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Sample records for aa genotype compared

  1. Overrepresentation of the COL3A1 AA genotype in Polish skiers with anterior cruciate ligament injury.

    PubMed

    Stępień-Słodkowska, M; Ficek, K; Maciejewska-Karłowska, A; Sawczuk, M; Ziętek, P; Król, P; Zmijewski, P; Pokrywka, A; Cięszczyk, P

    2015-06-01

    Although various intrinsic and extrinsic risk factors for anterior cruciate ligament (ACL) rupture have been identified, the exact aetiology of the injury is not yet fully understood. Type III collagen is an important factor in the repair of connective tissue, and certain gene polymorphisms may impair the tensile strength. The aim of this study was to examine the association of the COL3A1 rs1800255 polymorphism with ACL rupture in Polish male recreational skiers. A total of 321 male Polish recreational skiers were recruited for this study; 138 had surgically diagnosed primary ACL ruptures (ACL-injured group) and 183 were apparently healthy male skiers (control group - CON) who had no self-reported history of ligament or tendon injury. Both groups had a comparable level of exposure to ACL injury. Genomic DNA was extracted from the oral epithelial cells. All samples were genotyped on a real-time polymerase chain reaction instrument. The genotype distribution in the ACL-injured group was significantly different than in CON (respectively: AA=10.1 vs 2.2%, AG=22.5 vs 36.1, GG=67.4 vs 61.8%; p=0.0087). The AA vs AG+GG genotype of COL3A1 (odds ratio (OR)=5.05; 95% confidence interval (CI), 1.62-15.71, p=0.003) was significantly overrepresented in the ACL-injured group compared with CON. The frequency of the A allele was higher in the ACL-injured group (21.4%) compared with CON (20.2%), but the difference was not statistically significant (p=0.72). This study revealed an association between the COL3A1 rs1800255 polymorphism and ACL ruptures in Polish skiers. PMID:26060338

  2. HHEX_23 AA Genotype Exacerbates Effect of Diabetes on Dementia and Alzheimer Disease: A Population-Based Longitudinal Study

    PubMed Central

    Xu, Wei-Li; Pedersen, Nancy L.; Keller, Lina; Kalpouzos, Grégoria; Wang, Hui-Xin; Graff, Caroline; Winblad, Bengt; Bäckman, Lars; Fratiglioni, Laura

    2015-01-01

    Background Research has suggested that variations within the IDE/HHEX gene region may underlie the association of type 2 diabetes with Alzheimer disease (AD). We sought to explore whether IDE genes play a role in the association of diabetes with dementia, AD, and structural brain changes using data from two community-based cohorts of older adults and a subsample with structural MRI. Methods and Findings The first cohort, which included dementia-free adults aged ≥75 y (n = 970) at baseline, was followed for 9 y to detect incident dementia (n = 358) and AD (n = 271) cases. The second cohort (for replication), which included 2,060 dementia-free participants aged ≥60 y at baseline, was followed for 6 y to identify incident dementia (n = 166) and AD (n = 121) cases. A subsample (n = 338) of dementia-free participants from the second cohort underwent MRI. HHEX_23 and IDE_9 were genotyped, and diabetes (here including type 2 diabetes and prediabetes) was assessed. In the first cohort, diabetes led to an adjusted hazard ratio (HR) of 1.73 (95% CI 1.19–2.32) and 1.66 (95% CI 1.06–2.40) for dementia and AD, respectively, among all participants. Compared to people carrying the GG genotype without diabetes, AA genotype carriers with diabetes had an adjusted HR of 5.54 (95% CI 2.40–7.18) and 4.81 (95% CI 1.88–8.50) for dementia and AD, respectively. There was a significant interaction between HHEX_23-AA and diabetes on dementia (HR 4.79, 95% CI 1.63–8.90, p = 0.013) and AD (HR 3.55, 95% CI 1.45–9.91, p = 0.025) compared to the GG genotype without diabetes. In the second cohort, the HRs were 1.68 (95% CI 1.04–2.99) and 1.64 (1.02–2.33) for the diabetes–AD and dementia–AD associations, respectively, and 4.06 (95% CI 1.06–7.58, p = 0.039) and 3.29 (95% CI 1.02–8.33, p = 0.044) for the interactions, respectively. MRI data showed that HHEX_23-AA carriers with diabetes had significant structural brain changes compared to HHEX_23-GG carriers without

  3. Comparative analysis of Paenibacillus larvae genotypes isolated in Connecticut.

    PubMed

    Dingman, Douglas W

    2015-08-01

    Ninety-six strains of Paenibacillus larvae, causative agent of American foulbrood in honey bee (Apis mellifera) larvae, collected from Connecticut, USA (CT), honey bees, and 12 P. larvae strains not from CT, were genotyped via ERIC-PCR and XbaI-RFLP analysis. All CT-isolates, five strains isolated in South America, three strains from North America (not CT), and one strain isolated in Australia grouped into the ERIC I genotype. Three P. larvae formerly subsp. pulvifaciens strains grouped into ERIC III and IV genotypes. XbaI-RFLP genotyping showed three genotypes within the CT-isolates, and two were identified as XbaI-RFLP Type I and III. The third XbaI-RFLP genotype (Type Ib) represented one of four new XbaI-RFLP genotypes identified. Comparison of genotype results for the P. larvae strains tested was used to develop a correlation between ERIC-PCR genotyping and XbaI-RFLP genotyping. Sixteen CT-isolates were tetracycline-resistant and demonstrated PCR amplification using oligonucleotide primers for tetL. All 16 isolates grouped within XbaI-RFLP Type Ib, suggesting limited introduction of a tetracycline-resistant strain into CT. PMID:25929327

  4. Influence of the Temperature and the Genotype of the HSP90AA1 Gene over Sperm Chromatin Stability in Manchega Rams

    PubMed Central

    Ramón, Manuel; Salces-Ortiz, Judit; González, Carmen; Pérez-Guzmán, M. Dolores; Garde, J. Julián; García-Álvarez, Olga; Maroto-Morales, Alejandro; Calvo, Jorge H.; Serrano, M. Magdalena

    2014-01-01

    The present study addresses the effect of heat stress on males' reproduction ability. For that, we have evaluated the sperm DNA fragmentation (DFI) by SCSA of ejaculates incubated at 37°C during 0, 24 and 48 hours after its collection, as a way to mimic the temperature circumstances to which spermatozoa will be subject to in the ewe uterus. The effects of temperature and temperature-humidity index (THI) from day 60 prior collection to the date of semen collection on DFI were examined. To better understand the causes determining the sensitivity of spermatozoa to heat, this study was conducted in 60 males with alternative genotypes for the SNP G/C−660 of the HSP90AA1 promoter, which encode for the Hsp90α protein. The Hsp90α protein predominates in the brain and testis, and its role in spermatogenesis has been described in several species. Ridge regression analyses showed that days 29 to 35 and 7 to 14 before sperm collection (bsc) were the most critical regarding the effect of heat stress over DFI values. Mixed model analyses revealed that DFI increases over a threshold of 30°C for maximum temperature and 22 for THI at days 29 to 35 and 7 to 14 bsc only in animals carrying the GG−660 genotype. The period 29–35 bsc coincide with the meiosis I process for which the effect of the Hsp90α has been described in mice. The period 7–14 bsc may correspond with later stages of the meiosis II and early stages of epididymal maturation in which the replacement of histones by protamines occurs. Because of GG−660 genotype has been associated to lower levels of HSP90AA1 expression, suboptimal amounts of HSP90AA1 mRNA in GG−660 animals under heat stress conditions make spermatozoa DNA more susceptible to be fragmented. Thus, selecting against the GG−660 genotype could decrease the DNA fragmentation and spermatozoa thermal susceptibility in the heat season, and its putative subsequent fertility gains. PMID:24465903

  5. Enhanced active metabolite generation and platelet inhibition with prasugrel compared to clopidogrel regardless of genotype in thienopyridine metabolic pathways.

    PubMed

    Braun, Oscar Ö; Angiolillo, Dominick J; Ferreiro, Jose L; Jakubowski, Joseph A; Winters, Kenneth J; Effron, Mark B; Duvvuru, Suman; Costigan, Timothy M; Sundseth, Scott; Walker, Joseph R; Saucedo, Jorge F; Kleiman, Neal S; Varenhorst, Christoph

    2013-12-01

    Clopidogrel response varies according to the presence of genetic polymorphisms. The CYP2C19*2 allele has been associated with impaired response; conflicting results have been reported for CYP2C19*17, ABCB1, and PON1 genotypes. We assessed the impact of CYP2C19, PON1, and ABCB1 polymorphisms on clopidogrel and prasugrel pharmacodynamic (PD) and pharmacokinetic (PK) parameters. Aspirin-treated patients (N=194) with coronary artery disease from two independent, prospective, randomised, multi-centre studies comparing clopidogrel (75 mg) and prasugrel (10 mg) were genotyped and classified by predicted CYP2C19 metaboliser phenotype (ultra metabolisers [UM] = *17 carriers; extensive metabolisers [EM] = *1/1 homozygotes; reduced metabolisers [RM] = *2 carriers). ABCB1 T/T and C/T polymorphisms and PON1 A/A, A/G and G/G polymorphisms were also genotyped. PD parameters were assessed using VerifyNow® P2Y12 and vasodilator stimulated phosphoprotein (VASP) expressed as platelet reactivity index (PRI) after 14 days of maintenance dosing. Clopidogrel and prasugrel active metabolite (AM) exposure was calculated in a cohort of 96 patients. For clopidogrel, genetic variants in CYP2C19, but not ABCB1 or PON1, affected PK and PD. For prasugrel, none of the measured genetic variants affected PK or PD. Compared with clopidogrel, platelet inhibition with prasugrel was greater even in the CYP2C19 UM phenotype. Prasugrel generated more AM and achieved greater platelet inhibition than clopidogrel irrespective of CYP2C19, ABCB1, and PON1 polymorphisms. The lack of effect from genetic variants on prasugrel AM generation or antiplatelet activity is consistent with previous studies in healthy volunteers and is consistent with improved efficacy in acute coronary syndrome patients managed with percutaneous coronary intervention. PMID:24009042

  6. Comparative Morphophysiological Analyses and Molecular Profiling Reveal Pi-Efficient Strategies of a Traditional Rice Genotype

    PubMed Central

    Mehra, Poonam; Pandey, Bipin K.; Giri, Jitender

    2016-01-01

    Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice genotypes are naturally compatible with low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes, Dular (low Pi tolerant), and PB1 (low Pi sensitive), have been selected. Comparative morphophysiological, global transcriptome and lipidome analyses of root and shoot tissues of both genotypes grown under Pi deficient and sufficient conditions revealed potential low Pi tolerance mechanisms of the traditional genotype. Most of the genes associated with enhanced internal Pi utilization (phospholipid remobilization) and modulation of root system architecture (RSA) were highly induced in the traditional rice genotype, Dular. Higher reserves of phospholipids and greater accumulation of galactolipids under low Pi in Dular indicated it has more efficient Pi utilization. Furthermore, Dular also maintained greater root growth than PB1 under low Pi, resulting in larger root surface area due to increased lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of the traditional genotype can be exploited to improve the low Pi tolerance of modern high yielding rice cultivars. PMID:26779218

  7. Comparative study of two chitin-active and two cellulose-active AA10-type lytic polysaccharide monooxygenases.

    PubMed

    Forsberg, Zarah; Røhr, Asmund Kjendseth; Mekasha, Sophanit; Andersson, K Kristoffer; Eijsink, Vincent G H; Vaaje-Kolstad, Gustav; Sørlie, Morten

    2014-03-18

    Lytic polysaccharide monooxygenases (LPMOs), found in family 9 (previously GH61), family 10 (previously CBM33), and the newly discovered family 11 of auxiliary activities (AA) in the carbohydrate-active enzyme classification system, are copper-dependent enzymes that oxidize sp(3)-carbons in recalcitrant polysaccharides such as chitin and cellulose in the presence of an external electron donor. In this study, we describe the activity of two AA10-type LPMOs whose activities have not been described before and we compare in total four different AA10-type LPMOs with the aim of finding possible correlations between their substrate specificities, sequences, and EPR signals. EPR spectra indicate that the electronic environment of the copper varies within the AA10 family even though amino acids directly interacting with the copper atom are identical in all four enzymes. This variation seems to be correlated to substrate specificity and is likely caused by sequence variation in areas that affect substrate binding geometry and/or by variation in a cluster of conserved aromatic residues likely involved in electron transfer. Interestingly, EPR signals for cellulose-active AA10 enzymes were similar to those previously observed for cellulose-active AA9 enzymes. Mutation of the conserved phenylalanine positioned in close proximity to the copper center in AA10-type LPMOs to Tyr (the corresponding residue in most AA9-type LPMOs) or Ala, led to complete or partial inactivation, respectively, while in both cases the ability to bind copper was maintained. Moreover, substrate binding affinity and degradation ability seemed hardly correlated, further emphasizing the crucial role of the active site configuration in determining LPMO functionality. PMID:24559135

  8. Warfarin Dosing in a Patient with CYP2C9(∗)3(∗)3 and VKORC1-1639 AA Genotypes.

    PubMed

    Johnson, Mark; Richard, Craig; Bogdan, Renee; Kidd, Robert

    2014-01-01

    Genetic factors most correlated with warfarin dose requirements are variations in the genes encoding the enzymes cytochrome P450 2C9 (CYP2C9) and vitamin K epoxide reductase (VKOR). Patients receiving warfarin who possess one or more genetic variations in CYP2C9 and VKORC1 are at increased risk of adverse drug events and require significant dose reductions to achieve a therapeutic international normalized ratio (INR). A 74-year-old white female with atrial fibrillation was initiated on a warfarin dose of 2 mg PO daily, which resulted in multiple elevated INR measurements and three clinically significant hemorrhagic events and four vitamin K antidote treatments over a period of less than two weeks. Genetic analysis later revealed that she had the homozygous variant genotypes of CYP2C9∗3∗3 and VKORC1-1639 AA. Warfarin dosing was subsequently restarted and stabilized at 0.5 mg PO daily with therapeutic INRs. This is the first case report of a white female with these genotypes stabilized on warfarin, and it highlights the value of pharmacogenetic testing prior to the initiation of warfarin therapy to maximize efficacy and minimize the risk of adverse drug events. PMID:24627811

  9. Warfarin Dosing in a Patient with CYP2C9∗3∗3 and VKORC1-1639 AA Genotypes

    PubMed Central

    Bogdan, Renee

    2014-01-01

    Genetic factors most correlated with warfarin dose requirements are variations in the genes encoding the enzymes cytochrome P450 2C9 (CYP2C9) and vitamin K epoxide reductase (VKOR). Patients receiving warfarin who possess one or more genetic variations in CYP2C9 and VKORC1 are at increased risk of adverse drug events and require significant dose reductions to achieve a therapeutic international normalized ratio (INR). A 74-year-old white female with atrial fibrillation was initiated on a warfarin dose of 2 mg PO daily, which resulted in multiple elevated INR measurements and three clinically significant hemorrhagic events and four vitamin K antidote treatments over a period of less than two weeks. Genetic analysis later revealed that she had the homozygous variant genotypes of CYP2C9∗3∗3 and VKORC1-1639 AA. Warfarin dosing was subsequently restarted and stabilized at 0.5 mg PO daily with therapeutic INRs. This is the first case report of a white female with these genotypes stabilized on warfarin, and it highlights the value of pharmacogenetic testing prior to the initiation of warfarin therapy to maximize efficacy and minimize the risk of adverse drug events. PMID:24627811

  10. The IL1B-511 Polymorphism (rs16944 AA Genotype) Is Increased in Aspirin-Exacerbated Respiratory Disease in Mexican Population

    PubMed Central

    Falfán-Valencia, Ramcés; Pavón-Romero, Gandhi F.; Camarena, Angel; García, María de la Luz; Galicia-Negrete, Gustavo; Negrete-García, María Cristina; Teran, Luis Manuel

    2012-01-01

    Aspirin exacerbated respiratory disease (AERD) is characterized by chronic hyperplastic rhinosinusitis, nasal polyposis, asthma, and aspirin sensitivity. The mechanisms which produce these manifestations of intolerance are not fully defined, current research focuses on cyclooxygenase 1 (COX-1) inhibition, metabolism of arachidonic acid, and the COX pathway to the lipoxygenase (LO) route, inducing increased synthesis of leukotrienes (LT). The biological plausibility of this model has led to the search for polymorphisms in genes responsible for proinflammatory cytokines synthesis, such as IL1B and IL8. We performed a genetic association study between IL8-251 (rs4073) and IL1B-511 (rs16944) polymorphisms in AERD, aspirin-tolerant asthma (ATA), and healthy control subjects. Using allelic discrimination by real-time PCR, we found statistically nonsignificant associations between AERD, ATA, and healthy control subjects for the GG and GA genotypes of IL1B (rs16944). Interestingly, the AA genotype showed an increased frequency in the AERD patients versus the ATA group (GF = 0.19 versus 0.07, p = 0.018, OR 2.98, and 95% CI 1.17–7.82). This is the first observation that IL1B polymorphisms are involved in AERD. Thus, future studies must investigate whether interleukin-1β is released in the airways of AERD patients and whether it relates to genetic polymorphisms in the IL1B gene. PMID:22132000

  11. Comparative Transcriptome Profiling of Chilling Stress Responsiveness in Two Contrasting Rice Genotypes

    PubMed Central

    Zhang, Ting; Zhao, Xiuqin; Wang, Wensheng; Pan, Yajiao; Huang, Liyu; Liu, Xiaoyue; Zong, Ying; Zhu, Linghua; Yang, Daichang; Fu, Binying

    2012-01-01

    Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed a differential constitutive gene expression prior to stress and distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in chilling-tolerant LTH compared with chilling-sensitive IR29, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in the chilling- tolerant genotype and strong repression in chilling-sensitive genotype. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in the chilling-tolerant genotype, while the chilling-sensitive genotype displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance. A number of the chilling-regulated genes identified in this study were co-localized onto previously fine-mapped cold-tolerance-related QTLs, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for chilling tolerance in rice. PMID:22912843

  12. Comparative genotyping of Streptococcus mutans by repetitive extragenic palindromic polymerase chain reaction and multilocus sequence typing.

    PubMed

    Momeni, S S; Whiddon, J; Moser, S A; Cheon, K; Ruby, J D; Childers, N K

    2013-02-01

    The genetic diversity of Streptococcus mutans has been extensively studied using a variety of genotyping methods. Repetitive extragenic palindromic-polymerase chain reaction (rep-PCR) is a genotyping approach used for screening large numbers of bacterial isolates. This two-part study used multilocus sequence typing (MLST) analysis to evaluate genotypes previously identified as unique using rep-PCR. In part one, an isolate was selected from each of the 22 S. mutans rep-PCR genotype groups representing 8000 clinical isolates. For part two, four additional isolates were selected from the six most commonly occurring genotype groups (GG) for further analysis. Real-time PCR was performed using eight housekeeping S. mutans gene loci and the amplicons were sequenced. Sequence data analysis was performed using CLC DNA Workbench and alleles were compared with the PubMLST database for Oral Streptococcus using the Nakano scheme. Concatenated sequences were evaluated with MEGA using a minimum evolution method with bootstrap. All 22 rep-PCR genotypes were unique by MLST analysis. Within rep-PCR GGs, MLST matched rep-PCR in three groups demonstrating clonality; three groups exhibited more diversity with MLST. The discovery of three clonal groups is unique to this study and suggests that S. mutans genotypes are shared between unrelated subjects. Furthermore, MLST defined 19 new alleles and 26 new sequence types that have been confirmed and registered with PubMLST. Methods for processing were streamlined and a process for using MLST with rep-PCR is suggested. In conclusion, MLST verified that rep-PCR is a reliable and cost-effective method for screening large numbers of S. mutans strains for epidemiological study. PMID:23194334

  13. Comparative proteome analysis of metabolic changes by low phosphorus stress in two Brassica napus genotypes.

    PubMed

    Yao, Yinan; Sun, Haiyan; Xu, Fangsen; Zhang, Xuejiang; Liu, Shengyi

    2011-03-01

    In an attempt to determine the adaptation strategy to phosphorous (Pi) deficiency in oilseed rape, comparative proteome analyses were conducted to investigate the differences of metabolic changes in two oilseed rape genotypes with different tolerance to low phosphorus (LP). Generally in either roots or leaves, there existed few low phosphorus (LP)-induced proteins shared in the two lines. The LP-tolerant genotype 102 maintained higher Pi concentrations than LP-sensitive genotype 105 when growing hydroponically under the 5-μM phosphorus condition. In 102 we observed the downregulation of the proteins related to gene transcription, protein translation, carbon metabolism, and energy transfer in leaves and roots, and the downregulation of proteins related to leaf growth and root cellular organization. But the proteins related to the formation of lateral root were upregulated, such as the auxin-responsive family proteins in roots and the sucrose-phosphate synthase-like protein in roots and leaves. On the other hand, the LP-sensitive genotype 105 maintained the low level of Pi concentrations and suffered high oxidative pressure under the LP condition, and stress-shocking proteins were pronouncedly upregulated such as the proteins for signal transduction, gene transcription, secondary metabolism, universal stress family proteins, as well as the proteins involved in lipid oxygenation and the disease resistance in both leaves and roots. Although the leaf proteins for growth in 105 were downregulated, the protein expressions in roots related to glycolysis and tricarboxylic acid (TCA) cycle were enhanced to satisfy the requirement of organic acid secretion. PMID:21110039

  14. Comparative Genotyping of Campylobacter jejuni Strains from Patients with Guillain-Barré Syndrome in Bangladesh

    PubMed Central

    Islam, Zhahirul; van Belkum, Alex; Wagenaar, Jaap A.; Cody, Alison J.; de Boer, Albert G.; Tabor, Helen; Jacobs, Bart C.; Talukder, Kaisar A.; Endtz, Hubert P.

    2009-01-01

    Background Campylobacter jejuni is a common cause of acute gastroenteritis and is associated with post-infectious neuropathies such as the Guillain-Barré syndrome (GBS) and the Miller Fisher syndrome (MFS). We here present comparative genotyping of 49 C. jejuni strains from Bangladesh that were recovered from patients with enteritis or GBS. All strains were serotyped and analyzed by lipo-oligosaccharide (LOS) genotyping, amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). Methodology/Principal Findings C. jejuni HS:23 was a predominant serotype among GBS patients (50%), and no specific serotype was significantly associated with GBS compared to enteritis. PCR screening showed that 38/49 (78%) of strains could be assigned to LOS classes A, B, C, or E. The class A locus (4/7 vs 3/39; p<0.01) was significantly associated in the GBS-related strains as compared to enteritis strains. All GBS/oculomotor related strains contained the class B locus; which was also detected in 46% of control strains. Overlapping clonal groups were defined by MLST, AFLP and PFGE for strains from patients with gastroenteritis and GBS. MLST defined 22 sequence types (STs) and 7 clonal complexes including 7 STs not previously identified (ST-3742, ST-3741, ST-3743, ST-3748, ST-3968, ST-3969 and ST-3970). C. jejuni HS:23 strains from patients with GBS or enteritis were clonal and all strains belonged to ST-403 complex. Concordance between LOS class B and ST-403 complex was revealed. AFLP defined 25 different types at 90% similarity. The predominant AFLP type AF-20 coincided with the C. jejuni HS:23 and ST-403 complex. Conclusion/Significance LOS genotyping, MLST, AFLP and PFGE helped to identify the HS:23 strains from GBS or enteritis patients as clonal. Overall, genotypes exclusive for enteritis or for GBS-related strains were not obtained although LOS class A was significantly associated with GBS strains

  15. Comparative analysis of cervical cytology and human papillomavirus genotyping by three different methods in a routine diagnostic setting.

    PubMed

    Padalko, Elizaveta; Ali-Risasi, Catherine; Mesmaekers, Stéphanie; Ryckaert, Inge; Van Renterghem, Lieve; Lambein, Kathleen; Bamelis, Mieke; De Mey, Anja; Sturtewagen, Yolande; Vastenavond, Hilde; Broeck, Davy Vanden; Weyers, Steven; Praet, Marleen

    2015-09-01

    Application of Bethesda guidelines on cervical cytology involves human papillomavirus (HPV) determinations on all ASC-US and ASC-H results. We compared HPV DNA results in view of the eventual development of a cervical intraepithelial neoplasia lesion determined either on cytology or histology. A total of 214 liquid-based cytology samples were analysed. Three different HPV DNA methods were applied: the Abbott RealTime High Risk HPV test, INNO-Lipa HPV Genotyping Extra and Full Spectrum PCR HPV Amplification and Detection/Genotyping System by Lab2Lab Diagnostic Service. A comparison of these three methods showed full concordance only for 49 samples (23%), and 27 (13%) of the samples were discordant in indicating the presence of the high-risk HPV type. Out of 214 patients, 88 were selected who presented with a cervical intraepithelial neoplasia or a VAIN lesion at follow-up cytology or histology. In this group, full concordance with HPV genotyping was present only in 19 (22%) follow-up samples. Nine (10%) follow-up samples showed discordant results for the presence of a high-risk genotype between the three genotyping methods tested either by negativity for high-risk HPV by one of the methods (n=6) or by failure to genotype HPV (n=2), or by a combination of both (n=1). Moreover, discordance for the detection of HPV16 or HPV18 was observed between the three HPV DNA genotyping methods used in 9 (10%) follow-up samples. In addition, the performance of genotyping methods on 20 external quality samples was assessed, showing discordant results for HPV16 and HPV18. Major differences were found in the genotyping results according to the HPV DNA method. Our findings highlight the importance of careful interpretation of data from studies using different HPV genotyping methods and underline the need for standardization by method validation in clinical laboratories, especially in the setting of primary HPV screening. PMID:25370681

  16. Comparative Analysis of the Performance of Aspergillus flavus on Resistant and Susceptible Maize Genotypes during Infection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aspergillus, a mycotoxicogenic fungal genus, produces carcinogenic aflatoxins in crops like peanuts and maize. Development of fungal resistant maize cultivars is one strategy used to decrease contamination. Successful development and identification of resistant maize genotypes requires evaluation o...

  17. Comparative analysis of gene expression in response to cold stress in diverse rice genotypes.

    PubMed

    Moraes de Freitas, Gabriela Peres; Basu, Supratim; Ramegowda, Venkategowda; Braga, Eugenia Bolacel; Pereira, Andy

    2016-02-26

    Cold stress is a major factor affecting rice (Oryza sativa) growth and productivity, limiting its distribution worldwide. Rice production is affected primarily due to its vulnerability to cold stress at seedling stage, as well as reproductive stage leading to spikelet sterility. We report here the analysis of 21 diverse rice genotypes from the USDA mini-core collection for cold tolerance and categorized their tolerance levels on the basis of reduction in growth measured by root and shoot length. The screening identified 12 cold tolerant genotypes from which six tolerant genotypes were characterized at the vegetative stage for cold tolerance and gas-exchange parameters. Two tolerant and two sensitive genotypes were used further for gene expression analysis. Lipid Transfer Protein (LTP) genes showed a clear difference in expression between cold tolerant and sensitive genotypes suggesting that they are good candidates for engineering cold tolerance in rice. Nipponbare was identified as a cold tolerant genotype with stress tolerance mechanism potentially operating via both ABA dependent and independent pathways. PMID:26855133

  18. Comparative sensitivity of commercial tests for hepatitis E genotype 3 virus antibody detection.

    PubMed

    Avellon, Ana; Morago, Lucia; Garcia-Galera del Carmen, Maria; Munoz, Milagros; Echevarría, Jose-Manuel

    2015-11-01

    Hepatitis E virus (HEV) acute infection is often diagnosed only by anti-HEV IgM ELISA methods, whose sensitivity varies, according to different reports. Reports assessing the specificity of commercial assays for anti-HEV IgG testing are scarce, and estimates of sensitivity and specificity are both controversial. The aim of this work is to assess the sensitivity of different commercial techniques for HEV genotype 3 antibody (anti-HEV) IgM and IgG detection in entirely specific sample panels including both high and low antibody concentrations. The anti-HEV IgM and IgG ELISA methods compared were: DSI, Mikrogen, Wantai, Euroimmun, MP, and Dia.pro. The rapid test All Diag was also included in the anti-HEV IgM comparison. Our results show that low anti-HEV IgM concentrations were better detected by DSI, Mikrogen, and All Diag, these tests being the most sensitive in our study. Euroimmun, MP and Dia.pro gave concordant results, showing lower sensitivity than the others. Regarding anti-HEV IgG our results revealed similar anti-HEV IgG sensitivity. Furthermore, there was a striking overall lack of concordance among the results. We present a thorough review of previous comparative reports, with particular reference to the anti-HEV IgG comparison, since published results differ from ours. This discrepancy may be related to the improved versions of the tests for MP and Dia.pro that we employed. PMID:25959136

  19. Comparing simple root phenotyping methods on a core set of rice genotypes.

    PubMed

    Shrestha, R; Al-Shugeairy, Z; Al-Ogaidi, F; Munasinghe, M; Radermacher, M; Vandenhirtz, J; Price, A H

    2014-05-01

    Interest in belowground plant growth is increasing, especially in relation to arguments that shallow-rooted cultivars are efficient at exploiting soil phosphorus while deep-rooted ones will access water at depth. However, methods for assessing roots in large numbers of plants are diverse and direct comparisons of methods are rare. Three methods for measuring root growth traits were evaluated for utility in discriminating rice cultivars: soil-filled rhizotrons, hydroponics and soil-filled pots whose bottom was sealed with a non-woven fabric (a potential method for assessing root penetration ability). A set of 38 rice genotypes including the OryzaSNP set of 20 cultivars, additional parents of mapping populations and products of marker-assisted selection for root QTLs were assessed. A novel method of image analysis for assessing rooting angles from rhizotron photographs was employed. The non-woven fabric was the easiest yet least discriminatory method, while the rhizotron was highly discriminatory and allowed the most traits to be measured but required more than three times the labour of the other methods. The hydroponics was both easy and discriminatory, allowed temporal measurements, but is most likely to suffer from artefacts. Image analysis of rhizotrons compared favourably to manual methods for discriminating between cultivars. Previous observations that cultivars from the indica subpopulation have shallower rooting angles than aus or japonica cultivars were confirmed in the rhizotrons, and indica and temperate japonicas had lower maximum root lengths in rhizotrons and hydroponics. It is concluded that rhizotrons are the preferred method for root screening, particularly since root angles can be assessed. PMID:24015692

  20. Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes under Salinity Stress during the Vegetative Growth Stage

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice (Oryza sativa), a salt-sensitive species, has considerable genetic variation for salt tolerance within the cultivated gene pool. Two indica rice genotypes, FL478, a recombinant inbred line derived from a population developed for salinity tolerance studies, and IR29, the sensitive parent of the ...

  1. Comparative Transcriptome Profiling of Two Tibetan Wild Barley Genotypes in Responses to Low Potassium

    PubMed Central

    Zeng, Jianbin; He, Xiaoyan; Wu, Dezhi; Zhu, Bo; Cai, Shengguan; Nadira, Umme Aktari; Jabeen, Zahra; Zhang, Guoping

    2014-01-01

    Potassium (K) deficiency is one of the major factors affecting crop growth and productivity. Development of low-K tolerant crops is an effective approach to solve the nutritional deficiency in agricultural production. Tibetan annual wild barley is rich in genetic diversity and can grow normally under poor soils, including low-K supply. However, the molecular mechanism about low K tolerance is still poorly understood. In this study, Illumina RNA-Sequencing was performed using two Tibetan wild barley genotypes differing in low K tolerance (XZ153, tolerant and XZ141, sensitive), to determine the genotypic difference in transcriptome profiling. We identified a total of 692 differentially expressed genes (DEGs) in two genotypes at 6 h and 48 h after low-K treatment, including transcription factors, transporters and kinases, oxidative stress and hormone signaling related genes. Meanwhile, 294 low-K tolerant associated DEGs were assigned to transporter and antioxidant activities, stimulus response, and other gene ontology (GO), which were mainly involved in starch and sucrose metabolism, lipid metabolism and ethylene biosynthesis. Finally, a hypothetical model of low-K tolerance mechanism in XZ153 was presented. It may be concluded that wild barley accession XZ153 has a higher capability of K absorption and use efficiency than XZ141 under low K stress. A rapid response to low K stress in XZ153 is attributed to its more K uptake and accumulation in plants, resulting in higher low K tolerance. The ethylene response pathway may account for the genotypic difference in low-K tolerance. PMID:24949953

  2. Omics-Based Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes during Early Infestation by Small Brown Planthopper.

    PubMed

    Zhang, Weilin; Yang, Ling; Li, Mei; Ma, Bojun; Yan, Chengqi; Chen, Jianping

    2015-01-01

    The small brown planthopper (SBPH) is one of the destructive pests of rice. Although different biochemical pathways that are involved in rice responding to planthopper infestation have been documented, it is unclear which individual metabolic pathways are responsive to planthopper infestation. In this study, an omics-based comparative transcriptional profiling of two contrasting rice genotypes, an SBPH-resistant and an SBPH-susceptible rice line, was assessed for rice individual metabolic pathways responsive to SBPH infestation. When exposed to SBPH, 166 metabolic pathways were differentially regulated; of these, more than one-third of metabolic pathways displayed similar change patterns between these two contrasting rice genotypes; the difference of change pattern between these two contrasting rice genotypes mostly lies in biosynthetic pathways and the obvious difference of change pattern lies in energy metabolism pathways. Combining the Pathway Tools Omics Viewer with the web tool Venn, 21 and 6 metabolic pathways which potentially associated with SBPH resistance and susceptibility, respectively were identified. This study presents an omics-based comparative transcriptional profiling of SBPH-resistant and SBPH-susceptible rice plants during early infestation by SBPH, which will be very informative in studying rice-insect interaction. The results will provide insight into how rice plants respond to early infestation by SBPH from the biochemical pathways perspective. PMID:26633389

  3. Omics-Based Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes during Early Infestation by Small Brown Planthopper

    PubMed Central

    Zhang, Weilin; Yang, Ling; Li, Mei; Ma, Bojun; Yan, Chengqi; Chen, Jianping

    2015-01-01

    The small brown planthopper (SBPH) is one of the destructive pests of rice. Although different biochemical pathways that are involved in rice responding to planthopper infestation have been documented, it is unclear which individual metabolic pathways are responsive to planthopper infestation. In this study, an omics-based comparative transcriptional profiling of two contrasting rice genotypes, an SBPH-resistant and an SBPH-susceptible rice line, was assessed for rice individual metabolic pathways responsive to SBPH infestation. When exposed to SBPH, 166 metabolic pathways were differentially regulated; of these, more than one-third of metabolic pathways displayed similar change patterns between these two contrasting rice genotypes; the difference of change pattern between these two contrasting rice genotypes mostly lies in biosynthetic pathways and the obvious difference of change pattern lies in energy metabolism pathways. Combining the Pathway Tools Omics Viewer with the web tool Venn, 21 and 6 metabolic pathways which potentially associated with SBPH resistance and susceptibility, respectively were identified. This study presents an omics-based comparative transcriptional profiling of SBPH-resistant and SBPH-susceptible rice plants during early infestation by SBPH, which will be very informative in studying rice-insect interaction. The results will provide insight into how rice plants respond to early infestation by SBPH from the biochemical pathways perspective. PMID:26633389

  4. Comparative Transcriptome Analysis of Resistant and Susceptible Common Bean Genotypes in Response to Soybean Cyst Nematode Infection

    PubMed Central

    Jain, Shalu; Chittem, Kishore; Brueggeman, Robert; Osorno, Juan M.; Richards, Jonathan; Nelson, Berlin D.

    2016-01-01

    Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) reproduces on the roots of common bean (Phaseolus vulgaris L.) and can cause reductions in plant growth and seed yield. The molecular changes in common bean roots caused by SCN infection are unknown. Identification of genetic factors associated with SCN resistance could help in development of improved bean varieties with high SCN resistance. Gene expression profiling was conducted on common bean roots infected by SCN HG type 0 using next generation RNA sequencing technology. Two pinto bean genotypes, PI533561 and GTS-900, resistant and susceptible to SCN infection, respectively, were used as RNA sources eight days post inoculation. Total reads generated ranged between ~ 3.2 and 5.7 million per library and were mapped to the common bean reference genome. Approximately 70–90% of filtered RNA-seq reads uniquely mapped to the reference genome. In the inoculated roots of resistant genotype PI533561, a total of 353 genes were differentially expressed with 154 up-regulated genes and 199 down-regulated genes when compared to the transcriptome of non- inoculated roots. On the other hand, 990 genes were differentially expressed in SCN-inoculated roots of susceptible genotype GTS-900 with 406 up-regulated and 584 down-regulated genes when compared to non-inoculated roots. Genes encoding nucleotide-binding site leucine-rich repeat resistance (NLR) proteins, WRKY transcription factors, pathogenesis-related (PR) proteins and heat shock proteins involved in diverse biological processes were differentially expressed in both resistant and susceptible genotypes. Overall, suppression of the photosystem was observed in both the responses. Furthermore, RNA-seq results were validated through quantitative real time PCR. This is the first report describing genes/transcripts involved in SCN-common bean interaction and the results will have important implications for further characterization of SCN resistance genes in common bean

  5. Comparative Transcriptome Analysis of Resistant and Susceptible Common Bean Genotypes in Response to Soybean Cyst Nematode Infection.

    PubMed

    Jain, Shalu; Chittem, Kishore; Brueggeman, Robert; Osorno, Juan M; Richards, Jonathan; Nelson, Berlin D

    2016-01-01

    Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) reproduces on the roots of common bean (Phaseolus vulgaris L.) and can cause reductions in plant growth and seed yield. The molecular changes in common bean roots caused by SCN infection are unknown. Identification of genetic factors associated with SCN resistance could help in development of improved bean varieties with high SCN resistance. Gene expression profiling was conducted on common bean roots infected by SCN HG type 0 using next generation RNA sequencing technology. Two pinto bean genotypes, PI533561 and GTS-900, resistant and susceptible to SCN infection, respectively, were used as RNA sources eight days post inoculation. Total reads generated ranged between ~ 3.2 and 5.7 million per library and were mapped to the common bean reference genome. Approximately 70-90% of filtered RNA-seq reads uniquely mapped to the reference genome. In the inoculated roots of resistant genotype PI533561, a total of 353 genes were differentially expressed with 154 up-regulated genes and 199 down-regulated genes when compared to the transcriptome of non- inoculated roots. On the other hand, 990 genes were differentially expressed in SCN-inoculated roots of susceptible genotype GTS-900 with 406 up-regulated and 584 down-regulated genes when compared to non-inoculated roots. Genes encoding nucleotide-binding site leucine-rich repeat resistance (NLR) proteins, WRKY transcription factors, pathogenesis-related (PR) proteins and heat shock proteins involved in diverse biological processes were differentially expressed in both resistant and susceptible genotypes. Overall, suppression of the photosystem was observed in both the responses. Furthermore, RNA-seq results were validated through quantitative real time PCR. This is the first report describing genes/transcripts involved in SCN-common bean interaction and the results will have important implications for further characterization of SCN resistance genes in common bean

  6. Comparative study of the biological properties of Trypanosoma cruzi I genotypes in a murine experimental model.

    PubMed

    Cruz, Lissa; Vivas, Angie; Montilla, Marleny; Hernández, Carolina; Flórez, Carolina; Parra, Edgar; Ramírez, Juan David

    2015-01-01

    Chagas disease is an endemic zoonosis in Latin America and caused by the parasite Trypanosoma cruzi. This kinetoplastid displays remarkable genetic variability, allowing its classification into six Discrete Typing Units (DTUs) from TcI to TcVI. T. cruzi I presents the broadest geographical distribution in the continent and has been associated to severe forms of cardiomyopathies. Recently, a particular genotype associated to human infections has been reported and named as TcIDOM (previously named TcIa-b). This genotype shows to be clonal and adapted to the domestic cycle but so far no studies have determined the biological properties of domestic (TcIDOM) and sylvatic TcI strains (previously named TcIc-e). Hence, the aim of this study was to untangle the biological features of these genotypes in murine models. We infected ICR-CD1 mice with five TcI strains (two domestic, two sylvatic and one natural mixture) and determined the course of infection during 91 days (acute and chronic phase of the disease) in terms of parasitemia, tissue tropism, immune response (IgG titers) and tissue invasion by means of histopathology studies. Statistically significant differences were observed in terms of parasitemia curves and prepatent period between domestic (TcIDOM) and sylvatic strains. There were no differences in terms of IgG antibodies response across the mice infected with the five strains. Regarding the histopathology, our results indicate that domestic strains present higher parasitemias and low levels of histopathological damage. In contrast, sylvatic strains showed lower parasitemias and high levels of histopathological damage. These results highlight the sympatric and behavioral differences of domestic and sylvatic TcI strains; the clinical and epidemiological implications are herein discussed. PMID:25461848

  7. Comparative Analyses of Phenotypic and Genotypic Methods for Detection of Enterotoxigenic Escherichia coli Toxins and Colonization Factors▿

    PubMed Central

    Sjöling, Å.; Wiklund, G.; Savarino, S. J.; Cohen, D. I.; Svennerholm, A.-M.

    2007-01-01

    Enterotoxigenic Escherichia coli (ETEC) is one of the main causes of childhood diarrhea in developing countries and in travelers. However, this pathogen has often not been reported in surveys of diarrheal pathogens, due to lack of simple standardized methods to detect ETEC in many laboratories. ETEC expresses one or both of two different enterotoxin subtypes: heat-stable toxins, a heat-labile toxin (LT), and more than 22 different colonization factors (CFs) that mediate adherence to the intestinal cell wall. Here we compare established phenotypic and genotypic detection methods and newly developed PCR detection methods with respect to sensitivity, specificity, positive predictive value, and ease of performance. The methods include GM1-enzyme-linked immunosorbent assay and dot blot techniques using specific monoclonal antibodies (MAbs) for phenotypic detection of the toxins and CFs, respectively, as well as different PCR and DNA/DNA hybridization techniques, including new PCR assays, for genotypic identification of the toxin and CF genes, respectively. We found very good general agreement in results derived from genotypic and phenotypic methods. In a few strains, LT and CFs were identified genetically but not phenotypically. Based on our analyses, we recommend initial screening for ETEC in clinical samples by multiplex toxin gene PCR. Toxin-positive strains may then be analyzed by dot blot tests for detection of the CFs expressed on the bacterial surface and by PCR for determination of additional CFs for which MAbs are currently lacking as well as for strains that harbor silent CF genes. PMID:17687011

  8. Comparative quantification and statistical analysis of η′ and η precipitates in aluminum alloy AA7075-T651 by TEM and AFM

    SciTech Connect

    Garcia-Garcia, Adrian Luis Dominguez-Lopez, Ivan Lopez-Jimenez, Luis Barceinas-Sanchez, J.D. Oscar

    2014-01-15

    Quantification of nanometric precipitates in metallic alloys has been traditionally performed using transmission electron microscopy, which is nominally a low throughput technique. This work presents a comparative study of quantification of η′ and η precipitates in aluminum alloy AA7075-T651 using transmission electron microscopy (TEM) and non-contact atomic force microscopy (AFM). AFM quantification was compared with 2-D stereological results reported elsewhere. Also, a method was developed, using specialized software, to characterize nanometric size precipitates observed in dark-field TEM micrographs. Statistical analysis of the quantification results from both measurement techniques supports the use of AFM for precipitate characterization. Once the precipitate stoichiometry has been determined by appropriate analytical techniques like TEM, as it is the case for η′ and η in AA7075-T651, the relative ease with which specimens are prepared for AFM analysis could be advantageous in product and process development, and quality control, where a large number of samples are expected for analysis on a regular basis. - Highlights: • Nanometric MgZn{sub 2} precipitates in AA7075-T651 were characterized using AFM and TEM. • Phase-contrast AFM was used to differentiate metal matrix from MgZn{sub 2} precipitates. • TEM and AFM micrographs were analyzed using commercially available software. • AFM image analysis and TEM 2-D stereology render statistically equivalent results.

  9. Comparing different post-mortem human samples as DNA sources for downstream genotyping and identification.

    PubMed

    Calacal, Gayvelline C; Apaga, Dame Loveliness T; Salvador, Jazelyn M; Jimenez, Joseph Andrew D; Lagat, Ludivino J; Villacorta, Renato Pio F; Lim, Maria Cecilia F; Fortun, Raquel D R; Datar, Francisco A; De Ungria, Maria Corazon A

    2015-11-01

    The capability of DNA laboratories to perform genotyping procedures from post-mortem remains, including those that had undergone putrefaction, continues to be a challenge in the Philippines, a country characterized by very humid and warm conditions all year round. These environmental conditions accelerate the decomposition of human remains that were recovered after a disaster and those that were left abandoned after a crime. When considerable tissue decomposition of human remains has taken place, there is no other option but to extract DNA from bone and/or teeth samples. Routinely, femur shafts are obtained from recovered bodies for human identification because the calcium matrix protects the DNA contained in the osteocytes. In the Philippines, there is difficulty in collecting femur samples after natural disasters or even human-made disasters, because these events are usually characterized by a large number of fatalities. Identification of casualties is further delayed by limitation in human and material resources. Hence, it is imperative to test other types of biological samples that are easier to collect, transport, process and store. We analyzed DNA that were obtained from body fluid, bone marrow, muscle tissue, clavicle, femur, metatarsal, patella, rib and vertebral samples from five recently deceased untreated male cadavers and seven male human remains that were embalmed, buried for ∼ 1 month and then exhumed. The bodies had undergone different environmental conditions and were in various stages of putrefaction. A DNA extraction method utilizing a detergent-washing step followed by an organic procedure was used. The utility of bone marrow and vitreous fluid including bone marrow and vitreous fluid that was transferred on FTA(®) cards and subjected to autosomal STR and Y-STR DNA typing were also evaluated. DNA yield was measured and the presence or absence of PCR inhibitors in DNA extracts was assessed using Plexor(®)HY. All samples were amplified using

  10. A large maize (Zea Mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection for accelerated breeding. We report the establishment of a large SNP array for maize and i...

  11. Towards Development of Clustering Applications for Large-Scale Comparative Genotyping and Kinship Analysis Using Y-Short Tandem Repeats

    PubMed Central

    Sapawi, Azizian Mohd; Salleh, Mohd Zaki

    2015-01-01

    Abstract Y-chromosome short tandem repeats (Y-STRs) are genetic markers with practical applications in human identification. However, where mass identification is required (e.g., in the aftermath of disasters with significant fatalities), the efficiency of the process could be improved with new statistical approaches. Clustering applications are relatively new tools for large-scale comparative genotyping, and the k-Approximate Modal Haplotype (k-AMH), an efficient algorithm for clustering large-scale Y-STR data, represents a promising method for developing these tools. In this study we improved the k-AMH and produced three new algorithms: the Nk-AMH I (including a new initial cluster center selection), the Nk-AMH II (including a new dominant weighting value), and the Nk-AMH III (combining I and II). The Nk-AMH III was the superior algorithm, with mean clustering accuracy that increased in four out of six datasets and remained at 100% in the other two. Additionally, the Nk-AMH III achieved a 2% higher overall mean clustering accuracy score than the k-AMH, as well as optimal accuracy for all datasets (0.84–1.00). With inclusion of the two new methods, the Nk-AMH III produced an optimal solution for clustering Y-STR data; thus, the algorithm has potential for further development towards fully automatic clustering of any large-scale genotypic data. PMID:25945508

  12. Data in support of comparative physiology and proteomic analysis of two wheat genotypes contrasting in drought tolerance.

    PubMed

    Faghani, Elham; Gharechahi, Javad; Komatsu, Setsuko; Mirzaei, Mehdi; Ali Khavarinejad, Ramzan; Najafi, Farzaneh; Karimi Farsad, Laleh; Salekdeh, Ghasem Hosseini

    2015-03-01

    Here, we present the data from a comparative physiology and proteomics approach used to analyze the response of two wheat genotypes (SERI M 82 (SE) and SW89.5193/kAu2 (SW)) with contrasting responses to drought stress. Proteomic analysis resulted in identification of 49 unique proteins with significant change in abundance (2-fold) under water shortage in roots and leaves. Gene ontology analysis of drought-responsive proteins (DRPs) suggested an induction of proteins related to cell wall biogenesis, ATP synthesis, photosynthesis, and carbohydrate/energy metabolism in leaves under stress condition. A large fraction of root proteins were identified to be involved in defense and oxidative stress response. In addition, a significant change was detected in proteins related to protein synthesis, ATP synthesis, and germin-like proteins in response to drought stress. A detailed analysis of this data may be obtained from Ref. [1]. PMID:26217700

  13. Comparing the effects of genetic drift and fluctuating selection on genotype frequency changes in the scarlet tiger moth.

    PubMed

    O'Hara, R B

    2005-01-22

    One of the recurring arguments in evolutionary biology is whether evolution occurs principally through natural selection or through neutral processes such as genetic drift. A 60-year-long time series of changes in the genotype frequency of a colour polymorphism of the scarlet tiger moth, Callimorpha dominula, was used to compare the relative effects of genetic drift and variable natural selection. The analysis showed that most of the variation in frequency was the result of genetic drift. In addition, although selection was acting, mean fitness barely increased. This supports the 'Red Queen's hypothesis' that long-term improvements in fitness may not occur, because populations have to keep pace with changes in the environment. PMID:15695213

  14. Data in support of comparative physiology and proteomic analysis of two wheat genotypes contrasting in drought tolerance

    PubMed Central

    Faghani, Elham; Gharechahi, Javad; Komatsu, Setsuko; Mirzaei, Mehdi; Ali Khavarinejad, Ramzan; Najafi, Farzaneh; Karimi Farsad, Laleh; Hosseini Salekdeh, Ghasem

    2014-01-01

    Here, we present the data from a comparative physiology and proteomics approach used to analyze the response of two wheat genotypes (SERI M 82 (SE) and SW89.5193/kAu2 (SW)) with contrasting responses to drought stress. Proteomic analysis resulted in identification of 49 unique proteins with significant change in abundance (2-fold) under water shortage in roots and leaves. Gene ontology analysis of drought-responsive proteins (DRPs) suggested an induction of proteins related to cell wall biogenesis, ATP synthesis, photosynthesis, and carbohydrate/energy metabolism in leaves under stress condition. A large fraction of root proteins were identified to be involved in defense and oxidative stress response. In addition, a significant change was detected in proteins related to protein synthesis, ATP synthesis, and germin-like proteins in response to drought stress. A detailed analysis of this data may be obtained from Ref. [1]. PMID:26217700

  15. Comparative Transcriptome Analysis between Low- and High-Cadmium-Accumulating Genotypes of Pakchoi (Brassica chinensis L.) in Response to Cadmium Stress.

    PubMed

    Zhou, Qian; Guo, Jing-Jie; He, Chun-Tao; Shen, Chuang; Huang, Ying-Ying; Chen, Jing-Xin; Guo, Jian-Hua; Yuan, Jian-Gang; Yang, Zhong-Yi

    2016-06-21

    To reduce cadmium (Cd) pollution of food chains, screening and breeding of low-Cd-accumulating cultivars are the focus of much study. Two previously identified genotypes, a low-Cd-accumulating genotype (LAJK) and a high-Cd-accumulating genotype (HAJS) of pakchoi (Brassica chinesis L.), were stressed by Cd (12.5 μM) for 0 h (T0), 3 h (T3) and 24 h (T24). By comparative transcriptome analysis for root tissue, 3005 and 4343 differentially expressed genes (DEGs) were identified in LAJK at T3 (vs T0) and T24 (vs T3), respectively, whereas 8677 and 5081 DEGs were detected in HAJS. Gene expression pattern analysis suggested a delay of Cd responded transcriptional changes in LAJK compared to HAJS. DEG functional enrichments proposed genotype-specific biological processes coped with Cd stress. Cell wall biosynthesis and glutathione (GSH) metabolism were found to involve in Cd resistance in HAJS, whereas DNA repair and abscisic acid (ABA) signal transduction pathways played important roles in LAJK. Furthermore, the genes participating in Cd efflux such as PDR8 were overexpressed in LAJK, whereas those responsible for Cd transport such as YSL1 were more enhanced in HAJS, exhibiting different Cd transport processes between two genotypes. These novel findings should be useful for molecular assisted screening and breeding of low-Cd-accumulating genotypes for pakchoi. PMID:27228483

  16. Comparative morpho-physiological and biochemical responses of lentil and grass pea genotypes under water stress

    PubMed Central

    Talukdar, Dibyendu

    2013-01-01

    Background: Both lentil (Lens culinaris Medik.) and grass pea (Lathyrus sativus L.) in the family Fabaceae are two important cool-season food legumes, often experiencing water stress conditions during growth and maturity. Objective: The present study was undertaken to ascertain the response of these two crops under different water stress regimes. Materials and Methods: Different morpho-physiological and biochemical parameters were studied in a pot experiment under controlled environmental conditions. Along with control (proper irrigation, 0 stress), three sets of plants were subjected to mild (6 d), moderate (13 d) and severe (20 d) water stress by withholding irrigation at the appropriate time. Results: Compared with control, plant growth traits and seed yield components reduced significantly in both crops with increasing period of water stress, resulting in lowering of dry mass with more severe effect on lentil compared with grass pea. Foliar Relative Water Content (RWC) (%), K+/Na+ ratio, chlorophyll (chl) a, chl a/b ratio, stomatal conductance and net photosynthetic rate declined considerably in both crops under water stress. Leaf-free proline level increased significantly in both crops, but it decreased markedly in nodules of lentil and remained unchanged in grass pea. Nodulation was also affected due to water stress. The impairment in growth traits and physio-biochemical parameters under water stress was manifested in reduction of drought tolerance efficiency of both crops. Conclusion: Impact of water stress was more severe on lentil compared with grass pea, and modulation of growth traits signified necessity of a detailed strategy in breeding of food legumes under water stress. PMID:24082740

  17. Comparative study using phenotypic, genotypic, and proteomics methods for identification of coagulase-negative staphylococci.

    PubMed

    Loonen, Anne J M; Jansz, Arjan R; Bergland, Jeandery N B; Valkenburg, Marion; Wolffs, Petra F G; van den Brule, Adriaan J C

    2012-04-01

    Five methods were compared to determine the most accurate method for identification of coagulase-negative staphylococci (CoNS) (n = 142 strains). Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) showed the best results for rapid and accurate CoNS differentiation (99.3% of strains correctly identified). An alternative to this approach could be Vitek2 combined with partial tuf gene sequencing (100% of strains correctly identified when both methods are performed simultaneously). PMID:22238435

  18. Comparative Evaluation of Ligation-Mediated PCR and Spoligotyping as Screening Methods for Genotyping of Mycobacterium tuberculosis Strains

    PubMed Central

    Bonora, Stefano; Gutierrez, M. Cristina; Di Perri, Giovanni; Brunello, Francesca; Allegranzi, Benedetta; Ligozzi, Marco; Fontana, Roberta; Concia, Ercole; Vincent, Veronique

    1999-01-01

    Spoligotyping has been suggested as a screening test in multistep genotyping of Mycobacterium tuberculosis strains. Relying on restriction fragment length polymorphism (RFLP) analysis with IS6110 (IS6110 RFLP analysis) as a “gold standard,” we performed a comparative evaluation of spoligotyping and ligation-mediated PCR (LMPCR), a recently described PCR-based typing method, as rapid screening tests for fingerprinting of 158 M. tuberculosis strains collected in Verona, Italy. LMPCR seemed to be comparable to spoligotyping in terms both of feasibility with rapidly extracted DNA and of generation of software-analyzable images. Moreover, LMPCR grouped considerably fewer strains than spoligotyping (38 versus 67%) and was found to reduce the cluster overestimation rate (26.3 versus 58%) and to give a better discriminatory index (0.992 versus 0.970) compared to spoligotyping. In our geographical region, where there was no evidence of clustered strains carrying fewer than six IS6110 copies, LMPCR was found to be more discriminatory than spoligotyping. We also evaluated two models of three-step typing strategies, involving the use of spoligotyping and LMPCR as screening methods and IS6110 RFLP analysis as a further supporting test. LMPCR proved to be a more effective first-step test than spoligotyping, significantly reducing the need for subtyping. LMPCR should be considered an alternative to spoligotyping as a rapid screening method for M. tuberculosis fingerprinting, particularly in areas with a low prevalence of M. tuberculosis strains carrying few copies of IS6110. PMID:10488164

  19. International collaborative study to compare reverse transcriptase PCR assays for detection and genotyping of noroviruses.

    PubMed

    Vinjé, Jan; Vennema, Harry; Maunula, Leena; von Bonsdorff, Carl-Henrik; Hoehne, Marina; Schreier, Eckart; Richards, Alison; Green, Jon; Brown, David; Beard, Suzanne S; Monroe, Stephan S; de Bruin, Erwin; Svensson, Lennart; Koopmans, Marion P G

    2003-04-01

    To allow more rapid and internationally standardized assessment of the spread of noroviruses (previously called Norwalk-like viruses [NLVs]) as important food-borne pathogens, harmonization of methods for their detection is needed. Diagnosis of NLVs in clinical diagnostic laboratories is usually performed by reverse transciptase PCR (RT-PCR) assays. In the present study, the performance of five different RT-PCR assays for the detection of NLVs was evaluated in an international collaborative study by five laboratories in five countries with a coded panel of 91 fecal specimens. The assays were tested for their sensitivity, detection limit, and ease of standardization. In total, NLVs could be detected by at least one RT-PCR assay in 69 (84%) of the samples that originally tested positive. Sensitivity ranged from 52 to 73% overall and from 54 to 100% and 58 to 85% for genogroup I and II viruses, respectively. In all, 64% of the false-negative results were obtained with a set of diluted stools (n = 20) that may have lost quality upon storage. Sensitivity was improved when these samples were excluded from analysis. No one single assay stood out as the best, although the p1 assay demonstrated the most satisfactory overall performance. To promote comparability of data, this assay will be recommended for newly starting groups in future collaborative studies. PMID:12682125

  20. Comparative Study Using Amplified Fragment Length Polymorphism Fingerprinting, PCR Genotyping, and Phenotyping To Differentiate Campylobacter fetus Strains Isolated from Animals

    PubMed Central

    Wagenaar, Jaap A.; van Bergen, Marcel A. P.; Newell, Diane G.; Grogono-Thomas, Rose; Duim, Birgitta

    2001-01-01

    A collection of Campylobacter fetus strains, including both C. fetus subsp. fetus and C. fetus subsp. venerealis, were phenotypically identified to the subspecies level and genotypically typed by PCR and amplified fragment length polymorphism (AFLP) analysis. Phenotypic subspecies determination methods were unreliable. Genotyping of the strains by PCR and AFLP showed a clear discrimination between the two subspecies. PMID:11376071

  1. Comparative Transcriptional Profiling of Two Wheat Genotypes, with Contrasting Levels of Minerals in Grains, Shows Expression Differences during Grain Filling

    PubMed Central

    Singh, Sudhir P.; Jeet, Raja; Kumar, Jitendra; Shukla, Vishnu; Srivastava, Rakesh; Mantri, Shrikant S.; Tuli, Rakesh

    2014-01-01

    Wheat is one of the most important cereal crops in the world. To identify the candidate genes for mineral accumulation, it is important to examine differential transcriptome between wheat genotypes, with contrasting levels of minerals in grains. A transcriptional comparison of developing grains was carried out between two wheat genotypes- Triticum aestivum Cv. WL711 (low grain mineral), and T. aestivum L. IITR26 (high grain mineral), using Affymetrix GeneChip Wheat Genome Array. The study identified a total of 580 probe sets as differentially expressed (with log2 fold change of ≥2 at p≤0.01) between the two genotypes, during grain filling. Transcripts with significant differences in induction or repression between the two genotypes included genes related to metal homeostasis, metal tolerance, lignin and flavonoid biosynthesis, amino acid and protein transport, vacuolar-sorting receptor, aquaporins, and stress responses. Meta-analysis revealed spatial and temporal signatures of a majority of the differentially regulated transcripts. PMID:25364903

  2. Comparative Genotypic and Phenotypic Characterisation of Methicillin-Resistant Staphylococcus aureus ST398 Isolated from Animals and Humans

    PubMed Central

    Jamrozy, Dorota M.; Fielder, Mark D.; Butaye, Patrick; Coldham, Nick G.

    2012-01-01

    The high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) ST398 among pigs in certain European countries and North America and its occurrence in other animal species raises a question concerning the molecular mechanisms mediating the success of this lineage. In this study a panel of S. aureus strains belonging to sequence type (ST) 5 (n = 4), ST8 (n = 5), ST15 (n = 5), ST22 (n = 8), clonal complex (CC) 30 (n = 8), CC97 (n = 8), CC130 (n = 4), CC151 (n = 4) and ST398 (n = 18) were screened by DNA microarray and PCR for the carriage of virulence and antimicrobial resistance genes. Isolates belonging to the same sequence type/clonal complex (ST/CC) were found to share similar virulence gene profiles. The ST398 lineage displayed the lowest content of virulence genes, which consisted mainly of genes detected among the majority or all of the analysed lineages. All MRSA ST398 isolates lacked accessory virulence genes that were detected in other ST/CC. In contrast to virulence genotype, the antimicrobial resistance genes profiles varied between isolates belonging to the same ST/CC and profile similarities could be observed for isolates from different lineages. MRSA ST398 isolates in particular displayed significant diversity and high content of antimicrobial resistance genes. This was comparable with certain MRSA belonging to other sequence types particularly the equine MRSA ST8. The apparent lack of significant virulence genes among MRSA ST398 strains, demonstrates that the lineage features a unique genetic background but no ST398-specific virulence markers could be identified. PMID:22792335

  3. Comparative genotypic and phenotypic characterisation of methicillin-resistant Staphylococcus aureus ST398 isolated from animals and humans.

    PubMed

    Jamrozy, Dorota M; Fielder, Mark D; Butaye, Patrick; Coldham, Nick G

    2012-01-01

    The high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) ST398 among pigs in certain European countries and North America and its occurrence in other animal species raises a question concerning the molecular mechanisms mediating the success of this lineage. In this study a panel of S. aureus strains belonging to sequence type (ST) 5 (n = 4), ST8 (n = 5), ST15 (n = 5), ST22 (n = 8), clonal complex (CC) 30 (n = 8), CC97 (n = 8), CC130 (n = 4), CC151 (n = 4) and ST398 (n = 18) were screened by DNA microarray and PCR for the carriage of virulence and antimicrobial resistance genes. Isolates belonging to the same sequence type/clonal complex (ST/CC) were found to share similar virulence gene profiles. The ST398 lineage displayed the lowest content of virulence genes, which consisted mainly of genes detected among the majority or all of the analysed lineages. All MRSA ST398 isolates lacked accessory virulence genes that were detected in other ST/CC. In contrast to virulence genotype, the antimicrobial resistance genes profiles varied between isolates belonging to the same ST/CC and profile similarities could be observed for isolates from different lineages. MRSA ST398 isolates in particular displayed significant diversity and high content of antimicrobial resistance genes. This was comparable with certain MRSA belonging to other sequence types particularly the equine MRSA ST8. The apparent lack of significant virulence genes among MRSA ST398 strains, demonstrates that the lineage features a unique genetic background but no ST398-specific virulence markers could be identified. PMID:22792335

  4. A comparative study on low cycle fatigue behaviour of nano and micro Al2O3 reinforced AA2014 particulate hybrid composites

    NASA Astrophysics Data System (ADS)

    Senthilkumar, R.; Arunkumar, N.; Manzoor Hussian, M.

    Aluminium based metal matrix composites have drawn more attraction due to their improved properties in structural applications for the past two decades. The fatigue behaviour of composite materials needs to be studied for their structural applications. In this work, powder metallurgy based aluminium (AA2014) alloy reinforced with micro and nano-sized alumina particles were fabricated and consolidated with the hot extrusion process. The evaluation of mechanical properties in the extruded composite was carried out. This composite was subjected to low cycle fatigue test with a constant strain rate. Scanning Electron Microscope (SEM) and Transmission Electron Microscope (TEM) images were used to evaluate the fatigue behaviour of aluminium-nano composite samples. Enhanced mechanical properties were exhibited by the nano alumina reinforced aluminium composites, when compared to the micron sized alumina reinforced composites. The failure cycle is observed to be higher for the nano alumina reinforced composites when compared with micron sized alumina composites due to a lower order of induced plastic strain.

  5. Comparative Transcriptional Analysis of Human Macrophages Exposed to Animal and Human isolates of Mycobacterium avium subspecies paratuberculosis with Diverse Genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Interactions between Mycobacterium avium subsp. paratuberculosis and host macrophages represent critical early events in the pathogenesis of Johne’s disease. We present here a genome-wide characterization of the transcriptional changes within macrophages in responses to different genotypes of M. par...

  6. Lower response to simeprevir and sofosbuvir in HCV genotype 1 in routine practice compared with clinical trials

    PubMed Central

    Yee, Brittany E; Nguyen, Nghia H; Jin, Minjuan; Lutchman, Glen; Lim, Joseph K; Nguyen, Mindie H

    2016-01-01

    Background High sustained virological response at 12 weeks after end of treatment (SVR12) with 12 weeks of simeprevir and sofosbuvir±ribavirin (SMV+SOF±RBV) has been demonstrated in hepatitis C virus genotype 1 (HCV-1) but is based on limited data. Therefore, we performed a meta-analysis of available data evaluating the effectiveness of SMV+SOF±RBV in HCV-1. Methods We performed a comprehensive literature search in June 2015 to identify randomised controlled trials (RCTs) and observational studies of HCV-1 patients treated with 12 weeks of SMV+SOF±RBV. Original studies with SVR12 data in ≥5 HCV-1 patients were included. We excluded studies on liver transplant recipients and/or patients co-infected with HIV or hepatitis B/D. We estimated pooled effect sizes using a random-effects model and evaluated heterogeneity with Cochrane Q-test, p≤0.10 and I2 statistic ≥50%. Results Pooled SVR12 was 85.6% (CI 81.3% to 89.0%) in 1389 HCV-1 patients from 15 studies. On subgroup analysis, SVR12 was 83.9% (CI 79.4% to 87.5%) in observational studies, which was lower than 93.5% (CI 85.7% to 97.2%) in RCTs. A trend showed SVR12 was higher in mild fibrosis, 93.0% (CI 86.2% to 96.6%) compared with advanced fibrosis, 81.5% (CI 75.7% to 86.1%), OR 2.22 (CI 0.79 to 6.25, p=0.131). There was no significant difference in SVR12 rates between HCV-1a, 89.9% (CI 81.9% to 94.6%) and HCV-1b, 89.0% (CI 78.9% to 94.6%) with OR 1.35 (CI 0.75 to 2.42, p=0.322). The most common pooled side effects were: headache 15.2% (n=55/361), fatigue 12.1% (n=78/646), nausea 9.5% (n=50/527) and rash 9.3% (n=68/728). Conclusions SMV+SOF±RBV is an effective regimen in HCV-1 patients. The SVR12 rate in observational studies was lower than that in RCTs, which may reflect the more diverse patient population in real-world settings. PMID:26966547

  7. High-resolution mapping of genotype-phenotype relationships in cridu chat syndrome using array comparative genomic hybridization

    SciTech Connect

    Zhang, Xiaoxiao; Snijders, Antoine; Segraves, Richard; Zhang,Xiuqing; Niebuhr, Anita; Albertson, Donna; Yang, Huanming; Gray, Joe; Niebuhr, Erik; Bolund, Lars; Pinkel, Dan

    2007-07-03

    We have used array comparative genomic hybridization to map DNA copy-number changes in 94 patients with cri du chat syndrome who had been carefully evaluated for the presence of the characteristic cry, speech delay, facial dysmorphology, and level of mental retardation (MR). Most subjects had simple deletions involving 5p (67 terminal and 12 interstitial). Genotype-phenotype correlations localized the region associated with the cry to 1.5 Mb in distal 5p15.31, between bacterial artificial chromosomes (BACs) containing markers D5S2054 and D5S676; speech delay to 3.2 Mb in 5p15.32-15.33, between BACs containing D5S417 and D5S635; and the region associated with facial dysmorphology to 2.4 Mb in 5p15.2-15.31, between BACs containing D5S208 and D5S2887. These results overlap and refine those reported in previous publications. MR depended approximately on the 5p deletion size and location, but there were many cases in which the retardation was disproportionately severe, given the 5p deletion. All 15 of these cases, approximately two-thirds of the severely retarded patients, were found to have copy-number aberrations in addition to the 5p deletion. Restriction of consideration to patients with only 5p deletions clarified the effect of such deletions and suggested the presence of three regions, MRI-III, with differing effect on retardation. Deletions including MRI, a 1.2-Mb region overlapping the previously defined cri du chat critical region but not including MRII and MRIII, produced a moderate level of retardation. Deletions restricted to MRII, located just proximal to MRI, produced a milder level of retardation, whereas deletions restricted to the still-more proximal MRIII produced no discernible phenotype. However, MR increased as deletions that included MRI extended progressively into MRII and MRIII, and MR became profound when all three regions were deleted.

  8. Identification and Comparative Analysis of MicroRNAs Associated with Low-N Tolerance in Rice Genotypes

    PubMed Central

    Nischal, Lata; Mohsin, Mohd; Khan, Ishrat; Kardam, Hemant; Wadhwa, Asha; Abrol, Yash Pal; Iqbal, Muhammad; Ahmad, Altaf

    2012-01-01

    Background Nitrogen [N] is a critical limiting nutrient for plants and has to be exogenously supplied to many crops, to achieve high yield with significant economic and environmental costs, specifically for rice. Development of low-input nitrogen sustainable crop is necessary for sustainable agriculture. Identification of regulatory elements associated with low-N tolerance is imperative for formulating innovative approaches for developing low-N tolerant crop plants, using gene manipulation. MicroRNAs (miRNAs) are known to play crucial roles in the modulation of gene expression in plants under various environmental conditions. Methodology/Principal Findings MiRNAs associated with low-N tolerance have not been identified so far. In this study, we investigated microarray-based miRNA expression in low-N tolerant and low-N sensitive rice genotypes under low N condition. Expressions of 32 miRNAs differed significantly in the two genotypes. Of these 32 miRNAs, expressions of nine miRNAs were further validated experimentally in leaves as well as in roots. Of these differentially expressed miRNAs, six miRNAs (miR156, miR164, miR528, miR820, miR821 and miR1318) were reported in leaves and four (miR164, miR167, miR168 and miR528) in roots. Target genes of all the 32 miRNAs were predicted, which encode transcription factors, and proteins associated with metabolic processes or stress responses. Expression levels of some of the corresponding miRNA targets were analysed and found to be significantly higher in low N-tolerant genotype than low-N sensitive genotype. These findings suggested that miRNAs played an important role in low-N tolerance in rice. Conclusions/Significance Genome-wide differences in expression of miRNA in low N-tolerant and low N-sensitive rice genotypes were reported. This provides a platform for selection as well as manipulation of genotypes for better N utilization efficiency. PMID:23227161

  9. Correlation of microscopic phenotype with genotype in a formalin-fixed, paraffin-embedded testicular germ cell tumor with universal DNA amplification, comparative genomic hybridization, and interphase cytogenetics.

    PubMed Central

    Speicher, M. R.; Jauch, A.; Walt, H.; du Manoir, S.; Ried, T.; Jochum, W.; Sulser, T.; Cremer, T.

    1995-01-01

    We present a strategy for the evaluation of numerical copy number changes of DNA segments within a solid tumor genome that allows the correlation of microscopic phenotype with genotype in formalin-fixed, paraffin-embedded tumor material. Cells from a human testicular germ cell tumor and adjacent tissue areas with normal seminiferous tubules were selected separately from microscopically analyzed histological tissue sections, and DNA was extracted from the selected areas. After universal DNA amplification, the amplification products were subjected to comparative genomic hybridization. The results confirmed balanced chromosome copy numbers for the normal tissue area, although the analysis of the tumor tissue area revealed numerous gains and losses of chromosome segments. The comparative genomic hybridization results were used to select DNA probes for interphase cytogenetics on serial sections. We conclude that this technique allows the screening of selected tissue areas for numerical DNA alterations, thus enabling a direct phenotype-genotype comparison. Images Figure 1 Figure 2 Figure 4 PMID:7778673

  10. An intervention study demonstrates effects of MC4R genotype on boar taint and performances of growing-finishing pigs.

    PubMed

    Van den Broeke, A; Aluwé, M; Tuyttens, F A M; Ampe, B; Vanhaecke, L; Wauters, J; Janssens, S; Coussé, A; Buys, N; Millet, S

    2015-03-01

    The Asp298Asn polymorphism of the melanocortin-4 receptor (MC4R) in pigs is known to affect economically important traits such as growth rate and backfat thickness. We have assessed the possible use of this polymorphism as a molecular marker to perform genetic selection toward lower boar taint levels without compromising growth performance and carcass and meat quality in commercial boars and gilts. Homozygous boars and gilts of the AA genotype and GG genotype were compared in an intervention study with a 2 × 2 design to assess main effects and possible interactions between sex and genotype. The concentrations of the 3 boar taint compounds androstenone ( = 0.044), skatole ( = 0.049), and indole ( = 0.006) were significantly higher in fat of AA boars compared to GG boars. However, no effect on the sensory analysis of the fat samples could be observed. Between 20 and 115 kg BW, AA pigs showed higher ADFI than GG pigs ( < 0.001). An interaction between genotype and sex was observed for ADG ( = 0.044): AA boars had a significantly higher ADG than GG boars but there was no significant difference between the gilts. Daily lean meat gain tended to be higher in boars compared to gilts ( = 0.051), independent of genotype. Similarly, boars showed higher G:F compared to gilts ( < 0.001), without effect of genotype. Genotype and sex affected several carcass quality parameters but there was no interaction. Pigs of the AA genotype displayed a lower dressing percentage ( = 0.005), lower ham width ( = 0.024), lower muscle thickness ( = 0.011), and higher fat thickness ( < 0.001), resulting in a lower lean meat percentage ( < 0.001) in comparison with GG pigs. Gilts had a significantly higher dressing percentage ( < 0.001), higher muscle thickness ( < 0.001), higher ham width ( < 0.001), and lower ham angle ( < 0.001) compared to boars. Other than the boar taint compounds, meat quality was not affected by genotype. Pork of gilts was darker ( = 0.014) and less exudative during

  11. A Randomized Controlled Trial Comparing the Efficacy of Cyp3a5 Genotype-Based With Body-Weight-Based Tacrolimus Dosing After Living Donor Kidney Transplantation.

