Parental Participation and Retention in an Alcohol Preventive Family-Focused Programme

ERIC Educational Resources Information Center

Skarstrand, Eva; Branstrom, Richard; Sundell, Knut; Kallmen, Hakan; Andreassen, Sven

2009-01-01

Purpose: The purpose of this paper is to examine factors predicting parental participation and retention in a Swedish version of the Strengthening Families Programme (SFP). Design/methodology/approach: This study is based on data from a randomised controlled trial to evaluate the effects of the Swedish version of the SFP. The sample involves 441…

Comparing soluble ferric pyrophosphate to common iron salts and chelates as sources of bioavailable iron in a Caco-2 cell culture model.

PubMed

Zhu, Le; Glahn, Raymond P; Nelson, Deanna; Miller, Dennis D

2009-06-10

Iron bioavailability from supplements and fortificants varies depending upon the form of the iron and the presence or absence of iron absorption enhancers and inhibitors. Our objectives were to compare the effects of pH and selected enhancers and inhibitors and food matrices on the bioavailability of iron in soluble ferric pyrophosphate (SFP) to other iron fortificants using a Caco-2 cell culture model with or without the combination of in vitro digestion. Ferritin formation was the highest in cells treated with SFP compared to those treated with other iron compounds or chelates. Exposure to pH 2 followed by adjustment to pH 7 markedly decreased FeSO(4) bioavailability but had a smaller effect on bioavailabilities from SFP and sodium iron(III) ethylenediaminetetraacetate (NaFeEDTA), suggesting that chelating agents minimize the effects of pH on iron bioavailability. Adding ascorbic acid (AA) and cysteine to SFP in a 20:1 molar ratio increased ferritin formation by 3- and 2-fold, respectively, whereas adding citrate had no significant effect on the bioavailability of SFP. Adding phytic acid (10:1) and tannic acid (1:1) to iron decreased iron bioavailability from SFP by 91 and 99%, respectively. The addition of zinc had a marked inhibitory effect on iron bioavailability. Calcium and magnesium also inhibited iron bioavailability but to a lesser extent. Incorporating SFP in rice greatly reduced iron bioavailability from SFP, but this effect can be partially reversed with the addition of AA. SFP and FeSO(4) were taken up similarly when added to nonfat dry milk. Our results suggest that dietary factors known to enhance and inhibit iron bioavailability from various iron sources affect iron bioavailability from SFP in similar directions. However, the magnitude of the effects of iron absorption inhibitors on SFP iron appears to be smaller than on iron salts, such as FeSO(4) and FeCl(3). This supports the hypothesis that SFP is a promising iron source for food fortification and dietary supplements.

Novel Sfp1 Transcriptional Regulation of Saccharomyces cerevisiae Gene Expression Changes During Spaceflight

NASA Astrophysics Data System (ADS)

Coleman, Chasity B.; Allen, Patricia L.; Rupert, Mark; Goulart, Carla; Hoehn, Alexander; Stodieck, Louis S.; Hammond, Timothy G.

2008-12-01

This study identifies transcriptional regulation of stress response element (STRE) genes in space in the model eukaryotic organism, Saccharomyces cerevisiae. To determine transcription-factor dependence, gene expression changes in space were examined in strains bearing green fluorescent protein tagged (GFP-tagged) reporters for YIL052C (Sfp1 dependent with stress), YST-2 (Sfp1/Rap1 dependent with stress), or SSA4 (Msn4 dependent with stress), along with strains of SSA4-GFP and YIL052C-GFP with individual deletions of the Msn4 or Sfp1. When compared to parallel ground controls, spaceflight induces significant gene expression changes in SSA4 (35% decrease) and YIL052C (45% decrease), while expression of YST-2 (0.08% decrease) did not change. In space, deletion of Sfp1 reversed the SSA4 gene expression effect (0.00% change), but Msn4 deletion yielded a similar decrease in SSA4 expression (34% change), which indicates that SSA4 gene expression is dependent on the Sfp1 transcription factor in space, unlike other stresses. For YIL052C, deletion of Sfp1 reversed the effect (0.01% change), and the Msn4 deletion maintained the decrease in expression (30% change), which indicates that expression of YIL052C is also dependent on Sfp1 in space. Spaceflight has selective and specific effects on SSA4 and YIL052C gene expression, indicated by novel dependence on Sfp1.

Can pelvic tilt be predicated by the sacrofemoral-pubic angel in patients with thoracolumbar kyphosis secondary to ankylosing spondylitis?

PubMed

Hu, Jun; Ji, Ming-liang; Qian, Bang-ping; Qiu, Yong; Wang, Bin; Yu, Yang; Zhu, Ze-Zhang; Jiang, Jun

2014-11-01

A retrospective radiographical study. To construct a predictive model for pelvic tilt (PT) based on the sacrofemoral-pubic (SFP) angle in patients with thoracolumbar kyphosis secondary to ankylosing spondylitis (or AS). PT is a key pelvic parameter in the regulation of spine sagittal alignment that can be used to plan the appropriate osteotomy angle in patients with AS with thoracolumbar kyphosis. However, it could be difficult to measure PT in patients with femoral heads poorly visualized on lateral radiographs. Previous studies showed that the SFP angle could be used to evaluate PT in adult patients with scoliosis. However, this method has not been validated in patients with AS. A total of 115 patients with AS with thoracolumbar kyphosis were included. Full-length anteroposterior and lateral spine radiographs were all available, with spinal and pelvic anatomical landmarks clearly identified. PT, SFP angle, and global kyphosis were measured. The patients were randomly divided into group A (n=65) and group B (n=50). In group A, the predictive model for PT was constructed by the results of the linear regression analysis. In group B, the predictive ability and accuracy of the predictive model were investigated. In group A, the Pearson correlation analysis revealed a strong correlation between the SFP angle and PT (r=0.852; P<0.001). The predictive model for PT was constructed as PT=72.3-0.82×(SFP angle). In group B, PT was predicted by the model with a mean error of 4.6° (SD=4.5°) with a predictive value of 78%. PT can be accurately predicted by the SFP angle using the current model: PT=72.3-0.82×(SFP angle), when the femur heads are poorly visualized on lateral radiographs in patients with AS with thoracolumbar kyphosis. 4.

Complementary effect of Phloxine B on the insecticidal efficacy of Isaria fumosorosea SFP-198 wettable powder against greenhouse whitefly, Trialeurodes vaporariorum West.

PubMed

Kim, Jae Su; Je, Yeon Ho; Choi, Jae Young

2010-12-01

Insecticidal activities of five photoactive dyes against greenhouse whitefly (GWF), Trialeurodes vaporariorum West., in tomatoes were investigated to improve the control efficacy of an entomopathogenic fungal product, Isaria fumosorosea SFP-198 wettable powder (WP). Azorubine, Eosin B, Erythrosine, Brilliant Green and Phloxine B were used in this work, accompanying pyriproxyfen emulsifiable concentrate (EC) as a commercial standard for comparison. Phloxine B had the highest control efficacy in glasshouse conditions. The most suitable dose of Phloxine B was determined as 0.005 g L(-1) , given the dosage-dependent control efficacy and phytotoxicity of the dye, and its influence on the germination of SFP-198 conidia. In field conditions, SFP-198 WP + Phloxine B (2 + 0.005 g L(-1) ; tank mix) showed 89.1 and 95.3% control efficacy 7 and 14 days post-application, which was significantly higher than the efficacy of SFP-198 WP alone (43.5 and 64.0%), Phloxine B (47.5 and 30.7%) or pyriproxyfen EC (67.7 and 80.2%). Phloxine B cooperates with SFP-198 WP complementarily, possibly in the order of killing action (early: Phloxine B; late: SFP-198 WP). The dye can be incorporated into SFP-198 WP to improve its efficacy and applied to other Hypocrelean entomopathogenic fungal products. Copyright © 2010 Society of Chemical Industry.

