25, BARI Gom 26, BAW 1111, BAW 1146, BAW 1154 and BAW 1156 were identified as salt tolerant (STI = >0.70); BAW 1130, BAW 1135 and BAW 1142 were salt sensitive (STI = <0.60) and other ten were screened as moderately salt tolerant (STI = 0.60 to 0.70) wheat genotypes. Out of twenty genotypes, two salt tolerant (Shatabdi and BARI Gom 25) and two salt sensitive (BAW 1130 and BAW 1142) wheat genotypes were grown in pot irrigated with three levels of saline water (control, 6 dS m/sup -1/ and 12 dS m/sup -1/). Salt tolerant wheat genotypes maintained lower level of leaf Na, higher level of leaf K, greater K to Na ratio, increased level of flag leaf proline and greater flag leaf SPAD value in saline condition than the sensitive ones. Salt sensitive genotypes affected more in spikes plant-1, grains spike/sup -1/, grain dry weight spike-1, 100 grain weight and grain yield plant-1 under saline condition than salt tolerant genotypes. (author)

Distress of ostracism: oxytocin receptor gene polymorphism confers sensitivity to social exclusion.

Science.gov (United States)

McQuaid, Robyn J; McInnis, Opal A; Matheson, Kimberly; Anisman, Hymie

2015-08-01

A single-nucleotide polymorphism on the oxytocin receptor gene (OXTR), rs53576, involving a guanine (G) to adenine (A) substitution has been associated with altered prosocial features. Specifically, individuals with the GG genotype (i.e. the absence of the polymorphism) display beneficial traits including enhanced trust, empathy and self-esteem. However, because G carriers might also be more socially sensitive, this may render them more vulnerable to the adverse effects of a negative social stressor. The current investigation, conducted among 128 white female undergraduate students, demonstrated that relative to individuals with AA genotype, G carriers were more emotionally sensitive (lower self-esteem) in response to social ostracism promoted through an on-line ball tossing game (Cyberball). Furthermore, GG individuals also exhibited altered blood pressure and cortisol levels following rejection, effects not apparent among A carriers. The data support the view that the presence of the G allele not only promotes prosocial behaviors but also favors sensitivity to a negative social stressor. © The Author (2015). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

The influence of al-madinah al-munawwara treated and untreated domestic wastewater on growth and physiology of three tomato (lycopersicon esculentum mill.) genotypes

International Nuclear Information System (INIS)

Akhkha, A.; Boutraa, T.; Shoaibi, A.K.

2017-01-01

The impact of irrigation with Al-Madinah Al-Munawwara domestic wastewater on three tomato genotypes (AL, P and VF) was investigated. Five treatments including Tap water, untreated (TN), primary (T1), secondary (T2) and tertiary (T3) treated wastewaters were used for irrigation. The physico-chemical characteristics of wastewater were determined. Leaves were analysed for N, P, K and heavy metals (Copper, Cadmium, Lead and Nickel). The growth parameters assessed were % germination, plant height, shoot and root dry weights, and total leaf dry weight. Some physiological parameters such as photosynthetic light response curve, maximum gross photosynthesis (Amax), dark respiration (DR), chlorophyll fluorescence parameters (Fo, Fm and Fv / Fm), chlorophyll content index and stomatal conductance were detected. % germination was decreased in both A1 and P genotype, with no effect on VF genotype. Most growth parameters were increased in genotype A1, followed by VF then P genotype which had a sensitive leaf dry weight to T2 and T3. Photosynthesis was mainly increased in A1 genotype with a decrease in VF genotype. DR was negatively affected in VF genotype with no response of A1 genotype. Chlorophyll fluorescence showed an increase in Fo in VF genotype but a decrease in Fv / Fm in both A1 and VF genotypes. Chlorophyll content index was decreased but only in A1 and VF genotypes under TN. Treatment with TN and / or T1 decreased stomatal conductance in all genotypes. The levels of heavy metals in wastewaters used were lower than the standard limits; however, plant chemical analysis showed that the leaves of the three tomato genotypes accumulated heavy metals but differently with higher levels at TN and lower levels at T3. (author)

Tenofovir alafenamide demonstrates broad cross-genotype activity against wild-type HBV clinical isolates and maintains susceptibility to drug-resistant HBV isolates in vitro.

Science.gov (United States)

Liu, Yang; Miller, Michael D; Kitrinos, Kathryn M

2017-03-01

Tenofovir alafenamide (TAF) is a novel prodrug of tenofovir (TFV). This study evaluated the antiviral activity of TAF against wild-type genotype A-H HBV clinical isolates as well as adefovir-resistant, lamivudine-resistant, and entecavir-resistant HBV isolates. Full length HBV genomes or the polymerase/reverse transcriptase (pol/RT) region from treatment-naïve patients infected with HBV genotypes A-H were amplified and cloned into an expression vector under the control of a CMV promoter. In addition, 11 drug resistant HBV constructs were created by site-directed mutagenesis of a full length genotype D construct. Activity of TAF was measured by transfection of each construct into HepG2 cells and assessment of HBV DNA levels following treatment across a range of TAF concentrations. TAF activity in vitro was similar against wild-type genotype A-H HBV clinical isolates. All lamivudine- and entecavir-resistant isolates and 4/5 adefovir-resistant isolates were found to be sensitive to inhibition by TAF in vitro as compared to the wild-type isolate. The adefovir-resistant isolate rtA181V + rtN236T exhibited low-level reduced susceptibility to TAF. TAF is similarly active in vitro against wild-type genotype A-H HBV clinical isolates. The TAF sensitivity results for all drug-resistant isolates are consistent with what has been observed with the parent drug TFV. The in vitro cell-based HBV phenotyping assay results support the use of TAF in treatment of HBV infected subjects with diverse HBV genotypes, in both treatment-naive and treatment-experienced HBV infected patients. Copyright © 2016 Elsevier B.V. All rights reserved.

An evaluation of water deficit tolerance screening in pigmented indica rice genotypes

International Nuclear Information System (INIS)

Chutipaijit, S.; Sompornpailin, K.