    PubMed

    Shuker, N; Bouamar, R; van Schaik, R H N; Clahsen-van Groningen, M C; Damman, J; Baan, C C; van de Wetering, J; Rowshani, A T; Weimar, W; van Gelder, T; Hesselink, D A

    2016-07-01

    Patients expressing the cytochrome P450 (CYP) 3A5 gene require a higher tacrolimus dose to achieve therapeutic exposure compared with nonexpressers. This randomized-controlled study investigated whether adaptation of the tacrolimus starting dose according to CYP3A5 genotype increases the proportion of kidney transplant recipients being within the target tacrolimus predose concentration range (10-15 ng/mL) at first steady-state. Two hundred forty living-donor, renal transplant recipients were assigned to either receive a standard, body-weight-based or a CYP3A5 genotype-based tacrolimus starting dose. At day 3, no difference in the proportion of patients having a tacrolimus exposure within the target range was observed between the standard-dose and genotype-based groups: 37.4% versus 35.6%, respectively; p = 0.79. The proportion of patients with a subtherapeutic (i.e. <10 ng/mL) or a supratherapeutic (i.e. >15 ng/mL) Tac predose concentration in the two groups was also not significantly different. The incidence of acute rejection was comparable between both groups (p = 0.82). Pharmacogenetic adaptation of the tacrolimus starting dose does not increase the number of patients having therapeutic tacrolimus exposure early after transplantation and does not lead to improved clinical outcome in a low immunological risk population. PMID:26714287

  12. Effects of prolactin receptor genotype on the litter size of Mangalica.

    PubMed

    Tempfli, Károly; Farkas, Gergely; Simon, Zsolt; Bali Papp, Agnes

    2011-06-01

    The aim of this study was to detect different alleles of the prolactin receptor (PRLR) gene and to examine their effects on the litter size of the indigenous Hungarian pig, the Mangalica. G1789A single nucleotide polymorphism (SNP) was investigated as a candidate for litter size. Samples from 80 purebred Mangalica sows and data of their 335 litters were provided by Olmos & Tóth Ltd. Hair follicles were used to isolate the required DNA. Allelic discrimination was performed by means of the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method using the AluI restriction enzyme and agarose gel electrophoresis. In the population examined, the A allele was found to be preferable in the Mangalica breed group. The most advantageous AA genotype was the least prevalent (8.75%), while the frequencies of AB and BB were 40% and 51.25%, respectively. Remarkably, the average number of piglets born alive per litter was 1.11 ± 0.39 higher in sows with AA as compared to those with BB genotype. By raising the frequency of the AA genotype, the litter size is likely to increase. However, the effect of PRLR genotypes can differ among pig breeds and even lines. Further studies may be required to observe and estimate possible pleiotropic effects of this polymorphism on other traits. PMID:21665580

  13. Determination of ABO blood group genotypes using the real-time loop-mediated isothermal amplification method

    PubMed Central

    ZHANG, CHAO; ZHU, JUANLI; YANG, JIANGCUN; WAN, YINSHENG; MA, TING; CUI, YALI

    2015-01-01

    ABO genotyping is commonly used in several situations, including blood transfusion, personal identification and disease detection. The present study developed a novel method for ABO genotyping, using loop-mediated isothermal amplification (LAMP). This method allows the simultaneous determination of six ABO genotypes under 40 min at a constant temperature of 62°C. The genotypes of 101 blood samples were determined to be AA (n=6), AO (n=38), BB (n=12), BO (n =29), AB (n=8) and OO (n=8) by the LAMP assay. The results were compared with the phenotypes determined by serological assay and the genotypes determined by direct sequencing, and no discrepancies were observed. This novel and rapid method, with good accuracy and reasonably cost effective, provides a supplement to routine serological ABO typing and may also be useful in other point-of-care testing. PMID:26238310

  14. Allelic frequency and genotypes of prion protein at codon 136 and 171 in Iranian Ghezel sheep breeds

    PubMed Central

    Zadeh, Reza Ashrafi; Omrani, Mir Davood; Ramezani, Fatemeh; Amniattalab, Amir

    2011-01-01

    PrP genotypes at codons 136 and 171 in 120 Iranian Ghezel sheep breeds were studied using allele-specific PCR amplification and compared with the well-known sheep breeds in North America, the United States and Europe. The frequency of V allele and VV genotype at codon 136 of Ghezel sheep breed was significantly lower than AA and AV. At codon 171, the frequency of allele H was significantly lower than Q and R. Despite the similarities of PrP genotypes at codons 136 and 171 between Iranian Ghezel sheep breeds and some of the studied breeds, significant differences were found with others. Planning of effective breeding control and successful eradication of susceptible genotypes in Iranian Ghezel sheep breeds will not be possible unless the susceptibility of various genotypes in Ghezel sheep breeds to natural or experimental scrapie has been elucidated. PMID:21778818

  15. Comparative analysis of caffeoylquinic acids and lignans in roots and seeds among various burdock (Arctium lappa) genotypes with high antioxidant activity.

    PubMed

    Liu, Jingyi; Cai, Yi-Zhong; Wong, Ricky Ngok Shun; Lee, Calvin Kai-Fai; Tang, Sydney Chi Wai; Sze, Stephen Cho Wing; Tong, Yao; Zhang, Yanbo

    2012-04-25

    Caffeoylquinic acids and lignans in the crude extracts of both roots and seeds from different burdock ( Arctium lappa L.) genotypes were simultaneously characterized and systematically compared by LC-MS and matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (MALDI-QIT-TOF MS), and their antioxidant activities were also investigated. A total of 14 lignans were identified in burdock seeds and 12 caffeoylquinic acids in burdock roots. High levels of caffeoylquinic acids were also detected in burdock seeds, but only trace amounts of lignans were found in burdock roots. Burdock seeds contained higher concentrations of lignans and caffeoylquinic acids than burdock roots. Quantitative analysis of caffeoylquinic acids and lignans in roots and seeds of various burdock genotypes was reported for the first time. Great variations in contents of both individual and total phenolic compounds as well as antioxidant activities were found among different genotypes. Burdock as a root vegetable or medicinal plants possessed considerably stronger antioxidant activity than common vegetables and fruits. PMID:22497441

  16. Investigations on the efficacy of routinely used phenotypic methods compared to genotypic approaches for the identification of staphylococcal species isolated from companion animals in Irish veterinary hospitals

    PubMed Central

    2013-01-01

    Background Identification of Staphylococci to species level in veterinary microbiology is important to inform therapeutic intervention and management. We report on the efficacy of three routinely used commercial phenotypic methods for staphylococcal species identification, namely API Staph 32 (bioMérieux), RapID (Remel) and Staph-Zym (Rosco Diagnostica) compared to genotyping as a reference method to identify 52 staphylococcal clinical isolates (23 coagulase positive; 29 coagulase negative) from companion animals in Irish veterinary hospitals. Results Genotyping of a 412 bp fragment of the staphylococcal tuf gene and coagulase testing were carried out on all 52 veterinary samples along with 7 reference strains. In addition, genotyping of the staphylococcal rpoB gene, as well as PCR-RFLP of the pta gene, were performed to definitively identify members of the Staphylococcus intermedius group (SIG). The API Staph 32 correctly identified all S. aureus isolates (11/11), 83% (10/12) of the SIG species, and 66% (19/29) of the coagulase negative species. RapID and Staph-Zym correctly identified 61% (14/23) and 0% (0/23) respectively of the coagulase-positives, and 10% (3/29) and 3% (1/29) respectively of the coagulase-negative species. Conclusions Commercially available phenotypic species identification tests are inadequate for the correct identification of both coagulase negative and coagulase positive staphylococcal species from companion animals. Genotyping using the tuf gene sequence is superior to phenotyping for identification of staphylococcal species of animal origin. However, use of PCR-RFLP of pta gene or rpoB sequencing is recommended as a confirmatory method for discriminating between SIG isolates. PMID:23635328

  17. Standardized ileal digestibility of amino acids in eight genotypes of soft winter wheat fed to growing pigs.

    PubMed

    Rosenfelder, P; Mosenthin, R; Spindler, H K; Jørgensen, H; Bach Knudsen, K E; Sauer, N; Htoo, J K; Eklund, M

    2015-03-01

    A study with growing pigs was conducted to determine the chemical composition and standardized ileal digestibility (SID) of CP and AA of 8 wheat genotypes that have recently been added to the German Descriptive Variety List. These genotypes included Tabasco, KWS Erasmus, Tobak, Skalmeje, Mulan, Event, Tommi, and Adler. The 8 genotypes were grown under identical environmental conditions on the same site, and they were harvested and processed under the same conditions. Nine barrows with an initial BW of 32 ± 2 kg were surgically fitted with simple ileal T-cannulas and allotted to a row-column design with 9 pigs and 8 periods of 6 d each. Wheat was the sole dietary source of CP and AA. Among the 8 wheat genotypes, contents of CP ranged from 10.9 to 13.3% (as-fed basis), whereas contents of total nonstarch polysaccharides ranged from 8.0 to 9.4% (as-fed basis). The SID of CP in the 8 genotypes ranged from 83 to 87%, with greatest ( = 0.01) values for Event and lowest ( = 0.01) for all other wheat genotypes. Intermediate SID of CP values were obtained for Adler and KWS Erasmus. For Lys, greater ( < 0.05) SID was observed in Adler (73%) and KWS Erasmus (74%) in comparison to Tommi, Tobak, and Mulan (69%). Adler had greater SID of Met (88%; = 0.01) when compared to Tabasco (86%); Tobak, Skalmeje, and Mulan (85%); and Tommi (84%). Among the 8 wheat genotypes, standardized ileal digestible content (cSID) of CP followed total CP content and ranged from 9.1 to 11.3% (as-fed basis). Standardized ileal digestible content of both CP and AA were greater ( < 0.001) in Adler compared to all other genotypes. For most AA, Tabasco had the lowest ( < 0.001; except for His, Trp, Asp, and Cys) cSID values of all wheat genotypes. The cSID of CP decreased ( < 0.001) as the starch content in the 8 wheat genotypes increased, but cSID of CP increased ( < 0.001) as the CP content in the 8 genotypes increased. Because SID and cSID of CP and most AA increased ( < 0.05) with lower test weight

  18. Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress.

    PubMed

    Bai, Bin; Wu, Jun; Sheng, Wen-Tao; Zhou, Bo; Zhou, Li-Jie; Zhuang, Wen; Yao, Dong-Ping; Deng, Qi-Yun

    2015-01-01

    Rice is highly sensitive to cold stress during reproductive developmental stages, and little is known about the mechanisms of cold responses in rice anther. Using the HiSeq™ 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Pei'ai64S) were analyzed at the fertility sensitive stage under cold stress. Approximately 243 million clean reads were obtained from four libraries and aligned against the oryza indica genome and 1497 and 5652 differentially expressed genes (DEGs) were identified in P64S and Y58S, respectively. Both gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for these DEGs. Functional classification of DEGs was also carried out. The DEGs common to both genotypes were mainly involved in signal transduction, metabolism, transport, and transcriptional regulation. Most of the DEGs were unique for each comparison group. We observed that there were more differentially expressed MYB (Myeloblastosis) and zinc finger family transcription factors and signal transduction components such as calmodulin/calcium dependent protein kinases in the Y58S comparison group. It was also found that ribosome-related DEGs may play key roles in cold stress signal transduction. These results presented here would be particularly useful for further studies on investigating the molecular mechanisms of rice responses to cold stress. PMID:25993302

  19. Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress

    PubMed Central

    Bai, Bin; Wu, Jun; Sheng, Wen-Tao; Zhou, Bo; Zhou, Li-Jie; Zhuang, Wen; Yao, Dong-Ping; Deng, Qi-Yun

    2015-01-01

    Rice is highly sensitive to cold stress during reproductive developmental stages, and little is known about the mechanisms of cold responses in rice anther. Using the HiSeq™ 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Pei’ai64S) were analyzed at the fertility sensitive stage under cold stress. Approximately 243 million clean reads were obtained from four libraries and aligned against the oryza indica genome and 1497 and 5652 differentially expressed genes (DEGs) were identified in P64S and Y58S, respectively. Both gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for these DEGs. Functional classification of DEGs was also carried out. The DEGs common to both genotypes were mainly involved in signal transduction, metabolism, transport, and transcriptional regulation. Most of the DEGs were unique for each comparison group. We observed that there were more differentially expressed MYB (Myeloblastosis) and zinc finger family transcription factors and signal transduction components such as calmodulin/calcium dependent protein kinases in the Y58S comparison group. It was also found that ribosome-related DEGs may play key roles in cold stress signal transduction. These results presented here would be particularly useful for further studies on investigating the molecular mechanisms of rice responses to cold stress. PMID:25993302

  20. Co-dependence of genotype and dietary protein intake to affect expression on amino acid/peptide transporters in porcine skeletal muscle.

    PubMed

    Liu, Y; Kong, X; Li, F; Tan, B; Li, Y; Duan, Y; Yin, Y; He, J; Hu, C; Blachier, F; Wu, Guoyao

    2016-01-01

    A total of 96 barrows (48 pure-bred Bama mini-pigs representing fatty genotype, and 48 Landrace pigs representing lean genotype) were randomly assigned to either a low- or adequate-protein treatment diet. The experimental period commenced at 5 weeks of age and extended to the finishing period. After euthanasia, blood and skeletal muscle samples were collected from pigs at the nursery, growing, and finishing phases. Our results indicate that the concentrations of free AAs in the plasma and muscle decreased as the age of the pigs increased. In addition, a strain × growth phase interaction (P < 0.05) was observed for the free AA pool in the plasma and muscle. The low-protein diet upregulated (P < 0.05) the mRNA levels for T1R1/T1R3 involved in glutamate binding, but downregulated (P < 0.05) the mRNA levels for PAT1, PAT2, and ASCT2, which transport neutral AAs into muscles. Bama mini-pigs had higher (P < 0.05) mRNA levels for LAT1, SNAT2, and EAAC1, but a lower (P < 0.05) mRNA level for PepT1, compared with Landrace pigs. Collectively, our findings indicate that adequate provision of dietary protein plays an important role in regulating profiles of free AA pools and expression of key AA/peptide transporters/transceptors in a genotype- and tissue-specific manner. PMID:26255284

  1. Vitamin D-related gene polymorphisms do not influence the outcome and serum vitamin D level in pegylated interferon/ribavirin therapy combined with protease inhibitor for patients with genotype 1b chronic hepatitis C.

    PubMed

    Arai, Taeang; Atsukawa, Masanori; Tsubota, Akihito; Kondo, Chisa; Shimada, Noritomo; Abe, Hiroshi; Itokawa, Norio; Nakagawa, Ai; Okubo, Tomomi; Aizawa, Yoshio; Iwakiri, Katsuhiko

    2015-11-01

    Although several vitamin D-related gene polymorphisms were reported to affect the outcome of pegylated interferon/ribavirin (PR) therapy in chronic hepatitis C patients, there are no reports on the impact of the vitamin D-related gene polymorphisms in PR therapy combined with protease inhibitor (PI). Vitamin D-related gene polymorphisms were determined in 177 genotype 1b-infected chronic hepatitis C patients who received 12 weeks of PR therapy with telaprevir, a first-generation PI, followed by 12 weeks of PR therapy. The sustained virologic response (SVR) rate was 83.1% (147 of 177 patients). The frequencies of vitamin D-related gene polymorphisms were: 83 non-TT and 94 TT genotypes for GC, 97 non-AA and 80 AA genotypes for DHCR7, 151 non-AA and 26 AA genotypes for CYP2R1, 162 non-GG and 15 GG genotypes for CYP27B1, and 105 non-GG and 72 GG genotypes for VDR gene. Multivariate analysis extracted IL28B TT genotype (P = 2.05 × 10(-6)) and serum 25(OH) D3 level (P = 0.024) as independent factors contributing to the achieving of SVR. The SVR rate in IL28B TT genotype patients with serum 25(OH) D3 level of < 25 ng/ml was significantly low compared to other patients. None of the vitamin D-related gene polymorphisms affected the treatment outcome and serum 25(OH) D3 level. In conclusions, the IL28B polymorphism and serum 25(OH) D3 level contributed significantly and independently to SVR in PR combined with PI for genotype 1b-infected chronic hepatitis C patients. However, none of vitamin D-related gene polymorphisms had an impact on the treatment outcome and serum 25(OH) D3 level. PMID:25964133

  2. Methylenetetrahydrofolate reductase genotypes and haplotypes associated with susceptibility to colorectal cancer in an eastern Chinese Han population.

    PubMed

    Li, H; Xu, W L; Shen, H L; Chen, Q Y; Hui, L L; Long, L L; Zhu, X L

    2011-01-01

    Methylenetetrahydrofolate reductase (MTHFR) plays an important role in folate metabolism and is involved in DNA synthesis, DNA repair and DNA methylation. The two common functional polymorphisms of MTHFR, C677T and A1298C have been associated with several diseases, including cancer. We made a case-control study to analyze a possible association of MTHFR gene polymorphisms C677T and A1298C with risk for colorectal cancer in an eastern Chinese Han population of 137 patients with a confirmed histopathological diagnosis of CRC and 145 age- and gender-matched controls with no history of cancer. DNA was isolated from peripheral blood samples and the genotypes were determined by PCR-RFLP. The concentrations of folate in plasma were measured by chemiluminescence immunoassay. The MTHFR 677TT genotype had a protective effect against colorectal cancer, with an odds ratio (OR) = 0.467 (95% confidence interval (CI) = 0.225-0.966). The 1298CC genotype was significantly correlated with a reduced risk of colorectal cancer (OR = 0.192; 95%CI = 0.040-0.916). Compared with the MTHFR 677CC and MTHFR 1298 AA genotypes, for individuals who carried both MTHFR 677CC and 1298CC genotypes, the OR of colorectal cancer was 0.103 (95%CI = 0.012-0.900); among individuals who carried both MTHFR 677TT and 1298AC genotypes, the OR for risk of colorectal cancer was 0.169 (95%CI = 0.044-0.654). MTHFR 677TT+CT genotypes had a significantly lower plasma folate concentration than those with the MTHFR 677CC genotype. MTHFR 1298AC+CC genotypes had a lower plasma folate concentration than those with the MTHFR 1298AA genotype (P < 0.05). In conclusion, subjects with the MTHFR 677TT and MTHFR 1298CC genotypes appeared to have a significantly lower risk for colorectal cancer. MTHFR haplotypes 677CC/1298CC and 677TT/1298AC were less common in cases than in controls. These haplotypes, when compared to the most common haplotype 677CC/1298AA, were associated with a decreased risk for colorectal cancer. We

  3. Identification and Comparative Analysis of Cadmium Tolerance-Associated miRNAs and Their Targets in Two Soybean Genotypes

    PubMed Central

    Ma, Qibin; Huang, Yian; Wang, Peng; Zhang, Jie; Nian, Hai; Yang, Cunyi

    2013-01-01

    MicroRNAs (miRNAs) play crucial roles in regulating the expression of various stress responses genes in plants. To investigate soybean (Glycine max) miRNAs involved in the response to cadmium (Cd), microarrays containing 953 unique miRNA probes were employed to identify differences in the expression patterns of the miRNAs between different genotypes, Huaxia3 (HX3, Cd-tolerant) and Zhonghuang24 (ZH24, Cd-sensitive). Twenty six Cd-responsive miRNAs were identified in total. Among them, nine were detected in both cultivars, while five were expressed only in HX3 and 12 were only in ZH24. The expression of 16 miRNAs was tested by qRT-PCR and most of the identified miRNAs were found to have similar expression patterns with microarray. Three hundred and seventy six target genes were identified for 204 miRNAs from a mixture degradome library, which was constructed from the root of HX3 and ZH24 with or without Cd treatment. Fifty five genes were identified to be cleaved by 14 Cd-responsive miRNAs. Gene ontology (GO) annotations showed that these target transcripts are implicated in a broad range of biological processes. In addition, the expression patterns of ten target genes were validated by qRT-PCR. The characterization of the miRNAs and the associated target genes in response to Cd exposure provides a framework for understanding the molecular mechanism of heavy metal tolerance in plants. PMID:24363811

  4. Comparative Analysis of Muscle Transcriptome between Pig Genotypes Identifies Genes and Regulatory Mechanisms Associated to Growth, Fatness and Metabolism

    PubMed Central

    Ayuso, Miriam; Fernández, Almudena; Núñez, Yolanda; Benítez, Rita; Isabel, Beatriz; Barragán, Carmen; Fernández, Ana Isabel; Rey, Ana Isabel; Medrano, Juan F.; Cánovas, Ángela; González-Bulnes, Antonio; López-Bote, Clemente; Ovilo, Cristina

    2015-01-01

    Iberian ham production includes both purebred (IB) and Duroc-crossbred (IBxDU) Iberian pigs, which show important differences in meat quality and production traits, such as muscle growth and fatness. This experiment was conducted to investigate gene expression differences, transcriptional regulation and genetic polymorphisms that could be associated with the observed phenotypic differences between IB and IBxDU pigs. Nine IB and 10 IBxDU pigs were slaughtered at birth. Morphometric measures and blood samples were obtained and samples from Biceps femoris muscle were employed for compositional and transcriptome analysis by RNA-Seq technology. Phenotypic differences were evident at this early age, including greater body size and weight in IBxDU and greater Biceps femoris intramuscular fat and plasma cholesterol content in IB newborns. We detected 149 differentially expressed genes between IB and IBxDU neonates (p < 0.01 and Fold-Change > 1. 5). Several were related to adipose and muscle tissues development (DLK1, FGF21 or UBC). The functional interpretation of the transcriptomic differences revealed enrichment of functions and pathways related to lipid metabolism in IB and to cellular and muscle growth in IBxDU pigs. Protein catabolism, cholesterol biosynthesis and immune system were functions enriched in both genotypes. We identified transcription factors potentially affecting the observed gene expression differences. Some of them have known functions on adipogenesis (CEBPA, EGRs), lipid metabolism (PPARGC1B) and myogenesis (FOXOs, MEF2D, MYOD1), which suggest a key role in the meat quality differences existing between IB and IBxDU hams. We also identified several polymorphisms showing differential segregation between IB and IBxDU pigs. Among them, non-synonymous variants were detected in several transcription factors as PPARGC1B and TRIM63 genes, which could be associated to altered gene function. Taken together, these results provide information about candidate

  5. AAS 227: Day 1

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    The mission was featured on the front pages of 450 newspapers worldwide on every single continent (including Antartica!)New Horizons reached the Moon in9 HOURSafter launch (compared to the ~3 days it took the Apollo missions)The mission controllers were aiming for a 100km window of space all the way from EarthThere was a window of ~400seconds which the probe had to arrive within the probe arrived90 seconds early! Putting tardy astronomers everywhere to shame.Charon was the only satellite of Pluto known at the time of the mission proposalThe canyon found on Charon is not only bigger than the Grand Canyon but bigger than Mariner Valley on Mars which is already4000 km (2500 mi) long and reaches depths of up to 7 km (4 mi)!Charons surface. Tectonic feature runs about 1500 km, around 10 km deep. Eat it, Mars. #aas227 pic.twitter.com/blewwJaXEn Danny Barringer (@HeavyFe_H) January 5, 2016The mountains ringing the Sputnik Planum (aka the heart of Pluto) are over 4km high and are snow capped with methane icePlutos mountain ranges. Means surface nitrogen layer is thin, probably water ice according to @AlanStern. #aas227 pic.twitter.com/0yyHZvpBOE Danny Barringer (@HeavyFe_H) January 5, 2016Plutos atmosphere has a dozendistincthaze layers but how they arecreated is a mystery#aas227 hazes on Pluto wow pic.twitter.com/VPx99ZhPj1 Lisa StorrieLombardi (@lisajsl) January 5, 2016Alan also spoke about the future of New Horizons there is a new mission proposal for a fly by of a Kuiper Belt object 2014MU69 in Jan 2019 which should give us a better understanding of this icy frontier at the edge ofthe Solar System. As a parting gift Alan playedthemost gorgeously detailed fly over video of Plutos surface that had all in the room melting into their flip flops. Its safe to say that the whole room is now Pluto-curious and wondering whether a change of discipline is in order!Press Conference: Black Holes and Exoplanets (by Susanna Kohler)This morning marked the first press conference of the meeting

  6. Clinical severity of pediatric respiratory illness with enterovirus D68 compared with rhinovirus or other enterovirus genotypes

    PubMed Central

    Mertz, Dominik; Alawfi, Abdulsalam; Pernica, Jeffrey M.; Rutherford, Candy; Luinstra, Kathy; Smieja, Marek

    2015-01-01

    Background: Enterovirus D68 (EV-D68) resulted in a reported increase in the number of children needing hospital or critical care admission because of respiratory insufficiency during 2014. It remains unclear, however, whether EV-D68 infections were more severe than rhinovirus or non–EV-D68 enterovirus infections. Methods: We evaluated consecutive children presenting to a pediatric hospital between Aug. 1 and Oct. 31, 2014, with positive nasopharyngeal swabs for rhinovirus or enterovirus that were sent automatically for EV-D68 testing. We compared characteristics and outcomes of patients with EV-D68 with those with rhinovirus or non–EV-D68 enterovirus in a matched cohort study. Results: A total of 93/297 (31.3%) of rhinovirus or enterovirus samples tested positive for EV-D68, and it was possible to compare 87 matched pairs. Children with EV-D68 infection were more likely to have difficulty breathing (odds ratio [OR] 3.00, 95% confidence interval [CI] 1.47–6.14). There was no significant difference in admission to the critical care unit or death among children with EV-D68 infection compared with those with other rhinovirus or enterovirus infections (adjusted OR 1.47, 95% CI 0.61–3.52). Children with EV-D68 infection were more often admitted to hospital, but not significantly so (adjusted OR 2.29, 95% CI 0.96–5.46). Interpretation: Enterovirus D68 seems to be a more virulent pulmonary pathogen than rhinovirus or non–EV-D68 enterovirus, but we did not find a significant difference in death or need for critical care. PMID:26464137

  7. Comparative sensitivity, mechanisms, and whole plant physiological implications of responses of loblolly pine genotypes to ozone and acid deposition

    SciTech Connect

    McLaughlin, S.B.; Adams, M.B.; Edwards, N.T.; Hanson, P.J.; Layton, P.A.; O'Neill, E.G.; Roy, W.K.

    1988-09-01

    A quantitative and mechanistic basis for evaluating the potential effects of atmospheric pollutants on physiology and growth of seedlings of loblolly pine, an important timber species in southern commercial forests, was evaluated in laboratory and controlled field studies. Fifty-three half-sib families of loblolly pine were examined. Primary objectives were to (1) quantify differences in growth responses of these 53 half-sib families to the individual and interactive effects of simulated acid rain and ozone in the field, (2) characterize the physiological basis of observed responses in field and laboratory studies, (3) compare and contrast results obtained with similar experimental protocols in field and laboratory approaches, and (4) develop experimental protocols for quantifying physiological and growth responses of large trees in the field. 152 refs., 41 figs., 42 tabs.

  8. Comparative studies on pheno- and genotypic properties of Staphylococcus aureus isolated from bovine subclinical mastitis in central Java in Indonesia and Hesse in Germany.

    PubMed

    Salasia, Siti Isrina Oktavia; Khusnan, Zaini; Lammler, Christoph; Zschock, Michael

    2004-06-01

    In the present study, 35 Staphylococcal strain isolated from milk samples of 16 cows from eight farms of three different geographic locations in Central Java, Indonesia, and from milk samples of 19 cows from 19 farms of different geographic locations in Hesse, Germany, were compared pheno- and genotypically. On the basis of cultural and biochemical properties as well as by amplification of the 23S rRNA specific to Staphylococcus aureus, all isolates could be identified as S. aureus. In addition, all S. aureus isolates harboured the genes clfA and coa encoding staphylococcal clumping factor and coagulase, and the gene segments encoding the immunoglobulin G binding region and the X-region of protein A gene spa. By PCR amplification, the genes seb, seg, seh, and sei was observed for the S. aureus cultures isolated in Central Java, Indonesia and the genes sec, sed, seg, seh, sei, sej and tst for the S. aureus cultures isolated in Hesse, Germany. None of the S. aureus of both origins harboured the genes sea, see, eta and etb. All isolates were additionally positive for the genes nuc, fnbA, hla, and set1. The gene hlb was found for 6 cultures from Central Java, Indonesia and 16 cultures from Hesse, Germany. However, the gene fnbB and the gene segments cnaA and cnaB were not present among the strains isolated in Central Java, Indonesia and rare among the strains isolated in Hesse, Germany. It was of interest that most of the S. aureus isolated in Central Java, Indonesia harboured the gene cap5 and most of the strains isolated in Hesse, Germany the gene cap8. The phenotypic and genotypic results of the present study might help to understand the distribution of prevalent S. aureus clones among bovine mastitis isolates of both countries and might help to control S. aureus infections in dairy herds. PMID:15192336

  9. Development and Validation of a Comparative Genomic Fingerprinting Method for High-Resolution Genotyping of Campylobacter jejuni

    PubMed Central

    Ross, Susan L.; Mutschall, Steven K.; MacKinnon, Joanne M.; Roberts, Michael J.; Buchanan, Cody J.; Kruczkiewicz, Peter; Jokinen, Cassandra C.; Thomas, James E.; Nash, John H. E.; Gannon, Victor P. J.; Marshall, Barbara; Pollari, Frank; Clark, Clifford G.

    2012-01-01

    Campylobacter spp. are a leading cause of bacterial gastroenteritis worldwide. The need for molecular subtyping methods with enhanced discrimination in the context of surveillance- and outbreak-based epidemiologic investigations of Campylobacter spp. is critical to our understanding of sources and routes of transmission and the development of mitigation strategies to reduce the incidence of campylobacteriosis. We describe the development and validation of a rapid and high-resolution comparative genomic fingerprinting (CGF) method for C. jejuni. A total of 412 isolates from agricultural, environmental, retail, and human clinical sources obtained from the Canadian national integrated enteric pathogen surveillance program (C-EnterNet) were analyzed using a 40-gene assay (CGF40) and multilocus sequence typing (MLST). The significantly higher Simpson's index of diversity (ID) obtained with CGF40 (ID = 0.994) suggests that it has a higher discriminatory power than MLST at both the level of clonal complex (ID = 0.873) and sequence type (ID = 0.935). High Wallace coefficients obtained when CGF40 was used as the primary typing method suggest that CGF and MLST are highly concordant, and we show that isolates with identical MLST profiles are comprised of isolates with distinct but highly similar CGF profiles. The high concordance with MLST coupled with the ability to discriminate between closely related isolates suggests that CFG40 is useful in differentiating highly prevalent sequence types, such as ST21 and ST45. CGF40 is a high-resolution comparative genomics-based method for C. jejuni subtyping with high discriminatory power that is also rapid, low cost, and easily deployable for routine epidemiologic surveillance and outbreak investigations. PMID:22170908

  10. AAS 227: Day 3

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    many orbits has made it a powerhouse for learning about the temperatures, atmospheres, and orbits of exoplanets. The list of examples that Fazio provided included the first global temperature map of an exoplanet (HD 189733b), the detection of the closest transiting exoplanet (HD 219134b), and the measurement of thermal emission from a super-Earth (55 Cnc e). Spitzers large distance from the Earth (specifically, the ground-based telescopes on Earth) even allowed astronomers to observe an exoplanet via gravitational microlensing using a special technique called space-based parallax.Spitzer has also been extremely useful for observing everything from Solar System scales (such as the enormous infrared dust ring around Saturn) to galactic structures. Comparing images of galaxies observed at visible wavelengths with Spitzer images of the same galaxies at infrared wavelengths has allowed us to probe the structure and composition of galaxies at a new level.Astronomers have also used Spitzer to explore the evolution of stars. Thanks to its infrared detectors, Spitzer can look through large clouds of dust that are opaque at visible wavelengths, and observe young stellar objects in their birth environments. Cosmologists can use Spitzer to study the early universe and the formation of galaxies over twelve billion years ago. Fazio used all of these examples and more to demonstrate that Spitzer has truly changed our understanding of the universe.Climate Change for Astronomers (Meredith Rawls)Every astronomer at #aas227 wants to learn about climate change! WOW this room is ridiculously full. pic.twitter.com/ud9an0gLJG Meredith Rawls (@merrdiff) January 7, 2016The second half of the session was a presentation by Doug Duncan featuring an activity from his 101-level college course. He uses climate change as a way to teach critical thinking and scientific reasoning. Members of the audience were walked through an exercise that included interpreting plots of changing surface temperatures

  11. Section AA Pre2004 Fire, Section AA 2009, Section AA, South ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Section A-A Pre-2004 Fire, Section A-A 2009, Section A-A, South Elevation - Boston & Maine Railroad, Berlin Branch Bridge #148.81, Formerly spanning Moose Brook at former Boston & Maine Railroad, Gorham, Coos County, NH

  12. AAS 227: Day 1

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    The mission was featured on the front pages of 450 newspapers worldwide on every single continent (including Antartica!)New Horizons reached the Moon in9 HOURSafter launch (compared to the ~3 days it took the Apollo missions)The mission controllers were aiming for a 100km window of space all the way from EarthThere was a window of ~400seconds which the probe had to arrive within the probe arrived90 seconds early! Putting tardy astronomers everywhere to shame.Charon was the only satellite of Pluto known at the time of the mission proposalThe canyon found on Charon is not only bigger than the Grand Canyon but bigger than Mariner Valley on Mars which is already4000 km (2500 mi) long and reaches depths of up to 7 km (4 mi)!Charons surface. Tectonic feature runs about 1500 km, around 10 km deep. Eat it, Mars. #aas227 pic.twitter.com/blewwJaXEn Danny Barringer (@HeavyFe_H) January 5, 2016The mountains ringing the Sputnik Planum (aka the heart of Pluto) are over 4km high and are snow capped with methane icePlutos mountain ranges. Means surface nitrogen layer is thin, probably water ice according to @AlanStern. #aas227 pic.twitter.com/0yyHZvpBOE Danny Barringer (@HeavyFe_H) January 5, 2016Plutos atmosphere has a dozendistincthaze layers but how they arecreated is a mystery#aas227 hazes on Pluto wow pic.twitter.com/VPx99ZhPj1 Lisa StorrieLombardi (@lisajsl) January 5, 2016Alan also spoke about the future of New Horizons there is a new mission proposal for a fly by of a Kuiper Belt object 2014MU69 in Jan 2019 which should give us a better understanding of this icy frontier at the edge ofthe Solar System. As a parting gift Alan playedthemost gorgeously detailed fly over video of Plutos surface that had all in the room melting into their flip flops. Its safe to say that the whole room is now Pluto-curious and wondering whether a change of discipline is in order!Press Conference: Black Holes and Exoplanets (by Susanna Kohler)This morning marked the first press conference of the meeting

  13. Anal Cytology and Human Papillomavirus Genotyping in Women With a History of Lower Genital Tract Neoplasia Compared With Low-Risk Women

    PubMed Central

    Robison, Katina; Cronin, Beth; Bregar, Amy; Luis, Christine; DiSilvestro, Paul; Schechter, Steven; Pisharodi, Latha; Raker, Christina; Clark, Melissa

    2016-01-01

    OBJECTIVE To compare the prevalence of abnormal anal cytology and high-risk human papillomavirus (HPV) among women with a history of HPV-related genital neoplasia with women without a history of HPV-related genital neoplasia. METHODS A cross-sectional cohort study was performed from December 2012 to February 2014. Women were recruited from outpatient clinics at an academic medical center. Women with a history of high-grade cervical, vulvar, or vaginal cytology, dysplasia, or cancer were considered the high-risk group. Women with no history of high-grade anogenital dysplasia or cancer were considered the low-risk group. Human immunodeficiency virus–positive women were excluded. Anal cytology and HPV genotyping were performed. Women with abnormal anal cytology were referred for high-resolution anoscopy. RESULTS There were 190 women in the high-risk group and 83 in the low-risk group. The high-risk group was slightly older: 57 years compared with 47 years (P=.045); 21.7% of low-risk women had abnormal anal cytology compared with 41.2% of high-risk women (P=.006). High-risk HPV was detected in the anal canal of 1.2% of the low-risk group compared with 20.8% of the high-risk group (P<.001). Among women who underwent anoscopy, no anal dysplasia was detected in the low-risk group, whereas 13.4% in the high-risk group had anal dysplasia with 4.2% having anal intraepithelial neoplasia 2 or greater (P<.001). CONCLUSION Human immunodeficiency virus–negative women with a history of lower genital tract neoplasia are more likely to have positive anal cytology, anal high-risk HPV, and anal intraepithelial neoplasia. Anal cancer screening should be considered for these high-risk women. PMID:26551180

  14. Novel SNP identification in exon 3 of HSP90AA1 gene and their association with heat tolerance traits in Karan Fries (Bos taurus × Bos indicus) cows under tropical climatic condition.

    PubMed

    Kumar, Rakesh; Gupta, Ishwar Dayal; Verma, Archana; Singh, Sohan Vir; Verma, Nishant; Vineeth, M R; Magotra, Ankit; Das, Ramendra

    2016-04-01

    Heat shock proteins (HSPs) act as molecular chaperones those are preferentially transcribed in respose to heat stress and the polymorphism in HSP genes associated with heat tolerance traits in cows. HSP90AA1 gene has been mapped on Bos taurus autosome 21 (BTA-21) and spans nearly 5368 bp comprising of 11 exons out of which the first exon does not translate. The present study was done on Karan Fries (5/8 HF × 3/8 Tharparkar) cows reared in tropical climate with the objectives of identifying single-nucleotide polymorphisms (SNPs) in targeted regions (exon 3) of HSP90AA1 gene and analyzing their association with heat tolerance traits in Karan Fries cows. Respiration rate (RR) and rectal temperature (RT) were recorded once daily for four consecutive days during probable extreme hours in different seasons or temperature humidity index (THI), viz., winter, spring, and summer. For detecting single-nucleotide polymorphisms, sequence data were analyzed using BioEdit software (version 7.2). Comparative sequence analysis of HSP90AA1 gene showed point mutation, viz., g.1209A>G (exon 3) as compared to Bos taurus (NCBI Ref Seq: AC_000178.1). Association analysis indicated that THI was influenced (P < 0.01) by RR, RT, and HTC. Similarly, SNPs at locus g.1209A>G were categorized into three genotypes, i.e., AA, AG, and GG, and the least squares means (LSMEANS) of RR, RT, and HTC for GG (homozygous) genotype were significantly lower (P < 0.01) than AA (homozygous) and AG (heterozygous) genotypes. These findings may partly suggest that cows with GG genotypes were favored for heat tolerance trait, which can be used as an aid to selection for thermo-tolerance Karan Fries cows for better adaptation in subtropical and tropical hot climate. PMID:26898694

  15. The AAS Workforce Survey

    NASA Astrophysics Data System (ADS)

    Postman, Marc; Norman, D. J.; Evans, N. R.; Ivie, R.

    2014-01-01

    The AAS Demographics Committee, on behalf of the AAS, was tasked with initiating a biennial survey to improve the Society's ability to serve its members and to inform the community about changes in the community's demographics. A survey, based in part on similar surveys for other scientific societies, was developed in the summer of 2012 and was publicly launched in January 2013. The survey randomly targeted 2500 astronomers who are members of the AAS. The survey was closed 4 months later (April 2013). The response rate was excellent - 63% (1583 people) completed the survey. I will summarize the results from this survey, highlighting key results and plans for their broad dissemination.

  16. Serum Proteome Changes in Healthy Subjects with Different Genotypes of NOS1AP in the Chinese Population

    PubMed Central

    Jiang, Feng; Wang, Congrong; Li, Rongxia; Hu, Cheng; Zhang, Rong; Fang, Qichen; Bao, Yuqian; Xiang, Kunsan; Zeng, Rong; Jia, Weiping

    2013-01-01

    Type 2 diabetes and its chronic complications have become a worldwide epidemic nowadays. However, its molecular mechanism is still unknown. We have previously identified a novel variant rs12742393 of NOS1AP for type 2 diabetes susceptibility in the Chinese population. In this study, we analyzed the total serum profiling among three genotypes of rs12742393 to discover potential crosstalk under the variant and the disease through proteomic analyses for the first time. We used OFFGEL peptide fractionation, LC-MS/MS analysis, and label-free quantification to profile the fasting human serum samples of the genotypes in rs12742393 (n = 4, for CC, AC, and AA, resp.). Four proteins were identified, including apoA4, alpha1-ACT, HABP2, and keratin 10, with blood levels changed significantly between CC and AA homozygotes of rs12742393. Compared with AA group, the levels of apoA4 increased (P = 0.000265), whereas the concentration of alpha1-ACT, HABP2, and keratin 10 decreased in CC group (P = 0.011116, 0.021175, and 0.015661, resp.). Then we selected additional fasting serum samples for ELISA and western blot validation. However, no significant differences were identified by neither ELISA nor western blot (P > 0.05). The protein profiling changes between the genotypes of rs12742393 indicated that this SNP might play a role in the development of type 2 diabetes. PMID:23671866

  17. AAS 227: Day 3

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    many orbits has made it a powerhouse for learning about the temperatures, atmospheres, and orbits of exoplanets. The list of examples that Fazio provided included the first global temperature map of an exoplanet (HD 189733b), the detection of the closest transiting exoplanet (HD 219134b), and the measurement of thermal emission from a super-Earth (55 Cnc e). Spitzers large distance from the Earth (specifically, the ground-based telescopes on Earth) even allowed astronomers to observe an exoplanet via gravitational microlensing using a special technique called space-based parallax.Spitzer has also been extremely useful for observing everything from Solar System scales (such as the enormous infrared dust ring around Saturn) to galactic structures. Comparing images of galaxies observed at visible wavelengths with Spitzer images of the same galaxies at infrared wavelengths has allowed us to probe the structure and composition of galaxies at a new level.Astronomers have also used Spitzer to explore the evolution of stars. Thanks to its infrared detectors, Spitzer can look through large clouds of dust that are opaque at visible wavelengths, and observe young stellar objects in their birth environments. Cosmologists can use Spitzer to study the early universe and the formation of galaxies over twelve billion years ago. Fazio used all of these examples and more to demonstrate that Spitzer has truly changed our understanding of the universe.Climate Change for Astronomers (Meredith Rawls)Every astronomer at #aas227 wants to learn about climate change! WOW this room is ridiculously full. pic.twitter.com/ud9an0gLJG Meredith Rawls (@merrdiff) January 7, 2016The second half of the session was a presentation by Doug Duncan featuring an activity from his 101-level college course. He uses climate change as a way to teach critical thinking and scientific reasoning. Members of the audience were walked through an exercise that included interpreting plots of changing surface temperatures

  18. AAS 227: Welcome!

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    Greetings from the 227th American Astronomical Society meeting in Kissimmee, Florida! This week, along with several fellow authors from astrobites, Iwill bewritingupdates on selectedevents at themeeting and posting at the end of each day. You can follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.If youre an author or referee (or plan to be!) and youre here at the meeting, consider joining us at our Author and Referee Workshop on Wednesday in the Tallahassee room, where well be sharingsome of the exciting new features of the AAS journals. You can drop intoeither of the two-hour sessions(10 AM 12 PM or 1 PM 3 PM), and there will be afree buffet lunch at noon.Heres the agenda:Morning SessionTopic Speaker10:00 am 10:05 amIntroductionsJulie Steffen10:05 am 10:35 amChanges at AAS Journals; How to Be a Successful AAS AuthorEthan Vishniac10:35 am 11:00 amThe Peer Review ProcessButler Burton11:00 am 11:15 amAAS Nova: Sharing AAS Authors Research with the Broader CommunitySusanna Kohler11:15 am 11:30 amFixing Software and Instrumentation Publishing: New Paper Styles in AAS JournalsChris Lintott11:30 am 11:45 amMaking Article Writing Easier with the New AASTeX v6.0Greg Schwarz11:45 am 12:00 pmBringing JavaScript and Interactivity to Your AAS Journal FiguresGus MuenchLunch SessionTopic Speaker12:00 pm 12:15 pmUnified Astronomy ThesaurusKatie Frey12:15 pm 12:30 pmAAS/ADS ORCID Integration ToolAlberto Accomazzi12:30 pm 12:45 pmWorldWide Telescope and Video AbstractsJosh Peek12:45 pm 01:00 pmArizona Astronomical Data Hub (AADH)Bryan HeidornAfternoon SessionTopic Speaker01:00 pm 01:05 pmIntroductionsJulie Steffen01:05 pm 01:35 pmChanges at AAS Journals; How to Be a Successful AAS AuthorEthan Vishniac01:35 pm 02:00 pmThe Peer Review ProcessButler Burton02:00 pm 02:15 pmAAS Nova: Sharing AAS Authors Research with the Broader CommunitySusanna Kohler02:15 pm 02:30 pm

  19. AAS 228: Welcome!

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Greetings from the 228th American Astronomical Society meeting in San Diego, California! This week, along with a team of fellow authorsfrom astrobites, Iwill bewritingupdates on selectedevents at themeeting and posting twiceeach day. You can follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.If youre at the meeting, come stop by the AAS booth (Booth #211-213) to learn about the newly-announced partnership between AAS and astrobites and pick up some swag.And dont forget to visit the IOP booth in the Exhibit Hall (Booth #223) to learn more about the new corridors for AAS Journals and to pick up a badge pin to representyour corridor!

  20. Compressed Genotyping

    PubMed Central

    Erlich, Yaniv; Gordon, Assaf; Brand, Michael; Hannon, Gregory J.; Mitra, Partha P.

    2011-01-01

    Over the past three decades we have steadily increased our knowledge on the genetic basis of many severe disorders. Nevertheless, there are still great challenges in applying this knowledge routinely in the clinic, mainly due to the relatively tedious and expensive process of genotyping. Since the genetic variations that underlie the disorders are relatively rare in the population, they can be thought of as a sparse signal. Using methods and ideas from compressed sensing and group testing, we have developed a cost-effective genotyping protocol to detect carriers for severe genetic disorders. In particular, we have adapted our scheme to a recently developed class of high throughput DNA sequencing technologies. The mathematical framework presented here has some important distinctions from the ’traditional’ compressed sensing and group testing frameworks in order to address biological and technical constraints of our setting. PMID:21451737

  1. Comparative analysis of cytokine transcript profiles within mediastinal lymph node compartments of pigs after infection with porcine reproductive and respiratory syndrome genotype 1 strains differing in pathogenicity.

    PubMed

    García-Nicolás, Obdulio; Rosales, Rubén S; Pallarés, Francisco J; Risco, David; Quereda, Juan J; Graham, Simon P; Frossard, Jean-Pierre; Morgan, Sophie B; Steinbach, Falko; Drew, Trevor W; Strickland, Tony S; Salguero, Francisco J

    2015-01-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) induces a weak immune response enabling it to persist in different organs of infected pigs. This has been attributed to the ability of PRRSV to influence the induction of cytokine responses. In this study, we investigated the cytokine transcriptional profiles in different compartments of the mediastinal lymph node of pigs infected with three genotype 1 PRRSV strains of differing pathogenicity: the low virulence prototype Lelystad virus (LV), and UK field strain 215-06 and the highly virulent subtype 3 SU1-Bel isolate from Belarus. We have used a combination of laser capture micro-dissection (LCM) followed by real time quantitative PCR (RT-qPCR) and immunohistochemical (IHC) detection of immune cell markers (CD3, CD79a and MAC387) and RT-qPCR quantification of PRRSV and cytokine transcripts. Compared to mock infected pigs, we found a significant downregulation of TNF-α and IFN-α in follicular and interfollicular areas of the mediastinal lymph node from 3 days post-infection (dpi) in animals infected with all three strains. This was accompanied by a transient B cell depletion and T cell and macrophage infiltration in the follicles together with T cell depletion in the interfollicular areas. A delayed upregulation of IFN-γ and IL-23p19 was observed mainly in the follicles. The PRRSV load was higher in all areas and time-points studied in the animals infected with the SU1-Bel strain. This paper describes the first application of LCM to study the cytokine transcript profiles and virus distribution in different compartments of the lymph node of pigs. PMID:25889072

  2. Comparative cDNA-AFLP analysis of Cd-tolerant and -sensitive genotypes derived from crosses between the Cd hyperaccumulator Arabidopsis halleri and Arabidopsis lyrata ssp. petraea.

    PubMed

    Craciun, Adrian Radu; Courbot, Mikael; Bourgis, Fabienne; Salis, Pietrino; Saumitou-Laprade, Pierre; Verbruggen, Nathalie

    2006-01-01

    Cadmium (Cd) tolerance seems to be a constitutive species-level trait in Arabidopsis halleri. In order to identify genes potentially implicated in Cd tolerance, a backcross (BC1) segregating population was produced from crosses between A. halleri ssp. halleri and its closest non-tolerant relative A. lyrata ssp. petraea. The most sensitive and tolerant genotypes of the BC1 were analysed on a transcriptome-wide scale by cDNA-amplified fragment length polymorphism (AFLP). A hundred and thirty-four genes expressed more in the root of tolerant genotypes than in sensitive genotypes were identified. Most of the identified genes showed no regulation in their expression when exposed to Cd in a hydroponic culture medium and belonged to diverse functional classes, including reactive oxygen species (ROS) detoxification, cellular repair, metal sequestration, water transport, signal transduction, transcription regulation, and protein degradation, which are discussed. PMID:16916885

  3. Ascorbic acid (AA) metabolism in protection against radiation damage

    SciTech Connect

    Rose, R.C.; Koch, M.J.

    1986-03-05

    The possibility is considered that AA protects tissues against radiation damage by scavenging free radicals that result from radiolysis of water. A physiologic buffer (pH 6.7) was incubated with /sup 14/C-AA and 1 mM thiourea (to slow spontaneous oxidation of AA). Aliquots were assayed by HPLC and scintillation spectrometry to identify the /sup 14/C-label. Samples exposed to Cobalt-60 radiation had a half time of AA decay of < 3 minutes compared with nonirradiated samples (t/sub 1/2/ > 30 minutes) indicating that AA scavenges radiation-induced free radicals and forms the ascorbate free radical (AFR). Pairs of /sup 14/C-AFR disproportionate, with the net effect of /sup 14/C-dehydroascorbic acid formation from /sup 14/C-AA. Having established that AFR result from ionizing radiation in an aqueous solution, the possibility was evaluated that a tissue factor reduces AFR. Cortical tissue from the kidneys of male rats was minced, homogenized in buffer and centrifuged at 8000 xg. The supernatant was found to slow the rate of radiation-induced AA degradation by > 90% when incubated at 23/sup 0/C in the presence of 15 ..mu..M /sup 14/C-AA. Samples of supernatant maintained at 100/sup 0/C for 10 minutes or precipitated with 5% PCA did not prevent radiation-induced AA degradation. AA may have a specific role in scavenging free radicals generated by ionizing radiation and thereby protect body tissues.

  4. Gender-Dimorphic Impact of PXR Genotype and Haplotype on Hepatotoxicity During Antituberculosis Treatment

    PubMed Central

    Wang, Jann Yuan; Tsai, Ching Hui; Lee, Yungling Leo; Lee, Li Na; Hsu, Chia Lin; Chang, Hsiu Ching; Chen, Jong Ming; Hsu, Cheng An; Yu, Chong Jen; Yang, Pan Chyr

    2015-01-01

    Abstract Women have a higher risk of drug-induced hepatotoxicity during antituberculosis treatment (HATT) than men. We hypothesized that single nucleotide polymorphism (SNP) genotype and derived haplotype of pregnane X receptor (PXR) gene, which could regulate the expression of phase I enzyme cytochrome P450 (CYP) 3A4, had a sex-specific influence on the risk of HATT. Six SNPs of the PXR gene were sequenced. Genotypes and haplotypes of the PXR SNPs, and other potential risk factors for HATT were compared between pulmonary TB patients with and those without HATT. HATT was defined as an increase in serum transaminase level >3 times the upper limit of normal (ULN) with symptoms, or >5 times ULN without symptoms. We performed the study in a derivation and a validation cohort. Among the 355 patients with pulmonary TB in the derivation cohort, 70 (19.7%) developed HATT. Logistic regression analysis revealed the risk of HATT increased in female genotype AA at rs2461823 (OR: 6.87 [2.55–18.52]) and decreased in female genotype AA at rs7643645 (OR: 0.14 [0.02–1.02]) of PXR gene. Haplotype analysis showed that female h001101 (OR: 2.30 [1.22–4.32]) and female h000110 (OR: 2.25 [1.08–4.69]) haplotype were associated with increased HATT risk. The identified predictors were also significantly associated with female HATT risk among the 182 patients in the validation cohort. Two PXR SNP genotypes and 2 haplotypes influenced the risk of HATT only in females. The PXR SNP showed a sex-specific impact that contributed to an increased HATT risk in females.

  5. Low Lignin (Brown Mid-rib) Sorghum Genotypes Restrict Growth of Fusarium Spp. as Compared with Near-Isogenic Wild-Type Sorghum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To increase usability of sorghum for bioenergy and forages, two different brown midrib (bmr) genes, bmr-6 and bmr-12, were backcrossed into five elite backgrounds, resulting in reduced lignin near-isogenic genotypes. Field-grown grain from bmr-6 and bmr-12 plants had significantly reduced colonizati...

  6. Genotyping methods.

    PubMed

    Tümmler, Burkhard

    2014-01-01

    Genotyping allows for the identification of bacterial isolates to the strain level and provides basic information about the evolutionary biology, population biology, taxonomy, ecology, and genetics of bacteria. Depending on the underlying question and available resources, Pseudomonas aeruginosa strains may be typed by anonymous fingerprinting techniques or electronically portable sequence-based typing methods such as multiple locus variable number tandem repeat (VNTR) analysis (MLVA), multilocus sequence typing, or oligonucleotide microarray. Macrorestriction fragment pattern analysis is a genotyping method that is globally applicable to all bacteria and hence has been and still is the reference method for strain typing in bacteriology. Agarose-embedded chromosomal DNA is cleaved with a rare-cutting restriction endonuclease and the generated 20-70 fragments are then separated by pulsed-field gel electrophoresis. The chapter provides a detailed step-by-step manual for SpeI genome fingerprinting of Pseudomonas chromosomes that has been optimized for SpeI fragment pattern analysis of P. aeruginosa. PMID:24818895

  7. AAS Career Services

    NASA Astrophysics Data System (ADS)

    Marvel, Kevin B.

    2012-08-01

    The American Astronomical Society provides substantial programs in the area of Career Services.Motivated by the Society's mission to enhance and share humanity's understanding of the Universe, the AAS provides a central resource for advertising positions, interviewing opportunities at its annual winter meeting and information, workshops and networks to enable astronomers to find employment.The programs of the Society in this area are overseen by an active committee on employment and the AAS Council itself.Additional resources that help characterize the field, its growth and facts about employment such as salaries and type of jobs available are regularly summarized and reported on by the American Institute of Physics.

  8. Fat mass- and obesity-associated genotype, dietary intakes and anthropometric measures in European adults: the Food4Me study.

    PubMed

    Livingstone, Katherine M; Celis-Morales, Carlos; Navas-Carretero, Santiago; San-Cristobal, Rodrigo; Forster, Hannah; O'Donovan, Clare B; Woolhead, Clara; Marsaux, Cyril F M; Macready, Anna L; Fallaize, Rosalind; Kolossa, Silvia; Tsirigoti, Lydia; Lambrinou, Christina P; Moschonis, George; Godlewska, Magdalena; Surwiłło, Agnieszka; Drevon, Christian A; Manios, Yannis; Traczyk, Iwona; Gibney, Eileen R; Brennan, Lorraine; Walsh, Marianne C; Lovegrove, Julie A; Martinez, J Alfredo; Saris, Wim H M; Daniel, Hannelore; Gibney, Mike; Mathers, John C

    2016-02-14

    The interplay between the fat mass- and obesity-associated (FTO) gene variants and diet has been implicated in the development of obesity. The aim of the present analysis was to investigate associations between FTO genotype, dietary intakes and anthropometrics among European adults. Participants in the Food4Me randomised controlled trial were genotyped for FTO genotype (rs9939609) and their dietary intakes, and diet quality scores (Healthy Eating Index and PREDIMED-based Mediterranean diet score) were estimated from FFQ. Relationships between FTO genotype, diet and anthropometrics (weight, waist circumference (WC) and BMI) were evaluated at baseline. European adults with the FTO risk genotype had greater WC (AA v. TT: +1·4 cm; P=0·003) and BMI (+0·9 kg/m2; P=0·001) than individuals with no risk alleles. Subjects with the lowest fried food consumption and two copies of the FTO risk variant had on average 1·4 kg/m2 greater BMI (Ptrend=0·028) and 3·1 cm greater WC (Ptrend=0·045) compared with individuals with no copies of the risk allele and with the lowest fried food consumption. However, there was no evidence of interactions between FTO genotype and dietary intakes on BMI and WC, and thus further research is required to confirm or refute these findings. PMID:26620191

  9. HBV Genotypic Variability in Cuba

    PubMed Central

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

    2015-01-01

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

  10. Comparative evaluation of p5+14 with SAP and peptide p5 by dual-energy SPECT imaging of mice with AA amyloidosis

    PubMed Central

    Martin, Emily B.; Williams, Angela; Richey, Tina; Stuckey, Alan; Heidel, R. Eric; Kennel, Stephen J.; Wall, Jonathan S.

    2016-01-01

    Amyloidosis is a protein-misfolding disorder characterized by the extracellular deposition of amyloid, a complex matrix composed of protein fibrils, hyper-sulphated glycosaminoglycans and serum amyloid P component (SAP). Accumulation of amyloid in visceral organs results in the destruction of tissue architecture leading to organ dysfunction and failure. Early differential diagnosis and disease monitoring are critical for improving patient outcomes; thus, whole body amyloid imaging would be beneficial in this regard. Non-invasive molecular imaging of systemic amyloid is performed in Europe by using iodine-123-labelled SAP; however, this tracer is not available in the US. Therefore, we evaluated synthetic, poly-basic peptides, designated p5 and p5+14, as alternative radiotracers for detecting systemic amyloidosis. Herein, we perform a comparative effectiveness evaluation of radiolabelled peptide p5+14 with p5 and SAP, in amyloid-laden mice, using dual-energy SPECT imaging and tissue biodistribution measurements. All three radiotracers selectively bound amyloid in vivo; however, p5+14 was significantly more effective as compared to p5 in certain organs. Moreover, SAP bound principally to hepatosplenic amyloid, whereas p5+14 was broadly distributed in numerous amyloid-laden anatomic sites, including the spleen, liver, pancreas, intestines and heart. These data support clinical validation of p5+14 as an amyloid radiotracer for patients in the US. PMID:26936002

  11. AAS Oral History Project

    NASA Astrophysics Data System (ADS)

    Buxner, Sanlyn; Holbrook, Jarita; AAS Oral History Team

    2016-06-01

    Now in its fourth year, the AAS Oral History Project has interviewed over 80 astronomers from all over the world. Led by the AAS Historical Astronomy Division (HAD) and partially funded by the American Institute of Physics Niels Bohr Library and ongoing support from the AAS, volunteers have collected oral histories from astronomers at professional meetings starting in 2015, including AAS, DPS, and the IAU general assembly. Each interview lasts one and a half to two hours and focuses on interviewees’ personal and professional lives. Questions include those about one’s family, childhood, strong influences on one’s scientific career, career path, successes and challenges, perspectives on how astronomy is changing as a field, and advice to the next generation. Each interview is audio recorded and transcribed, the content of which is checked with each interviewee. Once complete, interview transcripts are posted online as part of a larger oral history library at https://www.aip.org/history-programs/niels-bohr-library/oral-histories. Future analysis will reveal a rich story of astronomers and will help the community address issues of diversity, controversies, and the changing landscape of science. We are still recruiting individuals to be interviewed from all stages of career from undergraduate students to retired and emeritus astronomers. Contact Jarita Holbrook to schedule an interview or to find out more information about the project (astroholbrook@gmail.com). Also, contact Jarita Holbrook if you would like to become an interviewer for the project.

  12. American Astronomical Society (AAS)

    NASA Astrophysics Data System (ADS)

    Murdin, P.

    2000-11-01

    Founded in 1899, the AAS is a non-profit scientific society created to promote the advancement of astronomy and closely related branches of science. Its membership consists primarily of professional researchers in the astronomical sciences, but also includes educators, students and others interested in the advancement of astronomical research. About 85% of the membership is drawn from North Ame...

  13. Tracing QTLs for Leaf Blast Resistance and Agronomic Performance of Finger Millet (Eleusine coracana (L.) Gaertn.) Genotypes through Association Mapping and in silico Comparative Genomics Analyses.

    PubMed

    Ramakrishnan, M; Antony Ceasar, S; Duraipandiyan, V; Vinod, K K; Kalpana, Krishnan; Al-Dhabi, N A; Ignacimuthu, S

    2016-01-01

    Finger millet is one of the small millets with high nutritive value. This crop is vulnerable to blast disease caused by Pyricularia grisea, which occurs annually during rainy and winter seasons. Leaf blast occurs at early crop stage and is highly damaging. Mapping of resistance genes and other quantitative trait loci (QTLs) for agronomic performance can be of great use for improving finger millet genotypes. Evaluation of one hundred and twenty-eight finger millet genotypes in natural field conditions revealed that leaf blast caused severe setback on agronomic performance for susceptible genotypes, most significant traits being plant height and root length. Plant height was reduced under disease severity while root length was increased. Among the genotypes, IE4795 showed superior response in terms of both disease resistance and better agronomic performance. A total of seven unambiguous QTLs were found to be associated with various agronomic traits including leaf blast resistance by association mapping analysis. The markers, UGEP101 and UGEP95, were strongly associated with blast resistance. UGEP98 was associated with tiller number and UGEP9 was associated with root length and seed yield. Cross species validation of markers revealed that 12 candidate genes were associated with 8 QTLs in the genomes of grass species such as rice, foxtail millet, maize, Brachypodium stacei, B. distachyon, Panicum hallii and switchgrass. Several candidate genes were found proximal to orthologous sequences of the identified QTLs such as 1,4-β-glucanase for leaf blast resistance, cytokinin dehydrogenase (CKX) for tiller production, calmodulin (CaM) binding protein for seed yield and pectin methylesterase inhibitor (PMEI) for root growth and development. Most of these QTLs and their putatively associated candidate genes are reported for first time in finger millet. On validation, these novel QTLs may be utilized in future for marker assisted breeding for the development of fungal

  14. Tracing QTLs for Leaf Blast Resistance and Agronomic Performance of Finger Millet (Eleusine coracana (L.) Gaertn.) Genotypes through Association Mapping and in silico Comparative Genomics Analyses

    PubMed Central

    Ramakrishnan, M.; Antony Ceasar, S.; Duraipandiyan, V.; Vinod, K. K.; Kalpana, Krishnan; Al-Dhabi, N. A.; Ignacimuthu, S.

    2016-01-01

    Finger millet is one of the small millets with high nutritive value. This crop is vulnerable to blast disease caused by Pyricularia grisea, which occurs annually during rainy and winter seasons. Leaf blast occurs at early crop stage and is highly damaging. Mapping of resistance genes and other quantitative trait loci (QTLs) for agronomic performance can be of great use for improving finger millet genotypes. Evaluation of one hundred and twenty-eight finger millet genotypes in natural field conditions revealed that leaf blast caused severe setback on agronomic performance for susceptible genotypes, most significant traits being plant height and root length. Plant height was reduced under disease severity while root length was increased. Among the genotypes, IE4795 showed superior response in terms of both disease resistance and better agronomic performance. A total of seven unambiguous QTLs were found to be associated with various agronomic traits including leaf blast resistance by association mapping analysis. The markers, UGEP101 and UGEP95, were strongly associated with blast resistance. UGEP98 was associated with tiller number and UGEP9 was associated with root length and seed yield. Cross species validation of markers revealed that 12 candidate genes were associated with 8 QTLs in the genomes of grass species such as rice, foxtail millet, maize, Brachypodium stacei, B. distachyon, Panicum hallii and switchgrass. Several candidate genes were found proximal to orthologous sequences of the identified QTLs such as 1,4-β-glucanase for leaf blast resistance, cytokinin dehydrogenase (CKX) for tiller production, calmodulin (CaM) binding protein for seed yield and pectin methylesterase inhibitor (PMEI) for root growth and development. Most of these QTLs and their putatively associated candidate genes are reported for first time in finger millet. On validation, these novel QTLs may be utilized in future for marker assisted breeding for the development of fungal

  15. Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity

    PubMed Central

    Ashraf, Nasheeman; Ghai, Deepali; Barman, Pranjan; Basu, Swaraj; Gangisetty, Nagaraju; Mandal, Mihir K; Chakraborty, Niranjan; Datta, Asis; Chakraborty, Subhra

    2009-01-01

    Background The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. Chickpea is the world's third most important food legume grown in over 40 countries representing all the continents. Despite its importance in plant evolution, role in human nutrition and stress adaptation, very little ESTs and differential transcriptome data is available, let alone genotype-specific gene signatures. Present study focuses on Fusarium wilt responsive gene expression in chickpea. Results We report 6272 gene sequences of immune-response pathway that would provide genotype-dependent spatial information on the presence and relative abundance of each gene. The sequence assembly led to the identification of a CaUnigene set of 2013 transcripts comprising of 973 contigs and 1040 singletons, two-third of which represent new chickpea genes hitherto undiscovered. We identified 209 gene families and 262 genotype-specific SNPs. Further, several novel transcription regulators were identified indicating their possible role in immune response. The transcriptomic analysis revealed 649 non-cannonical genes besides many unexpected candidates with known biochemical functions, which have never been associated with pathostress-responsive transcriptome. Conclusion Our study establishes a comprehensive catalogue of the immune-responsive root transcriptome with insight into their identity and function. The development, detailed analysis of CaEST datasets and global gene expression by microarray provide new insight into the commonality and diversity of organ-specific immune-responsive transcript signatures and their regulated expression shaping the species specificity at genotype level. This is the first report on differential transcriptome of an unsequenced genome during vascular wilt. PMID:19732460

  16. A Comparative Study of Proteolytic Mechanisms during Leaf Senescence of Four Genotypes of Winter Oilseed Rape Highlighted Relevant Physiological and Molecular Traits for NRE Improvement.

    PubMed

    Girondé, Alexandra; Poret, Marine; Etienne, Philippe; Trouverie, Jacques; Bouchereau, Alain; Le Cahérec, Françoise; Leport, Laurent; Niogret, Marie-Françoise; Avice, Jean-Christophe

    2015-01-01

    Winter oilseed rape is characterized by a low N use efficiency related to a weak leaf N remobilization efficiency (NRE) at vegetative stages. By investigating the natural genotypic variability of leaf NRE, our goal was to characterize the relevant physiological traits and the main protease classes associated with an efficient proteolysis and high leaf NRE in response to ample or restricted nitrate supply. The degradation rate of soluble proteins and D1 protein (a thylakoid-bound protein) were correlated to N remobilization, except for the genotype Samouraï which showed a low NRE despite high levels of proteolysis. Under restricted nitrate conditions, high levels of soluble protein degradation were associated with serine, cysteine and aspartic proteases at acidic pH. Low leaf NRE was related to a weak proteolysis of both soluble and thylakoid-bound proteins. The results obtained on the genotype Samouraï suggest that the timing between the onset of proteolysis and abscission could be a determinant. The specific involvement of acidic proteases suggests that autophagy and/or senescence-associated vacuoles are implicated in N remobilization under low N conditions. The data revealed that the rate of D1 degradation could be a relevant indicator of leaf NRE and might be used as a tool for plant breeding. PMID:27135221

  17. Comparative Transcriptome Analysis of Two Ipomoea aquatica Forsk. Cultivars Targeted To Explore Possible Mechanism of Genotype-Dependent Accumulation of Cadmium.

    PubMed

    Huang, Ying-Ying; Shen, Chuang; Chen, Jing-Xin; He, Chun-Tao; Zhou, Qian; Tan, Xiao; Yuan, Jian-Gang; Yang, Zhong-Yi

    2016-06-29

    A low-shoot-Cd (QLQ) and a high-shoot-Cd cultivar (T308) of water spinach (Ipomoea aquatica Forsk.) were used to investigate molecular mechanism of the genotype difference in cadmium (Cd) accumulation. RNA-Seq under 9 and 72 h cadmium exposures (5 mg L(-1)) were undertaken to explore Cd induced genotype differences in molecular processes. In total, 253 747 540 clean reads were assembled into 57 524 unigenes. Among them, 6136 and 10 064 unigenes were differentially expressed in QLQ and T308, respectively. Cell wall biosynthesis genes, such as GAUT and laccase, and three Cd efflux genes (Nramp5, MATE9, and YSL7) had higher expression levels in QLQ, while the genes in sulfur and glutathione metabolism pathway, e.g., sulfate transporter and cysteine synthase, showed higher expression levels in T308. These findings would be useful for further understanding of the mechanisms related to genotype-dependent Cd accumulation and developing the molecular assisted screening and breeding of low-shoot-Cd cultivars for water spinach. PMID:27267580

  18. A Comparative Study of Proteolytic Mechanisms during Leaf Senescence of Four Genotypes of Winter Oilseed Rape Highlighted Relevant Physiological and Molecular Traits for NRE Improvement

    PubMed Central

    Girondé, Alexandra; Poret, Marine; Etienne, Philippe; Trouverie, Jacques; Bouchereau, Alain; Le Cahérec, Françoise; Leport, Laurent; Niogret, Marie-Françoise; Avice, Jean-Christophe

    2015-01-01

    Winter oilseed rape is characterized by a low N use efficiency related to a weak leaf N remobilization efficiency (NRE) at vegetative stages. By investigating the natural genotypic variability of leaf NRE, our goal was to characterize the relevant physiological traits and the main protease classes associated with an efficient proteolysis and high leaf NRE in response to ample or restricted nitrate supply. The degradation rate of soluble proteins and D1 protein (a thylakoid-bound protein) were correlated to N remobilization, except for the genotype Samouraï which showed a low NRE despite high levels of proteolysis. Under restricted nitrate conditions, high levels of soluble protein degradation were associated with serine, cysteine and aspartic proteases at acidic pH. Low leaf NRE was related to a weak proteolysis of both soluble and thylakoid-bound proteins. The results obtained on the genotype Samouraï suggest that the timing between the onset of proteolysis and abscission could be a determinant. The specific involvement of acidic proteases suggests that autophagy and/or senescence-associated vacuoles are implicated in N remobilization under low N conditions. The data revealed that the rate of D1 degradation could be a relevant indicator of leaf NRE and might be used as a tool for plant breeding. PMID:27135221

  19. Racial Differences in CYP3A4 Genotype and Survival Among Men Treated on Radiation Therapy Oncology Group (RTOG) 9202: A Phase III Randomized Trial

    SciTech Connect

    Roach, Mack Silvio, Michelle de; Rebbick, Timothy; Grignon, David; Rotman, Marvin; Wolkov, Harvey; Fisher, Barbara; Hanks, Gerald; Shipley, William U.; Pollack, Alan; Sandler, Howard; Watkins-Bruner, Deborah Ph.D.

    2007-09-01

    Purpose: Inherited genotypes may explain the inferior outcomes of African American (AA) men with prostate cancer. To understand how variation in CYP3A4 correlated with outcomes, a retrospective examination of the CYP3A4*1B genotype was performed on men treated with Radiation Therapy Oncology Group (RTOG) 92-02. Methods and Materials: From 1,514 cases, we evaluated 56 (28.4%) of 197 AA and 54 (4.3%) of 1,274 European American (EA) patients. All patients received goserelin and flutamide for 2 months before and during RT (STAD-RT) {+-} 24 months of goserelin (long-term androgen deprivation plus radiation [LTAD-RT]). Events studied included overall survival and biochemical progression using American Society for Therapeutic Radiology and Oncology consensus guidelines. Results: There were no differences in outcome in patients in with or without CYP3A4 data. There was an association between race and CYP3A4 polymorphisms with 75% of EAs having the Wild Type compared to only 25% of AA men (p <0.0001). There was no association between CYP3A4 classification or race and survival or progression. Conclusions: The samples analyzed support previously reported observations about the distribution of CYP3A4*1B genotype by race, but race was not associated with poorer outcome. However, patient numbers were limited, and selection bias cannot be completely ruled out.

  20. Differences in genotype frequencies of salt-sensitive genes between fishing and nonfishing communities in Japan

    PubMed Central

    Harada, Masanori; Takeshima, Taro; Okayama, Masanobu; Kajii, Eiji

    2016-01-01

    Purpose To identify the differences in genotype frequencies of salt-sensitive genes between residents of fishing communities (FCs) and nonfishing communities (NFCs). Methods The subjects included 18,156 individuals (8,043 males [44%] and 10,113 females [56%]; average age: 57.2±16.1 years) from the general population who were registered with large-scale genome banks and resided in 30 prefectures and 78 different regions in Japan. The measurement items were age, sex, blood pressure, presence or absence of hypertension, body mass index, alcohol consumption, and smoking habit. Furthermore, to analyze the genotype frequencies of salt-sensitive genes, α-adducin 1 (ADD1), angiotensinogen (AGT), angiotensin II receptor type 1 (AT1), and guanine nucleotide-binding protein β peptide 3 (GNB3) were measured. According to the 2004 government classification of municipalities (cities, towns, and villages), communities existing in areas bordering an ocean and with an ocean port were defined as FCs (28 areas). The others were defined as NFCs (50 areas). A logistic regression model was used for comparison of genotype frequencies between subjects residing in FCs and NFCs. Results Of the included subjects, 4,916 (27.0%) and 13,240 (73.0%) resided in FCs and NFCs, respectively. In FCs, the mean age was 59.4±16.7 years and men accounted for 41.0% of the cohort (n=2,015). In NFCs, the mean age was 56.4±15.8 years and men accounted for 45.5% of the cohort (n=6,028). The adjusted odds ratios of the AA and AG genotypes compared with the GG genotype for AGT were 0.80 (95% confidence interval [CI]: 0.68–0.95) and 0.76 (95% CI: 0.64–0.91), respectively. The adjusted odds ratio of the CC genotype compared with AA for AT1 was 0.63 (95% CI: 0.40–0.93). Conclusion The incidence of the salt-sensitive genotypes AGT and AT1 in residents of FCs were significantly lower than in NFCs. PMID:27110136

  1. Processing and Optimization of Dissimilar Friction Stir Welding of AA 2219 and AA 7039 Alloys

    NASA Astrophysics Data System (ADS)

    Venkateswarlu, D.; Nageswara rao, P.; Mahapatra, M. M.; Harsha, S. P.; Mandal, N. R.

    2015-12-01

    The present paper discusses the optimization of dissimilar friction stir welding of AA 2219 and AA 7039 alloys with respect to tool design issues including microstructural study of weld. The optimized ultimate tensile strength was ~280 MPa, and % elongation was ~11.5. It was observed that the extent of tool shoulder flat surface and tool rotational speed influenced the weld quality significantly. A mathematical model was also developed using response surface regression analysis to predict the effects of tool geometry and process variables on dissimilar AA 2219 and AA 7039 alloys welds. The microstructure evolution and mechanical properties were investigated by employing electron backscatter diffraction technique, Vickers microhardness, and tensile testing, respectively. The microstructural observations indicated that the grain size obtained at advancing side (AA 2219 alloy side) was much finer compared to the retreating side (AA 7039 alloy side). Hardness distribution in the stir zone was inhomogeneous, which might be due to inadequate mixing of weld zone material. The hardness values observed at the weld zone were lower than that in the base materials.

  2. Genotyping analysis of 3 RET polymorphisms demonstrates low somatic mutation rate in Chinese Hirschsprung disease patients

    PubMed Central

    Zhang, Zhen; Jiang, Qian; Li, Qi; Cheng, Wei; Qiao, Guoliang; Xiao, Ping; Gan, Liang; Su, Lin; Miao, Chunyue; Li, Long

    2015-01-01

    Background: Genetic mosaicism has been reported for both coding and non-coding sequences in the RET gene in Hirschsprung disease (HSCR) patients. This study aimed to investigate somatic mutation rate in Chinese population by comparing both homozygous genotype percentage and risk allele frequency of 3 RET single nucleotide polymorphisms (SNPs) among blood and colon samples. Methods: DNA was extracted from 59 HSCR blood samples, 59 control blood samples and 76 fresh frozen colon tissue samples (grouped into ganglionic, transitional and aganglionic level). Genotype status of rs2435357 and rs2506030 was examined by competitive allele specific hydrolysis probes (Taqman) PCR technology, and rs2506004 was examined by Sanger sequencing. Homozygous genotype percentage and risk allele frequency were calculated for each type of sample and compared by chi-square test. P<0.05 was regarded as being statistically significant. Results: Colon tissue DNA samples showed similar frequency of SNPs as that of the blood DNA samples in HSCR patients, both of which are significantly higher than the control blood group (rs2435357 TT genotype: 71.2%, 74.7% versus 22.0% in HSCR blood, HSCR colon and control blood DNA respectively, P=0.000; rs2506004 AA genotype: 72.4%, 83.1% versus 25.5%, P=0.000; rs2506030 GG genotype: 79.7%, 77.2% versus 54.2%, P=0.000 and 0.004). With respect to DNA extracted from ganglionic, transitional and aganglionic levels, no statistically significant difference was demonstrated in those 3 regions (rs2435357: P=0.897; rs2506004: P=0.740; rs2506030: P=0.901). Conclusion: Our data does not support the notion that high frequency of somatic changes as an underlying etiology of Chinese HSCR population. PMID:26191260

  3. Profound reduction in the tamoxifen active metabolite endoxifen in a patient on phenytoin for epilepsy compared with a CYP2D6 genotype matched cohort.

    PubMed

    Gryn, Steven E; Teft, Wendy A; Kim, Richard B

    2014-07-01

    Tamoxifen is a prodrug, requiring cytochrome P450 enzyme-mediated metabolism to form the active metabolite endoxifen. We identified a case of drug-drug interaction involving tamoxifen and phenytoin, associated with a markedly lower endoxifen level than predicted. The patient is a 49-year-old woman, genotyped as a cytochrome P450 2D6 (CYP2D6) extensive metabolizer, chronically taking phenytoin for a seizure disorder. The plasma endoxifen level 2 months after starting tamoxifen was 4.72 nmol/l, the lowest level we have seen in our clinic among patients with CYP2D6 extensive metabolizer genotypes (n=195). To our knowledge, this is the first report documenting the extent of induction in terms of both tamoxifen and endoxifen levels during concomitant phenytoin therapy, and this effect would likely result in loss of therapeutic benefit from tamoxifen. Phenytoin should therefore not be used concurrently with tamoxifen for extended periods of time unless a therapeutic drug (endoxifen) monitoring strategy is utilized. PMID:24915025

  4. The Influence of Genotype Polymorphism on Morphine Analgesic Effect for Postoperative Pain in Children

    PubMed Central

    Lee, Mi Geum; Kim, Hyun Jung; Lee, Keun Hwa

    2016-01-01

    Background Although opioids are the most commonly used medications to control postoperative pain in children, the analgesic effects could have a large inter-individual variability according to genotypes. The aim of this study was to investigate the association between single nucleotide polymorphisms and the analgesic effect of morphine for postoperative pain in children. Methods A prospective study was conducted in 88 healthy children undergoing tonsillectomy, who received morphine during the operation. The postoperative pain score, frequency of rescue analgesics, and side effects of morphine were assessed in the post-anesthesia care unit. The children were genotyped for OPRM1 A118G, ABCB1 C3435T, and COMT Val158Met. Results Children with at least one G allele for OPRM1 (AG/GG) had higher postoperative pain scores compared with those with the AA genotype at the time of discharge from the post-anesthesia care unit (P = 0.025). Other recovery profiles were not significantly different between the two groups. There was no significant relationship between genotypes and postoperative pain scores in analysis of ABCB1 and COMT polymorphisms. Conclusions Genetic polymorphism at OPRM1 A118G, but not at ABCB1 C3435T and COMT Val158Met, influences the analgesic effect of morphine for immediate acute postoperative pain in children. PMID:26839669

  5. Comparison between ARB and CARB processes on an AA5754/AA6061 composite

    NASA Astrophysics Data System (ADS)

    Verstraete, K.; Helbert, A.-L.; Brisset, F.; Baudin, T.