Children with Elevated Psychosocial Risk Load Benefit Most from a Family-Based Preventive Intervention: Exploratory Differential Analyses from the German "Strengthening Families Program 10-14" Adaptation Trial.

PubMed

Bröning, Sonja; Baldus, Christiane; Thomsen, Monika; Sack, Peter-Michael; Arnaud, Nicolas; Thomasius, Rainer

2017-11-01

While the effectiveness of substance use prevention programs such as the Strengthening Families Program 10-14 (SFP) has been demonstrated in the USA, European SFP adaptations have not replicated these sizable effects. Following the rationale of the risk moderation hypothesis positing that elevated risk groups may benefit more from a preventive intervention than lower-risk groups, we reanalyzed evaluation data from a randomized controlled trial testing the adapted German version of SFP (SFP-D). We hypothesized a differential impact of risk status on intervention results. The study employed a minimal control condition. Of the N = 292 participating children, 73.5% qualified as at-risk because they lived in a deprived urban district, and 26.5% qualified as high risk because they additionally scored as "difficult" in the German Strengths and Difficulty Questionnaire (parents' reports using gender- and age-specific German norms). Outcomes were children's self-reports on substance use, mental health, family functioning, and quality of life. Data were analyzed with repeated measures linear mixed models and relative risk analyses. The high-risk group in the SFP-D condition achieved the best results compared with all other groups, especially in mental health and quality of life. Relative risk analyses on tobacco [alcohol] abstinence showed that an additional percentage of 29.8% [16.0%] of high-risk children in nonabstinent controls would have remained abstinent if they had participated in SFP-D. We conclude that risk load influences the impact of substance use prevention programs and discuss to what extent differential analyses can add value to prevention research.

Early-stage primary school children attending a school in the Malawian School Feeding Program (SFP) have better reversal learning and lean muscle mass growth than those attending a non-SFP school.

PubMed

Nkhoma, Owen W W; Duffy, Maresa E; Cory-Slechta, Deborah A; Davidson, Philip W; McSorley, Emeir M; Strain, J J; O'Brien, Gerard M

2013-08-01

In developing countries, schoolchildren encounter a number of challenges, including failure to complete school, poor health and nutrition, and poor academic performance. Implementation of school feeding programs (SFPs) in less developed countries is increasing and yet there is mixed evidence regarding their positive effects on nutrition, education, and cognition at the population level. This study evaluated cognitive and anthropometric outcomes in entry-level primary school children in Malawi with the aim of generating evidence for the ongoing debate about SFPs in Malawi and other developing countries. A total of 226 schoolchildren aged 6-8 y in 2 rural Malawian public primary schools were followed for one school year. Children attending one school (SFP school) received a daily ration of corn-soy blend porridge, while those attending the other (non-SFP school) did not. Baseline and post-baseline outcomes included the Cambridge Neurological Test Automated Battery cognitive tests of paired associate learning, rapid visual information processing and intra-extra dimensional shift, and anthropometric measurements of weight, height, and mid-upper arm circumference (MUAC). At follow-up, the SFP subcohort had a greater reduction than the non-SFP subcohort in the number of intra-extra predimensional shift errors made (mean 18.5 and 24.9, respectively; P-interaction = 0.02) and also showed an increase in MUAC (from 16.3 to 17.0; P-interaction <0.0001). The results indicate that the SFP in Malawi is associated with an improvement in reversal learning and catch-up growth in lean muscle mass in children in the SFP school compared with children in the non-SFP school. These findings suggest that the Malawian SFP, if well managed and ration sizes are sustained, may have the potential to improve nutritional and cognitive indicators of the most disadvantaged children.

School feeding contributes to micronutrient adequacy of Ghanaian schoolchildren.

PubMed

Abizari, Abdul-Razak; Buxton, Christiana; Kwara, Lugutuah; Mensah-Homiah, Joseph; Armar-Klemesu, Margaret; Brouwer, Inge D

2014-09-28

Without gains in nutritional outcomes, it is unlikely that school feeding programmes (SFP) could improve cognition and academic performance of schoolchildren despite the improvements in school enrolment. We compared the nutrient intake adequacy and Fe and nutritional status of SFP and non-SFP participants in a cross-sectional survey involving 383 schoolchildren (aged 5-13 years). Quantitative 24 h recalls and weighed food records, repeated in 20% subsample, were used to estimate energy and nutrient intakes adjusted for day-to-day variations. The probability of adequacy (PA) was calculated for selected micronutrients and the mean of all PA (MPA) was calculated. The concentrations of Hb, serum ferritin, and soluble transferrin receptor (sTfR) and anthropometric measurements were used to determine Fe and nutritional status. Energy and nutrient intakes and their adequacies were significantly higher among SFP participants (P<0·001). The MPA of micronutrients was significantly higher among SFP participants (0·61 v. 0·18; P<0·001), and the multiple-micronutrient-fortified corn soya blend was a key contributor to micronutrient adequacy. In SFP participants, 6 g/l higher Hb concentrations (P<0·001) and about 10% points lower anaemia prevalence (P=0·06) were observed. The concentration of sTfR was significantly lower among SFP participants (11·2 v. 124 mg/l; P=0·04); however, there was no difference in the prevalence of Fe deficiency and Fe-deficiency anaemia between SFP and non-SFP participants. There was also no significant difference in the prevalence of thinness, underweight and stunting. In conclusion, the present results indicate that school feeding is associated with higher intakes and adequacies of energy and nutrients, but not with the prevalence of Fe and nutritional status indicators. The results also indicate an important role for micronutrient-dense foods in the achievement of micronutrient adequacy within SFP.

Parents and Early Life Environment Affect Behavioral Development of Laying Hen Chickens

PubMed Central

de Haas, Elske N.; Bolhuis, J. Elizabeth; Kemp, Bas; Groothuis, Ton G. G.; Rodenburg, T. Bas

2014-01-01

Severe feather pecking (SFP) in commercial laying hens is a maladaptive behavior which is associated with anxiety traits. Many experimental studies have shown that stress in the parents can affect anxiety in the offspring, but until now these effects have been neglected in addressing the problem of SFP in commercially kept laying hens. We therefore studied whether parental stock (PS) affected the development of SFP and anxiety in their offspring. We used flocks from a brown and white genetic hybrid because genetic background can affect SFP and anxiety. As SFP can also be influenced by housing conditions on the rearing farm, we included effects of housing system and litter availability in the analysis. Forty-seven rearing flocks, originating from ten PS flocks were followed. Behavioral and physiological parameters related to anxiety and SFP were studied in the PS at 40 weeks of age and in the rearing flocks at one, five, ten and fifteen weeks of age. We found that PS had an effect on SFP at one week of age and on anxiety at one and five weeks of age. In the white hybrid, but not in the brown hybrid, high levels of maternal corticosterone, maternal feather damage and maternal whole-blood serotonin levels showed positive relations with offsprings’ SFP at one week and offsprings’ anxiety at one and five weeks of age. Disruption and limitation of litter supply at an early age on the rearing farms increased SFP, feather damage and fearfulness. These effects were most prominent in the brown hybrid. It appeared that hens from a brown hybrid are more affected by environmental conditions, while hens from a white hybrid were more strongly affected by parental effects. These results are important for designing measures to prevent the development of SFP, which may require a different approach in brown and white flocks. PMID:24603500