2011-01-01

Eight pigmented genotypes of indica subspecies were geminated and then treated by mannitol-induced water deficit stress. A change of growth characteristics, photosynthetic pigments, lipid peroxidation, DNA content, proline content and anthocyanin accumulation in stressed seedling (100 mM mannitol) and control plant (0 mM mannitol) were calculated. Growth performances, photosynthetic pigment concentrations , and DNA contents in all rice genotypes were dropped whereas proline, anthocyanin contents and the lipid peroxidation levels were enriched. The stabilization in total photosynthetic pigment concentrations of stressed-seedlings were positively correlated to the proline or anthocyanin accumulation. In contrast, MDA content, the increases in the percentages of drought-stressed seedlings were negatively correlated to the proline or anthocyanin accumulation. The changes in biochemical, physiological and growth parameters were subjected to Wards cluster analysis for water deficit tolerance. These cultivars could be classified into two groups, water deficit sensitive, SY, KD, KLD and TD49 and water deficit tolerance, KS, KK1, KK2 and BSR. (author)

A genotype, environment and management (GxExM) analysis of adaptation in winter wheat to climate change in Denmark

DEFF Research Database (Denmark)

Montesino San Martin, Manuel; Olesen, Jørgen Eivind; Porter, John Roy

2014-01-01

version of AFRCWHEAT2 to model several combinations of genotypes (varying in crop growth, development and tolerance to water and nitrogen scarcity) and management (sowing dates and nitrogen fertilization rate). The simulations showed a slight improvement of grain yields (0.3–1.2 Mg ha−1) in the medium...... consistently points towards need for cultivars with a longer reproductive phases (2.9–7.5% per 1 °C) and lower photoperiod sensitivities. Due to the positive synergies between several genotypic characteristics, multiple-target breeding programmes would be necessary, possibly assisted by model-based assessments...... of optimal phenotypic characteristics....

Effects of the Chinese herbal formula "Zuojin Pill" on the pharmacokinetics of dextromethorphan in healthy Chinese volunteers with CYP2D6*10 genotype.

Science.gov (United States)

Qiu, Furong; Liu, Songcan; Miao, Ping; Zeng, Jin; Zhu, Leilei; Zhao, TongFang; Ye, Yujie; Jiang, Jian

2016-06-01

Zuojin Pill has been shown to inhibit the cytochrome P450 (CYP) 2D6 isoenzyme in vitro. In Chinese individuals, CYP 2D6*10 is the most common allele with reduced enzyme activity. In this study, we investigated the pharmacokinetic interaction between Zuojin Pill and the sensitive CYP2D6 probe dextromethorphan in healthy Chinese volunteers with CYP2D6*10 genotype. A pharmacokinetics interaction study was carried out in three groups with CYP2D6*1/*1 (n = 6), CYP2D6*1/*10 (n = 6), and CYP2D6*10/*10 (n = 6) genotypes. Each participant received a single oral dose of dextromethorphan (15 mg) followed by Zuojin Pill (3 g twice daily) for 7 days, and received 3 g Zuojin Pill with 15 mg dextromethorphan in the last day. Blood samples (0-24 h) and urine samples (0-12 h) were collected at baseline and after the administration of Zuojin Pill, and the samples' concentration of dextromethorphan and its main metabolite dextrorphan was determined. Compared to baseline values, co-administration of Zuojin Pill (3 g twice daily) for 7 days increased the AUC0-24 of dextromethorphan [mean (90 % CI)] by 3.00-fold (2.49∼3.61) and 1.71-fold (1.42∼2.06), and decreased oral clearance(CL/F) by 0.27-fold (0.2-0.40) and 0.57-fold (0.48-0.67) in the participants with CYP2D6*1/*1 and CYP2D6*1/*10 genotypes, respectively. In contrast, no significant change was observed in these pharmacokinetic parameters of the participants with CYP2D6*10/*10 genotype. These data demonstrated that administration of Zuojin Pill inhibited moderately CYP2D6-mediated metabolism of dextromethorphan in healthy volunteers. The inhibitory influence of CYP2D6 was greater in CYP2D6*1/*1 and CYP2D6*1/*10 groups than CYP2D6 *10/*10 group.

Evaluation of moderately cooled pure NaI as a scintillator for position-sensitive PET detectors

International Nuclear Information System (INIS)

Wear, J.A.; Karp, J.S.; Haigh, A.T.; Freifelder, R.

1996-01-01

A new evaluation of pure NaI has been performed to determine if moderate cooling would lead to better performance than that of existing, activated NaI(Tl) position-sensitive detectors, particularly at high countrates. Using a freezer, an initial effort was performed to cool the crystal assembly to -90 C (183 K). At this temperature, pure NaI has a decay constant of 35 nsec, a light output which is about 20% that of room temperature NaI(Tl), and an energy resolution of 15%. For the PET applications the signal of room temperature (25 C) NaI(Tl) is normally pulse clipped, reducing the light output to 40% of the unclipped signal and yielding an energy resolution of 10.5%. Since the long decay of NaI(Tl) causes it to suffer more significantly than pure NaI from pre-pulse pileup, the difference in energy resolution between the two crystals at high countrates will be reduced. Also, a significantly shorter trigger deadtime with pure NaI will lead to a reduction in coincidence deadtime losses in PET. Computer simulations of large-area crystals operating at high countrates have been performed to quantify their trigger deadtime behavior and position resolution as a function of light output and pulse decay time. Having gained experience with the practical issues of cooling large crystals, measurements of position resolution have been performed with a NaI bar detector of similar geometry to the NaI(Tl) detectors in use in the PENN-PET scanner

The BDNF Val66Met polymorphism moderates the relationship between Posttraumatic Stress Disorder and fear extinction learning.