    2014-08-01

    The present work aims to compare two processes: Accumulative Roll Bonding and Cross Accumulative Roll Bonding (CARB). Both processes consist in the repetition of rolling but the second technique adds a 90° rotation of the sheet around its normal direction between each rolling. Microstructure, mechanical properties and texture were compared for both processes on an AA5754/AA6061 composite. As a result a thinner and less elongated microstructure was obtained in the CARB process leading to an isotropy and an improvement of the mechanical properties. Besides, the texture was characterized by the rotated Cube component for both processes but for CARB it is of less strength.

  6. Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination.

    PubMed

    Schouls, Leo M; Reulen, Sanne; Duim, Birgitta; Wagenaar, Jaap A; Willems, Rob J L; Dingle, Kate E; Colles, Frances M; Van Embden, Jan D A

    2003-01-01

    Three molecular typing methods were used to study the relationships among 184 Campylobacter strains isolated from humans, cattle, and chickens. All strains were genotyped by amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), and sequence analysis of a genomic region with short tandem repeats designated clustered regularly interspaced short palindromic repeats (CRISPRs). MLST and AFLP analysis yielded more than 100 different profiles and patterns, respectively. These multiple-locus typing methods resulted in similar genetic clustering, indicating that both are useful in disclosing genetic relationships between Campylobacter jejuni isolates. Group separation analysis of the AFLP analysis and MLST data revealed an unexpected association between cattle and human strains, suggesting a common source of infection. Analysis of the polymorphic CRISPR region carrying short repeats allowed about two-thirds of the typeable strains to be distinguished, similar to AFLP analysis and MLST. The three methods proved to be equally powerful in identifying strains from outbreaks of human campylobacteriosis. Analysis of the MLST data showed that intra- and interspecies recombination occurs frequently and that the role of recombination in sequence variation is 50 times greater than that of mutation. Examination of strains cultured from cecum swabs revealed that individual chickens harbored multiple Campylobacter strain types and that some genotypes were found in more than one chicken. We conclude that typing of Campylobacter strains is useful for identification of outbreaks but is probably not useful for source tracing and global epidemiology because of carriage of strains of multiple types and an extremely high diversity of strains in animals. PMID:12517820

  7. [Bioactive Effect of the Preparation Biostyl on the Reproductive Function of Different Genotypes of American Mink].

    PubMed

    Trapezov, O V; Zemljanitskajia, E I; Rasputina, O V; Naumkin, I V; Trapezova, L I

    2016-01-01

    The different role of coat color mutations in the American mink on the per os effect of the biologically active preparation Biostyl was shown. The number of kits per female was the same in all control genotypes, including Standard (+/+ +/+), sapphire (a/a p/p), and lavender (a/a m/m): 4.4 ± 0.4, 4.4 ± 0.5, and 4.3 ± 0.5, respectively. Experimental groups of these genotypes have shown a great contrast among each other: stimulation of the reproductive function was 5.2 ± 0.3 in Standard minks, while suppression of the reproductive function was 3.8 ± 0.6, and 2.3 ± 0.5 in the double recessive mutants sapphire and lavender, respectively. The differentiation in body mass between experimental and control newborn Standard kits was not revealed. A significant decrease in the body mass of newborn experimental sapphire kits as compared to control group in a sex-specific manner was registered. PMID:27183801

  8. Caffeine and 3-km cycling performance: Effects of mouth rinsing, genotype, and time of day.

    PubMed

    Pataky, M W; Womack, C J; Saunders, M J; Goffe, J L; D'Lugos, A C; El-Sohemy, A; Luden, N D

    2016-06-01

    We assessed the efficacy of caffeine mouth rinsing on 3-km cycling performance and determined whether caffeine mouth rinsing affects performance gains influenced by the CYP1A2 polymorphism. Thirty-eight recreational cyclists completed four simulated 3-km time trials (TT). Subjects ingested either 6 mg/kg BW of caffeine or placebo 1 h prior to each TT. Additionally, 25 mL of 1.14% caffeine or placebo solution were mouth rinsed before each TT. The treatments were Placebo, caffeine Ingestion, caffeine Rinse and Ingestion+Rinse. Subjects were genotyped and classified as AA homozygotes or AC heterozygotes for the rs762551 polymorphism of the CYP1A2 gene involved in caffeine metabolism. Magnitude-based inferences were used to evaluate treatment differences in mean power output based on a predetermined meaningful treatment effect of 1.0%. AC heterozygotes (4.1%) and AA homozygotes (3.4%) benefited from Ingestion+Rinse, but only AC performed better with Ingestion (6.0%). Additionally, Rinse and Ingestion+Rinse elicited better performance relative to Placebo among subjects that performed prior to 10:00 h (Early) compared with after 10:00 h (Late). The present study provides additional evidence of genotype and time of day factors that affect the ergogenic value of caffeine intake that may allow for more personalized caffeine intake strategies to maximize performance. PMID:26062916

  9. Quantitative analysis of texture evolution of cold-rolled direct-chill-cast and continuous-cast AA5052 and AA5182 aluminum alloys during isothermal annealing

    NASA Astrophysics Data System (ADS)

    Zhao, Y. M.; Liu, W. C.; Morris, J. G.

    2004-11-01

    The as-received direct-chill-cast (DC) and continuous-cast (CC) AA5052 and AA5182 hot bands were preheated at 454 °C for 4 hours, followed by cold rolling to an 80 pct reduction in thickness. The texture evolution of these cold-rolled samples during isothermal annealing was investigated by X-ray diffraction. The variation in texture volume fractions with annealing time was quantitatively analyzed by using the Johnson-Mehl-Avrami-Kolmogorov (JMAK) equation. The differences in recrystallization textures between the AA5052 and AA5182 alloys and between the DC and CC alloys were compared. It was found that the AA5052 alloy possessed a stronger cube recrystallization texture than the AA5182 alloy for the DC and CC materials. The recrystallization textures of the AA5182 alloy were affected strongly by the annealing temperature. As the annealing temperature increased, the cube recrystallization texture strengthened, whereas the R texture weakened. The annealing temperature had little influence on the recrystallization textures of the AA5052 alloy. The DC AA5052 and 5182 alloys also exhibited stronger cube recrystallization textures than the corresponding CC alloys. For the DC and CC AA5052 alloys, the n value in the JMAK-type equation increased with an increase in the annealing temperature, while the n values varied only slightly with the annealing temperature for the DC and CC AA5182 alloys.

  10. Effect of CSN1S1-CSN3 (α(S1)-κ-casein) composite genotype on milk production traits and milk coagulation properties in Mediterranean water buffalo.

    PubMed

    Bonfatti, V; Giantin, M; Gervaso, M; Coletta, A; Dacasto, M; Carnier, P

    2012-06-01

    The aim of this study was to estimate effects of CSN1S1-CSN3 (α(S1)-κ-casein) composite genotypes on milk production traits and milk coagulation properties (MCP) in Mediterranean water buffalo. Genotypes at CSN1S1 and CSN3 and coagulation properties [rennet clotting time (RCT), curd firming time (K₂₀), and curd firmness (A₃₀)] were assessed by reversed-phase HPLC and computerized renneting meter analysis, respectively, using single test-day milk samples of 536 animals. Alternative protein variants of α(S1)-CN and κ-CN were detected by HPLC, and identification of the corresponding genetic variants was carried out by DNA analysis. Two genetic variants were detected at CSN1S1 (A and B variants) and 2 at CSN3 (X1 and X2 variants). Statistical inference was based on a linear model including the CSN1S1-CSN3 composite genotype effect (7 genotypes), the effects of herd-test-day (8 levels), and a combined days in milk (DIM)-parity class. Composite genotype AB-X2X2 was associated with decreased test-day milk yield [-0.21 standard deviation (SD) units of the trait] relative to genotype BB-X2X2. Genotypes did not affect milk protein content, but genotype AB-X1X1 was associated with increased fat content compared with genotype BB-X2X2 (+0.28 SD units of the trait) and AB-X1X1 (+0.43 SD units of the trait). For RCT, the largest difference (+1.91 min; i.e., 0.61 SD units of the trait) was observed between genotype AA-X1X2 and AB-X1X1. Direction of genotype effects on K(20) was consistent with that for RCT. The maximum variation in K₂₀ due to genotype effects (between AA-X1X2 and AB-X1X1 genotypes) was almost 0.9 SD units of the trait. Magnitude of genotype effects was smaller for A₃₀ than for RCT and K₂₀, with a maximum difference of 0.5 SD units of the trait between genotype AA-X1X2 and AA-X1X1. The B allele at CSN1S1 was associated with increased RCT and K₂₀ and with weaker curds compared with allele A. Allele X2 at CSN3 exerted opposite effects on

  11. Genotype imputation via matrix completion.

    PubMed

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

    2013-03-01

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

  12. Strategic Change in AAS Publishing

    NASA Astrophysics Data System (ADS)

    Steffen, Julie

    2015-08-01

    The American Astronomical Society has embarked on a process of strategic change in its publishing program. The process has incuded authors, AAS leaders, editors, publishing experts, librarians, and data scientists. This session will outline the still ongoing process and present some both upcoming and already available new AAS Publishing features and services to the global astronomy community.

  13. AAS 227: Day 2

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    Editors Note:This week were at the 227th AAS Meeting in Kissimmee, FL. Along with several fellow authors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting at the end of each day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Welcome to Day 2 of the winter American Astronomical Society (AAS) meeting in Kissimmee! Several of us are attending the conference this year, and we will report highlights from each day here on astrobites. If youd like to see more timely updates during the day, we encourage you to follow @astrobites on twitter or search the #aas227 hashtag.Plenary Session: Black Hole Physics with the Event Horizon Telescope (by Susanna Kohler)If anyone needed motivation to wake up early this morning, they got it in the form of Feryal Ozel (University of Arizona) enthralling us all with exciting pictures, videos, and words about black holes and the Event Horizon Telescope. Ozel spoke to a packed room (at 8:30am!) about where the project currently stands, and where its heading in the future.The EHT has pretty much the coolest goal ever: actually image the event horizons of black holes in our universe. The problem is that the largest black hole we can look at (Sgr A*, in the center of our galaxy) has an event horizon size of 50 as. For this kind of resolution roughly equivalent to trying to image a DVD on the Moon! wed need an Earth-sized telescope. EHT has solved this problem by linking telescopes around the world, creating one giant, mm-wavelength effective telescope with a baseline the size of Earth.Besides producing awesome images, the EHT will be able to test properties of black-hole spacetime, the no-hair theorem, and general relativity (GR) in new regimes.Ozel walked us through some of the theory prep work we need to do now in order to get the most science out of the EHT, including devising new

  14. AAS 227: Day 2

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    Editors Note:This week were at the 227th AAS Meeting in Kissimmee, FL. Along with several fellow authors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting at the end of each day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Welcome to Day 2 of the winter American Astronomical Society (AAS) meeting in Kissimmee! Several of us are attending the conference this year, and we will report highlights from each day here on astrobites. If youd like to see more timely updates during the day, we encourage you to follow @astrobites on twitter or search the #aas227 hashtag.Plenary Session: Black Hole Physics with the Event Horizon Telescope (by Susanna Kohler)If anyone needed motivation to wake up early this morning, they got it in the form of Feryal Ozel (University of Arizona) enthralling us all with exciting pictures, videos, and words about black holes and the Event Horizon Telescope. Ozel spoke to a packed room (at 8:30am!) about where the project currently stands, and where its heading in the future.The EHT has pretty much the coolest goal ever: actually image the event horizons of black holes in our universe. The problem is that the largest black hole we can look at (Sgr A*, in the center of our galaxy) has an event horizon size of 50 as. For this kind of resolution roughly equivalent to trying to image a DVD on the Moon! wed need an Earth-sized telescope. EHT has solved this problem by linking telescopes around the world, creating one giant, mm-wavelength effective telescope with a baseline the size of Earth.Besides producing awesome images, the EHT will be able to test properties of black-hole spacetime, the no-hair theorem, and general relativity (GR) in new regimes.Ozel walked us through some of the theory prep work we need to do now in order to get the most science out of the EHT, including devising new

  15. Resting-State Brain and the FTO Obesity Risk Allele: Default Mode, Sensorimotor, and Salience Network Connectivity Underlying Different Somatosensory Integration and Reward Processing between Genotypes.

    PubMed

    Olivo, Gaia; Wiemerslage, Lyle; Nilsson, Emil K; Solstrand Dahlberg, Linda; Larsen, Anna L; Olaya Búcaro, Marcela; Gustafsson, Veronica P; Titova, Olga E; Bandstein, Marcus; Larsson, Elna-Marie; Benedict, Christian; Brooks, Samantha J; Schiöth, Helgi B

    2016-01-01

    Single-nucleotide polymorphisms (SNPs) of the fat mass and obesity associated (FTO) gene are linked to obesity, but how these SNPs influence resting-state neural activation is unknown. Few brain-imaging studies have investigated the influence of obesity-related SNPs on neural activity, and no study has investigated resting-state connectivity patterns. We tested connectivity within three, main resting-state networks: default mode (DMN), sensorimotor (SMN), and salience network (SN) in 30 male participants, grouped based on genotype for the rs9939609 FTO SNP, as well as punishment and reward sensitivity measured by the Behavioral Inhibition (BIS) and Behavioral Activation System (BAS) questionnaires. Because obesity is associated with anomalies in both systems, we calculated a BIS/BAS ratio (BBr) accounting for features of both scores. A prominence of BIS over BAS (higher BBr) resulted in increased connectivity in frontal and paralimbic regions. These alterations were more evident in the obesity-associated AA genotype, where a high BBr was also associated with increased SN connectivity in dopaminergic circuitries, and in a subnetwork involved in somatosensory integration regarding food. Participants with AA genotype and high BBr, compared to corresponding participants in the TT genotype, also showed greater DMN connectivity in regions involved in the processing of food cues, and in the SMN for regions involved in visceral perception and reward-based learning. These findings suggest that neural connectivity patterns influence the sensitivity toward punishment and reward more closely in the AA carriers, predisposing them to developing obesity. Our work explains a complex interaction between genetics, neural patterns, and behavioral measures in determining the risk for obesity and may help develop individually-tailored strategies for obesity prevention. PMID:26924971

  16. Resting-State Brain and the FTO Obesity Risk Allele: Default Mode, Sensorimotor, and Salience Network Connectivity Underlying Different Somatosensory Integration and Reward Processing between Genotypes

    PubMed Central

    Olivo, Gaia; Wiemerslage, Lyle; Nilsson, Emil K.; Solstrand Dahlberg, Linda; Larsen, Anna L.; Olaya Búcaro, Marcela; Gustafsson, Veronica P.; Titova, Olga E.; Bandstein, Marcus; Larsson, Elna-Marie; Benedict, Christian; Brooks, Samantha J.; Schiöth, Helgi B.

    2016-01-01

    Single-nucleotide polymorphisms (SNPs) of the fat mass and obesity associated (FTO) gene are linked to obesity, but how these SNPs influence resting-state neural activation is unknown. Few brain-imaging studies have investigated the influence of obesity-related SNPs on neural activity, and no study has investigated resting-state connectivity patterns. We tested connectivity within three, main resting-state networks: default mode (DMN), sensorimotor (SMN), and salience network (SN) in 30 male participants, grouped based on genotype for the rs9939609 FTO SNP, as well as punishment and reward sensitivity measured by the Behavioral Inhibition (BIS) and Behavioral Activation System (BAS) questionnaires. Because obesity is associated with anomalies in both systems, we calculated a BIS/BAS ratio (BBr) accounting for features of both scores. A prominence of BIS over BAS (higher BBr) resulted in increased connectivity in frontal and paralimbic regions. These alterations were more evident in the obesity-associated AA genotype, where a high BBr was also associated with increased SN connectivity in dopaminergic circuitries, and in a subnetwork involved in somatosensory integration regarding food. Participants with AA genotype and high BBr, compared to corresponding participants in the TT genotype, also showed greater DMN connectivity in regions involved in the processing of food cues, and in the SMN for regions involved in visceral perception and reward-based learning. These findings suggest that neural connectivity patterns influence the sensitivity toward punishment and reward more closely in the AA carriers, predisposing them to developing obesity. Our work explains a complex interaction between genetics, neural patterns, and behavioral measures in determining the risk for obesity and may help develop individually-tailored strategies for obesity prevention. PMID:26924971

  17. AAS 228: Day 1 morning

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Jeffrey Coughlin and colleagues to improve our ability to automatically detect and confirm exoplanet candidates with the traditional transit technique. They have developed a robotic technique called DAVE (Discovery And Vetting of K2 Exoplanets), which does an impressive job of eliminating false positive eclipse signals. To complement K2 observations of exoplanet transits, astrobites alumna Courtney Dressing presented a method which incorporates observations from the infrared Spitzer Space Telescope to better refine planet properties such as radius. @AstroDressing: Spitzer lets us refine Kepler planet radii, orbits, and even masses in prep for the Webb. #aas228 pic.twitter.com/qAUHeUSMYa Meredith Rawls (@merrdiff) June 13, 2016One of the challenges of K2 compared to Kepler is noise introduced by the spacecrafts less precise ability to point. Derek Buzasi implored us to not consider any one pipeline that removes this jitter as necessarily best, but rather to try several and recognize that different science goals will need different approaches to data processing.There isnt one best K2 pipeline! Depends strongly on your science goals. Buzasi begs us not to rank them. #aas228 pic.twitter.com/ykl89WqKNk Meredith Rawls (@merrdiff) June 13, 2016Jeffrey Van Cleve showed examples of what can be accomplished when K2 data is appropriately processed: just like Kepler, K2 can use asteroseismology to see the ringing oscillations of acoustic waves inside evolved stars. More gorgeous asteroseismology coming out of K2! Thanks to K2P2 pipelines handling of calibrated pixels. #aas228 pic.twitter.com/dGY6DcZHlV Meredith Rawls (@merrdiff) June 13, 2016Finally, several speakers including Buzasi presented their work on stellar astrophysics with K2. In addition to stellar activity and asteroseismology, presenters discussed spots and flares on cool brown dwarfs (John Gizis) and using eclipses together with stellar models to measure distances to star clusters (Keivan Stassun). Not a bad roundup for

  18. AAS 228: Day 4

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note: Lastweek we were at the 228th AAS Meeting in San Diego, CA. Here is a final post aboutselectedevents on the last day of the meeting, written by authors fromastrobites.com, a grad-student collaborative project with which we recently announced a new partnership! Starting in July,keep an eye out for astrobites postsat AAS Nova in between Highlights(i.e., on Tuesdays and Thursdays).Were excited to be working together to bring you more recent astronomy research from AAS journals!Extrasolar Planets: Detection (by Leonardo dos Santos)Thursdays first session on exoplanets was about detecting these distant worlds, and the opening talk was given by Robert Siverd (Las Cumbres Observatory). He describes the NRES, a network of spectrographs that will look for exoplanets using the radial velocity method. One of the coolest aspects of this instrument is that it will feature an on the fly scheduling system that will perform observations as efficiently as possible. The spectrograph is still being tested, but a unit will be deployed at CTIO later this year.@lcogt contracted by @NASA_TESS for follow up of their candidates. #aas228 Jessie Christiansen (@aussiastronomer) June 16, 2016Measuring the depths of transits and eclipses in Spitzer has been problematic in the past, since the Spitzer instrument IRAC (InfraRed Array Camera) has a non-uniform response in its detectors pixels. But, as reported by James Ingalls (Spitzer Science Center, Caltech), observers are circumventing this issue by using what they call the staring mode (avoiding large pointing jumps) and an algorithm to pick sweet spot pixels. Moreover, the results from the IRAC Data Challenge are helping to better understand its behavior. Giuseppe Morello (University College London), on the other hand, explained how his research group gets rid of instrumental effects from IRAC using machine learning. This method removes systematics from exoplanet transit data no matter if the noise source is from an instrument or

  19. Comparing the performance of FAM19A4 methylation analysis, cytology and HPV16/18 genotyping for the detection of cervical (pre)cancer in high-risk HPV-positive women of a gynecologic outpatient population (COMETH study).

    PubMed

    Luttmer, Roosmarijn; De Strooper, Lise M A; Berkhof, Johannes; Snijders, Peter J F; Dijkstra, Maaike G; Uijterwaal, Margot H; Steenbergen, Renske D M; van Kemenade, Folkert J; Rozendaal, Lawrence; Helmerhorst, Theo J M; Verheijen, Rene H M; Ter Harmsel, W Abraham; Van Baal, W Marchien; Graziosi, Peppino G C M; Quint, Wim G V; Heideman, Daniëlle A M; Meijer, Chris J L M

    2016-02-15

    Recently, DNA methylation analysis of FAM19A4 in cervical scrapes has been shown to adequately detect high-grade cervical intraepithelial neoplasia and cervical cancer (≥ CIN3) in high-risk HPV (hrHPV)-positive women. Here, we compared the clinical performance of FAM19A4 methylation analysis to cytology and HPV16/18 genotyping, separately and in combination, for ≥ CIN3 detection in hrHPV-positive women participating in a prospective observational multi-center cohort study. The study population comprised hrHPV-positive women aged 18-66 years, visiting a gynecological outpatient clinic. From these women, cervical scrapes and colposcopy-directed biopsies (for histological confirmation) were obtained. Cervical scrapes were analyzed for FAM19A4 gene promoter methylation, cytology and HPV16/18 genotyping. Methylation analysis was performed by quantitative methylation-specific PCR (qMSP). Sensitivities and specificities for ≥ CIN3 were compared between tests. Stratified analyses were performed for variables that potentially influence marker performance. Of all 508 hrHPV-positive women, the sensitivities for ≥ CIN3 of cytology, FAM19A4 methylation analysis, and cytology combined with HPV16/18 genotyping were 85.6, 75.6 and 92.2%, respectively, with corresponding specificities of 49.8, 71.1 and 29.4%, respectively. Both sensitivity and specificity of FAM19A4 methylation analysis were associated with age (p ≤ 0.001 each). In women ≥ 30 years (n = 287), ≥ CIN3 sensitivity of FAM19A4 methylation analysis was 88.3% (95%CI: 80.2-96.5) which was noninferior to that of cytology [85.5% (95%CI: 76.0-94.0)], at a significantly higher specificity [62.1% (95%CI: 55.8-68.4) compared to 47.6% (95%CI: 41.1-54.1)]. In conclusion, among hrHPV-positive women from an outpatient population aged ≥ 30 years, methylation analysis of FAM19A4 is an attractive marker for the identification of women with ≥ CIN3. PMID:26317579

  20. The 3-D Structural Basis for the Pgi Genotypic Differences in the Performance of the Butterfly Melitaea cinxia at Different Temperatures.

    PubMed

    Li, Yuan; Andersson, Stefan

    2016-01-01

    Although genotype-by-environment interaction has long been used to unveil the genetic variation that affects Darwinian fitness, the mechanisms underlying the interaction usually remain unknown. Genetic variation at the dimeric glycolytic enzyme phosphoglucoisomerase (Pgi) has been observed to interact with temperature to explain the variation in the individual performance of the butterfly Melitaea cinxia. At relatively high temperature, individuals with Pgi-non-f genotypes generally surpass those with Pgi-f genotypes, while the opposite applies at relatively low temperature. In this study, we did protein structure predictions and BlastP homology searches with the aim to understand the structural basis for this temperature-dependent difference in the performance of M. cinxia. Our results show that, at amino acid (AA) site 372, one of the two sites that distinguish Pgi-f (the translated polypeptide of the Pgi-f allele) from Pgi-non-f (the translated polypeptide of the Pgi-non-f allele), the Pgi-non-f-related residue strengthens an electrostatic attraction between a pair of residues (Glu373-Lys472) that are from different monomers, compared to the Pgi-f-related residue. Further, BlastP searches of animal protein sequences reveal a dramatic excess of electrostatically attractive combinations of the residues at the Pgi AA sites equivalent to sites 373 and 472 in M. cinxia. This suggests that factors enhancing the inter-monomer interaction between these two sites, and therefore helping the tight association of two Pgi monomers, are favourable. Our homology-modelling results also show that, at the second AA site that distinguishes Pgi-f from Pgi-non-f in M. cinxia, the Pgi-non-f-related residue is more entropy-favourable (leading to higher structural stability) than the Pgi-f-related residue. To sum up, this study suggests a higher structural stability of the protein products of the Pgi-non-f genotypes than those of the Pgi-f genotypes, which may explain why individuals

  1. The 3-D Structural Basis for the Pgi Genotypic Differences in the Performance of the Butterfly Melitaea cinxia at Different Temperatures

    PubMed Central

    Li, Yuan; Andersson, Stefan

    2016-01-01

    Although genotype-by-environment interaction has long been used to unveil the genetic variation that affects Darwinian fitness, the mechanisms underlying the interaction usually remain unknown. Genetic variation at the dimeric glycolytic enzyme phosphoglucoisomerase (Pgi) has been observed to interact with temperature to explain the variation in the individual performance of the butterfly Melitaea cinxia. At relatively high temperature, individuals with Pgi-non-f genotypes generally surpass those with Pgi-f genotypes, while the opposite applies at relatively low temperature. In this study, we did protein structure predictions and BlastP homology searches with the aim to understand the structural basis for this temperature-dependent difference in the performance of M. cinxia. Our results show that, at amino acid (AA) site 372, one of the two sites that distinguish Pgi-f (the translated polypeptide of the Pgi-f allele) from Pgi-non-f (the translated polypeptide of the Pgi-non-f allele), the Pgi-non-f-related residue strengthens an electrostatic attraction between a pair of residues (Glu373-Lys472) that are from different monomers, compared to the Pgi-f-related residue. Further, BlastP searches of animal protein sequences reveal a dramatic excess of electrostatically attractive combinations of the residues at the Pgi AA sites equivalent to sites 373 and 472 in M. cinxia. This suggests that factors enhancing the inter-monomer interaction between these two sites, and therefore helping the tight association of two Pgi monomers, are favourable. Our homology-modelling results also show that, at the second AA site that distinguishes Pgi-f from Pgi-non-f in M. cinxia, the Pgi-non-f-related residue is more entropy-favourable (leading to higher structural stability) than the Pgi-f-related residue. To sum up, this study suggests a higher structural stability of the protein products of the Pgi-non-f genotypes than those of the Pgi-f genotypes, which may explain why individuals

  2. AA9 and AA10: from enigmatic to essential enzymes.

    PubMed

    Corrêa, Thamy Lívia Ribeiro; dos Santos, Leandro Vieira; Pereira, Gonçalo Amarante Guimarães

    2016-01-01

    The lignocellulosic biomass, comprised mainly of cellulose, hemicellulose, and lignin, is a strong competitor for petroleum to obtain fuels and other products because of its renewable nature, low cost, and non-competitiveness with food production when obtained from agricultural waste. Due to its recalcitrance, lignocellulosic material requires an arsenal of enzymes for its deconstruction and the consequent release of fermentable sugars. In this context, enzymes currently classified as auxiliary activity 9 (AA9/formerly GH61) and 10 (AA10/formerly CBM 33) or lytic polysaccharide monooxygenases (LPMO) have emerged as cellulase boosting enzymes. AA9 and AA10 are the new paradigm for deconstruction of lignocellulosic biomass by enhancing the activity and decreasing the loading of classical enzymes to the reaction and, consequently, reducing costs of the hydrolysis step in the second-generation ethanol production chain. In view of that disclosed above, the goal of this work is to review experimental data that supports the relevance of AA9 and AA10 for the biomass deconstruction field. PMID:26476647

  3. MTHFR 677 CT/MTHFR 1298 CC genotypes are associated with increased risk of hypertension in Indians.

    PubMed

    Markan, Suchita; Sachdeva, Meenakshi; Sehrawat, Badan Singh; Kumari, Savita; Jain, Sanjay; Khullar, Madhu

    2007-08-01

    The goals of our present study were to measure plasma homocysteine levels and determine their association with methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms (C677T and A1298C) in essential hypertensive subjects. Plasma total homocysteine and folic acid levels were measured in essential hypertensive patients (n = 153) before and after oral supplementation with either 5 mg folic acid tablet/day or 5 mg placebo/day for 4 weeks and compared with age and sex matched normotensive controls (n = 133). MTHFR gene polymorphisms (C677T and A1298C) were studied by restriction fragment length polymorphism and correlated with plasma homocysteine levels. Homocysteine levels were significantly higher in hypertensive patients as compared to controls and showed a negative correlation with plasma folate levels. Folic acid supplementation (5 mg/day) for 4 weeks resulted in a significant decrease in plasma homocysteine concentrations in these patients. Patients carrying MTHFR 677T allele (OR = 1.90; 95%CI: 1.14-3.19) or MTHFR 1298C (OR = 2.6, 95%CI: 1.55-4.40) allele were at increased risk of hypertension. The frequency of co-occurrence of MTHFR 677 CT/1298 CC genotypes was significantly higher in the patients compared to controls (P < 0.05) and was associated with increased risk of hypertension (OR = 3.54, 95%CI: 0.37-4.30). Subjects with MTHFR 1298 CC genotype had significantly higher homocysteine levels compared to those with MTHFR 1298 AA genotype (P < 0.05). Our results indicate that MTHFR 677T and 1298C alleles and co-occurrence of MTHFR 677 CT/MTHFR 1298 CC genotypes are associated with increased risk of hypertension and MTHFR 1298 CC genotype is associated with higher homocysteine levels in our subjects. PMID:17333388

  4. AAS 227: Day 4

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    Editors Note:This week were at the 227th AAS Meeting in Kissimmee, FL. Along with several fellow authors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting at the end of each day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Welcome to Day 4 of the winter American Astronomical Society (AAS) meeting in Kissimmee! Several of us are attending the conference this year, and we will report highlights from each day here on astrobites. If youd like to see more timely updates during the day, we encourage you to follow @astrobites on twitter or search the #aas227 hashtag.Helen B. Warner Prize: Origins of Structure in Planetary Systems (by Erika Nesvold)Another excellent prize lecture started off todays sessions. The Helen B. Warner Prize is awarded for achievement in observational or theoretical astrophysics by a young researcher (no more than eight years after their Ph.D.). This years Warner Prize was presented to Ruth Murray-Clay of UC Santa Barbara. For her award lecture, Murray-Clay told us all about planetary system architecture: the number, masses, and orbits of planets in a given system.Ruth Murray-Clay [photo from http://web.physics.ucsb.edu/ ~murray/biocv.html]The underlying question motivating this type of research is: How rare is the Solar System? In other words, how likely is it that a given planetary system will have rocky planets close to their star, gas giants farther out, and ice giants at the outer reaches of the system? Answering this question will help us solve the physics problem of how and where planets form, and will also help us on our search for other planets like Earth.The data on exoplanet population from transit and radial velocity observations and from direct imaging tell us that our Solar System is not common (many systems we observe have much more eccentric gas giants), but that doesnt

  5. Smarter clustering methods for SNP genotype calling

    PubMed Central

    Lin, Yan; Tseng, George C.; Cheong, Soo Yeon; Bean, Lora J. H.; Sherman, Stephanie L.; Feingold, Eleanor

    2008-01-01

    Motivation: Most genotyping technologies for single nucleotide polymorphism (SNP) markers use standard clustering methods to ‘call’ the SNP genotypes. These methods are not always optimal in distinguishing the genotype clusters of a SNP because they do not take advantage of specific features of the genotype calling problem. In particular, when family data are available, pedigree information is ignored. Furthermore, prior information about the distribution of the measurements for each cluster can be used to choose an appropriate model-based clustering method and can significantly improve the genotype calls. One special genotyping problem that has never been discussed in the literature is that of genotyping of trisomic individuals, such as individuals with Down syndrome. Calling trisomic genotypes is a more complicated problem, and the addition of external information becomes very important. Results: In this article, we discuss the impact of incorporating external information into clustering algorithms to call the genotypes for both disomic and trisomic data. We also propose two new methods to call genotypes using family data. One is a modification of the K-means method and uses the pedigree information by updating all members of a family together. The other is a likelihood-based method that combines the Gaussian or beta-mixture model with pedigree information. We compare the performance of these two methods and some other existing methods using simulation studies. We also compare the performance of these methods on a real dataset generated by the Illumina platform (www.illumina.com). Availability: The R code for the family-based genotype calling methods (SNPCaller) is available to be downloaded from the following website: http://watson.hgen.pitt.edu/register. Contact: liny@upmc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18826959

  6. Genotyping Campylobacter jejuni by comparative genome indexing: an evaluation with pulsed-field gel electrophoresis and flaA SVR sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: Comparative genome indexing (CGI) using whole-genome DNA microarrays was evaluated as a means of genotying Campylobacter jejuni relative to two standard methods, pulsed-field gel electrophoresis (PFGE) and flaA short variable region sequencing (flaA SVR typing). Methods and Results: Thirty-six...

  7. AAS 228: Day 4

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note: Lastweek we were at the 228th AAS Meeting in San Diego, CA. Here is a final post aboutselectedevents on the last day of the meeting, written by authors fromastrobites.com, a grad-student collaborative project with which we recently announced a new partnership! Starting in July,keep an eye out for astrobites postsat AAS Nova in between Highlights(i.e., on Tuesdays and Thursdays).Were excited to be working together to bring you more recent astronomy research from AAS journals!Extrasolar Planets: Detection (by Leonardo dos Santos)Thursdays first session on exoplanets was about detecting these distant worlds, and the opening talk was given by Robert Siverd (Las Cumbres Observatory). He describes the NRES, a network of spectrographs that will look for exoplanets using the radial velocity method. One of the coolest aspects of this instrument is that it will feature an on the fly scheduling system that will perform observations as efficiently as possible. The spectrograph is still being tested, but a unit will be deployed at CTIO later this year.@lcogt contracted by @NASA_TESS for follow up of their candidates. #aas228 Jessie Christiansen (@aussiastronomer) June 16, 2016Measuring the depths of transits and eclipses in Spitzer has been problematic in the past, since the Spitzer instrument IRAC (InfraRed Array Camera) has a non-uniform response in its detectors pixels. But, as reported by James Ingalls (Spitzer Science Center, Caltech), observers are circumventing this issue by using what they call the staring mode (avoiding large pointing jumps) and an algorithm to pick sweet spot pixels. Moreover, the results from the IRAC Data Challenge are helping to better understand its behavior. Giuseppe Morello (University College London), on the other hand, explained how his research group gets rid of instrumental effects from IRAC using machine learning. This method removes systematics from exoplanet transit data no matter if the noise source is from an instrument or

  8. Use of immuno-dominant epitope derived from genotype 4 as a diagnostic reagent for detecting the antibodies against Hepatitis E Virus

    PubMed Central

    2013-01-01

    Background Despite the genotype 4 has become the dominant cause of hepatitis E disease in China, none antigen derived from genotype 4 of hepatitis E virus (HEV) was used in current commercial anti-HEV immunoassay, and the serological reactivity of antigen derive from genotype 4 is not well-charactered. Methods We expressed and purified the 4 main immuno-dominant epitopes derived from genotype 1 and 4 including ORF2 (410-621aa) of genotype 4, ORF3 (47-114aa) of genotype 4, ORF2 (396-606aa) of genotype 1 and ORF3 (56-123aa) of genotype 4. Results The ORF2 of genotype 4 displayed good diagnostics performance according to ROC analysis using in-house panel, and the immunoassays based the ORF2 of genotype 4 was then developed to detect the anti-HEV IgG antibodies and evaluated further in 530 anti-HEV IgG positive specimens and 380 negative specimens. The sensitivity and the specificity is 98.1% (520/530) and 94.7% (360/380) for immunoassay based on ORF2 of genotype 4, 96.6% (512/530) and 92.6% (352/380) for commercial immunoassay based on genotype 1. It is noted that all of the positive samples will be detected by combing two assays together. The anti-HEV immunoassays based on genotype 4 are in accordance with Chinese anti-HEV national standard,and show an good agreement of 95.8% with commercial assay (kappa=0.913, P=0.014). Conclusions The immunoassay based on ORF2G4 displays good performance, and combining assay based on genotype 1 together with genotype 4 will benefit the HEV diagnosis in large scale samples. PMID:23618011

  9. AAS 227: Day 4

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    Editors Note:This week were at the 227th AAS Meeting in Kissimmee, FL. Along with several fellow authors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting at the end of each day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Welcome to Day 4 of the winter American Astronomical Society (AAS) meeting in Kissimmee! Several of us are attending the conference this year, and we will report highlights from each day here on astrobites. If youd like to see more timely updates during the day, we encourage you to follow @astrobites on twitter or search the #aas227 hashtag.Helen B. Warner Prize: Origins of Structure in Planetary Systems (by Erika Nesvold)Another excellent prize lecture started off todays sessions. The Helen B. Warner Prize is awarded for achievement in observational or theoretical astrophysics by a young researcher (no more than eight years after their Ph.D.). This years Warner Prize was presented to Ruth Murray-Clay of UC Santa Barbara. For her award lecture, Murray-Clay told us all about planetary system architecture: the number, masses, and orbits of planets in a given system.Ruth Murray-Clay [photo from http://web.physics.ucsb.edu/ ~murray/biocv.html]The underlying question motivating this type of research is: How rare is the Solar System? In other words, how likely is it that a given planetary system will have rocky planets close to their star, gas giants farther out, and ice giants at the outer reaches of the system? Answering this question will help us solve the physics problem of how and where planets form, and will also help us on our search for other planets like Earth.The data on exoplanet population from transit and radial velocity observations and from direct imaging tell us that our Solar System is not common (many systems we observe have much more eccentric gas giants), but that doesnt

  10. AAS 228: Day 3 morning

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Plenary Session 2015 Newton Lacy Pierce Prize Lecture: The Elephant in the Room: Effects of Distant, Massive Companions on Planetary System Architectures (by Leonardo dos Santos)The first session on Wednesday at 228th AAS Meeting was the Newton Lacy Pierce Prize Lecture by Heather Knutson (California Institute of Technology). This talk featured a broad range of research efforts on exoplanets, with the main focus on how we study the composition of their atmospheres, and how multi-body interactions carve the structure of the planetary systems we observe.One of her first points is the well-known idea that the Solar System is an oddball, compared to the exoplanet systems we have found so far: most of these systems contain hot Jupiters and mini-Neptunes at very close-in orbits around their host stars. Moreover, even when studying their transmission spectra, it is difficult to know the exact composition of their atmospheres.Knutson: it is difficult to constrain atmospheric composition of exoplanets (H-poor or H-rich+clouds?) #aas228pic.twitter.com/LdyN4o9RC7 astrobites (@astrobites) June 15, 2016The main proposal on how these systems formed is the migration scenario. In order to validate this idea, Dr. Knutson and her group The Friends of Hot Jupiters study systems with close-in gas giants and their frequency of binary companions, which are supposed to be the main culprits causing gas-giant migration. They found that approximately half of the observed systems have long-distance companions, providing strong validation of the migration scenario. Moreover, Dr. Knutson speculates that wide binaries have more

  11. Analyses of Genotypes and Phenotypes of Ten Chinese Patients with Wolf-Hirschhorn Syndrome by Multiplex Ligation-dependent Probe Amplification and Array Comparative Genomic Hybridization

    PubMed Central

    Yang, Wen-Xu; Pan, Hong; Li, Lin; Wu, Hai-Rong; Wang, Song-Tao; Bao, Xin-Hua; Jiang, Yu-Wu; Qi, Yu

    2016-01-01

    Background: Wolf-Hirschhorn syndrome (WHS) is a contiguous gene syndrome that is typically caused by a deletion of the distal portion of the short arm of chromosome 4. However, there are few reports about the features of Chinese WHS patients. This study aimed to characterize the clinical and molecular cytogenetic features of Chinese WHS patients using the combination of multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (array CGH). Methods: Clinical information was collected from ten patients with WHS. Genomic DNA was extracted from the peripheral blood of the patients. The deletions were analyzed by MLPA and array CGH. Results: All patients exhibited the core clinical symptoms of WHS, including severe growth delay, a Greek warrior helmet facial appearance, differing degrees of intellectual disability, and epilepsy or electroencephalogram anomalies. The 4p deletions ranged from 2.62 Mb to 17.25 Mb in size and included LETM1, WHSC1, and FGFR3. Conclusions: The combined use of MLPA and array CGH is an effective and specific means to diagnose WHS and allows for the precise identification of the breakpoints and sizes of deletions. The deletion of genes in the WHS candidate region is closely correlated with the core WHS phenotype. PMID:26960370

  12. Comparative Genotypic and Phenotypic Analysis of Cronobacter Species Cultured from Four Powdered Infant Formula Production Facilities: Indication of Pathoadaptation along the Food Chain

    PubMed Central

    Yan, Qiongqiong; Wang, Juan; Gangiredla, Jayanthi; Cao, Yu; Martins, Marta; Gopinath, Gopal R.; Stephan, Roger; Lampel, Keith; Tall, Ben D.

    2015-01-01

    Cronobacter species are opportunistic pathogens commonly found in the environment. Among the seven Cronobacter species, Cronobacter sakazakii sequence type 4 (ST-4) is predominantly associated with recorded cases of infantile meningitis. This study reports on a 26-month powdered infant formula (PIF) surveillance program in four production facilities located in distinct geographic regions. The objective was to identify the ST(s) in PIF production environments and to investigate the phenotypic features that support their survival. Of all 168 Cronobacter isolates, 133 were recovered from a PIF production environment, 31 were of clinical origin, and 4 were laboratory type strains. Sequence type 1 (n = 84 isolates; 63.9%) was the dominant type in PIF production environments. The majority of these isolates clustered with an indistinguishable pulsotype and persisted for at least an 18-month period. Moreover, DNA microarray results identified two phylogenetic lineages among ST-4 strains tested. Thereafter, the ST-1 and -4 isolates were phenotypically compared. Differences were noted based on the phenotypes expressed by these isolates. The ST-1 PIF isolates produced stronger biofilms at both 28°C and 37°C, while the ST-4 clinical isolates exhibited greater swimming activity and increased binding to Congo red dye. Given the fact that PIF is a low-moisture environment and that the clinical environment provides for an interaction between the pathogen and its host, these differences may be consistent with a form of pathoadaptation. These findings help to extend our current understanding of the epidemiology and ecology of Cronobacter species in PIF production environments. PMID:25911470

  13. Comparative Genotypic and Phenotypic Analysis of Cronobacter Species Cultured from Four Powdered Infant Formula Production Facilities: Indication of Pathoadaptation along the Food Chain.

    PubMed

    Yan, Qiongqiong; Wang, Juan; Gangiredla, Jayanthi; Cao, Yu; Martins, Marta; Gopinath, Gopal R; Stephan, Roger; Lampel, Keith; Tall, Ben D; Fanning, Séamus

    2015-07-01

    Cronobacter species are opportunistic pathogens commonly found in the environment. Among the seven Cronobacter species, Cronobacter sakazakii sequence type 4 (ST-4) is predominantly associated with recorded cases of infantile meningitis. This study reports on a 26-month powdered infant formula (PIF) surveillance program in four production facilities located in distinct geographic regions. The objective was to identify the ST(s) in PIF production environments and to investigate the phenotypic features that support their survival. Of all 168 Cronobacter isolates, 133 were recovered from a PIF production environment, 31 were of clinical origin, and 4 were laboratory type strains. Sequence type 1 (n = 84 isolates; 63.9%) was the dominant type in PIF production environments. The majority of these isolates clustered with an indistinguishable pulsotype and persisted for at least an 18-month period. Moreover, DNA microarray results identified two phylogenetic lineages among ST-4 strains tested. Thereafter, the ST-1 and -4 isolates were phenotypically compared. Differences were noted based on the phenotypes expressed by these isolates. The ST-1 PIF isolates produced stronger biofilms at both 28°C and 37°C, while the ST-4 clinical isolates exhibited greater swimming activity and increased binding to Congo red dye. Given the fact that PIF is a low-moisture environment and that the clinical environment provides for an interaction between the pathogen and its host, these differences may be consistent with a form of pathoadaptation. These findings help to extend our current understanding of the epidemiology and ecology of Cronobacter species in PIF production environments. PMID:25911470

  14. AAS 228: Day 3 morning

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Plenary Session 2015 Newton Lacy Pierce Prize Lecture: The Elephant in the Room: Effects of Distant, Massive Companions on Planetary System Architectures (by Leonardo dos Santos)The first session on Wednesday at 228th AAS Meeting was the Newton Lacy Pierce Prize Lecture by Heather Knutson (California Institute of Technology). This talk featured a broad range of research efforts on exoplanets, with the main focus on how we study the composition of their atmospheres, and how multi-body interactions carve the structure of the planetary systems we observe.One of her first points is the well-known idea that the Solar System is an oddball, compared to the exoplanet systems we have found so far: most of these systems contain hot Jupiters and mini-Neptunes at very close-in orbits around their host stars. Moreover, even when studying their transmission spectra, it is difficult to know the exact composition of their atmospheres.Knutson: it is difficult to constrain atmospheric composition of exoplanets (H-poor or H-rich+clouds?) #aas228pic.twitter.com/LdyN4o9RC7 astrobites (@astrobites) June 15, 2016The main proposal on how these systems formed is the migration scenario. In order to validate this idea, Dr. Knutson and her group The Friends of Hot Jupiters study systems with close-in gas giants and their frequency of binary companions, which are supposed to be the main culprits causing gas-giant migration. They found that approximately half of the observed systems have long-distance companions, providing strong validation of the migration scenario. Moreover, Dr. Knutson speculates that wide binaries have more

  15. Comparative Genotypes, Staphylococcal Cassette Chromosome mec (SCCmec) Genes and Antimicrobial Resistance amongst Staphylococcus epidermidis and Staphylococcus haemolyticus Isolates from Infections in Humans and Companion Animals

    PubMed Central

    McManus, Brenda A.; Coleman, David C.; Deasy, Emily C.; Brennan, Gráinne I.; O’ Connell, Brian; Monecke, Stefan; Ehricht, Ralf; Leggett, Bernadette; Leonard, Nola; Shore, Anna C.

    2015-01-01

    This study compares the characteristics of Staphylococcus epidermidis (SE) and Staphylococcus haemolyticus (SH) isolates from epidemiologically unrelated infections in humans (Hu) (28 SE-Hu; 8 SH-Hu) and companion animals (CpA) (12 SE-CpA; 13 SH-CpA). All isolates underwent antimicrobial susceptibility testing, multilocus sequence typing and DNA microarray profiling to detect antimicrobial resistance and SCCmec-associated genes. All methicillin-resistant (MR) isolates (33/40 SE, 20/21 SH) underwent dru and mecA allele typing. Isolates were predominantly assigned to sequence types (STs) within a single clonal complex (CC2, SE, 84.8%; CC1, SH, 95.2%). SCCmec IV predominated among MRSE with ST2-MRSE-IVc common to both Hu (40.9%) and CpA (54.5%). Identical mecA alleles and nontypeable dru types (dts) were identified in one ST2-MRSE-IVc Hu and CpA isolate, however, all mecA alleles and 2/4 dts detected among 18 ST2-MRSE-IVc isolates were closely related, sharing >96.5% DNA sequence homology. Although only one ST-SCCmec type combination (ST1 with a non-typeable [NT] SCCmec NT9 [class C mec and ccrB4]) was common to four MRSH-Hu and one MRSH-CpA, all MRSH isolates were closely related based on similar STs, SCCmec genes (V/VT or components thereof), mecA alleles and dts. Overall, 39.6% of MR isolates harbored NT SCCmec elements, and ACME was more common amongst MRSE and CpA isolates. Multidrug resistance (MDR) was detected among 96.7% of isolates but they differed in the prevalence of specific macrolide, aminoglycoside and trimethoprim resistance genes amongst SE and SH isolates. Ciprofloxacin, rifampicin, chloramphenicol [fexA, cat-pC221], tetracycline [tet(K)], aminoglycosides [aadD, aphA3] and fusidic acid [fusB] resistance was significantly more common amongst CpA isolates. SE and SH isolates causing infections in Hu and CpA hosts belong predominantly to STs within a single lineage, harboring similar but variable SCCmec genes, mecA alleles and dts. Host and

  16. Genotype-specific mutations in the polymerase gene of hepatitis B virus potentially associated with resistance to oral antiviral therapy.

    PubMed

    Mirandola, Silvia; Sebastiani, Giada; Rossi, Cristina; Velo, Emanuela; Erne, Elke Maria; Vario, Alessandro; Tempesta, Diego; Romualdi, Chiara; Campagnolo, Davide; Alberti, Alfredo

    2012-12-01

    The evolution of hepatitis B virus (HBV) and the role of different variants during antiviral therapy may be influenced by HBV genotype. We have therefore analysed substitutions potentially related to nucleos(t)ide analogues (NAs) resistance at 42 positions within RT-region in a cohort of patients with chronic hepatitis B in relation to HBV-genotype. RT mutations analysis was performed by direct sequencing in 200 NAs-naïve patients and in 64 LAM or LAM+ADV experienced patients with NAs resistance, infected mainly by HBV-genotypes D and A. 27 polymorphic-sites were identified among the 42 positions analysed and 64 novel mutations were detected in 23 positions. Genotype-D displayed the highest mutation frequency (6.4%) among all HBV-genotypes analysed. Single or multiple mutations were detected in 80% of naïve patients. Overall, the most frequent single mutations were at residues rt54, rt53 and rt91 which may associate with significantly lower HBV-DNA levels (p=0.001). Comparison with sequencing data of patients failing LMV or LAM+ADV therapy revealed an higher frequency of novel genotype-specific mutations if compared with naïve patients: 3 mutations under LAM monotherapy in HBV-D (rtS85F; rtL91I; rtC256G) and 3 mutations under ADV therapy in HBV-A (rtI53V; rtW153R; rtF221Y). In HBV-D treated patients the dominant resistance mutation was rtL80V (31.4%) and rtM204I (60%) in LAM+ADV group while LAM-treated patients showed a preference of rtM204V (51.9%). Interestingly, none of HBV-A patients had mutation rtM204I under ADV add-on treatment but all of them had the "V" AA substitution. These results suggested that in patients with CHB, HBV-genotype might be relevant in the evolution and development of drug resistance showing also different mutation patterns in the YMDD motif between HBV genotype D and A. PMID:23026293

  17. Systematic Review and Network Meta-Analysis of Randomized Controlled Trials: Comparative Effectiveness and Safety of Direct-Acting Antiviral Agents for Treatment-Naive Hepatitis C Genotype 1.

    PubMed

    Zhu, Gui-Qi; Zou, Zhuo-Lin; Zheng, Ji-Na; Chen, Da-Zhi; Zou, Tian-Tian; Shi, Ke-Qing; Zheng, Ming-Hua

    2016-03-01

    All possible direct-acting antiviral agent (DAA) regimens for treatment-naive hepatitis C genotype 1 were evaluated by many randomized controlled trials (RCTs). However, the optimum regimen remains inconclusive. We aim to compare interventions in terms of sustained virological response at 12 (SVR12) and 24 (SVR24) weeks after the end of treatment and adverse effects (AEs) (fatigue, headache, nausea, insomnia). PubMed, Embase, and the Cochrane Library were searched for RCTs until July 31, 2015. We estimated odds ratios (ORs) between treatments on clinical outcomes. Twenty-two eligible RCTs were included. Compared with peginterferon-ribavirin (PR), daclatasvir plus PR (OR 8.90, P < 0.001), faldaprevir plus PR (OR 3.72, P < 0.001), simeprevir plus PR (OR 3.59, P < 0.001), sofosbuvir plus PR (OR 4.69, P < 0.001) yield a significant effect in improving SVR12. Consistently, simeprevir plus PR (OR 3.49, P < 0.001), sofosbuvir plus PR (OR 4.51, P < 0.001), daclatasvir plus PR (OR 4.77, P < 0.001) also improved the rates of SVR24 significantly compared with PR. With respect to AEs, compared with PR, ledipasvir plus sofosbuvir plus PR (OR 2.13, P < 0.001) confer a significant AE in nausea, whereas daclatasvir plus PR (OR 0.20, P < 0.001 and OR 0.18, P < 0.001, respectively) lowered the incidence of fatigue and nausea significantly when compared with ledipasvir plus sofosbuvir plus PR. Daclatasvir plus PR was the most effective in SVR12 and SVR24, but caused an increased AEs profile (headache and insomnia). Combined ledipasvir with sofosbuvir or combination of PR was associated with higher incidence of fatigue and nausea. PMID:26945424

  18. Water limitation and rootstock genotype interact to alter grape berry metabolism through transcriptome reprogramming

    PubMed Central

    Berdeja, Mariam; Nicolas, Philippe; Kappel, Christian; Dai, Zhan Wu; Hilbert, Ghislaine; Peccoux, Anthony; Lafontaine, Magali; Ollat, Nathalie; Gomès, Eric; Delrot, Serge

    2015-01-01

    Grapevine is a perennial crop often cultivated by grafting a scion cultivar on a suitable rootstock. Rootstocks influence scions, particularly with regard to water uptake and vigor. Therefore, one of the possibilities to adapt viticulture to the extended drought stress periods is to select rootstocks conferring increased tolerance to drought. However, the molecular mechanisms associated with the ability of rootstock/scion combination to influence grape berry metabolism under drought stress are still poorly understood. The transcriptomic changes induced by drought stress in grape berries (cv. Pinot noir) from vines grafted on either 110R (drought-tolerant) or 125AA (drought-sensitive) rootstock were compared. The experiments were conducted in the vineyard for two years and two grape berry developmental stages (50% and 100% veraison). The genome-wide microarray approach showed that water stress strongly impacts gene expression in the berries, through ontology categories that cover cell wall metabolism, primary and secondary metabolism, signaling, stress, and hormones, and that some of these effects strongly depend on the rootstock genotype. Indeed, under drought stress, berries from vines grafted on 110R displayed a different transcriptional response compared to 125AA-concerning genes related to jasmonate (JA), phenylpropanoid metabolism, and pathogenesis-related proteins. The data also suggest a link between JA and secondary metabolism in water-stressed berries. Overall, genes related to secondary metabolism and JA are more induced and/or less repressed by drought stress in the berries grafted on the drought-sensitive rootstock 125AA. These rootstock-dependent gene expression changes are relevant for berry composition and sensory properties. PMID:26504567

  19. Association of RBP4 Genotype with Phenotypic Reproductive Traits of Sows.

    PubMed

    Marantidis, A; Laliotis, G P; Avdi, M

    2016-01-01

    PCR-RFLP was applied to a commercial crossbred pig population in order to investigate the association between polymorphism (SNP) of Retinol-binding protein 4 (RBP4) gene and reproductive performance. 400 sows were genotyped and 2000 records of reproductive traits were used in order to retrieve information about the allele frequencies and the association of the RBP4 gene with main reproductive characteristics of the population. A deviation from the Hardy-Weinberg equilibrium was observed as a result of the AB genotype excess. In addition, the AA genotype saw statistically significant higher values of (i) the total number of born piglets (p < 0.05), (ii) the number of piglets born alive (p < 0.01), and (iii) the number of weaned piglets (p < 0.01). The number of the mummified piglets and the number of the piglets born dead did not differ between the various RBP4 genotypes. Interestingly, the AA genotype had a negative impact (p < 0.05) on the number of piglets born dead, resulting indirectly in a larger litter size. In conclusion, the AA genotype and in extension the A allele of RBP4 gene are in favor of producing larger litter size, suggesting that the RBP4 gene may be used in Marker-Assisted Selection (MAS) programs for a rapid improvement of the reproductive characteristics in pigs. PMID:26885398

  20. Association of RBP4 Genotype with Phenotypic Reproductive Traits of Sows

    PubMed Central

    Marantidis, A.; Laliotis, G. P.; Avdi, M.

    2016-01-01

    PCR-RFLP was applied to a commercial crossbred pig population in order to investigate the association between polymorphism (SNP) of Retinol-binding protein 4 (RBP4) gene and reproductive performance. 400 sows were genotyped and 2000 records of reproductive traits were used in order to retrieve information about the allele frequencies and the association of the RBP4 gene with main reproductive characteristics of the population. A deviation from the Hardy-Weinberg equilibrium was observed as a result of the AB genotype excess. In addition, the AA genotype saw statistically significant higher values of (i) the total number of born piglets (p < 0.05), (ii) the number of piglets born alive (p < 0.01), and (iii) the number of weaned piglets (p < 0.01). The number of the mummified piglets and the number of the piglets born dead did not differ between the various RBP4 genotypes. Interestingly, the AA genotype had a negative impact (p < 0.05) on the number of piglets born dead, resulting indirectly in a larger litter size. In conclusion, the AA genotype and in extension the A allele of RBP4 gene are in favor of producing larger litter size, suggesting that the RBP4 gene may be used in Marker-Assisted Selection (MAS) programs for a rapid improvement of the reproductive characteristics in pigs. PMID:26885398

  1. Distribution of Hepatitis C Virus Genotypes in Bahrain

    PubMed Central

    Janahi, Essam M.; Al-Mannai, Mariam; Singh, Hemlata; Jahromi, Mohamed M.

    2015-01-01

    Background: Approximately 170 million people are infected with Hepatitis C virus (HCV) worldwide, making it one of the world’s major infectious diseases. There are no published population based studies about the prevalence of HCV genotypes in Bahrain. Objectives: Therefore, the aim of the present study was to investigate the prevalence and distribution of HCV genotypes and subtypes among a large sample of patients with chronic HCV infection in Bahrain. Patients and Methods: Serum samples were collected from 202 HCV positive patients; of them 128 had a viral load (> 500 IU/mL) suitable for the type-specific genotyping assay. Gender-wise and age-wise differences in the distribution of HCV genotypes were determined by Chi Square and Fisher’s Exact tests. Results: The predominant genotype among Bahraini patients was type 1 (36.71%), followed by genotypes 3 and 4 (15.6% each) and the lowest frequency was found for genotype 2 (3.9%). Among genotype 1, subtype 1b had the highest frequency (21.09%), followed by subtype 1a (14.06%). Among genotype 3, subtype 3a had the highest frequency (11.72%), while among genotype 4, most of subtypes were undetermined. The frequency of all different HCV genotypes was higher in male patients compared to female patients. Genotype 1 was most common in the age group of 51 - 60 years (38.3%), genotype 2 in 21 - 30 years (60%) and genotype 3 in 51 - 60 years (30%), while genotype 4 was most frequent among the age group > 61 (40%). Conclusions: The most common HCV genotype in Bahrain was subtype 1b followed by 1a and 3a. Further studies involving sources of transmission in Bahrain are required to enhance control measures for HCV infection. PMID:26977163

  2. Donor KIR B Genotype Improves Progression-Free Survival of Non-Hodgkin Lymphoma Patients Receiving Unrelated Donor Transplantation.

    PubMed

    Bachanova, Veronika; Weisdorf, Daniel J; Wang, Tao; Marsh, Steven G E; Trachtenberg, Elizabeth; Haagenson, Michael D; Spellman, Stephen R; Ladner, Martha; Guethlein, Lisbeth A; Parham, Peter; Miller, Jeffrey S; Cooley, Sarah A

    2016-09-01

    Donor killer immunoglobulin-like receptor (KIR) genotypes are associated with relapse protection and survival after allotransplantation for acute myelogenous leukemia. We examined the possibility of a similar effect in a cohort of 614 non-Hodgkin lymphoma (NHL) patients receiving unrelated donor (URD) T cell-replete marrow or peripheral blood grafts. Sixty-four percent (n = 396) of donor-recipient pairs were 10/10 allele HLA matched and 26% were 9/10 allele matched. Seventy percent of donors had KIR B/x genotype; the others had KIR A/A genotype. NHL patients receiving 10/10 HLA-matched URD grafts with KIR B/x donors experienced significantly lower relapse at 5 years (26%; 95% confidence interval [CI], 21% to 32% versus 37%; 95% CI, 27% to 46%; P = .05) compared with KIR A/A donors, resulting in improved 5-year progression-free survival (PFS) (35%; 95% CI, 26% to 44% versus 22%; 95% CI, 11% to 35%; P = .007). In multivariate analysis, use of KIR B/x donors was associated with significantly reduced relapse risk (relative risk [RR], .63, P = .02) and improved PFS (RR, .71, P = .008). The relapse protection afforded by KIR B/x donors was not observed in HLA-mismatched transplantations and was not specific to any particular KIR-B gene. Selecting 10/10 HLA-matched and KIR B/x donors should benefit patients with NHL receiving URD allogeneic transplantation. PMID:27220262

  3. Genotype-Dependent Effects of Dalcetrapib on Cholesterol Efflux and Inflammation

    PubMed Central

    Rhainds, David; Brodeur, Mathieu; Feroz Zada, Yassamin; Fouodjio, René; Provost, Sylvie; Boulé, Marie; Alem, Sonia; Grégoire, Jean C.; L’Allier, Philippe L.; Ibrahim, Reda; Guertin, Marie-Claude; Mongrain, Ian; Olsson, Anders G.; Schwartz, Gregory G.; Rhéaume, Eric

    2016-01-01

    Background— Dalcetrapib effects on cardiovascular outcomes are determined by adenylate cyclase 9 gene polymorphisms. Our aim was to determine whether these clinical end point results are also associated with changes in reverse cholesterol transport and inflammation. Methods and Results— Participants of the dal-OUTCOMES and dal-PLAQUE-2 trials were randomly assigned to receive dalcetrapib or placebo in addition to standard care. High-sensitivity C-reactive protein was measured at baseline and at end of study in 5243 patients from dal-OUTCOMES also genotyped for the rs1967309 polymorphism in adenylate cyclase 9. Cholesterol efflux capacity of high-density lipoproteins from J774 macrophages after cAMP stimulation was determined at baseline and 12 months in 171 genotyped patients from dal-PLAQUE-2. Treatment with dalcetrapib resulted in placebo-adjusted geometric mean percent increases in high-sensitivity C-reactive protein from baseline to end of trial of 18.1% (P=0.0009) and 18.7% (P=0.00001) in participants with the GG and AG genotypes, respectively, but the change was −1.0% (P=0.89) in those with the protective AA genotype. There was an interaction between the treatment arm and the genotype groups (P=0.02). Although the mean change in cholesterol efflux was similar among study arms in patients with GG genotype (mean: 7.8% and 7.4%), increases were 22.3% and 3.5% with dalcetrapib and placebo for those with AA genotype (P=0.005). There was a significant genetic effect for change in efflux for dalcetrapib (P=0.02), but not with placebo. Conclusions— Genotype-dependent effects on C-reactive protein and cholesterol efflux are supportive of dalcetrapib benefits on atherosclerotic cardiovascular outcomes in patients with the AA genotype at polymorphism rs1967309. Clinical Trials Registration— ClinicalTrials.gov; Unique Identifiers: NCT00658515 and NCT01059682. PMID:27418594

  4. Antioxidant Bioactive Compounds Changes in Fruit of Quince Genotypes Over Cold Storage.

    PubMed

    Moradi, Samira; Koushesh Saba, Mahmoud; Mozafari, Ali Akbar; Abdollahi, Hamid

    2016-07-01

    Quince fruit has many benefits to human health and is excellent source of bioactive compounds. The fruit of 15 quince genotypes stored at 2 °C for 5 mo to study fruit quality changes during cold storage. Fruit were sampled monthly and stored at 20 °C for 24 h. Fruit ascorbic acid (AA), total phenol (TP), and total flavonoid (TF) concentrations, total antioxidant activity (TAA), flesh browning (FB) incidence, polyphenol oxidase (PPO), peroxidase (POX), and superoxide dismutase (SOD) activities were measured during storage. A high variation in bioactive compounds was observed across genotypes. The range of 26.8 to 44.4 mg/100 g FW for AA, 86.7% to 98.2% for TAA, 157.7 to 380.7 mg GAE 100(-1) g FW for TP, and 5.3 to 10.7 mg/100 g FW for TF were observed across genotypes at harvest time. The overall AA, TAA, TP, TF, and SOD decreased while PPO and POX increased during storage. FB was first observed after 4 mo and increased thereafter while the FB index was different across genotypes. Higher bioactive content may prevent or reduce FB index so that a negative correlation was found between FB and AA, TAA, TP, TF, and SOD. PMID:27273124

  5. HIV Genotypic Resistance Testing

    MedlinePlus

    ... be limited. Home Visit Global Sites Search Help? HIV Antiretroviral Drug Resistance Testing, Genotypic Share this page: Was this page helpful? Also known as: Anti-retroviral Drug Resistance Testing; ARV Resistance Testing Formal name: ...

  6. HCV genotypes in Morocco.

    PubMed

    Benani, A; El-Turk, J; Benjelloun, S; Sekkat, S; Nadifi, S; Hda, N; Benslimane, A

    1997-08-01

    To determine the hepatitis C virus (HCV) genotypes circulating in Morocco, virus isolates from 105 chronically infected and 19 hemodialysis patients were examined using the line probe assay. Genotypes 1 and 2 only were found among Moroccan patients. Subtypes 1b (47.6%) and 2a/2c (37.1%) were the most common, whereas subtype 1a (2.8%) was less common. Among the hemodialysis patients, only genotype 1 was found with a prevalence of 68.4% for subtype 1b and 15.8% for the subtype 1a. It was also shown that the HCV genotypes distribution varies with age in both studied populations. Subtype 1b was most prevalent among older patients, whereas subtype 2a/2c was mainly found among younger ones. Although Morocco belongs to the African continent, the circulating HCV strains are similar to those observed in some American and European countries. PMID:9260687

  7. APOE Genotyping, Cardiovascular Disease

    MedlinePlus

    ... Risk Assessment ; HDL Cholesterol ; LDL Cholesterol ; Lipid Profile ; Triglycerides Were you looking instead for APOE genotyping ordered ... the skin called xanthomas, a high level of triglycerides in the blood, and atherosclerosis that develops at ...

  8. Genotype imputation in the domestic dog.

    PubMed

    Friedenberg, S G; Meurs, K M

    2016-10-01

    Application of imputation methods to accurately predict a dense array of SNP genotypes in the dog could provide an important supplement to current analyses of array-based genotyping data. Here, we developed a reference panel of 4,885,283 SNPs in 83 dogs across 15 breeds using whole genome sequencing. We used this panel to predict the genotypes of 268 dogs across three breeds with 84,193 SNP array-derived genotypes as inputs. We then (1) performed breed clustering of the actual and imputed data; (2) evaluated several reference panel breed combinations to determine an optimal reference panel composition; and (3) compared the accuracy of two commonly used software algorithms (Beagle and IMPUTE2). Breed clustering was well preserved in the imputation process across eigenvalues representing 75 % of the variation in the imputed data. Using Beagle with a target panel from a single breed, genotype concordance was highest using a multi-breed reference panel (92.4 %) compared to a breed-specific reference panel (87.0 %) or a reference panel containing no breeds overlapping with the target panel (74.9 %). This finding was confirmed using target panels derived from two other breeds. Additionally, using the multi-breed reference panel, genotype concordance was slightly higher with IMPUTE2 (94.1 %) compared to Beagle; Pearson correlation coefficients were slightly higher for both software packages (0.946 for Beagle, 0.961 for IMPUTE2). Our findings demonstrate that genotype imputation from SNP array-derived data to whole genome-level genotypes is both feasible and accurate in the dog with appropriate breed overlap between the target and reference panels. PMID:27129452

  9. Signaling Pathways Related to Protein Synthesis and Amino Acid Concentration in Pig Skeletal Muscles Depend on the Dietary Protein Level, Genotype and Developmental Stages

    PubMed Central

    Liu, Yingying; Li, Fengna; Kong, Xiangfeng; Tan, Bie; Li, Yinghui; Duan, Yehui; Blachier, François; Hu, Chien-An A.; Yin, Yulong

    2015-01-01

    Muscle growth is regulated by the homeostatic balance of the biosynthesis and degradation of muscle proteins. To elucidate the molecular interactions among diet, pig genotype, and physiological stage, we examined the effect of dietary protein concentration, pig genotype, and physiological stages on amino acid (AA) pools, protein deposition, and related signaling pathways in different types of skeletal muscles. The study used 48 Landrace pigs and 48 pure-bred Bama mini-pigs assigned to each of 2 dietary treatments: lower/GB (Chinese conventional diet)- or higher/NRC (National Research Council)-protein diet. Diets were fed from 5 weeks of age to respective market weights of each genotype. Samples of biceps femoris muscle (BFM, type I) and longissimus dorsi muscle (LDM, type II) were collected at nursery, growing, and finishing phases according to the physiological stage of each genotype, to determine the AA concentrations, mRNA levels for growth-related genes in muscles, and protein abundances of mechanistic target of rapamycin (mTOR) signaling pathway. Our data showed that the concentrations of most AAs in LDM and BFM of pigs increased (P<0.05) gradually with increasing age. Bama mini-pigs had generally higher (P<0.05) muscle concentrations of flavor-related AA, including Met, Phe, Tyr, Pro, and Ser, compared with Landrace pigs. The mRNA levels for myogenic determining factor, myogenin, myocyte-specific enhancer binding factor 2 A, and myostatin of Bama mini-pigs were higher (P<0.05) than those of Landrace pigs, while total and phosphorylated protein levels for protein kinase B, mTOR, and p70 ribosomal protein S6 kinases (p70S6K), and ratios of p-mTOR/mTOR, p-AKT/AKT, and p-p70S6K/p70S6K were lower (P<0.05). There was a significant pig genotype-dependent effect of dietary protein on the levels for mTOR and p70S6K. When compared with the higher protein-NRC diet, the lower protein-GB diet increased (P<0.05) the levels for mTOR and p70S6K in Bama mini-pigs, but

  10. Signaling Pathways Related to Protein Synthesis and Amino Acid Concentration in Pig Skeletal Muscles Depend on the Dietary Protein Level, Genotype and Developmental Stages.

    PubMed

    Liu, Yingying; Li, Fengna; Kong, Xiangfeng; Tan, Bie; Li, Yinghui; Duan, Yehui; Blachier, François; Hu, Chien-An A; Yin, Yulong

    2015-01-01

    Muscle growth is regulated by the homeostatic balance of the biosynthesis and degradation of muscle proteins. To elucidate the molecular interactions among diet, pig genotype, and physiological stage, we examined the effect of dietary protein concentration, pig genotype, and physiological stages on amino acid (AA) pools, protein deposition, and related signaling pathways in different types of skeletal muscles. The study used 48 Landrace pigs and 48 pure-bred Bama mini-pigs assigned to each of 2 dietary treatments: lower/GB (Chinese conventional diet)- or higher/NRC (National Research Council)-protein diet. Diets were fed from 5 weeks of age to respective market weights of each genotype. Samples of biceps femoris muscle (BFM, type I) and longissimus dorsi muscle (LDM, type II) were collected at nursery, growing, and finishing phases according to the physiological stage of each genotype, to determine the AA concentrations, mRNA levels for growth-related genes in muscles, and protein abundances of mechanistic target of rapamycin (mTOR) signaling pathway. Our data showed that the concentrations of most AAs in LDM and BFM of pigs increased (P<0.05) gradually with increasing age. Bama mini-pigs had generally higher (P<0.05) muscle concentrations of flavor-related AA, including Met, Phe, Tyr, Pro, and Ser, compared with Landrace pigs. The mRNA levels for myogenic determining factor, myogenin, myocyte-specific enhancer binding factor 2 A, and myostatin of Bama mini-pigs were higher (P<0.05) than those of Landrace pigs, while total and phosphorylated protein levels for protein kinase B, mTOR, and p70 ribosomal protein S6 kinases (p70S6K), and ratios of p-mTOR/mTOR, p-AKT/AKT, and p-p70S6K/p70S6K were lower (P<0.05). There was a significant pig genotype-dependent effect of dietary protein on the levels for mTOR and p70S6K. When compared with the higher protein-NRC diet, the lower protein-GB diet increased (P<0.05) the levels for mTOR and p70S6K in Bama mini-pigs, but

  11. Comparative Phenotypic and Molecular Genetic Profiling of Wild Lactococcus lactis subsp. lactis Strains of the L. lactis subsp. lactis and L. lactis subsp. cremoris Genotypes, Isolated from Starter-Free Cheeses Made of Raw Milk▿

    PubMed Central

    Fernández, Elena; Alegría, Ángel; Delgado, Susana; Martín, M. Cruz; Mayo, Baltasar

    2011-01-01

    Twenty Lactococcus lactis strains with an L. lactis subsp. lactis phenotype isolated from five traditional cheeses made of raw milk with no added starters belonging to the L. lactis subsp. lactis and L. lactis subsp. cremoris genotypes (lactis and cremoris genotypes, respectively; 10 strains each) were subjected to a series of phenotypic and genetic typing methods, with the aims of determining their phylogenetic relationships and suitability as starters. Pulsed-field gel electrophoresis (PFGE) analysis of intact genomes digested with SalI and SmaI proved that all strains were different except for three isolates of the cremoris genotype, which showed identical PFGE profiles. Multilocus sequence typing (MLST) analysis using internal sequences of seven loci (namely, atpA, rpoA, pheS, pepN, bcaT, pepX, and 16S rRNA gene) revealed considerable intergenotype nucleotide polymorphism, although deduced amino acid changes were scarce. Analysis of the MLST data for the present strains and others from other dairy and nondairy sources showed that all of them clustered into the cremoris or lactis genotype group, by using both independent and combined gene sequences. These two groups of strains also showed distinctive carbohydrate fermentation and enzyme activity profiles, with the strains in the cremoris group showing broader profiles. However, the profiles of resistance/susceptibility to 16 antibiotics were very similar, showing no atypical resistance, except for tetracycline resistance in three identical cremoris genotype isolates. The numbers and concentrations of volatile compounds produced in milk by the strains belonging to these two groups were clearly different, with the cremoris genotype strains producing higher concentrations of more branched-chain, derived compounds. Together, the present results support the idea that the lactis and cremoris genotypes of phenotypic Lactococcus lactis subsp. lactis actually represent true subspecies. Some strains of the two subspecies

  12. Comparative Evaluation of GenoType MTBDRplus Line Probe Assay with Solid Culture Method in Early Diagnosis of Multidrug Resistant Tuberculosis (MDR-TB) at a Tertiary Care Centre in India

    PubMed Central

    Yadav, Raj N.; Singh, Binit K.; Sharma, Surendra K.; Sharma, Rohini; Soneja, Manish; Sreenivas, Vishnubhatla; Myneedu, Vithal P.; Hanif, Mahmud; Kumar, Ashok; Sachdeva, Kuldeep S.; Paramasivan, Chinnambedu N.; Vollepore, Balasangameshwra; Thakur, Rahul; Raizada, Neeraj; Arora, Suresh K.; Sinha, Sanjeev

    2013-01-01

    Background The objectives of the study were to compare the performance of line probe assay (GenoType MTBDRplus) with solid culture method for an early diagnosis of multidrug resistant tuberculosis (MDR-TB), and to study the mutation patterns associated with rpoB, katG and inhA genes at a tertiary care centre in north India. Methods In this cross-sectional study, 269 previously treated sputum-smear acid-fast bacilli (AFB) positive MDR-TB suspects were enrolled from January to September 2012 at the All India Institute of Medical Sciences hospital, New Delhi. Line probe assay (LPA) was performed directly on the sputum specimens and the results were compared with that of conventional drug susceptibility testing (DST) on solid media [Lowenstein Jensen (LJ) method]. Results DST results by LPA and LJ methods were compared in 242 MDR-TB suspects. The LPA detected rifampicin (RIF) resistance in 70 of 71 cases, isoniazid (INH) resistance in 86 of 93 cases, and MDR-TB in 66 of 68 cases as compared to the conventional method. Overall (rifampicin, isoniazid and MDR-TB) concordance of the LPA with the conventional DST was 96%. Sensitivity and specificity were 98% and 99% respectively for detection of RIF resistance; 92% and 99% respectively for detection of INH resistance; 97% and 100% respectively for detection of MDR-TB. Frequencies of katG gene, inhA gene and combined katG and inhA gene mutations conferring all INH resistance were 72/87 (83%), 10/87 (11%) and 5/87 (6%) respectively. The turnaround time of the LPA test was 48 hours. Conclusion The LPA test provides an early diagnosis of monoresistance to isoniazid and rifampicin and is highly sensitive and specific for an early diagnosis of MDR-TB. Based on these findings, it is concluded that the LPA test can be useful in early diagnosis of drug resistant TB in high TB burden countries. PMID:24039735

  13. Association of the vitamin D receptor genotype with bone metastases in breast cancer patients.

    PubMed

    Schöndorf, Thomas; Eisberg, Carsten; Wassmer, Gernot; Warm, Mathias; Becker, Martina; Rein, Daniel T; Göhring, Uwe-Jochen

    2003-01-01

    This study was designed in order to evaluate specific vitamin D receptor (VDR) genotypes as indicators of the likelihood of developing osseous metastases in breast cancer patients. Therefore, we determined polymorphisms of the VDR gene in a study group comprising 183 breast cancer patients. Specific fragments spanning over intron 8 and exon 9 of the VDR gene were amplified by polymerase chain reaction. The fragments were then incubated with each of the specific endonucleases APAI, BSMI or TAQI, respectively. The VDR gene polymorphisms were detected by the presence or absence of the particular restriction site using agarose gel electrophoresis. Statistical analyses revealed a significant correlation between both the VDR gene polymorphisms indicated as AA (absence of the APAI restriction site in both alleles) or TT (absence of the TAQI restriction site in both alleles), respectively, and the occurrence of bone metastases. Patients with the AA genotype have a 1.7-fold increased risk of developing bone metastases, whereas patients with the TT genotype have a 0.5-fold risk. Neither other genotypes nor allelic combinations displayed any further correlation with the clinical stage. The data suggest that the AA genotype of the VDR gene might be useful to identify breast cancer patients with a high probability of forming occult bone metastases who are considered to benefit from an adjuvant bone-protective therapy. PMID:12566913

  14. Antigenic composition and immunoreactivity differences between HEV recombinant capsid proteins generated from different genotypes.