Attachment in the Making: Mother and Father Sensitivity and Infants’ Responses during the Still-Face Paradigm

PubMed Central

Braungart-Rieker, Julia M.; Zentall, Shannon; Lickenbrock, Diane M.; Ekas, Naomi V.; Oshio, Toko; Planalp, Elizabeth

2014-01-01

This study examined the extent to which infant and parent response trajectories during the Still-Face-Paradigm (SFP) in early infancy predicted later infant-mother and infant-father attachment. Families (n = 135) participated in the SFP when infants were 3, 5, and 7 months and the Strange Situation when infants were 12 (mothers) and 14 months (fathers). Multilevel models showed that parent sensitivity assessed during the SFP was related to infants’ affective and behavioral response trajectories during the SFP, and that sensitivity and infant response trajectories predicted attachment. Results from the present study support the notion that parent and infant responses in the SFP with mothers and fathers during Bowlby’s Attachment in the Making phase provide insight into the developing parent-child attachment relationship. PMID:24833270

Fungal Peritonitis: Underestimated Disease in Critically Ill Patients with Liver Cirrhosis and Spontaneous Peritonitis.

PubMed

Lahmer, Tobias; Brandl, Andreas; Rasch, Sebastian; Schmid, Roland M; Huber, Wolfgang

2016-01-01

Spontaneous peritonitis, especially spontaneous fungal peritonitis (SFP), is an important and potentially fatal complication in patients with endstage liver disaese. We evaluated potential risk factors, microbiological findings, and outcome of patients with SFP compared to spontaneous bacterial peritonitis (SBP) in critically ill patients. Retrospective analyses of critically ill patients with suspected spontaneous peritonitis. Out of 205 patients, 20 (10%) had SFP, 28 (14%) had SBP, 48 (24%) had peritonitis without microbiological findings (SP) and 109 (52%) had no-peritonitis (NP). APACHE II and SOFA score were significantly higher in patients with SFP (26; 22-28; p<0.004 and 16; 14-18; p<0.002), SBP (26; 22-28; p<0.004 and 16; 14-18; p<0.002) and SP (24; 18-30; p<0.045 and 14; 10-18; p<0.044) as compared to NP (22; 16-24 and 12; 10-14). CHILD Pugh classification was mainly CHILD C and MELD Score was in patients with SFP (34; 18-40; p<0.001), SBP (32;12-40 p<0.002) and SP (29; 14-40 p<0.003) significantly higher as compared to NP (25;8-40). Nosocomial peritonitis could be significantly more often found in patients with SFP (65%; p<0.023) and SBP (62%, p<0.030) as compared to SP (51 p = 0.243) and NP (45%). Antibiotic pretreatment last 3 month prior peritonitis was significantly more often in patients with SFP (85%; p<0.002), SBP (71%, p<0.033), and SP (56; p<0.040) as compared to NP (33%). Candida albicans (60%; 12/20) was the most common isolated fungus, followed by Candida glabrata (13%) and Candida krusei (13%). Mortality rate was significantly higher in patients with SFP (90%, p<0.001), followed by SBP (75%; p<0.001) and SP (69%; p<0.001) as compared to NP (45%). SFP is not a rare complication in end stage liver disease which is associated with increased mortality. Physicians should be aware of SFP in patients with CHILD C liver cirrhosis, elevated MELD score, antibiotic pretreatment and nosocomial peritonitis.

Evaluation of Saccharomyces cerevisiae fermentation product as an alternative to monensin on growth performance, cost of gain, and carcass characteristics of heavy-weight yearling beef steers.

PubMed

Swyers, K L; Wagner, J J; Dorton, K L; Archibeque, S L

2014-06-01

Two hundred fifty-two cross-bred yearling steers (406 ± 24 kg BW) were used in a completely randomized block design with a 2 × 2 factorial arrangement of treatments (7 pens/treatment) to evaluate the effects of dietary Saccharomyces cerevisiae fermentation product (SFP) and monensin (MON) on growth performance and carcass characteristics. Dietary treatments arranged as a 2 × 2 factorial were 1) with or without SFP and 2) with or without MON. Finishing diets contained 19.7% of DM as dried distiller's grains with solubles. Both SFP and MON were added in the total mixed ration in place of an equal amount of cornmeal (DM basis; target intake = 2.8 g of SFP and 33 mg of MON/kg of dietary DM). Each treatment group was offered ad libitum access to a transition ration from d 1 to 8 and then to the finishing ration from d 9 to 125. Body weights were collected on d 0, 28, 56, 84, 110, and 125. Initial and final BW was an average of 2-d weights (d -1 and 0 and d 124 and 125, respectively). Steers were shipped for harvest on d 125. Overall ADG was decreased (P = 0.03) in steers supplemented with SFP, but final BW was similar among treatments. Feeding SFP was associated with lighter (P < 0.01) HCW and a greater (P = 0.01) number of carcasses grading USDA Choice. Twelfth rib fat thickness was not affected by SFP (P = 0.82) or MON (P = 0.35), but numerical decreases in 12th rib fat thickness among cattle receiving SFP or MON alone contributed to a tendency (P = 0.07) for greater 12 rib fat thickness when SFP and MON were provided. There was no effect of treatment on cost of gain (P ≥ 0.21). The effects of SFP in the current study may have been limited in heavy yearling steers due to consumption of a finishing diet containing 19.7% dried distiller's grains with solubles.

A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence.

PubMed

Drost, Derek R; Novaes, Evandro; Boaventura-Novaes, Carolina; Benedict, Catherine I; Brown, Ryan S; Yin, Tongming; Tuskan, Gerald A; Kirst, Matias

2009-06-01

Microarrays have demonstrated significant power for genome-wide analyses of gene expression, and recently have also revolutionized the genetic analysis of segregating populations by genotyping thousands of loci in a single assay. Although microarray-based genotyping approaches have been successfully applied in yeast and several inbred plant species, their power has not been proven in an outcrossing species with extensive genetic diversity. Here we have developed methods for high-throughput microarray-based genotyping in such species using a pseudo-backcross progeny of 154 individuals of Populus trichocarpa and P. deltoides analyzed with long-oligonucleotide in situ-synthesized microarray probes. Our analysis resulted in high-confidence genotypes for 719 single-feature polymorphism (SFP) and 1014 gene expression marker (GEM) candidates. Using these genotypes and an established microsatellite (SSR) framework map, we produced a high-density genetic map comprising over 600 SFPs, GEMs and SSRs. The abundance of gene-based markers allowed us to localize over 35 million base pairs of previously unplaced whole-genome shotgun (WGS) scaffold sequence to putative locations in the genome of P. trichocarpa. A high proportion of sampled scaffolds could be verified for their placement with independently mapped SSRs, demonstrating the previously un-utilized power that high-density genotyping can provide in the context of map-based WGS sequence reassembly. Our results provide a substantial contribution to the continued improvement of the Populus genome assembly, while demonstrating the feasibility of microarray-based genotyping in a highly heterozygous population. The strategies presented are applicable to genetic mapping efforts in all plant species with similarly high levels of genetic diversity.