Science.gov (United States)

Felmingham, Kim L; Zuj, Daniel V; Hsu, Ken Chia Ming; Nicholson, Emma; Palmer, Matthew A; Stuart, Kimberley; Vickers, James C; Malhi, Gin S; Bryant, Richard A

2018-05-01

The low expression Met allele of the BDNF Val66Met polymorphism is associated with impaired fear extinction in healthy controls, and poorer response to exposure therapy in patients with Posttraumatic Stress Disorder (PTSD). Given that fear extinction underlies exposure therapy, this raises the question of the impact of BDNFVal66Met polymorphism on fear extinction in PTSD, yet this question has not yet been examined. One hundred and six participants (22 PTSD, 46 trauma-exposed controls (TC) and 38 non-trauma exposed controls (NTC)) completed a fear conditioning and extinction task and saliva samples were taken for DNA extraction and genotyped for the BDNF Val66Met polymorphism. Moderation analyses using PROCESS examined whether BDNF genotype (Val-Val vs Met carriers) moderated the relationship between PTSD symptom severity (and diagnostic status) and skin conductance response (SCR) amplitude during fear extinction. The PTSD group displayed significantly slower fear extinction learning compared to TC and NTC in the early extinction phase. The BDNF Val66Met polymorphism moderated the relationship between PTSD and fear extinction learning, such that poorer fear extinction learning was associated with greater PTSD symptom severity (and PTSD diagnostic status) in individuals with the low-expression Met allele, but no relationship was demonstrated in individuals with the Val-Val allele. This study reveals that impaired fear extinction learning is particularly evident in individuals with PTSD who carry the low-expression BDNF Met allele and importantly not in those with the Val-Val allele. This provides novel evidence of a link between BDNF and impaired fear extinction learning in PTSD, which may contribute to poorer response to exposure therapy. Copyright © 2018 Elsevier Ltd. All rights reserved.

Single-tube multiplex PCR using type-specific E6/E7 primers and capillary electrophoresis genotypes 21 human papillomaviruses in neoplasia

Directory of Open Access Journals (Sweden)

Warenholt Janina

2011-01-01

Full Text Available Abstract Background Human papillomavirus (HPV E6/E7 type-specific oncogenes are required for cervical carcinogenesis. Current PCR protocols for genotyping high-risk HPV in cervical screening are not standardized and usually use consensus primers targeting HPV capsid genes, which are often deleted in neoplasia. PCR fragments are detected using specialized equipment and extra steps, including probe hybridization or primer extension. In published papers, analytical sensitivity is typically compared with a different protocol on the same sample set. A single-tube multiplex PCR containing type-specific primers was developed to target the E6/E7 genes of two low-risk and 19 high-risk genotypes (HPV6, 11 and 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 70, 73 and 82 and the resulting short fragments were directly genotyped by high-resolution fluorescence capillary electrophoresis. Results The method was validated using long oligonucleotide templates, plasmid clones and 207 clinical samples of DNA from liquid-based cytology, fresh and formalin-fixed specimens and FTA Microcards® imprinted with cut tumor surfaces, swabbed cervical cancers or ejected aspirates from nodal metastases of head and neck carcinomas. Between one and five long oligonucleotide targets per sample were detected without false calls. Each of the 21 genotypes was detected in the clinical sample set with up to five types simultaneously detected in individual specimens. All 101 significant cervical neoplasias (CIN 2 and above, except one adenocarcinoma, contained E6/E7 genes. The resulting genotype distribution accorded with the national pattern with HPV16 and 18 accounting for 69% of tumors. Rare HPV types 70 and 73 were present as the sole genotype in one carcinoma each. One cervical SCC contained DNA from HPV6 and 11 only. Six of twelve oropharyngeal cancer metastases and three neck metastases of unknown origin bore E6/E7 DNA; all but one were HPV16. One neck

Mathematical Ability and Socio-Economic Background: IRT Modeling to Estimate Genotype by Environment Interaction.

Science.gov (United States)

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

2017-12-01

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

Genotype x environment interaction and optimum resource ...

African Journals Online (AJOL)

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

Comparative shoot proteome analysis of two potato (Solanum tuberosum L.) genotypes contrasting in nitrogen deficiency responses in vitro.

Science.gov (United States)

Meise, Philipp; Jozefowicz, Anna Maria; Uptmoor, Ralf; Mock, Hans-Peter; Ordon, Frank; Schum, Annegret

2017-08-23

Aiming at a better understanding of the physiological and biochemical background of nitrogen use efficiency, alterations in the shoot proteome under N-deficiency were investigated in two contrasting potato genotypes grown in vitro with 60 and 7.5mM N, respectively. A gel based proteomic approach was applied to identify candidate proteins associated with genotype specific responses to N-deficiency. 21% of the detected proteins differed in abundance between the two genotypes. Between control and N-deficiency conditions 19.5% were differentially accumulated in the sensitive and 15% in the tolerant genotype. 93% of the highly N-deficiency responsive proteins were identified by MALDI TOF/TOF mass spectrometry. The major part was associated with photosynthesis, carbohydrate metabolism, stress response and regulation. Differential accumulation of enzymes involved in the Calvin cycle and glycolysis suggest activation of alternative carbohydrate pathways. In the tolerant genotype, increased abundance under N-deficiency was also found for enzymes involved in chlorophyll synthesis and stability of enzymes, which increase photosynthetic carbon fixation efficiency. Out of a total of 106 differentially abundant proteins, only eight were detected in both genotypes. Our findings suggest that mutually responsive proteins reflect universal stress responses while adaptation to N-deficiency in metabolic pathways is more genotype specific. Nitrogen losses from arable farm land considerably contribute to environmental pollution. In potato, this is a special problem due cultivation on light soils, irrigation and the shallow root system. Therefore, breeding of cultivars with improved nitrogen use efficiency and stable yields under reduced N fertilization is an important issue. Knowledge of genotype dependent adaptation to N-deficiency at the proteome level can help to understand regulation of N efficiency and development of N-efficient cultivars. Copyright © 2017 Elsevier B.V. All rights

PER1 rs3027172 Genotype Interacts with Early Life Stress to Predict Problematic Alcohol Use, but Not Reward-Related Ventral Striatum Activity

Science.gov (United States)