    PubMed

    Behloul, Nouredine; Wen, Jiyue; Dai, Xing; Dong, Chen; Meng, Jihong

    2015-08-01

    Appreciable variability has been observed in hepatitis E virus (HEV) serological diagnostics. Four recombinant proteins (p166s) were generated from position 452 to 617 aa of ORF2 of different HEV genotypes and used in an indirect ELISA to detect anti-HEV IgMs and IgGs in serially diluted sera of patients infected with different HEV genotypes (genotype 1, n=15; genotype 3, n=12; genotype 4, n=17). To evaluate the differences at a conformational level, 3D-structure models of p166s were predicted, and different bioinformatics tools were used to analyze the antigenic composition. With both anti-HEV IgMs and IgGs antibodies, there was a considerable variability between the four antigens immunoreactivities. In silico results revealed the region 483-533 aa with the highest antigenic potential and contains six key aa at positions 488, 489, 512, 533, 483 and 530. This immunoreactivity variation could affect diagnosis results and seroprevalence estimations and the identification in silico of a region highly antigenic would guide the development of efficient serological assays and epitope-based vaccines. PMID:26122075

  15. Blood Group ABO Genotyping in Paternity Testing

    PubMed Central

    Bugert, Peter; Rink, Gabriele; Kemp, Katharina; Klüter, Harald

    2012-01-01

    Background The ABO blood groups result from DNA sequence variations, predominantly single nucleotide and insertion/deletion polymorphisms (SNPs and indels), in the ABO gene encoding a glycosyltransferase. The ABO blood groups A1, A2, B and O predominantly result from the wild type allele A1 and the major gene variants that are characterized by four diallelic markers (261G>del, 802G>A, 803G>C, 1061C>del). Here, we were interested to evaluate the impact of ABO genotyping compared to ABO phenotyping in paternity testing. Methods The major ABO alleles were determined by PCR amplification with sequence-specific primers (PCR-SSP) in a representative sample of 1,335 blood donors. The genotypes were compared to the ABO blood groups registered in the blood donor files. Then, the ABO phenotypes and genotypes were determined in 95 paternity trio cases that have been investigated by 12 short tandem repeat (STR) markers before. We compared statistical parameters (PL, paternity likelihood; PE, power of exclusion) of both blood grouping approaches. Results The prevalence of the major ABO alleles and genotypes corresponded to the expected occurrence of ABO blood groups in a Caucasian population. The low resolution genotyping of 4 diallelic markers revealed a correct genotype-phenotype correlation in 1,331 of 1,335 samples (99.7%). In 60 paternity trios with confirmed paternity of the alleged father based on STR analysis both PL and PE of the ABO genotype was significantly higher than of the ABO phenotype. In 12 of 35 exclusion cases (34.3%) the ABO genotype also excluded the alleged father, whereas the ABO phenotype excluded the alleged father only in 7 cases (20%). Conclusion In paternity testing ABO genotyping is superior to ABO phenotyping with regard to PL and PE, however, ABO genotyping is not sufficient for valid paternity testing. Due to the much lower mutation rate compared to STR markers, blood group SNPs in addition to anonymous SNPs could be considered for future

  16. Systemic AA amyloidosis in the common marmoset.

    PubMed

    Ludlage, E; Murphy, C L; Davern, S M; Solomon, A; Weiss, D T; Glenn-Smith, D; Dworkin, S; Mansfield, K G

    2005-03-01

    The common marmoset (Callithrix jacchus) is a small New World primate native to Brazil that has been used extensively in biomedical research. A retrospective analysis of archived hematoxylin and eosin-stained tissue sections and clinical records was conducted at the New England Primate Research Center on 86 marmosets more than 1 year of age that were euthanized during the past decade because of morbidity and failure to thrive. Approximately 17% (15 of 86) were found to have amyloid deposits in one or more organs, including the liver, adrenal glands, kidneys, and intestine. This material was shown by amino acid sequence analysis to be composed of serum amyloid A (SAA)-related protein. This type of amyloidosis, designated AA or "secondary," is associated typically with an inflammatory process that induces elevated levels of the SAA amyloidogenic precursor molecule. Notably, there were no significant pathologic differences or other distinguishing features in animals with amyloid versus those without; furthermore, on the basis of the limited number of serum specimens available for analysis, the SAA concentrations in the two groups were comparable, thus suggesting the possible inheritable nature of the disorder. In this respect, the common marmoset provides a unique experimental model for study of the pathogenesis and treatment of AA and other forms of systemic amyloidosis. PMID:15753464

  17. Antibodies Targeting Novel Neutralizing Epitopes of Hepatitis C Virus Glycoprotein Preclude Genotype 2 Virus Infection.

    PubMed

    Deng, Kai; Liu, Ruyu; Rao, Huiying; Jiang, Dong; Wang, Jianghua; Xie, Xingwang; Wei, Lai

    2015-01-01

    Currently, there is no effective vaccine to prevent hepatitis C virus (HCV) infection, partly due to our insufficient understanding of the virus glycoprotein immunology. Most neutralizing antibodies (nAbs) were identified using glycoprotein immunogens, such as recombinant E1E2, HCV pseudoparticles or cell culture derived HCV. However, the fact that in the HCV acute infection phase, only a small proportion of patients are self-resolved accompanied with the emergence of nAbs, indicates the limited immunogenicity of glycoprotein itself to induce effective antibodies against a highly evolved virus. Secondly, in previous reports, the immunogen sequence was mostly the genotype of the 1a H77 strain. Rarely, other genotypes/subtypes have been studied, although theoretically one genotype/subtype immunogen is able to induce cross-genotype neutralizing antibodies. To overcome these drawbacks and find potential novel neutralizing epitopes, 57 overlapping peptides encompassing the full-length glycoprotein E1E2 of subtype 1b were synthesized to immunize BALB/c mice, and the neutralizing reactive of the induced antisera against HCVpp genotypes 1-6 was determined. We defined a domain comprising amino acids (aa) 192-221, 232-251, 262-281 and 292-331 of E1, and 421-543, 564-583, 594-618 and 634-673 of E2, as the neutralizing regions of HCV glycoprotein. Peptides PUHI26 (aa 444-463) and PUHI45 (aa 604-618)-induced antisera displayed the most potent broad neutralizing reactive. Two monoclonal antibodies recognizing the PUHI26 and PUHI45 epitopes efficiently precluded genotype 2 viral (HCVcc JFH and J6 strains) infection, but they did not neutralize other genotypes. Our study mapped a neutralizing epitope region of HCV glycoprotein using a novel immunization strategy, and identified two monoclonal antibodies effective in preventing genotype 2 virus infection. PMID:26406225

  18. Antibodies Targeting Novel Neutralizing Epitopes of Hepatitis C Virus Glycoprotein Preclude Genotype 2 Virus Infection

    PubMed Central

    Rao, Huiying; Jiang, Dong; Wang, Jianghua; Xie, Xingwang; Wei, Lai

    2015-01-01

    Currently, there is no effective vaccine to prevent hepatitis C virus (HCV) infection, partly due to our insufficient understanding of the virus glycoprotein immunology. Most neutralizing antibodies (nAbs) were identified using glycoprotein immunogens, such as recombinant E1E2, HCV pseudoparticles or cell culture derived HCV. However, the fact that in the HCV acute infection phase, only a small proportion of patients are self-resolved accompanied with the emergence of nAbs, indicates the limited immunogenicity of glycoprotein itself to induce effective antibodies against a highly evolved virus. Secondly, in previous reports, the immunogen sequence was mostly the genotype of the 1a H77 strain. Rarely, other genotypes/subtypes have been studied, although theoretically one genotype/subtype immunogen is able to induce cross-genotype neutralizing antibodies. To overcome these drawbacks and find potential novel neutralizing epitopes, 57 overlapping peptides encompassing the full-length glycoprotein E1E2 of subtype 1b were synthesized to immunize BALB/c mice, and the neutralizing reactive of the induced antisera against HCVpp genotypes 1–6 was determined. We defined a domain comprising amino acids (aa) 192–221, 232–251, 262–281 and 292–331 of E1, and 421–543, 564–583, 594–618 and 634–673 of E2, as the neutralizing regions of HCV glycoprotein. Peptides PUHI26 (aa 444–463) and PUHI45 (aa 604–618)-induced antisera displayed the most potent broad neutralizing reactive. Two monoclonal antibodies recognizing the PUHI26 and PUHI45 epitopes efficiently precluded genotype 2 viral (HCVcc JFH and J6 strains) infection, but they did not neutralize other genotypes. Our study mapped a neutralizing epitope region of HCV glycoprotein using a novel immunization strategy, and identified two monoclonal antibodies effective in preventing genotype 2 virus infection. PMID:26406225

  19. Plant genotypic diversity reduces the rate of consumer resource utilization

    PubMed Central

    McArt, Scott H.; Thaler, Jennifer S.

    2013-01-01

    While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore—the Japanese beetle (Popillia japonica)—increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore. PMID:23658201

  20. Laboratory Astrophysics Division of The AAS (LAD)

    NASA Astrophysics Data System (ADS)

    Salama, Farid; Drake, R. P.; Federman, S. R.; Haxton, W. C.; Savin, D. W.

    2012-10-01

    The purpose of the Laboratory Astrophysics Division (LAD) is to advance our understanding of the Universe through the promotion of fundamental theoretical and experimental research into the underlying processes that drive the Cosmos. LAD represents all areas of astrophysics and planetary sciences. The first new AAS Division in more than 30 years, the LAD traces its history back to the recommendation from the scientific community via the White Paper from the 2006 NASA-sponsored Laboratory Astrophysics Workshop. This recommendation was endorsed by the Astronomy and Astrophysics Advisory Committee (AAAC), which advises the National Science Foundation (NSF), the National Aeronautics and Space Administration (NASA), and the U.S. Department of Energy (DOE) on selected issues within the fields of astronomy and astrophysics that are of mutual interest and concern to the agencies. In January 2007, at the 209th AAS meeting, the AAS Council set up a Steering Committee to formulate Bylaws for a Working Group on Laboratory Astrophysics (WGLA). The AAS Council formally established the WGLA with a five-year mandate in May 2007, at the 210th AAS meeting. From 2008 through 2012, the WGLA annually sponsored Meetings in-a-Meeting at the AAS Summer Meetings. In May 2011, at the 218th AAS meeting, the AAS Council voted to convert the WGLA, at the end of its mandate, into a Division of the AAS and requested draft Bylaws from the Steering Committee. In January 2012, at the 219th AAS Meeting, the AAS Council formally approved the Bylaws and the creation of the LAD. The inaugural gathering and the first business meeting of the LAD were held at the 220th AAS meeting in Anchorage in June 2012. You can learn more about LAD by visiting its website at http://lad.aas.org/ and by subscribing to its mailing list.

  1. Laboratory Astrophysics Division of the AAS (LAD)

    NASA Technical Reports Server (NTRS)

    Salama, Farid; Drake, R. P.; Federman, S. R.; Haxton, W. C.; Savin, D. W.

    2012-01-01

    The purpose of the Laboratory Astrophysics Division (LAD) is to advance our understanding of the Universe through the promotion of fundamental theoretical and experimental research into the underlying processes that drive the Cosmos. LAD represents all areas of astrophysics and planetary sciences. The first new AAS Division in more than 30 years, the LAD traces its history back to the recommendation from the scientific community via the White Paper from the 2006 NASA-sponsored Laboratory Astrophysics Workshop. This recommendation was endorsed by the Astronomy and Astrophysics Advisory Committee (AAAC), which advises the National Science Foundation (NSF), the National Aeronautics and Space Administration (NASA), and the U.S. Department of Energy (DOE) on selected issues within the fields of astronomy and astrophysics that are of mutual interest and concern to the agencies. In January 2007, at the 209th AAS meeting, the AAS Council set up a Steering Committee to formulate Bylaws for a Working Group on Laboratory Astrophysics (WGLA). The AAS Council formally established the WGLA with a five-year mandate in May 2007, at the 210th AAS meeting. From 2008 through 2012, the WGLA annually sponsored Meetings in-a-Meeting at the AAS Summer Meetings. In May 2011, at the 218th AAS meeting, the AAS Council voted to convert the WGLA, at the end of its mandate, into a Division of the AAS and requested draft Bylaws from the Steering Committee. In January 2012, at the 219th AAS Meeting, the AAS Council formally approved the Bylaws and the creation of the LAD. The inaugural gathering and the first business meeting of the LAD were held at the 220th AAS meeting in Anchorage in June 2012. You can learn more about LAD by visiting its website at http://lad.aas.org/ and by subscribing to its mailing list.

  2. Fetal Vegf Genotype is More Important for Abortion Risk than Mother Genotype

    PubMed Central

    Yalcintepe, Sinem Atik; Silan, Fatma; Hacivelioglu, Servet Ozden; Uludag, Ahmet; Cosar, Emine; Ozdemir, Ozturk

    2014-01-01

    VEGF gene has been reported to be related with many diseases and recurrent pregnancy loss in various studies. Concerning the role of VEGF polymorphisms in pregnancy losses, generally mothers genotypes have been analyzed. To evaluate the association between VEGF A +405G/C (rs2010963), −460T/C (rs833061), +936C/T (rs3025039) and - 2578A/C (rs699947) polymorphisms and spontaneous abortion, we studied the genotypes of spontaneously aborted fetuses, their mothers and healthy controls. 23 spontaneously aborted fetal materials, 22 mothers who had these abortions and 86 healthy controls were included in this study. rs2010963, rs833061, rs3025039 and rs699947 polymorphisms were analyzed by Real Time PCR technique after genomic DNA isolation from all subjects. The frequencies of VEGF A rs2010963 GG genotype and rs2010963 G allele were higher in fetuses compared both with mothers and healthy controls. VEGF A rs3025039 TT genotype and rs3025039 T allele frequencies were higher in fetuses comparing with mothers. VEGF A rs833061 CT and TT genotypes frequencies were higher in fetuses comparing with mothers. We ascertained that VEGF A rs2010963, rs833061 and rs3025039 are the risk factors for spontaneous abortion in fetal genotypes comparing with their mothers and healthy controls. PMID:25035858

  3. Constitutive behavior of as-cast AA1050, AA3104, and AA5182

    NASA Astrophysics Data System (ADS)

    van Haaften, W. M.; Magnin, B.; Kool, W. H.; Katgerman, L.

    2002-07-01

    Recent thermomechanical modeling to calculate the stress field in industrially direct-chill (DC) cast-aluminum slabs has been successful, but lack of material data limits the accuracy of these calculations. Therefore, the constitutive behavior of three aluminum alloys (AA1050, AA3104, and AA5182) was determined in the as-cast condition using tensile tests at low strain rates and from room temperature to solidus temperature. The parameters of two constitutive equations, the extended Ludwik equation and a combination of the Sellars-Tegart equation with a hardening law, were determined. In order to study the effect of recovery, the constitutive behavior after prestraining at higher temperatures was also investigated. To evaluate the quantified constitutive equations, tensile tests were performed simulating the deformation and cooling history experienced by the material during casting. It is concluded that both constitutive equations perform well, but the combined hardening-Sellars-Tegart (HST) equation has temperature-independent parameters, which makes it easier to implement in a DC casting model. Further, the deformation history of the ingot should be taken into account for accurate stress calculations.

  4. Influence of fresh forage-based diets and αs₁-casein (CSN1S1) genotype on nutrient intake and productive, metabolic, and hormonal responses in milking goats.

    PubMed

    Bonanno, A; Di Grigoli, A; Di Trana, A; Di Gregorio, P; Tornambè, G; Bellina, V; Claps, S; Maggio, G; Todaro, M

    2013-04-01

    Polymorphism at the αS1-casein locus (CSN1S1) in goats influences several milk production traits. Milk from goats carrying strong alleles, which are associated with high αS1-casein (αS1-CN) synthesis, has higher fat and casein contents, longer coagulation time and higher curd firmness than milk from goats with weak alleles linked to low αS1-CN content. Nutrition also affects these milk properties; therefore, it is important to better understand the interaction between dietary characteristics and the CSN1S1 genotype in goats. This study aimed to investigate the effect of fresh forage based diet or energy supplement on feeding behavior, milk production, and metabolic and hormonal parameters of Girgentana goats with different genotypes at CSN1S1 loci. From a group of goats genotyped by PCR at the DNA level, 12 were selected because they had the same genotype for αS2-CN, β-CN, and κ-CN but a different genotype for αS1-CN: 6 were homozygous for strong alleles at the CSN1S1 loci (AA) and 6 were heterozygous for a weak allele (AF). Goats of each genotype were allocated to 3 subgroups and fed 3 diets ad libitum in a 3×3 Latin square design. The diets were sulla (Hedysarum coronarium L.) fresh forage, sulla fresh forage plus 800 g/d of barley meal (SFB), and mixed hay plus 800 g/d of barley meal (MHB). Diet had a stronger effect than CSN1S1 genotype. The SFB diet led to the highest energy intake, dry matter (DM) digestibility, and milk yield. The fresh forage diets (SFF and SFB) increased DM and crude protein (CP) intake, CP digestibility, and milk CN compared with the MHB diet. The diets supplemented with energy (SFB, MHB) reduced milk fat and urea, improved CP utilization for casein synthesis, and limited body fat mobilization, in accordance with a lower level of nonesterified fatty acids and higher levels of glucose and IGF-1. With regard to CSN1S1 genotype, AA goats showed higher CP digestibility and lower free thyroxine hormone and cholesterol levels than AF

  5. AAS 228: Day 1 morning

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Come visit astrobites at the AAS booth we have swag!Things kicked off last night at our undergraduate reception booth. Thanks to all of you who stopped by we were delightedto hear from undergrads who already know and love the site, educators who want to use it in their classrooms, and students who had not yet been introduced to astrobites and were excited about a new resource!For the rest of the meeting we will be stationed at theAAS booth in the exhibit hall (booth #211-213), so drop by if you want to learn more (or pick up swag: weve got lots of stickers and sunglasses)!Mondaymorning was the official start of the meeting. Here are just a few of the talks and workshops astrobiters attended this morning.Opening Address(by Susanna Kohler)AAS President Meg Urry kicked off the meeting this morning at 8am with an overview of some of the great endeavors AAS is supporting. We astrobiters had personal motivation to drag ourselves out of bed that early: during this session, Urryannounced the new partnership between AAS and astrobites!Urry touched on some difficult topics in her welcome, including yesterdays tragedy in Orlando. Shereiteratedthe AASs support fortheCommittee for Sexual-Orientation and Gender Minorities in Astronomy (SGMA). She also reminded meeting attendees about the importance ofkeeping conference interactions professional, and pointed to the meetings anti-harassment policy.Partnership Announcement (by Michael Zevin)This morning, the American Astronomical Society announced the new partnership that it will have with Astrobites! We are beyond excited to embark on this new partnership with the

  6. Transmission of systemic AA amyloidosis in animals.

    PubMed

    Murakami, T; Ishiguro, N; Higuchi, K

    2014-03-01

    Amyloidoses are a group of protein-misfolding disorders that are characterized by the deposition of amyloid fibrils in organs and/or tissues. In reactive amyloid A (AA) amyloidosis, serum AA (SAA) protein forms deposits in mice, domestic and wild animals, and humans that experience chronic inflammation. AA amyloid fibrils are abnormal β-sheet-rich forms of the serum precursor SAA, with conformational changes that promote fibril formation. Extracellular deposition of amyloid fibrils causes disease in affected animals. Recent findings suggest that AA amyloidosis could be transmissible. Similar to the pathogenesis of transmissible prion diseases, amyloid fibrils induce a seeding-nucleation process that may lead to development of AA amyloidosis. We review studies of possible transmission in bovine, avian, mouse, and cheetah AA amyloidosis. PMID:24280941

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

    PubMed Central

    2012-01-01

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

  8. Distribution of geriatric disease-related genotypes in the National Institute for Longevity Sciences, Longitudinal Study of Aging (NILS-LSA).

    PubMed

    Shimokata, H; Yamada, Y; Nakagawa, M; Okubo, R; Saido, T; Funakoshi, A; Miyasaka, K; Ohta, S; Tsujimoto, G; Tanaka, M; Ando, F; Niino, N

    2000-04-01

    Phenotypes of various genes related to geriatric diseases and the aging process were assessed in the National Institute for Longevity Sciences, Longitudinal Study of Aging (NILS-LSA). The subjects were 1,297 participants in the NILS-LSA. They were community-living males and females aged 40 to 79 years who were randomly selected from the area of the NILS. Genotypic and allelic frequencies of genes in the subjects were analyzed. Age and gender differences in the distribution of genotypes were also tested. The genotypic frequencies were as follows: (1) Angiotensin I-converting enzyme (ACE) genotype was I/I 46.2%, I/D 38.3% and D/D 15.5%. (2) alpha 1-adrenoreceptor genotype was C/C 84.4%, C/T 12.7%, and T/T 3.0%. (3) Apolipoprotein E genotype was epsilon 2/epsilon 2 0%, epsilon 2/epsilon 3 7.9%, epsilon 3/epsilon 3 70.0%, epsilon 3/epsilon 4 20.8%, epsilon 2/epsilon 4 0%, and epsilon 4/epsilon 4 1.4%. (4) Cholecystokinin type-A receptor (CCKAR) nucleotide-81 (nt-81) genotype was A/A 59.1%, A/G 35.1%, and G/G 5.9%. The CCKAR nucleotide-128 genotype (nt-128) was G/G 74.3%, G/T 23.6%, and T/T 2.2%. The combination of nucleotide (nt-81, nt-128) was (A/A, G/G) 59.1%, (A/G, G/G) 14.1%, (G/G, G/G) 1.1%, (A/G, G/T) 21.0%, (G/G, G/T) 2.6%, and (G/G, T/T) 2.1%. There were no subjects with (A/A, G/T), (A/A, T/T) or (A/G, T/T) genotypic combinations. (5) beta 3-adrenoreceptor genotype was T/T 66.8%, T/A 28.5%, and A/A 4.7%. (6) Dihydrolipoamide succinyltransferase (DLST) nucleotide 19117 genotype was A/A 25.1%, A/G 49.7%, and G/G 25.1%. The DLST nucleotide 19183 genotype was C/C 55.8%, C/T 38.2%, and T/T 5.9%. The combination of nucleotide (nt19117, nt19183) was (A/A, C/C) 6.7%, (A/G, C/C) 24.1%, (G/G, C/C) 25.1%, (A/G, C/T) 25.6%, (A/A, T/T) 5.9%, and (A/A, C/T) 12.6%. There were no subjects with (A/G, T/T), (G/G, T/T) or (G/G, T/C) genotypic combinations. (7) Transforming growth factor-beta 1 genotype T/T 35.2%, T/C 44.6%, and C/C 20.2%. (8) The platelet-activating factor

  9. Axiom turkey genotyping array

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  10. AAS 228: Day 2 afternoon

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.The Limits of Scientific Cosmology: Setting the Stage: Accepted Facts, and Testing Limitations in Theory and Data (by Gourav Khullar)With a stellar lineup of speakers to talk about current and future prospects of cosmology and its limits (or lack thereof), the first session kicked off with talks by Risa Wechsler, Joseph Silk, and Sean Carroll (his talk on Multiverses is described below, by Nathan Sanders). Risa set the stage with an elaborate description of the current accepted facts in the era of precision cosmology including the standard model of concordance cosmology, described by seven parameters and an accepted Lambda-CDM paradigm (with a cosmological constant and cold dark matter). The talk stressed on the fact that all these parameters are understood to a percent order precision, which is a remarkable deviation from the time in 1990s when according to Risa, Alan Guth never thought that any of these numbers could be measured precisely!Risa Wechsler describing our current constraints on what Dark Matter could constitute.Joseph Silk discussing limits on cosmological parameters.The CMB measurements, Big Bang Nucleosynthesis estimates and galaxy clustering statistics all contribute to locking down the description of our universe. She emphasized on the tensions between different probes to measure expansion rate H0 of the universe, and small scale predictions of cold dark matter simulations, but she is hopeful that these shall be resolved eventually. Joe Silk followed this up with his interpretation of trying to understand our place in the universe and placing limits on different parameters and

  11. Measles viruses of genotype H1 evade recognition by vaccine-induced neutralizing antibodies targeting the linear haemagglutinin noose epitope.

    PubMed

    Finsterbusch, Tim; Wolbert, Anne; Deitemeier, Ingrid; Meyer, Kerstin; Mosquera, Maria Mar; Mankertz, Annette; Santibanez, Sabine

    2009-11-01

    The linear haemagglutinin noose epitope (HNE; aa 379-410) is a protective B-cell epitope and considered to be highly conserved in both the vaccine and the wild-type measles virus (MeV) haemagglutinin (H) proteins. Vaccine virus-derived monoclonal antibodies (mAbs) BH6 and BH216, which target the HNE, neutralized MeVs of genotypes B3, C2, D4, D5, D6, D7 and D8, and the vaccine strain Edmonston Zagreb. In the case of genotype H1, only strain Berlin.DEU/44.01 was neutralized by these mAbs, whereas strains Shenyang.CHN/22.99 and Sofia.BGR/19.05 were not. The H gene sequences of these two strains showed an exchange of proline 397 (P397) to leucine (L397). Mutated H proteins, with P397 exchanged to L and vice versa, were compared with original H proteins by indirect fluorescence assay. H proteins exhibiting P397 but not those with L397 were recognized by BH6 and BH216. This indicates that L397 leads to the loss of the neutralizing HNE. In contrast, human sera obtained from vaccinees (n=10) did not discriminate between genotype H1 variants P397 and L397. This concurs with the epidemiological observation that the live-attenuated vaccine protects against both H1 variants. Furthermore, we demonstrated that MeVs of genotype H1 also lack the neutralizing epitopes defined by the vaccine virus-induced mAbs BH15, BH125 and BH47. The loss of several neutralizing epitopes, as shown for H1 viruses currently circulating endemically in Asia, implies that epitope monitoring should be considered to be included in measles surveillance. PMID:19625457

  12. Genotype 1 hepatitis C virus envelope features that determine antiviral response assessed through optimal covariance networks.

    PubMed

    Murray, John M; Moenne-Loccoz, Rémy; Velay, Aurélie; Habersetzer, François; Doffoël, Michel; Gut, Jean-Pierre; Fofana, Isabel; Zeisel, Mirjam B; Stoll-Keller, Françoise; Baumert, Thomas F; Schvoerer, Evelyne

    2013-01-01

    The poor response to the combined antiviral therapy of pegylated alfa-interferon and ribavarin for hepatitis C virus (HCV) infection may be linked to mutations in the viral envelope gene E1E2 (env), which can result in escape from the immune response and higher efficacy of viral entry. Mutations that result in failure of therapy most likely require compensatory mutations to achieve sufficient change in envelope structure and function. Compensatory mutations were investigated by determining positions in the E1E2 gene where amino acids (aa) covaried across groups of individuals. We assessed networks of covarying positions in E1E2 sequences that differentiated sustained virological response (SVR) from non-response (NR) in 43 genotype 1a (17 SVR), and 49 genotype 1b (25 SVR) chronically HCV-infected individuals. Binary integer programming over covariance networks was used to extract aa combinations that differed between response groups. Genotype 1a E1E2 sequences exhibited higher degrees of covariance and clustered into 3 main groups while 1b sequences exhibited no clustering. Between 5 and 9 aa pairs were required to separate SVR from NR in each genotype. aa in hypervariable region 1 were 6 times more likely than chance to occur in the optimal networks. The pair 531-626 (EI) appeared frequently in the optimal networks and was present in 6 of 9 NR in one of the 1a clusters. The most frequent pairs representing SVR were 431-481 (EE), 500-522 (QA) in 1a, and 407-434 (AQ) in 1b. Optimal networks based on covarying aa pairs in HCV envelope can indicate features that are associated with failure or success to antiviral therapy. PMID:23840641

  13. AAS 228: Day 2 morning

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    tendency to prefer sugars and proteins that are one chirality only, but it is unknown whether this is a universal preference or a quirk of Earth-based life. Carroll and McGuires new detection in a star-forming cloud of material near the center of the Milky Way does not distinguish whether the propylene oxide is left- or right-handed, but it does show that the cosmos is capable of producing complex molecules that are essential to biology. In the future, they hope to use polarized light to directly measure chirality.Next, Joel Green from STScI presented how a young star surrounded by a bright protoplanetary disk, FU Orionis, has changed since a bright outburst in 1936. Since then, it has consumed some 80 Jupiters worth of material! By comparing observations of the disks brightness taken twelve years apart, Green showed that the hottest inner regions of the disk have faded significantly while the cooler regions farther out have not. In other words, the star has consumed the hot parts of the disk closest to it and altered the chemical composition in the disk that remains. This is likely what our own Sun experienced as a young star, and has implications for planet formation because the chemical composition of the disk affects what materials are available for forming planets. Green hopes that future observations with the Webb telescope will complement existing Spitzer and SOFIA data.A gluttonous star may hold clues to #planet formation: https://t.co/bTcFJM3xcY#aas228pic.twitter.com/nDWLF3bXVN NASA PlanetQuest (@PlanetQuest) June 14, 2016

  14. Dysregulation Of Innate Immunity In HCV Genotype 1 IL28B Unfavorable Genotype Patients: Impaired Viral Kinetics And Therapeutic Response

    PubMed Central

    Naggie, Susanna; Osinusi, Anu; Katsounas, Antonios; Lempicki, Richard; Herrmann, Eva; Thompson, Alexander J; Clark, Paul J; Patel, Keyur; Muir, Andrew J; McHutchison, John G; Schlaak, Joerg F; Trippler, Martin; Shivakumar, Bhavana; Masur, Henry; Polis, Michael A.; Kottilil, Shyam

    2012-01-01

    Recent studies have shown that a single nucleotide polymorphism upstream of the interleukin (IL)-28B gene plays a major role in predicting therapeutic response in HCV-infected patients treated with pegylated interferon-alpha (IFN)/ribavirin. We sought to investigate the mechanism of the IL28B polymorphism, specifically as it relates to early HCV viral kinetics (VK), IFN pharmacokinetics (PK), IFN pharmacodynamics (PD), and gene expression profiles. Two prospective cohorts (HIV/HCV co-infected and HCV mono-infected) completing treatment with IFN/ribavirin were enrolled. Patients (N=88; 44 HIV/HCV and 44 HCV) were genotyped at the polymorphic site rs12979860. In the HIV/HCV cohort frequent serum sampling was completed for HCV RNA and IFN-levels. DNA microarray of PBMCs and individual expression of interferon stimulated genes (ISGs) were quantified on IFN-therapy. The IL28B favorable (CC) genotype was associated with improved therapeutic response compared to unfavorable (CT/TT) genotypes. Patients with favorable genotype had greater first and second phase VK (P=0.004 and P=0.036, respectively), IFN maximum anti-viral efficiency (P=0.007) and infected cell death loss (P=0.009) compared to unfavorable genotypes. Functional annotation analysis of DNA microarray data was consistent with depressed innate immune function, particularly of NK cells, from patients with unfavorable genotypes (P<0.004). Induction of innate immunity genes was also lower in unfavorable genotype. ISG expression at baseline and induction with IFN was independent of IL28B genotype. Conclusions Carriers of the IL28B favorable genotype were more likely to have superior innate immune response to IFN-therapy compared to unfavorable genotypes, this suggests the unfavorable genotype has aberrant baseline induction of innate immune response pathways resulting in impaired virologic response. IL28B genotype is associated with more rapid viral kinetics and improved treatment response outcomes independent of

  15. AAS 228: Day 3 afternoon

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Wikipedia Year of Science Editathon (by Meredith Rawls)Whats your first go-to source for an unfamiliar topic on the internet? If you said Wikipedia, youre not alone. For many people, Wikipedia is the primary source of information about astronomy and science. However, many Wikipedia articles about science topics are incomplete or missing, and women are underrepresented among scientists with biographies.To address this, the AAS Astronomy Education Board teamed up with the Wiki Education Foundation to host an edit-a-thon as part of the Wikipedia Year of Science. More than forty attendees spent the better part of three hours working through tutorials, creating new articles, and editing existing ones. The session was generously sponsored by the Simons Foundation.The Year of Science initiative seeks to bring Wikipedia editing skills to the classroom and help new editors find sustainable ways to contribute to Wikipedia in the long term. Anybody can create a free account and start editing!As a first-time Wikipedia contributor, I took the time to go through nearly all the tutorial exercises and familiarize myself with the process of editing a page. I decided to flesh out one section in an existing page about asteroseismology. Others created biography pages from scratch or selected various astronomical topics to write about. To me, the editing process felt like a cross between writing a blog post and a journal article, in a hack day type environment. Working through the tutorial and some examples renewed my empathy for learners who are tackling a new skill set for the first time. A full summary of our

  16. Bacillus thuringiensis subsp. israelensis Cyt1Aa synergizes Cry11Aa toxin by functioning as a membrane-bound receptor.

    PubMed

    Pérez, Claudia; Fernandez, Luisa E; Sun, Jianguang; Folch, Jorge Luis; Gill, Sarjeet S; Soberón, Mario; Bravo, Alejandra

    2005-12-20

    Bacillus thuringiensis subsp. israelensis produces crystal proteins, Cry (4Aa, 4Ba, 10Aa, and 11Aa) and Cyt (1Aa and 2Ba) proteins, toxic to mosquito vectors of human diseases. Cyt1Aa overcomes insect resistance to Cry11Aa and Cry4 toxins and synergizes the toxicity of these toxins. However, the molecular mechanism of synergism remains unsolved. Here, we provide evidence that Cyt1Aa functions as a receptor of Cry11Aa. Sequential-binding analysis of Cyt1Aa and Cry11Aa revealed that Cyt1Aa binding to Aedes aegypti brush border membrane vesicles enhanced the binding of biotinylated-Cry11Aa. The Cyt1Aa- and Cry11Aa-binding epitopes were mapped by means of the yeast two-hybrid system, peptide arrays, and heterologous competition assays with synthetic peptides. Two exposed regions in Cyt1Aa, loop beta6-alphaE and part of beta7, bind Cry11Aa. On the other side, Cry11Aa binds Cyt1Aa proteins by means of domain II-loop alpha8 and beta-4, which are also involved in midgut receptor interaction. Characterization of single-point mutations in Cry11Aa and Cyt1Aa revealed key Cry11Aa (S259 and E266) and Cyt1Aa (K198, E204 and K225) residues involved in the interaction of both proteins and in synergism. Additionally, a Cyt1Aa loop beta6-alphaE mutant (K198A) with enhanced synergism to Cry11Aa was isolated. Data provided here strongly indicates that Cyt1Aa synergizes or suppresses resistance to Cry11Aa toxin by functioning as a membrane-bound receptor. Bacillus thuringiensis subsp. israelensis is a highly effective pathogenic bacterium because it produces a toxin and also its functional receptor, promoting toxin binding to the target membrane and causing toxicity. PMID:16339907

  17. Mass genotyping by sequencing technology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Large scale genotyping of a moderate number of loci is cost prohibitive with current chip-based technologies. We demonstrate the ability to use next generation sequencing technologies to genotype many DNA samples for a moderate number of loci – a mass genotyping by sequencing technology (MGST). Ou...

  18. AAS 228: Day 3 afternoon

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Wikipedia Year of Science Editathon (by Meredith Rawls)Whats your first go-to source for an unfamiliar topic on the internet? If you said Wikipedia, youre not alone. For many people, Wikipedia is the primary source of information about astronomy and science. However, many Wikipedia articles about science topics are incomplete or missing, and women are underrepresented among scientists with biographies.To address this, the AAS Astronomy Education Board teamed up with the Wiki Education Foundation to host an edit-a-thon as part of the Wikipedia Year of Science. More than forty attendees spent the better part of three hours working through tutorials, creating new articles, and editing existing ones. The session was generously sponsored by the Simons Foundation.The Year of Science initiative seeks to bring Wikipedia editing skills to the classroom and help new editors find sustainable ways to contribute to Wikipedia in the long term. Anybody can create a free account and start editing!As a first-time Wikipedia contributor, I took the time to go through nearly all the tutorial exercises and familiarize myself with the process of editing a page. I decided to flesh out one section in an existing page about asteroseismology. Others created biography pages from scratch or selected various astronomical topics to write about. To me, the editing process felt like a cross between writing a blog post and a journal article, in a hack day type environment. Working through the tutorial and some examples renewed my empathy for learners who are tackling a new skill set for the first time. A full summary of our

  19. A Comparison of Aggregatibacter actinomycetemcomitans (Aa) Virulence Traits in a Rat Model for Periodontal Disease

    PubMed Central

    Schreiner, Helen; Li, Yu; Cline, Joshua; Tsiagbe, Vincent K.; Fine, Daniel H.

    2013-01-01

    Our aim was to explore the effects of Cytolethal Distending toxin (Cdt) in a well established rat model of periodontal disease where leukotoxin (LtxA) was thought to have no known effect. In vitro studies, were used to assess CdtB activity using Aa Leukotoxin as a negative control. These studies showed that both CdtB and LtxA (unexpectedly) exerted significant effects on CD4+ T cells. As a result we decided to compare the effects of these two prominent Aa virulence factors on bone loss using our rat model of Aa-induced periodontitis. In this model, Aa strains, mutant in cdtB and ltxA, were compared to their parent non-mutant strains and evaluated for colonization, antibody response to Aa, bone loss and disease. We found that bone loss/disease caused by the ltxA mutant strain, in which cdtB was expressed, was significantly less (p<0.05) than that due to the wild type strain. On the other hand, the disease caused by cdtB mutant strain, in which ltxA was expressed, was not significantly different from the wild type strain. This data indicates that Aa LtxA exerts a greater effect on bone loss than Cdt in this rat model of periodontal disease and supports the utility of this model to dissect specific virulence factors as they relate to immunopathology in studies of Aa-induced disease. PMID:23936002

  20. Distribution pattern of HCV genotypes & its association with viral load

    PubMed Central

    Chakravarti, Anita; Dogra, Gaurav; Verma, Vikas; Srivastava, Amit Parkash

    2011-01-01

    Background & objectives: Hepatitis C virus (HCV) has emerged as a leading cause of chronic hepatitis, liver cirrhosis and hepatocellular carcinoma worldwide. Genotyping and assessment of the viral load in HCV patients is important for designing the therapeutic strategies. Thus the present study was designed to determine the distribution pattern of HCV genotypes in chronic hepatitis patients and their association with the viral load and biochemical profiles. Methods: Seventy one HCV RNA positive patients were included in the study. HCV genotyping was carried out by restriction fragment length polymorphism (RFLP) followed by the direct sequencing of the core region. Viral load estimation was carried out by Taqman real time PCR system. Results: Sixty three per cent (45/71) of cases were infected with genotype 3 followed by genotype 1 in 30.98 per cent (22/71) and genotype 2 in 5.63 per cent (4/71) of cases. Genotype 1 was associated with a significantly (P<0.001) higher viral load as compared to genotypes 3 and 2. There was no significant difference seen in the biochemical profile between the three groups of genotypes except in the levels of SGOT. The commonest mode of transmission was parenteral which accounted for 68 per cent of all the infected cases. Interpretation & conclusions: The present study revealed that HCV genotype 3 and 1 accounted for approximately 95 per cent of the HCV infection in Delhi and surrounding areas. Also two atypical subtypes like 3i and 3f were identified. Genotype 1 was associated with more severity of liver disease as compared to genotypes 3 and 2 as assessed by viral load. PMID:21441689

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A simulation study was carried out to develop an alternative method of selecting animals to be genotyped and to compare the proposed method to other known procedures. The simulated pedigrees included 5,000 animals and were assigned genotypes for a bi-allelic gene based on assumed allelic frequencie...

  2. Sugarcane Genotype Selection for Sand Soils in Florida

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Selection of high yielding sugarcane (Saccharum spp.) genotypes for organic (muck) soils in Florida has been more successful than for sand soils. The purpose of this study was to compare the performance of 31 sugarcane genotypes on sand soils with and without mill mud added at the rate of 1510 cubic...

  3. The thioacetate-ω(γ-lactam carboxamide) HDAC inhibitor ST7612AA1 as HIV-1 latency reactivation agent.

    PubMed

    Badia, Roger; Grau, Judith; Riveira-Muñoz, Eva; Ballana, Ester; Giannini, Giuseppe; Esté, José A

    2015-11-01

    Antiretroviral therapy (ART) is unable to cure HIV infection. The ability of HIV to establish a subset of latent infected CD4(+) T cells, which remain undetectable to the immune system, becomes a major roadblock to achieve viral eradication. Histone deacetylase inhibitors (HDACi) have been shown to potently induce the reactivation of latent HIV. Here, we show that a new thiol-based HDACi, the thioacetate-ω(γ-lactam carboxamide) derivative ST7612AA1, is a potent inducer of HIV reactivation. We evaluated HIV reactivation activity of ST7612AA1 compared to panobinostat (PNB), romidepsin (RMD) and vorinostat (VOR) in cell culture models of HIV-1 latency, in latently infected primary CD4(+) T lymphocytes and in PBMCs from HIV(+) patients. ST7612AA1 potently induced HIV-1 reactivation at submicromolar concentrations with comparable potency to panobinostat or superior to vorinostat. The presence of known antiretrovirals did not affect ST7612AA1-induced reactivation and their activity was not affected by ST7612AA1. Cell proliferation and cell activation were not affected by ST7612AA1, or any other HDACi used. In conclusion, our results indicate that ST7612AA1 is a potent activator of latent HIV and that reactivation activity of ST7612AA1 is exerted without activation or proliferation of CD4(+) T cells. ST7612AA1 is a suitable candidate for further studies of HIV reactivation strategies and potential new therapies to eradicate the viral reservoirs. PMID:26348004

  4. Interface Formation During Fusion™ Casting of AA3003/AA4045 Aluminum Alloy Ingots

    NASA Astrophysics Data System (ADS)

    Di Ciano, Massimo; Caron, E. J. F. R.; Weckman, D. C.; Wells, M. A.

    2015-12-01

    Fusion™ casting is a unique Direct Chill continuous casting process whereby two different alloys can be cast simultaneously, producing a laminated ingot for rolling into clad sheet metal such as AA3003/AA4045 brazing sheet. Better understanding of the wetting and interface formation process during Fusion™ casting is required to further improve process yields and also explore use of other alloy systems for new applications. In this research, AA3003-core/AA4045-clad ingots were cast using a well-instrumented lab-scale Fusion™ casting system. As-cast Fusion™ interfaces were examined metallurgically and by mechanical testing. Computational fluid dynamic analyses of the FusionTM casts were also performed. It was shown that the liquid AA4045-clad alloy was able to successfully wet and create an oxide-free, metallurgical, and mechanically sound interface with the lightly oxidized AA3003-core shell material. Based on the results of this study, it is proposed that the bond formation process at the alloys interface during casting is a result of discrete penetration of AA4045 liquid at defects in the preexisting AA3003 oxide, dissolution of underlying AA3003 by liquid AA4045, and subsequent bridging between penetration sites. Spot exudation on the AA3003 chill cast surface due to remelting and inverse segregation may also improve the wetting and bonding process.

  5. The CYP1A2 genotype modifies the association between coffee consumption and breast cancer risk among BRCA1 mutation carriers.

    PubMed

    Kotsopoulos, Joanne; Ghadirian, Parviz; El-Sohemy, Ahmed; Lynch, Henry T; Snyder, Carrie; Daly, Mary; Domchek, Susan; Randall, Susan; Karlan, Beth; Zhang, Phil; Zhang, Shiyu; Sun, Ping; Narod, Steven A

    2007-05-01

    We have recently reported that, among BRCA1 mutation carriers, the consumption of caffeinated coffee was associated with a significant reduction in breast cancer risk. Because the metabolism of caffeine is primarily by CYP1A2, we examined whether or not the CYP1A2 genotype modifies the association between a history of coffee consumption and the risk of breast cancer. A common A to C polymorphism in the CYP1A2 gene is associated with decreased enzyme inducibility and impaired caffeine metabolism. Information regarding coffee consumption habits and the CYP1A2 genotype was available for 411 BRCA1 mutation carriers (170 cases and 241 controls). We estimated the odds ratios (ORs) and 95% confidence intervals (95% CIs) for breast cancer associated with the CYP1A2 genotype and a history of coffee consumption before age 35, adjusting for potential confounders. The CYP1A2 genotype did not affect breast cancer risk. Among women with at least one variant C allele (AC or CC), those who consumed coffee had a 64% reduction in breast cancer risk, compared with women who never consumed coffee (OR, 0.36; 95% CI, 0.18-0.73). A significant protective effect of coffee consumption was not observed among women with the CYP1A2 AA genotype (OR, 0.93; 95% CI, 0.49-1.77). Similar results were obtained when the analysis was restricted to caffeinated coffee. This study suggests that caffeine protects against breast cancer in women with a BRCA1 mutation and illustrates the importance of integrating individual genetic variability when assessing diet-disease associations. PMID:17507615

  6. Development of a Laboratory Project to Determine Human ABO Genotypes--Limitations Lead to Further Student Explorations

    ERIC Educational Resources Information Center

    Salerno, Theresa A.

    2009-01-01

    A multiplex allele-specific PCR analysis was developed to identify six "common" genotypes: AA, AO, BB, BO, OO, and AB. This project included a pre-laboratory exercise that provided active learning experiences and developed critical thinking skills. This laboratory resulted in many successful analyses, which were verified by student knowledge of…

  7. Genotype-guided tacrolimus dosing in African American kidney transplant recipients

    PubMed Central

    Sanghavi, K.; Brundage, RC.; Miller, MB.; Schladt, DP.; Israni, AK.; Guan, W.; Oettin, WS.; Mannon, RB.; Remme, RP.; Matas, AJ.; Jacobson, PA.

    2015-01-01

    Tacrolimus is dependent on CYP3A5 enzyme for metabolism. Expression of the CYP3A5 enzyme is controlled by several alleles including CYP3A5*1, CYP3A5*3, CYP3A5*6 and CYP3A5*7. African Americans (AA) have on average higher tacrolimus dose requirements than Caucasians; however, some have requirements similar to Caucasians. Studies in AA have primarily evaluated the CYP3A5*3 variant; however, there are common nonfunctional variants in AA (CYP3A5*6 and CYP3A5*7) which do not occur in Caucasians. These variants are associated with lower dose requirements and may explain why some AA are metabolically similar to Caucasians. We created a tacrolimus clearance model in 354 AA using a development and validation cohort. Time posttransplant, steroid and antiviral use, age, CYP3A5*1, *3, *6 and *7 alleles were significant towards clearance. This study is the first to develop an AA specific genotype-guided tacrolimus dosing model to personalize therapy. PMID:26667830

  8. Gas chromatography-mass spectrometry metabolomics of goat milk with different polymorphism at the αS1-casein genotype locus.

    PubMed

    Caboni, Pierluigi; Murgia, Antonio; Porcu, Alessandra; Demuru, Martina; Pulina, Giuseppe; Nudda, Anna

    2016-08-01

    Hyphenated gas chromatography-mass spectrometry (GC-MS) and multivariate data analysis techniques were used to uncover milk metabolite differences in different αS1-casein genotypes of goats. By a discriminant GC-MS metabolomics approach, we characterized milk polar metabolites of 28 goats. Animals were selected on the basis of their genotypes as 7 goats classified heterozygous for weak or null alleles, 5 for the genotype EE, 9 for the genotypes AE and BE, and finally 7 for the strong genotype AA. Low molecular weight polar metabolite profile was tightly related to the different goat genotypes, milk production, and protein levels. Results of multivariate statistical analysis of GC-MS data demonstrate that different heterozygous and homozygous genotypes expressed different metabolites such as citric and aconitic acid for the strong allele class with different sugars and polyols for the weak class. PMID:27289154

  9. Halothane genotype and pork quality. 3. Comminuted meat products derived from the three halothane genotypes.

    PubMed

    Fisher, P; Mellett, F D; Hoffman, L C

    2000-02-01

    The effect of the halothane gene on cured meat products was investigated using the meat from 60 Landrace×Large White pigs of known halothane genotype (NN=25, Nn=19, nn=16). Results for the two types of fresh sausage manufactured (with and without rusk) indicated that the NN pigs (15.7%) had lower total moisture losses (P<0.05) compared to the nn pigs (18.9%), with Nn being intermediate (17.4%) for the sausage without rusk. Where rusk was added, there were no significant differences between genotypes for moisture losses (NN=12.6%, Nn=13. 0%, nn=14.2%). Taste panel evaluations of the fresh sausages made without rusk indicated no genotypic influence for juiciness, however the sausage made with the rusk was judged the juiciest for the nn genotype, with Nn being intermediate and NN the least juiciest. The smoking and cooking losses during manufacturing of the emulsion product (vienna) indicated that the nn genotype (12.5%) had significantly (P<0.05) higher total losses than the Nn genotype (11. 3%), with NN being intermediate (12.4%). PMID:22060606

  10. Association of Interleukin-6 and Interleukin-10 Genotypes With Radiographic Damage in Rheumatoid Arthritis Is Dependent on Autoantibody Status

    PubMed Central

    Marinou, I; Healy, J; Mewar, D; Moore, D J; Dickson, M C; Binks, M H; Montgomery, D S; Walters, K; Wilson, A G

    2007-01-01

    Objective Recent evidence has highlighted a major genetic contribution to radiographic damage in rheumatoid arthritis (RA). The objective of this study was to determine whether genetic variants in the loci for interleukin-1 (IL-1), IL-6, IL-10, protein tyrosine phosphatase N22 (PTPN22), and selenoprotein S are associated with radiographic damage. Methods Modified Larsen scores of radiographic damage were determined in a cross-sectional population of patients with RA (n = 964). Rheumatoid factor (RF) and anti–cyclic citrullinated peptide (anti-CCP) were also assayed. The Kruskal-Wallis nonparametric test was used to compare median radiographic damage scores across genotype groups, followed by the Cuzick nonparametric test for trend to assess gene-dose effects. Results An allele-dose association of IL-6 −174G with increasing radiographic damage was present (P = 0.005), but only in patients who were RF positive (P = 0.004) or anti-CCP positive (P = 0.01). Patients with the IL-10 −592CC genotype had more extensive radiographic damage than did those with the AC or AA genotype (P = 0.006), but this was observed only among patients who were RF negative (P = 0.002) or anti-CCP negative (P = 0.002). However, RF status and anti-CCP status were not associated with the IL-6 or IL-10 genotype. No other genetic associations were detected, apart from a marginal association of PTPN22 +1858T with increased radiographic damage. Conclusion The reported associations of IL-6 −174G with high IL-6 production and IL-10 −592 with low IL-10 production and our own results support a role of genetically determined dysregulated cytokine production in disease severity. The lack of association of these genotypes with RF and anti-CCP antibody status suggests that they act downstream of autoantibody production. We conclude that IL-6 and IL-10 genotypes may be useful in predicting disease severity in autoantibody-positive and autoantibody-negative patients, respectively. PMID:17665434

  11. minimac2: faster genotype imputation

    PubMed Central

    Fuchsberger, Christian; Abecasis, Gonçalo R.; Hinds, David A.

    2015-01-01

    Summary: Genotype imputation is a key step in the analysis of genome-wide association studies. Upcoming very large reference panels, such as those from The 1000 Genomes Project and the Haplotype Consortium, will improve imputation quality of rare and less common variants, but will also increase the computational burden. Here, we demonstrate how the application of software engineering techniques can help to keep imputation broadly accessible. Overall, these improvements speed up imputation by an order of magnitude compared with our previous implementation. Availability and implementation: minimac2, including source code, documentation, and examples is available at http://genome.sph.umich.edu/wiki/Minimac2 Contact: cfuchsb@umich.edu, goncalo@umich.edu PMID:25338720

  12. Novel polymorphism of AA-NAT gene in Indian goat breeds differing in reproductive traits.

    PubMed

    Sharma, R; Ahlawat, S; Tantia, M S

    2015-01-01

    This is the first description of the polymorphisms of arylalkylamine-N-acetyltransferase (AA-NAT) gene in Indian goats with different reproductive traits (twinning percentage and age of sexual maturity). Based on the important role of AA-NAT in reproduction, it is considered as a possible candidate gene for this trait. Two novel synonymous SNPs, C825T (exon2) and C1249T (exon3) were identified. All three possible genotypes (CC, CT and TT) were identified for C825T mutation whereas two genotypes were observed (CC and CT) for C1249T mutation. SNPs C825T and C1249T changed recognition site of restriction enzyme BtsCI (GGA T G) and AciI (C C GC) and thus can be genotyped by the relatively simple and cost effective technique of PCR-RFLP for establishing further association with reproductive traits. Present results add to the meager existing knowledge and extend the spectrum of genetic variation of caprine candidate genes of reproductive traits, which is another step towards improvement of goat genetic resources and breeding. PMID:27175207

  13. Genotyping Sleep Disorders Patients

    PubMed Central

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

    2010-01-01

    Objective The genetic susceptibility factors underlying sleep disorders might help us predict prognoses and responses to treatment. Several candidate polymorphisms for sleep disorders have been proposed, but there has as yet inadequate replication or validation that the candidates may be useful in the clinical setting. Methods To assess the validity of several candidate associations, we obtained saliva deoxyribonucleic acid (DNA) samples and clinical information from 360 consenting research participants who were undergoing clinical polysomnograms. Ten single nucleotide polymorphisms (SNPs) were genotyped. These were thought to be related to depression, circadian sleep disorders, sleep apnea, restless legs syndrome (RLS), excessive sleepiness, or to slow waves in sleep. Results With multivariate generalized linear models, the association of TEF rs738499 with depressive symptoms was confirmed. Equivocal statistical evidence of association of rs1801260 (the C3111T SNP in the CLOCK gene) with morningness/eveningness and an association of Apolipoprotein E (APOE) rs429358 with the Epworth Sleepiness Scale (ESS) were obtained, but these associations were not strong enough to be of clinical value by themselves. Predicted association of SNPs with sleep apnea, RLS, and slow wave sleep were not confirmed. Conclusion The SNPs tested would not, by themselves, be of use for clinical genotyping in a sleep clinic. PMID:20396431

  14. Vip3Aa induces apoptosis in cultured Spodoptera frugiperda (Sf9) cells.

    PubMed

    Jiang, Kun; Mei, Si-Qi; Wang, Ting-Ting; Pan, Jin-Hua; Chen, Yue-Hua; Cai, Jun

    2016-09-15

    The vegetative insecticidal proteins (Vip) secreted by many Bacillus thuringiensis strains during their vegetative growth stage are regarded as second generation insecticidal proteins, as they share no sequence or structural homology with known crystal insecticidal proteins (Cry) and have a broad insecticidal spectrum. Compared with insecticidal crystal proteins (ICPs), the insecticidal mechanisms of Vips have been little studied. Here we investigated the mechanism responsible for Vip3Aa toxicity in cultured insect cells. Using, flow cytometry analyzes, TUNEL staining and DNA fragmentation assays, we show that Vip3Aa can induce apoptosis in Spodoptera frugiperda (Sf9) cells and cause cells to arrest at the G2/M phase. We also show that Vip3Aa can disrupt mitochondrial membrane potential (ΔΨm), leading to the activation of Sf-caspase-1, suggesting that a mitochondrial mediated and caspase dependent pathway may be involved in Vip3Aa-induced apoptosis in Sf9 cells. PMID:27476462

  15. Southeast Asian patients with chronic hepatitis C: the impact of novel genotypes and race on treatment outcome.

    PubMed

    Dev, Anouk T; McCaw, Rhonda; Sundararajan, Vijaya; Bowden, Scott; Sievert, William

    2002-11-01

    Hepatitis C virus (HCV) genotype and other host and viral factors influence treatment outcome in chronic HCV infection. We evaluated the effect of race and genotype on interferon and ribavirin treatment outcome in 70 Southeast Asian (SEA) and 50 white patients. Genotype was based on the 5' untranslated region (5'UTR) with a commonly used line probe assay (INNO-LiPA HCV II) that may mistype genotype 7, 8, or 9 as 1b. HCV core region sequencing resulted in reclassification of 8 genotype 1 and 25 genotype 1b SEA subjects as genotype 7, 8, or 9. Twenty-six SEA genotype 7, 8, and 9 (79%) and 10 SEA true genotype 1b (59%) patients achieved a sustained virologic response (SVR) compared with 15 (34%) white genotype 1b patients. Logistic regression analysis showed that SEA patients with genotype 7, 8, or 9 were more likely to achieve a SVR than white genotype 1b patients (OR 16.56; 95%CI 4.16, 65.91) as were SEA true genotype 1b patients compared with white genotype 1b patients (OR 4.63; 95%CI 1.19, 18.04). In conclusion, a proportion of SEA patients classified by INNO-LiPA as genotype 1b were in reality genotype 7, 8, or 9. In comparison with white genotype 1b patients, both SEA genotype 1b and SEA genotype 7, 8, and 9 patients showed a significantly greater SVR. HCV core sequencing was necessary to determine genotype accurately in persons potentially exposed to HCV genotypes 7, 8, or 9. This study also supports the concept that race and ethnicity are important determinants of treatment outcome in HCV infected patients. PMID:12395338

  16. AA amyloidosis in vaccinated growing chickens.

    PubMed

    Murakami, T; Inoshima, Y; Sakamoto, E; Fukushi, H; Sakai, H; Yanai, T; Ishiguro, N

    2013-01-01

    Systemic amyloid-A (AA) amyloidosis in birds occurs most frequently in waterfowl such as Pekin ducks. In chickens, AA amyloidosis is observed as amyloid arthropathy. Outbreaks of systemic amyloidosis in flocks of layers are known to be induced by repeated inflammatory stimulation, such as those resulting from multiple vaccinations with oil-emulsified bacterins. Outbreaks of fatal AA amyloidosis were observed in growing chickens in a large scale poultry farm within 3 weeks of vaccination with multiple co-administered vaccines. This study documents the histopathological changes in tissues from these birds. Amyloid deposits were also observed at a high rate in the tissues of apparently healthy chickens. Vaccination should therefore be considered as a potential risk factor for the development of AA amyloidosis in poultry. PMID:23570943

  17. Homocysteine induced cardiovascular events: a consequence of long term anabolic‐androgenic steroid (AAS) abuse

    PubMed Central

    Graham, M R; Grace, F M; Boobier, W; Hullin, D; Kicman, A; Cowan, D; Davies, B; Baker, J S

    2006-01-01

    Objectives The long term effects (>20 years) of anabolic‐androgenic steroid (AAS) use on plasma concentrations of homocysteine (HCY), folate, testosterone, sex hormone binding globulin (SHBG), free androgen index, urea, creatinine, haematocrit (HCT), vitamin B12, and urinary testosterone/epitestosterone (T/E) ratio, were examined in a cohort of self‐prescribing bodybuilders. Methods Subjects (n = 40) were divided into four distinct groups: (1) AAS users still using AAS (SU; n = 10); (2) AAS users abstinent from AAS administration for 3 months (SA; n = 10); (3) non‐drug using bodybuilding controls (BC; n = 10); and (4) sedentary male controls (SC; n = 10). Results HCY levels were significantly higher in SU compared with BC and SC (p<0.01), and with SA (p<0.05). Fat free mass was significantly higher in both groups of AAS users (p<0.01). Daily energy intake (kJ) and daily protein intake (g/day) were significantly higher in SU and SA (p<0.05) compared with BC and SC, but were unlikely to be responsible for the observed HCY increases. HCT concentrations were significantly higher in the SU group (p<0.01). A significant linear inverse relationship was observed in the SU group between SHBG and HCY (r = −0.828, p<0.01), indicating a possible influence of the sex hormones in determining HCY levels. Conclusions With mounting evidence linking AAS to adverse effects on some clotting factors, the significantly higher levels of HCY and HCT observed in the SU group suggest long term AAS users have increased risk of future thromboembolic events. PMID:16488899

  18. Quantitative analysis of interstitial mast cells in AA and AL renal amyloidosis.

    PubMed

    Danilewicz, Marian; Wagrowska-Danilewicz, Małgorzata

    2002-01-01

    Eighteen renal biopsy specimens obtained from patients with AA-type renal amyloidosis (AA) and 11 from patients with AL-type renal amyloidosis (AL), for whom both light and electron microscopy as well as immunofluorescence microscopy and full clinical data were available, were examined quantitatively. The cases were selected on the basis of immunohistochemical studies. As a control, we used 10 biopsy specimens from the kidneys removed because of trauma. Morphometric investigations were carried out by a computer image analysis system to find an answer to the question of whether mast cells can correlate with tubulointerstitial fibrosis in AA and AL renal amyloidosis, and to examine the relationship between mast cells and interstitial alpha-smooth muscle actin (alpha-SMA) expression and interstitial infiltrates. The morphometric study revealed that the mean values of the interstitial tryptase-positive cells, expression of alpha-SMA, interstitial volume, CD68+, CD45RB+, CD43+ and CD20+ cells were increased in AA as compared with the AL group, most of them significantly. Most of these parameters were also significantly increased in both AA and AL patients as compared with the control group. In both the AA group and the AL group, there existed some significant positive correlations between interstitial tryptase-positive cells and interstitial expression of alpha-SMA, interstitial volume and CD68+ cells. Interestingly, in AA cases, but not in AL cases, we noted a significant relationship between interstitial tryptase-positive cells and CD43+ cells. Our findings demonstrate that mast cells belong to the constitutive cell types in the interstitium in renal amyloidosis, in particular in amyloid type A. In addition, in both the AA group and the AL group, the significant positive correlations between interstitial mast cell count and relative interstitial volume and interstitial expression of alpha-SMA suggest that these cells play a role in the development of interstitial

  19. The Changing Shape of the AAS

    NASA Astrophysics Data System (ADS)

    Boyce, P. B.

    1995-12-01

    What is the astronomical workforce like? Where do astronomers work? How old are they? How permanent are their jobs? As we move into a period of increased uncertainty in federal funding for science it is important to know the answers to these questions. There are four sources of information for answers: 1. Information from the AAS membership database. 2. A survey of the AAS membership. 3. Surveys of samples of the AAS membership by AIP. 4. Information from the NRC and NSF. We have gender and age data from 1. A survey of the AAS membershWe will have age and gender data from 1. We will complete and analyze a new membersip survey shortly. The latest AIP data is from 1994. They will do a new sample in 1996. Much of the NRC data is aggregated with physics, and that does not give information about astronomers. Nevertheless, we do have some interesting information. The ages and genders of AAS members are available for 1972, 1990 and 1995. The time sequence provides an interesting look at the AAS. For instance, from 1990 to 1995 the number of women in each 5-year age group below the the age of 65 increased. Contrary to popular perception, women are not leaving the Society as they get older. However, the number of men actually decreased in each age group above the age of 35. This and other interesting trends will be discussed.

  20. The Prevalence of Hepatitis C Virus Core Amino Acid 70 Substitution and Genotypes of Polymorphisms Near the IFNL3 Gene in Iranian Patients With Chronic Hepatitis C

    PubMed Central

    Kadjbaf, Danesh; Keshvari, Maryam; Alavian, Seyed Moayed; Pouryasin, Ali; Behnava, Bita; Salimi, Shima; Mehrnoush, Leila; Karimi Elizee, Pegah; Sharafi, Heidar

    2016-01-01

    Background Molecular studies have demonstrated that the hepatitis C virus (HCV) genotype and host genetics play predictive roles in the management of patients infected with HCV. Objectives This study aimed to investigate the HCV genotype, core amino acid (aa) 70 substitution, and polymorphisms near the IFNL3 gene (including rs12979860 and rs8099917) among Iranian patients with chronic hepatitis C (CHC). Patients and Methods In this cross-sectional study, the molecular profiles of the HCV genotype, core aa 70 substitution, and rs12979860 and rs8099917 polymorphisms and plasma HCV RNA levels were determined in 429 CHC patients including 141 hemophilic, 84 thalassemic, and 204 non-hemophilic, non-thalassemic patients. Results The hepatitis C virus subtype 1a was the most common subtype in the study population. Core aa substitution Arg70Gln was strongly associated with cirrhosis (OR = 2.49; 95% CI = 1.13 - 5.50; P = 0.020). Core aa 70 substitutions were more frequently observed in patients with the HCV subtype 1b than in patients with any other HCV subtypes (P < 0.001). Core aa 70 substitutions were also more common in patients with the rs12979860 TT genotype than in patients with non-TT genotypes (17.3% vs. 8.5%, P = 0.022) and also in rs8099917 non-TT genotypes than in the TT genotype (14.0% vs. 7.0%, P = 0.026). The HCV genotypes and rs8099917 polymorphisms were correlated in which HCV subtype 1b was in favor of rs8099917 GG and HCV subtype 3a favored rs8099917 TT (P = 0.021). Furthermore, the rs12979860 TT and rs8099917 GG genotypes showed significantly lower HCV RNA levels than the other genotypes (P < 0.001). Conclusions There is an as yet unexplained association between HCV and host parameters with unknown mechanisms in patients with chronic HCV infection. The assessments of core aa 70 substitution and polymorphisms near the IFNL3 gene could offer promising steps to improve the management of patients with HCV.

  1. AAS 228: Day 1 afternoon

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Plenary Session: From Space Archeology to Serving the World Today: A 20-year Journey from the Jungles of Guatemala to a Network of Satellite Remote Sensing Facilities Around the World(by Michael Zevin)In the conferences second plenary session, NASAs Daniel Irwin turned the eyes of the conference back to Earth by highlighting the huge impact that NASA missions play in protecting and developing our own planet.Daniel Irwin: using satellite imagery to detect differences in vegetation and find ancient Mayan cities. #aas228 pic.twitter.com/9LFPQdCHTM astrobites (@astrobites) June 13, 2016Irwin came to be involved in NASA through his work mapping Guatemalan jungles, where he would spend 22 days at a time exploring the treacherous jungles on foot armed with a 1st generation GPS, a compass, and a machete. A colleague introduced Irwin to the satellite imagery thathe was exploring, demonstratinghow these images are a strong complement to field work. The sharing of this satellite data with nearby villages helped to show the encroachment of agriculture and the necessity of connecting space to the village. Satellite imagery also played a role in archeological endeavors, uncovering dozens of Mayan cities that have been buried for over a millennia by vegetation, and it provided evidence that the fall of the Mayan civilization may have been due to massive deforestation that ledto drought.Glacial retreat in Chile imaged by ISERV.Irwin displayed the constellation of NASAs Earth-monitoring satellites that have played an integral role in conserving our planet and alerting the world of natural disasters. He also showed

  2. Development of an improved genotyping assay for the detection of hepatitis C virus genotypes and subtypes in Pakistan.

    PubMed

    Idrees, Muhammad

    2008-06-01

    A new genotyping system was established for the specific detection of HCV genotypes 1a, 1b, 1c, 2a, 2b, 2c, 3a, 3b, 3c, 4a-h, 5a and 6a during the course of this study. The system is based on entire core region and a part of 5' noncoding region (5'NCR) with genotype-specific primers. Genotype-specific primers were designed on the basis of 114 HCV isolates. Serum samples with known genotypes were used as positive controls to validate the assay developed and to generate PCR band patterns. Band patterns generated from the clinical serum samples from HCV patients were compared to the patterns produced from these control samples. In addition, the type-specific bands were sequenced from the test patients and control clinical samples to validate further the test results. To determine sensitivity and specificity of the assay, a total 260 samples were analyzed simultaneously by this HCV genotyping method and that developed by Ohno and Murex HCV Serotyping 1-6 Assay. The system showed 79.2% concordance with Ohno's system and 65.38% with serotyping system. Samples with discordant results were sequenced and their genotypes were determined by molecular evolutionary analysis. The data indicate that the method described in this study may offer better sensitivity and specificity for the detection directly of HCV genotypes present at low levels in HCV patient samples. PMID:18423633

  3. IL-18, TNF, and IFN-γ alleles and genotypes are associated with susceptibility to chronic hepatitis B infection and severity of liver injury.

    PubMed

    Ferreira, Sandro da Costa; Chachá, Silvana Gama Florêncio; Souza, Fernanda Fernandes; Teixeira, Andreza Corrêa; Santana, Rodrigo de Carvalho; Deghaide, Neifi Hassan Saloun; Rodrigues, Sandra; Marano, Leonardo Arduíno; Mendes-Junior, Celso Teixeira; Zucoloto, Sérgio; Donadi, Eduardo Antônio; Martinelli, Ana de Lourdes Candolo

    2015-10-01

    This study evaluated the association of polymorphisms in the IL-18 (-607C/A and -137C/G), IFNγ (+874 A/T), and TNF (-238 A/G and -308 A/G) genes with susceptibility to HBV infection and severity of liver injury. A total of 259 chronic HBV-infected patients followed at the University Hospital, Faculty of Medicine of Ribeirão Preto, São Paulo, Brazil, and 202 healthy individuals were studied. Four Single Nucleotide Polymorphisms (SNPs) were amplified by Polymerase Chain Reaction (PCR). Liver biopsy was performed in 212 HBV-infected patients and classified according to severity of liver fibrosis (scores 0-4) and necroinflammatory activity (HAI scores 0-18). TNF-308*A allele (P < 0.001; OR = 2.16) and TNF -308 AA genotype (P = 0.026; OR = 5.43) were associated with susceptibility to HBV infection. An association was found between severe liver fibrosis when compared to mild fibrosis and the following polymorphisms: Alleles IL-18 -137*G (P = 0.004; OR = 3.45), TNF -308*A (P < 0.001; OR = 3.39), and IFNγ +874*T (P = 0.029; OR = 1.85) and IL-18 -137 GG genotype (P = 0.009; OR = 3.70). No significant association was found between IL-18 (-607 A/C) polymorphism and severity of liver fibrosis. Alleles IL-18 -137*G (P = 0.028; OR = 2.64) and TNF-308*A (P = 0.002; OR = 3.06) and IL-18 -137 GG genotype (P = 0.011; OR = 4.20) were associated with severe necroinflammatory activity (HAI>12) when compared to mild necroinflammatory activity (HAI 1-8). The results suggest that IL-18 -137C/G, TNF-308 G/A and IFNγ +874 A/T SNPs were associated to more severe liver injury in chronic HBV infection. TNF -308*A allele and TNF -308 AA genotype could play a role in the susceptibility to HBV infection. PMID:25952099

  4. Analysis of hepatitis B virus genotype changes in patients with chronic hepatitis B infection on tenofovir therapy.

    PubMed

    Chauhan, Ranjit; Singh, Avishek K; Rooge, Sheetalnath; Varshney, Aditi; Kumar, Manoj; Sarin, Shiv K

    2016-08-01

    Antiviral therapy for chronic hepatitis B (CHB) is often required for prolonged periods. We investigated the instance of one HBV genotype switching to another during tenofovir therapy. Of the 67 patients, genotype A was present in 6 (8.9%), D in 43 (65.6%), C in 1 (1.5%), and mixed in 17 (23.8%) patients. Genotype changes were detected in 51 (76.1%) patients on therapy during a follow-up of 192 (range 52-312) weeks. Inter-genotype changes were seen in 17 (33.3%) and intra-genotype in 28 (55%) and both inter- and intra-genotype in 6 of 51 (11.7%) patients. The distribution of genotypes in patients achieving complete virological response was genotype D, 32/43 (74.4%); genotype A, 6/6 (100%); and mixed genotypes, 13/17 (76.47%). The cumulative time of genotype switch among genotype A was 12 months (range 6-18), in genotype D, 12 months (range 6-48), and mixed genotype, 18 months (range 6-24). The type of inter-genotype switch most frequently detected among genotype A1 was from A1 to D1 5/6 (83.3%), followed by mixed to genotype D3 7/13 (54%) and among intra-genotype changes, from D1 to D3 in 14/20 (70%). Pretreatment HBV genotype was the only factor predicting inter-genotype switches with genotype A or mixed genotypes more likely to undergo inter-genotype switches as compared to genotype D patients (OR 66.6 [13.6-327.0, P < 0.001]). Compared to genotype D, genotype A, and mixed genotypes are more inclined to switch while on tenofovir therapy. Genotypes tend to switch and select to a particular type possibly due to constant antiviral drug pressure. J. Med. Virol. 88:1364-1375, 2016. © 2016 Wiley Periodicals, Inc. PMID:26858138

  5. AAS 228: Day 1 afternoon

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Plenary Session: From Space Archeology to Serving the World Today: A 20-year Journey from the Jungles of Guatemala to a Network of Satellite Remote Sensing Facilities Around the World(by Michael Zevin)In the conferences second plenary session, NASAs Daniel Irwin turned the eyes of the conference back to Earth by highlighting the huge impact that NASA missions play in protecting and developing our own planet.Daniel Irwin: using satellite imagery to detect differences in vegetation and find ancient Mayan cities. #aas228 pic.twitter.com/9LFPQdCHTM astrobites (@astrobites) June 13, 2016Irwin came to be involved in NASA through his work mapping Guatemalan jungles, where he would spend 22 days at a time exploring the treacherous jungles on foot armed with a 1st generation GPS, a compass, and a machete. A colleague introduced Irwin to the satellite imagery thathe was exploring, demonstratinghow these images are a strong complement to field work. The sharing of this satellite data with nearby villages helped to show the encroachment of agriculture and the necessity of connecting space to the village. Satellite imagery also played a role in archeological endeavors, uncovering dozens of Mayan cities that have been buried for over a millennia by vegetation, and it provided evidence that the fall of the Mayan civilization may have been due to massive deforestation that ledto drought.Glacial retreat in Chile imaged by ISERV.Irwin displayed the constellation of NASAs Earth-monitoring satellites that have played an integral role in conserving our planet and alerting the world of natural disasters. He also showed

  6. Intermolecular interaction between Cry2Aa and Cyt1Aa and its effect on larvicidal activity against Culex quinquefasciatus.