Remedial self-fulfilling prophecy: two field experiments to prevent Golem effects among disadvantaged women.

PubMed

Davidson, O B; Eden, D

2000-06-01

The Pygmalion effect is a self-fulfilling prophecy (SFP) in which raising leader expectations boosts subordinate performance. Although attempts to produce Pygmalion effects have been successful repeatedly among men, attempts to produce Pygmalion effects with female leaders have yielded null results. Also, only 1 experiment has demonstrated the Golem effect (i.e., negative SFP in which low leader expectations impair subordinate performance). In 2 field experiments testing the SFP hypothesis among women leading disadvantaged women, experimental leaders were led to believe that their trainees had higher than usual potential. In reality, the trainees had been assigned randomly. Manipulation checks confirmed that the treatment raised leader expectations toward experimental trainees. Analysis of variance of performance detected the predicted SFP effects in both experiments. These were the first-ever experimental confirmations of SFP among women as leaders.

Transport and uptake effects of marine complex lipid liposomes in small intestinal epithelial cell models.

PubMed

Du, Lei; Yang, Yu-Hong; Xu, Jie; Wang, Yu-Ming; Xue, Chang-Hu; Kurihara, Hideyuki; Takahashi, Koretaro

2016-04-01

Nowadays, marine complex lipids, including starfish phospholipids (SFP) and cerebrosides (SFC) separated from Asterias amurensis as well as sea cucumber phospholipids (SCP) and cerebrosides (SCC) isolated from Cucumaria frondosa, have received much attention because of their potent biological activities. However, little information is known on the transport and uptake of these lipids in liposome forms in small intestinal cells. Therefore, this study was undertaken to investigate the effects of these complex lipid liposomes on transport and uptake in Caco-2 and M cell monolayer models. The results revealed that SFP and SCP contained 42% and 47.9% eicosapentaenoic acid (EPA), respectively. The average particle sizes of liposomes prepared in this study were from 169 to 189 nm. We found that the transport of the liposomes across the M cell monolayer model was much higher than the Caco-2 cell monolayer model. The liposomes consisting of SFP or SCP showed significantly higher transport and uptake than soy phospholipid (soy-PL) liposomes in both Caco-2 and M cell monolayer models. Our results also exhibited that treatment with 1 mM liposomes composed of SFP or SCP for 3 h tended to increase the EPA content in phospholipid fractions of both differentiated Caco-2 and M cells. Moreover, it was also found that the hybrid liposomes consisting of SFP/SFC/cholesterol (Chol) revealed higher transport and uptake across the M cell monolayer in comparison with other liposomes. Furthermore, treatment with SFP/SFC/Chol liposomes could notably decrease the trans-epithelial electrical resistance (TEER) values of Caco-2 and M cell monolayers. The present data also showed that the cell viability of differentiated Caco-2 and M cells was not affected after the treatment with marine complex lipids or soy-PL liposomes. Based on the data in this study, it was suggested that marine complex lipid liposomes exhibit prominent transport and uptake in small intestinal epithelial cell models.

Seminal fluid protein depletion and replenishment in the fruit fly, Drosophila melanogaster: an ELISA-based method for tracking individual ejaculates

PubMed Central

Sirot, Laura K.; Wolfner, Mariana F.

2014-01-01

In many species, seminal fluid proteins (SFPs) affect female post-mating behavioral patterns, including sperm storage, egg laying, feeding, and remating. Yet, few studies have investigated the patterns of allocation, depletion, and replenishment of SFPs in male animals, despite the importance of these proteins to male and female reproductive success. To investigate such SFP dynamics, it is necessary to have a sensitive method for quantifying SFP levels in males and mated females. We developed such a method by adapting the enzyme-linked immunosorbent assay (ELISA) using anti-SFP antibodies. Here, we first use two Drosophila melanogaster SFPs (ovulin and sex peptide) to demonstrate that ELISAs provide accurate measures of SFP levels. We find that, consistent with previous data from Western blotting or immunofluorescence studies, levels of both ovulin and sex peptide decline in the mated female with time since mating, but they do so at different rates. We then use ELISAs to show that males become depleted of SFPs with repeated matings, but that previously mated males are able to transfer “virgin” levels of SFPs after 3 days of sexual inactivity. Finally, we demonstrate that ELISAs can detect SFPs from wild-caught D. melanogaster males and, thus, potentially can be used to track mating patterns in the wild. This method of measuring SFP dynamics can be used in a wide range of species to address questions related to male reproductive investment, female mating history, and variation in female post-mating behavioral changes. PMID:24733957

Evaluation to Improve a High School Summer Science Outreach Program †

PubMed Central

Chiappinelli, Katherine B.; Moss, Britney L.; Lenz, Devjanee Swain; Tonge, Natasha A.; Joyce, Adam; Holt, Glen E.; Holt, Leslie Edmonds; Woolsey, Thomas A.

2016-01-01

The goal of the Young Scientist Program (YSP) at Washington University School of Medicine in St. Louis (WUSM) is to broaden science literacy and recruit talent for the scientific future. In particular, YSP seeks to expose underrepresented minority high school students from St. Louis public schools (SLPS) to a wide variety of careers in the sciences. The centerpiece of YSP, the Summer Focus Program (SFP), is a nine-week, intensive research experience for competitively chosen rising high school seniors (Scholars). Scholars are paired with volunteer graduate student, medical student, or postdoctoral fellow mentors who are active members of the practicing scientific community and serve as guides and exemplars of scientific careers. The SFP seeks to increase the number of underrepresented minority students pursuing STEM undergraduate degrees by making the Scholars more comfortable with science and science literacy. The data presented here provide results of the objective, quick, and simple methods developed by YSP to assess the efficacy of the SFP from 2006 to 2013. We demonstrate that the SFP successfully used formative evaluation to continuously improve the various activities within the SFP over the course of several years and in turn enhance student experiences within the SFP. Additionally we show that the SFP effectively broadened confidence in science literacy among participating high school students and successfully graduated a high percentage of students who went on to pursue science, technology, engineering, and mathematics (STEM) majors at the undergraduate level. PMID:27158303

Evaluation to Improve a High School Summer Science Outreach Program.

PubMed

Chiappinelli, Katherine B; Moss, Britney L; Lenz, Devjanee Swain; Tonge, Natasha A; Joyce, Adam; Holt, Glen E; Holt, Leslie Edmonds; Woolsey, Thomas A

2016-05-01

The goal of the Young Scientist Program (YSP) at Washington University School of Medicine in St. Louis (WUSM) is to broaden science literacy and recruit talent for the scientific future. In particular, YSP seeks to expose underrepresented minority high school students from St. Louis public schools (SLPS) to a wide variety of careers in the sciences. The centerpiece of YSP, the Summer Focus Program (SFP), is a nine-week, intensive research experience for competitively chosen rising high school seniors (Scholars). Scholars are paired with volunteer graduate student, medical student, or postdoctoral fellow mentors who are active members of the practicing scientific community and serve as guides and exemplars of scientific careers. The SFP seeks to increase the number of underrepresented minority students pursuing STEM undergraduate degrees by making the Scholars more comfortable with science and science literacy. The data presented here provide results of the objective, quick, and simple methods developed by YSP to assess the efficacy of the SFP from 2006 to 2013. We demonstrate that the SFP successfully used formative evaluation to continuously improve the various activities within the SFP over the course of several years and in turn enhance student experiences within the SFP. Additionally we show that the SFP effectively broadened confidence in science literacy among participating high school students and successfully graduated a high percentage of students who went on to pursue science, technology, engineering, and mathematics (STEM) majors at the undergraduate level.