Baranger, David A. A.; Ifrah, Chloé; Prather, Aric A.; Carey, Caitlin E.; Corral-Frías, Nadia S.; Drabant Conley, Emily; Hariri, Ahmad R.; Bogdan, Ryan

2016-01-01

Increasing evidence suggests that the circadian and stress regulatory systems contribute to alcohol use disorder (AUD) risk, which may partially arise through effects on reward-related neural function. The C allele of the PER1 rs3027172 single nucleotide polymorphism (SNP) reduces PER1 expression in cells incubated with cortisol and has been associated with increased risk for adult AUD and problematic drinking among adolescents exposed to high levels of familial psychosocial adversity. Using data from undergraduate students who completed the ongoing Duke Neurogenetics Study (DNS) (n = 665), we tested whether exposure to early life stress (ELS; Childhood Trauma Questionnaire) moderates the association between rs3027172 genotype and later problematic alcohol use (Alcohol Use Disorders Identification Test) as well as ventral striatum (VS) reactivity to reward (card-guessing task while functional magnetic resonance imaging data were acquired). Initial analyses found that PER1 rs3027172 genotype interacted with ELS to predict both problematic drinking and VS reactivity; minor C allele carriers, who were also exposed to elevated ELS reported greater problematic drinking and exhibited greater ventral striatum reactivity to reward-related stimuli. When gene × covariate and environment × covariate interactions were controlled for, the interaction predicting problematic alcohol use remained significant (p < 0.05, corrected) while the interaction predicting VS reactivity was no longer significant. These results extend our understanding of relationships between PER1 genotype, ELS, and problematic alcohol use, and serve as a cautionary tale on the importance of controlling for potential confounders in studies of moderation including gene × environment interactions. PMID:27065929

PER1 rs3027172 genotype interacts with early life stress to predict problematic alcohol use, but not reward-related ventral striatum activity

Directory of Open Access Journals (Sweden)

David eBaranger

2016-03-01

Full Text Available Increasing evidence suggests that the circadian and stress regulatory systems contribute to alcohol use disorder (AUD risk, which may partially arise through effects on reward-related neural function. The C allele of the PER1 rs3027172 single nucleotide polymorphism reduces PER1 expression in cells incubated with cortisol and has been associated with increased risk for adult AUD and problematic drinking among adolescents exposed to high levels of familial psychosocial adversity. Using data from undergraduate students who completed the ongoing Duke Neurogenetics Study (n=665, we tested whether exposure to early life stress (ELS; Childhood Trauma Questionnaire moderates the association between rs3027172 genotype and later problematic alcohol use (Alcohol Use Disorders Identification Test as well as ventral striatum (VS reactivity to reward (card-guessing task while functional magnetic resonance imaging data were acquired. Initial analyses found that PER1 rs3027172 genotype interacted with ELS to predict both problematic drinking and VS reactivity; minor C allele carriers, who were also exposed to elevated ELS reported greater problematic drinking and exhibited greater ventral striatum reactivity to reward-related stimuli. When gene x covariate and environment x covariate interactions were controlled for, the interaction predicting problematic alcohol use remained significant (p<0.05, corrected while the interaction predicting VS reactivity was no longer significant. These results extend our understanding of relationships between PER1 genotype, early life stress, and problematic alcohol use, and serve as a cautionary tale on the importance of controlling for potential confounders in studies of moderation including gene x environment interactions.

Does Apolipoprotein e4 Status Moderate the Association of Family Environment with Long-Term Child Functioning following Early Moderate to Severe Traumatic Brain Injury? A Preliminary Study.

Science.gov (United States)

Treble-Barna, Amery; Zang, Huaiyu; Zhang, Nanhua; Martin, Lisa J; Yeates, Keith Owen; Taylor, H Gerry; Wade, Shari L; Kurowski, Brad G

2016-09-01

To examine whether apolipoprotein e4 (APOE) status moderates the association of family environment with child functioning following early traumatic brain injury (TBI). Sixty-five children with moderate to severe TBI and 70 children with orthopedic injury (OI) completed assessments 6, 12, 18 months, and 3.5 and 6.8 years post injury. DNA was extracted from saliva samples and genotyped for APOE e4 status. Linear mixed models examined moderating effects of APOE e4 status on associations between two family environment factors (parenting style, home environment) and three child outcomes (executive functioning, behavioral adjustment, adaptive functioning). Children with TBI who were carriers of the e4 allele showed poorer adaptive functioning relative to non-carriers with TBI and children with OI in the context of low authoritarianism. At high levels of authoritarianism, non-carriers with TBI showed the poorest adaptive functioning among groups. There were no main effects or interactions involving APOE and executive functioning or behavioral adjustment. The APOE e4 allele was detrimental for long-term adaptive functioning in the context of positive parenting, whereas in less optimal parenting contexts, being a non-carrier was detrimental. We provide preliminary evidence for an interaction of APOE e4 status and parenting style in predicting long-term outcomes following early TBI. (JINS, 2016, 22, 859-864).

Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions.

Science.gov (United States)

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

2011-02-01

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

Hepatitis C Virus: Virology and Genotypes

KAUST Repository

Abdelaziz, Ahmed

2017-01-01

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

Genotype-by-environment interactions leads to variable selection on life-history strategy in Common Evening Primrose (Oenothera biennis).

Science.gov (United States)

Johnson, M T J

2007-01-01

Monocarpic plant species, where reproduction is fatal, frequently exhibit variation in the length of their prereproductive period prior to flowering. If this life-history variation in flowering strategy has a genetic basis, genotype-by-environment interactions (G x E) may maintain phenotypic diversity in flowering strategy. The native monocarpic plant Common Evening Primrose (Oenothera biennis L., Onagraceae) exhibits phenotypic variation for annual vs. biennial flowering strategies. I tested whether there was a genetic basis to variation in flowering strategy in O. biennis, and whether environmental variation causes G x E that imposes variable selection on flowering strategy. In a field experiment, I randomized more than 900 plants from 14 clonal families (genotypes) into five distinct habitats that represented a natural productivity gradient. G x E strongly affected the lifetime fruit production of O. biennis, with the rank-order in relative fitness of genotypes changing substantially between habitats. I detected genetic variation in annual vs. biennial strategies in most habitats, as well as a G x E effect on flowering strategy. This variation in flowering strategy was correlated with genetic variation in relative fitness, and phenotypic and genotypic selection analyses revealed that environmental variation resulted in variable directional selection on annual vs. biennial strategies. Specifically, a biennial strategy was favoured in moderately productive environments, whereas an annual strategy was favoured in low-productivity environments. These results highlight the importance of variable selection for the maintenance of genetic variation in the life-history strategy of a monocarpic plant.