    PubMed

    Bideshi, Dennis K; Waldrop, Greer; Fernandez-Luna, Maria Teresa; Diaz-Mendoza, Mercedes; Wirth, Margaret C; Johnson, Jeffrey J; Park, Hyun-Woo; Federici, Brian A

    2013-08-01

    The Cyt1Aa protein of Bacillus thuringiensis susbp. israelensis elaborates demonstrable toxicity to mosquito larvae, but more importantly, it enhances the larvicidal activity of this species Cry proteins (Cry11Aa, Cry4Aa, and Cry4Ba) and delays the phenotypic expression of resistance to these that has evolved in Culex quinquefasciatus. It is also known that Cyt1Aa, which is highly lipophilic, synergizes Cry11Aa by functioning as a surrogate membrane-bound receptor for the latter protein. Little is known, however, about whether Cyt1Aa can interact similarly with other Cry proteins not primarily mosquitocidal; for example, Cry2Aa, which is active against lepidopteran larvae, but essentially inactive or has very low toxicity to mosquito larvae. Here we demonstrate by ligand binding and enzyme-linked immunosorbent assays that Cyt1Aa and Cry2Aa form intermolecular complexes in vitro, and in addition show that Cyt1Aa facilitates binding of Cry2Aa throughout the midgut of C. quinquefasciatus larvae. As Cry2Aa and Cry11Aa share structural similarity in domain II, the interaction between Cyt1Aa and Cry2Aa could be a result of a similar mechanism previously proposed for Cry11Aa and Cyt1Aa. Finally, despite the observed interaction between Cry2Aa and Cyt1Aa, only a 2-fold enhancement in toxicity resulted against C. quinquefasciatus. Regardless, our results suggest that Cry2Aa could be a useful component of mosquitocidal endotoxin complements being developed for recombinant strains of B. thuringiensis subsp. israelensis and B. sphaericus aimed at improving the efficacy of commercial products and avoiding resistance. PMID:23727800

  7. Palindromic-nucleotide substitutions (PNS) of hepatitis C virus genotypes 1 and 5a from South Africa.

    PubMed

    Prabdial-Sing, N; Giangaspero, M; Puren, A J; Mahlangu, J; Barrow, P; Bowyer, S M

    2011-08-01

    The HCV stem-loop subdomains III-a, -b and -c have been shown to reflect the characteristics of the virus and identify isolates by genus, genotype and subtype. The aim of this study was to investigate the genotype-specific PNS within the 5'UTR of prevalent HCV genotypes (1 and 5a) found in South Africa. The genotype 5a (N = 35) and genotype 1 sequences (N=20) were from patients presenting with liver disease or haemophilia, respectively. PNS HCV typing characteristics, defined previously, were observed. The PNS method differentiated subtypes 1a and 1c from subtype 1b by the base change at nucleotide position 243. A lack of structural data from the variable loci V1 of the 5'UTR did not allow us to further differentiate the subtypes of 1. A nucleotide change from a thymine (T) to a cytosine (C) at position 183 was found among genotype 5a sequences. This mutation changed the stable U-AA bond to a Y AA bulge at base-pair position 32. There was an insertion of a single adenine (A) at position 207. At present PNS analysis is labour intensive but, with development of further software to aid the computer analysis, it has the potential to provide a rapid, reliable alternative to phylogenetic analysis. PMID:21600241

  8. Direct-Chill Co-Casting of AA3003/AA4045 Aluminum Ingots via Fusion™ Technology

    NASA Astrophysics Data System (ADS)

    Caron, Etienne J. F. R.; Pelayo, Rosa E. Ortega; Baserinia, Amir R.; Wells, Mary A.; Weckman, David C.; Barker, Simon; Gallerneault, Mark

    2014-06-01

    Laboratory-scale experiments were conducted to cast AA3003/AA4045 clad ingots via Fusion™ Technology, a novel process developed by Novelis Inc. for the production of aluminum clad materials such as brazing sheet. Experimental results were used to validate a steady-state thermofluids model of the Fusion™ Technology co-casting process. The numerical model was able to accurately predict the temperature field within the AA3003/AA4045 clad ingot as well as the shape of the AA3003 liquid sump. The model was also used to quantify the temperature, fraction solid, and velocity fields in a clad ingot cast with an asymmetrical molten metal-feeding system. Feeding of core and clad molten metals at opposite corners of the mold was found to reduce the risks of hot spots and liquid metal breakthrough from the core sump to the clad side of the Fusion™ Technology mold. The use of a diffuser for the AA3003 core molten metal and of a vertical feeding tube for the AA4045 clad produced different flow patterns and liquid sump shapes on either side of the mold. The quality of the metallurgical bond at the core/clad interface appeared good near the clad inlet and at the ingot centerline, but poor near the edges of the ingot. SEM-EDS analysis of the chemical composition across the interface showed that a 1 to 20- μm-deep penetration of silicon from the AA4045 clad into the AA3003 core had occurred at visually acceptable interfaces, whereas silicon diffusion across poor interfaces was very limited. A study of the model-predicted fraction solid history at different points along the interface indicated that reheating of the AA3003 core is not required to form a visually acceptable metallurgical bond. However, a sufficient amount of interaction time between the solid AA3003 core shell and the silicon-rich AA4045 clad liquid is required to chemically dissolve the surface of the core and form a good metallurgical bond. An approximate dissolution depth of 750 to 1000 μm was observed along

  9. AN EVALUATION OF CRYPTOSPORIDIUM PARVUM GENOTYPING

    EPA Science Inventory

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

  10. Detection of AA76, a Common Form of Amyloid A Protein, as a Way of Diagnosing AA Amyloidosis.

    PubMed

    Sato, Junji; Okuda, Yasuaki; Kuroda, Takeshi; Yamada, Toshiyuki

    2016-03-01

    Reactive amyloid deposits consist of amyloid A (AA) proteins, the degradation products of serum amyloid A (SAA). Since the most common species of AA is the amino terminal portion produced by cleavage between residues 76 and 77 of SAA (AA76), the presence of AA76 in tissues could be a consequence of AA amyloid deposition. This study assessed the diagnostic significance of the detection of AA76 for AA amyloidosis using two different approaches. Biopsy specimens (n=130 from 54 subjects) from gastroduodenal mucosa or abdominal fat (n=9 from 9 subjects) of patients who had already been diagnosed with or were suspected of having AA amyloidosis were used. Fixed mucosal sections were subjected to immunohistochemistry using a newly developed antibody recognizing the carboxyl terminal end of AA76 (anti-AA76). The non-fixed materials from gastroduodenal mucosa or abdominal fat were subjected to immunoblotting for detection of the size of AA76. Among the gastroduodenal specimens (n=115) from already diagnosed patients, the positive rates of Congo red staining, immunohistochemistry using anti-AA76, and immunoblotting were 68.4%, 73.0%, and 92.2%, respectively. The anti-AA76 did not stain the supposed SAA in the blood or leakage, which was stained by anti-SAA antibody. AA76 was not detected either by immunohistochemistry or by immunoblot in the materials from patients in whom AA amyloidosis had been ruled out. In the abdominal fat, the immunoblot detected AA76 in 8 materials from 8 already diagnosed patients and did not in 1 patient whose gastroduodenal mucosa was negative. In conclusion, the detection of AA76 may alter the ability to diagnose AA amyloidosis. In immunohistochemistry for fixed specimens, the new anti-AA76 antibody can improve the specificity. Immunoblot for non-fixed materials, which can considerably improve the sensitivity, should be beneficial for small materials like abdominal fat. PMID:27098620

  11. MDCT evaluation of acute aortic syndrome (AAS).

    PubMed

    Valente, Tullio; Rossi, Giovanni; Lassandro, Francesco; Rea, Gaetano; Marino, Maurizio; Muto, Maurizio; Molino, Antonio; Scaglione, Mariano

    2016-05-01

    Non-traumatic acute thoracic aortic syndromes (AAS) describe a spectrum of life-threatening aortic pathologies with significant implications on diagnosis, therapy and management. There is a common pathway for the various manifestations of AAS that eventually leads to a breakdown of the aortic intima and media. Improvements in biology and health policy and diffusion of technology into the community resulted in an associated decrease in mortality and morbidity related to aortic therapeutic interventions. Hybrid procedures, branched and fenestrated endografts, and percutaneous aortic valves have emerged as potent and viable alternatives to traditional surgeries. In this context, current state-of-the art multidetector CT (MDCT) is actually the gold standard in the emergency setting because of its intrinsic diagnostic value. Management of acute aortic disease has changed with the increasing realization that endovascular therapies may offer distinct advantages in these situations. This article provides a summary of AAS, focusing especially on the MDCT technique, typical and atypical findings and common pitfalls of AAS, as well as recent concepts regarding the subtypes of AAS, consisting of aortic dissection, intramural haematoma, penetrating atherosclerotic ulcer and unstable aortic aneurysm or contained aortic rupture. MDCT findings will be related to pathophysiology, timing and management options to achieve a definite and timely diagnostic and therapeutic definition. In the present article, we review the aetiology, pathophysiology, clinical presentation, outcomes and therapeutic approaches to acute aortic syndromes. PMID:27033344

  12. Genotype Specification Language.

    PubMed

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

    2016-06-17

    We describe here the Genotype Specification Language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language based on traditional genetic notation, as well as a set of low-level DNA manipulation primitives. The language allows facile incorporation of parts from a library of cloned DNA constructs and from the "natural" library of parts in fully sequenced and annotated genomes. GSL was designed to engage genetic engineers in their native language while providing a framework for higher level abstract tooling. To this end we define four language levels, Level 0 (literal DNA sequence) through Level 3, with increasing abstraction of part selection and construction paths. GSL targets an intermediate language based on DNA slices that translates efficiently into a wide range of final output formats, such as FASTA and GenBank, and includes formats that specify instructions and materials such as oligonucleotide primers to allow the physical construction of the GSL designs by individual strain engineers or an automated DNA assembly core facility. PMID:26886161

  13. Genotypic diversity of the Killer Cell Immunoglobulin-like Receptors (KIR) and their HLA class I Ligands in a Saudi population

    PubMed Central

    Omar, Suliman Y. Al; Alkuriji, Afrah; Alwasel, Saleh; Dar, javid Ahmed; Alhammad, Alwaleed; Christmas, Stephen; Mansour, Lamjed

    2016-01-01

    Abstract Killer Cell Immunoglobulin-like Receptors (KIR) have been used as good markers for the study of genetic predisposition in many diseases and in human genetic population dynamics. In this context, we have investigated the genetic diversity of KIR genes and their main HLA class I ligands in Saudi population and compared the data with other studies of neighboring populations. One hundred and fourteen randomly selected healthy Saudi subjects were genotyped for the presence or absence of 16 KIR genes and their HLA-C1, -C2, -Bw4Thr80 and Bw4Ile80 groups, using a PCR-SSP technique. The results show the occurrence of the framework genes (3DL2, 3DL3 and 2DL4) and the pseudogenes (2DP1 and 3DP1) at highest frequencies. All inhibitory KIR (iKIR) genes appeared at higher frequencies than activating genes (aKIR), except for 2DS4 with a frequency of 90.35%. A total of 55 different genotypes were observed appearing at different frequencies, where 12 are considered novel. Two haplotypes were characterized, AA and Bx (BB and AB), which were observed in 24.5% and 75.5% respectively of the studied group. The frequencies of iKIR + HLA associations were found to be much higher than aKIR + HLA. KIR genes frequencies in the Saudi population are comparable with other Middle Eastern and North African populations. PMID:27007893

  14. Echinococcus granulosus genotypes in Iran

    PubMed Central

    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

  15. AAS 228: Day 2 morning

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Plenary Session (Day 1) The Galaxy Zoo(by Benny Tsang)Galaxy Zoo was so hot that the servers hosting the galaxy images got melted down soon after being launched.Kevin Schawinski from ETH Zurich took us on a tour ofhis wonderful Galaxy Zoo. It is a huge zoo with about a quarter million zookeepers, they are citizen astronomers who collaboratively classify galaxies by their looks as an attempt to understand galaxy evolution. The big question that is being answered is: how do blue, actively star-forming galaxies evolve into red, quiescent (non-star-forming) galaxies? The Zoo helped reveal that blue galaxies turn into red galaxies via two possible paths galaxies might run out of supply of gas and shut off star formation slowly; or they could merge with one another and turn off star formation by destroying the gas reservoir rapidly!The Galaxy Zoo project also led to the discoveries of:Green Peas: they are the living fossils of galaxy evolution; compact, bright, green galaxies that are actively forming starsOverlapping galaxies: they are pairs of galaxies that are separated physically but happen to lie on the same line of sight; they provide excellent laboratories for studying dust extinctionHannys Voorwerp: an unusual object named after Hanny the discoverer, which is believed to be the first detection of quasar light echoThe idea of Galaxy Zoo in getting help from citizen scientists was further extended into an award-winningproject known as the Zooniverse, which is an online platform for streamlined crowd-sourcing for scientific research that requires human input. The future of astronomy is going to be

  16. AAS 228: Day 2 afternoon

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.The Limits of Scientific Cosmology: Setting the Stage: Accepted Facts, and Testing Limitations in Theory and Data (by Gourav Khullar)With a stellar lineup of speakers to talk about current and future prospects of cosmology and its limits (or lack thereof), the first session kicked off with talks by Risa Wechsler, Joseph Silk, and Sean Carroll (his talk on Multiverses is described below, by Nathan Sanders). Risa set the stage with an elaborate description of the current accepted facts in the era of precision cosmology including the standard model of concordance cosmology, described by seven parameters and an accepted Lambda-CDM paradigm (with a cosmological constant and cold dark matter). The talk stressed on the fact that all these parameters are understood to a percent order precision, which is a remarkable deviation from the time in 1990s when according to Risa, Alan Guth never thought that any of these numbers could be measured precisely!Risa Wechsler describing our current constraints on what Dark Matter could constitute.Joseph Silk discussing limits on cosmological parameters.The CMB measurements, Big Bang Nucleosynthesis estimates and galaxy clustering statistics all contribute to locking down the description of our universe. She emphasized on the tensions between different probes to measure expansion rate H0 of the universe, and small scale predictions of cold dark matter simulations, but she is hopeful that these shall be resolved eventually. Joe Silk followed this up with his interpretation of trying to understand our place in the universe and placing limits on different parameters and

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

    PubMed Central

    Sabatti, Chiara; Lange, Kenneth

    2011-01-01

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

  18. The AAS: Its Next 100 Years

    NASA Astrophysics Data System (ADS)

    Wolff, S.

    1999-05-01

    The AAS: Its Next Hundred Years "We are probably nearing the limit of all we can know about astronomy."-- Simon Newcomb, 1888. The best way to celebrate the centennial of the AAS is to look forward, not backward, and to begin planning for the next 100 years. However, predicting the future is even more difficult than it was in Newcomb's time. We live in an era characterized by an unprecedented rate of change in the kinds of scientific questions we ask, the tools we use to answer them, and the way we communicate our results. This talk will highlight some of the issues that we will face as a community during the next 10--but not the next 100!--years and suggests that the AAS has a fundamental role to play in shaping the community response to these issues.

  19. Constant amplitude and post-overload fatigue crack growth behavior in PM aluminum alloy AA 8009

    NASA Technical Reports Server (NTRS)

    Reynolds, A. P.

    1991-01-01

    A recently developed, rapidly solidified, powder metallurgy, dispersion strengthened aluminum alloy, AA 8009, was fatigue tested at room temperature in lab air. Constant amplitude/constant delta kappa and single spike overload conditions were examined. High fatigue crack growth rates and low crack closure levels compared to typical ingot metallurgy aluminum alloys were observed. It was proposed that minimal crack roughness, crack path deflection, and limited slip reversibility, resulting from ultra-fine microstructure, were responsible for the relatively poor da/dN-delta kappa performance of AA 8009 as compared to that of typical IM aluminum alloys.

  20. Constant amplitude and post-overload fatigue crack growth behavior in PM aluminum alloy AA 8009

    NASA Technical Reports Server (NTRS)

    Reynolds, A. P.

    1992-01-01

    A recently developed, rapidly solidified, powder metallurgy, dispersion strengthened aluminum alloy, AA 8009, was fatigue tested at room temperature in lab air. Constant amplitude/constant delta kappa and single spike overload conditions were examined. High fatigue crack growth rates and low crack closure levels compared to typical ingot metallurgy aluminum alloys were observed. It was proposed that minimal crack roughness, crack path delection, and limited slip reversibility, resulting from ultra-fine microstructure, were responsible for the relatively poor da/dN-delta kappa performance of AA 8009 as compared to that of typical IM aluminum alloys.

  1. Cost-Effectiveness of Genotype Testing for Primary Resistance in Brazil

    PubMed Central

    Morris, Bethany L.; Grinsztejn, Beatriz; Freedberg, Kenneth A.; Veloso, Valdilea G.; Walensky, Rochelle P.; Losina, Elena; Nakamura, Yoriko M.; Girouard, Michael P.; Sax, Paul E.; Struchiner, Claudio J.; Paltiel, A. David

    2015-01-01

    Objective: HIV genotype-resistance testing can help identify more effective antiretroviral treatment (ART) regimens for patients, substantially increasing the likelihood of viral suppression and immune recovery. We sought to evaluate the cost-effectiveness of genotype-resistance testing before first-line ART initiation in Brazil. Design: We used a previously published microsimulation model of HIV disease (CEPAC-International) and data from Brazil to compare the clinical impact, costs, and cost-effectiveness of initial genotype testing (Genotype) with no initial genotype testing (No genotype). Methods: Model parameters were derived from the HIV Clinical Cohort at the Evandro Chagas Clinical Research Institute and from published data, using Brazilian sources whenever possible. Baseline patient characteristics included 69% male, mean age of 36 years (SD, 10 years), mean CD4 count of 347 per microliter (SD, 300/µL) at ART initiation, annual ART costs from 2012 US $1400 to US $13,400, genotype test cost of US $230, and primary resistance prevalence of 4.4%. Life expectancy and costs were discounted 3% per year. Genotype was defined as “cost-effective” compared with No Genotype if its incremental cost-effectiveness ratio was less than 3 times the 2012 Brazilian per capita GDP of US $12,300. Results: Compared with No genotype, Genotype increased life expectancy from 18.45 to 18.47 years and reduced lifetime cost from US $45,000 to $44,770; thus, in the base case, Genotype was cost saving. Genotype was cost-effective at primary resistance prevalence as low as 1.4% and remained cost-effective when subsequent-line ART costs decreased to 30% of baseline value. Cost-inefficient results were observed only when simultaneously holding multiple parameters to extremes of their plausible ranges. Conclusions: Genotype-resistance testing in ART-naive individuals in Brazil will improve survival and decrease costs and should be incorporated into HIV treatment guidelines in Brazil

  2. Ovine HSP90AA1 gene promoter: functional study and epigenetic modifications.

    PubMed

    Salces-Ortiz, Judit; González, Carmen; Bolado-Carrancio, Alfonso; Rodríguez-Rey, Jose Carlos; Calvo, Jorge H; Muñoz, Rubén; Serrano, M Magdalena

    2015-11-01

    When environmental temperatures exceed a certain threshold, the upregulation of the ovine HSP90AA1 gene is produced to cope with cellular injuries caused by heat stress. It has been previously pointed out that several polymorphisms located at the promoter region of this gene seem to be the main responsible for the differences in the heat stress response observed among alternative genotypes in terms of gene expression rate. The present study, focused on the functional study of those candidate polymorphisms by electrophoretic mobility shift assay (EMSA) and in vitro luciferase expression assays, has revealed that the observed differences in the transcriptional activity of the HSP90AA1 gene as response to heat stress are caused by the presence of a cytosine insertion (rs397514115) and a C to G transversion (rs397514116) at the promoter region. Next, we discovered the presence of epigenetic marks at the promoter and along the gene body founding an allele-specific methylation of the rs397514116 mutation in DNA extracted from blood samples. This regulatory mechanism interacts synergistically to modulate gene expression depending on environmental circumstances. Taking into account the results obtained, it is suggested that the transcription of the HSP90AA1 ovine gene is regulated by a cooperative action of transcription factors (TFs) whose binding sites are polymorphic and where the influence of epigenetic events should be also taken into account. PMID:26253285

  3. Correlated genotypes in friendship networks

    PubMed Central

    Fowler, James H.; Settle, Jaime E.; Christakis, Nicholas A.

    2011-01-01

    It is well known that humans tend to associate with other humans who have similar characteristics, but it is unclear whether this tendency has consequences for the distribution of genotypes in a population. Although geneticists have shown that populations tend to stratify genetically, this process results from geographic sorting or assortative mating, and it is unknown whether genotypes may be correlated as a consequence of nonreproductive associations or other processes. Here, we study six available genotypes from the National Longitudinal Study of Adolescent Health to test for genetic similarity between friends. Maps of the friendship networks show clustering of genotypes and, after we apply strict controls for population stratification, the results show that one genotype is positively correlated (homophily) and one genotype is negatively correlated (heterophily). A replication study in an independent sample from the Framingham Heart Study verifies that DRD2 exhibits significant homophily and that CYP2A6 exhibits significant heterophily. These unique results show that homophily and heterophily obtain on a genetic (indeed, an allelic) level, which has implications for the study of population genetics and social behavior. In particular, the results suggest that association tests should include friends’ genes and that theories of evolution should take into account the fact that humans might, in some sense, be metagenomic with respect to the humans around them. PMID:21245293

  4. Impact of OAS1 Exon 7 rs10774671 Genetic Variation on Liver Fibrosis Progression in Egyptian HCV Genotype 4 Patients.

    PubMed

    Bader El Din, Noha G; Anany, Mohamed A; Dawood, Reham M; Ibrahim, Marwa K; El-Shenawy, Reem; El Abd, Yasmin S; El Awady, Mostafa K

    2015-11-01

    The aim of this study was to assess the impact of genetic variants of oligoadenylate synthetase 1 (OAS1) single-nucleotide polymorphism (SNP) rs10774671 at the exon 7 splice acceptor site on liver fibrosis progression and hepatitis C virus (HCV) outcome in Egyptian HCV genotype 4 patients. In this study, 195 subjects were enrolled; 60 controls and 135 chronic HCV genotype 4 patients with different fibrosis grades. All subjects were genotyped for OAS1 SNP rs10774671 polymorphism by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. There was an increasing trend of liver fibrosis progression as 52.9% GG, 73.6% GA, and 83.3% AA genotypes were detected in late fibrosis patients (p = 0.025). The AA genotype was higher in the late fibrosis group than in the early fibrosis group (83.3% vs. 16.7%) (p = 0.001). The A allele was significantly affecting the liver fibrosis progression rate, more than the G allele (p = 0.001). The multivariate analysis showed that the OAS1 GA and AA genotypes were independent factors associated with liver progression (p = 0.009, odds ratio [OR] 3.467, 95% confidence interval [CI] 1.273-7.584). In addition, the A allele was associated with liver fibrosis progression (p = 0.014, OR 2.525, 95% CI 1.157-4.545). The polymorphism at OAS1 exon 7 rs3741981 might be a potential genetic marker and can be useful in the assessment of liver fibrosis progression and disease outcome in HCV-infected patients. PMID:26505957

  5. 7 CFR 51.596 - U.S. Grade AA.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Consumer Standards for Celery Stalks Grades § 51.596 U.S. Grade AA. U.S. Grade AA shall consist of stalks of celery of similar varietal characteristics, which are...

  6. 7 CFR 51.596 - U.S. Grade AA.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Consumer Standards for Celery Stalks Grades § 51.596 U.S. Grade AA. U.S. Grade AA shall consist of stalks of celery of similar varietal characteristics, which are...

  7. 7 CFR 51.596 - U.S. Grade AA.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Consumer Standards for Celery Stalks Grades § 51.596 U.S. Grade AA. U.S. Grade AA shall consist of stalks of celery of similar varietal characteristics, which are well developed, and have good...

  8. 7 CFR 51.596 - U.S. Grade AA.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Consumer Standards for Celery Stalks Grades § 51.596 U.S. Grade AA. U.S. Grade AA shall consist of stalks of celery of similar varietal characteristics, which are well developed, and have good...

  9. Integrity of genome-wide genotype data from low passage lymphoblastoid cell lines.

    PubMed

    McCarthy, Nina S; Allan, Spencer M; Chandler, David; Jablensky, Assen; Morar, Bharti

    2016-09-01

    We compared genotype data from the HumanExomeCore Array in peripheral blood mononuclear cells and low passage lymphoblastoid cell lines from the same 24 individuals to test for genotypic errors caused by the Epstein-Barr Virus transformation process. Genotype concordance across the 24 comparisons was 99.57% for unfiltered genotype data, and 99.63% following standard genotype quality control filters. Mendelian error rates and levels of heterozygosity were not significantly different between lymphoblastoid cell lines and their parent peripheral blood mononuclear cells. These results show that at low passage numbers, genotype discrepancies are minimal even before stringent quality control, and extend current evidence qualifying the use of low-passage lymphoblastoid cell lines as a reliable DNA source for genotype analysis. PMID:27330997

  10. Warfarin Sensitivity Genotyping: A Review of the Literature and Summary of Patient Experience

    PubMed Central

    Moyer, Thomas P.; O'Kane, Dennis J.; Baudhuin, Linnea M.; Wiley, Carmen L.; Fortini, Alexandre; Fisher, Pamela K.; Dupras, Denise M.; Chaudhry, Rajeev; Thapa, Prabin; Zinsmeister, Alan R.; Heit, John A.

    2009-01-01

    The antithrombotic benefits of warfarin are countered by a narrow therapeutic index that contributes to excessive bleeding or cerebrovascular clotting and stroke in some patients. This article reviews the current literature describing warfarin sensitivity genotyping and compares the results of that review to the findings of our study in 189 patients at Mayo Clinic conducted between June 2001 and April 2003. For the review of the literature, we identified relevant peer-reviewed articles by searching the Web of Knowledge using key word warfarin-related adverse event. For the 189 Mayo Clinic patients initiating warfarin therapy to achieve a target international normalized ratio (INR) in the range of 2.0 to 3.5, we analyzed the CYP2C9 (cytochrome P450 2C9) and VKORC1 (vitamin K epoxide reductase complex, subunit 1) genetic loci to study the relationship among the initial warfarin dose, steady-state dose, time to achieve steady-state dose, variations in INR, and allelic variance. Results were compared with those previously reported in the literature for 637 patients. The relationships between allelic variants and warfarin sensitivity found in our study of Mayo Clinic patients are fundamentally the same as in those reported by others. The Mayo Clinic population is predominantly white and shows considerable allelic variability in CYP2C9 and VKORC1. Certain of these alleles are associated with increased sensitivity to warfarin. Polymorphisms in CYP2C9 and VKORC1 have a considerable effect on warfarin dose in white people. A correlation between steady-state warfarin dose and allelic variants of CYP2C9 and VKORC1 has been demonstrated by many previous reports and is reconfirmed in this report. The allelic variants found to most affect warfarin sensitivity are CYP2C9*1*1-VKORC1BB (less warfarin sensitivity than typical); CYP2C9*1*1-VKORC1AA (considerable variance in INR throughout initiation); CYP2C9*1*2-VKORC1AB (more sensitivity to warfarin than typical); CYP2C9*1*3-VKORC1

  11. Newcastle disease: genotypic variation and gross pathology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are currently 18 genotypes described for class II Newcastle disease viruses and one genotype for class I. While class I viruses are globally distributed in wild birds, the class II genotypes are found more selectively in different countries. For instance the NDV isolates in genotype V are mo...

  12. Genotype Imputation with Millions of Reference Samples.

    PubMed

    Browning, Brian L; Browning, Sharon R

    2016-01-01

    We present a genotype imputation method that scales to millions of reference samples. The imputation method, based on the Li and Stephens model and implemented in Beagle v.4.1, is parallelized and memory efficient, making it well suited to multi-core computer processors. It achieves fast, accurate, and memory-efficient genotype imputation by restricting the probability model to markers that are genotyped in the target samples and by performing linear interpolation to impute ungenotyped variants. We compare Beagle v.4.1 with Impute2 and Minimac3 by using 1000 Genomes Project data, UK10K Project data, and simulated data. All three methods have similar accuracy but different memory requirements and different computation times. When imputing 10 Mb of sequence data from 50,000 reference samples, Beagle's throughput was more than 100× greater than Impute2's throughput on our computer servers. When imputing 10 Mb of sequence data from 200,000 reference samples in VCF format, Minimac3 consumed 26× more memory per computational thread and 15× more CPU time than Beagle. We demonstrate that Beagle v.4.1 scales to much larger reference panels by performing imputation from a simulated reference panel having 5 million samples and a mean marker density of one marker per four base pairs. PMID:26748515

  13. Genotype Imputation with Millions of Reference Samples

    PubMed Central

    Browning, Brian L.; Browning, Sharon R.

    2016-01-01

    We present a genotype imputation method that scales to millions of reference samples. The imputation method, based on the Li and Stephens model and implemented in Beagle v.4.1, is parallelized and memory efficient, making it well suited to multi-core computer processors. It achieves fast, accurate, and memory-efficient genotype imputation by restricting the probability model to markers that are genotyped in the target samples and by performing linear interpolation to impute ungenotyped variants. We compare Beagle v.4.1 with Impute2 and Minimac3 by using 1000 Genomes Project data, UK10K Project data, and simulated data. All three methods have similar accuracy but different memory requirements and different computation times. When imputing 10 Mb of sequence data from 50,000 reference samples, Beagle’s throughput was more than 100× greater than Impute2’s throughput on our computer servers. When imputing 10 Mb of sequence data from 200,000 reference samples in VCF format, Minimac3 consumed 26× more memory per computational thread and 15× more CPU time than Beagle. We demonstrate that Beagle v.4.1 scales to much larger reference panels by performing imputation from a simulated reference panel having 5 million samples and a mean marker density of one marker per four base pairs. PMID:26748515

  14. AaCAT1 of the Yellow Fever Mosquito, Aedes aegypti

    PubMed Central

    Hansen, Immo A.; Boudko, Dmitri Y.; Shiao, Shin-Hong; Voronov, Dmitri A.; Meleshkevitch, Ella A.; Drake, Lisa L.; Aguirre, Sarah E.; Fox, Jeffrey M.; Attardo, Geoffrey M.; Raikhel, Alexander S.

    2011-01-01

    Insect yolk protein precursor gene expression is regulated by nutritional and endocrine signals. A surge of amino acids in the hemolymph of blood-fed female mosquitoes activates a nutrient signaling system in the fat bodies, which subsequently derepresses yolk protein precursor genes and makes them responsive to activation by steroid hormones. Orphan transporters of the SLC7 family were identified as essential upstream components of the nutrient signaling system in the fat body of fruit flies and the yellow fever mosquito, Aedes aegypti. However, the transport function of these proteins was unknown. We report expression and functional characterization of AaCAT1, cloned from the fat body of A. aegypti. Expression of AaCAT1 transcript and protein undergoes dynamic changes during postembryonic development of the mosquito. Transcript expression was especially high in the third and fourth larval stages; however, the AaCAT1 protein was detected only in pupa and adult stages. Functional expression and analysis of AaCAT1 in Xenopus oocytes revealed that it acts as a sodium-independent cationic amino acid transporter, with unique selectivity to l-histidine at neutral pH (K0.5l-His = 0.34 ± 0.07 mm, pH 7.2). Acidification to pH 6.2 dramatically increases AaCAT1-specific His+-induced current. RNAi-mediated silencing of AaCAT1 reduces egg yield of subsequent ovipositions. Our data show that AaCAT1 has notable differences in its transport mechanism when compared with related mammalian cationic amino acid transporters. It may execute histidine-specific transport and signaling in mosquito tissues. PMID:21262963

  15. 7 CFR 51.596 - U.S. Grade AA.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false U.S. Grade AA. 51.596 Section 51.596 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Consumer Standards for Celery Stalks Grades § 51.596 U.S. Grade AA. U.S. Grade AA shall consist of...

  16. Systemic AA amyloidosis: epidemiology, diagnosis, and management

    PubMed Central

    Real de Asúa, Diego; Costa, Ramón; Galván, Jose María; Filigheddu, María Teresa; Trujillo, Davinia; Cadiñanos, Julen

    2014-01-01

    The term “amyloidosis” encompasses the heterogeneous group of diseases caused by the extracellular deposition of autologous fibrillar proteins. The global incidence of amyloidosis is estimated at five to nine cases per million patient-years. While amyloid light-chain (AL) amyloidosis is more frequent in developed countries, amyloid A (AA) amyloidosis is more common in some European regions and in developing countries. The spectrum of AA amyloidosis has changed in recent decades owing to: an increase in the median age at diagnosis; a percent increase in the frequency of primary AL amyloidosis with respect to the AA type; and a substantial change in the epidemiology of the underlying diseases. Diagnosis of amyloidosis is based on clinical organ involvement and histological evidence of amyloid deposits. Among the many tinctorial characteristics of amyloid deposits, avidity for Congo red and metachromatic birefringence under unidirectional polarized light remain the gold standard. Once the initial diagnosis has been made, the amyloid subtype must be identified and systemic organ involvement evaluated. In this sense, the 123I-labeled serum amyloid P component scintigraphy is a safe and noninvasive technique that has revolutionized the diagnosis and monitoring of treatment in systemic amyloidosis. It can successfully identify anatomical patterns of amyloid deposition throughout the body and enables not only an initial estimation of prognosis, but also the monitoring of the course of the disease and the response to treatment. Given the etiologic diversity of AA amyloidosis, common therapeutic strategies are scarce. All treatment options should be based upon a greater control of the underlying disease, adequate organ support, and treatment of symptoms. Nevertheless, novel therapeutic strategies targeting the formation of amyloid fibrils and amyloid deposition may generate new expectations for patients with AA amyloidosis. PMID:25378951

  17. The acute lymphoblastic leukemia prognostic scoring whether it is possible by BCL-2, BAX gene promoter genotyping

    PubMed Central

    Moazami-Goudarzi, Mozhagan; Farshdousti-Hagh, Majid; Hoseinpour-Feizi, Abbasali; Talebi, Mehdi; Movassaghpour-Akbari, Ali Akbar; Shams-Asanjan, Karim; Eyvazi-Ziyaee, Jamal; Seifi, Morteza

    2016-01-01

    Background: BCL-2 is the most important anti-apoptotic regulator and Bax is a pro-apoptotic protein. The status of these parameters or the ration of BCL-2 to BAX is important in malignant cell fate as well as normal cells. Methods: Sixty-two ALL patients and 62 healthy sex-and age-matched controls were studied. After genotyping, the promoter region of the BAX and BCL-2 genes by RFLP-PCR method the patients were classified in nine prognostic groups, after that, the overall survival ratio of each score was compared with others pair-wise or between groups. Results: The frequencies of the AA, AC, CC alleles of the BCL-2 C-938A polymorphism in patient group were 33 (53.23%), 18 (29.03%), 11 (17.74%), and in the control group were 13 (21.0%), 27 (43.5%), 22 (35.5%), respectively (P=0.003). Also, the frequencies of AA, AG, GG alleles of the BAX G-248A SNP were 15 (24.2%), 24 (38.7%), 23 (37.1%) in ALL group and 13 (21.0%), 25 (40.3%), 24 (38.7%) (p>0.05) in the control group. The survival time estimation and ratio were significantly different between different SNPs in BCL-2 (P=0.002). Conclusion: These findings showed that the BCL-2 promoter region polymorphism is more reliable than BAX gene promoter polymorphism in any ALL scoring system. But the establishment of complete scoring system requires further more clinical and laboratory findings along with genetic polymorphisms is necessary.

  18. Mechanism of decay of the cry1Aa mRNA in Bacillus subtilis.

    PubMed Central

    Vázquez-Cruz, C; Olmedo-Alvarez, G

    1997-01-01

    We undertook the study of the decay process of the cry1Aa mRNA of Bacillus thuringiensis expressed in B. subtilis. The cry1Aa transcript is a 3.7-kb mRNA expressed during sporulation whose transcriptional control has previously been studied in both B. subtilis and B. thuringiensis. We found that the cry1Aa mRNA has a half-life of around 9 min and that its decay occurs through endoribonucleolytic cleavages which result in three groups of high-molecular-weight mRNA intermediates ranging in size from 2.7 to 0.5 kb. A comparative study carried out with Escherichia coli showed a similar pattern of degradation intermediates. Primer extension analysis carried out on RNA from B. subtilis revealed that most cleavages occur within two regions located toward the 5' and 3' ends of the mRNA. The most prominent processing site observed for the cry1Aa mRNA isolated from B. subtilis is only two bases away from that occurring on RNA isolated from E. coli. Most cleavage sites occur at seemingly single-stranded RNA segments rich in A and U nucleotides, suggesting that a common and conserved mechanism may process the cry1Aa mRNA. PMID:9335281

  19. Using Focus Groups to Inform the Development of Stroke Recovery and Prevention Programs for Younger African-American (AA) Men

    PubMed Central

    Blixen, Carol; Perzynski, Adam; Cage, Jamie; Smyth, Kathleen; Moore, Shirley; Sila, Cathy; Pundik, Svetlana; Sajatovic, Martha

    2016-01-01

    Objective To assess perceived facilitators and recommendations for stroke recovery and prevention among younger AA men (< age 65) in order to inform the development and pilot testing of an intervention for this high risk group. Method Focus group methodology was used to collect data from ten community-dwelling AA stroke survivors and seven of their care partners (CPs) (N=17. Thematic analysis of session transcripts and the constant comparative method were used to generate themes. Results Participants cited facilitators to post-stroke care and recovery as Family Support, Stress Reduction and Dietary Changes. Specific person-level recommendations for AA men included following established stroke guidelines, use of complementary and alternative medicine, and never give up recovery efforts. Community-level recommendations included making a list of community resources available, providing support and education to care partners, using videos that feature AA men to deliver information and use AA men stroke survivors to help disseminate the information. Provider and health system recommendations included consolidation of medical bills, improving provider communication skills and making providers aware of needs specific to AA men and their families. Conclusions While AA men and their CPs acknowledged and welcomed learning more about the American Health Assocation Stroke Prevention Guidelines, it is clear they desired approaches that addressed their specific needs and preferences as young AA men who sometimes felt de-valued by their community and care providers. Specific person, community and care-system level approaches that are of perceived value to AA men offer potential to improve health outcomes and reduce health disparities. PMID:26084323

  20. Genomic analysis of 16 Colorado human NL63 coronaviruses identifies a new genotype, high sequence diversity in the N-terminal domain of the spike gene and evidence of recombination

    PubMed Central

    Sims, Gregory E.; Wentworth, David E.; Halpin, Rebecca A.; Robinson, Christine C.; Town, Christopher D.; Holmes, Kathryn V.

    2012-01-01

    This study compared the complete genome sequences of 16 NL63 strain human coronaviruses (hCoVs) from respiratory specimens of paediatric patients with respiratory disease in Colorado, USA, and characterized the epidemiology and clinical characteristics associated with circulating NL63 viruses over a 3-year period. From 1 January 2009 to 31 December 2011, 92 of 9380 respiratory specimens were found to be positive for NL63 RNA by PCR, an overall prevalence of 1 %. NL63 viruses were circulating during all 3 years, but there was considerable yearly variation in prevalence and the month of peak incidence. Phylogenetic analysis comparing the genome sequences of the 16 Colorado NL63 viruses with those of the prototypical hCoV-NL63 and three other NL63 viruses from the Netherlands demonstrated that there were three genotypes (A, B and C) circulating in Colorado from 2005 to 2010, and evidence of recombination between virus strains was found. Genotypes B and C co-circulated in Colorado in 2005, 2009 and 2010, but genotype A circulated only in 2005 when it was the predominant NL63 strain. Genotype C represents a new lineage that has not been described previously. The greatest variability in the NL63 virus genomes was found in the N-terminal domain (NTD) of the spike gene (nt 1–600, aa 1–200). Ten different amino acid sequences were found in the NTD of the spike protein among these NL63 strains and the 75 partial published sequences of NTDs from strains found at different times throughout the world. PMID:22837419

  1. Alkaline phosphatases and aminopeptidases are altered in a Cry11Aa resistant strain of Aedes aegypti

    PubMed Central

    Lee, Su-Bum; Aimanova, Karlygash G.; Gill, Sarjeet S.

    2014-01-01

    Bacillus thuringiensis subsp. israelensis (Bti) has been widely for the biological control of mosquito populations. However, the mechanism of Bti toxins is still not fully understood. To further elucidate the mechanism of Bti toxins, we developed an Aedes aegypti resistant strain that shows high-level resistance to Cry11Aa toxin. After 27 selections with Cry11Aa toxin, the larvae showed a 124-fold resistance ratio for Cry11Aa (strain G30). G30 larvae showed cross-resistance to Cry4Aa (66-fold resistance), less to Cry4Ba (13-fold), but not to Cry11Ba (2-fold). Midguts from these resistant larvae did not show detectable difference in the processing of the Cry11Aa toxin compared to that in susceptible larvae (WT). Brush border membrane vesicles (BBMV) from resistant larvae bound slightly less Cry11Aa compared to WT BBMV. To identify potential proteins associated with Cry11A resistance, not only transcript changes in the larval midgut were analyzed using Illumina sequencing and qPCR, but alterations of previously identified receptor proteins were investigated using immunoblots. The transcripts of 375 genes were significantly increased and those of 208 genes were down regulated in the resistant larvae midgut compared to the WT. None of the transcripts for previously identified receptors of Cry11Aa (Aedes cadherin, ALP1, APN1, and APN2) were altered in these analyses. The genes for the identified functional receptors in resistant larvae midgut did not contain any mutation in their sequences nor was there any change in their transcript expression levels compared to WT. However, ALP proteins were expressed at reduced levels (~40%) in the resistant strain BBMV. APN proteins and their activity were also slightly reduced in resistance strain. The transcript levels of ALPs (AAEL013330 and AAEL015070) and APNs (AAEL008158, AAEL008162) were significantly reduced. These results strongly suggest that ALPs and APNs could be associated with Cry11Aa resistance in Ae. aegypti. PMID

  2. Alkaline phosphatases and aminopeptidases are altered in a Cry11Aa resistant strain of Aedes aegypti.

    PubMed

    Lee, Su-Bum; Aimanova, Karlygash G; Gill, Sarjeet S

    2014-11-01

    Bacillus thuringiensis subsp. israelensis (Bti) is widely used for the biological control of mosquito populations. However, the mechanism of Bti toxins is still not fully understood. To further elucidate the mechanism of Bti toxins, we developed an Aedes aegypti resistant strain that shows high-level resistance to Cry11Aa toxin. After 27 selections with Cry11Aa toxin, the larvae showed a 124-fold resistance ratio for Cry11Aa (strain G30). G30 larvae showed cross-resistance to Cry4Aa (66-fold resistance), less to Cry4Ba (13-fold), but not to Cry11Ba (2-fold). Midguts from these resistant larvae did not show detectable difference in the processing of the Cry11Aa toxin compared to that in susceptible larvae (WT). Brush border membrane vesicles (BBMV) from resistant larvae bound slightly less Cry11Aa compared to WT BBMV. To identify potential proteins associated with Cry11A resistance, not only transcript changes in the larval midgut were analyzed using Illumina sequencing and qPCR, but alterations of previously identified receptor proteins were investigated using immunoblots. The transcripts of 375 genes were significantly increased and those of 208 genes were down regulated in the resistant larvae midgut compared to the WT. None of the transcripts for previously identified receptors of Cry11Aa (Aedes cadherin, ALP1, APN1, and APN2) were altered in these analyses. The genes for the identified functional receptors in resistant larvae midgut did not contain any mutation in their sequences nor was there any change in their transcript expression levels compared to WT. However, ALP proteins were expressed at reduced levels (∼ 40%) in the resistant strain BBMV. APN proteins and their activity were also slightly reduced in resistance strain. The transcript levels of ALPs (AAEL013330 and AAEL015070) and APNs (AAEL008158, AAEL008162) were significantly reduced. These results strongly suggest that ALPs and APNs could be associated with Cry11Aa resistance in Ae. aegypti. PMID

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

    PubMed

    Hyman, Glenn; Hodson, Dave; Jones, Peter

    2013-01-01

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

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

    PubMed Central

    Hyman, Glenn; Hodson, Dave; Jones, Peter

    2013-01-01

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

  5. Compression Behavior and Energy Absorption of Aluminum Alloy AA6061 Tubes with Multiple Holes

    NASA Astrophysics Data System (ADS)

    Simhachalam, Bade; Lakshmana Rao, C.; Srinivas, Krishna

    2014-05-01

    In this article, compression behavior and energy absorption of aluminum alloy AA6061 tubes are investigated both experimentally and numerically. Static and dynamic simulations are done using LS-Dyna Software for AA6061 tubes. True stress-plastic strain curves from the tensile test are used in the static and dynamic simulations of AA6061 tubes. The energy absorption values between experimental compression results and numeral simulation are found to be in good agreement. Dynamic simulations are done with drop velocity of up to 10 m/s to understand the inertia effects on energy absorption. The deformed modes from the numerical simulation are compared between tubes with and without holes in static and dynamic conditions.

  6. AA479 antiserum: new reagent for the serotype characterization of atypical variants of Shigella flexneri.

    PubMed

    van der Ploeg, Claudia A; Rogé, Ariel D; Bordagorria, Ximena L; de Urquiza, María T; Viñas, María R; Pichel, Mariana G; Bruno, Susana B

    2015-01-01

    Shigella flexneri is divided into 13 serotypes based on the combination of antigenic determinants present in the O-antigen. A new O-antigen modification with phosphoethanolamine has been identified. The presence of this antigenic determinant (called E1037) is recognized by monoclonal antibody MASF IV-1. Given the increasing incidence of these new variants and the difficulty in supplying the monoclonal antibody to our country, we produced a polyclonal antiserum (AA479) through immunization with a S. flexneri Xv strain. The antiserum specificity was assessed by slide agglutination against isolates from clinical cases and a culture collection representing all Shigella serotypes. The results obtained demonstrated a 100% correlation between AA479 absorbed antiserum and monoclonal antibody MASF IV-1. The availability of AA479 antiserum in every public hospital in Argentina will allow us to identify atypical S. flexneri isolates in order to strengthen Shigella surveillance in our country and to compare with global epidemiological data. PMID:25735215

  7. Comparison of preliminary results from Airborne Aster Simulator (AAS) with TIMS data

    NASA Technical Reports Server (NTRS)

    Kannari, Yoshiaki; Mills, Franklin; Watanabe, Hiroshi; Ezaka, Teruya; Narita, Tatsuhiko; Chang, Sheng-Huei

    1992-01-01

    The Japanese Advanced Spaceborne Thermal Emission and Reflection radiometer (ASTER), being developed for a NASA EOS-A satellite, will have 3 VNIR, 6 SWIR, and 5 TIR (8-12 micron) bands. An Airborne ASTER Simulator (AAS) was developed for Japan Resources Observation System Organization (JAROS) by the Geophysical Environmental Research Group (GER) Corp. to research surface temperature and emission features in the MWIR/TIR, to simulate ASTER's TIR bands, and to study further possibility of MWIR/TIR bands. ASTER Simulator has 1 VNIR, 3 MWIR (3-5 microns), and 20 (currently 24) TIR bands. Data was collected over 3 sites - Cuprite, Nevada; Long Valley/Mono Lake, California; and Death Valley, California - with simultaneous ground truth measurements. Preliminary data collected by AAS for Cuprite, Nevada is presented and AAS data is compared with Thermal Infrared Multispectral Scanner (TIMS) data.

  8. 40 CFR Appendix A to Subpart Aa of... - Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... (40 CFR Part 63, Subpart A) to Subpart AA A Appendix A to Subpart AA of Part 63 Protection of... Hazardous Air Pollutants From Phosphoric Acid Manufacturing Plants Pt. 63, Subpt. AA, App. A Appendix A to Subpart AA of Part 63—Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA 40...

  9. 40 CFR Appendix A to Subpart Aa of... - Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... (40 CFR Part 63, Subpart A) to Subpart AA A Appendix A to Subpart AA of Part 63 Protection of... Hazardous Air Pollutants From Phosphoric Acid Manufacturing Plants Pt. 63, Subpt. AA, App. A Appendix A to Subpart AA of Part 63—Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA 40...

  10. 40 CFR Appendix A to Subpart Aa of... - Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... (40 CFR Part 63, Subpart A) to Subpart AA A Appendix A to Subpart AA of Part 63 Protection of... Hazardous Air Pollutants From Phosphoric Acid Manufacturing Plants Pt. 63, Subpt. AA, App. A Appendix A to Subpart AA of Part 63—Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA 40...

  11. 40 CFR Appendix A to Subpart Aa of... - Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... (40 CFR Part 63, Subpart A) to Subpart AA A Appendix A to Subpart AA of Part 63 Protection of... Hazardous Air Pollutants From Phosphoric Acid Manufacturing Plants Pt. 63, Subpt. AA, App. A Appendix A to Subpart AA of Part 63—Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA 40...

  12. 40 CFR Appendix A to Subpart Aa of... - Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (40 CFR Part 63, Subpart A) to Subpart AA A Appendix A to Subpart AA of Part 63 Protection of... Hazardous Air Pollutants From Phosphoric Acid Manufacturing Plants Pt. 63, Subpt. AA, App. A Appendix A to Subpart AA of Part 63—Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA 40...

  13. [Relationship between genotypes at MyoD locus and carcass traits in cattle].

    PubMed

    Tian, Lu; Xu, Shang-Zhong; Yue, Wen-Bin; Li, Jun-Ya; Gao, Xue; Ren, Hong-Yan

    2007-03-01

    A 261 bp sequence of the bovine MyoD gene intron 2 was cloned and was found to bear no similarities to the human MyoD gene sequence. Polymorphisms of the Myod gene in cattle including three Chinese breeds (Luxi cattle, Jinnan cattle and Qinchuan cattle) and four cross-breeding populations (Limousin x Luxi cattle, Simmental x Luxi cattle, Charolais x Luxi cattle and Angus x Luxi cattle) were detected by PCR-SSCP. Two SSCP alleles (A and B) were detected, which caused by a C-->T at 39 bp and a C-->G transition at 112 bp. Only two genotypes AA and AB occurred in the population. In Chinese local cattle, B allele was dominant, and this locus was at Hardy-Weinberg equilibrium except for the Charolais x Luxi cattle and Angus x Luxi cattle. The association of these polymorphisms with cattle carcass traits was analyzed using the general linear model (GLM). Statistical analysis revealed a higher value of living weight, carcass weight and loin eye area for individuals with genotype AA than AB (P < 0.05). Further studies on a bigger population size are needed to confirm the observed effect of MyoD genotypes on carcass quality traits. PMID:17369152

  14. Human papillomavirus infection and P53 codon 72 genotypes in a Hispanic population at high-risk for cervical cancer.

    PubMed

    Haws, Andrea L Fuessel; Woeber, Sabine; Gomez, Miroslava; Garza, Noe; Gomez, Yvonne; Rady, Peter; He, Qin; Zhang, Lifang; Grady, James J; McCormick, Joseph B; Fisher-Hoch, Susan P; Tyring, Stephen K

    2005-10-01

    Cervical cancer mortality is high in Texas, especially among Hispanic women living in south Texas and adjacent Mexico. Though human papillomavirus (HPV) infection has a causal role in the development of cervical cancer, there are no published data on the prevalence of HPV genotypes in this underscreened region. We studied 398 Hispanic women on both sides of the border along the lower Rio Grande River to determine the prevalence of HPV genotypes and risk factors for cervical cancer. Using a nested PCR system HPV was detected in 62% of cervical specimens, including all the known high-risk HPV genotypes, with HPV16 and HPV18 the most frequent (30.6% and 23.0%, respectively). Multiple infections were common (29.4% of the infected specimens), and where this occurred we were more likely to find high-risk HPV genotypes. We examined host p53 codon 72 genotype frequencies and found that patients with cervical abnormalities and women with HPV16 and HPV18 infections had a lower genotype frequency of the homozygous (AA) previously reported to be associated with cervical cancer, than uninfected women with no abnormalities. In this US/Mexico border population high rates of potentially oncogenic HPV viruses and multiple infections are consistent with observed elevated cervical cancer rates. These data are further evidence that in this underserved population HPV infections are associated with high rates of malignancy, but that host p53 genotypic variations are unlikely to be primary factors in oncogenesis. PMID:16121365

  15. Amazonian head lice-specific genotypes are putatively pre-Columbian.

    PubMed

    Boutellis, Amina; Veracx, Aurélie; Abrahão, Jônatas; Raoult, Didier

    2013-06-01

    Head and body lice are strict obligate human ectoparasites with three mitochondrial phylotypes (A, B, and C). Using molecular methods for genotyping lice (Cytochrome b and multi-spacer typing), and comparing our results with all the sequences of human lice that were genotyped previously, we assessed the presence of a specific American genotype that most likely predates the Columbian era in head lice collected from Amazonia. PMID:23610158

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  18. Colchicine use in isolated renal AA amyloidosis.

    PubMed

    Meneses, Carlos F; Egües, César A; Uriarte, Miren; Belzunegui, Joaquín; Rezola, Marta

    2015-01-01

    We present the case of a 45-year-old woman, with two-year history of chronic renal insufficiency and proteinuria. A kidney biopsy showed the presence of AA amyloidosis (positive Congo red staining and immunohistochemistry). There was no evidence of amyloid deposits in other organs and there was no underlying disease. AA amyloidosis normally is secondary to chronic inflammatory or infectious diseases. High levels of IL-1, IL-6 and TNF-α play a role in the pathogenesis of amyloidosis and induce the synthesis of serum amyloid A protein (SAA), a precursor of tissue amyloid deposits. We empirically treated the patient with a low dose colchicine. The patient responded well. Colchicine has been used for the treatment of Familiar Mediterranean Fever and related auto-inflammatory diseases. To monitor treatment responses, we measured SAA finding low titers. Soon after treatment onset there were signs of improvement pertaining to proteinuria and stabilization of renal function. PMID:25453598

  19. Identification of G and P genotype-specific motifs in the predicted VP7 and VP4 amino acid sequences.

    PubMed

    Ma, Yongping

    2015-12-01

    Equine rotavirus (ERV) strain L338 (G13P[18]) has a unique G and P genotype. However, the evolutionary relationship of L338 with other ERVs is still unknown. Here whole genome analysis of the L338 ERV strain was independently performed. Its genotype constellations were determined as G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11, confirming previous genotype assignments. The L338 strain only shared the P[18] and I6 genotypes with other ERVs. The nucleotide sequences of the other 9 RNA segments were different from those of cogent genes of all other group A rotavirus (RVA) strains including ERVs and formed unique phylogenetic lineages. The L338 evolutionary footprints were tentatively identified in both VP7 and VP4 amino acid sequences: two regions were found in VP7 and twelve in VP4. The conserved regions shared between L338 and other group A rotavirus strains (RVAs) indicated that L338 was more closely related genomically to animal and human RVAs other than ERVs, suggesting that L338 may not be an endogenous equine RV but have emerged as an interspecies reassortant with other RVA strains. Furthermore, genotype-specific motifs of all 27 G and 37 P types were identified in regions 7-1a (aa 91-100) of VP7 and regions 8-1 (aa146-151) and 8-3 (aa113-118 and 125-135) of VP4 (VP8*). PMID:26321159

  20. The Effectiveness of the AAS REU Program

    NASA Astrophysics Data System (ADS)

    Hemenway, M. K.; Boyce, P. B.; Milkey, R. W.

    1996-05-01

    In an attempt to address the particular needs of astronomy faculty and undergraduate students, in 1991 the Education Office of the American Astronomical Society approached the National Science Foundation with a unique proposal for funding through the Research Experiences for Undergraduates program. The goals of the AAS program were to "slow the hemorrhage of students out of science...", extend the REU program to non-NSF-funded scientists, to reach under-represented women and minority students particularly in small educational institutions, and to encourage research scientists there to mentor students. As this grant has now expired, the AAS has surveyed the 44 mentors and their students to assess the program's effect on the mentor and the mentor's career; the educational institution; and the student's education and career choices. More than half the mentors responded by the abstract deadline. The program clearly had an effect upon the individuals involved. The greatest effect (in 85% of the cases) was to develop more interest in the mentor's research project both among the students and among the mentor's faculty colleagues. The mentors rated the grant to be a medium or strong factor in their student's decision to pursue graduate study, which 90% of them did. All but one of the AAS-REU students attended an AAS meeting and 3/4 of those gave a paper on their project research. Over 90% of the mentors felt that the research experience strongly promoted a greater interest in science, a greater understanding of science and a desire to continue in science. According to the mentors, this was a very positive and beneficial program for the students as well as for themselves.

  1. Spectroscopic observations and analysis of the peculiar SN1999aa

    SciTech Connect

    Garavini, G.; Folatelli, G.; Goobar, A.; Nobili, S.; Aldering,G.; Amadon, A.; Amanullah, R.; Astier, P.; Balland, C.; Blanc, G.; Burns,M.S.; Conley, A.; Dahlen, T.; Deustua, S.E.; Ellis, R.; Fabbro, S.; Fan,X.; Frye, B.; Gates, E.L.; Gibbons, R.; Goldhaber, G.; Goldman, B.; Groom, D.E.; Haissinski, J.; Hardin, D.; Hook, I.M.; Howell, D.A.; Kasen,D.; Kent, S.; Kim, A.G.; Knop, R.A.; Lee, B.C.; Lidman, C.; Mendez, J.; Miller, G.J.; Moniez, M.; Mourao, A.; Newberg, H.; Nugent, P.E.; Pain,R.; Perdereau, O.; Perlmutter, S.; Prasad, V.; Quimby, R.; Raux, J.; Regnault, N.; Rich, J.; Richards, G.T.; Ruiz-Lapuente, P.; Sainton, G.; Schaefer, B.E.; Schahmaneche, K.; Smith, E.; Spadafora, A.L.; Stanishev,V.; Walton, N.A.; Wang, L.; Wood-Vasey, W.M.

    2003-12-10

    We present an extensive new time series of spectroscopic data of the peculiar SN 1999aa in NGC 2595. Our data set includes 25 optical spectra between -11 and +58 days with respect to B-band maximum light, providing an unusually complete time history. The early spectra resemble those of an SN 1991T-like object but with a relatively strong CaH and K absorption feature. The first clear sign of Si II lambda 6355, characteristic of Type Ia supernovae, is found at day -7, and its velocity remains constant up to at least the first month after B-band maximum light. The transition to normal-looking spectra is found to occur earlier than in SN 1991T, suggesting SN 1999aa as a possible link between SN 1991T-like and Branch-normal supernovae. Comparing the observations with synthetic spectra, doubly ionized Fe, Si, and Ni are identified at early epochs. These are characteristic of SN 1991 T-like objects. Furthermore, in the day -11 spectrum, evidence is found for an absorption feature that could be identified as high velocity C II lambda 6580 or H alpha. At the same epoch C III lambda 4648.8 at photospheric velocity is probably responsible for the absorption feature at 4500 8. High-velocity Ca is found around maximum light together with Si II and Fe II confined in a narrow velocity window. Implied constraints on supernovae progenitor systems and explosion hydrodynamic models are briefly discussed.

  2. Association of angiotensin converting enzyme and angiotensin II type 1 receptor genotypes with left ventricular function and mass in patients with angiographically normal coronary arteries.

    PubMed Central

    Hamon, M.; Amant, C.; Bauters, C.; Richard, F.; Helbecque, N.; McFadden, E.; Lablanche, J. M.; Bertrand, M.; Amouyel, P.

    1997-01-01

    OBJECTIVE: To analyse the potential association of the angiotensin converting enzyme (ACE) and angiotensin II type 1 receptor (AT1R) gene polymorphisms on left ventricular function and mass in patients with normal coronary arteries. DESIGN: Consecutive sample. SETTING: University hospital. SUBJECTS: 141 consecutive white patients referred for coronary angiography and with angiographically normal coronary arteries. Patients with valvar diseases, cardiomyopathies, or a history of myocardial infarction were excluded. MAIN OUTCOME MEASURES: Left ventricular variables were measured for all patients. The ACE and AT1R genotypes were determined with a polymerase chain reaction based protocol using DNA prepared from white blood cells. A general linear model was used to compare data according to the ACE and to the AT1R genotypes. RESULTS: A strong association was observed between left ventricular mass and systemic hypertension (mean (SD) hypertension: 114 (31) g/m2; no hypertension 98 (23) g/m2; P < 0.003). However, no influence of ACE and AT1R polymorphisms on left ventricular mass was found, regardless of systemic hypertension. The subjects homozygous for the AT1R CC mutation had a significantly lower ejection fraction than those with allele A (AC+AA) (mean (SD) 62(12)% and 68(10)%, respectively, P < 0.05). No synergistic interaction of ACE and AT1R gene polymorphisms on left ventricular function and mass was found. CONCLUSIONS: These data do not support an association of the ACE and AT1R genotypes on left ventricular hypertrophy in white patients with normal coronary arteries. PMID:9227291

  3. The long non-coding RNA HNF1A-AS1 regulates proliferation and metastasis in lung adenocarcinoma

    PubMed Central

    Shi, Xuefei; Yao, Yanwen; Yang, Wen; Song, Yong

    2015-01-01

    Long noncoding RNAs (lncRNAs) have emerged as key regulators of tumor development and progression. The lncRNA HNF1A-antisense 1 (HNF1A-AS1) is a 2455-bp transcript on chromosome 12 with a potential oncogenic role in esophageal adenocarcinoma. Nevertheless, current understanding of the involvement of HNF1A-AS1 in lung adenocarcinoma tumorigenesis remains limited. In this study, we analyzed the roles of HNF1A-AS1 in 40 lung adenocarcinoma tissues and five lung cancer cell lines. Our results showed that HNF1A-AS1 was significantly up-regulated in lung adenocarcinoma tissues compared with corresponding non-tumor tissues, and its expression level was significantly correlated with TNM stage, tumor size, and lymph node metastasis. The UCSC Cancer Genomics Browser's Kaplan-Meier plot suggested that patients in the high HNF1A-AS1 expression subgroup experienced worse overall survival compared to the low expression subgroup. Moreover, HNF1A-AS1 was determined to promote tumor proliferation and metastasis, both in vitro and in vivo, by regulating cyclin D1, E-cadherin, N-cadherin and β-catenin expression. In addition, the binding of HNF1A-AS1 to DNMT1 may explain its regulation of E-cadherin. In conclusions, we demonstrated that increased HNF1A-AS1 expression could regulate cell proliferation and metastasis and identified it as a poor prognostic biomarker in lung adenocarcinoma. PMID:25863539

  4. AAS Publishing News: Astronomical Software Citation Workshop

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2015-07-01

    Do you write code for your research? Use astronomical software? Do you wish there were a better way of citing, sharing, archiving, or discovering software for astronomy research? You're not alone! In April 2015, AAS's publishing team joined other leaders in the astronomical software community in a meeting funded by the Sloan Foundation, with the purpose of discussing these issues and potential solutions. In attendance were representatives from academic astronomy, publishing, libraries, for-profit software sharing platforms, telescope facilities, and grantmaking institutions. The goal of the group was to establish “protocols, policies, and platforms for astronomical software citation, sharing, and archiving,” in the hopes of encouraging a set of normalized standards across the field. The AAS is now collaborating with leaders at GitHub to write grant proposals for a project to develop strategies for software discoverability and citation, in astronomy and beyond. If this topic interests you, you can find more details in this document released by the group after the meeting: http://astronomy-software-index.github.io/2015-workshop/ The group hopes to move this project forward with input and support from the broader community. Please share the above document, discuss it on social media using the hashtag #astroware (so that your conversations can be found!), or send private comments to julie.steffen@aas.org.

  5. Introducing the AAS Astronomy Ambassadors Program

    NASA Astrophysics Data System (ADS)

    Gurton, S.; Fienberg, R. T.; Fraknoi, A.; Prather, E. E.

    2013-04-01

    Newly established by the American Astronomical Society (AAS), the Astronomy Ambassadors program is designed to support early-career AAS members with training in resources and techniques for effective outreach to students and/or the public. A pilot Astronomy Ambassadors workshop will be held at the January 2013 AAS meeting. Workshop participants will learn to communicate effectively with public and school audiences; find outreach opportunities and establish ongoing partnerships with local schools, science centers, museums, parks, and/or community centers; reach audiences with personal stories, hands-on activities, and jargon-free language; identify strategies and techniques to improve their presentation skills; gain access to a menu of outreach resources that work in a variety of settings; and become part of an active community of astronomers who do outreach. Applications are welcome from advanced undergraduates (those doing research and committed to continuing in astronomy), graduate students, and postdocs and new faculty in their first two years after receipt of the PhD. We especially encourage applications from members of groups that are presently underrepresented in science.

  6. High cycle fatigue of AA6082 and AA6063 aluminum extrusions

    NASA Astrophysics Data System (ADS)

    Nanninga, Nicholas E.

    The high cycle fatigue behavior of hollow extruded AA6082 and AA6063 aluminum extrusions has been studied. Hollow extruded aluminum profiles can be processed into intricate shapes, and may be suitable replacements for fatigue critical automotive applications requiring reduced weight. There are several features inherent in hollow aluminum extrusions, such as seam welds, charge welds, microstructural variations and die lines. The effects of such extrusion variables on high cycle fatigue properties were studied by taking specimens from an actual car bumper extrusion. It appears that extrusion die lines create large anisotropy differences in fatigue properties, while welds themselves have little effect on fatigue lives. Removal of die lines greatly increased fatigue properties of AA6082 specimens taken transverse to the extrusion direction. Without die lines, anisotropy in fatigue properties between AA6082 specimens taken longitudinal and transverse to the extrusion direction, was significantly reduced, and properties associated with the orientation of the microstructure appears to be isotropic. A fibrous microstructure for AA6082 specimens showed great improvements in fatigue behavior. The effects of elevated temperatures and exposure of specimens to NaCl solutions was also studied. Exposure to the salt solution greatly reduced the fatigue lives of specimens, while elevated temperatures showed more moderate reductions in fatigue lives.

  7. Comparing Genetic Ancestry and Self-Described Race in African Americans Born in the United States and in Africa

    PubMed Central

    Yaeger, Rona; Avila-Bront, Alexa; Abdul, Kazeem; Nolan, Patricia C.; Grann, Victor R.; Birchette, Mark G.; Choudhry, Shweta; Burchard, Esteban G.; Beckman, Kenneth B.; Gorroochurn, Prakash; Ziv, Elad; Consedine, Nathan S.; Joe, Andrew K.

    2008-01-01

    Genetic association studies can be used to identify factors that may contribute to disparities in disease evident across different racial and ethnic populations. However, such studies may not account for potential confounding if study populations are genetically heterogeneous. Racial and ethnic classifications have been used as proxies for genetic relatedness. We investigated genetic admixture and developed a questionnaire to explore variables used in constructing racial identity in two cohorts – 50 African Americans (AAs) and 40 Nigerians. Genetic ancestry was determined by genotyping 107 ancestry informative markers. Ancestry estimates calculated with maximum likelihood estimation were compared with population stratification detected with principal component analysis. Ancestry was approximately 95% west African, 4% European, and 1% Native American in the Nigerian cohort and 83% west African, 15% European, and 2% Native American in the AA cohort. Therefore, self-identification as AA agreed well with inferred west African ancestry. However, the cohorts differed significantly in mean percentage west African and European ancestries (P < 0.0001) and in the variance for individual ancestry (P ≤ 0.01). Among AAs, no set of questionnaire items effectively estimated degree of west African ancestry, and self-report of a high degree of African ancestry in a three-generation family tree did not accurately predict degree of African ancestry. Our findings suggest that self-reported race and ancestry can predict ancestral clusters, but do not reveal the extent of admixture. Genetic classifications of ancestry may provide a more objective and accurate method of defining homogenous populations for the investigation of specific population-disease associations. PMID:18559547

  8. Representativeness of Tuberculosis Genotyping Surveillance in the United States, 2009-2010.

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

    Spangler, M L; Robbins, K R; Bertrand, J K; Macneil, M; Rekaya, R

    2009-06-01

    A simulation study was carried out to develop an alternative method of selecting animals to be genotyped. Simulated pedigrees included 5000 animals, each assigned genotypes for a bi-allelic single nucleotide polymorphism (SNP) based on assumed allelic frequencies of 0.7/0.3 and 0.5/0.5. In addition to simulated pedigrees, two beef cattle pedigrees, one from field data and the other from a research population, were used to test selected methods using simulated genotypes. The proposed method of ant colony optimization (ACO) was evaluated based on the number of alleles correctly assigned to ungenotyped animals (AK(P)), the probability of assigning true alleles (AK(G)) and the probability of correctly assigning genotypes (APTG). The proposed animal selection method of ant colony optimization was compared to selection using the diagonal elements of the inverse of the relationship matrix (A(-1)). Comparisons of these two methods showed that ACO yielded an increase in AK(P) ranging from 4.98% to 5.16% and an increase in APTG from 1.6% to 1.8% using simulated pedigrees. Gains in field data and research pedigrees were slightly lower. These results suggest that ACO can provide a better genotyping strategy, when compared to A(-1), with different pedigree sizes and structures. PMID:19220227

  11. The AAS Visiting Professor Programs: Three Anniversaries

    NASA Astrophysics Data System (ADS)

    Philip, A. G. Davis

    2003-05-01

    The AAS Program of Visiting Professors was started in 1958 with three astronomers as lecturers. They were Paul Merrill (Mt. Wilson and Palomar Observatories), Seth Nicholson (Mt. Wilson and Palomar Observatories) and Harlow Shapley (Harvard College Observatory). The program was run by a Committee on Visiting Professors from 1958 through 1963. The program was funded by grants from the National Science Foundation. The Executive Officer of the AAS, Paul Routley headed the program from the 1963 - 64 academic year through the 1968 - 69 academic year. Larry Fredrick headed the program for 1969 - 70 and then Hank Gurin headed it through 1973 -74, the last year of the program. At the end of this summer meeting, the combined Visiting Professors Program and the Shapley Program will be starting their 47th year. The Shapley Visiting Lectureships in Astronomy Program was started in the 1974 - 75 academic year under the leadership of Hank Gurin. The original funding came from the Perkin Fund and a three year grant from the Research Corporation. In 1975 the Shapley Endowment fund was set up to help pay the expenses of the program. In 1976 there was support from the Slipher fund which lasted through the 1978 - 79 academic year. From 1979 to the present the program is financed by the Shapley Endowment Fund and by the contributions made by institutions which host the visits. In the fall of 1998 the fee that Institutions pay to the AAS in support of their Shapley visits was reduced from 300 to 250 to make it easier for them to apply for visits. Members of the AAS have made contributions to the program over the years and we are very appreciative of this support. In 1974 there were 42 lecturers in the program, of whom four are still active giving lectures (George Carruthers, Larry Fredrick, Arlo Landolt and Davis Philip). After the summer meeting, the Shapley Program will be embarking on its 30th year. Now there are 82 astronomers in the program and we get from 40 to 60 requests a year

  12. Atypical Toxoplasma gondii genotype in feral cats from the Fernando de Noronha Island, northeastern Brazil.

    PubMed

    Melo, R P B; Almeida, J C; Lima, D C V; Pedrosa, C M; Magalhães, F J R; Alcântara, A M; Barros, L D; Vieira, R F C; Garcia, J L; Mota, R A

    2016-07-15

    Toxoplasma gondii isolates from Brazil have a different phenotypic and genotypic pattern, with predominance of virulent isolates and recombinant genotypes, compared to the North Hemisphere. Considering that a new T. gondii genotype, non-pathogenic to mice, was previously identified from free-range chickens from the Fernando de Noronha Island, Brazil, this study aimed to identify genotypes of this parasite in tissue samples of feral cats (Felis catus) from this Brazilian Island. Anti-T. gondii IgG antibodies were detected in 18/31 (58%) feral cats. Two non-virulent T. gondii isolates were obtained by mouse bioassay. Genotyping was performed by PCR-RFLP using 10 genetic markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, PK1, L358 and Apico) and an atypical strain of T. gondii (ToxoDB #146) was identified. This is the first report of this genotype in feral cats. PMID:27270396

  13. Measurements of experimental precision for trials with cowpea (Vigna unguiculata L. Walp.) genotypes.

    PubMed

    Teodoro, P E; Torres, F E; Santos, A D; Corrêa, A M; Nascimento, M; Barroso, L M A; Ceccon, G

    2016-01-01

    The aim of this study was to evaluate the suitability of statistics as experimental precision degree measures for trials with cowpea (Vigna unguiculata L. Walp.) genotypes. Cowpea genotype yields were evaluated in 29 trials conducted in Brazil between 2005 and 2012. The genotypes were evaluated with a randomized block design with four replications. Ten statistics that were estimated for each trial were compared using descriptive statistics, Pearson correlations, and path analysis. According to the class limits established, selective accuracy and F-test values for genotype, heritability, and the coefficient of determination adequately estimated the degree of experimental precision. Using these statistics, 86.21% of the trials had adequate experimental precision. Selective accuracy and the F-test values for genotype, heritability, and the coefficient of determination were directly related to each other, and were more suitable than the coefficient of variation and the least significant difference (by the Tukey test) to evaluate experimental precision in trials with cowpea genotypes. PMID:27173351

  14. Polymerase chain reaction-based genotype classification among human Blastocystis hominis populations isolated from different countries.

    PubMed

    Yoshikawa, Hisao; Wu, Zhiliang; Kimata, Isao; Iseki, Motohiro; Ali, Ibne Karim M D; Hossain, Momammad B; Zaman, Viqar; Haque, Rashidul; Takahashi, Yuzo

    2004-01-01

    Since the genotype of human Blastocystis hominis isolates is highly polymorphic, PCR-based genotype classification using known sequenced-tagged site (STS) primers would allow the identification or classification of different genotypes. Five populations of human B. hominis isolates obtained from Japan, Pakistan, Bangladesh, Germany, and Thailand were subjected to genotype analysis by using seven kinds of STS primers. Ninety-nine out of 102 isolates were identified as one of the known genotypes, while one isolate from Thailand showed two distinct genotypes and two isolates from Japan were negative with all the STS primers. The most dominant genotype among four populations, except for all four isolates from Thailand, was subtype 3 and it varied from 41.7% to 92.3%. The second most common genotype among four populations was either subtype 1 (7.7-25.0%) or subtype 4 (10.0-22.9%). Subtype 2, subtype 5, and/or subtype 7 were only rarely detected among the isolates from Japan and Germany, while subtype 6 was not detected. The phylogenetic position of the two isolates which were negative with all STS primers, was inferred from the small subunit rRNA (SSU rRNA) genes with the known sequence data of 20 Blastocystis isolates. Since the two isolates were positioned in an additional clade in the phylogenetic tree, this suggested they were a new genotype. These results demonstrated that PCR-based genotype classification is a powerful tool with which to analyse genotypes of Blastocystis isolates obtained from clinical samples. In addition, two groups of the isolates from 15 symptomatic and 11 asymptomatic patients in Bangladesh were compared with the PCR-based subtype classification. Since both groups were only classified into two distinct genotypes of subtype 1 or subtype 3 and no statistically significant difference was observed between the two groups, in this study it could not be shown that the specific genotype correlated with the pathogenic potential of B. hominis. PMID

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

    PubMed Central

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

    2015-01-01

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

  16. Cu(II)-catalyzed reactions in ternary [Cu(AA)(AA - H)]+ complexes (AA = Gly, Ala, Val, Leu, Ile, t-Leu, Phe).

    PubMed

    Wang, Ping; Ohanessian, Gilles; Wesdemiotis, Chrys

    2009-01-01

    The unimolecular chemistry of [Cu(II)AA(AA - H)](+) complexes, composed of an intact and a deprotonated amino acid (AA) ligand, have been probed in the gas phase by tandem and multistage mass spectrometry in an electrospray ionization quadrupole ion trap mass spectrometer. The amino acids examined include Gly, Ala, Val, Leu, Ile, t-Leu and Phe. Upon collisionally-activated dissociation (CAD), the [Cu(II)AA(AA - H)](+) complexes undergo decarboxylation with simultaneous reduction of Cu(II) to Cu(I); during this process, a radical site is created at the alpha-carbon of the decarboxylated ligand (H(2)N(1) - (*)C(alpha)H - C(beta)H(2) - R; R = side chain substituent). The radical site is able to move along the backbone of the decarboxylated amino acid to form two new radicals (HN(1)(*) - C(alpha)H(2) - C(beta)H(2) - R and H(2)N(1) - C(alpha)H(2) - (*)C(beta)H - R). From the complexes of Gly and t-Leu, only C(alpha) and N(1) radicals can be formed. The whole radical ligand can be lost to form [Cu(I)AA](+) from these three isomeric radicals. Alternatively, further radical induced dissociations can take place along the backbone of the decarboxylated amino acid ligand to yield [Cu(II)AA(AA - 2H - CO(2))](+), [Cu(I)AA((*)NH(2))](+), [Cu(I)AA(HN = C(alpha)H(2))](+), or [Cu(I)AA(H(2)N - C(alpha)H = C(beta)H - R'](+) (R' = partial side chain substituent). The sodiated copper complexes, [Cu(II)(AA - H + Na)(AA - H)](+), show the same fragmentation patterns as their non-sodiated counterparts; sodium ion is retained on the intact amino acid ligand and is not involved in the CAD pathways. The amino groups of both AA units, the carbonyl group of the intact amino acid, and the deprotonated hydroxyl oxygen coordinate Cu(II) in square-planar fashion. Ab initio calculations indicate that the metal ion facilitates hydrogen atom shuttling between the N(1), C(alpha) and C(beta) atoms of the decarboxylated amino acid ligand. The dissociations of the decarboxylated radical ions unveil

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

    PubMed

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

    2010-09-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5' untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored. PMID:20592136

  18. Epidemiology and Genetic Characterization of Hepatitis A Virus Genotype IIA▿

    PubMed Central

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

    2010-01-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5′ untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored. PMID:20592136

  19. SUGARCANE GENOTYPE SELECTION ON A SAND SOIL WITH AND WITHOUT ADDED MILL MUD

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Long-term results for identifying high yielding sugarcane Saccharum spp.) cultivars have been better for Histosols (muck soils) than sand soils in Florida. We examined whether genotype selection could be improved by comparing genotypes on a sand soil with and without added mill mud (in Florida, mill...