Integrating mindfulness with parent training: effects of the Mindfulness-Enhanced Strengthening Families Program.

PubMed

Coatsworth, J Douglas; Duncan, Larissa G; Nix, Robert L; Greenberg, Mark T; Gayles, Jochebed G; Bamberger, Katharine T; Berrena, Elaine; Demi, Mary Ann

2015-01-01

There is growing support for the efficacy of mindfulness training with parents as an intervention technique to improve parenting skills and reduce risk for youth problem behaviors. The evidence, however, has been limited to small scale studies, many with methodological shortcomings. This study sought to integrate mindfulness training with parents into the Strengthening Families Program: For Parents and Youth 10-14 (SFP 10-14), an empirically-validated family-based preventive intervention. It used a randomized-controlled comparative effectiveness study design (N = 432 families, 31% racial/ethnic minority) to test the efficacy of the Mindfulness-Enhanced Strengthening Families Program (MSFP), compared to standard SFP 10-14 and a minimal-treatment home study control condition. Results indicated that, in general, MSFP was as effective as SFP 10-14 in improving multiple dimensions of parenting, including interpersonal mindfulness in parenting, parent-youth relationship quality, youth behavior management, and parent well-being, according to both parent and youth reports at both postintervention and 1-year follow-up. This study also found that in some areas MSFP boosted and better sustained the effects of SFP 10-14, especially for fathers. Although the pattern of effects was not as uniform as hypothesized, this study provides intriguing evidence for the unique contribution of mindfulness activities to standard parent training.

Integrating Mindfulness with Parent Training: Effects of the Mindfulness-Enhanced Strengthening Families Program

PubMed Central

Coatsworth, J. Douglas; Duncan, Larissa G.; Nix, Robert L.; Greenberg, Mark T.; Gayles, Jochebed G.; Bamberger, Katharine T.; Berrena, Elaine; Demi, Mary Ann

2015-01-01

There is growing support for the efficacy of mindfulness training with parents as an intervention technique to improve parenting skills and reduce risk for youth problem behaviors. The evidence, however, has been limited to small scale studies, many with methodological shortcomings. This study sought to integrate mindfulness training with parents into the Strengthening Families Program: For Parents and Youth 10-14 (SFP 10-14), an empirically-validated family-based preventive intervention. It used a randomized-controlled comparative effectiveness study design (N = 432 families, 31% racial/ethnic minority) to test the efficacy of the Mindfulness-Enhanced Strengthening Families Program (MSFP), compared to standard SFP 10-14 and a minimal-treatment home study control condition. Results indicated that, in general, MSFP was as effective as SFP 10-14 in improving multiple dimensions of parenting, including interpersonal mindfulness in parenting, parent-youth relationship quality, youth behavior management, and parent well-being, according to both parent and youth reports at both post-intervention and one-year follow-up. This study also found that in some areas MSFP boosted and better sustained the effects of SFP 10-14, especially for fathers. Although the pattern of effects was not as uniform as hypothesized, this study provides intriguing evidence for the unique contribution of mindfulness activities to standard parent training. PMID:25365122

Comparison of virulence and antibiotic resistance genes of food poisoning outbreak isolates of Staphylococcus aureus with isolates obtained from bovine mastitis milk and pig carcasses.

PubMed

Johler, Sophia; Layer, Franziska; Stephan, Roger

2011-11-01

Staphylococcus aureus is the etiological agent in a variety of infections in humans and livestock and produces enterotoxins leading to staphylococcal food poisoning (SFP), one of the most prevalent foodborne intoxication diseases worldwide. Pork and bovine milk are considered possible sources of SFP because pig skin is often colonized by S. aureus and bovine mastitis caused by S. aureus is common, but conclusive data are limited. The objective of the present study was to compare S. aureus isolates associated with cases of SFP with isolates obtained from bovine mastitis milk and pig carcasses. DNA microarray analysis and spa gene typing were performed with 100 S. aureus isolates: 20 isolates related to outbreaks of SFP in humans, 39 isolates obtained from pig carcasses, and 41 isolates collected from bovine mastitis milk. No overlap in spa types was observed for SFP isolates (t008, t015, t018, t024, t056, t084, t279, t377, t383, t648, t733, t912, t1239, t1270, t4802, and t6969) and isolates gathered from milk or pork. The porcine isolates were assigned to t034, t208, t337, t524, t899, t1939, t2922, t2971, t4475, and t7006, and the bovine isolates belonged to t267, t524, t529, t1403, t2953, t7007, t7008, and t7013. Comparison of microarray profiles revealed similar virulence gene patterns for isolates collected from the same host (pigs or cattle) but few similarities between SFP isolate profiles and the profiles of isolates obtained from bovine mastitis milk and pig carcasses. Although only some bovine and porcine isolates possessed the β-lactamase gene blaZ (milk, 24%; pork, 28%), significantly higher numbers of SFP isolates contained blaZ (90%). Investigations of these isolates provided no evidence that pork or bovine mastitis milk represent common sources of SFP.

Object oriented classification of high resolution data for inventory of horticultural crops

NASA Astrophysics Data System (ADS)

Hebbar, R.; Ravishankar, H. M.; Trivedi, S.; Subramoniam, S. R.; Uday, R.; Dadhwal, V. K.

2014-11-01

High resolution satellite images are associated with large variance and thus, per pixel classifiers often result in poor accuracy especially in delineation of horticultural crops. In this context, object oriented techniques are powerful and promising methods for classification. In the present study, a semi-automatic object oriented feature extraction model has been used for delineation of horticultural fruit and plantation crops using Erdas Objective Imagine. Multi-resolution data from Resourcesat LISS-IV and Cartosat-1 have been used as source data in the feature extraction model. Spectral and textural information along with NDVI were used as inputs for generation of Spectral Feature Probability (SFP) layers using sample training pixels. The SFP layers were then converted into raster objects using threshold and clump function resulting in pixel probability layer. A set of raster and vector operators was employed in the subsequent steps for generating thematic layer in the vector format. This semi-automatic feature extraction model was employed for classification of major fruit and plantations crops viz., mango, banana, citrus, coffee and coconut grown under different agro-climatic conditions. In general, the classification accuracy of about 75-80 per cent was achieved for these crops using object based classification alone and the same was further improved using minimal visual editing of misclassified areas. A comparison of on-screen visual interpretation with object oriented approach showed good agreement. It was observed that old and mature plantations were classified more accurately while young and recently planted ones (3 years or less) showed poor classification accuracy due to mixed spectral signature, wider spacing and poor stands of plantations. The results indicated the potential use of object oriented approach for classification of high resolution data for delineation of horticultural fruit and plantation crops. The present methodology is applicable at local levels and future development is focused on up-scaling the methodology for generation of fruit and plantation crop maps at regional and national level which is important for creation of database for overall horticultural crop development.

Plasma pharmacokinetics and synovial concentrations of S-flurbiprofen plaster in humans.