Moral sensitivity and moral distress in Iranian critical care nurses.

Science.gov (United States)

Borhani, Fariba; Abbaszadeh, Abbas; Mohamadi, Elham; Ghasemi, Erfan; Hoseinabad-Farahani, Mohammad Javad

2017-06-01

Moral sensitivity is the foremost prerequisite to ethical performance; a review of literature shows that nurses are sometimes not sensitive enough for a variety of reasons. Moral distress is a frequent phenomenon in nursing, which may result in paradoxes in care, dealing with patients and rendering high-quality care. This may, in turn, hinder the meeting of care objectives, thus affecting social healthcare standards. The present research was conducted to determine the relationship between moral sensitivity and moral distress of nurses in intensive care units. This study is a descriptive-correlation research. Lutzen's moral sensitivity questionnaire and Corley Moral Distress Questionnaire were used to gather data. Participants and research context: A total of 153 qualified nurses working in the hospitals affiliated to Shahid Beheshti University of Medical Sciences were selected for this study. Subjects were selected by census method. Ethical considerations: After explaining the objectives of the study, all the participants completed and signed the written consent form. To conduct the study, permission was obtained from the selected hospitals. Nurses' average moral sensitivity grade was 68.6 ± 7.8, which shows a moderate level of moral sensitivity. On the other hand, nurses also experienced a moderate level of moral distress (44.8 ± 16.6). Moreover, there was no meaningful statistical relationship between moral sensitivity and moral distress (p = 0.26). Although the nurses' moral sensitivity and moral distress were expected to be high in the intensive care units, it was moderate. This finding is consistent with the results of some studies and contradicts with others. As moral sensitivity is a crucial factor in care, it is suggested that necessary training be provided to develop moral sensitivity in nurses in education and practical environments. Furthermore, removing factors that contribute to moral distress may help decrease it in nurses.

Prevalence of Porphyromonas gingivalis Four rag Locus Genotypes in Patients of Orthodontic Gingivitis and Periodontitis

Science.gov (United States)

Liu, Yi; Zhang, Yujie; Wang, Lili; Guo, Yang; Xiao, Shuiqing

2013-01-01

Porphyromonas gingivalis is considered as a major etiological agent in periodontal diseases and implied to result in gingival inflammation under orthodontic appliance. rag locus is a pathogenicity island found in Porphyromonas gingivalis. Four rag locus variants are different in pathogenicity of Porphyromonas gingivalis. Moreover, there are different racial and geographic differences in distribution of rag locus genotypes. In this study, we assessed the prevalence of Porphyromonas gingivalis and rag locus genotypes in 102 gingival crevicular fluid samples from 57 cases of gingivitis patients with orthodontic appliances, 25 cases of periodontitis patients and 20 cases of periodontally healthy people through a 16S rRNA-based PCR and a multiplex PCR. The correlations between Porphyromona.gingivalis/rag locus and clinical indices were analyzed. The prevalence of Porphyromonas gingivalis and rag locus genes in periodontitis group was the highest among three groups and higher in orthodontic gingivitis than healthy people (porthodontic gingivitis and mild-to-moderate periodontitis in Shandong. Porphyromonas.gingivalis carrying rag-1 has the strong virulence and could be associated with severe periodontitis. PMID:23593379

Genetic susceptibility factors for multiple chemical sensitivity revisited

DEFF Research Database (Denmark)

Berg, Nikolaj Drimer; Rasmussen, Henrik Berg; Linneberg, Allan

2010-01-01

of this study was to investigate genetic susceptibility factors for MCS and self-reported chemical sensitivity in a population sample. Ninety six MCS patients and 1,207 controls from a general population divided into four severity groups of chemical sensitivity were genotyped for variants in the genes encoding......Multiple chemical sensitivity (MCS) is characterised by adverse effects due to exposure to low levels of chemical substances. Various genes, especially genes of importance to the metabolism of xenobiotic compounds, have been associated with MCS, but findings are inconsistent. The purpose...... significant (OR=1.2, p=0.28). Fast arylamine N-acetyltransferase 2 metaboliser status was associated with severity of chemical sensitivity only in the most severely affected group in the population sample (OR=3.1, p=0.04). The cholecystokinin 2 receptor allele with 21 CT repeats was associated with MCS when...

Relative degree of susceptibility and resistance of different brassica campestris l. genotypes against aphid myzus persicae- a field investigation

International Nuclear Information System (INIS)

Sarwar, M.

2013-01-01

Field evaluation of twenty three Brassica campestris L. genotypes was conducted for aphid (Homoptera: Aphididae) resistance during 2008 crop season. The parameters used to assess tolerance of germplasm lines included pest population during growth season and grain yield at crop maturity. Aphids showed obvious preferences for all of the germplasm investigated; however, the evaluation for resistance to pest identified several genotypes with variable potential for tolerance and sensitivity. Estimated grain yield also varied significantly due to variable pest intensity noted, and seemed to be more appropriately dependent on the pest population conditions at the experimental site. Among the germplasm, the estimation obtained regarding both the parameters sorted out MM-II/02-3 and MM-I285 genotypes as most tolerant due to less pest infestation and damage. Peak infestations by aphid caused severe crop fatalities on S-9-S-97-0.75+75/55 and S-9-1006/95 genotypes, affecting the seed weight and resulting an immense reduction in grain Brassica genotypes appeared to be governed by means of varietals characteristics of diverse germplasms. The result of resistance test conducted under field environment is an effective and consistent approach in the practical selection of crop lines resistant or partially resistant to pests for use in future breeding programs. (author)

Relationship of some upland rice genotype after gamma irradiation

Science.gov (United States)

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

2018-02-01

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

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

Science.gov (United States)

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

2015-03-01

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

The moderator's moderator

International Nuclear Information System (INIS)

Williamson, G.K.