  20. Reliability increases from combining 50,000- and 777,000-marker genotypes from four countries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic predictions were compared on U.S. scale after combining 50,000 (50K) and 777,000 (HD) marker genotypes across countries. The genotyped Holsteins included 161,341 animals with five marker densities including 1,510 with HD. Imputation was more accurate with FImpute than with findhap across the...

  1. Phylogenetic Analysis of Hepatitis B Virus Genotypes Circulating in Different Risk Groups of Panama, Evidence of the Introduction of Genotype A2 in the Country

    PubMed Central

    Martínez, Alexander A.; Zaldívar, Yamitzel; Arteaga, Griselda; de Castillo, Zoila; Ortiz, Alma; Mendoza, Yaxelis; Castillero, Omar; Castillo, Juan A.; Cristina, Juan; Pascale, Juan M.

    2015-01-01

    The Hepatitis B Virus (HBV) can cause acute or chronic infection it is also associated with the development of liver cancer, thousands of new infections occur on a yearly basis, and many of these cases are located in certain areas of the Caribbean and Latin America. In these areas, the HBV prevalence is still high which makes this virus a serious public health concern to the entire region. Studies performed in Panama suggest a complex pattern in the distribution of HBV among the country’s different risk groups. We use phylogenetic analysis in order to determine which HBV genotypes were circulating in these specific groups; for this we used a fragment of the PreS2/2 region of the HBV genome. Subsequently whole HBV genome sequences were used for Bayesian analysis of phylodynamics and phylogeography. Two main genotypes were found: genotype A (54.5%) and genotype F (45.5%). There was a difference in the distribution of genotypes according to risk groups: 72.9% of high risk groups were associated to genotype A, and 55.0% of samples of genotype F were associated to the low risk group (p<0.002). The Bayesian analysis of phylogeny-traits association revealed a statistically significant geographical association (p<0.0001) with both genotypes and different regions of the country. The Bayesian time of most recent common ancestor analysis (tMRCA) revealed a recent tMRCA for genotype A2 circulating in Panama (1997, 95% HPD: 1986—2005), when it is compared with Panamanian genotype F1c sequences (1930, 95% HPD: 1810 – 2005). These results suggest a possible change in the distribution of HBV genotypes in Panama and Latin America as a whole. They also serve to encourage the implementation of vaccination programs in high-risk groups, in order to prevent an increase in the number of new HBV cases in Latin America and worldwide. PMID:26230260

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

    PubMed

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

    2016-01-01

    Recently, the genotype plus genotype x environment interaction (GGE) biplot methodology has been used to investigate genotype x environment interactions in several crop species, but has not been applied to the common bean (Phaseolus vulgaris L.) crop in Brazil. The aim of this study was to identify common bean genotypes that exhibit high grain yield and stability in the State of Mato Grosso do Sul, Brazil. We conducted 12 trials from 2000 to 2006 in the municipalities of Aquidauana and Dourados, and evaluated 13 genotypes in a randomized block design with three replications. Grain yield data were subjected to individual and joint analyses of variance. After analyzing the GE interaction, the adaptability and phenotypic stability of the common bean genotypes were analyzed using GGE biplot methodology. The genotypes EMGOPA-201, Xamego, and Aporé are recommended for growing in Mato Grosso do Sul, because they exhibited high grain yield and phenotypic stability. PMID:27525915

  3. Genotype GI.6 Norovirus, United States, 2010–2012

    PubMed Central

    Barclay, Leslie; Wikswo, Mary; Vega, Everardo; Gregoricus, Nicole; Parashar, Umesh D.; Vinjé, Jan; Hall, Aron J.

    2013-01-01

    We report an increase in the proportion of genotype GI.6 norovirus outbreaks in the United States from 1.4% in 2010 to 7.7% in 2012 (p<0.001). Compared with non-GI.6 outbreaks, GI.6 outbreaks were characterized by summer seasonality, foodborne transmission, and non–health care settings. PMID:23876252

  4. New Hepatitis E Virus Genotype in Camels, the Middle East

    PubMed Central

    Lau, Susanna K.P.; Teng, Jade L.L.; Tsang, Alan K. L.; Joseph, Marina; Wong, Emily Y.M.; Tang, Ying; Sivakumar, Saritha; Xie, Jun; Bai, Ru; Wernery, Renate; Wernery, Ulrich; Yuen, Kwok-Yung

    2014-01-01

    In a molecular epidemiology study of hepatitis E virus (HEV) in dromedaries in Dubai, United Arab Emirates, HEV was detected in fecal samples from 3 camels. Complete genome sequencing of 2 strains showed >20% overall nucleotide difference to known HEVs. Comparative genomic and phylogenetic analyses revealed a previously unrecognized HEV genotype. PMID:24856611

  5. Current software for genotype imputation.

    PubMed

    Ellinghaus, David; Schreiber, Stefan; Franke, Andre; Nothnagel, Michael

    2009-07-01

    Genotype imputation for single nucleotide polymorphisms (SNPs) has been shown to be a powerful means to include genetic markers in exploratory genetic association studies without having to genotype them, and is becoming a standard procedure. A number of different software programs are available. In our experience, user-friendliness is often the deciding factor in the choice of software to solve a particular task. We therefore evaluated the usability of three publicly available imputation programs: BEAGLE, IMPUTE and MACH. We found all three programs to perform well with HapMap reference data, with little effort needed for data preparation and subsequent association analysis. Each of them has different strengths and weaknesses, however, and none is optimal for all situations. PMID:19706367

  6. Predicting Tensile Stretchability of Trimmed AA6111-T4 Sheets

    SciTech Connect

    Hu, Xiaohua; Sun, Xin; Golovashchenko, Sergey F.

    2014-02-15

    An integrated manufacturing process simulation framework has been developed to predict the trimmed edge tensile stretchability of AA6111-T4 sheets by incorporating the burr geometry, damage, and plastic strain from trimming simulations into subsequent tensile stretchability simulations. The influence of the trimming die clearances on the predicted tensile stretching ductility (stretchability) is studied and quantitatively compared with experimental measurements. Stretchability is found to decrease with increasing cutting clearances, and simulation results have successfully captured experimentally observed edge crack initiation and failure mode variations for different trimming clearances. Subsequent computational sensitivity studies reveal that while deburring of previously trimmed edges has little influence on tensile stretchability, removal of trimmed edge initial plastic strain may significantly enhance the subsequent trimmed edge stretchability.

  7. Human cerebral malaria and Plasmodium falciparum genotypes in Malawi

    PubMed Central

    2012-01-01

    Background Cerebral malaria, a severe form of Plasmodium falciparum infection, is an important cause of mortality in sub-Saharan African children. A Taqman 24 Single Nucleotide Polymorphisms (SNP) molecular barcode assay was developed for use in laboratory parasites which estimates genotype number and identifies the predominant genotype. Methods The 24 SNP assay was used to determine predominant genotypes in blood and tissues from autopsy and clinical patients with cerebral malaria. Results Single genotypes were shared between the peripheral blood, the brain, and other tissues of cerebral malaria patients, while malaria-infected patients who died of non-malarial causes had mixed genetic signatures in tissues examined. Children with retinopathy-positive cerebral malaria had significantly less complex infections than those without retinopathy (OR = 3.7, 95% CI [1.51-9.10]).The complexity of infections significantly decreased over the malaria season in retinopathy-positive patients compared to retinopathy-negative patients. Conclusions Cerebral malaria patients harbour a single or small set of predominant parasites; patients with incidental parasitaemia sustain infections involving diverse genotypes. Limited diversity in the peripheral blood of cerebral malaria patients and correlation with tissues supports peripheral blood samples as appropriate for genome-wide association studies of parasite determinants of pathogenicity. PMID:22314206

  8. Identification of a new genotype of bovine leukemia virus.

    PubMed

    Balić, Davor; Lojkić, Ivana; Periškić, Marin; Bedeković, Tomislav; Jungić, Andreja; Lemo, Nina; Roić, Besi; Cač, Zeljko; Barbić, Ljubo; Madić, Josip

    2012-07-01

    To investigate the degree of genetic variability of bovine leukemia virus (BLV) strains circulating in Croatia, 29 isolates from the six largest dairy farms were examined by PCR for a segment of the gp51 env gene, followed by DNA sequencing and phylogenetic analysis. The nucleotide sequences were compared with other previously characterized BLV strains from different geographical areas, comprising all seven known BLV genotypes. The Croatian sequences showed six to eight nucleotide substitutions: six silent substitutions and two amino acid changes. Four of those substitutions were within epitopes. In comparison to the sequences of other BLV genotypes, our isolates showed the closest relationship to genotype 1 isolates PL-3252 (FJ808585) and AL-148 (FJ808573) from Argentina. The degree of variation between our sequences and those of genotype 1 was 0.2- 4.6 %. In phylogenetic trees based on 400-nt and 519-nt sequences, all of the Croatian sequences clustered separately from the other sequences, revealing a new genotype. PMID:22488472

  9. Super-Genotype: Global Monoclonality Defies the Odds of Nature

    PubMed Central

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

    2007-01-01

    The ability to respond to natural selection under novel conditions is critical for the establishment and persistence of introduced alien species and their ability to become invasive. Here we correlated neutral and quantitative genetic diversity of the weed Pennisetum setaceum Forsk. Chiov. (Poaceae) with differing global (North American and African) patterns of invasiveness and compared this diversity to native range populations. Numerous molecular markers indicate complete monoclonality within and among all of these areas (FST = 0.0) and is supported by extreme low quantitative trait variance (QST = 0.00065–0.00952). The results support the general-purpose-genotype hypothesis that can tolerate all environmental variation. However, a single global genotype and widespread invasiveness under numerous environmental conditions suggests a super-genotype. The super-genotype described here likely evolved high levels of plasticity in response to fluctuating environmental conditions during the Early to Mid Holocene. During the Late Holocene, when environmental conditions were predominantly constant but extremely inclement, strong selection resulted in only a few surviving genotypes. PMID:17611622

  10. [AA-type amyloidosis secondary to multidrug resistant pulmonary tuberculosis: implications for therapy].

    PubMed

    Baux, E; Henard, S; Alauzet, C; Goehringer, F; Laurain, C; Champigneulle, J; Vaillant, P; Hardy, A; Rabaud, C; May, T

    2015-10-01

    Multidrug resistant pulmonary tuberculosis was diagnosed to a 32-year-old man. An AA-amyloidosis was subsequently diagnosed on the renal biopsy performed for nephrotic syndrome and macroscopic hematuria. A 6-drug antibiotic treatment was delivered quickly after first results of genotypic antibiogram given the renal failure, and was secondarily adapted to the phenotypic antibiogram. Multidrug therapy was fairly well tolerated. Clinical and biological improving were slow. Although tuberculosis is a classic cause of amyloidosis, this is the first case reporting an association between a multidrug resistant case and an amyloidosis in adults. This case also raises the question of MDR probabilistic treatments in situations whether a vital organ prognosis is engaged. PMID:26198876

  11. AAS Special Session: Policy Making in Astronomy

    NASA Astrophysics Data System (ADS)

    Cardelli, J. A.; Massa, D.

    1995-12-01

    The professional astronomical community today is more diverse than at any time in its history. Individuals participating in creative research programs can be found in a wide range of positions. This type of diversity, which mixes research, education, and service (e.g. contract) work, represents the strength of contemporary astronomy. While recognizing the unavoidable reductions in funding and restructuring of organizations like NASA, it is imperative that the significance of the current diversity be considered during these processes. Creative ideas are one of the cornerstones of quality research, and they can originate anywhere. Consequently, it is essential that adequate research resources remain available for free and open competition by all astronomers. Our goal in this session is to bring together officials from the AAS, NASA, and the NSF to discuss how the policy and decision making process operates and whether it should be changed to better serve the general needs of the professional astronomical community. Examples of the issues we believe are important include: In establishing new policy, how can the needs of the average research astronomer be better addressed? How could input from such astronomers be provided to those who craft NASA/NSF policy? How can/should the AAS serve as an interface between policy/decision making bodies and its membership? Should the AAS membership become more actively/effectively involved in the decision making process and, if so, how? More information on this session and related issues can be found at the Association of Research Astronomers Home Page: http://www.phy.vill.edu/astro/faculty/ara/ara_home.htm

  12. Genotypic variability for protoplast regeneration in Saintpaulia ionantha (H. Wendl.).

    PubMed

    Winkelmann, T; Grunewaldt, J

    1995-08-01

    The behaviour of eleven Saintpaulia ionantha (H. Wendl.) genotypes in protoplast culture was compared. Isolation of protoplasts from young shootlets regenerated in vitro on leaf explants, yielded 0.7 to 1.8 × 10(6) protoplasts per gram fresh weight. In all cultivars and breeding lines tested, cell divisions were observed. The mean division frequencies varied between 1.0 and 5.0% after 14 days, and between 6.4 and 13.8% after 24 days of culture. In ten genotypes callussing and shoot regeneration were achieved. The difference between the genotypes in shoot regeneration rate, between 2 and 68%, was more pronounced. The comparison of four cytokinins indicated hat thidiazuron was most effective for shoot regeneration, but often resulted in poorer shoot quality than benzylaminopurine. PMID:24186626

  13. Impact resistance of AA6005 panels

    NASA Astrophysics Data System (ADS)

    Clausen, A. H.; Borvik, T.; Hopperstad, O. S.; Langseth, M.

    2003-09-01

    The interest regarding use of extruded aluminium panels as lightweight protective structures is cmrently increasing. Even so, there are few experimental and computational investigations considering such structures. This paper presents some perforation tests on AA6005-T6 aluminium panels impacted by ogival-nose steel projectiles, where special emphasis was paid to the determination of the ballistic limit. Moreover, a material test programme including high strain rate tests using a split-Hopkinson tension bar was carried out in order to calibrate the Johnson-Cook constitutive model. Results from numerical analyses with LS-DYNA are finally included.

  14. Study on Fabrication of AA4032/AA6069 Cladding Billet Using Direct Chill Casting Process

    NASA Astrophysics Data System (ADS)

    Han, Xing; Zhang, Haitao; Shao, Bo; Li, Lei; Liu, Xuan; Cui, Jianzhong

    2016-04-01

    AA4032/AA6069 cladding billet in size of φ130 mm/φ110 mm was prepared by the modified direct chill casting process, and the parametric effect on casting performance was investigated using numerical simulation. Microstructures, elements distribution, and mechanical properties of the bonding interface were examined. The results show that metallurgical bonding interface can be obtained with the optimal parameters: the casting speed of 130 to 140 mm/min, the internal liquid level height of 50 to 60 mm, and the contact height of 40 to 50 mm. The metallurgical bonding interface is free of any discontinuities due to the fact that the alloying elements diffused across the interface and formed Ni-containing phase. Tensile strength of the cladding billet reaches 225.3 MPa, and the fracture position was located in AA6069 side, suggesting that the interface bonding strength is higher than the strength of AA6069. The interfacial shearing strength is 159.3 MPa, indicating excellent metallurgical bonding.

  15. Activity of vegetative insecticidal proteins Vip3Aa58 and Vip3Aa59 of Bacillus thuringiensis against lepidopteran pests.

    PubMed

    Baranek, Jakub; Kaznowski, Adam; Konecka, Edyta; Naimov, Samir

    2015-09-01

    Vegetative insecticidal proteins (Vips) secreted by some isolates of Bacillus thuringiensis show activity against insects and are regarded as insecticides against pests. A number of B. thuringiensis strains harbouring vip3A genes were isolated from different sources and identified by using a PCR based approach. The isolates with the highest insecticidal activity were indicated in screening tests, and their vip genes were cloned and sequenced. The analysis revealed two polymorphic Vip protein forms, which were classified as Vip3Aa58 and Vip3Aa59. After expression of the vip genes, the proteins were isolated and characterized. The activity of both toxins was estimated against economically important lepidopteran pests of woodlands (Dendrolimus pini), orchards (Cydia pomonella) and field crops (Spodoptera exigua). Vip3Aa58 and Vip3Aa59 were highly toxic and their potency surpassed those of many Cry proteins used in commercial bioinsecticides. Vip3Aa59 revealed similar larvicidal activity as Vip3Aa58 against S. exigua and C. pomonella. Despite 98% similarity of amino acid sequences of both proteins, Vip3Aa59 was significantly more active against D. pini. Additionally the effect of proteolytic activation of Vip58Aa and Vip3Aa59 on toxicity of D. pini and S. exigua was studied. Both Vip3Aa proteins did not show any activity against Tenebrio molitor (Coleoptera) larvae. The results suggest that the Vip3Aa58 and Vip3Aa59 toxins might be useful for controlling populations of insect pests of crops and forests. PMID:26146224

  16. Chemical Composition and Yield of Six Genotypes of Common Purslane (Portulaca oleracea L.): An Alternative Source of Omega-3 Fatty Acids.

    PubMed

    Petropoulos, Spyridon Α; Karkanis, Anestis; Fernandes, Ângela; Barros, Lillian; Ferreira, Isabel C F R; Ntatsi, Georgia; Petrotos, Konstantinos; Lykas, Christos; Khah, Ebrahim

    2015-12-01

    Common purslane (Portulaca oleracea L.) is an annual weed rich in omega-3 fatty acids which is consumed for its edible leaves and stems. In the present study six different genotypes of common purslane (A-F) were evaluated for their nutritional value and chemical composition. Nutritional value and chemical composition depended on genotype. Oxalic acid content was the lowest for genotype D, whereas genotypes E and F are more promising for commercial cultivation, since they have low oxalic acid content. Genotype E had a very good antioxidant profile and a balanced composition of omega-3 and omega-6 fatty acids. Regarding yield, genotype A had the highest yield comparing to the other genotypes, whereas commercial varieties (E and F) did not differ from genotypes B and C. This study provides new information regarding common purslane bioactive compounds as affected by genotype and could be further implemented in food industry for products of high quality and increased added value. PMID:26510561

  17. Molecular characterisation and prevalence of a new genotype of Cyprinid herpesvirus 2 in mainland China.

    PubMed

    Li, Lijuan; Luo, Yangzhi; Gao, Zexia; Huang, Jian; Zheng, Xianghai; Nie, Huihui; Zhang, Junmei; Lin, Li; Yuan, Junfa

    2015-06-01

    Cyprinid herpesvirus 2 (CyHV-2, species Cyprinid herpesvirus 2) has been confirmed as a causative agent of the acute haematopoietic necrosis disease outbreak in farmed goldfish (Carassius auratus L.) and gibel carp (Carassius auratus gibelio Bloch). In this study, we present the genomic characteristics of a variant CyHV-2 strain (SY-C1) isolated from farmed gibel carp in mainland China and its comparative genomics analysis with the CyHV-2 reference strain ST-J1. Overall, the full-length genome of SY-C1 shares 98.8% homology with that of ST-J1. Sequence comparisons between SY-C1 and ST-J1 indicate that the variations include single-nucleotide mutations, insertions, deletions, and rearrangements, which suggested that SY-C1 is different from ST-J1 and represents a new genotype. Therefore, we propose that the identified CyHV-2 can be divided into 2 different genotypes and be named China genotype (C genotype) and Japan genotype (J genotype) according to their isolation loci. Furthermore, epidemiological surveys indicate that the dominant genotype of CyHV-2 circulating in mainland China is closer to the China genotype than the Japan genotype. PMID:25900131

  18. T-cell response relative to genotype and ethnicity during antiviral therapy for chronic hepatitis C.

    PubMed

    Kaplan, David E; Sugimoto, Kazushi; Ikeda, Fusao; Stadanlick, Jason; Valiga, Mary; Shetty, Kirti; Reddy, K Rajender; Chang, Kyong-Mi

    2005-06-01

    Viral genotype and host ethnicity are important predictors of viral clearance during antiviral therapy for chronic hepatitis C virus (HCV) infection. Based on the role of T cells in natural HCV clearance, we hypothesized that T cells may contribute to the genotypic and ethnic difference in treatment outcome. To test this hypothesis, T-cell response to HCV antigens (core, nonstructural NS3/4 and NS5) and control phytohemagglutinin (PHA) was monitored prospectively and was correlated with virological outcome in 41 patients chronically infected with HCV (27 genotype 1, 14 genotype 2 or 3; 19 black persons, 22 white persons) undergoing combined interferon alfa and ribavirin therapy. Interestingly, in patients with genotype 2 or 3 infection, enhanced virological response coincided with a greater T-cell response to HCV NS3/4 antigen at baseline (50% vs. 15%; P = .026) that augmented further during therapy (29% vs. 4%; P = .035) compared with genotype 1-infected patients. However, HCV-specific T-cell response remained weak in genotype 1-infected patients regardless of virological outcome or ethnicity. Furthermore, virological outcome was associated with a suppressed baseline proliferative response to phytohemagglutinin (P < .03) that increased during therapy (P < .003) independent of ethnicity or genotype. In conclusion, HCV-specific T-cell response was associated with HCV genotype but not with therapeutic clearance of HCV infection. The association between treatment outcome and phytohemagglutinin response suggests more global and antigen-nonspecific mechanisms for therapeutic HCV clearance. PMID:15915458

  19. ACTN3 genotype in Spanish elite swimmers: no "heterozygous advantage".

    PubMed

    Ruiz, J R; Santiago, C; Yvert, T; Muniesa, C; Díaz-Ureña, G; Bekendam, N; Fiuza-Luces, C; Gómez-Gallego, F; Femia, P; Lucia, A

    2013-06-01

    The aim of the present case-control study was to examine the association of the ACTN3 R577X genotype with elite swimming status. We compared a group of Spanish (Caucasian) elite swimmers (n = 88) with other cohorts of the same ethnic origin, i.e., nonathletic controls (n = 343) and other types of athletes who are in both end-points of the sports performance continuum, i.e., world-class power (n = 119) and endurance male athletes (n = 154). Swimmers had a lower odds ratio (OR) of having the RX genotype [1.815, 95% confidence intervals (CI): 0.899-3.664] compared with nonathletic controls, yet the association did not reach statistical significance (P = 0.096). Endurance athletes had greater OR of having the XX genotype (OR: 2.88, 95% CI: 1.162-7.135, P = 0.022), or the RX+XX genotype (OR: 1.903, 95% CI: 1.015-3.567, P = 0.045) compared with swimmers. No other association was found. In summary, we did not observe an association between the ACTN3 R577X polymorphism and elite swimmer's status, suggesting that any influence of this polymorphism is not of sufficient magnitude as to significantly influence elite swimming performance, at least in Spanish athletes. PMID:23317015

  20. Microstructure and Mechanical Properties of AA1235 Aluminum Foil Stocks Produced Directly from Electrolytic Aluminum Melt

    NASA Astrophysics Data System (ADS)

    Xiong, Hanqing; Yu, Kun; Wen, Li; Yao, Sujuan; Dai, Yilong; Wang, Zhifeng

    2016-02-01

    A new process is developed to obtain high-quality AA1235 aluminum foil stocks and to replace the traditional manufacture process. During the new manufacture process, AA1235 aluminum sheets are twin-roll casted directly through electrolytic aluminum melt (EAM), and subsequently the sheets are processed into aluminum foil stocks by cold rolling and annealing. Microstructure and mechanical properties of the AA1235 aluminum sheets produced through such new process are investigated in each state by optimal microscope, scanning electron microscopy, X-ray diffraction, orientation imaging microscopy, transmission electron microscopy, etc. The results show that compared with the traditional AA1235 aluminum foil stocks produced through re-melted aluminum melt (RAM), the amount of impurities is decreased in the EAM aluminum foil stocks. The EAM aluminum foil stock obtains less β-FeSiAl5 phases, but more α-Fe2SiAl8 phases. The elongation of EAM aluminum foil stocks is improved significantly owing to more cubic orientation. Especially, the elongation value of the EAM aluminum foil stocks is approximately 25 pct higher than that of the RAM aluminum foil stocks. As a result, the EAM aluminum foil stocks are at an advantage in increasing the processing performance for the aluminum foils during subsequent processes.

  1. The cytochrome P450 2AA gene cluster in zebrafish (Danio rerio); expression of CYP2AA1 and CYP2AA2 and response to phenobarbital-type inducers

    PubMed Central

    Kubota, Akira; Bainy, Afonso C.D.; Woodin, Bruce R.; Goldstone, Jared V.; Stegeman, John J.

    2013-01-01

    The cytochrome P450 (CYP) 2 gene family is the largest and most diverse CYP gene family in vertebrates. In zebrafish, we have identified 10 genes in a new subfamily CYP2AA, which does not show orthology to any human or other mammalian CYP genes. Here we report evolutionary and structural relationships of the 10 CYP2AA genes and expression of the first two genes, CYP2AA1 and CYP2AA2. Parsimony reconstruction of the tandem duplication pattern for the CYP2AA cluster suggests that CYP2AA1, CYP2AA2 and CYP2AA3 likely arose in the earlier duplication events and thus are most diverged in function from the other CYP2AAs. On the other hand, CYP2AA8 and CYP2AA9 are genes that arose in the latest duplication event, implying functional similarity between these two CYPs. A molecular model of CYP2AA1 showing the sequence conservation across the CYP2AA cluster reveals that the regions with the highest variability within the cluster map into CYP2AA1 near the substrate access channels, suggesting differing substrate specificity. Zebrafish CYP2AA1 transcript was expressed predominantly in intestine, while CYP2AA2 was most highly expressed in kidney, suggesting differing roles in physiology. In liver CYP2AA2 expression but not that of CYP2AA1, was increased by 1,4-bis [2-(3,5-dichloropyridyloxy)] benzene (TCPOBOP) and, to a lesser extent, by phenobarbital (PB). In contrast, pregnenolone 16α-carbonitrile (PCN) increased CYP2AA1, but not CYP2AA2 in liver. The results identify a CYP2 subfamily in zebrafish that includes genes apparently induced by PB-type chemicals and PXR agonists, the first concrete in vivo evidence for a PB-type response in fish. PMID:23726801

  2. Impact of Q139R substitution of MEB4-Cry2Aa toxin on its stability, accessibility and toxicity against Ephestia kuehniella.

    PubMed

    Nouha, Abdelmalek; Sameh, Sellami; Fakher, Frikha; Slim, Tounsi; Souad, Rouis

    2015-11-01

    The Bacillus thuringiensis subsp. kurstaki strain MEB4 was previously found to be highly toxic to Ephestia kuehniella. SDS-PAGE analysis of the recombinant strain DH5α (pBS-cry2Aa-MEB4) showed that Cry2Aa-MEB4 delta-endotoxins were forming inclusion bodies, and were 2.75 fold more toxic towards E. kuehniella than those of Cry2Aa-BNS3. Besides to the 65kDa active toxin, proteolysis activation of Cry2Aa-BNS3 protein with E. kuehniella midgut juice generated an extra proteolysis form of 49kDa, which was the result of another chymotrypsin cleavage located in Leu144. The amino acid sequences alignment of Cry2Aa-MEB4 and Cry2Aa-BNS3 showed that among the different 15 amino acids, the Q139R substitution was found to be interesting. In fact, due to its presence within the loop α3-α4, the chymotrypsin-like protease was unable to access to its site in Cry2Aa-MEB4, resulting to the production of only the 65kDa form. The accessible surface and the stability studies of the structure model of the Cry2Aa-BNS3-49 form showed a lower hydrophobicity surface due to the omission of 144 amino acids from the N-terminal comparing with the active Cry2Aa-MEB4 protein. All these features caused the diminishing of Cry2Aa-BNS3 toxicity towards E. kuehniella. PMID:26321422

  3. Milk Fat Content and DGAT1 Genotype Determine Lipid Composition of the Milk Fat Globule Membrane

    PubMed Central

    Argov-Argaman, Nurit; Mida, Kfir; Cohen, Bat-Chen; Visker, Marleen; Hettinga, Kasper

    2013-01-01

    During secretion of milk fat globules, triacylglycerol (TAG) droplets are enveloped by a phospholipid (PL) trilayer. Globule size has been found to be related to polar lipid composition and fat content, and milk fat content and fatty acid composition have been associated with the diacylglycerol acyltransferase 1 (DGAT1) K232A polymorphism; however, the association between the DGAT1 polymorphism and fat globule size and polar lipid composition has not been studied. The ratio between polar and neutral lipids as well as the composition of the polar lipids in milk has industrial as well as nutritional and health implications. Understanding phenotypic and genotypic factors influencing these parameters could contribute to improving milk lipid composition for dairy products. The focus of the present study was to determine the effect of both fat content and DGAT1 polymorphism on PL/TAG ratio, as a marker for milk fat globule size, and detailed PL composition. Milk samples were selected from 200 cows such that there were equal numbers of samples for the different fat contents as well as per DGAT1 genotype. Samples were analyzed for neutral and polar lipid concentration and composition. PL/TAG ratio was significantly associated with both fat content and DGAT1 genotype. Phosphatidylinositol and phosphatidylserine concentrations were associated with fat content*DGAT1 genotype with a stronger association for the AA than the KK genotype. Sphingomyelin concentration tended to interact with fat content*DGAT1 genotype. Phosphatidylethanolamine (PE) concentration showed a biphasic response to fat content, suggesting that multiple biological processes influence its concentration. These results provide a new direction for controlling polar lipid concentration and composition in milk through selective breeding of cows. PMID:23874734

  4. Methylenetetrahydrofolate reductase (MTHFR-677 and MTHFR-1298) genotypes and haplotypes and plasma homocysteine levels in patients with occlusive artery disease and deep venous thrombosis.

    PubMed

    Spiroski, Igor; Kedev, Sashko; Antov, Slobodan; Arsov, Todor; Krstevska, Marija; Dzhekova-Stojkova, Sloboda; Bosilkova, Gordana; Kostovska, Stojanka; Trajkov, Dejan; Petlichkovski, Aleksandar; Strezova, Ana; Efinska-Mladenovska, Olivija; Spiroski, Mirko

    2008-01-01

    The aim was to investigate different genotypes and haplotypes of methylenetetrahydrofolate reductase (MTHFR-677, -1298) and plasma concentration of total homocysteine (tHcy) in Macedonian patients with occlusive artery disease (OAD) and deep venous thrombosis (DVT). Investigated groups consists of 80 healthy, 74 patients with OAD, and 63 patients with DVT. Plasma tHcy was measured with Microplate Enzyme Immunoassay. Identification of MTHFR genotypes and haplotypes was done with CVD StripAssay. The probability level (P-value) was evaluated by the Student's t-test. Plasma concentration of tHcy in CC and CT genotypes of MTHFR C677T was significantly increased in patients with OAD and in patients with DVT. Plasma concentration of tHcy in AC genotype of MTHFR A1298C was increased in patients with OAD and in patients with DVT. Plasma concentration of tHcy was significantly increased in AA genotype of patients with OAD, but not in patients with DVT. We found a significant increase of plasma tHcy in patients with OAD in comparison with healthy respondents for normal:heterozygote (CC:AC), heterozygote:normal (CT:AA), and heterozygote:heterozygote (CT:AC) haplotypes. Plasma concentration of tHcy in patients with DVT in comparison with healthy respondents was significantly increased for normal:normal (CC:AA), normal heterozygote (CC:AC), and heterozygote:heterozygote (CT:AC) haplotypes. We conclude that MTHFR C677T and MTHFR A1289C genotypes and haplotypes are connected with tHcy plasma levels in Macedonian patients with OAD and DVT. PMID:18800176

  5. Prevalence of HCV genotypes in district Mardan

    PubMed Central

    2013-01-01

    Background Approximately 170 million people are infected with Hepatitis C virus (HCV) worldwide. The prevalence of chronic HCV infections in Pakistan is about 5%, with most individuals being infected with HCV genotype 3a. Data on HCV genotypes distribution across various districts of the country are scarce. One example is district Mardan from where such data is available only from 17 individuals. Accordingly, the present study aimed at determining HCV genotypes distribution among 177 HCV RNA positive individuals from district Mardan. Findings Serum samples (n = 215) from patients suspected of hepatitis C were collected and processed for Nested PCR based detection and subsequent genotyping. Gender-wise and age-wise differences in HCV prevalence and HCV genotypes distribution were determined by χ2 test. Out of the total 215 serum samples, 177 were found to be positive for HCV RNA. The genotype 3a was the most predominant genotype among HCV RNA positive samples with a prevalence of 90.3%, followed by genotype 1a (5.6%), mixed genotypes (2.8%), genotype 3b (0.6%) and genotype 4 (0.6%). The HCV prevalence was higher in young individuals than old people and was indicative of reduced survival rate beyond 40 years. Conclusion HCV genotype 3a is the most predominant genotype in district Mardan. The state of the art preventive and therapeutic strategies should be implemented to control the spread of HCV infections. Further temporal studies involving different geographical areas of Pakistan, are required to improve the control measures for HCV infection. PMID:23514695

  6. Tolerance of 42 bread wheat genotypes to drought stress after anthesis.

    PubMed

    Shahryari, Reza; Gurbanov, Elshad; Gadimov, Aladdin; Hassanpanah, Davoud

    2008-05-15

    The present research characterized yield and yield components of 42 wheat genotypes after terminal drought stress. The experiment was in twice replicated simple rectangular lattice design, conducted at irrigated and terminal stress conditions during 2006-2007. These study genotypes had significant differences for grain yield at level of 1%. Genotypes 4057, Viking/5/Gds/4.., Sabalan and 5041 respectively with 6.313, 6.159, 5.793 and 5.774 t ha(-1) had the highest yield and Gascogen has the lowest yield with 2.561 t ha(-1). Mean of total grain yield for under study genotypes was 5.628 t ha(-1) in non-stress and 3.305 t ha(-1) in drought stress conditions. Drought stress decreased amount of grain yield 2.323 t ha(-1) that was noticeable. Interaction of Genotype x environmental conditions was significant at probability level of 1% for grain yield. Yield of all genotypes in drought condition was lower than non-stress condition. Genotypes Viking/5/Gds/4/Anza/3/Pi.., Sabalan, 4061,4057 and 4041 had more yield in non-stress condition and MV17/Zrn, Sabalan, Saysonz and 4032 in stress condition. Stress intensity pay attention to total grain yield was 42%. Genotypes Viking/5/Gds/4/.. and Sabalan had high grain yield and was better than other genotypes and controls (Toos and Crosse Shahi), according to GMP, STI and MSTI. And had the most amount of stress tolerance index as compared with other genotypes confirms this subject. Correlation of yield with other traits was not significant in non-stress condition. In drought condition, correlation of grain yield with 1000 grain weight and total number of tillers per plant was positively significant. ANOVA showed significant differences between osmotic pressures for coleoptile length, between genotypes for mean and maximum coleoptile length and between interactions of genotypes x osmotic pressures for mean and maximum coleoptile length. Mean comparisons showed the highest total, mean and maximum coleoptile length in -7 bar PEG+I ml L

  7. Clustering of soybean genotypes via Ward-MLM and ANNs associated with mixed models.

    PubMed

    Teodoro, P E; Torres, F E; Corrêa, A M

    2016-01-01

    The objectives of this study were to use mixed models to confirm the presence of genetic variability in 16 soybean genotypes, to compare clusters generated by artificial neural networks (ANNs) with those created by the Ward modified location model (MLM) technique, and to indicate parental combinations that hold promise for obtaining superior segregating populations of soybean. A field trial was conducted between November 2014 and February 2015 at Universidade Estadual de Mato Grosso do Sul, Aquidauana, MS. The experimental design consisted of four replications of randomized blocks, each containing 16 treatments. We assessed the following agronomic traits: plant height, first pod height, number of branches per plant, number of pods per plant, number of grains per pod, hundred-grain weight, and grain yield. Mixed models were used to estimate variance components and genetic parameters, and obtain genotypic values for each trait. After verifying the presence of genetic variability for all traits, genotypic values were submitted to both a Ward-MLM procedure and ANNs to estimate genetic divergence among genotypes. The number of groups formed by both methods was the same, but there were differences in group constitutions. ANN analysis improved soybean genotypes clustering patterns compared to Ward-MLM procedure. Based on these methods, divergent crosses may be made between genotype 97R73 with genotypes AS3797 and SYN9070, whereas convergent crosses may be made between genotypes AS3797 and SYN9070. PMID:27525912

  8. Design of the MsAa-4 Moessbauer Spectrometer

    SciTech Connect

    Blachowski, A.; Ruebenbauer, K.; Zukrowski, J.; Gornicki, R.

    2008-10-28

    An entirely new Moessbauer spectrometer MsAa-4 is currently being under design and construction. New features as compared to the basic features of the previous generation MsAa-3 spectrometer could be summarized as follows. Completely digital processing of the {gamma}-ray detector signal beyond the Gaussian shape filter/amplifier is to be implemented. The spectrometer is going to be able to accommodate external multiple detector heads. Up to 128 {gamma}-ray spectra in 16384 channels of 32-bit each and up to 512 Moessbauer spectra in 4096 channels of 32-bit each could be collected simultaneously, provided the proper external multiple detector head is used. The count-rate per single detector is limited to about 10{sup 5} counts per second in total. Improved precision of the reference function from 12-bit to 16-bit is to be provided. The reference function is stored in 8192 channels per a complete cycle. Addition of the random noise to the reference corner prism of the Michelson-Morley calibration interferometer is to be introduced to avoid spurious fringes due to the phase lock-up. An integrated universal temperature controller being able to use a variety of the temperature sensors is to be interconnected properly with the spectrometer. The spectrometer is now a stand-alone network device as it is equipped with the Ethernet connection to the outside world. Fast and high precision digital oscilloscope is to be incorporated to the spectrometer as the intrinsic unit. This oscilloscope could monitor signals at various crucial points of the internal spectrometer electronics. Modular design and use of the strict standards allows easy reconfiguration for other applications than Moessbauer spectroscopy.

  9. SNP genotypes of olfactory receptor genes associated with olfactory ability in German Shepherd dogs.

    PubMed

    Yang, M; Geng, G-J; Zhang, W; Cui, L; Zhang, H-X; Zheng, J-L

    2016-04-01

    To find out the relationship between SNP genotypes of canine olfactory receptor genes and olfactory ability, 28 males and 20 females from German Shepherd dogs in police service were scored by odor detection tests and analyzed using the Beckman GenomeLab SNPstream. The representative 22 SNP loci from the exonic regions of 12 olfactory receptor genes were investigated, and three kinds of odor (human, ice drug and trinitrotoluene) were detected. The results showed that the SNP genotypes at the OR10H1-like:c.632C>T, OR10H1-like:c.770A>T, OR2K2-like:c.518G>A, OR4C11-like:c.511T>G and OR4C11-like:c.692G>A loci had a statistically significant effect on the scenting abilities (P < 0.001). The kind of odor influenced the performances of the dogs (P < 0.001). In addition, there were interactions between genotype and the kind of odor at the following loci: OR10H1-like:c.632C>T, OR10H1-like:c.770A>T, OR4C11-like:c.511T>G and OR4C11-like:c.692G>A (P < 0.001). The dogs with genotype CC at the OR10H1-like:c.632C>T, genotype AA at the OR10H1-like:c.770A>T, genotype TT at the OR4C11-like:c.511T>G and genotype GG at the OR4C11-like:c.692G>A loci did better at detecting the ice drug. We concluded that there was linkage between certain SNP genotypes and the olfactory ability of dogs and that SNP genotypes might be useful in determining dogs' scenting potential. PMID:26582499

  10. Floor Plans: Section "AA", Section "BB"; Floor Framing Plans: Section ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Floor Plans: Section "A-A", Section "B-B"; Floor Framing Plans: Section "A-A", Section "B-B" - Fort Washington, Fort Washington Light, Northeast side of Potomac River at Fort Washington Park, Fort Washington, Prince George's County, MD

  11. Idiopathic systemic AA-amyloidosis in a skunk (Mephitis mephitis).

    PubMed

    Elhensheri, Mohamed; Linke, Reinhold P; Blankenburg, Anja; Beineke, Andreas

    2012-03-01

    This report describes a case of systemic amyloidosis in a captive striped skunk. At necropsy, bilateral alopecia, as well as reno-, hepato-, and splenomegaly were present. Congo red staining and immunohistochemistry revealed depositions of AA-amyloid in different organs. The lack of a predisposing disease is suggestive of idiopathic systemic AA-amyloidosis. PMID:22448530

  12. Synergism and Rules of the new Combination drug Yiqijiedu Formulae (YQJD) on Ischemic Stroke based on amino acids (AAs) metabolism

    PubMed Central

    Gao, Jian; Chen, Chang; Chen, Jian-Xin; Wen, Li-Mei; Yang, Geng-Liang; Duan, Fei-Peng; Huang, Zhi-Ying; Li, De-Feng; Yu, Ding-Rong; Yang, Hong-Jun; Li, Shao-Jing

    2014-01-01

    The use of combination drugs is considered to be a promising strategy to control complex diseases such as ischemic stroke. The detection of metabolites has been used as a versatile tool to reveal the potential mechanism of diverse diseases. In this study, the levels of 12 endogenous AAs were simultaneously determined quantitatively in the MCAO rat brain using RRLC-QQQ method. Seven AAs were chosen as the potential biomarkers, and using PLS-DA analysis, the effects of the new combination drug YQJD, which is composed of ginsenosides, berberine, and jasminoidin, on those 7 AAs were evaluated. Four AAs, glutamic acid, homocysteine, methionine, and tryptophan, which changed significantly in the YQJD-treated groups compared to the vehicle groups (P < 0.05), were identified and designated as the AAs to use to further explore the synergism of YQJD. The result of a PCA showed that the combination of these three drugs exhibits the strongest synergistic effect compared to other combination groups and that ginsenosides might play a pivotal role, especially when combined with jasminoidin. We successfully explored the synergetic mechanism of multi-component and provided a new method for evaluating the integrated effects of combination drugs in the treatment of complex diseases. PMID:24889025

  13. [Genotypic specificity of schizophrenic psychoses].

    PubMed

    Shakhmatova-Pavlova, I V; Gindilis, V M; Rokhlina, M L; Kozlova, I A

    1980-01-01

    A total of 610 probands with a disease manifestation in childhood, middle and old age and their families were examined by the clinico-genealogical method. The results allowed conclusions that (1) there is an undoubted genetic relationship between schizophrenia of childhood, middle and old age; and that (2) among the closest relatives in families of the probands there is no significant (in comparison to the general population) accumulation of non-schizophrenic pathology. The latter indicates a high genotypic specificity of schizophrenia. PMID:7415694

  14. Amino acid substitution in the core protein has no impact on relapse in hepatitis C genotype 1 patients treated with peginterferon and ribavirin.

    PubMed

    Inoue, Yuko; Hiramatsu, Naoki; Oze, Tsugiko; Yakushijin, Takayuki; Mochizuki, Kiyoshi; Fukuda, Kazuto; Mita, Eiji; Haruna, Yoshimichi; Inoue, Atsuo; Imai, Yasuharu; Hosui, Atsushi; Miyagi, Takuya; Yoshida, Yuichi; Tatsumi, Tomohide; Kiso, Shinichi; Kanto, Tatsuya; Kasahara, Akinori; Takehara, Tetsuo; Hayashi, Norio

    2011-03-01

    Previous reports demonstrated that amino acid (aa) substitutions in the hepatitis C virus (HCV) core protein are predictors of non-virological responses to pegylated interferon (Peg-IFN) and ribavirin combination therapy. The aim of this study was to investigate the impact of core aa substitutions on viral kinetics during the treatment and relapse after the treatment. The 187 patients with HCV genotype 1 enrolled in this study were categorized into four groups according to core aa substitution patterns: double-wild group (n=92), Arg70/Leu91; 70-mutant group (n=42), Gln70/Leu91; 91-mutant group (n=31), Arg70/Met91; and double-mutant group (n=22), Gln70/Met91. The relationship between the core aa substitutions and the virological response was examined. Multivariate logistic regression analyses showed that substitution at aa 70 was significantly associated with a poor virological response during the first 12 weeks (decline of <1 log from baseline at week 4, <2 log at week 12), and substitution at aa 91 was significantly associated with detectable HCV RNA at week 24. With respect to relapse, only the ribavirin exposure (odds ratio (OR), 0.77; 95% confidence interval (CI), 0.60-0.98) and HCV RNA disappearance between weeks 13 and 24 (OR, 23.69; 95% CI, 5.44-103.08) were associated independently with relapse, with no correlation being found with the core aa substitutions and relapse. In conclusion, the results showed that core aa substitutions can be strong predictive factors at pretreatment of the non-response, but not for relapse, for virological responders with HCV RNA disappearance during treatment. PMID:21264862

  15. Rotavirus Genotypes in Belarus, 2008–2012

    PubMed Central

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

    2015-01-01

    This study describes group A rotavirus (RVA) genotype prevalence in Belarus from 2008–2012. In 2008, data from 3 sites in Belarus (Brest, Mogilev, Minsk) indicated that G4P[8] was the predominant genotype. Data from Minsk (2008–2012) showed that G4P[8] was the predominant RVA genotype in all years except in 2011 when G3P[8] was most frequently detected. Other RVA genotypes common in Europe (G1P[8], G2P[4]) were detected each year of the study. This study reveals the dominance of genotype G4P[8] in Belarus and helps to establish the baseline genotype prevalence prior to RVA vaccine introduction in the country. PMID:25218086

  16. States' Flexibility Waiver Plans for Alternate Assessments Based on Alternate Achievement Standards (AA-AAS). Synthesis Report 96

    ERIC Educational Resources Information Center

    Lazarus, Sheryl S.; Edwards, Lynn M.; Thurlow, Martha L.; Hodgson, Jennifer R.

    2014-01-01

    All states have alternate assessments based on alternate achievement standards (AA-AAS) for students with the most significant cognitive disabilities. For accountability purposes, the Elementary and Secondary Education Act (ESEA) allows up to 1% of students to be counted as proficient with this assessment option. In 2011 the U.S. Department of…

  17. Mutant Rep protein of the porcine circovirus type 2 N-glycosylation:23-25aa, 256-258aa mutation reduced virus replication but 286-288aa mutation enhanced virus replication in PK-15 cells.

    PubMed

    Shi, Jianli; Peng, Zhe; Fu, Fang; Xu, Shaojian; Xu, Shengnan; Cong, Xiaoyan; Yuan, Xiaoyuan; Yu, Jiang; Wu, Jiaqiang; Sun, Wenbo; Du, Yijun; Li, Jun; Wang, Jinbao

    2015-06-12

    Porcine circovirus type 2 (PCV2) Rep protein and the splice variant Rep' protein impact genome replication. The Rep protein contains three potential N-glycosylation at positions 23-25aa (NPS), 256-258aa (NQT) and 286-288aa (NAT). Three double copy infectious clones with Rep protein N-glycosylation at positions mutations 23-25aa (DPS), 256-258aa (DQT) and 286-288aa (DAT) were constructed and their function in virus replication in PK-15 cells was investigated. The results showed that the double copy infectious clone with N-glycosylation site mutation could be rescued in vitro and 23-25aa, 256-258aa mutation reduced virus replication but 286-288aa mutation enhanced virus replication. PMID:25829242

  18. The cytochrome P450 2AA gene cluster in zebrafish (Danio rerio): Expression of CYP2AA1 and CYP2AA2 and response to phenobarbital-type inducers

    SciTech Connect

    Kubota, Akira; Bainy, Afonso C.D.; Woodin, Bruce R.; Goldstone, Jared V.; Stegeman, John J.

    2013-10-01

    The cytochrome P450 (CYP) 2 gene family is the largest and most diverse CYP gene family in vertebrates. In zebrafish, we have identified 10 genes in a new subfamily, CYP2AA, which does not show orthology to any human or other mammalian CYP genes. Here we report evolutionary and structural relationships of the 10 CYP2AA genes and expression of the first two genes, CYP2AA1 and CYP2AA2. Parsimony reconstruction of the tandem duplication pattern for the CYP2AA cluster suggests that CYP2AA1, CYP2AA2 and CYP2AA3 likely arose in the earlier duplication events and thus are most diverged in function from the other CYP2AAs. On the other hand, CYP2AA8 and CYP2AA9 are genes that arose in the latest duplication event, implying functional similarity between these two CYPs. A molecular model of CYP2AA1 showing the sequence conservation across the CYP2AA cluster reveals that the regions with the highest variability within the cluster map onto CYP2AA1 near the substrate access channels, suggesting differing substrate specificities. Zebrafish CYP2AA1 transcript was expressed predominantly in the intestine, while CYP2AA2 was most highly expressed in the kidney, suggesting differing roles in physiology. In the liver CYP2AA2 expression but not that of CYP2AA1, was increased by 1,4-bis [2-(3,5-dichloropyridyloxy)] benzene (TCPOBOP) and, to a lesser extent, by phenobarbital (PB). In contrast, pregnenolone 16α-carbonitrile (PCN) increased CYP2AA1 expression, but not CYP2AA2 in the liver. The results identify a CYP2 subfamily in zebrafish that includes genes apparently induced by PB-type chemicals and PXR agonists, the first concrete in vivo evidence for a PB-type response in fish. - Highlights: • A tandemly duplicated cluster of ten CYP2AA genes was described in zebrafish. • Parsimony and duplication analyses suggest pathways to CYP2AA diversity. • Homology models reveal amino acid positions possibly related to functional diversity. • The CYP2AA locus does not share synteny with

  19. Differences in CYP2C9 Genotype and Enzyme Activity Between Swedes and Koreans of Relevance for Personalized Medicine: Role of Ethnicity, Genotype, Smoking, Age, and Sex.

    PubMed

    Hatta, Fazleen H M; Lundblad, Mia; Ramsjo, Margareta; Kang, Ju-Hee; Roh, Hyung-Keun; Bertilsson, Leif; Eliasson, Erik; Aklillu, Eleni

    2015-06-01

    Global personalized medicine demands the characterization of person-to-person and between-population differences in drug pharmacokinetics and pharmacodynamics. CYP2C9 pharmacokinetic pathway is subject to modulation by both genetic and environmental factors. CYP2C9 genotype-based dose recommendations (e.g., for warfarin) is advocated. However, the overall contribution of genotype for variation in enzyme activity may differ between populations. We evaluated the importance of ethnicity, genotype, smoking, body weight, age, and sex for CYP2C9 enzyme activity. CYP2C9 genotype and phenotype was determined in 148 Swedes and 146 Koreans using losartan as a probe. CYP2C9 enzyme activity was assessed using urinary losartan/metabolite E-3174 ratio. The frequency of CYP2C9 defective variant alleles (*2 and *3) was significantly higher in Swedes (10.8% and 12.5%) than in Koreans (0% and 5.8%). In matched genotypes, CYP2C9 enzyme activity was significantly lower in Swedes compared to Koreans (p<0.0001). In a univariate analysis, age, weight, ethnicity, genotype, and smoking were significant predictors of CYP2C9 phenotype. A stepwise multivariate analysis indicated ethnicity, genotype, and smoking remained as significant predictors of CYP2C9 enzyme activity, accounting for 50% of the total variance. In both study populations, CYP2C9 genotype was a significant predictor of CYP2C9 enzyme activity, but its contribution in explaining the total variance was lower in Koreans (26.6%) than Swedes (40%). In conclusion, we report significantly lower CYP2C9 enzyme activity in Swedes compared to Koreans, partly but not exclusively due to CYP2C9 pharmacogenetic variations. Ethnicity and environment factors need to be considered together with genotype for population-specific dose optimization and global personalized medicine. PMID:25977991

  20. [First case of hepatitis B virus genotype H infection in Turkey].

    PubMed

    Ural, Onur; Sayan, Murat; Akhan, Sıla; Sümer, Sua; Simşek, Funda

    2013-07-01

    Clinical studies reported from Turkey indicate that hepatitis B virus (HBV) genotype D is more prevalent than other genotypes. Epidemiological and clinical information on genotype H infection is currently limited. Genotype H infection is most likely due to its regional (Central and South America) prevalence throughout the world. The aim of this report is to present the first HBV genotype H infection in a chronic hepatitis B patient in Turkey. Laboratory findings of a 42 years old male patient admitted to our hospital revealed HBsAg (+), anti-HBs (-), HBeAg (-), anti-HBe (+), anti-HBc IgM (-), anti-HBc IgG (+), anti-HAV IgG (+), HBV-DNA: 5.689.776 IU/ml and high liver enzymes (ALT: 223 U/L, AST: 121 U/L). History of the patient indicated no risk factor (intravenous drug use, blood transfusion, suspicious sexual contact) related to HBV transmission. Since liver ultrasonography showed multiple hemangiomas, biopsy was performed and histologic activity index was found as 6/18 and fibrosis as 2/6, according to modified Knodell score system. HBV DNA isolated from the serum sample of the patient was amplified by polymerase chain reaction and polymerase gene segment of HBV was directly sequenced. UPGMA method was used for phylogenetic analysis, and the genotype of the virus was identified accordingly. The nucleotide sequence was compared to those from the international DNA data bank (GenBank). The genotyping of the patient revealed that the isolated HBV was genotype H. Treatment with tenofovir disoproxil fumarate was initiated and the patient responded to the treatment. This finding suggested that other HBV genotypes, except the predominant genotype D may also be in circulation in Turkey. In conclusion, detection of epidemiologic and molecular characteristics of HBV genotype H which is related to chronic hepatitis, seems to be necessary in order to better understand its circulation and progression around the world. PMID:23971934

  1. Transgenic plants expressing the AaIT/GNA fusion protein show increased resistance and toxicity to both chewing and sucking pests.

    PubMed

    Liu, Shu-Min; Li, Jie; Zhu, Jin-Qi; Wang, Xiao-Wei; Wang, Cheng-Shu; Liu, Shu-Sheng; Chen, Xue-Xin; Li, Sheng

    2016-04-01

    The adoption of pest-resistant transgenic plants to reduce yield losses and decrease pesticide use has been successful. To achieve the goal of controlling both chewing and sucking pests in a given transgenic plant, we generated transgenic tobacco, Arabidopsis, and rice plants expressing the fusion protein, AaIT/GNA, in which an insecticidal scorpion venom neurotoxin (Androctonus australis toxin, AaIT) is fused to snowdrop lectin (Galanthus nivalis agglutinin, GNA). Compared with transgenic tobacco and Arabidopsis plants expressing AaIT or GNA, transgenic plants expressing AaIT/GNA exhibited increased resistance and toxicity to one chewing pest, the cotton bollworm, Helicoverpa armigera. Transgenic tobacco and rice plants expressing AaIT/GNA showed increased resistance and toxicity to two sucking pests, the whitefly, Bemisia tabaci, and the rice brown planthopper, Nilaparvata lugens, respectively. Moreover, in the field, transgenic rice plants expressing AaIT/GNA exhibited a significant improvement in grain yield when infested with N. lugens. This study shows that expressing the AaIT/GNA fusion protein in transgenic plants can be a useful approach for controlling pests, particularly sucking pests which are not susceptible to the toxin in Bt crops. PMID:25641865

  2. Genotypic Diversity and Virulence Traits of Streptococcus mutans Isolated from Carious Dentin after Partial Caries Removal and Sealing

    PubMed Central

    Damé-Teixeira, Nailê; Arthur, Rodrigo Alex; Parolo, Clarissa Cavalcanti Fatturi

    2014-01-01

    The aim of this study was to compare the genotypic diversity and virulence traits of Streptococcus mutans isolated from carious dentin before and after partial dentin caries removal (PDR) and sealing. Carious dentin samples were obtained three months before and after the PDR and cavity sealing. Up to seven isolates of each morphological type of S. mutans were selected and strain identity was confirmed using gtfB primer. Genotyping was performed by arbitrary primer-PCR (AP-PCR). Acidogenesis and acidurance of the genotypes were evaluated as virulence traits. A paired t-test and a Wilcoxon test were used to compare the virulence of genotypes. A total of 48 representative S. mutans isolates were genotyped (31 before and 17 after the sealing). At least one of the genotypes found before the sealing was also found on dentin after the sealing. The number of genotypes found before the sealing ranged from 2 to 3 and after the sealing from 1 to 2 genotypes. No difference was observed in the acidogenesis and acidurance between genotypes isolated before and after the sealing. In conclusion, genotypic diversity of S. mutans decreased after the PDR and sealing, but the virulence traits of S. mutans remained unchangeable. PMID:24578618

  3. Hepatitis C virus genotypes in Myanmar.

    PubMed

    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. PMID:27468202

  4. Hepatitis B virus: the genotype E puzzle.

    PubMed

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

    2009-07-01

    Hepatitis B virus (HBV) is highly endemic throughout sub-Saharan Africa. One of the two genotypes A and E dominates in most countries. With several subgenotypes and variants, genotype A is more diverse in Africa (4.00%) than in the rest of the world (2.96%), suggesting an African origin and a long history on the continent. Despite the African slave trade, genotype E has only sporadically been found within the Americas, indicating that this genotype was introduced only during the past 200 years into the general African population. A short history for this genotype in Africa is also supported by its conspicuously low genetic diversity (1.75%), which contrasts, however, with its excessively high HBsAg prevalence and its extensive spread throughout the vast West-African genotype E crescent. We discuss the spread and routes of transmission of genotype E and suggest that the distribution and current high prevalence levels of HBV (genotype E) in Africa are the result of the extensive use of unsafe needles, potentially solving the current African genotype E puzzle and shedding new light on the high HBV prevalence in Africa. PMID:19475565

  5. Additional novel Cryptosporidium genotypes in ornamental fishes.

    PubMed

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

    2012-12-21

    Current knowledge on the prevalence and genotypes of Cryptosporidium in fishes is still limited. This study investigated the prevalence of Cryptosporidium species in 171 ornamental fishes, belonging to 33 species, collected from 8 commercial aquariums around Perth, Western Australia. All samples were screened by nested PCR targeting the 18S rRNA locus. A total of 6 positives were identified by PCR at the 18S locus from 4 different species of fishes (red eye tetra, Moenkhausia sanctaefilomenae; gold gourami, Trichogaster trichopterus; neon tetra, Paracheirodon innesi; goldfish, Carassius auratus auratus), giving an overall prevalence of 3.5% (6/171). Four different genotypes were identified, only one of which has been previously reported in fish; piscine genotype 4 in a neon tetra isolate, a rat genotype III-like isolate in a goldfish, a novel genotype in three isolates from red eye (piscine genotype 7) which exhibited a 3.5% genetic distance from piscine genotype 1 and a piscine genotype 6-like from a gold gourami (1% genetic distance). Further biological and genetic characterisation is required to determine the relationship of these genotypes to established species and strains of Cryptosporidium. PMID:22819587

  6. Hepatitis C virus genotypes in Myanmar

    PubMed Central

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

    2016-01-01

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

  7. Genotypic variation in a foundation tree (Populus tremula L.) explains community structure of associated epiphytes

    PubMed Central

    Davies, Chantel; Ellis, Christopher J.; Iason, Glenn R.; Ennos, Richard A.

    2014-01-01

    Community genetics hypothesizes that within a foundation species, the genotype of an individual significantly influences the assemblage of dependent organisms. To assess whether these intra-specific genetic effects are ecologically important, it is required to compare their impact on dependent organisms with that attributable to environmental variation experienced over relevant spatial scales. We assessed bark epiphytes on 27 aspen (Populus tremula L.) genotypes grown in a randomized experimental array at two contrasting sites spanning the environmental conditions from which the aspen genotypes were collected. We found that variation in aspen genotype significantly influenced bark epiphyte community composition, and to the same degree as environmental variation between the test sites. We conclude that maintaining genotypic diversity of foundation species may be crucial for conservation of associated biodiversity. PMID:24789141

  8. High Quality Genome-Wide Genotyping from Archived Dried Blood Spots without DNA Amplification

    PubMed Central

    St. Julien, Krystal R.; Jelliffe-Pawlowski, Laura L.; Shaw, Gary M.; Stevenson, David K.; O’Brodovich, Hugh M.; Krasnow, Mark A.

    2013-01-01

    Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping. Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA. PMID:23737996

  9. [Genotype diversity of the Bacillus anthracis strains isolated from the Caucasus region].

    PubMed

    Eremenko, E I; Riazanava, A G; Tsygankova, O I; Tsygankova, E A; Buravtseva, N P; Kulichenko, A N

    2012-01-01

    The study of the genotypes of Bacillus anthracis strains isolated from the Caucasus region was performed using MLVA. Among 149 strains, 32 distinctive MLVA-8 genotypes belonging to Ala, A3a, A4 and B1 molecular diversity groups were identified. 9 genotypes were not described previously; 6 genotypes were not found in other geographic regions and could be considered as endemic for Caucasus. The majority of the identified genotypes are widespread not only in Caucasus, but also throughout Eurasia, Africa, and America. Molecular diversity of Caucasian isolates is comparable to the worldwide diversity. This represents historical relations of this region, proximity to ancient trade routes and intensity of the anthrax epizootic in Caucasus. The obtained results are of interest from the theoretical point of view, as well as for the application in epidemiological research of the anthrax outbreaks. PMID:22937567

  10. Phenotyping two tomato genotypes with different nitrogen use efficiency.

    PubMed

    Abenavoli, Maria Rosa; Longo, Caterina; Lupini, Antonio; Miller, Anthony J; Araniti, Fabrizio; Mercati, Francesco; Princi, Maria P; Sunseri, Francesco

    2016-10-01

    Nitrogen (N) supply usually limits crop production and optimizing N-use efficiency (NUE) to minimize fertilizer loss is important. NUE is a complex trait that can be dissected into crop N uptake from the soil (NUpE) and N utilization (NUtE). We compared NUE in 14 genotypes of three week old tomatoes grown in sand or hydroponic culture supplied with nitrate (NO3(-)). Culture method influenced measured NUE for some cultivars, but Regina Ostuni (RO) and UC82 were consistently identified as high and low NUE genotypes. To identify why these genotypes had contrasting NUE some traits were compared growing under 0.1 and 5 mM NO3(-) supply. UC82 showed greater root (15)NO3(-) influx at low and high supply, and stronger SlNRT2.1/NAR2.1 transporter expression under low supply when compared with RO. Conversely, RO showed a higher total root length and thickness compared to UC82. Compared with UC82, RO showed higher shoot SlNRT2.3 expression and NO3(-) storage at high supply, but similar NO3(-) reductase activity. After N-starvation, root cell electrical potentials of RO were significantly more negative than UC82, but nitrate elicited similar responses in both root types. Overall for UC82 and RO, NUtE may play a greater role than NUpE for improved NUE. PMID:27235648

  11. Emergence of telaprevir-resistant variants detected by ultra-deep sequencing after triple therapy in patients infected with HCV genotype 1.

    PubMed

    Akuta, Norio; Suzuki, Fumitaka; Seko, Yuya; Kawamura, Yusuke; Sezaki, Hitomi; Suzuki, Yoshiyuki; Hosaka, Tetsuya; Kobayashi, Masahiro; Hara, Tasuku; Kobayashi, Mariko; Saitoh, Satoshi; Arase, Yasuji; Ikeda, Kenji; Kumada, Hiromitsu

    2013-06-01

    Using ultra-deep sequencing technology, the present was designed to investigate whether the emergence of telaprevir-resistant variants (amino acid substitutions of aa36, aa54, aa155, aa156, and aa170 positions in HCV NS3 region) after commencement of triple therapy of telaprevir/peginterferon (PEG-IFN)/ribavirin could be predicted at baseline in previous non-responders to dual therapy. Fourteen patients infected with HCV genotype 1 who did not respond to previous PEG-IFN/ribavirin, received a 24-week regimen of triple therapy, and were evaluated for appearance of telaprevir-resistant variants (amino acid substitutions of more than 0.2% among the total coverage) by ultra-deep sequencing. The sustained virological response rate was 28.6% (4 of 14 patients), which was significantly higher in patients with Arg70 (substitution at core aa70) and partial response (type of previous response to PEG-IFN/ribavirin) than in other patients. Telaprevir-resistant variants at baseline were detected in 7.1% (1 of 14 patients) by direct sequencing and in 21.4% (3 of 14 patients) by ultra-deep sequencing. The appearance of telaprevir-resistant variants was examined by ultra-deep sequencing in 10 who did not show sustained virological responders. De novo variants emerged at re-elevation of viral load, regardless of variant frequencies at baseline (one patient with very high frequency variants [T54S: 99.9%], two patients with very low frequency variants [V36A: 0.2%; and V170A: 0.4%], and seven patients of undetectable variants). It is concluded that it is difficult to predict at baseline the emergence of telaprevir-resistant variants after commencement of triple therapy in prior non-responders of HCV genotype 1, even with the use of ultra-deep sequencing. PMID:23588728

  12. Comprehensive Analysis and Characterization of Linear Antigenic Domains on HN Protein from Genotype VII Newcastle Disease Virus Using Yeast Surface Display System

    PubMed Central

    Li, Tao; Wang, Gaoling; Shi, Bingtian; Liu, Peixin; Si, Wei; Wang, Bin; Jiang, Li; Zhou, Lunjiang; Xiu, Jinsheng; Liu, Henggui

    2015-01-01

    Circulation of genotype VII Newcastle disease virus (NDV) has posed a great threat for the poultry industry worldwide. Antibodies against Hemagglutinin-neuraminidase (HN), a membrane protein of NDV with critical roles in NDV infection, have been reported to provide chickens protection from NDV infection. In this study, we comprehensively analyzed the in vivo antibody responses against the linear antigenic domains of the HN protein from genotype VII NDV using a yeast surface display system. The results revealed four distinct regions of HN, P1 (1-52aa), P2 (53-192aa), P3 (193-302aa) and P4 (303-571aa), respectively, according to their antigenic potency. Analysis by FACS and ELISA assay indicated P2 to be the dominant linear antigenic domain, with the immunogenic potency to protect the majority of chickens from NDV challenge. In contrast, the P1, P3 and P4 domains showed weak antigenicity in vivo and could not protect chickens from NDV challenge. These results provide important insight into the characteristic of humoral immune responses elicited by HN of NDV in vivo. PMID:26121247

  13. Genotype and haplotype distributions of MTHFR677C>T and 1298A>C single nucleotide polymorphisms: a meta-analysis.

    PubMed

    Ogino, Shuji; Wilson, Robert B

    2003-01-01

    Common single nucleotide polymorphisms (SNPs; 677C>T and 1298A>C) in the methylenetetrahydrofolate reductase gene ( MTHFR) decrease the activity of the enzyme, leading to hyperhomocysteinemia, particularly in folate-deficient states. We calculate herein the haplotype frequencies of the MTHFR 677 and 1298 polymorphisms in pooled general populations derived from published data. We selected 16 articles that provided reliable data on combined MTHFR genotypes in general populations ( n = 5389). The combined data comprised the following totals for each genotype at nucleotide positions 677 and 1298: 838 CC/AA (i.e., 677CC/1298AA), 1225 CC/AC, 489 CC/CC, 1120 CT/AA, 1093 CT/AC, 8 CT/CC, 606 TT/AA, 10 TT/AC, and 0 TT/CC. The estimated haplotype frequencies, and the fractional contribution of each, were 677C/1298A, 0.37; 677C/1298C, 0.31; 677T/1298A, 0.32; and 677T/1298C, 0.0023 to 0.0034. Thus, a vast majority of 677T alleles and 1298C alleles are associated with 1298A alleles and 677C alleles, respectively. There may be an increased frequency of the very rare cis 677T/1298C haplotype in some parts of the United Kingdom and Canada, possibly due to a founder effect. Further studies on both SNPs are needed to determine their exact role in various clinical settings. PMID:12560871

  14. Comprehensive Analysis and Characterization of Linear Antigenic Domains on HN Protein from Genotype VII Newcastle Disease Virus Using Yeast Surface Display System.

    PubMed

    Li, Tao; Wang, Gaoling; Shi, Bingtian; Liu, Peixin; Si, Wei; Wang, Bin; Jiang, Li; Zhou, Lunjiang; Xiu, Jinsheng; Liu, Henggui

    2015-01-01

    Circulation of genotype VII Newcastle disease virus (NDV) has posed a great threat for the poultry industry worldwide. Antibodies against Hemagglutinin-neuraminidase (HN), a membrane protein of NDV with critical roles in NDV infection, have been reported to provide chickens protection from NDV infection. In this study, we comprehensively analyzed the in vivo antibody responses against the linear antigenic domains of the HN protein from genotype VII NDV using a yeast surface display system. The results revealed four distinct regions of HN, P1 (1-52aa), P2 (53-192aa), P3 (193-302aa) and P4 (303-571aa), respectively, according to their antigenic potency. Analysis by FACS and ELISA assay indicated P2 to be the dominant linear antigenic domain, with the immunogenic potency to protect the majority of chickens from NDV challenge. In contrast, the P1, P3 and P4 domains showed weak antigenicity in vivo and could not protect chickens from NDV challenge. These results provide important insight into the characteristic of humoral immune responses elicited by HN of NDV in vivo. PMID:26121247

  15. Effects of challenge with a virulent genotype II strain of porcine reproductive and respiratory syndrome virus on piglets vaccinated with an attenuated genotype I strain vaccine.

    PubMed

    Roca, M; Gimeno, M; Bruguera, S; Segalés, J; Díaz, I; Galindo-Cardiel, I J; Martínez, E; Darwich, L; Fang, Y; Maldonado, J; March, R; Mateu, E

    2012-07-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) is endemic in most parts of Asia, where genotype I and II strains of diverse virulence may coexist. This study evaluated the outcome of infection with a highly virulent Asian genotype II PRRSV isolate in piglets vaccinated with a genotype I vaccine. Twenty-one 3-week-old piglets were divided in three groups: Pigs in group V (n=8) were vaccinated with an attenuated genotype I commercial PRRSV vaccine, while pigs in group U (n=8) and a control group (group C; n=5) were unvaccinated; 6 weeks later, pigs in groups V and U were challenged intranasally with a highly virulent strain of genotype II PRRSV (1×10(5) 50% tissue culture infectious doses/mL), while pigs in group C received a placebo. Over a period of 21 days after challenge, vaccinated pigs had significantly lower mortality (0/8 versus 2/8), fewer days of fever, a lower frequency of catarrhal bronchopneumonia, higher weight gains (13.4 versus 6.6 kg) and lower levels of viraemia compared to unvaccinated challenged pigs. Immunisation with a genotype I attenuated PRRSV vaccine provided partial protection against challenge with a highly virulent genotype II strain. PMID:22264642

  16. Deletion Genotypes Reduce Occlusion Body Potency but Increase Occlusion Body Production in a Colombian Spodoptera frugiperda Nucleopolyhedrovirus Population

    PubMed Central

    Barrera, Gloria; Williams, Trevor; Villamizar, Laura; Caballero, Primitivo; Simón, Oihane

    2013-01-01

    A Colombian field isolate (SfCOL-wt) of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) is a mixture of different genotypes. To evaluate the insecticidal properties of the different genotypic variants, 83 plaque purified virus were characterized. Ten distinct genotypes were identified (named A through J). SfCOL-A was the most prevalent (71±2%; mean ± SE) showing a PstI restriction profile indistinguishable to that of SfCOL-wt. The remaining nine genotypes presented genomic deletions of 3.8 - 21.8 Kb located mainly between nucleotides 11,436 and 33,883 in the reference genome SfMNPV-B, affecting the region between open reading frames (ORFs) sf20 and sf33. The insecticidal activity of each genotype from SfCOL-wt and several mixtures of genotypes was compared to that of SfCOL-wt. The potency of SfCOL-A occlusion bodies (OBs) was 4.4-fold higher than SfCOL-wt OBs, whereas the speed of kill of SfCOL-A was similar to that of SfCOL-wt. Deletion genotype OBs were similarly or less potent than SfCOL-wt but six deletion genotypes were faster killing than SfCOL-wt. The potency of genotype mixtures co-occluded within OBs were consistently reduced in two-genotype mixtures involving equal proportions of SfCOL-A and one of three deletion genotypes (SfCOL-C, -D or -F). Speed of kill and OB production were improved only when the certain genotype mixtures were co-occluded, although OB production was higher in the SfCOL-wt isolate than in any of the component genotypes, or mixtures thereof. Deleted genotypes reduced OB potency but increased OB production of the SfCOL-wt population, which is structured to maximize the production of OBs in each infected host. PMID:24116220

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

    PubMed Central

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

    2015-01-01

    Objective: 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. Methods: 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. Results: 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. Conclusion: 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. PMID:26649001

  18. Occupational Tuberculosis in Denmark through 21 Years Analysed by Nationwide Genotyping

    PubMed Central

    Andersen, Aase Bengaard; Andersen, Peter Henrik; Svensson, Erik; Jensen, Sidse Graff; Lillebaek, Troels

    2016-01-01

    Tuberculosis (TB) is a well-known occupational hazard. Based on more than two decades (1992–2012) of centralized nationwide genotyping of all Mycobacterium tuberculosis culture-positive TB patients in Denmark, we compared M. tuberculosis genotypes from all cases notified as presumed occupational (N = 130) with M. tuberculosis genotypes from all TB cases present in the country (N = 7,127). From 1992 through 2006, the IS6110 Restriction Fragment Length Polymorphism (RFLP) method was used for genotyping, whereas from 2005 to present, the 24-locus-based Mycobacterial Interspersed Repetitive Unit-Variable Number of Tandem Repeat (MIRU-VNTR) was used. An occupational TB case was classified as clustered if the genotype was 100% identical to at least one other genotype. Subsequently, based on genotype, time period, smear positivity, geography, susceptibility pattern, and any reported epidemiological links between the occupational cases and any potential source cases, the occupational case was categorized as confirmed, likely, possible or unlikely occupationally infected. Among the 130 notified presumed occupational cases, 12 (9.2%) could be classified as confirmed and 46 (35.4%) as unlikely, accounting for nearly half of all cases (44.6%). The remaining 72 cases (55.4%) were categorized as possible. Within this group, 15 cases (11.5%) were assessed to be likely occupational. Our study shows that genotyping can serve as an important tool for disentangle occupational TB in high-income low incidence settings, but still needs to be combined with good epidemiological linkage information. PMID:27082745

  19. LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms.

    PubMed

    Money, Daniel; Gardner, Kyle; Migicovsky, Zoë; Schwaninger, Heidi; Zhong, Gan-Yuan; Myles, Sean

    2015-11-01

    Obtaining genome-wide genotype data from a set of individuals is the first step in many genomic studies, including genome-wide association and genomic selection. All genotyping methods suffer from some level of missing data, and genotype imputation can be used to fill in the missing data and improve the power of downstream analyses. Model organisms like human and cattle benefit from high-quality reference genomes and panels of reference genotypes that aid in imputation accuracy. In nonmodel organisms, however, genetic and physical maps often are either of poor quality or are completely absent, and there are no panels of reference genotypes available. There is therefore a need for imputation methods designed specifically for nonmodel organisms in which genomic resources are poorly developed and marker order is unreliable or unknown. Here we introduce LinkImpute, a software package based on a k-nearest neighbor genotype imputation method, LD-kNNi, which is designed for unordered markers. No physical or genetic maps are required, and it is designed to work on unphased genotype data from heterozygous species. It exploits the fact that markers useful for imputation often are not physically close to the missing genotype but rather distributed throughout the genome. Using genotyping-by-sequencing data from diverse and heterozygous accessions of apples, grapes, and maize, we compare LD-kNNi with several genotype imputation methods and show that LD-kNNi is fast, comparable in accuracy to the best-existing methods, and exhibits the least bias in allele frequency estimates. PMID:26377960

  20. Genotypic Variation for Drought Tolerance in Beta vulgaris

    PubMed Central

    OBER, E. S.; LUTERBACHER, M. C.