PubMed

Yataba, Ikuko; Otsuka, Noboru; Matsushita, Isao; Kamezawa, Miho; Yamada, Ichimaro; Sasaki, Sigeru; Uebaba, Kazuo; Matsumoto, Hideo; Hoshino, Yuichi

2016-01-01

The purpose of this study is to investigate the pharmacokinetics and deep tissue penetration capability of the newly developed S-flurbiprofen plaster (SFPP) in humans. Study 1: SFPP tape-type patch (2-60 mg) was applied to the lower back for 24 h in healthy adult volunteers. S-flurbiprofen (SFP) plasma concentration was measured over time to examine SFP pharmacokinetics. Study 2: SFPP (20 mg) was applied for 12 h to the affected knee of osteoarthritis (OA) patients who were scheduled for total knee arthroplasty. Deep tissues (synovial tissue and synovial fluid) were collected during surgery to compare SFP concentrations after application of SFPP or a commercially available flurbiprofen (FP) gel-type patch. Study 1: The plasma concentration of SFP was sustained during 24-h topical application of the SFPP, showing a high percutaneous absorption ratio of 51.4-72.2 %. Cmax and AUC0-∞ were dose-proportional. Study 2: After application of the SFPP for 12 h, SFP concentrations in the synovial tissue and synovial fluid were 14.8-fold (p = 0.002) and 32.7-fold (p < 0.001) higher, respectively, than those achieved by the FP patch. Sustained plasma concentration of SFP and high percutaneous absorption ratio was observed after 24-h topical application of the SFPP. Compared to the FP patch, the SFPP showed superior percutaneous absorption and greater tissue penetration of SFP into the synovial tissue. Greater tissue penetration of the SFPP seemed to be primarily due to its formulation. Thus, SFPP is expected to show higher efficacy for the treatment of knee OA.

[Children with Multiple Risk Factor Exposition Benefit from the German "Strengthening Families Program"].

PubMed

Bröning, Sonja; Sack, Peter-Michael; Thomsen, Monika; Thomasius, Rainer

2016-09-01

Children with Multiple Risk Factor Exposition Benefit from the German "Strengthening Families Program" The German adaptation of the substance use-preventive family-based Strengthening Families Program 10-14 (SFP, Iowa version) was evaluated in a longitudinal two-year follow-up trial. Participants were N = 292 children with a mean age of twelve years at baseline, and N = 292 parents. We employed a multi-centric, randomized-controlled, two-armed (SFP vs. minimal control condition) study design. Following a "risk moderation hypothesis", we assumed that children with an elevated risk-exposition R(+) would benefit more than children with a low risk-exposition R(-) irrespective of the preventive intervention, and that R(+) under SFP would benefit more than R(+) under the minimal control condition. "Risk-exposition" was measured in correspondence with the Communities That Care Youth Survey-questionnaire. A total of 28 % of children were classified with an elevated risk level. Children's reports confirmed our hypothesis: R(+) report a total of eleven improvements, four of these being significantly more distinct than in the other groups (Anxiety-Depressivity, Punitive Parenting of mother, Punitive Parenting of father, Unbalanced family functioning). In three measures an improvement appears solely in R(+) under SFP (Satisfaction with family functioning, School Attachment and Peer Relationship Quality, Quality of Life). Parents' reports showed a similar tendency, but were less pronounced.

Modulation of Frontoparietal Neurovascular Dynamics in Working Memory

PubMed Central

Ardestani, Allen; Shen, Wei; Darvas, Felix; Toga, Arthur W.; Fuster, Joaquin M.

2016-01-01

Our perception of the world is represented in widespread, overlapping, and interactive neuronal networks of the cerebral cortex. A majority of physiological studies on the subject have focused on oscillatory synchrony as the binding mechanism for representation and transmission of neural information. Little is known, however, about the stability of that synchrony during prolonged cognitive operations that span more than just a few seconds. The present research, in primates, investigated the dynamic patterns of oscillatory synchrony by two complementary recording methods, surface field potentials (SFPs) and near-infrared spectroscopy (NIRS). The signals were first recorded during the resting state to examine intrinsic functional connectivity. The temporal modulation of coactivation was then examined on both signals during performance of working memory ( WM) tasks with long delays (memory retention epochs). In both signals, the peristimulus period exhibited characteristic features in frontal and parietal regions. Examination of SFP signals over delays lasting tens of seconds, however, revealed alternations of synchronization and desynchronization. These alternations occurred within the same frequency bands observed in the peristimulus epoch, without a specific correspondence between any definite cognitive process (e.g., WM) and synchrony within a given frequency band. What emerged instead was a correlation between the degree of SFP signal fragmentation (in time, frequency, and brain space) and the complexity and efficiency of the task being performed. In other words, the incidence and extent of SFP transitions between synchronization and desynchronization—rather than the absolute degree of synchrony—augmented in correct task performance compared with incorrect performance or in a control task without WM demand. An opposite relationship was found in NIRS: increasing task complexity induced more uniform, rather than fragmented, NIRS coactivations. These findings indicate that the particular features of neural oscillations cannot be linearly mapped to cognitive functions. Rather, information and the cognitive operations performed on it are primarily reflected in their modulations over time. The increased complexity and fragmentation of electrical frequencies in WM may reflect the activation of hierarchically diverse cognits (cognitive networks) in that condition. Conversely, the homogeneity in coherence of NIRS responses may reflect the cumulative vascular reactions that accompany that neuroelectrical proliferation of frequencies and the longer time constant of the NIRS signal. These findings are directly relevant to the mechanisms mediating cognitive processes and to physiologically based interpretations of functional brain imaging. PMID:26679214

School feeding program has resulted in improved dietary diversity, nutritional status and class attendance of school children.

PubMed

Zenebe, Mastewal; Gebremedhin, Samson; Henry, Carol J; Regassa, Nigatu

2018-01-23

School Feeding Program (SFP) is a targeted safety net program designed to provide educational and health benefits to vulnerable children. However, limited evidence exists regarding the effect of the intervention on the nutritional status and school attendance of children. The study is aimed at examining the effects of SFP on dietary diversity, nutritional status and class attendance of school children in Boricha district, Southern Ethiopia. The study was conducted based on a representative data collected from 290 students drawn from the district. A school-based comparative cross-sectional study was conducted on school children aged 10-14 years. Data were collected using structured pretested questionnaire. The effects of SFP on dietary diversity score (DDS), class attendance rate, body-mass-index for age (BAZ) and height-for-age (HAZ) Z-scores were assessed using multivariable linear regression model. The finding showed significantly higher mean (±SD) of DDS in SFP beneficiaries (5.8 ± 1.1) than the non-beneficiaries (3.5 ± 0.7) (P < 0.001). BAZ and HAZ of the beneficiaries were also higher than their counterparts, which were (0.07 ± 0.93), (- 0.50 ± 0.86) and (- 1.45 ± 1.38), (- 2.17 ± 1.15) respectively (P < 0.001). The mean (±SD) days of absence from school for non-beneficiaries (2.6 ± 1.6) was significantly higher than that of the beneficiaries (1.3 ± 1.7) (P < 0.05). Given the positive effects of the program in improving the DDS, nutritional status, and class attendance of school children, we strongly recommend scaling up the program to other food insecure areas.

Induction of surfactin production in Bacillus subtilis by gsp, a gene located upstream of the gramicidin S operon in Bacillus brevis.