1990-01-01

A brief account is given of the development of graphite moderators for Magnox and advanced gas cooled reactors. The accident at Windscale in 1957 brought to worldwide attention the importance of irradiation damage in graphite and the consequent storage of Wigner energy. In spite of the Windscale setback, preparations for the civil programme of Magnox reactors went ahead apace. Some of the background to the disastrous Dungeness B tender is presented. In spite of all the difficulties and uncertainties, the graphite in UK reactors has performed well. In all cases, as far as the author is aware, the behaviour of the graphite moderators will not prevent design life being achieved. (author)

Forensic SNP genotyping with SNaPshot

DEFF Research Database (Denmark)

Fondevila, M; Børsting, C; Phillips, C

2017-01-01

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

Partial resistance to fruit necrosis associated to Colletotrichum spp. among arabic coffee genotypes

Directory of Open Access Journals (Sweden)

Gustavo Hiroshi Sera

2007-05-01

Full Text Available The aim of this study was to evaluate the resistance to fruit necrosis associated to Colletotrichum spp. in Coffea arabica L.. Twenty-two arabic coffee genotypes were performed in a randomized block design, with three replications and ten plants per plot. They were evaluated for the variables fruit necrosis, luminosity index inside of the plant canopy and fruits per productive nodes of the plants. There was genetic variability for the resistance to fruit necrosis. Different partial resistance levels, varying from highly susceptible (score = 3.89 to moderately resistant (score = 1.77 were observed. The genotypes that presented moderate resistance were the cultivars IPR-100, IPR-103, IPR-105 and IPR-108 and the coffee selection IAPAR-00023.Diferentes espécies de fungo do gênero têm sido associadas a perdas na cafeicultura brasileira. O objetivo deste trabalho foi avaliar a resistência à necrose de frutos associada ao Colletotrichum spp. em Coffea arabica L.. Vinte e dois genótipos de café foram avaliados no delineamento em blocos ao acaso com três repetições e dez plantas por parcela. As avaliações foram realizadas no IAPAR, Londrina, em janeiro de 2004 para as variáveis necrose de frutos, índice de luminosidade dentro da copa da planta e frutos por nó produtivo. Existe variabilidade genética em cafeeiros arábicos para a resistência à necrose de frutos. Foi observado diferentes níveis de resistência parcial, variando de altamente suscetível (nota = 3,89 a moderadamente resistente (nota = 1,77. Os genótipos que apresentaram moderada resistência foram as cultivares IPR-100, IPR-103, IPR-105 e IPR-108 e a seleção de café IAPAR-00023.

Validation of clinical testing for warfarin sensitivity: comparison of CYP2C9-VKORC1 genotyping assays and warfarin-dosing algorithms.

Science.gov (United States)

Langley, Michael R; Booker, Jessica K; Evans, James P; McLeod, Howard L; Weck, Karen E

2009-05-01

Responses to warfarin (Coumadin) anticoagulation therapy are affected by genetic variability in both the CYP2C9 and VKORC1 genes. Validation of pharmacogenetic testing for warfarin responses includes demonstration of analytical validity of testing platforms and of the clinical validity of testing. We compared four platforms for determining the relevant single nucleotide polymorphisms (SNPs) in both CYP2C9 and VKORC1 that are associated with warfarin sensitivity (Third Wave Invader Plus, ParagonDx/Cepheid Smart Cycler, Idaho Technology LightCycler, and AutoGenomics Infiniti). Each method was examined for accuracy, cost, and turnaround time. All genotyping methods demonstrated greater than 95% accuracy for identifying the relevant SNPs (CYP2C9 *2 and *3; VKORC1 -1639 or 1173). The ParagonDx and Idaho Technology assays had the shortest turnaround and hands-on times. The Third Wave assay was readily scalable to higher test volumes but had the longest hands-on time. The AutoGenomics assay interrogated the largest number of SNPs but had the longest turnaround time. Four published warfarin-dosing algorithms (Washington University, UCSF, Louisville, and Newcastle) were compared for accuracy for predicting warfarin dose in a retrospective analysis of a local patient population on long-term, stable warfarin therapy. The predicted doses from both the Washington University and UCSF algorithms demonstrated the best correlation with actual warfarin doses.

Differential zinc uptake of rice genotypes as established by radiotracer technique

International Nuclear Information System (INIS)

Sudhalakshmi, C.; Krishnasamy, R.; Meena, S.

2017-01-01

Rice is a sensitive crop to zinc (Zn 2+ ) deficiency and its uptake, transport and metabolism is imperative in bio-fortification process. A pot culture experiment was conducted at Tamil Nadu Agricultural University, Coimbatore to establish the differential zinc use efficiency of rice genotypes viz., Zn efficient Norungan and Zn inefficient PMK 3 and to assess the partitioning of Zn in shoot and root of genotypes employing radiotracer technique. Graded levels of Zn (0, 12.5, 25.0, 37.5 and 50 kg ha -1 of ZnSO 4 ) as 65 Zn labeled ZnSO 4 were applied. Zinc uptake from fertilizer increased with increased dose of applied zinc up to 37.5 kg ha -1 for PMK 3 whereas in Norungan, it was up to 25 kg ZnSO 4 ha -1 and thereafter it declined. The per cent zinc derived from fertilizer (% Zndff) was the highest in PMK 3 which apparently implies its inability to mobilize soil nutrient reserve and respond to elevated doses of applied zinc. The % Zndfs was higher in Norungan. In both the genotypes, the 'A value' showed a conspicuous increase with increased dose of applied zinc. Norungan registered a higher 'A value' than PMK 3 irrespective of the stages of sampling. Zn efficient Norungan had better Zn translocation to the shoots whereas in Zn inefficient PMK 3, vacuolar sequestration in root cells was higher. (author)