    2002-01-01

    Insufficient soil moisture during summer months is now the major cause of sugar beet yield losses in the UK. However, selection for increased drought tolerance has not been a breeding priority until recently. Genetic variation for drought tolerance is an essential prerequisite for the development of more stress‐tolerant varieties, but commercial sugar beet varieties seem to have similar yield responses to drought. The objective of this study was to assess the degree of genotypic variation for drought tolerance within a wide range of sugar beet germplasm and genebank accessions within Beta. Thirty sugar beet genotypes were screened under field drought conditions, and putative drought tolerant and sensitive lines (in terms of yield reduction in polythene‐covered vs. irrigated plots) were identified. Significant genotype × water treatment interactions were found for dry matter yield and relative leaf expansion rate. Genotypic differences for drought susceptibility index were also significant. Differential sensitivity of seedling shoot growth to water deficit was examined by comparing 350 genebank accessions in a simple growth chamber screen. Methods of data management were devised to highlight lines for entry into subsequent field tests. The results of the field and seedling screens indicate that there is variation for tolerance to water deficits within sugar beet and related types, and that there are lines that show greater drought tolerance than selected commercial varieties. Divergent lines showing contrasting behaviour should aid in the identification of key morpho‐physiological traits that confer drought tolerance. PMID:12102517

  1. Reverse genetics studies of attenuation of the ca A/AA/6/60 influenza virus: the role of the matrix gene.

    PubMed

    Sweet, T M; Maassab, H F; Herlocher, M L

    2004-11-01

    The matrix (M) gene of influenza virus has been implicated in the attenuation phenotype of the cold adapted (ca) A/AA/6/60 vaccine. Previous studies have evaluated the ca M from A/AA/6/60 in different wild type (wt) virus backgrounds with varying results. In experiments described here, the ca M gene was transfected into the background of its own wt A/AA/6/60 to eliminate the possibility of confounding gene constellation effects. Comparison of the sequence of the wt and the ca A/AA/6/60 revealed one substitution in the nucleotide sequence of M. The molecular techniques of reverse genetics were used to rescue the ca M gene into the virulent wt A/AA/6/60 virus. The selection system used to identify the desired transfectant virus was amantadine resistance, which was introduced into the M2 gene using mutagenesis. The ca A/AA/6/60, the wt A/AA/6/60, a virus which contained wt M and was wt in the remaining seven genes and amantadine resistant (wt/969), a virus which contained the ca M but wt in the other seven genes (ca/969) were all evaluated in mice determine the effect of the ca M. The ca/969 virus was not attenuated in the mouse model when compared to the wt/969 virus, indicating that the ca A/AA/6/60 M does not independently contribute to the attenuation phenotype attributed to the ca A/AA/6/60 vaccine virus. PMID:15511608

  2. SNP genotyping by heteroduplex analysis.

    PubMed

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

    2015-01-01

    Heteroduplex-based genotyping methods have proven to be technologically effective and economically efficient for low- to medium-range throughput single-nucleotide polymorphism (SNP) determination. In this chapter we describe two protocols that were successfully applied for SNP detection and haplotype analysis of candidate genes in association studies. The protocols involve (1) enzymatic mismatch cleavage with endonuclease CEL1 from celery, associated with fragment separation using capillary electrophoresis (CEL1 cleavage), and (2) differential retention of the homo/heteroduplex DNA molecules under partial denaturing conditions on ion pair reversed-phase liquid chromatography (dHPLC). Both methods are complementary since dHPLC is more versatile than CEL1 cleavage for identifying multiple SNP per target region, and the latter is easily optimized for sequences with fewer SNPs or small insertion/deletion polymorphisms. Besides, CEL1 cleavage is a powerful method to localize the position of the mutation when fragment resolution is done using capillary electrophoresis. PMID:25373754

  3. The effects of female sex, viral genotype and IL28B genotype on spontaneous clearance of acute hepatitis C virus infection

    PubMed Central

    Grebely, Jason; Page, Kimberly; Sacks-Davis, Rachel; van der Loeff, Maarten Schim; Rice, Thomas M.; Bruneau, Julie; Morris, Meghan D.; Hajarizadeh, Behzad; Amin, Janaki; Cox, Andrea L.; Kim, Arthur Y.; McGovern, Barbara H.; Schinkel, Janke; George, Jacob; Shoukry, Naglaa H.; Lauer, Georg M.; Maher, Lisa; Lloyd, Andrew R.; Hellard, Margaret; Dore, Gregory J.; Prins, Maria

    2014-01-01

    Although 20–40% of persons with acute HCV infection demonstrate spontaneous clearance, the time-course and factors associated with clearance remain poorly understood. We investigated the time to spontaneous clearance and predictors among participants with acute HCV using Cox proportional hazards analyses. Data for this analysis were drawn from an international collaboration of nine prospective cohorts evaluating outcomes following acute HCV infection. Among 632 participants with acute HCV, 35% were female, 82% were Caucasian, 49% had IL28B CC genotype (rs12979860), 96% had injected drugs ever, 47% were infected with HCV genotype 1 and 5% had HIV co-infection. Twenty-eight percent were HCV antibody negative/RNA positive at the time of acute HCV detection (early acute HCV). During follow-up, spontaneous clearance occurred in 173 of 632 and at one year following infection, 25% (95%CI: 21%, 29%) had cleared virus. Among those with clearance, the median time to clearance was 16.5 weeks (IQR: 10.5, 33.4 weeks), with 34%, 67% and 83% demonstrating clearance at three, six and twelve months. Adjusting for age, factors independently associated with time to spontaneous clearance included female sex [adjusted hazards ratio (AHR) 2.16; 95%CI 1.48, 3.18], IL28B CC genotype (vs. CT/TT, AHR 2.26; 95%CI 1.52, 3.34), and HCV genotype 1 (vs. non-genotype 1, AHR 1.56; 95%CI 1.06, 2.30). The effect of IL28B genotype and HCV genotype on spontaneous clearance was greater among females compared to males. Conclusions Female sex, favorable IL28B genotype and HCV genotype 1 are independent predictors of spontaneous clearance. Further research is required to elucidate the observed sex-based differences in HCV control. PMID:23908124

  4. Estimating Genotype- and Environment-Specific Heritabilities

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  5. Filling in missing genotypes using haplotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Unknown genotypes can be made known (imputed) from observed genotypes at the same or nearby loci of relatives using pedigree haplotyping, or from matching allele patterns (regardless of pedigree) using population haplotyping. Fortran program findhap.f90 was designed to combine population and pedigre...

  6. Using genotypic information to reduce disease

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. Genotype imputation efficiency in Nelore Cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  8. Genomic evaluations with many more genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background Genomic evaluations have quickly become more reliable over the last two years in many countries as more animals were genotyped for 50,000 markers. Evaluations can also include animals genotyped with more or fewer markers using new tools such as 777,000 or 2,900 marker chips recently intr...

  9. Determination of elements in ayurvedic medicinal plants by AAS

    NASA Astrophysics Data System (ADS)

    Teerthe, Santoshkumar S.; Kerur, B. R.

    2015-08-01

    India has a rich country for the uses of Ayurvedic medicinal plants for treatment and also the north- Karnataka boasts an unparallel diversity of medicinal plants. The present study attempts to estimate and compare the level of trace and heavy metals in some selected leaves and root samples of Ayurvedic medicinal plants such as Mg, Al, K, Cr, Mn, Fe, Cu, Zn, and Cd. The samples are collected from different places of North-Karnataka regions and sample solutions prepared as the ratio of 1:25:25+950ml=1000ppm.the trace and heavy elemental concentration was estimated using Atomic Absorption Spectrometric (AAS) Method. The average concentrations of Mg, Mn, Fe and Zn, are ranging from 2ppm to 5250.2ppm and potassium (K) has more concentration as compare to all other. The other elements likes Al, Cr, Cu, and Cd were also estimed and presented in the table. Therefore, these medicinal plants are rich in some essential minerals, especially K, Mg, Mn, Fe and Zn which are essential for human health

  10. Determination of elements in ayurvedic medicinal plants by AAS

    SciTech Connect

    Teerthe, Santoshkumar S.; Kerur, B. R.

    2015-08-28

    India has a rich country for the uses of Ayurvedic medicinal plants for treatment and also the north- Karnataka boasts an unparallel diversity of medicinal plants. The present study attempts to estimate and compare the level of trace and heavy metals in some selected leaves and root samples of Ayurvedic medicinal plants such as Mg, Al, K, Cr, Mn, Fe, Cu, Zn, and Cd. The samples are collected from different places of North-Karnataka regions and sample solutions prepared as the ratio of 1:25:25+950ml=1000ppm.the trace and heavy elemental concentration was estimated using Atomic Absorption Spectrometric (AAS) Method. The average concentrations of Mg, Mn, Fe and Zn, are ranging from 2ppm to 5250.2ppm and potassium (K) has more concentration as compare to all other. The other elements likes Al, Cr, Cu, and Cd were also estimed and presented in the table. Therefore, these medicinal plants are rich in some essential minerals, especially K, Mg, Mn, Fe and Zn which are essential for human health.

  11. A novel method for multiplex genotyping in a single reactor using GTPlex-PyroSeq: genotyping HPV as a prototype.

    PubMed

    Oh, Myungsok; Hoehn, Benjamin Douglass; Moon, Youngho; Oh, Taejeong; Ko, Youngbok; An, Sungwhan

    2012-07-01

    Herein, we describe a novel multiplex genotyping method, GTPlex-PyroSeq. This method consists of two phases: multiplex PCR followed by a single reaction of pyrosequencing. This study demonstrates how GTPlex-PyroSeq can be adapted for the determination of multiple human papillomavirus (HPV) genotypes. A biotinylated consensus primer, GP6+, and 15 high-risk HPV type-specific primers are used for multiplex PCR. Each type-specific primer has a 5'-tag unique ID sequence connected to a pyrosequencing primer binding region. The unique ID sequence is composed of three parts: i) a single nucleotide ID representing a specific genotype; ii) a sign post; and iii) an end mark. This design allows multiple genotype determination under an ID sequence-dependent nucleotide dispensation order during pyrosequencing. Following initial studies using HPV plasmids and cell lines, we evaluated the clinical utility and effectiveness by comparing our assay with direct sequencing and HPV DNA chip analysis of 80 samples from high-risk, HPV-positive patients. We found in single-type infections, 100% concordance with direct sequencing (70 of 80 perfect matches) and 97.5% concordance with HPV DNA chip data (50 of 80 perfect matches). Additionally, our system was superior to direct sequencing in detection of multiple infections (12 of 80), with a limit of detection of 100 copies. The scalability of this multiplex system, with its open-platform design and ability to use various sample types, makes the GTPlex applicable for use in multiple settings. PMID:22575716

  12. Influence of ascorbic acid (AA) on iron (Fe) utilization in copper (Cu) deficient male and female rats

    SciTech Connect

    Johnson, M.A. )

    1989-02-09

    Interactions between Cu status (-Cu: 1.0 mg Cu/kg diet or +Cu: 5.8 mg Cu/kg diet) and AA (0 or 1% of the diet) were compared in male and female weanling rats. Food intakes were controlled so that final body weights were similar on day 23 when rats were killed. On day 17 rats were given an oral dose of 4 uCi of Fe-59 and feces were collected for 5 days. Heart weights (g/100 g body weight) were increased in both male and female -Cu rats. Among -Cu rats, AA increased heart weight by 25% in females but by only 6% in males. Similarly, among -Cu rats AA increased liver weight (g/100 g body weight) by 16% in females but not at all in males. Hematocrits (%) were similar among +Cu rats but were decreased in -Cu rats to a greater in male than in female rats. However, among -Cu rats AA decreased hematocrits from 34.1 to 26.4% in females but from only 30.0 to 26.8% in males. Compared to -Cu rats, +Cu rats apparently absorbed 2-times more Fe-59 and retained 2.5- times more absorbed Fe-59 in their whole blood. Among -Cu rats, AA decreased the absorption of Fe-59 and whole blood Fe-59 to a greater extent in female than in male rats. These results suggest that female rats may be somewhat more sensitive to the adverse effects of AA during Cu deficiency than are male rats.

  13. AAS and spectrophotometric methods for the determination metoprolol tartrate in tablets

    NASA Astrophysics Data System (ADS)

    Alpdoğan, Güzin; Sungur, Sidika

    1999-11-01

    Sensitive and specific atomic adsorption spectroscopy (AAS) and spectrophotometric methods have been developed for the determination of beta adrenergic blocking drug, metoprolol tartrate.The method is based on the formation of Cu(II) dithiocarbamate complex by derivatization of the secondary amino group of metoprolol with CS 2 and CuCl 2 in the presence of ammonia.The copper-bis(dithiocarbamate) complex was extracted into chloroform and the concentration of metoprolol tartrate was determined directly by spectrophotometric and indirectly by AAS measurement of copper.The two methods developed were applied to the assay of metoprolol tartrate in commercial tablet formulations.The methods were compared statistically with each other and with the high performance liquid chromatography (HPLC) method of USPXXII using t- and F-tests.

  14. Surface Tension of Organic Liquids Using the OPLS/AA Force Field.

    PubMed

    Zubillaga, Rafael A; Labastida, Ariana; Cruz, Bibiana; Martínez, Juan Carlos; Sánchez, Enrique; Alejandre, José

    2013-03-12

    Molecular dynamics simulations are performed to obtain the surface tension of 61 organic liquids using the OPLS/AA (all-atom optimized potential for liquid simulations). The force field parameters are the same as those recently used (Caleman et al. J. Chem. Theory Comput.2012, 8, 61) to determine several thermodynamic properties of 146 organic liquids. The correct evaluation of surface tension using slab simulations of liquids requires one to properly take into account the long-range interactions (Trukhymchuk and Alejandre J. Chem. Phys.1999, 111, 8510). In addition, the liquid density from slab simulations has to be the same as that obtained in liquid simulations at constant temperature and pressure. The new results of surface tensions from this work improve those reported by Caleman et al. The OPLS/AA force field gives good surface tensions compared with experimental data for most of the systems studied in this work, although it was developed to simulate liquids. PMID:26587622

  15. Work capacity and anticipation in A.A. Ukhtomsky's concept of dominance

    NASA Astrophysics Data System (ADS)

    Pavlova, L. P.

    2015-08-01

    This paper presents the results of theoretical and experimental investigations of human activity and anticipation based on A.A. Ukhtomsky's concept of brain dominance - a non-equilibrium system-forming factor in living systems. Facts on the stages of dominance formation are presented in relation to the creative abilities of the human brain and the role of fatigue as a "lever" for increasing systems' work capacity on the basis of "trace exaltation". Individually, specific features of dominantogenesis are compared with variations in behavioural types. On the basis of chronotopic EEG analysis, we delineate cortical dominants that underlie individual specifics of cognitive processes. The relation is shown between anticipation and the "expansion of dominants" - the broadening of "distal perception" in time and space, as framed by A.A. Ukhtomsky.

  16. Effects of simulated ice on the performance of price type-AA current meter rotors

    USGS Publications Warehouse

    Fulford, Janice M.

    1994-01-01

    Slush ice readily adheres to the standard metal rotor of the winter Price type-AA current meter and affects the ability of the meter to measure the flow velocity accurately. Tests conducted at the U.S. Geological Survey Hydraulics Laboratory at Stennis Space Center, Mississippi, attempt to quantify the effects of slush ice on the performance of standard Price type-AA meter metal rotors. Test data obtained for rotors filled with simulated slush are compared with data for solid-cup polymer and standard hollow-cup metal rotors. Partial filling of the cups only marginally affects rotor performance at velocities greater than 15.24 centimeters per second. However, when cups are filled or over-filled with simulated slush, rotor performance is noticeably affected. Errors associated with slush over-filling and filling of cups are also significant when flows are angled vertically.

  17. Mechanical and microstructural characterization of single and double pass Aluminum AA6061 friction stir weld joints

    NASA Astrophysics Data System (ADS)

    Othman, N. H.; Shah, L. H.; Ishak, M.

    2015-12-01

    This study focuses on the effect of single pass (SP), double sided pass (DSP) and normal double pass (NDP) method on friction stir welding of aluminum AA6061. Two pieces of AA6061 alloy with thickness of 6 mm were friction stir welded by using conventional milling machine. The rotational speeds that were used in this study were 800 rpm, 1000 rpm and 1200 rpm, respectively. The welding speed is fixed to 100 mm/min. Microstructure observation of welded area was studied by using optical microscope. Tensile test and Vickers hardness test were used to evaluate the mechanical properties of this specimen. Mechanical property analysis results indicate that at low rotational speeds, defects such as surface lack of fill and tunneling in the welded area can be observed. Vickers hardness of specimens however did not vary much when rotational speed is varied. Welded specimens using single pass method shows higher tensile strength and hardness value compared to both double pass methods up to 180.61 MPa. Moreover, DSP showed better tensile test and hardness test compared to NDP method. The optimum parameters were found to be single pass method with 1200 rpm of rotational speed. Therefore economically sound to only perform SP method to obtain maximum tensile strength for AA6061 FSW with thickness of 6 mm.

  18. Role of ledipasvir/sofosbuvir combination for genotype 1 hepatitis C virus infection

    PubMed Central

    Sundaram, Vinay; Kowdley, Kris V

    2016-01-01

    Chronic hepatitis C virus (HCV) infection is one of the most common etiologies of liver-related mortality throughout the world. Among the six HCV genotypes, genotype 1 was significantly more aggressive when utilizing the combination of pegylated interferon and ribavirin, as genotype 1-infected patients had the lowest likelihood of achieving cure (40%–50%) and required twice as long duration of treatment, as compared to genotypes 2 and 3. Recently, however, significant advances have been made with the advent of all-oral direct-acting antiviral agents, which have significantly improved the safety, efficacy, and tolerability of the treatment of HCV genotype 1. Among the available treatments for HCV genotype 1, the combination therapy of ledipasvir/sofosbuvir provides several advantages compared to other regimens, including use of a single-pill regimen, possibility to shorten the duration of treatment to 8 weeks, efficacy in patients exposed to protease inhibitors, safety in decompensated cirrhosis, and potential to avoid ribavirin. In this review, we discuss the pharmacotherapy of the combination of ledipasvir/sofosbuvir therapy and summarize the results of the Phase III clinical trials for this treatment in HCV genotype 1 patients. We will also discuss the data for special populations, including decompensated cirrhosis, human immunodeficiency virus (HIV) coinfected patients, African-Americans, the elderly, and those who failed sofosbuvir-containing regimens. PMID:27418860

  19. Role of ledipasvir/sofosbuvir combination for genotype 1 hepatitis C virus infection.

    PubMed

    Sundaram, Vinay; Kowdley, Kris V

    2016-01-01

    Chronic hepatitis C virus (HCV) infection is one of the most common etiologies of liver-related mortality throughout the world. Among the six HCV genotypes, genotype 1 was significantly more aggressive when utilizing the combination of pegylated interferon and ribavirin, as genotype 1-infected patients had the lowest likelihood of achieving cure (40%-50%) and required twice as long duration of treatment, as compared to genotypes 2 and 3. Recently, however, significant advances have been made with the advent of all-oral direct-acting antiviral agents, which have significantly improved the safety, efficacy, and tolerability of the treatment of HCV genotype 1. Among the available treatments for HCV genotype 1, the combination therapy of ledipasvir/sofosbuvir provides several advantages compared to other regimens, including use of a single-pill regimen, possibility to shorten the duration of treatment to 8 weeks, efficacy in patients exposed to protease inhibitors, safety in decompensated cirrhosis, and potential to avoid ribavirin. In this review, we discuss the pharmacotherapy of the combination of ledipasvir/sofosbuvir therapy and summarize the results of the Phase III clinical trials for this treatment in HCV genotype 1 patients. We will also discuss the data for special populations, including decompensated cirrhosis, human immunodeficiency virus (HIV) coinfected patients, African-Americans, the elderly, and those who failed sofosbuvir-containing regimens. PMID:27418860

  20. Parallel genotypic adaptation: when evolution repeats itself

    PubMed Central

    Wood, Troy E.; Burke, John M.; Rieseberg, Loren H.

    2008-01-01

    Until recently, parallel genotypic adaptation was considered unlikely because phenotypic differences were thought to be controlled by many genes. There is increasing evidence, however, that phenotypic variation sometimes has a simple genetic basis and that parallel adaptation at the genotypic level may be more frequent than previously believed. Here, we review evidence for parallel genotypic adaptation derived from a survey of the experimental evolution, phylogenetic, and quantitative genetic literature. The most convincing evidence of parallel genotypic adaptation comes from artificial selection experiments involving microbial populations. In some experiments, up to half of the nucleotide substitutions found in independent lineages under uniform selection are the same. Phylogenetic studies provide a means for studying parallel genotypic adaptation in non-experimental systems, but conclusive evidence may be difficult to obtain because homoplasy can arise for other reasons. Nonetheless, phylogenetic approaches have provided evidence of parallel genotypic adaptation across all taxonomic levels, not just microbes. Quantitative genetic approaches also suggest parallel genotypic evolution across both closely and distantly related taxa, but it is important to note that this approach cannot distinguish between parallel changes at homologous loci versus convergent changes at closely linked non-homologous loci. The finding that parallel genotypic adaptation appears to be frequent and occurs at all taxonomic levels has important implications for phylogenetic and evolutionary studies. With respect to phylogenetic analyses, parallel genotypic changes, if common, may result in faulty estimates of phylogenetic relationships. From an evolutionary perspective, the occurrence of parallel genotypic adaptation provides increasing support for determinism in evolution and may provide a partial explanation for how species with low levels of gene flow are held together. PMID:15881688

  1. African American Women's Perception of Their Own Weight Status Compared to Measured Weight Status

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous research indicates that African American (AA) women may be more accepting of larger body sizes compared with women of other races. This study assessed whether AA women perceived their own weight status accurately, when compared with their actual weight classification. Participants were 528 ...

  2. Two distinct human parainfluenza virus type 1 genotypes detected during the 1991 Milwaukee epidemic.

    PubMed Central

    Henrickson, K J; Savatski, L L

    1996-01-01

    The extent of genetic and antigenic variation found in a population of human parainfluenza virus type 1 (HPIV-1) during a single local epidemic was investigated. Fifteen HPIV-1 strains isolated from children in 1991 were analyzed. Nucleotide sequence variation in the hemagglutinin-neuraminidase protein (HN) gene demonstrated two distinct genotypes (genotypes C and D). Unique patterns were identified involving 62 nucleotide and 10 amino acid positions. These patterns represented 40% of all mutations within the HN gene. The remaining mutations were randomly distributed, and 74% involved only one (55%) or two isolates. Genotypes were statistically different from each other at both the nucleotide (P = 0.001) and amino acid (P = 0.001) levels and demonstrated unique potential N-linked glycosylation patterns. Thirty-eight monoclonal antibodies (MAbs) made to four different viral proteins (22 HN, 2 fusion [F], 1 phosphoprotein, and 13 nucleoprotein) (originating from two different genotypes [genotypes A and D]) were compared for their ability to bind to the clinical isolates in enzyme-linked immunosorbent assays (ELISAs) and hemagglutinin-inhibition (HI) assays. Twenty-one MAbs bound well to all clinical isolates in ELISAs and HI assays. The remaining 17 MAbs showed variation in all four structural proteins. Three HN MAbs demonstrated genotype C- and D-specific antigenic and neutralization differences. Evolutionary analysis using parsimony methods confirmed the differences between the two genotypes. No differences in either clinical presentation or disease severity between the two genotypes were found. Geographically localized HPIV-1 epidemics can be caused by at least two distinct genotypes with minor but specific antigenic changes. The clinical and immunologic roles of HPIV-1 genotypes have not been determined. PMID:8904440

  3. Epigenomics and bolting tolerance in sugar beet genotypes.

    PubMed

    Hébrard, Claire; Peterson, Daniel G; Willems, Glenda; Delaunay, Alain; Jesson, Béline; Lefèbvre, Marc; Barnes, Steve; Maury, Stéphane

    2016-01-01

    In sugar beet (Beta vulgaris altissima), bolting tolerance is an essential agronomic trait reflecting the bolting response of genotypes after vernalization. Genes involved in induction of sugar beet bolting have now been identified, and evidence suggests that epigenetic factors are involved in their control. Indeed, the time course and amplitude of DNA methylation variations in the shoot apical meristem have been shown to be critical in inducing sugar beet bolting, and a few functional targets of DNA methylation during vernalization have been identified. However, molecular mechanisms controlling bolting tolerance levels among genotypes are still poorly understood. Here, gene expression and DNA methylation profiles were compared in shoot apical meristems of three bolting-resistant and three bolting-sensitive genotypes after vernalization. Using Cot fractionation followed by 454 sequencing of the isolated low-copy DNA, 6231 contigs were obtained that were used along with public sugar beet DNA sequences to design custom Agilent microarrays for expression (56k) and methylation (244k) analyses. A total of 169 differentially expressed genes and 111 differentially methylated regions were identified between resistant and sensitive vernalized genotypes. Fourteen sequences were both differentially expressed and differentially methylated, with a negative correlation between their methylation and expression levels. Genes involved in cold perception, phytohormone signalling, and flowering induction were over-represented and collectively represent an integrative gene network from environmental perception to bolting induction. Altogether, the data suggest that the genotype-dependent control of DNA methylation and expression of an integrative gene network participate in bolting tolerance in sugar beet, opening up perspectives for crop improvement. PMID:26463996

  4. APOE genotype alters immunoglobulin subtypes in knock-in mice

    PubMed Central

    Zhou, Ye; Zhao, Wenjuan; Al-muhtasib, Nour; Rebeck, G. William

    2016-01-01

    Apolipoprotein E (APOE) alleles are strongly related to the risk of Alzheimer’s disease (AD). APOE genotype also affects inflammatory processes in response to damage. We tested whether APOE genotype affected the levels of specific immunoglobulins in healthy, uninfected APOE knock-in mice. We measured specific immunoglobulins in brain, spleen and plasma. Levels of total IgG in brain and spleen were highest in APOE-ε3 mice, significantly higher than in APOE-ε2 and APOE-ε4 mice; no differences were observed for levels of total IgG plasma. We also measured specific subtypes of IgG. IgG1 was only detectable in plasma, and did not differ by APOE genotype. IgG3 was detectable in plasma and spleen, and also did not differ by APOE genotype. IgG2b showed the same pattern as levels of total IgG by APOE genotype, with the highest levels of IgG2b in brain, spleen, and plasma of APOE-ε3 mice. IgG2a showed an entirely different pattern, with significantly higher levels in spleen and plasma of APOE-ε4 mice compared to APOE-ε2 and APOE-ε3 mice. We also measured IgM and IgA in spleens and plasma of these mice. In spleen, APOE-ε4 mice had the lowest IgA levels and the highest levels of IgM; both being significantly different from APOE-ε2 mice. In total, murine IgG2a and IgM were highest in APOE-ε4 mice, while total IgG and Ig2b were highest in APOE-ε3 mice. These dramatically different distributions of immunoglobulins could allow for human AD risk biomarkers based on specific immunoglobulin subtypes. PMID:25737044

  5. Epigenomics and bolting tolerance in sugar beet genotypes

    PubMed Central

    Hébrard, Claire; Peterson, Daniel G.; Willems, Glenda; Delaunay, Alain; Jesson, Béline; Lefèbvre, Marc; Barnes, Steve; Maury, Stéphane

    2016-01-01

    In sugar beet (Beta vulgaris altissima), bolting tolerance is an essential agronomic trait reflecting the bolting response of genotypes after vernalization. Genes involved in induction of sugar beet bolting have now been identified, and evidence suggests that epigenetic factors are involved in their control. Indeed, the time course and amplitude of DNA methylation variations in the shoot apical meristem have been shown to be critical in inducing sugar beet bolting, and a few functional targets of DNA methylation during vernalization have been identified. However, molecular mechanisms controlling bolting tolerance levels among genotypes are still poorly understood. Here, gene expression and DNA methylation profiles were compared in shoot apical meristems of three bolting-resistant and three bolting-sensitive genotypes after vernalization. Using Cot fractionation followed by 454 sequencing of the isolated low-copy DNA, 6231 contigs were obtained that were used along with public sugar beet DNA sequences to design custom Agilent microarrays for expression (56k) and methylation (244k) analyses. A total of 169 differentially expressed genes and 111 differentially methylated regions were identified between resistant and sensitive vernalized genotypes. Fourteen sequences were both differentially expressed and differentially methylated, with a negative correlation between their methylation and expression levels. Genes involved in cold perception, phytohormone signalling, and flowering induction were over-represented and collectively represent an integrative gene network from environmental perception to bolting induction. Altogether, the data suggest that the genotype-dependent control of DNA methylation and expression of an integrative gene network participate in bolting tolerance in sugar beet, opening up perspectives for crop improvement. PMID:26463996

  6. Nephrotic Syndrome Associated with Lung Cancer: A Rare Case of Malignancy Associated with AA Amyloidosis

    PubMed Central

    Gueutin, Victor; Langlois, Anne-Lyse; Shehwaro, Nathalie; Elharraqui, Ryme; Rouvier, Philippe; Izzedine, Hassane

    2013-01-01

    Nonhematologic malignancies are rarely reported to be associated with AA amyloidosis. Although the association between renal cell carcinoma and systemic AA amyloidosis has been established, the evidence linking pulmonary cancer to AA amyloidosis is scarce. Here, a case of biopsy-proven renal AA amyloidosis complicated with nephrotic syndrome associated with lung carcinoma is reported. PMID:24558629

  7. Hepatitis C virus genotype 3a with phylogenetically distinct origin is circulating in Pakistan

    PubMed Central

    2011-01-01

    Background Hepatitis C virus (HCV) is one of the leading causes of viral hepatitis worldwide and its genotype 3a is predominant in vast areas of Pakistan. Findings The present study reports the first full sequence of HCV 3a isolate PK-1 from Pakistan. This nucleotide sequence was compared with six other HCV genotype 3a full length sequences from different regions of the world by using statistical methods of phylogenetic analysis. Conclusion The nucleotide difference of these seven sequences shows that HCV genotype 3a of phylogenetically distinct origin is circulating in Pakistan. PMID:21211024

  8. Dependence of deodorant usage on ABCC11 genotype: scope for personalized genetics in personal hygiene.

    PubMed

    Rodriguez, Santiago; Steer, Colin D; Farrow, Alexandra; Golding, Jean; Day, Ian N M

    2013-07-01

    Earwax type and axillary odor are genetically determined by rs17822931, a single-nucleotide polymorphism (SNP) located in the ABCC11 gene. The literature has been concerned with the Mendelian trait of earwax, although axillary odor is also Mendelian. Ethnic diversity in rs17822931 exists, with higher frequency of allele A in east Asians. Influence on deodorant usage has not been investigated. In this work, we present a detailed analysis of the rs17822931 effect on deodorant usage in a large (N∼17,000 individuals) population cohort (the Avon Longitudinal Study of Parents and Children (ALSPAC)). We found strong evidence (P=3.7 × 10(-20)) indicating differential deodorant usage according to the rs17822931 genotype. AA homozygotes were almost 5-fold overrepresented in categories of never using deodorant or using it infrequently. However, 77.8% of white European genotypically nonodorous individuals still used deodorant, and 4.7% genotypically odorous individuals did not. We provide evidence of a behavioral effect associated with rs17822931. This effect has a biological basis that can result in a change in the family's environment if an aerosol deodorant is used. It also indicates potential cost saving to the nonodorous and scope for personalized genetics usage in personal hygiene choices, with consequent reduction of inappropriate chemical exposures for some. PMID:23325016

  9. Effects of CSN1S2 Genotypes on Economic Traits in Chinese Dairy Goats

    PubMed Central

    Yue, X. P.; Fang, Q.; Zhang, X.; Mao, C. C.; Lan, X. Y.; Chen, H.; Lei, C. Z.

    2013-01-01

    The aim of this study was to investigate allele frequencies at the CSN1S2 locus in two Chinese dairy goat breeds and the effects of its variation on dairy goat economic traits. Seven hundred and eight goats from Xinong Saanen (XS, n = 268) and Guanzhong (GZ, N = 440) breeds were selected. The milk samples of 268 XS goats were collected during the middle of lactation, body size parameters (708 goats) and daily milk yield (202 goats) were registered. The RFLP (restriction fragment length polymorphism) and SSCP (single strand conformation polymorphism) were used to detect the polymorphisms in CSN1S2. The Hardy-Weinberg (HW) equilibrium and the associations between body size, milk yield and composition and the genotypes were calculated. The results revealed that only A and F CSN1S2 alleles were found in the two Chinese dairy goat breeds. Allelic frequencies of A and F were 0.795, 0.205 and 0.739, 0.261 in Xinong Saanen and Guanzhong population respectively. Xinong Saanen breed was in Hardy-Weinberg equilibrium, while Guanzhong breed deviated from Hardy-Weinberg equilibrium (p<0.05). The association of polymorphism with economic traits indicated that the goats with FF genotype have higher milk fat and total solid concentration than those with AA and AF genotypes (p<0.05). PMID:25049867

  10. Section BB, Section DD, Plan AA, Plan CC, Typical Framing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Section B-B, Section D-D, Plan A-A, Plan C-C, Typical Framing Detail of Upper Stringers, Typical Framing Detail of Lower Stringers - Covered Bridge, Spanning Connecticut River, Orford, Grafton County, NH

  11. Genotypic differences in behavioural entropy: unpredictable genotypes are composed of unpredictable individuals

    PubMed Central

    Stamps, Judy A.; Saltz, Julia B.; Krishnan, V.V.

    2013-01-01

    Intra-genotypic variability (IGV) occurs when individuals with the same genotype, raised in the same environment and then tested under the same conditions, express different trait values. Game theoretical and bet-hedging models have suggested two ways that a single genotype might generate variable behaviour when behavioural variation is discrete rather than continuous: behavioural polyphenism (a genotype produces different types of individuals, each of which consistently expresses a different type of behaviour) or stochastic variability (a genotype produces one type of individual who randomly expresses different types of behaviour over time). We first demonstrated significant differences across 14 natural genotypes of male Drosophila melanogaster in the variability (as measured by entropy) of their microhabitat choice, in an experiment in which each fly was allowed free access to four different types of habitat. We then tested four hypotheses about ways that within-individual variability might contribute to differences across genotypes in the variability of microhabitat choice. There was no empirical support for three hypotheses (behavioural polymorphism, consistent choice, or time-based choice), nor could our results be attributed to genotypic differences in activity levels. The stochastic variability hypothesis accurately predicted the slope and the intercept of the relationship across genotypes between entropy at the individual level and entropy at the genotype level. However, our initial version of the stochastic model slightly but significantly overestimated the values of individual entropy for each genotype, pointing to specific assumptions of this model that might need to be adjusted in future studies of the IGV of microhabitat choice. This is among a handful of recent studies to document genotypic differences in behavioural IGV, and the first to explore ways that genotypic differences in within-individual variability might contribute to differences among

  12. Cost–effectiveness of CYP2B6 genotyping to optimize efavirenz dosing in HIV clinical practice

    PubMed Central

    Schackman, Bruce R; Haas, David W; Park, Sanghee S; Li, X Cynthia; Freedberg, Kenneth A

    2016-01-01

    Aims To assess the cost–effectiveness of CYP2B6 genotyping to guide efavirenz dosing for initial HIV therapy in the USA. Methods We used the Cost–Effectiveness of Preventing AIDS Complications (CEPAC) microsimulation model to project quality-adjusted life expectancy and lifetime costs (2014 US dollars) for efavirenz-based HIV therapy with or without CYP2B6 genotyping. We assumed that with genotyping 60% of patients would be eligible to receive lower doses. Results Current care without CYP2B6 genotyping has an incremental cost–effectiveness ratio >$100,000/QALY compared with genotype-guided dosing, even if lower dosing reduces efficacy. When we assumed generic efavirenz availability, conclusions were similar unless lower dosing reduces efficacy by 6% or more. Conclusion CYP2B6 genotyping can inform efavirenz dosing and decrease HIV therapy cost. PMID:26607811

  13. A Comparison of Pigment-Protein Complexes among Normal, Chlorophyll-Deficient and Senescent Soybean Genotypes 1

    PubMed Central

    Eskins, Kenneth; Delmastro, Dean; Harris, Leland

    1983-01-01

    Pigment-protein complexes were isolated from chloroplasts of normal green and several types of chlorophyll-deficient soybeans. The complexes were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and comparisons were made between normal and chlorophyll-deficient genotypes of the relative amounts of chlorophyll associated with Photosystem I (PSI), Photosystem II (PSII), light-harvesting, and free pigment complexes. Chlorophyll-deficient genotypes, compared to normal green genotypes, have fewer light-harvesting complexes and a higher ratio of PSII to PSI complexes. Chlorophyll associated with PSII in yellow genotypes is in relatively higher amounts in spite of the fact that these genotypes have much less grana stacking than normal green genotypes. Although PSII activity has been associated with appressed regions of grana in normal plants, our work shows that the association does not always hold true. PMID:16663184

  14. AAS Committee on Employment Panel Introduction

    NASA Astrophysics Data System (ADS)

    Borne, Kirk; Fanelli, M. N.; Storrie-Lombardi, L. J.; Krishnamurthi, A.

    2006-12-01

    Many younger astronomers are unaware of the dangers and pitfalls that await them in the job market. Issues related to fringe benefits (if any), moving expenses, medical coverage for family members, teaching versus research expectations, etc. can lead to misunderstandings and to serious difficulties if these are not addressed early in the job interview process. The AAS Committee on Employment has often received letters from concerned junior members of the society, who feel that they needed more guidance and assistance in entering the job market for the first time. The major areas of concern have included those just listed, but there may be others. The session is structured as a panel presentation, whose members are asked to prepare in advance their top 10 questions that job applicants should ask, and we will instruct our panel members not to discuss their list at all with the other panel members prior to their presentations. This will ensure independent viewpoints and novel responses. The panel will consist of astronomers who have different perspectives on this issue, including old and young, postdoc and beyond, academic and non-academic. To kick off the session, we will invite a brief humorous presentation of the Top Ten List, in the style of The Night Show host David Letterman.

  15. Microstructure and properties of AA 2090 weldments

    SciTech Connect

    Sunwoo, A.J.; Morris, J.W. Jr.

    1988-06-01

    The effects of welding on AA 2090 are examined along with the metallurgical changes associated with welding and aging. The results of the study show that the GTA and EB weldment properties are controlled by the precipitate size and distribution. There is a trade-off between strength and elongation. In the as-welded condition, solid solution strengthening is the primary strengthening mechanism present. As a result, the weldment strengths are less than 200 MPa, but the elongations are greater than 4%. In the post-weld aged condition, an inhomogeneous distribution of solutes results in an inhomogeneous distribution of precipitates, causing strain localization. Although the weldment strengths increase, the weldment elongations decrease precipitously. The peak strengths of EB and GTA weldments are obtained aging at 160{degree}C for 32 hours with 75% joint efficiency and at 190{degree}C for 16 hours with 65% joint efficiency, respectively. Aging at 230{degree}C leads to coarsening of precipitates as well as the intermetallic constituents; the weldment strengths deteriorate rapidly, but the elongations improve. The best overall weldment properties are obtained in the solution heat treated and aged conditions, and are associated with a homogeneous distribution of strengthening precipitates. 13 refs.

  16. Recrystallization behaviour of AA6063 extrusions

    NASA Astrophysics Data System (ADS)

    Zhang, K.; Pettersen, T.; Paulsen, C. O.; Marthinsen, K.; Holmedal, B.; Segatori, A.

    2015-08-01

    Cylindrical profiles of an AA6063 aluminium alloy were produced in a lab-scale direct extrusion set-up. The extrusion was performed at 300 °C, 450 °C and 550 °C, respectively, with the same ram speed. Immediate water quenching was applied to the profiles and the end of billet (butt-end) after extrusion. Microstructure and texture of the material in different states were measured by electron back-scattered diffraction. Only the profile extruded at 300 °C, was found in the deformed state after extrusion, featuring a fibrous grain structure and a strong <111> and weak <100> double fibre texture. Post-extrusion annealing of this profile at 450 °C resulted in an almost fully recrystallized structure (recrystallized fraction of 87%) and with a texture similar to that of the as-deformed state. The profile extruded at 450 °C was almost fully recrystallized (recrystallization fraction 91%) already after quenching, and with a texture characterized by a weak <111> and strong <100> double fibre. The profile extruded at 550 °C showed a partially recrystallized grain structure with recrystallization fraction of 71%, and with a texture dominated by a <100> fibre. The influence of the deformation conditions on the recrystallization behaviour, in terms of recrystallization kinetics and mechanisms, are discussed in view of these results.

  17. Molecular and Phenotypic Characterization of Genotypic Candida albicans Subgroups and Comparison with Candida dubliniensis and Candida stellatoidea

    PubMed Central

    McCullough, Michael J.; Clemons, Karl V.; Stevens, David A.

    1999-01-01

    There have been increased reports of the isolation of unusual genotypic groups of Candida albicans (groups C and D) based on a well-defined genotypic method; this method uses cellular DNA digested with the EcoRI enzyme and the restriction fragment length polymorphisms (RFLPs) generated by agarose gel electrophoresis. The aim of the present study was to use additional molecular tools to characterize these unusual strains and to compare them with authentic strains of C. dubliniensis, a recently delineated species, and type I C. stellatoidea. The RFLPs of PCR products generated from the intergenic transcribed spacer (ITS) region did not differentiate among C. albicans genotypes A, B, and C and type I C. stellatoidea. However, this method did differentiate the C. albicans genotype D strains, which were identical to C. dubliniensis. The RFLPs generated by HaeIII digestion of the PCR products of the V3 region of the 25S rRNA gene (rDNA) could differentiate the same groups as RFLP analysis of the PCR amplicon of the ITS region. C. albicans genotype B isolates have been shown to have a transposable intron in the 25S rDNA, whereas genotype A isolates do not; C. dubliniensis strains also have an intron that is larger than that in genotype B C. albicans strains but that is in the same location. PCR designed to span this region resulted in a single product for C. albicans genotype A (450 bp), B (840 bp), type 1 C. stellatoidea (840 bp), and C. dubliniensis (1,080 bp), whereas the C. albicans genotype C isolates had two major products (450 and 840 bp). All C. albicans genotype D isolates gave a PCR product identical to that given by C. dubliniensis. These results indicate that those strains previously designated C. albicans genotype D are in fact C. dubliniensis, that no differences were found between type 1 C. stellatoidea and C. albicans genotype B strains, and that the C. albicans genotype C strains appear to have the transposable intron incompletely inserted throughout the

  18. Outcomes From AAS Hack Day at the 227th AAS Meeting

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    Editors Note:This is a final post from the 227th AAS Meeting in Kissimmee, FL. This special summary of AAS Hack Day, a meeting of AAS members to collaboratively work on various small projects, was written by Meredith Rawls (@Merrdiff) and was originally posted on astrobites.com.As the 227thAmerican Astronomical Society meeting drew to a close (see highlights from Day 1, Day 2, Day 3, and Day 4), a group of at least 50 attendees spent Day 4working on small projects fondly called hacks. Thanks to sponsorship from LSST and Northrup Grumman, the industrious hackers werewell-caffeinated and fed so we could devote time and energy toworking in groups on one-day projects.TheHack Day beganat 10am with pitches. Anybody with a project idea was welcome to briefly speak and try to convince others to work with them. Only someideas panned out, but the enthusiasm was palpable. Its not every day you get a full room of astronomers and affiliates eager to spend hours working on fun and useful projects to benefit the community.#hackAAS is getting underway! #aas227 pic.twitter.com/yX7jlOnSCK James R A Davenport (@jradavenport) January 8, 2016Here is a rundown of what we accomplished. Pretty impressive for a single day! Many thanks to fellow astrobiter Erika Nesvold (now at Carnegie DTM; @erikanesvold) whose hack was live-documenting all the other hacks. Her tweets as @astrobites appeared with the #hackaas hashtag, and her notes made this recap post infinitely easier to write.Interested in joining the fun? Sign up for Hack Day at the 2017 JanuaryAAS meeting (its free with meeting registration), and consider applying for the .Astronomy conference this summer.Towards Optimal Session Scheduling:Adrian Price-Whelan (Columbia), David Hogg (NYU), and Scott Idem (AAS) began writing a program to take all submitted abstracts to a conference like AAS and sort them using keywords to avoid scheduling similar talks in parallel sessions. Its impossible to make everyone happy, but minimizing conflicts

  19. Asiago spectroscopic classification of SN2016aa in PGC 22658

    NASA Astrophysics Data System (ADS)

    Ciabattari, F.; Tomasella, L.; Pastorello, A.; Benetti, S.; Cappellaro, E.; Elias-Rosa, N.; Ochner, P.; Tartaglia, L.; Terreran, G.; Turatto, M.; Briganti, F.; Caimmi, M.; Campaner, P.; Donati, S.; Mazzoni, E.

    2016-02-01

    We report the spectroscopic classification of SN2016aa in PGC 22658 through observations obtained with the 1.82-m Copernico Telescope in Asiago (+ AFOSC; range 340-820 nm, resolution 1.3 nm). A low signal-to-noise spectrogram obtained on Jan 04.97 UT indicates that SN2016aa is a Type II SNe, a few weeks after the explosion.

  20. Section AA through main entrance gates & west stairs. San ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Section AA through main entrance gates & west stairs. San Bernardino Valley Union Junior College, Science Building. Also includes plans and sections of boys' and girls' toilets. Howard E. Jones, Architect, San Bernardino, California. Sheet 5, job no. 311. Scales 1/4 inch to the foot (section AA) and 1/2 inch to the foot (toilet rooms). February 15, 1927. - San Bernardino Valley College, Life Science Building, 701 South Mount Vernon Avenue, San Bernardino, San Bernardino County, CA

  1. Prion genotypes of scrapie-infected Canadian sheep 1998–2008

    PubMed Central

    Harrington, Noel P.; O’Rourke, Katherine I.; Feng, Yuqin; Rendulich, Jasmine; DiFruscio, Cathleen; Balachandran, Aru

    2010-01-01

    This report describes the genetics of the prion protein gene (PRNP) at codons 136, 154, and 171 for sheep diagnosed with naturally acquired classical scrapie in Canada between 1998 and 2008. Genotyping analysis was performed on 249 sheep with confirmed classical scrapie infection representing 98 flocks from 6 provinces. A further case-control analysis of 3 of these flocks compared the genotypes between infected sheep (n = 72) and those of their healthy flockmates (n = 1990). The incidence of classical scrapie in the Canadian sheep population was highly associated with the ARQ haplotype (91.8%) and the ARQ/ARQ genotype (91.6%). In addition, the ARQ haplotype was found at significantly higher frequency in scrapie-infected sheep when compared with their healthy flockmates. Comparison with other published data suggests that the scrapie risk of PRNP genotypes differs between Canada and countries where the VRQ allele is associated with the highest susceptibility to infection. PMID:20885849

  2. Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content

    PubMed Central

    Kostadinov, Rumen; Maley, Carlo C.; Kuhner, Mary K.

    2016-01-01

    When multiple samples are taken from the neoplastic tissues of a single patient, it is natural to compare their mutation content. This is often done by bulk genotyping of whole biopsies, but the chance that a mutation will be detected in bulk genotyping depends on its local frequency in the sample. When the underlying mutation count per cell is equal, homogenous biopsies will have more high-frequency mutations, and thus more detectable mutations, than heterogeneous ones. Using simulations, we show that bulk genotyping of data simulated under a neutral model of somatic evolution generates strong spurious evidence for non-neutrality, because the pattern of tissue growth systematically generates differences in biopsy heterogeneity. Any experiment which compares mutation content across bulk-genotyped biopsies may therefore suggest mutation rate or selection intensity variation even when these forces are absent. We discuss computational and experimental approaches for resolving this problem. PMID:27105344

  3. Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content.

    PubMed

    Kostadinov, Rumen; Maley, Carlo C; Kuhner, Mary K

    2016-04-01

    When multiple samples are taken from the neoplastic tissues of a single patient, it is natural to compare their mutation content. This is often done by bulk genotyping of whole biopsies, but the chance that a mutation will be detected in bulk genotyping depends on its local frequency in the sample. When the underlying mutation count per cell is equal, homogenous biopsies will have more high-frequency mutations, and thus more detectable mutations, than heterogeneous ones. Using simulations, we show that bulk genotyping of data simulated under a neutral model of somatic evolution generates strong spurious evidence for non-neutrality, because the pattern of tissue growth systematically generates differences in biopsy heterogeneity. Any experiment which compares mutation content across bulk-genotyped biopsies may therefore suggest mutation rate or selection intensity variation even when these forces are absent. We discuss computational and experimental approaches for resolving this problem. PMID:27105344

  4. AA amyloidosis as a complication of primary lymphedema.

    PubMed

    Beloncle, François; Sayegh, Johnny; Eymerit-Morin, Caroline; Duveau, Agnès; Augusto, Jean-François

    2014-03-01

    Primary lymphedema is a rare disease caused by a disorder of lymphangiogenesis. Clinical presentation and age at onset are variable. AA amyloidosis is usually due to chronic inflammatory diseases, malignant tumors or less frequently chronic infectious diseases. We report here the first two cases of AA amyloidosis present with renal failure and nephrotic syndrome in patients with primary lymphedema-induced chronic leg ulcers. The first patient was a 62-year-old female who presented with chronic untreated leg ulcers for 8 years secondary to primary lymphedema. A kidney biopsy done for nephrotic syndrome allowed the diagnosis of AA amyloidosis. The second patient was a 54-year-old male who presented with hereditary lymphedema and elephantiasis since the age of 12. A salivary gland biopsy allowed the diagnosis of AA amyloidosis. Renal function deteriorated progressively needing chronic haemodialysis. Chronic leg ulcers have been rarely reported to induce AA amyloidosis. Only five other cases have been reported in the literature, but none of them with chronic lymphedema. We believe that the relation between lymphedema, chronic leg ulcers and AA amyloidosis is underestimated. PMID:23964754

  5. Different methods of selecting animals for genotyping to maximize the amount of genetic information known in the population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A simulation study was carried out to develop and compare different methods of sampling animals to be genotyped. The simulated pedigrees included 5,000 animals and were assigned genotypes based on assumed allelic frequencies (favorable/unfavorable) of 0.3/0.7, 0.5/0.5, and 0.8/0.2. A real beef cat...

  6. Periodic barrier structure in AA-stacked bilayer graphene

    NASA Astrophysics Data System (ADS)

    Redouani, Ilham; Jellal, Ahmed

    2016-06-01

    We study the charge carriers transport in an AA-stacked bilayer graphene modulated by a lateral one-dimensional multibarrier structure. We investigate the band structures of our system, that is made up of two shifted Dirac cones, for finite and zero gap. We use the boundary conditions to explicitly determine the transmission probability of each individual cone (τ =+/- 1) for single, double and finite periodic barrier structure. We find that the Klein tunneling is only possible when the band structure is gapless and can occur at normal incidence as a result of the Dirac nature of the quasiparticles. We observe that the band structure of the barriers can have more than one Dirac points for finite periodic barrier. The resonance peaks appear in the transmission probability, which correspond to the positions of new cones index like associated with τ =+/- 1. Two conductance channels through different cones (τ =+/- 1) are found where the total conductance has been studied and compared to the cases of single layer and AB-stacked bilayer graphene.

  7. COST-EFFECTIVENESS OF USING HUMAN PAPILLOMAVIRUS 16/18 GENOTYPE TRIAGE IN CERVICAL CANCER SCREENING

    PubMed Central

    Vijayaraghavan, Arthi; Efrusy, Molly; Mazonson, Peter; Goodman, Karyn; Santas, Christopher; Huh, Warner

    2015-01-01

    Objective Testing for human papillomavirus (HPV) 16 and 18 genotypes, which are known to cause more than 65-70% of invasive cervical cancer cases, may allow clinicians to identify women at highest risk for underlying high-grade dysplasia missed by Pap cytology. Our objective was to determine the cost-effectiveness of adding HPV-16 and 18 genotype triage to current cervical cancer screening strategies in the United States. Methods We developed a lifetime Markov model to assess the cost-effectiveness of adding HPV genotyping to current cervical cancer screening algorithms. All costs were estimated from a payer perspective in 2007 U.S. dollars. Outcome measures included lifetime risk of cervical cancer, quality-adjusted life-years saved (QALYs), and incremental cost-effectiveness ratios (ICERs). Results In our model, the use of HPV genotype triage prevented 51-73 deaths per 100,000 women screened compared to screening using liquid-based cytology (LBC) followed by HPV triage and 4-26 deaths compared to co-screening with LBC and HPV. Use of HPV genotyping to triage all high-risk HPV-positive women every three years had an ICER of $34,074 per QALY compared to HPV and LBC co-screening. HPV genotyping with co-screening was the most effective strategy and had an ICER of $33,807 per QALY compared to HPV genotyping for all high-risk HPV-positive women. Conclusion The addition of HPV-16 and -18 genotype triage to current adjunctive HPV screening with LBC is a cost-effective screening strategy in the United States. PMID:20713299

  8. Evolutionary escape on complex genotype-phenotype networks.

    PubMed

    Ibáñez-Marcelo, Esther; Alarcón, Tomás

    2016-04-01

    We study the problem of evolutionary escape that is the process whereby a population under sudden changes in the selective pressures acting upon it try to evade extinction by evolving from previously well-adapted phenotypes to those that are favoured by the new selective pressure. We perform a comparative analysis between results obtained by modelling genotype space as a regular hypercube (H-graphs), which is the scenario considered in previous work on the subject, to those corresponding to a complex genotype-phenotype network (B-graphs). In order to analyse the properties of the escape process on both these graphs, we apply a general theory based on multi-type branching processes to compute the evolutionary dynamics and probability of escape. We show that the distribution of distances between phenotypes in B-graphs exhibits a much larger degree of heterogeneity than in H-graphs. This property, one of the main structural differences between both types of graphs, causes heterogeneous behaviour in all results associated to the escape problem. We further show that, due to the heterogeneity characterising escape on B-graphs, escape probability can be underestimated by assuming a regular hypercube genotype network, even if we compare phenotypes at the same distance in H-graphs. Similarly, it appears that the complex structure of B-graphs slows down the rate of escape. PMID:26802479

  9. Analyses and comparison of accuracy of different genotype imputation methods.

    PubMed

    Pei, Yu-Fang; Li, Jian; Zhang, Lei; Papasian, Christopher J; Deng, Hong-Wen

    2008-01-01

    The power of genetic association analyses is often compromised by missing genotypic data which contributes to lack of significant findings, e.g., in in silico replication studies. One solution is to impute untyped SNPs from typed flanking markers, based on known linkage disequilibrium (LD) relationships. Several imputation methods are available and their usefulness in association studies has been demonstrated, but factors affecting their relative performance in accuracy have not been systematically investigated. Therefore, we investigated and compared the performance of five popular genotype imputation methods, MACH, IMPUTE, fastPHASE, PLINK and Beagle, to assess and compare the effects of factors that affect imputation accuracy rates (ARs). Our results showed that a stronger LD and a lower MAF for an untyped marker produced better ARs for all the five methods. We also observed that a greater number of haplotypes in the reference sample resulted in higher ARs for MACH, IMPUTE, PLINK and Beagle, but had little influence on the ARs for fastPHASE. In general, MACH and IMPUTE produced similar results and these two methods consistently outperformed fastPHASE, PLINK and Beagle. Our study is helpful in guiding application of imputation methods in association analyses when genotype data are missing. PMID:18958166

  10. Genotype imputation reference panel selection using maximal phylogenetic diversity.

    PubMed

    Zhang, Peng; Zhan, Xiaowei; Rosenberg, Noah A; Zöllner, Sebastian

    2013-10-01

    The recent dramatic cost reduction of next-generation sequencing technology enables investigators to assess most variants in the human genome to identify risk variants for complex diseases. However, sequencing large samples remains very expensive. For a study sample with existing genotype data, such as array data from genome-wide association studies, a cost-effective approach is to sequence a subset of the study sample and then to impute the rest of the study sample, using the sequenced subset as a reference panel. The use of such an internal reference panel identifies population-specific variants and avoids the problem of a substantial mismatch in ancestry background between the study population and the reference population. To efficiently select an internal panel, we introduce an idea of phylogenetic diversity from mathematical phylogenetics and comparative genomics. We propose the "most diverse reference panel", defined as the subset with the maximal "phylogenetic diversity", thereby incorporating individuals that span a diverse range of genotypes within the sample. Using data both from simulations and from the 1000 Genomes Project, we show that the most diverse reference panel can substantially improve the imputation accuracy compared to randomly selected reference panels, especially for the imputation of rare variants. The improvement in imputation accuracy holds across different marker densities, reference panel sizes, and lengths for the imputed segments. We thus propose a novel strategy for planning sequencing studies on samples with existing genotype data. PMID:23934887

  11. Analyses and Comparison of Accuracy of Different Genotype Imputation Methods

    PubMed Central

    Pei, Yu-Fang; Li, Jian; Zhang, Lei; Papasian, Christopher J.; Deng, Hong-Wen

    2008-01-01

    The power of genetic association analyses is often compromised by missing genotypic data which contributes to lack of significant findings, e.g., in in silico replication studies. One solution is to impute untyped SNPs from typed flanking markers, based on known linkage disequilibrium (LD) relationships. Several imputation methods are available and their usefulness in association studies has been demonstrated, but factors affecting their relative performance in accuracy have not been systematically investigated. Therefore, we investigated and compared the performance of five popular genotype imputation methods, MACH, IMPUTE, fastPHASE, PLINK and Beagle, to assess and compare the effects of factors that affect imputation accuracy rates (ARs). Our results showed that a stronger LD and a lower MAF for an untyped marker produced better ARs for all the five methods. We also observed that a greater number of haplotypes in the reference sample resulted in higher ARs for MACH, IMPUTE, PLINK and Beagle, but had little influence on the ARs for fastPHASE. In general, MACH and IMPUTE produced similar results and these two methods consistently outperformed fastPHASE, PLINK and Beagle. Our study is helpful in guiding application of imputation methods in association analyses when genotype data are missing. PMID:18958166

  12. Comparison of INNO-LiPA HPV Genotyping v2 with PCR product subcloning and sequencing for identification of genital human papillomavirus genotypes in African women.

    PubMed

    Didelot-Rousseau, Marie-Noëlle; Courgnaud, Valérie; Nagot, Nicolas; Ouedraogo, Abdoulaye; Konate, Issouf; Mayaud, Philippe; Weiss, Helen; Van de Perre, Philippe; Segondy, Michel

    2006-08-01

    The performance characteristics of the INNO-LiPA Genotyping v2 test for human papillomavirus (HPV) identification were assessed by comparing results with those obtained by PCR product sequencing after subcloning, in genital samples from 20 highly sexually exposed African women. The INNO-LiPA HPV Genotyping v2 test identified more HPV types than subcloning/sequencing (56 versus 37, respectively). Overall, 86.5% (32/37) of the HPV types identified by subcloning/sequencing were identified by the INNO-LiPA HPV Genotyping v2 test, whereas 57.1% (32/56) of the HPV types identified by the INNO-LiPA HPV Genotyping v2 test were identified by subcloning/sequencing. Of the 20 clinical samples tested, 7 had identical types detected under both methods and a further 11 had more types detected under INNO-LiPA HPV Genotyping v2 than subcloning/sequencing. Of the remaining two samples, the same number of types were detected under both methods, but different types were detected. INNO-LiPA HPV Genotyping v2 test appears as a valid method for identifying HPV subtypes in women with multiple HPV infection. PMID:16675035

  13. 40 CFR Table Aa-2 to Subpart Aa of... - Kraft Lime Kiln and Calciner Emissions Factors for CH4 and N2O

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Kraft Lime Kiln and Calciner Emissions... Manufacturing Pt. 98, Subpt. AA, Table AA -2 Table AA-2 to Subpart AA of Part 98—Kraft Lime Kiln and Calciner Emissions Factors for CH4 and N2O Fuel Fossil fuel-based emissions factors (kg/mmBtu HHV) Kraft lime...

  14. Donor-Recipient Matching for KIR Genotypes Reduces Chronic GVHD and Missing Inhibitory KIR Ligands Protect against Relapse after Myeloablative, HLA Matched Hematopoietic Cell Transplantation

    PubMed Central

    Faridi, Rehan Mujeeb; Kemp, Taylor J.; Dharmani-Khan, Poonam; Lewis, Victor; Rajalingam, Raja; Berka, Noureddine; Storek, Jan; Masood Khan, Faisal

    2016-01-01

    Background Allogeneic hematopoietic cell transplantation (HCT) can be curative for many hematologic diseases. However, complications such as graft-versus-host disease (GVHD) and relapse of primary malignancy remain significant and are the leading causes of morbidity and mortality. Effects of killer Ig-like receptors (KIR)-influenced NK cells on HCT outcomes have been extensively pursued over the last decade. However, the relevance of the reported algorithms on HLA matched myeloablative HCT with rabbit antithymocyte globulin (ATG) is used for GVHD prophylaxis remains elusive. Here we examined the role of KIR and KIR-ligands of donor-recipient pairs in modifying the outcomes of ATG conditioned HLA matched sibling and unrelated donor HCT Methods and Findings The study cohort consisted of 281 HLA matched sibling and unrelated donor-recipient pairs of first allogeneic marrow or blood stem cell transplantation allocated into ‘discovery’ (135 pairs) and ‘validation’ (146 pairs) cohorts. High resolution HLA typing was obtained from the medical charts and KIR gene repertoires were obtained by a Luminex® based SSO method. All surviving patients were followed-up for a minimum of two years. KIR and HLA class I distributions of HCT pairs were stratified as per applicable definitions and were tested for their association with cause specific outcomes [acute GVHD grade II-IV (aGVHD), chronic GVHD needing systemic therapy (cGVHD) and relapse] using a multivariate competing risks regression model as well as with survival outcomes [relapse-free survival (RFS), cGVHD & relapse free survival (cGRFS) and overall survival (OS)] by multivariate Cox proportional hazards regression model. A significant association between KIR genotype mismatching (KIR-B/x donor into KIR-AA recipient or vice versa) and cGVHD was found in both discovery (p = 0.001; SHR = 2.78; 95%CI: 1.50–5.17) and validation cohorts (p = 0.005; SHR = 2.61; 95%CI: 1.33–5.11). High incidence of cGVHD associated

  15. Dengue 2 genotypes in the state of Oaxaca, Mexico.

    PubMed

    Cisneros, A; Díaz-Badillo, A; Cruz-Martínez, G; Tovar, R; Ramírez-Palacios, L R; Jiménez-Rojas, F; Beaty, B; Black, W C; de Lourdes Muñoz, M

    2006-01-01

    To genetically characterize dengue 2 (DEN-2) viruses in Oaxaca, Mexico, the C protein, and a portion of the prM protein genes of 8 isolates from the 2001 DEN epidemic were sequenced. The sequences were compared to those of prototype DEN-2 viruses from various parts of the world. Phylogenetic analysis suggested that the 2001 isolates of DEN-2 were of the American/Asian genotype and were most similar to the Jamaica and Venezuelan isolates MARA3, LARD1996 and LARD1910. Molecular analyses confirmed the origin of the isolates. This study indicates that DEN-2 strains of American/Asian genotype probably from Southeast Asian are circulating in Oaxaca. PMID:16096709

  16. High-throughput real-time PCR-based genotyping without DNA purification

    PubMed Central

    2012-01-01

    Background While improvements in genotyping technology have allowed for increased throughput and reduced time and expense, protocols remain hindered by the slow upstream steps of isolating, purifying, and normalizing DNA. Various methods exist for genotyping samples directly through blood, without having to purify the DNA first. These procedures were designed to be used on smaller throughput systems, however, and have not yet been tested for use on current high-throughput real-time (q)PCR based genotyping platforms. In this paper, a method of quantitative qPCR-based genotyping on blood without DNA purification was developed using a high-throughput qPCR platform. Findings The performances of either DNA purified from blood or the same blood samples without DNA purification were evaluated through qPCR-based genotyping. First, 60 different mutations prevalent in the Ashkenazi Jewish population were genotyped in 12 Ashkenazi Jewish individuals using the QuantStudio™12K Flex Real-Time PCR System. Genotyping directly from blood gave a call rate of 99.21%, and an accuracy of 100%, while the purified DNA gave a call rate of 92.49%, and an accuracy of 99.74%. Although no statistical difference was found for these parameters, an F test comparing the standard deviations of the wild type clusters for the two different methods indicated significantly less variation when genotyping directly from blood instead of after DNA purification. To further establish the ability to perform high-throughput qPCR based genotyping directly from blood, 96 individuals of Ashkenazi Jewish decent were genotyped for the same 60 mutations (5,760 genotypes in 5 hours) and resulted in a call rate of 98.38% and a diagnostic accuracy of 99.77%. Conclusion This study shows that accurate qPCR-based high-throughput genotyping can be performed without DNA purification. The direct use of blood may further expedite the entire genotyping process, reduce costs, and avoid tracking errors which can occur during

  17. The Complete Genome Phylogeny of Geographically Distinct Dengue Virus Serotype 2 Isolates (1944-2013) Supports Further Groupings within the Cosmopolitan Genotype

    PubMed Central

    Ali, Akhtar; Ali, Ijaz

    2015-01-01

    Dengue virus serotype 2 (DENV-2) isolates have been implicated in deadly outbreaks of dengue fever (DF) and dengue hemorrhagic fever (DHF) in several regions of the world. Phylogenetic analysis of DENV-2 isolates collected from particular countries has been performed using partial or individual genes but only a few studies have examined complete whole-genome sequences collected worldwide. Herein, 50 complete genome sequences of DENV-2 isolates, reported over the past 70 years from 19 different countries, were downloaded from GenBank. Phylogenetic analysis was conducted and evolutionary distances of the 50 DENV-2 isolates were determined using maximum likelihood (ML) trees or Bayesian phylogenetic analysis created from complete genome nucleotide (nt) and amino acid (aa) sequences or individual gene sequences. The results showed that all DENV-2 isolates fell into seven main groups containing five previously defined genotypes. A Cosmopolitan genotype showed further division into three groups (C-I, C-II, and C-III) with the C-I group containing two subgroups (C-IA and C-IB). Comparison of the aa sequences showed specific mutations among the various groups of DENV-2 isolates. A maximum number of aa mutations was observed in the NS5 gene, followed by the NS2A, NS3 and NS1 genes, while the smallest number of aa substitutions was recorded in the capsid gene, followed by the PrM/M, NS4A, and NS4B genes. Maximum evolutionary distances were found in the NS2A gene, followed by the NS4A and NS4B genes. Based on these results, we propose that genotyping of DENV-2 isolates in future studies should be performed on entire genome sequences in order to gain a complete understanding of the evolution of various isolates reported from different geographical locations around the world. PMID:26414178

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

    PubMed Central

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

    2007-01-01

    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 isolates belonged to

  19. Genotyping NAT2 with only two SNPs (rs1041983 and rs1801280) outperforms the tagging SNP rs1495741 and is equivalent to the conventional 7-SNP NAT2 genotype.

    PubMed

    Selinski, Silvia; Blaszkewicz, Meinolf; Lehmann, Marie-Louise; Ovsiannikov, Daniel; Moormann, Oliver; Guballa, Christoph; Kress, Alexander; Truss, Michael C; Gerullis, Holger; Otto, Thomas; Barski, Dimitri; Niegisch, Günter; Albers, Peter; Frees, Sebastian; Brenner, Walburgis; Thüroff, Joachim W; Angeli-Greaves, Miriam; Seidel, Thilo; Roth, Gerhard; Dietrich, Holger; Ebbinghaus, Rainer; Prager, Hans M; Bolt, Hermann M; Falkenstein, Michael; Zimmermann, Anna; Klein, Torsten; Reckwitz, Thomas; Roemer, Hermann C; Löhlein, Dietrich; Weistenhöfer, Wobbeke; Schöps, Wolfgang; Hassan Rizvi, Syed Adibul; Aslam, Muhammad; Bánfi, Gergely; Romics, Imre; Steffens, Michael; Ekici, Arif B; Winterpacht, Andreas; Ickstadt, Katja; Schwender, Holger; Hengstler, Jan G; Golka, Klaus

    2011-10-01

    Genotyping N-acetyltransferase 2 (NAT2) is of high relevance for individualized dosing of antituberculosis drugs and bladder cancer epidemiology. In this study we compared a recently published tagging single nucleotide polymorphism (SNP) (rs1495741) to the conventional 7-SNP genotype (G191A, C282T, T341C, C481T, G590A, A803G and G857A haplotype pairs) and systematically analysed if novel SNP combinations outperform the latter. For this purpose, we studied 3177 individuals by PCR and phenotyped 344 individuals by the caffeine test. Although the tagSNP and the 7-SNP genotype showed a high degree of correlation (R=0.933, P<0.0001) the 7-SNP genotype nevertheless outperformed the tagging SNP with respect to specificity (1.0 vs. 0.9444, P=0.0065). Considering all possible SNP combinations in a receiver operating characteristic analysis we identified a 2-SNP genotype (C282T, T341C) that outperformed the tagging SNP and was equivalent to the 7-SNP genotype. The 2-SNP genotype predicted the correct phenotype with a sensitivity of 0.8643 and a specificity of 1.0. In addition, it predicted the 7-SNP genotype with sensitivity and specificity of 0.9993 and 0.9880, respectively. The prediction of the NAT2 genotype by the 2-SNP genotype performed similar in populations of Caucasian, Venezuelan and Pakistani background. A 2-SNP genotype predicts NAT2 phenotypes with similar sensitivity and specificity as the conventional 7-SNP genotype. This procedure represents a facilitation in individualized dosing of NAT2 substrates without losing sensitivity or specificity. PMID:21750470

  20. Cloning and epitope mapping of Cry11Aa-binding sites in the Cry11Aa-receptor alkaline phosphatase from Aedes aegypti.

    PubMed

    Fernandez, Luisa E; Martinez-Anaya, Claudia; Lira, Erandi; Chen, Jianwu; Evans, Amy; Hernández-Martínez, Salvador; Lanz-Mendoza, Humberto; Bravo, Alejandra; Gill, Sarjeet S; Soberón, Mario

    2009-09-22

    Cry11Aa is the most active Bacillus thuringiensis israelensis toxin against Aedes aegypti larvae. Ae. aegypti alkaline phosphatase (ALP) was previously identified as a Cry11Aa receptor mediating toxicity. Here we report the cloning and functional characterization of this Ae. aegypti Cry11Aa-ALP receptor. Of three ALP's cDNA clones, the recombinant produced ALP1 isoform was shown to bind Cry11Aa and P1.BBMV peptide phage that specifically binds the midgut ALP-Cry11Aa receptor. An anti-ALP1 antibody inhibited binding to brush border membrane vesicles and toxicity of Cry11Aa in isolated cultured guts. Two ALP1 Cry11Aa binding regions (R59-G102 and N257-I296) were mapped by characterizing binding of Cry11Aa to nine recombinant overlapping peptides covering the ALP1 sequence. Finally, by using a peptide spot array of Cry11Aa domain III and site-directed mutagenesis, we show that the ALP1 R59-G102 region binds Cry11Aa through domain II loop alpha-8 while ALP1 N257-I296 interacts with Cry11Aa through domain III 561RVQSQNSGNN570 located in beta18-beta19. Our results show that Cry11Aa domain II and domain III are involved in the binding with two distinct binding sites in the ALP1 receptor. PMID:19697959

  1. Cloning and Epitope Mapping of Cry11Aa-Binding Sites in the Cry11Aa-Receptor Alkaline Phosphatase from Aedes aegypti†

    PubMed Central

    Fernandez, Luisa E.; Martinez-Anaya, Claudia; Lira, Erandi; Chen, Jianwu; Evans, Amy; Hernández-Martínez, Salvador; Lanz-Mendoza, Humberto; Bravo, Alejandra; Gill, Sarjeet S.; Soberón, Mario

    2013-01-01

    Cry11Aa is the most active Bacillus thuringiensis israelensis toxin against Aedes aegypti larvae. Ae. aegypti alkaline phosphatase (ALP) was previously identified as a Cry11Aa receptor mediating toxicity. Here we report the cloning and functional characterization of this Ae. aegypti Cry11Aa-ALP receptor. Of three ALP’s cDNA clones, the recombinant produced ALP1 isoform was shown to bind Cry11Aa and P1.BBMV peptide phage that specifically binds the midgut ALP-Cry11Aa receptor. An anti-ALP1 antibody inhibited binding to brush border membrane vesicles and toxicity of Cry11Aa in isolated cultured guts. Two ALP1 Cry11Aa binding regions (R59–G102 and N257–I296) were mapped by characterizing binding of Cry11Aa to nine recombinant overlapping peptides covering the ALP1 sequence. Finally, by using a peptide spot array of Cry11Aa domain III and site-directed mutagenesis, we show that the ALP1 R59–G102 region binds Cry11Aa through domain II loop α-8 while ALP1 N257–I296 interacts with Cry11Aa through domain III 561RVQSQNSGNN570 located in β18-β19. Our results show that Cry11Aa domain II and domain III are involved in the binding with two distinct binding sites in the ALP1 receptor. PMID:19697959

  2. Isolation and partial sequence of the A-protein gene of Thermus thermophilus cytochrome c/sub 1/aa/sub 3/

    SciTech Connect

    Fee, J.A.; Mather, M.W.; Springer, P.; Hensel, S.; Buse, G.

    1988-01-01

    Thermus thermophilus is a strictly aerobic eubacterium which grows optimally near 70/degree/C. Its respiratory system is very similar to that of eukaryotic mitochondria, and the organism has proven to be a particularly good source of stable, comparatively simple respiratory enzymes. There are at least two terminal oxidases: The recently discovered cytochrome ba/sub 3//sup 3/ and cytochrome c/sub 1/aa/sub 3//sup 2/. Cytochrome ba/sub 3/ is analog of aa/sub 3/ in which the heme A of cytochrome a is replaced with protoporphyrin IX (heme B) while its order redox components appear to be largely identical to those of the now classical mammalian cytochrome aa/sub 3/; it has only a single 35 kD protein subunit. Cytochrome c/sub 1/aa/sub 3/ consists of two polypeptides. The /approximately/33 kD C-protein covalently binds one heme C, while the /approximately/55 kD protein is thought to bind the four canonical redox centers of aa/sub 3/, two heme A, and two Cu. Toward our goal of unequivocally establishing the distribution of the metal centers in cytochrome c/sub 1/aa/sub 3/, we have isolated the structural gene of the A-protein. 20 refs., 4 figs.

  3. Carbon Dots and 9AA as a Binary Matrix for the Detection of Small Molecules by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Chen, Yongli; Gao, Dan; Bai, Hangrui; Liu, Hongxia; Lin, Shuo; Jiang, Yuyang

    2016-07-01

    Application of matrix-assisted laser-desorption/ionization mass spectrometry (MALDI MS) to analyze small molecules have some limitations, due to the inhomogeneous analyte/matrix co-crystallization and interference of matrix-related peaks in low m/z region. In this work, carbon dots (CDs) were for the first time applied as a binary matrix with 9-Aminoacridine (9AA) in MALDI MS for small molecules analysis. By 9AA/CDs assisted desorption/ionization (D/I) process, a wide range of small molecules, including nucleosides, amino acids, oligosaccharides, peptides, and anticancer drugs with a higher sensitivity were demonstrated in the positive ion mode. A detection limit down to 5 fmol was achieved for cytidine. 9AA/CDs matrix also exhibited excellent reproducibility compared with 9AA matrix. Moreover, by exploring the ionization mechanism of the matrix, the influence factors might be attributed to the four parts: (1) the strong UV absorption of 9AA/CDs due to their π-conjugated network; (2) the carboxyl groups modified on the CDs surface act as protonation sites for proton transfer in positive ion mode; (3) the thin layer crystal of 9AA/CDs could reach a high surface temperature more easily and lower transfer energy for LDI MS; (4) CDs could serve as a matrix additive to suppress 9AA ionization. Furthermore, this matrix was allowed for the analysis of glucose as well as nucleosides in human urine, and the level of cytidine was quantified with a linear range of 0.05-5 mM (R2 > 0.99). Therefore, the 9AA/CDs matrix was proven to be an effective MALDI matrix for the analysis of small molecules with improved sensitivity and reproducibility. This work provides an alternative solution for small molecules detection that can be further used in complex samples analysis.

  4. Carbon Dots and 9AA as a Binary Matrix for the Detection of Small Molecules by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry.