PubMed Central

Borchert, S; Stachelhaus, T; Marahiel, M A

1994-01-01

The deduced amino acid sequence of the gsp gene, located upstream of the 5' end of the gramicidin S operon (grs operon) in Bacillus brevis, showed a high degree of similarity to the sfp gene product, which is located downstream of the srfA operon in B. subtilis. The gsp gene complemented in trans a defect in the sfp gene (sfpO) and promoted production of the lipopeptide antibiotic surfactin. The functional homology of Gsp and Sfp and the sequence similarity of these two proteins to EntD suggest that the three proteins represent a new class of proteins involved in peptide secretion, in support of a hypothesis published previously (T. H. Grossman, M. Tuckman, S. Ellestad, and M. S. Osburne, J. Bacteriol. 175:6203-6211, 1993). Images PMID:7512553

Digital disruption? Maternal mobile device use is related to infant social-emotional functioning.

PubMed

Myruski, Sarah; Gulyayeva, Olga; Birk, Samantha; Pérez-Edgar, Koraly; Buss, Kristin A; Dennis-Tiwary, Tracy A

2017-09-24

Mobile device use has become increasingly prevalent, yet its impact on infant development remains largely unknown. When parents use mobile devices in front of infants, the parent is physically present but most likely distracted and unresponsive. Research using the classic Still Face Paradigm (SFP) suggests that parental withdrawal and unresponsiveness may have negative consequences for children's social-emotional development. In the present study, 50 infants aged 7.20 to 23.60 months (M = 15.40, SD = 4.74) and their mothers completed a modified SFP. The SFP consisted of three phases: free play (FP; parent and infant play and interact), still face (SF; parent withdraws attention and becomes unresponsive), and reunion (RU; parent resumes normal interaction). The modified SFP incorporated mobile device use in the SF phase. Parents reported on their typical mobile device use and infant temperament. Consistent with the standard SFP, infants showed more negative affect and less positive affect during SF versus FP. Infants also showed more toy engagement and more engagement with mother during FP versus SF and RU. Infants showed the most social bids during SF and more room exploration in SF than RU. More frequent reported mobile device use was associated with less room exploration and positive affect during SF, and less recovery (i.e., engagement with mother, room exploration positive affect) during RU, even when controlling for individual differences in temperament. Findings suggest that the SFP represents a promising theoretical framework for understanding the impact of parent's mobile device use on infant social-emotional functioning and parent-infant interactions. © 2017 John Wiley & Sons Ltd.

Analgesic Effect of the Newly Developed S(+)-Flurbiprofen Plaster on Inflammatory Pain in a Rat Adjuvant-Induced Arthritis Model.

PubMed

Sugimoto, Masanori; Toda, Yoshihisa; Hori, Miyuki; Mitani, Akiko; Ichihara, Takahiro; Sekine, Shingo; Hirose, Takuya; Endo, Hiromi; Futaki, Nobuko; Kaku, Shinsuke; Otsuka, Noboru; Matsumoto, Hideo

2016-02-01

Preclinical Research This article describes the properties of a novel topical NSAID (Nonsteroidal anti-inflammatory drug) patch, SFPP (S(+)-flurbiprofen plaster), containing the potent cyclooxygenase (COX) inhibitor, S(+)-flurbiprofen (SFP). The present studies were conducted to confirm human COX inhibition and absorption of SFP and to evaluate the analgesic efficacy of SFPP in a rat adjuvant-induced arthritis (AIA) model. COX inhibition by SFP, ketoprofen and loxoprofen was evaluated using human recombinant COX proteins. Absorption of SFPP, ketoprofen and loxoprofen from patches through rat skin was assessed 24 h after application. The AIA model was induced by injecting Mycobacterium tuberculosis followed 20 days later by the evaluation of the prostaglandin PGE2 content of the inflamed paw and the pain threshold. SFP exhibited more potent inhibitory activity against COX-1 (IC50  = 8.97 nM) and COX-2 (IC50  = 2.94 nM) than the other NSAIDs evaluated. Absorption of SFP was 92.9%, greater than that of ketoprofen and loxoprofen from their respective patches. Application of SFPP decreased PGE2 content from 15 min to 6 h and reduced paw hyperalgesia compared with the control, ketoprofen and loxoprofen patches. SFPP showed analgesic efficacy, and was superior to the ketoprofen and loxoprofen patches, which could be through the potent COX inhibitory activity of SFP and greater skin absorption. The results suggested SFPP can be expected to exert analgesic effect clinically. © 2016 The Authors Drug Development Research Published by Wiley Periodicals, Inc.

Analgesic Effect of the Newly Developed S(+)‐Flurbiprofen Plaster on Inflammatory Pain in a Rat Adjuvant‐Induced Arthritis Model

PubMed Central

Toda, Yoshihisa; Hori, Miyuki; Mitani, Akiko; Ichihara, Takahiro; Sekine, Shingo; Hirose, Takuya; Endo, Hiromi; Futaki, Nobuko; Kaku, Shinsuke; Otsuka, Noboru; Matsumoto, Hideo

2016-01-01

ABSTRACT Preclinical Research This article describes the properties of a novel topical NSAID (Nonsteroidal anti‐inflammatory drug) patch, SFPP (S(+)‐flurbiprofen plaster), containing the potent cyclooxygenase (COX) inhibitor, S(+)‐flurbiprofen (SFP). The present studies were conducted to confirm human COX inhibition and absorption of SFP and to evaluate the analgesic efficacy of SFPP in a rat adjuvant‐induced arthritis (AIA) model. COX inhibition by SFP, ketoprofen and loxoprofen was evaluated using human recombinant COX proteins. Absorption of SFPP, ketoprofen and loxoprofen from patches through rat skin was assessed 24 h after application. The AIA model was induced by injecting Mycobacterium tuberculosis followed 20 days later by the evaluation of the prostaglandin PGE2 content of the inflamed paw and the pain threshold. SFP exhibited more potent inhibitory activity against COX‐1 (IC50 = 8.97 nM) and COX‐2 (IC50 = 2.94 nM) than the other NSAIDs evaluated. Absorption of SFP was 92.9%, greater than that of ketoprofen and loxoprofen from their respective patches. Application of SFPP decreased PGE2 content from 15 min to 6 h and reduced paw hyperalgesia compared with the control, ketoprofen and loxoprofen patches. SFPP showed analgesic efficacy, and was superior to the ketoprofen and loxoprofen patches, which could be through the potent COX inhibitory activity of SFP and greater skin absorption. The results suggested SFPP can be expected to exert analgesic effect clinically. Drug Dev Res 76 : 20–28, 2016. © 2016 Wiley Periodicals, Inc. PMID:26763139

Quantifying immediate radiative forcing by black carbon and organic matter with the Specific Forcing Pulse

NASA Astrophysics Data System (ADS)

Bond, T. C.; Zarzycki, C.; Flanner, M. G.; Koch, D. M.