Variations in the growth, oil quantity and quality, and mineral nutrients of chamomile genotypes under salinity stress

Directory of Open Access Journals (Sweden)

Omid Askari-Khorasgani

2017-03-01

Full Text Available Understanding how plants respond to salinity, which severely restricts plant growth, productivity, and survival, is highly important in agriculture. Using three genotypes of Matricaria recutita L. (Shiraz, Ahvaz, and Isfahan with different sensitivity to NaCl, the effect of long-term (about 110 days NaCl treatments (2.5, 6, 9, and 12 dS*m-1 on crop growth, oil quality and quantity, and nutrient variations were investigated to underpin its agricultural management in the future. The adaptation strategy and plant responses were influenced by salinity level, genotype, and genotype × salinity interactions. With higher productivity compared to the Isfahan genotype, the Shiraz and Ahvaz genotypes had efficient Na+ exclusion at root surface as an avoidance strategy; however, under higher NaCl concentration, their higher performance were mainly attributed to the Na+ sequestration in root vacuoles and higher Ca2+/Na+, Mg2+/Na+, and root/shoot ratios as tolerance strategies. The higher oil yield and chamazulene percentage in the Isfahan genotype were not affected by salinity level and were only genotype dependent. Under 12 dS*m-1 NaCl, roots of the Shiraz and Ahvaz genotypes accumulated markedly higher Ca2+ (2.5% and 1.5% respectively and Mg2+ (1.6% and 1.3% respectively, required for membrane stability and chlorophyll synthesis, respectively, more than the Isfahan genotype (0.2% Ca and 0.1% Mg2+ and considerably more than the control plants to keep low concentrations of ion toxicity of Na2+ and Cl- in shoots. Overall, greater salt tolerance found in the Shiraz and Ahvaz genotypes could be due to a variety of mechanisms, including higher efficiency of nutrient uptake (Ca2+, Mg2+, and Zn2+, utilization (N, P, Ca2+, and Mg2+, compartmentation (Na in roots, and maintenance of higher root/shoot ratios. Taking flower and oil yield as well as chamazulene percentage into consideration, the findings recommended cultivation of the Ahvaz genotype in the absence of

Poorer frontolimbic white matter integrity is associated with chronic cannabis use, FAAH genotype, and increased depressive and apathy symptoms in adolescents and young adults

Directory of Open Access Journals (Sweden)

Skyler G. Shollenbarger

2015-01-01

Conclusions: Consistent with prior findings, cannabis use was associated with reduced frontolimbic WM integrity. WM integrity was also moderated by FAAH genotype, in that cannabis-using FAAH C/C carriers and A carrying controls had reduced WM integrity compared to control C/C carriers. Observed frontolimbic white matter abnormalities were linked with increased depressive and apathy symptoms in the cannabis users.

Genetic moderation of the association between regulatory focus and reward responsiveness: a proof-of-concept study.

Science.gov (United States)

Goetz, Elena L; Hariri, Ahmad R; Pizzagalli, Diego A; Strauman, Timothy J

2013-02-01

Recent studies implicate individual differences in regulatory focus as contributing to self-regulatory dysfunction, particularly not responding to positive outcomes. How such individual differences emerge, however, is unclear. We conducted a proof-of-concept study to examine the moderating effects of genetically driven variation in dopamine signaling, a key modulator of neural reward circuits, on the association between regulatory focus and reward cue responsiveness. Healthy Caucasians (N=59) completed a measure of chronic regulatory focus and a probabilistic reward task. A common functional genetic polymorphism impacting prefrontal dopamine signaling (COMT rs4680) was evaluated. Response bias, the participants' propensity to modulate behavior as a function of reward, was predicted by an interaction of regulatory focus and COMT genotype. Specifically, self-perceived success at achieving promotion goals predicted total response bias, but only for individuals with the COMT genotype (Val/Val) associated with relatively increased phasic dopamine signaling and cognitive flexibility. The combination of success in promotion goal pursuit and Val/Val genotype appears to facilitate responding to reward opportunities in the environment. This study is among the first to integrate an assessment of self-regulatory style with an examination of genetic variability that underlies responsiveness to positive outcomes in goal pursuit.

Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan

OpenAIRE

Sonuga-Barke, E.; Lasky-Su, J.; Neale, B.; Oades, R.D.; Chen, W.; Franke, B.; Buitelaar, J.K.; Banaschewski, T.; Ebstein, R.; Gill, M.; Anney, R.J.; Miranda, A.; Mulas, F.; Roeyers, H.; Rothenberger, A.

2008-01-01

Studies of gene x environment (G x E) interaction in ADHD have previously focused on known risk genes for ADHD and environmentally mediated biological risk. Here we use G x E analysis in the context of a genome-wide association scan to identify novel genes whose effects on ADHD symptoms and comorbid conduct disorder are moderated by high maternal expressed emotion (EE). SNPs (600,000) were genotyped in 958 ADHD proband-parent trios. After applying data cleaning procedures we examined 429,981 ...

Enhanced muscle insulin sensitivity after contraction/exercise is mediated by AMPK

DEFF Research Database (Denmark)

Kjøbsted, Rasmus; Munk-Hansen, Nanna; Birk, Jesper Bratz

2017-01-01

muscle and whole body insulin sensitivity in wild type (WT) mice, respectively. These effects were not found in AMPKα1α2 muscle-specific knockout mice. Prior in situ contraction did not increase insulin sensitivity in m. soleus from either genotype. Improvement in muscle insulin sensitivity....... Collectively, our data suggest that the AMPK-TBC1D4 signaling axis is likely mediating the improved muscle insulin sensitivity after contraction/exercise and illuminates an important and physiological relevant role of AMPK in skeletal muscle.......Earlier studies have demonstrated that muscle insulin sensitivity to stimulate glucose uptake is enhanced several hours after an acute bout of exercise. Using 5-aminoimidazole-4-carboxamide-ribonucleotide (AICAR), we recently demonstrated that prior activation of AMPK is sufficient to increase...