    PubMed

    Chen, Yongli; Gao, Dan; Bai, Hangrui; Liu, Hongxia; Lin, Shuo; Jiang, Yuyang

    2016-07-01

    Application of matrix-assisted laser-desorption/ionization mass spectrometry (MALDI MS) to analyze small molecules have some limitations, due to the inhomogeneous analyte/matrix co-crystallization and interference of matrix-related peaks in low m/z region. In this work, carbon dots (CDs) were for the first time applied as a binary matrix with 9-Aminoacridine (9AA) in MALDI MS for small molecules analysis. By 9AA/CDs assisted desorption/ionization (D/I) process, a wide range of small molecules, including nucleosides, amino acids, oligosaccharides, peptides, and anticancer drugs with a higher sensitivity were demonstrated in the positive ion mode. A detection limit down to 5 fmol was achieved for cytidine. 9AA/CDs matrix also exhibited excellent reproducibility compared with 9AA matrix. Moreover, by exploring the ionization mechanism of the matrix, the influence factors might be attributed to the four parts: (1) the strong UV absorption of 9AA/CDs due to their π-conjugated network; (2) the carboxyl groups modified on the CDs surface act as protonation sites for proton transfer in positive ion mode; (3) the thin layer crystal of 9AA/CDs could reach a high surface temperature more easily and lower transfer energy for LDI MS; (4) CDs could serve as a matrix additive to suppress 9AA ionization. Furthermore, this matrix was allowed for the analysis of glucose as well as nucleosides in human urine, and the level of cytidine was quantified with a linear range of 0.05-5 mM (R(2) > 0.99). Therefore, the 9AA/CDs matrix was proven to be an effective MALDI matrix for the analysis of small molecules with improved sensitivity and reproducibility. This work provides an alternative solution for small molecules detection that can be further used in complex samples analysis. Graphical Abstract ᅟ. PMID:27075876

  5. Carbon Dots and 9AA as a Binary Matrix for the Detection of Small Molecules by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Chen, Yongli; Gao, Dan; Bai, Hangrui; Liu, Hongxia; Lin, Shuo; Jiang, Yuyang

    2016-04-01

    Application of matrix-assisted laser-desorption/ionization mass spectrometry (MALDI MS) to analyze small molecules have some limitations, due to the inhomogeneous analyte/matrix co-crystallization and interference of matrix-related peaks in low m/z region. In this work, carbon dots (CDs) were for the first time applied as a binary matrix with 9-Aminoacridine (9AA) in MALDI MS for small molecules analysis. By 9AA/CDs assisted desorption/ionization (D/I) process, a wide range of small molecules, including nucleosides, amino acids, oligosaccharides, peptides, and anticancer drugs with a higher sensitivity were demonstrated in the positive ion mode. A detection limit down to 5 fmol was achieved for cytidine. 9AA/CDs matrix also exhibited excellent reproducibility compared with 9AA matrix. Moreover, by exploring the ionization mechanism of the matrix, the influence factors might be attributed to the four parts: (1) the strong UV absorption of 9AA/CDs due to their π-conjugated network; (2) the carboxyl groups modified on the CDs surface act as protonation sites for proton transfer in positive ion mode; (3) the thin layer crystal of 9AA/CDs could reach a high surface temperature more easily and lower transfer energy for LDI MS; (4) CDs could serve as a matrix additive to suppress 9AA ionization. Furthermore, this matrix was allowed for the analysis of glucose as well as nucleosides in human urine, and the level of cytidine was quantified with a linear range of 0.05-5 mM (R2 > 0.99). Therefore, the 9AA/CDs matrix was proven to be an effective MALDI matrix for the analysis of small molecules with improved sensitivity and reproducibility. This work provides an alternative solution for small molecules detection that can be further used in complex samples analysis.

  6. Amino acid substitutions in the hepatitis C virus core region of genotype 1b affect very early viral dynamics during treatment with telaprevir, peginterferon, and ribavirin.

    PubMed

    Akuta, Norio; Suzuki, Fumitaka; Hirakawa, Miharu; Kawamura, Yusuke; Yatsuji, Hiromi; Sezaki, Hitomi; Suzuki, Yoshiyuki; Hosaka, Tetsuya; Kobayashi, Masahiro; Kobayashi, Mariko; Saitoh, Satoshi; Arase, Yasuji; Ikeda, Kenji; Kumada, Hiromitsu

    2010-04-01

    Substitution of amino acid (aa) 70 and 91 in the core region of hepatitis C virus (HCV) genotype 1b can predict the response to pegylated interferon (PEG-IFN)/ribavirin combination therapy, but its impact on triple therapy of telaprevir/PEG-IFN/ribavirin is not clear. The aims of this study were to investigate the rate of HCV RNA loss following 12-week triple therapy, and determine the effect of aa substitutions on very early (within 48 hr) viral dynamics. Sixty-seven patients infected with HCV genotype 1b (HCV-1b) and high viral load who received 12-week triple therapy were studied. RNA loss could be achieved in 2%, 34%, 80%, 92%, 95%, 94%, and 90% of the patients after 1, 2, 4, 6, 8, 10, and 12 weeks of triple therapy, respectively. After 24-hr treatment, the proportion of patients with Arg70 and Leu91 substitutions with > or = 3.0 log fall in HCV RNA was significantly higher than those with < 3.0 log fall (P = 0.008). However, the aa substitution patterns in the core region did not influence the fall in HCV RNA after 48-hr treatment. Multivariate analysis identified substitutions of aa 70 and 91 (P = 0.014) and level of viremia at baseline (> or = 7.0 log IU/ml; P = 0.085) as independent parameters that determined the > or = 3.0 log fall in HCV RNA level after 24-hr triple therapy. It is concluded that 12-week triple therapy achieved high rates of loss of HCV RNA in Japanese patients infected with HCV-1b and high viral load, and that the aa substitution pattern in the core region seems to influence very early viral dynamics. PMID:20166188

  7. Genotypic distribution of hepatitis C virus in Thailand and Southeast Asia.

    PubMed

    Wasitthankasem, Rujipat; Vongpunsawad, Sompong; Siripon, Nipaporn; Suya, Chutima; Chulothok, Phrutsada; Chaiear, Kasemporn; Rujirojindakul, Pairaya; Kanjana, Sawan; Theamboonlers, Apiradee; Tangkijvanich, Pisit; Poovorawan, Yong

    2015-01-01

    The majority of hepatitis C virus (HCV) infection results in chronic infection, which can lead to liver cirrhosis and hepatocellular carcinoma. Global burden of hepatitis C virus (HCV) is estimated at 150 million individuals, or 3% of the world's population. The distribution of the seven major genotypes of HCV varies with geographical regions. Since Asia has a high incidence of HCV, we assessed the distribution of HCV genotypes in Thailand and Southeast Asia. From 588 HCV-positive samples obtained throughout Thailand, we characterized the HCV 5' untranslated region, Core, and NS5B regions by nested PCR. Nucleotide sequences obtained from both the Core and NS5B of these isolates were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. Results were compared to the epidemiological data of HCV genotypes identified within Southeast Asian. Among the HCV subtypes characterized in the Thai samples, subtype 3a was the most predominant (36.4%), followed by 1a (19.9%), 1b (12.6%), 3b (9.7%) and 2a (0.5%). While genotype 1 was prevalent throughout Thailand (27-36%), genotype 3 was more common in the south. Genotype 6 (20.9%) constituted subtype 6f (7.8%), 6n (7.7%), 6i (3.4%), 6j and 6m (0.7% each), 6c (0.3%), 6v and 6xa (0.2% each) and its prevalence was significantly lower in southern Thailand compared to the north and northeast (p = 0.027 and p = 0.030, respectively). Within Southeast Asia, high prevalence of genotype 6 occurred in northern countries such as Myanmar, Laos, and Vietnam, while genotype 3 was prevalent in Thailand and Malaysia. Island nations of Singapore, Indonesia and Philippines demonstrated prevalence of genotype 1. This study further provides regional HCV genotype information that may be useful in fostering sound public health policy and tracking future patterns of HCV spread. PMID:25962112

  8. [Determination of hepatitis B virus genotypes by DNA sequence analysis in patients from Ankara, Turkey].

    PubMed

    Külah, Canan; Cirak, Meltem Yalinay

    2010-04-01

    Hepatitis B virus (HBV) genotypes vary depending on the geographical region. The HBV genotype determined in Turkey has been genotype D which is found as the homogenously disseminated single genotype. The aim of this study was to determine HBV genotypes in a group of HBV infected patients who were admitted to a university hospital in Ankara, Turkey. Serum samples from HBsAg positive and anti-HBs negative 84 (52 male, 32 female) patients with HBV infection were included into the study. Anti-HBc was positive in 95.2%, HBeAg was positive in 47.6% and anti-HBe was positive in 11.9% of the patients. Mean HBV-DNA levels of the patients were 5.7 x 10(7) +/- 4.6 x 10(7) IU/ml; mean ALT levels were 131 +/- 171 IU/ml and mean AST levels were 98 +/- 170 IU/ml. HBV-DNA was extracted from serum by the phenol-chloroform method and PCR was performed to amplify the S gene region of HBV-DNA. Cycle sequencing of PCR products was performed by a commercial "Cy5/Cy5.5 Dye Primer Cycle Sequencing Kit" (Visible Genetics, Canada) based on dideoxy chain termination method. The sequences were read and analyzed in an automated fluorescence-based DNA-sequencing system (Long-Read Tower System, Visible Genetics, Canada). The nucleotide sequences of the patient samples were compared with the previously reported sequences in gene bank for each genotype. According to the comparative analysis of S-sequences of all patient samples with the published sequences of the genotypes in gene bank, all of the 84 hepatitis B strains (100%) were shown to be related to D genotypic group, subtype ayw. A phylogenetic analysis was performed and phylogenetic trees were constructed using programs in the PHYLIP phylogeny inference package. The patient samples clustered within the genotypic group D. According to these results, the main HBV genotype in our patients was genotype D in accordance with the previous molecular epidemiologic information on HBV in this geographic area. HBV genotype determination may help to

  9. Genotypic Distribution of Hepatitis C Virus in Thailand and Southeast Asia

    PubMed Central

    Wasitthankasem, Rujipat; Vongpunsawad, Sompong; Siripon, Nipaporn; Suya, Chutima; Chulothok, Phrutsada; Chaiear, Kasemporn; Rujirojindakul, Pairaya; Kanjana, Sawan; Theamboonlers, Apiradee; Tangkijvanich, Pisit; Poovorawan, Yong

    2015-01-01

    The majority of hepatitis C virus (HCV) infection results in chronic infection, which can lead to liver cirrhosis and hepatocellular carcinoma. Global burden of hepatitis C virus (HCV) is estimated at 150 million individuals, or 3% of the world’s population. The distribution of the seven major genotypes of HCV varies with geographical regions. Since Asia has a high incidence of HCV, we assessed the distribution of HCV genotypes in Thailand and Southeast Asia. From 588 HCV-positive samples obtained throughout Thailand, we characterized the HCV 5’ untranslated region, Core, and NS5B regions by nested PCR. Nucleotide sequences obtained from both the Core and NS5B of these isolates were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. Results were compared to the epidemiological data of HCV genotypes identified within Southeast Asian. Among the HCV subtypes characterized in the Thai samples, subtype 3a was the most predominant (36.4%), followed by 1a (19.9%), 1b (12.6%), 3b (9.7%) and 2a (0.5%). While genotype 1 was prevalent throughout Thailand (27–36%), genotype 3 was more common in the south. Genotype 6 (20.9%) constituted subtype 6f (7.8%), 6n (7.7%), 6i (3.4%), 6j and 6m (0.7% each), 6c (0.3%), 6v and 6xa (0.2% each) and its prevalence was significantly lower in southern Thailand compared to the north and northeast (p = 0.027 and p = 0.030, respectively). Within Southeast Asia, high prevalence of genotype 6 occurred in northern countries such as Myanmar, Laos, and Vietnam, while genotype 3 was prevalent in Thailand and Malaysia. Island nations of Singapore, Indonesia and Philippines demonstrated prevalence of genotype 1. This study further provides regional HCV genotype information that may be useful in fostering sound public health policy and tracking future patterns of HCV spread. PMID:25962112

  10. Genotypic Diversity of Escherichia coli in the Water and Soil of Tropical Watersheds in Hawaii ▿

    PubMed Central

    Goto, Dustin K.; Yan, Tao

    2011-01-01

    High levels of Escherichia coli were frequently detected in tropical soils in Hawaii, which present important environmental sources of E. coli to water bodies. This study systematically examined E. coli isolates from water and soil of several watersheds in Hawaii and observed high overall genotypic diversity (35.5% unique genotypes). In the Manoa watershed, fewer than 9.3% of the observed E. coli genotypes in water and 6.6% in soil were shared between different sampling sites, suggesting the lack of dominant fecal sources in the watershed. High temporal variability of E. coli genotypes in soil was also observed, which suggests a dynamic E. coli population corresponding with the frequently observed high concentrations in tropical soils. When E. coli genotypes detected from the same sampling events were compared, limited sharing between the soil and water samples was observed in the majority of comparisons (73.5%). However, several comparisons reported up to 33.3% overlap of E. coli genotypes between soil and water, illustrating the potential for soil-water interactions under favorable environmental conditions. In addition, genotype accumulation curves for E. coli from water and soil indicated that the sampling efforts in the Manoa watershed could not exhaust the overall genotypic diversity. Comparisons of E. coli genotypes from other watersheds on Oahu, Hawaii, identified no apparent grouping according to sampling locations. The results of the present study demonstrate the complexity of using E. coli as a fecal indicator bacterium in tropical watersheds and highlight the need to differentiate environmental sources of E. coli from fecal sources in water quality monitoring. PMID:21515724

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

    PubMed

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

    2015-10-01

    Rotavirus (RV) is one of the most important viral etiologic agents of acute gastroenteritis (AGE) in children. Although effective RV vaccines (RVVs) are now used worldwide, novel genotypes and outbreaks resulting from rare genotype combinations have emerged. This study documented RV genotypes in a Korean population of children with AGE 5 yr after the introduction of RVV and assessed potential genotype differences based on vaccination status or vaccine type. Children less than 5-yr-old diagnosed with AGE between October 2012 and September 2013 admitted to 9 medical institutions from 8 provinces in Korea were prospectively enrolled. Stool samples were tested for RV by enzyme immunoassay and genotyped by multiplex reverse-transcription polymerase chain reaction. In 346 patients, 114 (32.9%) were RV-positive. Among them, 87 (76.3%) patients were infected with RV alone. Eighty-six of 114 RV-positive stool samples were successfully genotyped, and their combinations of genotypes were G1P[8] (36, 41.9%), G2P[4] (12, 14.0%), and G3P[8] (6, 7.0%). RV was detected in 27.8% of patients in the vaccinated group and 39.8% in the unvaccinated group (P=0.035). Vaccination history was available for 67 of 86 cases with successfully genotyped RV-positive stool samples; RotaTeq (20, 29.9%), Rotarix (7, 10.4%), unvaccinated (40, 59.7%). The incidence of RV AGE is lower in the RV-vaccinated group compared to the unvaccinated group with no evidence of substitution with unusual genotype combinations. PMID:26425045

  12. Evolution and mutations of hepatitis B virus quasispecies in genotype B and C during vertical transmission.

    PubMed

    Wu, Quanxin; Xu, Cheng; Li, Junnan; Li, Li; Yan, Guohua; Yue, Liangliang; Zeng, Yi; Huang, Hongfei; Deng, Guohong; Wang, Yuming

    2016-06-01

    Evolution patterns of HBV QS between genotype B and C during vertical transmission are not well understood. In this study, we enrolled 10 HBV infected mother-infant pairs (four pairs with genotype B, four pairs with genotype C, and two with co-infection) without anti-viral therapy. Serum HBV DNA of mothers and infants were sequenced, HBV QS complexity and diversity were analyzed, polymorphisms and mutation sites were recorded, and phylogenetic trees were performed. Our result showed that the QS complexities in P (amino acid), C/PreC (amino acid), and PreS1 (nucleotide) gene were significantly higher in mothers than in infants in pairs with genotype C (P < 0.05), however, full-length and other genes showed non-significant differences (P > 0.05). Unlike genotype C, QS complexity of P gene (nucleotide) was significantly higher in infants than in mothers (P < 0.05) in pairs with genotype B, similarly, QS complexities of full-length and other genes (except Pre S2) were also higher in infants than in mothers but without significant differences (P > 0.05). QS diversities of full-length and most genes in genotype B were comparable between mothers and their infants (P > 0.05), in pairs with genotype C, dS of P, X, RT genes, genetic distance of Pre S1 gene (amino acid) and dN of Pre S1 gene were significant higher in mothers than in infants (P < 0.05). Several HBV mutations correlated with immune escape, e antigen loss and drug resistance were observed in infants. The results indicated that differences of HBV QS evolution patterns between genotype B and C during vertical transmission might contribute to distinct prognosis. J. Med. Virol. 88:1018-1026, 2016. © 2015 Wiley Periodicals, Inc. PMID:26531675

  13. Using NS5B Sequencing for Hepatitis C Virus Genotyping Reveals Discordances with Commercial Platforms

    PubMed Central

    Chueca, Natalia; Rivadulla, Isidro; Lovatti, Rubén; Reina, Gabriel; Blanco, Ana; Fernandez-Caballero, Jose Angel; Cardeñoso, Laura; Rodriguez-Granjer, Javier; Fernandez-Alonso, Miriam; Aguilera, Antonio; Alvarez, Marta

    2016-01-01

    We aimed to evaluate the correct assignment of HCV genotypes by three commercial methods—Trugene HCV genotyping kit (Siemens), VERSANT HCV Genotype 2.0 assay (Siemens), and Real-Time HCV genotype II (Abbott)—compared to NS5B sequencing. We studied 327 clinical samples that carried representative HCV genotypes of the most frequent geno/subtypes in Spain. After commercial genotyping, the sequencing of a 367 bp fragment in the NS5B gene was used to assign genotypes. Major discrepancies were defined, e.g. differences in the assigned genotype by one of the three methods and NS5B sequencing, including misclassification of subtypes 1a and 1b. Minor discrepancies were considered when differences at subtype levels, other than 1a and 1b, were observed. The overall discordance with the reference method was 34% for Trugene and 15% for VERSANT HCV2.0. The Abbott assay correctly identified all 1a and 1b subtypes, but did not subtype all the 2, 3, 4 and 5 (34%) genotypes. Major discordances were found in 16% of cases for Trugene HCV, and the majority were 1b- to 1a-related discordances; major discordances were found for VERSANT HCV 2.0 in 6% of cases, which were all but one 1b to 1a cases. These results indicated that the Trugene assay especially, and to a lesser extent, Versant HCV 2.0, can fail to differentiate HCV subtypes 1a and 1b, and lead to critical errors in clinical practice for correctly using directly acting antiviral agents. PMID:27097040

  14. Using NS5B Sequencing for Hepatitis C Virus Genotyping Reveals Discordances with Commercial Platforms.

    PubMed

    Chueca, Natalia; Rivadulla, Isidro; Lovatti, Rubén; Reina, Gabriel; Blanco, Ana; Fernandez-Caballero, Jose Angel; Cardeñoso, Laura; Rodriguez-Granjer, Javier; Fernandez-Alonso, Miriam; Aguilera, Antonio; Alvarez, Marta; Galán, Juan Carlos; García, Federico

    2016-01-01

    We aimed to evaluate the correct assignment of HCV genotypes by three commercial methods-Trugene HCV genotyping kit (Siemens), VERSANT HCV Genotype 2.0 assay (Siemens), and Real-Time HCV genotype II (Abbott)-compared to NS5B sequencing. We studied 327 clinical samples that carried representative HCV genotypes of the most frequent geno/subtypes in Spain. After commercial genotyping, the sequencing of a 367 bp fragment in the NS5B gene was used to assign genotypes. Major discrepancies were defined, e.g. differences in the assigned genotype by one of the three methods and NS5B sequencing, including misclassification of subtypes 1a and 1b. Minor discrepancies were considered when differences at subtype levels, other than 1a and 1b, were observed. The overall discordance with the reference method was 34% for Trugene and 15% for VERSANT HCV2.0. The Abbott assay correctly identified all 1a and 1b subtypes, but did not subtype all the 2, 3, 4 and 5 (34%) genotypes. Major discordances were found in 16% of cases for Trugene HCV, and the majority were 1b- to 1a-related discordances; major discordances were found for VERSANT HCV 2.0 in 6% of cases, which were all but one 1b to 1a cases. These results indicated that the Trugene assay especially, and to a lesser extent, Versant HCV 2.0, can fail to differentiate HCV subtypes 1a and 1b, and lead to critical errors in clinical practice for correctly using directly acting antiviral agents. PMID:27097040

  15. Temporal Dynamics and Decay of Putatively Allochthonous and Autochthonous Viral Genotypes in Contrasting Freshwater Lakes

    PubMed Central

    Barbosa, Jorge G.; Brown, Julia M.; Donelan, Ryan P.; Eaglesham, James B.; Eggleston, Erin M.; LaBarre, Brenna A.

    2012-01-01

    Aquatic viruses play important roles in the biogeochemistry and ecology of lacustrine ecosystems; however, their composition, dynamics, and interactions with viruses of terrestrial origin are less extensively studied. We used a viral shotgun metagenomic approach to elucidate candidate autochthonous (i.e., produced within the lake) and allochthonous (i.e., washed in from other habitats) viral genotypes for a comparative study of their dynamics in lake waters. Based on shotgun metagenomes prepared from catchment soil and freshwater samples from two contrasting lakes (Cayuga Lake and Fayetteville Green Lake), we selected two putatively autochthonous viral genotypes (phycodnaviruses likely infecting algae and cyanomyoviruses likely infecting picocyanobacteria) and two putatively allochthonous viral genotypes (geminiviruses likely infecting terrestrial plants and circoviruses infecting unknown hosts but common in soil libraries) for analysis by genotype-specific quantitative PCR (TaqMan) applied to DNAs from viruses in the viral size fraction of lake plankton, i.e., 0.2 μm > virus > 0.02 μm. The abundance of autochthonous genotypes largely reflected expected host abundance, while the abundance of allochthonous genotypes corresponded with rainfall and storm events in the respective catchments, suggesting that viruses with these genotypes may have been transported to the lake in runoff. The decay rates of allochthonous and autochthonous genotypes, assessed in incubations where all potential hosts were killed, were generally lower (0.13 to 1.50% h−1) than those reported for marine virioplankton but similar to those for freshwater virioplankton. Both allochthonous and autochthonous viral genotypes were detected at higher concentrations in subsurface sediments than at the water-sediment interface. Our data indicate that putatively allochthonous viruses are present in lake plankton and sediments, where their temporal dynamics reflect active transport to the lake during

  16. Role of cytochrome P450 genotype in the steps toward personalized drug therapy

    PubMed Central

    Cavallari, Larisa H; Jeong, Hyunyoung; Bress, Adam

    2011-01-01

    Genetic polymorphism for cytochrome 450 (P450) enzymes leads to interindividual variability in the plasma concentrations of many drugs. In some cases, P450 genotype results in decreased enzyme activity and an increased risk for adverse drug effects. For example, individuals with the CYP2D6 loss-of-function genotype are at increased risk for ventricular arrhythmia if treated with usual does of thioridazine. In other cases, P450 genotype may influence the dose of a drug required to achieve a desired effect. This is the case with warfarin, with lower doses often necessary in carriers of a variant CYP2C9*2 or *3 allele to avoid supratherapeutic anticoagulation. When a prodrug, such as clopidogrel or codeine, must undergo hepatic biotransformation to its active form, a loss-of-function P450 genotype leads to reduced concentrations of the active drug and decreased drug efficacy. In contrast, patients with multiple CYP2D6 gene copies are at risk for opioid-related toxicity if treated with usual doses of codeine-containing analgesics. At least 25 drugs contain information in their US Food and Drug Administration-approved labeling regarding P450 genotype. The CYP2C9, CYP2C19, and CYP2D6 genes are the P450 genes most often cited. To date, integration of P450 genetic information into clinical decision making is limited. However, some institutions are beginning to embrace routine P450 genotyping to assist in the treatment of their patients. Genotyping for P450 variants may carry less risk for discrimination compared with genotyping for disease-associated variants. As such, P450 genotyping is likely to lead the way in the clinical implementation of pharmacogenomics. This review discusses variability in the CYP2C9, CYP2C19, and CYP2D6 genes and the implications of this for drug efficacy and safety. PMID:23226058

  17. Hepatitis B virus genotype A: design of reference sequences for sub-genotypes.

    PubMed

    Cai, Qun; Zhu, Huilan; Zhang, Yafei; Li, Xu; Zhang, Zhenhua

    2016-06-01

    Genotype A of hepatitis B virus (HBV/A) is widespread and is currently divided into six sub-genotypes. Suitable reference sequences for different sub-genotypes can facilitate research on HBV/A. However, the current reference sequences for this virus are insufficient. In the present work, we retrieved 442 full-length HBV/A genomic sequences from the GenBank database and classified them into sub-genotypes by phylogenetic analysis. By the maximum likelihood method using the MEGA6.0 software, we established the reference sequences for different HBV/A sub-genotypes. Our analyses demonstrated that these reference sequences clustered phylogenetically with known strains, indicating that the reference sequences we established indeed belonged to the right sub-genotypes. HBV/A subtype sequences were selected by geographic origins and grouped as sub-genotypes including A1-South Africa, A2-Europe, A3-Cameroon, and A5-Haiti. Reference sequences of sub-genotypes A1, A2, A3, and A5 were constructed and deposited into GenBank (KP234050-KP234053). By applying phylogenetic analyses, we further determined the time to most recent common ancestor of HBV/A lineages. In conclusion, these newly established reference sequences can provide suitable reference standards for studies on the molecular biology and virology of HBV genotype A. PMID:27002608

  18. Inferring haplotypes from genotypes on a pedigree with mutations, genotyping errors and missing alleles.

    PubMed

    Wang, Wei-Bung; Jiang, Tao

    2011-04-01

    Inferring the haplotypes of the members of a pedigree from their genotypes has been extensively studied. However, most studies do not consider genotyping errors and de novo mutations. In this paper, we study how to infer haplotypes from genotype data that may contain genotyping errors, de novo mutations, and missing alleles. We assume that there are no recombinants in the genotype data, which is usually true for tightly linked markers. We introduce a combinatorial optimization problem, called haplotype configuration with mutations and errors (HCME), which calls for haplotype configurations consistent with the given genotypes that incur no recombinants and require the minimum number of mutations and errors. HCME is NP-hard. To solve the problem, we propose a heuristic algorithm, the core of which is an integer linear program (ILP) using the system of linear equations over Galois field GF(2). Our algorithm can detect and locate genotyping errors that cannot be detected by simply checking the Mendelian law of inheritance. The algorithm also offers error correction in genotypes/haplotypes rather than just detecting inconsistencies and deleting the involved loci. Our experimental results show that the algorithm can infer haplotypes with a very high accuracy and recover 65%-94% of genotyping errors depending on the pedigree topology. PMID:21523936

  19. Observations of AA Tau requested to schedule XMM-Newton

    NASA Astrophysics Data System (ADS)

    Waagen, Elizabeth O.

    2013-08-01

    Dr. Hans Moritz Guenther (Harvard-Smithsonian Center for Astrophysics) has requested nightly observations of the classical T Tauri star AA Tau in order to schedule x-ray observations with XMM-Newton that have been planned for between 2013 August 15 and September 15. The purpose of the AAVSO observations is to determine whether AA Tau is at a suitable magnitude for the satellite observations. Taurus is difficult to observe during this time period but that is exactly why AAVSO assistance is needed! AA Tau is a morning object, and also, many of the professional ground-based telescopes are offline because of the US southwest monsoon season. Since it is critical to know the brightness of AA Tau, AAVSO observations will be truly essential. Nightly visual and snapshot (not more than once per night) observations beginning now and continuing through September 20 are needed. Coverage beginning ahead of the XMM window is requested because there is a one- to two-week lead time for the target to be inserted into the telescope schedule. Continuing the nightly observations a few days beyond the end of the XMM window will give better optical context for the x-ray data. AA Tau ranges between ~12.8V and ~16.1V; since December 2011 or earlier it has been at ~14.5V. The most recent observation in the AAVSO International Database shows it at 14.779V on 2013 Feb 5 (J. Roe, Bourbon, MO). Dr. Guenther writes, "AA Tau is surrounded by a thick accretion disk which is seen nearly edge-on. For decades the light curve of AA Tau showed regular eclipsing events when the accretion funnel rotated through the line of sight. However, earlier this year J. Bouvier and his group found that this behavior changed dramatically: AA Tau now seems to be deeply absorbed all the time (V band 14.5 mag). In collaboration with this group we will perform X-ray observations of AA Tau with the XMM-Newton satellite." Finder charts with sequence may be created using the AAVSO Variable Star Plo! tter (http

  20. Changes in whole grain polyphenols and antioxidant activity of six sorghum genotypes under different irrigation treatments.

    PubMed

    Wu, Gangcheng; Johnson, Stuart K; Bornman, Janet F; Bennett, Sarita J; Fang, Zhongxiang

    2017-01-01

    Sorghum grain containing elevated polyphenolic antioxidant content may provide foods with benefits to human health. A study was undertaken to determine the potential role of irrigation on the content of polyphenols and antioxidant levels in sorghum grain. Bound, free and total polyphenols were investigated in six diverse sorghum genotypes grown under either full irrigation or a deficit irrigation regime. Results showed genotype, irrigation and their interaction had a significant effect on polyphenols and antioxidant activity (P⩽0.05). The deficit irrigation treatment significantly increased polyphenol content and antioxidant activity compared to the full irrigation treatment. Of the six genotypes Shawaya black short 1 and IS1311C (brown) showed the highest polyphenols levels and antioxidant activity. Therefore, both irrigation treatments and genotype need to be considered by sorghum breeders and farmers during sorghum production to produce grain with the required levels of polyphenolics and antioxidant activity for targeted end-use. PMID:27507466

  1. New Lyssavirus Genotype from the Lesser Mouse-eared Bat (Myotis blythi), Kyrghyzstan

    PubMed Central

    Kuzmin, Ivan V.; Kameoka, Yosuke; Botvinkin, Alexandr D.

    2003-01-01

    The Aravan virus was isolated from a Lesser Mouse-eared Bat (Myotis blythi) in the Osh region of Kyrghyzstan, central Asia, in 1991. We determined the complete sequence of the nucleoprotein (N) gene and compared it with those of 26 representative lyssaviruses obtained from databases. The Aravan virus was distinguished from seven distinct genotypes on the basis of nucleotide and amino acid identity. Phylogenetic analysis based on both nucleotide and amino acid sequences showed that the Aravan virus was more closely related to genotypes 4, 5, and—to a lesser extent—6, which circulates among insectivorus bats in Europe and Africa. The Aravan virus does not belong to any of the seven known genotypes of lyssaviruses, namely, rabies, Lagos bat, Mokola, and Duvenhage viruses and European bat lyssavirus 1, European bat lyssavirus 2, and Australian bat lyssavirus. Based on these data, we propose a new genotype for the Lyssavirus genus. PMID:12643828

  2. The Pasadena Recommendations: Five Years After AAS Endorsement

    NASA Astrophysics Data System (ADS)

    Knezek, Patricia; Frattare, L.; Ulvestad, J.

    2010-01-01

    It has been five years since the AAS Council unanimously endorsed the document, known as "Equity Now: The Pasadena Recommendations for Gender Equality in Astronomy," in January 2005. This document was the main product of the conference entitled "Women in Astronomy II: Ten Years After” (WIA II), held in June 2003 in Pasadena, CA. Participants of that 2003 meeting assessed the progress for women in science, offering insights into causes of the slower advancement of women, and discussed strategies to accelerate the achievement of equality. These insights and strategies were then incorporated into the "Pasadena Recommendations" by the CSWA. It was subsequently released to the entire AAS community for review and comments prior to its endorsement by the AAS. We will discuss the Recommendations and their impact since the endorsement by the AAS, including the process that is in place for organizations and departments to formally endorse the Pasadena Recommendations, thus making an organizational commitment to their implementation (see http://www.aas.org/cswa/pasadena_endorse.html).

  3. Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling

    PubMed Central

    2014-01-01

    Background Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having differential response to low-N stress. Results Illumina RNA-sequencing detected several common differentially expressed genes (DEGs) between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk). In sensitive genotypes, N-stress increased the abundance of DEG transcripts associated with stress responses including oxidative stress and stimuli were abundant. The tolerant genotypes adapt to N deficiency by producing greater root mass for efficient uptake of nutrients. In tolerant genotypes, higher abundance of transcripts related to high affinity nitrate transporters (NRT2.2, NRT2.3, NRT2.5, and NRT2.6) and lysine histidine transporter 1 (LHT1), may suggest an improved uptake efficiency of inorganic and organic forms of nitrogen. Higher abundance of SEC14 cytosolic factor family protein transcript in tolerant genotypes could lead to increased membrane stability and tolerance to N-stress. Conclusions Comparison of transcriptomes between N-stress tolerant and sensitive genotypes revealed several common DEG transcripts. Some of these DEGs were evaluated further by comparing the transcriptomes of genotypes grown under full N. The DEG transcripts showed higher expression in tolerant genotypes could be used for transgenic over-expression in sensitive genotypes of sorghum and related crops for increased tolerance to N-stress, which results in increased nitrogen use efficiency for sustainable

  4. Outcomes From AAS Hack Day at the 227th AAS Meeting

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    Editors Note:This is a final post from the 227th AAS Meeting in Kissimmee, FL. This special summary of AAS Hack Day, a meeting of AAS members to collaboratively work on various small projects, was written by Meredith Rawls (@Merrdiff) and was originally posted on astrobites.com.As the 227thAmerican Astronomical Society meeting drew to a close (see highlights from Day 1, Day 2, Day 3, and Day 4), a group of at least 50 attendees spent Day 4working on small projects fondly called hacks. Thanks to sponsorship from LSST and Northrup Grumman, the industrious hackers werewell-caffeinated and fed so we could devote time and energy toworking in groups on one-day projects.TheHack Day beganat 10am with pitches. Anybody with a project idea was welcome to briefly speak and try to convince others to work with them. Only someideas panned out, but the enthusiasm was palpable. Its not every day you get a full room of astronomers and affiliates eager to spend hours working on fun and useful projects to benefit the community.#hackAAS is getting underway! #aas227 pic.twitter.com/yX7jlOnSCK James R A Davenport (@jradavenport) January 8, 2016Here is a rundown of what we accomplished. Pretty impressive for a single day! Many thanks to fellow astrobiter Erika Nesvold (now at Carnegie DTM; @erikanesvold) whose hack was live-documenting all the other hacks. Her tweets as @astrobites appeared with the #hackaas hashtag, and her notes made this recap post infinitely easier to write.Interested in joining the fun? Sign up for Hack Day at the 2017 JanuaryAAS meeting (its free with meeting registration), and consider applying for the .Astronomy conference this summer.Towards Optimal Session Scheduling:Adrian Price-Whelan (Columbia), David Hogg (NYU), and Scott Idem (AAS) began writing a program to take all submitted abstracts to a conference like AAS and sort them using keywords to avoid scheduling similar talks in parallel sessions. Its impossible to make everyone happy, but minimizing conflicts

  5. A new genotype of Cryptosporidium from giant panda (Ailuropoda melanoleuca) in China.

    PubMed

    Liu, Xuehan; He, Tingmei; Zhong, Zhijun; Zhang, Hemin; Wang, Rongjun; Dong, Haiju; Wang, Chengdong; Li, Desheng; Deng, Jiabo; Peng, Guangneng; Zhang, Longxian

    2013-10-01

    Fifty-seven fecal samples were collected from giant pandas (Ailuropoda melanoleuca) in the China Conservation and Research Centre for the Giant Panda (CCRCGP) in Sichuan and examined for Cryptosporidium oocysts by Sheather's sugar flotation technique. An 18-year-old male giant panda was Cryptosporidium positive, with oocysts of an average size of 4.60×3.99 μm (n=50). The isolate was genetically analyzed using the partial 18S rRNA, 70 kDa heat shock protein (HSP70), Cryptosporidium oocyst wall protein (COWP) and actin genes. Multi-locus genetic characterization indicated that the present isolate was different from known Cryptosporidium species and genotypes. The closest relative was the Cryptosporidium bear genotype, with 11, 10, and 6 nucleotide differences in the 18S rRNA, HSP70, and actin genes, respectively. Significant differences were also observed in the COWP gene compared to Cryptosporidium mongoose genotype. The homology to the bear genotype at the 18S rRNA locus was 98.6%, which is comparable to that between Cryptosporidium parvum and Cryptosporidium hominis (99.2%), or between Cryptosporidium muris and Cryptosporidium andersoni (99.4%). Therefore, the Cryptosporidium in giant pandas in this study is considered as a new genotype: the Cryptosporidium giant panda genotype. PMID:23810821

  6. Comparison of Leaf Proteomes of Cassava (Manihot esculenta Crantz) Cultivar NZ199 Diploid and Autotetraploid Genotypes

    PubMed Central

    An, Feifei; Fan, Jie; Li, Jun; Li, Qing X.; Li, Kaimian; Zhu, Wenli; Wen, Feng; Carvalho, Luiz J. C. B.; Chen, Songbi

    2014-01-01

    Cassava polyploid breeding has drastically improved our knowledge on increasing root yield and its significant tolerance to stresses. In polyploid cassava plants, increases in DNA content highly affect cell volumes and anatomical structures. However, the mechanism of this effect is poorly understood. The purpose of the present study was to compare and validate the changes between cassava cultivar NZ199 diploid and autotetraploid at proteomic levels. The results showed that leaf proteome of cassava cultivar NZ199 diploid was clearly differentiated from its autotetraploid genotype using 2-DE combined MS technique. Sixty-five differential protein spots were seen in 2-DE image of autotetraploid genotype in comparison with that of diploid. Fifty-two proteins were identified by MALDI-TOF-MS/MS, of which 47 were up-regulated and 5 were down-regulated in autotetraploid genotype compared with diploid genotype. The classified functions of 32 up-regulated proteins were associated with photosynthesis, defense system, hydrocyanic acid (HCN) metabolism, protein biosynthesis, chaperones, amino acid metabolism and signal transduction. The remarkable variation in photosynthetic activity, HCN content and resistance to salt stress between diploid and autotetraploid genotypes is closely linked with expression levels of proteomic profiles. The analysis of protein interaction networks indicated there are direct interactions between the 15 up-regulation proteins involved in the pathways described above. This work provides an insight into understanding the protein regulation mechanism of cassava polyploid genotype, and gives a clue to improve cassava polyploidy breeding in increasing photosynthesis and resistance efficiencies. PMID:24727655

  7. Comparison of leaf proteomes of cassava (Manihot esculenta Crantz) cultivar NZ199 diploid and autotetraploid genotypes.

    PubMed

    An, Feifei; Fan, Jie; Li, Jun; Li, Qing X; Li, Kaimian; Zhu, Wenli; Wen, Feng; Carvalho, Luiz J C B; Chen, Songbi

    2014-01-01

    Cassava polyploid breeding has drastically improved our knowledge on increasing root yield and its significant tolerance to stresses. In polyploid cassava plants, increases in DNA content highly affect cell volumes and anatomical structures. However, the mechanism of this effect is poorly understood. The purpose of the present study was to compare and validate the changes between cassava cultivar NZ199 diploid and autotetraploid at proteomic levels. The results showed that leaf proteome of cassava cultivar NZ199 diploid was clearly differentiated from its autotetraploid genotype using 2-DE combined MS technique. Sixty-five differential protein spots were seen in 2-DE image of autotetraploid genotype in comparison with that of diploid. Fifty-two proteins were identified by MALDI-TOF-MS/MS, of which 47 were up-regulated and 5 were down-regulated in autotetraploid genotype compared with diploid genotype. The classified functions of 32 up-regulated proteins were associated with photosynthesis, defense system, hydrocyanic acid (HCN) metabolism, protein biosynthesis, chaperones, amino acid metabolism and signal transduction. The remarkable variation in photosynthetic activity, HCN content and resistance to salt stress between diploid and autotetraploid genotypes is closely linked with expression levels of proteomic profiles. The analysis of protein interaction networks indicated there are direct interactions between the 15 up-regulation proteins involved in the pathways described above. This work provides an insight into understanding the protein regulation mechanism of cassava polyploid genotype, and gives a clue to improve cassava polyploidy breeding in increasing photosynthesis and resistance efficiencies. PMID:24727655

  8. Phasing of many thousands of genotyped samples.

    PubMed

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

    2012-08-10

    Haplotypes are an important resource for a large number of applications in human genetics, but computationally inferred haplotypes are subject to switch errors that decrease their utility. The accuracy of computationally inferred haplotypes increases with sample size, and although ever larger genotypic data sets are being generated, the fact that existing methods require substantial computational resources limits their applicability to data sets containing tens or hundreds of thousands of samples. Here, we present HAPI-UR (haplotype inference for unrelated samples), an algorithm that is designed to handle unrelated and/or trio and duo family data, that has accuracy comparable to or greater than existing methods, and that is computationally efficient and can be applied to 100,000 samples or more. We use HAPI-UR to phase a data set with 58,207 samples and show that it achieves practical runtime and that switch errors decrease with sample size even with the use of samples from multiple ethnicities. Using a data set with 16,353 samples, we compare HAPI-UR to Beagle, MaCH, IMPUTE2, and SHAPEIT and show that HAPI-UR runs 18× faster than all methods and has a lower switch-error rate than do other methods except for Beagle; with the use of consensus phasing, running HAPI-UR three times gives a slightly lower switch-error rate than Beagle does and is more than six times faster. We demonstrate results similar to those from Beagle on another data set with a higher marker density. Lastly, we show that HAPI-UR has better runtime scaling properties than does Beagle so that for larger data sets, HAPI-UR will be practical and will have an even larger runtime advantage. HAPI-UR is available online (see Web Resources). PMID:22883141

  9. Phasing of Many Thousands of Genotyped Samples

    PubMed Central

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

    2012-01-01

    Haplotypes are an important resource for a large number of applications in human genetics, but computationally inferred haplotypes are subject to switch errors that decrease their utility. The accuracy of computationally inferred haplotypes increases with sample size, and although ever larger genotypic data sets are being generated, the fact that existing methods require substantial computational resources limits their applicability to data sets containing tens or hundreds of thousands of samples. Here, we present HAPI-UR (haplotype inference for unrelated samples), an algorithm that is designed to handle unrelated and/or trio and duo family data, that has accuracy comparable to or greater than existing methods, and that is computationally efficient and can be applied to 100,000 samples or more. We use HAPI-UR to phase a data set with 58,207 samples and show that it achieves practical runtime and that switch errors decrease with sample size even with the use of samples from multiple ethnicities. Using a data set with 16,353 samples, we compare HAPI-UR to Beagle, MaCH, IMPUTE2, and SHAPEIT and show that HAPI-UR runs 18× faster than all methods and has a lower switch-error rate than do other methods except for Beagle; with the use of consensus phasing, running HAPI-UR three times gives a slightly lower switch-error rate than Beagle does and is more than six times faster. We demonstrate results similar to those from Beagle on another data set with a higher marker density. Lastly, we show that HAPI-UR has better runtime scaling properties than does Beagle so that for larger data sets, HAPI-UR will be practical and will have an even larger runtime advantage. HAPI-UR is available online (see Web Resources). PMID:22883141

  10. Combined identification of long non-coding RNA XIST and HIF1A-AS1 in serum as an effective screening for non-small cell lung cancer

    PubMed Central

    Tantai, Jicheng; Hu, Dingzhong; Yang, Yu; Geng, Junfeng

    2015-01-01

    Objective: Long non-coding RNAs (lncRNAs) XIST and HIF1A-AS1 have been shown to play important regulatory roles in cancer biology, and lncRNA-XIST and HIF1A-AS1 are upregulated in several cancers such as glioblastoma, breast cancer and thoracoabdominal aorta aneurysm, however, its value in the diagnosis of non-small cell lung cancer (NSCLC) is unclear. The aim of this study is to evaluate the clinical significance of serum XIST and HIF1A-AS1 as a biomarker in the screening of NSCLC. Methods: Expression levels of lncRNA-XIST and HIF1A-AS1 in tumor tissues and serum from NSCLC patients were evaluated by quantitative real-time PCR, and its association with overall survival of patients was analyzed by statistical analysis. Moreover, the XIST and lncRNA-XIST expression correlation between tumor tissues and plasma was demonstrated by linear regression analysis. Results: The levels of XIST (P < 0.05) and HIF1A-AS1 (P < 0.05) were significantly increased in tumor tissues or serum from NSCLC patients as compared to those of control group. Correlation of lncRNA-XIST or HIF1A-AS1 expression between tumor tissues and serum from the same individuals was confirmed in NSCLC patients. Moreover, serum levels of XIST and HIF1A-AS1 were significantly decreased after surgical treatment as compared to pre-operative. The ROC curves illustrated strong separation between the NSCLC patients and control group, with an AUC of 0.834 (95% CI: 0.726-0.935; P < 0.001) for XIST and 0.876 (95% CI: 0.793-0.965; P < 0.001) for HIF1A-AS1, however, the combination of XIST and HIF1A-AS1 yielded an AUC of 0.931 (95% CI: 0.869-0.990; P < 0.001), which was significantly improved as compared to XIST or HIF1A-AS1 alone. Conclusion: Our results demonstrated that increased serum XIST and HIF1A-AS1 could be used as a predictive biomarker for NSCLC screening, and that combination of XIST and HIF1A-AS1 had a higher positive diagnostic efficiency of NSCLC than XIST or HIF1A-AS1 alone. PMID:26339353

  11. Hepatic steatosis in hepatitis C virus genotype 3 infection: does it correlate with body mass index, fibrosis, and HCV risk factors?

    PubMed

    Sharma, Pratima; Balan, Vijayan; Hernandez, Jose; Rosati, Marianne; Williams, James; Rodriguez-Luna, Hector; Schwartz, Joan; Harrison, Edwyn; Anderson, Monte; Byrne, Thomas; Vargas, Hugo E; Douglas, David D; Rakela, Jorge

    2004-01-01

    Hepatic steatosis is a recognized feature of hepatitis C viral infection, particularly in genotype 3. The demographics and the associations contributing to moderate to severe steatosis in genotype 3 are not very well studied. The aim of this study is to determine the demographics and association of steatosis with fibrosis, obesity, diabetes, lipid levels, and risk factors among patients with hepatitis C virus (HCV) genotype 3. Two hundred ninety-three consecutive HCV patients (genotype 1, n = 218; genotype 2, n = 43; genotype 3, n = 32) at our institution were studied retrospectively. Demographic information such as height, weight, genotype, risk factors, serum cholesterol and triglyceride, and liver biopsy was collected. Steatosis was graded using the Brunt classification. HCV genotype 3-infected patients were younger (P < 0.04) and had lower serum cholesterol levels (P < 0.02) compared to nongenotype 3 patients. Moderate to severe steatosis was more prevalent in HCV genotype 3 patients (P < 0.001) with intravenous drug abuse as a risk factor (P = 0.04). Genotype 3 was the independent predictor of steatosis in all patients. There was no statistical association between grade of steatosis and body mass index, fibrosis, necroinflammation, or hyperlipidemia when only HCV genotype 3 patients were included in the multivariate logistic model. Hepatic steatosis is a feature of genotype 3. Patients with HCV genotype 3 are younger and have lower serum cholesterol levels. Genotype 3 is the independent predictor for steatosis in HCV patients. HCV genotype 3 patients with moderate to severe steatosis are more likely to have intravenous drug use as a risk factor. PMID:14992430

  12. Legionella prevention in the Netherlands: an evaluation using genotype distribution.

    PubMed

    Euser, S M; Bruin, J P; Brandsema, P; Reijnen, L; Boers, S A; Den Boer, J W

    2013-08-01

    Legionnaires' disease (LD) is an acute pneumonia caused by the inhalation or aspiration of aerosols contaminated with Legionella bacteria. The watery environment is considered to be the natural habitat for these bacteria. Therefore, drinking water legislation is used in the primary prevention of LD, focussing on the different water sources to which the general public is exposed. For 10 years, secondary prevention of LD in the Netherlands has been organised using an outbreak detection programme that eliminates potential sources of infection that LD patients have been exposed to during their incubation period. To evaluate the two prevention strategies, we compared the distribution of Legionella pneumophila serogroup 1 genotypes isolated from patient material (n = 179) with the distribution resulting from primary (n = 182) and secondary (n = 60) prevention actions, respectively. The sequence type profiles were generated using the HiMLST method that employs next generation sequencing. We found that genotypes collected during primary prevention differ to a large extent from those isolated from patients. Genotypes collected during secondary prevention efforts had a greater similarity to that of patient isolates, but could be further improved. Our results suggest that primary prevention is not aiming at the correct reservoir, whereas secondary prevention is only partially focussed. It seems that there is a still unknown reservoir. PMID:23430195

  13. Robust, high-throughput solution for blood group genotyping.

    PubMed

    Le Goff, Gaelle C; Brès, Jean-Charles; Rigal, Dominique; Blum, Loïc J; Marquette, Christophe A

    2010-07-15

    With the concomitant increase of blood transfusions and safety rules, there is a growing need to integrate high-throughput and multiparametric assays within blood qualification centers. Using a robust and automated solution, we describe a new method for extended blood group genotyping (HiFi-Blood 96) bringing together the throughput possibilities of complete automation and the microarray multiplexed analysis potential. Our approach provides a useful resource for upgrading blood qualification center facilities. A set of six single-nucleotide polymorphisms (SNPs) associated with clinically important blood group antigens (Kell, Kidd, Duffy, and MNS systems) were selected and the corresponding genotyping assays developed. A panel of 293 blood samples was used to validate the approach. The resulting genotypes were compared to phenotypes previously determined by standard serologic techniques, and excellent correlations were found for five SNPs out of six. For the Kell, Kidd, Duffy, and MNS3/MNS4 systems, high matching percentages of 100%, 98.9%, 97.7%, and 97.4% were obtained, respectively, whereas a concordance percentage of 83.3% only was attained for the MNS1/MNS2 polymorphism. PMID:20560530

  14. Single nucleotide polymorphism genotyping using BeadChip microarrays.

    PubMed

    Lambert, Gilliam; Tsinajinnie, Darwin; Duggan, David

    2013-07-01

    The genotyping of single nucleotide polymorphisms (SNPs) has successfully contributed to the study of complex diseases more than any other technology to date. Genome-wide association studies (GWAS) using 10,000s to >1,000,000 SNPs have identified 1000s of statistically significant SNPs pertaining to 17 different human disease and trait categories. Post-GWAS fine-mapping studies using 10,000s to 100,000s SNPs on a microarray have narrowed the region of interest for many of these GWAS findings; in addition, independent signals within the original GWAS region have been identified. Focused content, SNP-based microarrays such as the human exome, for example, have too been used successfully to identify novel disease associations. Success has come to studies where 100s to 10,000s (mostly) to >100,000 samples were genotyped. For the time being, SNP-based microarrays remain cost-effective especially when studying large numbers of samples compared to other "genotyping" technologies including next generation sequencing. In this unit, protocols for manual (LIMS-free), semi-manual, and automated processing of BeadChip microarrays are presented. Lower throughput studies will find value in the manual and semi-manual protocols, while all types of studies--low-, medium-, and high-throughput--will find value in the semi-manual and automated protocols. PMID:23853082

  15. Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

    PubMed Central

    Waman, Vaishali P.; Kolekar, Pandurang; Ramtirthkar, Mukund R.; Kale, Mohan M.

    2016-01-01

    Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae). There are four serotypes of Dengue Virus (DENV-1 to DENV-4), each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. Methods Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. Results DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. Discussion Complete genome-based analysis revealed that the

  16. Predictive Factors for Sustained Virological Response after Treatment with Pegylated Interferon α-2a and Ribavirin in Patients Infected with HCV Genotypes 2 and 3

    PubMed Central

    Niederau, Claus; Mauss, Stefan; Schober, Andreas; Stoehr, Albrecht; Zimmermann, Tim; Waizmann, Michael; Moog, Gero; Pape, Stefan; Weber, Bernd; Isernhagen, Konrad; Sandow, Petra; Bokemeyer, Bernd; Alshuth, Ulrich; Steffens, Hermann; Hüppe, Dietrich

    2014-01-01

    Background Previous trials have often defined genotype 2 and 3 patients as an “easy to treat” group and guidelines recommend similar management. Aims The present study looks for differences between the two genotypes and analyzes predictive factors for SVR. Methods Prospective, community-based cohort study involving 421 physicians throughout Germany. The analysis includes 2,347 patients with untreated chronic HCV genotype 2 (n = 391) and 3 (n = 1,956) infection treated with PEG-IFN α-2a plus ribavirin between August 2007 and July 2012. Results When compared with genotype 2 patients, those with genotype 3 were younger, had a shorter duration of infection, lower values of total cholesterol, LDL cholesterol and BMI, a higher frequency of drug use as infection mode and male gender (p<0.0001, respectively), and a higher APRI score (p<0.005). SVR was higher in genotype 2 when compared with genotype 3 (64.7% vs. 56.9%, p = 0.004). By multivariate analysis of genotype 2 patients, low baseline γ -GT and RVR predicted SVR. In genotype 3 age ≤45 years, cholesterol>130 mg/dl, a low APRI score, and a γ-GT ≥3-times ULN, RVR, and RBV starting dose were associated with SVR by multivariate analysis. Conclusions The present study corroborates that liver fibrosis is more pronounced in genotype 3 vs. 2. SVR is higher in genotype 2 versus genotype 3 partly because of follow-up problems in genotype 3 patients, in particular in those infected by drug use. Thus, subgroups of genotype 3 patients have adherence problems and need special attention also because they often have significant liver fibrosis. Trial Registration Verband Forschender Arzneimittelhersteller e.V., Berlin, Germany ML21645 ClinicalTrials.gov NCT02106156 PMID:25238535

  17. Simultaneous voltammetric determination for DA, AA and NO₂⁻ based on graphene/poly-cyclodextrin/MWCNTs nanocomposite platform.

    PubMed

    Zhang, Yu; Yuan, Ruo; Chai, Yaqin; Li, Wenjuan; Zhong, Xia; Zhong, Huaan

    2011-05-15

    In the present work, graphene sheets (GS) and multiwall carbon nanotubes (MWCNTs) were dispersed in the mixed solution of cyclodextrin (CD) and cyclodextrin prepolymer (pre-CD) and were used as modifier to fabricate chemical modified electrode to simultaneous detect dopamine (DA), ascorbic acid (AA) and nitrite (NO2(-)). CD cross-linked pre-CD (CDP) displays excellent film forming ability, which made the electrode stable. Comparing with CDP-GS, CDP-MWCNTs and CDP-GS-MWCNTs modified electrodes, the CDP-GS-MWCNTs displays higher catalytic activity and selectivity toward the oxidation of DA, AA and NO2(-), revealing that MWCNTs effectively inhibited the stacking of individual GS and enhanced the utilization of GS based composites. The host-guest chemical reaction ability of CD and π-π stacking interaction between detected molecules and GS-MWCNTs surface were considered as the main reasons of the successfully simultaneous detection of DA, AA and NO2(-). Cyclic voltammetry (CV), scanning electron microscopy (SEM) and different pulse voltammetry (DPV) were employed to characterize the biosensor. The linear response range for AA, DA and NO2(-) were 5 μM-0.48 mM, 0.15-21.65 μM and 5 μM-6.75 mM, respectively and the detection limits were 1.65 μM, 0.05 μM and 1.65 μM. PMID:21497078

  18. Regulation of tillering in sorghum: genotypic effects

    PubMed Central

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

    2010-01-01

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

  19. Imputation of ungenotyped parental genotypes in dairy and beef cattle from progeny genotypes.

    PubMed

    Berry, D P; McParland, S; Kearney, J F; Sargolzaei, M; Mullen, M P

    2014-06-01

    The objective of this study was to quantify the accuracy of imputing the genotype of parents using information on the genotype of their progeny and a family-based and population-based imputation algorithm. Two separate data sets were used, one containing both dairy and beef animals (n=3122) with high-density genotypes (735 151 single nucleotide polymorphisms (SNPs)) and the other containing just dairy animals (n=5489) with medium-density genotypes (51 602 SNPs). Imputation accuracy of three different genotype density panels were evaluated representing low (i.e. 6501 SNPs), medium and high density. The full genotypes of sires with genotyped half-sib progeny were masked and subsequently imputed. Genotyped half-sib progeny group sizes were altered from 4 up to 12 and the impact on imputation accuracy was quantified. Up to 157 and 258 sires were used to test the accuracy of imputation in the dairy plus beef data set and the dairy-only data set, respectively. The efficiency and accuracy of imputation was quantified as the proportion of genotypes that could not be imputed, and as both the genotype concordance rate and allele concordance rate. The median proportion of genotypes per animal that could not be imputed in the imputation process decreased as the number of genotyped half-sib progeny increased; values for the medium-density panel ranged from a median of 0.015 with a half-sib progeny group size of 4 to a median of 0.0014 to 0.0015 with a half-sib progeny group size of 8. The accuracy of imputation across different paternal half-sib progeny group sizes was similar in both data sets. Concordance rates increased considerably as the number of genotyped half-sib progeny increased from four (mean animal allele concordance rate of 0.94 in both data sets for the medium-density genotype panel) to five (mean animal allele concordance rate of 0.96 in both data sets for the medium-density genotype panel) after which it was relatively stable up to a half-sib progeny group size

  20. Long noncoding RNA HIF1A-AS1A reduces apoptosis of vascular smooth muscle cells: implications for the pathogenesis of thoracoabdominal aorta aneurysm.

    PubMed

    He, Qing; Tan, Jinyun; Yu, Bo; Shi, Weihao; Liang, Kun

    2015-05-01

    Long non-coding RNAs (IncRNAs) play important roles in various biological processes, such as transcriptional regulation, cell growth and tumorigenesis. However, little is known about the role of IncRNA HIF 1 alpha-antisense RNA 1 (HIF1a-AS1) in regulating the proliferation and apoptosis of vascular smooth muscle cells (VSMCs) and the expression of HIF1a-AS1 in serum of thoracoabdominal aortic aneurysm (TAAA) patients. The cell viability was detected by the CCK8 assay. The cell apoptosis was assessed by annexin V-PI double-labeling staining. Expression of genes and proteins were analyzed by real-time PCR and western blotting, respectively. Cells were transfected with siRNAs as a gene silencing method. In serum of TAAA patients, the expression of HIF1a-AS1 was significantly increased (superior to 6-fold) compared to the normal control. Moreover, Palmitic acid (PA) induced cell apoptosis in VSMCs in a time- and dose-dependent manner, and the proportion of the apoptotic cells had gained as compared to untreatment group. PA also induced up-regulation expression of HIF1a-AS1. We also found that transfection of cells with HIF1a-AS1 siRNA decreased the expression of caspase-3 and caspase-8 and increased the expression of Bcl2, and protected PA-induced cell apoptosis in VSMCs. HIF1a-AS1 was overexpressed in the TAAA and the interaction between HIF1a-AS1 and apoptotic proteins plays a key role in the proliferation and apoptosis of VSMCs in vitro, which may contribute to the pathogenesis of TAAA. PMID:26062299

  1. Oestradiol metabolism and androgen receptor genotypes are associated with right ventricular function

    PubMed Central

    Ventetuolo, Corey E.; Mitra, Nandita; Wan, Fei; Manichaikul, Ani; Barr, R. Graham; Johnson, Craig; Bluemke, David A.; Lima, Joao A.C.; Tandri, Hari; Ouyang, Pamela; Kawut, Steven M.

    2016-01-01

    Sex hormones are linked to right ventricular (RV) function, but the relationship between genetic variation in these pathways and RV function is unknown. We performed a cross-sectional study of 2761 genotyped adults without cardiovascular disease. The relationships between RV measures and single nucleotide polymorphisms (SNPs) in 10 candidate genes were assessed. Urinary oestradiol (E2) metabolites produced by cytochrome P4501B1 (CYP1B1) and serum testosterone were measured in women and men respectively. In African-American (AA) women, the CYP1B1 SNP rs162561 was associated with RV ejection fraction (RVEF), such that each copy of the A allele was associated with a 2.0% increase in RVEF. Haplotype analysis revealed associations with RVEF in AA (global p<7.2×10−6) and white (global p=0.05) women. In white subjects, higher E2 metabolite levels were associated with significantly higher RVEF. In men, androgen receptors SNPs (rs1337080; rs5918764) were significantly associated with all RV measures and modified the relationship between testosterone and RVEF. Genetic variation in E2 metabolism and androgen signalling was associated with RV morphology in a sex-specific manner. The CYP1B1 SNP identified is in tight linkage disequilibrium with SNPs associated with pulmonary hypertension and oncogenesis, suggesting these pathways may underpin sexual dimorphism in RV failure. PMID:26647441

  2. Oestradiol metabolism and androgen receptor genotypes are associated with right ventricular function.

    PubMed

    Ventetuolo, Corey E; Mitra, Nandita; Wan, Fei; Manichaikul, Ani; Barr, R Graham; Johnson, Craig; Bluemke, David A; Lima, Joao A C; Tandri, Hari; Ouyang, Pamela; Kawut, Steven M

    2016-02-01

    Sex hormones are linked to right ventricular (RV) function, but the relationship between genetic variation in these pathways and RV function is unknown.We performed a cross-sectional study of 2761 genotyped adults without cardiovascular disease. The relationships between RV measures and single nucleotide polymorphisms (SNPs) in 10 candidate genes were assessed. Urinary oestradiol (E2) metabolites produced by cytochrome P4501B1 (CYP1B1) and serum testosterone were measured in women and men respectively.In African-American (AA) women, the CYP1B1 SNP rs162561 was associated with RV ejection fraction (RVEF), such that each copy of the A allele was associated with a 2.0% increase in RVEF. Haplotype analysis revealed associations with RVEF in AA (global p<7.2×10(-6)) and white (global p=0.05) women. In white subjects, higher E2 metabolite levels were associated with significantly higher RVEF. In men, androgen receptors SNPs (rs1337080; rs5918764) were significantly associated with all RV measures and modified the relationship between testosterone and RVEF.Genetic variation in E2 metabolism and androgen signalling was associated with RV morphology in a sex-specific manner. The CYP1B1 SNP identified is in tight linkage disequilibrium with SNPs associated with pulmonary hypertension and oncogenesis, suggesting these pathways may underpin sexual dimorphism in RV failure. PMID:26647441

  3. Tolerant and Susceptible Sesame Genotypes Reveal Waterlogging Stress Response Patterns

    PubMed Central

    Wang, Linhai; Li, Donghua; Zhang, Yanxin; Gao, Yuan; Yu, Jingyin; Wei, Xin; Zhang, Xiurong

    2016-01-01

    Waterlogging is a common adverse environmental condition that limits plant growth. Sesame (Sesamum indicum) is considered a drought-tolerant oil crop but is typically susceptible to harmful effects from waterlogging. The present study used comparative analysis to explore the waterlogging stress response associated with two sesame genotypes. The RNA-seq dataset generated during a time course of 0, 3, 9 and 15 h of waterlogging as well as 20 h post-drainage indicated that stress gradually suppressed the expression of sesame genes, with 9 h as the critical time point for the response of sesame to waterlogging stress. Of the 19,316 genes expressed during waterlogging, 72.1% were affected significantly. Sesame of both tolerant and susceptible genotypes showed decreased numbers of upregulated differentially expressed genes (DEGs) but increased numbers of downregulated DEGs at the onset of waterlogging. However, the tolerant-genotype sesame exhibited 25.5% more upregulated DEGs and 29.7% fewer downregulated DEGs than those of the susceptible-genotype strain between 3 and 15 h. The results indicated that the tolerant sesame displayed a more positive gene response to waterlogging. A total of 1,379 genes were significantly induced and commonly expressed in sesame under waterlogging conditions from 3 to 15 h regardless of tolerance level; of these genes, 98 are known homologous stress responsive genes, while the remaining 1,281 are newly reported here. This gene set may represent the core genes that function in response to waterlogging, including those related mainly to energy metabolism and phenylpropanoid biosynthesis. Furthermore, a set of 3,016 genes functioning in energy supply and cell repair or formation was activated in sesame recovery from waterlogging stress. A comparative analysis between sesame of the tolerant and susceptible genotypes revealed 66 genes that may be candidates for improving sesame tolerance to waterlogging. This study provided a comprehensive

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  5. Field Response of Sugarcane Genotypes to Freeze Stress with Genotype x Environment Effects on Quality Traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Freeze stress is a constraint to sugarcane (Saccharum sp.) with negative effect on sucrose yield, particularly during the harvest season. To understand its impact on the performance of genotypes developed by the Canal Point (CP) breeding program, the genotype by environment (GxE) interaction was app...

  6. Bending Properties of Locally Laser Heat Treated AA2024-T3 Aluminium Alloy

    NASA Astrophysics Data System (ADS)

    Mohammadi, Amirahmad; Vanhove, Hans; Van Bael, Albert; Duflou, Joost R.

    The bending properties of AA2024-T3 aluminium alloy after localized laser assisted softening have been studied and compared to untreated material. Single and multi-path laser scanning strategies are applied for achieving a predictable and minimized springback. Process parameters for softening have been chosen based on FE modeling. In order to investigate the softening, and to characterize the size of this softened region, hardness measurements were carried out. Using a triple scanning path strategy springback was reduced by about 43% without changing the bending radius.

  7. Severe hidradenitis suppurativa complicated by renal AA amyloidosis.

    PubMed

    Utrera-Busquets, M; Romero-Maté, A; Castaño, Á; Alegre, L; García-Donoso, C; Borbujo, J

    2016-04-01

    Hidradenitis suppurativa (HS) is a chronic, recurrent inflammatory disease affecting the skin folds. Multiple therapeutic options have been proposed for severe cases, but persistent responses are rarely seen. Important complications of HS are uncommon, and usually seen only in severe and unresponsive disease. Amyloid A (AA) amyloidosis is secondary to inflammatory chronic diseases, and is an uncommon complication of dermatological diseases. Only a few cases related with HS have been reported. We report the case of a 37-year-old patient who developed AA amyloidosis secondary to severe HS. PMID:26206410

  8. Modeling of the Effect of Temperature, Frequency, and Phase Transformations on the Viscoelastic Properties of AA 7075-T6 and AA 2024-T3 Aluminum Alloys

    NASA Astrophysics Data System (ADS)

    Rojas, Jose I.; Crespo, Daniel

    2012-12-01

    The viscoelastic response of commercial aluminum alloys 7075-T6 and 2024-T3 as a function of temperature is presented. Experimental data are obtained with a dynamic-mechanical analyzer (DMA) at different loading frequencies and compared with the available transmission electron microscopy (TEM) and differential scanning calorimetry (DSC) data. The effect of successive microstructural transformations (particle precipitation and redissolution) is revealed. An analytical model is developed, which fits the mechanical response up to 573 K (300 °C). The model takes into account the concentration of Guinier-Preston Zones (GPZ) and metastable precipitates ( η' in AA 7075-T6 and θ'/S' in AA 2024-T3), allowing us to determine the kinetic parameters of these transformations. The activation energies were previously obtained by several authors from DSC measurements and other techniques, showing considerable dispersion. The presented data, obtained with a completely different technique, allow us to reduce the uncertainty on these data and show the potential of DMA measurements in the study of microstructural transformations.

  9. Precise genotyping and recombination detection of Enterovirus

    PubMed Central

    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

  10. Precise genotyping and recombination detection of Enterovirus.

    PubMed

    Lin, Chieh-Hua; Wang, Yu-Bin; Chen, Shu-Hwa; Hsiung, Chao Agnes; Lin, Chung-Yen

    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

  11. Estimation of Genotype Distributions and Posterior Genotype Probabilities for β-Mannosidosis in Salers Cattle

    PubMed Central

    Taylor, J. F.; Abbitt, B.; Walter, J. P.; Davis, S. K.; Jaques, J. T.; Ochoa, R. F.

    1993-01-01

    β-Mannosidosis is a lethal lysosomal storage disease inherited as an autosomal recessive in man, cattle and goats. Laboratory assay data of plasma β-mannosidase activity represent a mixture of homozygous normal and carrier genotype distributions in a proportion determined by genotype frequency. A maximum likelihood approach employing data transformations for each genotype distribution and assuming a diallelic model of inheritance is described. Estimates of the transformation and genotype distribution parameters, gene frequency, genotype fitness and carrier probability were obtained simultaneously from a sample of 2,812 observations on U.S. purebred Salers cattle with enzyme activity, age, gender, month of pregnancy, month of testing, and parents identified. Transformations to normality were not required, estimated gene and carrier genotype frequencies of 0.074 and 0.148 were high, and the estimated relative fitness of heterozygotes was 1.36. The apparent overdominance in fitness may be due to a nonrandom sampling of progeny genotypes within families. The mean of plasma enzyme activity was higher for males than females, higher in winter months, lower in summer months and decreased with increased age. Estimates of carrier probabilities indicate that the test is most effective when animals are sampled as calves, although effectiveness of the plasma assay was less for males than females. Test effectiveness was enhanced through averaging repeated assays of enzyme activity on each animal. Our approach contributes to medical diagnostics in several ways. Rather than assume underlying normality for the distributions comprising the mixture, we estimate transformations to normality for each genotype distribution simultaneously with all other model parameters. This process also excludes potential biases due to data preadjustment for systematic effects. We also provide a method for partitioning phenotypic variation within each genotypic distribution which allows an assessment

  12. CSI 2264: Probing the inner disks of AA Tauri-like systems in NGC 2264

    NASA Astrophysics Data System (ADS)

    McGinnis, P. T.; Alencar, S. H. P.; Guimarães, M. M.; Sousa, A. P.; Stauffer, J.; Bouvier, J.; Rebull, L.; Fonseca, N. N. J.; Venuti, L.; Hillenbrand, L.; Cody, A. M.; Teixeira, P. S.; Aigrain, S.; Favata, F.; Fűrész, G.; Vrba, F. J.; Flaccomio, E.; Turner, N. J.; Gameiro, J. F.; Dougados, C.; Herbst, W.; Morales-Calderón, M.; Micela, G.

    2015-05-01

    Context. The classical T Tauri star (CTTS) AA Tau has presented photometric variability that was attributed to an inner disk warp, caused by the interaction between the inner disk and an inclined magnetosphere. Previous studies of the young cluster NGC 2264 have shown that similar photometric behavior is common among CTTS. Aims: The goal of this work is to investigate the main causes of the observed photometric variability of CTTS in NGC 2264 that present AA Tau-like light curves, and verify if an inner disk warp could be responsible for their observed variability. Methods: In order to understand the mechanism causing these stars' photometric behavior, we investigate veiling variability in their spectra and u - r color variations and estimate parameters of the inner disk warp using an occultation model proposed for AA Tau. We also compare infrared Spitzer IRAC and optical CoRoT light curves to analyze the dust responsible for the occultations. Results: AA Tau-like variability proved to be transient on a timescale of a few years. We ascribe this variability to stable accretion regimes and aperiodic variability to unstable accretion regimes and show that a transition, and even coexistence, between the two is common. We find evidence of hot spots associated with occultations, indicating that the occulting structures could be located at the base of accretion columns. We find average values of warp maximum height of 0.23 times its radial location, consistent with AA Tau, with variations of on average 11% between rotation cycles. We also show that extinction laws in the inner disk indicate the presence of grains larger than interstellar grains. Conclusions: The inner disk warp scenario is consistent with observations for all but one star with AA Tau-like variability in our sample. AA Tau-like systems are fairly common, comprising 14% of CTTS observed in NGC 2264, though this number increases to 35% among systems of mass 0.7 M⊙ ≲ M ≲ 2.0 M⊙. Assuming random

  13. Concordance between CYP2D6 genotypes obtained from tumor-derived and germline DNA.

    PubMed

    Rae, James M; Regan, Meredith M; Thibert, Jacklyn N; Gersch, Christina; Thomas, Dafydd; Leyland-Jones, Brian; Viale, Giuseppe; Pusztai, Lajos; Hayes, Daniel F; Skaar, Todd; Van Poznak, Catherine

    2013-09-01

    Formalin-fixed, paraffin-embedded tumors (FFPETs) are a valuable source of DNA for genotype association studies and are often the only germline DNA resource from cancer clinical trials. The anti-estrogen tamoxifen is metabolized into endoxifen by CYP2D6, leading to the hypothesis that patients with certain CYP2D6 genotypes may not receive benefit because of their inability to activate the drug. Studies testing this hypothesis using FFPETs have provided conflicting results. It has been postulated that CYP2D6 genotype determined using FFPET may not be accurate because of somatic tumor alterations. In this study, we determined the concordance between CYP2D6 genotypes generated using 3 tissue sources (FFPETs; formalin-fixed, paraffin-embedded unaffected lymph nodes [FFPELNs]; and whole blood cells [WBCs]) from 122 breast cancer patients. Compared with WBCs, FFPET and FFPELN genotypes were highly concordant (>94%), as were the predicted CYP2D6 metabolic phenotypes (>97%). We conclude that CYP2D6 genotypes obtained from FFPETs accurately represent the patient's CYP2D6 metabolic phenotype. PMID:23958736

  14. The COL5A1 genotype is associated with range of motion

    PubMed Central

    Lim, Seung-Taek; Kim, Chang-Sun; Kim, Woo-Nam; Min, Seok-Ki

    2015-01-01

    [Purpose] The aim of our study was to investigate the association between COL5A1 genotype and Range of Motion as measured by the passive straight leg raise (SLR) and whole body join laxity (WBJL) in Asian population. [Methods] One hundred and seventy seven participants including Korean and Japanese college students (male = 109, female = 68) participated in the study. Each subject performed the passive straight leg raise and whole body join laxity test. Genotyping for the COL5A1 (rs 12722) polymorphism was performed using the TaqMan approach. The COL5A1 genotype exhibited a Hardy-Weinberg equilibrium distribution in our population. [Results] The physical parameters including height, weight, and BMI were higher in < 90° group than > 90° group. The SLR exhibited significant difference among the COL5A1 group. However, the WBJL did not differ significantly among the COL5A1 genotype, but significant difference was seen in CC genotype when compared to CT (2.99 ± 1.72) or TT (2.70 ± 1.52) genotype. [Conclusion] We concluded that COL5A1 gene polymorphism is associated with increased SLR ROM in Asian population. PMID:26244122

  15. A novel MALDI-TOF based methodology for genotyping single nucleotide polymorphisms.

    PubMed

    Blondal, Thorarinn; Waage, Benedikt G; Smarason, Sigurdur V; Jonsson, Frosti; Fjalldal, Sigridur B; Stefansson, Kari; Gulcher, Jeffery; Smith, Albert V

    2003-12-15

    A new MALDI-TOF based detection assay was developed for analysis of single nucleotide polymorphisms (SNPs). It is a significant modification on the classic three-step minisequencing method, which includes a polymerase chain reaction (PCR), removal of excess nucleotides and primers, followed by primer extension in the presence of dideoxynucleotides using modified thermostable DNA polymerase. The key feature of this novel assay is reliance upon deoxynucleotide mixes, lacking one of the nucleotides at the polymorphic position. During primer extension in the presence of depleted nucleotide mixes, standard thermostable DNA polymerases dissociate from the template at positions requiring a depleted nucleotide; this principal was harnessed to create a genotyping assay. The assay design requires a primer- extension primer having its 3'-end one nucleotide upstream from the interrogated site. The assay further utilizes the same DNA polymerase in both PCR and the primer extension step. This not only simplifies the assay but also greatly reduces the cost per genotype compared to minisequencing methodology. We demonstrate accurate genotyping using this methodology for two SNPs run in both singleplex and duplex reactions. We term this assay nucleotide depletion genotyping (NUDGE). Nucleotide depletion genotyping could be extended to other genotyping assays based on primer extension such as detection by gel or capillary electrophoresis. PMID:14654708

  16. Genotype-environment interactions in mouse behavior: a way out of the problem.

    PubMed

    Kafkafi, Neri; Benjamini, Yoav; Sakov, Anat; Elmer, Greg I; Golani, Ilan

    2005-03-22

    In behavior genetics, behavioral patterns of mouse genotypes, such as inbred strains, crosses, and knockouts, are characterized and compared to associate them with particular gene loci. Such genotype differences, however, are usually established in single-laboratory experiments, and questions have been raised regarding the replicability of the results in other laboratories. A recent multilaboratory experiment found significant laboratory effects and genotype x laboratory interactions even after rigorous standardization, raising the concern that results are idiosyncratic to a particular laboratory. This finding may be regarded by some critics as a serious shortcoming in behavior genetics. A different strategy is offered here: (i) recognize that even after investing much effort in identifying and eliminating causes for laboratory differences, genotype x laboratory interaction is an unavoidable fact of life. (ii) Incorporate this understanding into the statistical analysis of multilaboratory experiments using the mixed model. Such a statistical approach sets a higher benchmark for finding significant genotype differences. (iii) Develop behavioral assays and endpoints that are able to discriminate genetic differences even over the background of the interaction. (iv) Use the publicly available multilaboratory results in single-laboratory experiments. We use software-based strategy for exploring exploration (see) to analyze the open-field behavior in eight genotypes across three laboratories. Our results demonstrate that replicable behavioral measures can be practically established. Even though we address the replicability problem in behavioral genetics, our strategy is also applicable in other areas where concern about replicability has been raised. PMID:15764701

  17. Color and antioxidant characteristics of some fresh fig (Ficus carica L.) genotypes from northeastern Turkey.

    PubMed

    Ercisli, Sezai; Tosun, Murat; Karlidag, Huseyin; Dzubur, Ahmed; Hadziabulic, Semina; Aliman, Yasmina

    2012-09-01

    Fruit skin color, total phenolics, total anthocyanins, soluble solids content, titratable acidity and total antioxidant capacity in fresh fruits of a number of local and well-known fig (Ficus carica L.) genotypes and cultiva