An epidemiologic survey of methicillin-resistant Staphylococcus aureus by combined use of mec-HVR genotyping and toxin genotyping in a university hospital in Japan.

Science.gov (United States)

Nishi, Junichiro; Yoshinaga, Masao; Miyanohara, Hiroaki; Kawahara, Motoshi; Kawabata, Masaharu; Motoya, Toshiro; Owaki, Tetsuhiro; Oiso, Shigeru; Kawakami, Masayuki; Kamewari, Shigeko; Koyama, Yumiko; Wakimoto, Naoko; Tokuda, Koichi; Manago, Kunihiro; Maruyama, Ikuro

2002-09-01

To evaluate the usefulness of an assay using two polymerase chain reaction-based genotyping methods in the practical surveillance of methicillin-resistant Staphylococcus aureus (MRSA). Nosocomial infection and colonization were surveyed monthly in a university hospital in Japan for 20 months. Genotyping with mec-HVR is based on the size of the mec-associated hypervariable region amplified by polymerase chain reaction. Toxin genotyping uses a multiplex polymerase chain reaction method to amplify eight staphylococcal toxin genes. Eight hundred nine MRSA isolates were classified into 49 genotypes. We observed differing prevalences of genotypes for different hospital wards, and could rapidly demonstrate the similarity of genotype for outbreak isolates. The incidence of genotype D: SEC/TSST1 was significantly higher in isolates causing nosocomial infections (49.5%; 48 of 97) than in nasal isolates (31.4%; 54 of 172) (P = .004), suggesting that this genotype may represent the nosocomial strains. The combined use of these two genotyping methods resulted in improved discriminatory ability and should be further investigated.

Moderators of noise-induced cognitive change in healthy adults.

Science.gov (United States)

Wright, Bernice Al; Peters, Emmanuelle R; Ettinger, Ulrich; Kuipers, Elizabeth; Kumari, Veena

2016-01-01

Environmental noise causes cognitive impairment, particularly in executive function and episodic memory domains, in healthy populations. However, the possible moderating influences on this relationship are less clear. This study assessed 54 healthy participants (24 men) on a cognitive battery (measuring psychomotor speed, attention, executive function, working memory, and verbal learning and memory) under three (quiet, urban, and social) noise conditions. IQ, subjective noise sensitivity, sleep, personality, paranoia, depression, anxiety, stress, and schizotypy were assessed on a single occasion. We found significantly slower psychomotor speed (urban), reduced working memory and episodic memory (urban and social), and more cautious decision-making (executive function, urban) under noise conditions. There was no effect of sex. Variance in urban noise-induced changes in psychomotor speed, attention, Trail Making B-A (executive function), and immediate recall and social noise-induced changes in verbal fluency (executive function) and immediate recall were explained by a combination of baseline cognition and paranoia, noise sensitivity, sleep, or cognitive disorganization. Higher baseline cognition (but not IQ) predicted greater impairment under urban and social noise for most cognitive variables. Paranoia predicted psychomotor speed, attention, and executive function impairment. Subjective noise sensitivity predicted executive function and memory impairment. Poor sleep quality predicted less memory impairment. Finally, lower levels of cognitive disorganization predicted slower psychomotor speed and greater memory impairment. The identified moderators should be considered in studies aiming to reduce the detrimental effects of occupational and residential noise. These results highlight the importance of studying noise effects in clinical populations characterized by high levels of the paranoia, sleep disturbances, noise sensitivity, and cognitive disorganization.

1 H MR spectroscopy in cervical carcinoma using external phase array body coil at 3.0 Tesla: Prediction of poor prognostic human papillomavirus genotypes.

Science.gov (United States)

Lin, Gigin; Lai, Chyong-Huey; Tsai, Shang-Yueh; Lin, Yu-Chun; Huang, Yu-Ting; Wu, Ren-Chin; Yang, Lan-Yan; Lu, Hsin-Ying; Chao, Angel; Wang, Chiun-Chieh; Ng, Koon-Kwan; Ng, Shu-Hang; Chou, Hung-Hsueh; Yen, Tzu-Chen; Hung, Ji-Hong

2017-03-01

To assess the clinical value of proton ( 1 H) MR spectroscopy in cervical carcinomas, in the prediction of poor prognostic human papillomavirus (HPV) genotypes as well as persistent disease following concurrent chemoradiotherapy (CCRT). 1 H MR spectroscopy using external phase array coil was performed in 52 consecutive cervical cancer patients at 3 Tesla (T). Poor prognostic HPV genotypes (alpha-7 species or absence of HPV infection) and persistent cervical carcinoma after CCRT were recorded. Statistical significance was calculated with the Mann-Whitney two-sided nonparametric test and areas under the receiver operating characteristics curve (AUC) analysis. A 4.3-fold (P = 0.032) increased level of methyl resonance at 0.9 ppm was found in the poor prognostic HPV genotypes, mainly attributed to the presence of HPV18, with a sensitivity of 75%, a specificity of 81%, and an AUC of 0.76. Poor prognostic HPV genotypes were more frequently observed in patients with adeno-/adenosquamous carcinoma (Chi-square, P < 0.0001). In prediction of the four patients with persistent disease after CCRT, elevated methyl resonance demonstrated a sensitivity of 100%, a specificity of 74%, and an AUC of 0.82. 1 H MR spectroscopy at 3T can be used to depict the elevated lipid resonance levels in cervical carcinomas, as well as help to predict the poor prognostic HPV genotypes and persistent disease following CCRT. Further large studies with longer follow up times are warranted to validate our initial findings. 1 J. Magn. Reson. Imaging 2017;45:899-907. © 2016 International Society for Magnetic Resonance in Medicine.

Two-temperature LATE-PCR endpoint genotyping

Directory of Open Access Journals (Sweden)

Reis Arthur H

2006-12-01

Full Text Available Abstract Background In conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay. Results Two-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of

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 ...