2010-06-01

We propose a measure to quantify climate warming or cooling by pollutants with atmospheric lifetimes of less than one year: the Specific Forcing Pulse (SFP). SFP is the amount of energy added to the Earth system per mass of pollutant emitted. Global average SFP for black carbon, including atmosphere and cryosphere, is 1.12 GJ g-1 and that for organic matter is -0.061 GJ g-1. We provide regional values for black carbon (BC) and organic matter (OM) emitted from 23 source-region combinations, divided between atmosphere and cryosphere impacts and identifying forcing by latitude. Regional SFP varies by about 40% for black carbon. This variation is relatively small because of compensating effects; particles from regions that affect ice albedo typically have shorter atmospheric lifetimes because of lower convection. The ratio between BC and OM SFP implies that, for direct forcing, an OM:BC mass ratio of 15 has a neutral effect on top-of-atmosphere direct forcing for any region, and any lower ratio induces direct warming. However, important processes, particularly cloud changes that tend toward cooling, have not been included here. We demonstrate ensemble adjustment, in which we produce a "best estimate" by combining a suite of diverse but simple models and enhanced models of greater complexity. Adjustments for black carbon internal mixing and for regional variability are discussed; regions with convection are implicated in greater model diversity. SFP expresses scientific uncertainty and separates it from policy uncertainty; the latter is caused by disagreements about the relevant time horizon, impact, or spatial scale of interest. However, metrics used in policy discussions, such as global warming potentials, are easily derived from SFP. Global-average SFP for biofuel and fossil fuel emissions translates to a 100-year GWP of about 760 for black carbon and -40 for organic matter when snow forcing is included. Ensemble-adjusted estimates of atmospheric radiative impact by black and organic matter using year 2000 emissions are +0.46 W m-2 and -0.17 W m-2, respectively; anthropogenic forcing is +0.38 W m-2 and -0.12 W m-2. The black carbon value is only 11% higher than that of the Intergovernmental Panel on Climate Change (IPCC), although this value includes enhanced absorption due to internal mixing.

Quantifying immediate radiative forcing by black carbon and organic matter with the Specific Forcing Pulse

NASA Astrophysics Data System (ADS)

Bond, T. C.; Zarzycki, C.; Flanner, M. G.; Koch, D. M.

2011-02-01

Climatic effects of short-lived climate forcers (SLCFs) differ from those of long-lived greenhouse gases, because they occur rapidly after emission and because they depend upon the region of emission. The distinctive temporal and spatial nature of these impacts is not captured by measures that rely on global averages or long time integrations. Here, we propose a simple measure, the Specific Forcing Pulse (SFP), to quantify climate warming or cooling by these pollutants, where we define "immediate" as occurring primarily within the first year after emission. SFP is the amount of energy added to or removed from a receptor region in the Earth-atmosphere system by a chemical species, per mass of emission in a source region. We limit the application of SFP to species that remain in the atmosphere for less than one year. Metrics used in policy discussions, such as total forcing or global warming potential, are easily derived from SFP. However, SFP conveys purely physical information without incurring the policy implications of choosing a time horizon for the global warming potential. Using one model (Community Atmosphere Model, or CAM), we calculate values of SFP for black carbon (BC) and organic matter (OM) emitted from 23 source-region combinations. Global SFP for both atmosphere and cryosphere impacts is divided among receptor latitudes. SFP is usually greater for open-burning emissions than for energy-related (fossil-fuel and biofuel) emissions because of the timing of emission. Global SFP for BC varies by about 45% for energy-related emissions from different regions. This variation would be larger except for compensating effects. When emitted aerosol has larger cryosphere forcing, it often has lower atmosphere forcing because of less deep convection and a shorter atmospheric lifetime. A single model result is insufficient to capture uncertainty. We develop a best estimate and uncertainties for SFP by combining forcing results from 12 additional models. We outline a framework for combining a large number of simple models with a smaller number of enhanced models that have greater complexity. Adjustments for black carbon internal mixing and for regional variability are discussed. Emitting regions with more deep convection have greater model diversity. Our best estimate of global-mean SFP is +1.03 ± 0.52 GJ g-1 for direct atmosphere forcing of black carbon, +1.15 ± 0.53 GJ g-1 for black carbon including direct and cryosphere forcing, and -0.064 (-0.02, -0.13) GJ g-1 for organic matter. These values depend on the region and timing of emission. The lowest OM:BC mass ratio required to produce a neutral effect on top-of-atmosphere direct forcing is 15:1 for any region. Any lower ratio results in positive direct forcing. However, important processes, particularly cloud changes that tend toward cooling, have not been included here. Global-average SFP for energy-related emissions can be converted to a 100-year GWP of about 740 ± 370 for BC without snow forcing, and 830 ± 440 with snow forcing. 100-year GWP for OM is -46 (-18, -92). Best estimates of atmospheric radiative impact (without snow forcing) by black and organic matter are +0.47 ± 0.26 W m-2 and -0.17 (-0.07, -0.35) W m-2 for BC and OM, respectively, assuming total emission rates of 7.4 and 45 Tg yr-1. Anthropogenic forcing is +0.40 ± 0.18 W m-2 and -0.13 (-0.05, -0.25) W m-2 for BC and OM, respectively, assuming anthropogenic emission rates of 6.3 and 32.6 Tg yr-1. Black carbon forcing is only 18% higher than that given by the Intergovernmental Panel on Climate Change (IPCC), although the value presented here includes enhanced absorption due to internal mixing.

[Collective scombroid fish poisoning following tuna consumption in Castellon].

PubMed

Arnedo Pena, A; Bellido Blasco, J B; Pac Sa, M R; González Morán, F; Criado Juárez, J; Mesanza del Notario, I; Rodríguez Merquero, N; Balagué López, A

1996-11-16

To investigate and control of a collective scombroid-fish poisoning (SFP) outbreak, that took place in Castellón, Spain. Description of the outbreak and case-control study in order to identify risk factors. Active surveillance of SFP cases, and inspection of implicated markets. Histamine determination in urine of cases and foods. During June 1994, 15 cases of SFP were found out, with 12 cases occurred on June, 28 and 29. Five families were affected (attack rate 68.2%). The median incubation period was 45 minutes. Disease symptoms included facial or general flushing, headache, diarrhea, nausea, abdominal pain, and peppery taste. Implicated food was fresh tuna, bought in a hypermarket of Castellón (odds ratio = 26.4, 95% confidence intervals: 1.05-666.8), adjusted by age and sex using logistic regression analysis. Four samples of urine from cases presented histamine concentration above 35 micrograms/l. Three samples of tuna consumed by cases and one sample of tuna from the hypermarket had histamine concentration above a 200 ppm. Considering the situation of risk, remaining suspected tuna was confiscated from the hypermarket. Rest unknown if the descompositions of tuna occurred in the hypermarket or during capture and distribution. SFP was caused by fresh tuna ingestion with epidemiologic and analytic confirmation. Determination of histamine in urine of patients could permit to confirm SFP.

The Codacs™ direct acoustic cochlear implant actuator: exploring alternative stimulation sites and their stimulation efficiency.

PubMed

Grossöhmichen, Martin; Salcher, Rolf; Kreipe, Hans-Heinrich; Lenarz, Thomas; Maier, Hannes

2015-01-01

This work assesses the efficiency of the Codacs system actuator (Cochlear Ltd., Sydney Australia) in different inner ear stimulation modalities. Originally the actuator was intended for direct perilymph stimulation after stapedotomy using a piston prosthesis. A possible alternative application is the stimulation of middle ear structures or the round window (RW). Here the perilymph stimulation with a K-piston through a stapes footplate (SFP) fenestration (N = 10) as well as stimulation of the stapes head (SH) with a Bell prosthesis (N = 9), SFP stimulation with an Omega/Aerial prosthesis (N = 8) and reverse RW stimulation (N = 10) were performed in cadaveric human temporal bones (TBs). Codacs actuator output is expressed as equivalent sound pressure level (eq. SPL) using RW and SFP displacement responses, measured by Laser Doppler velocimetry as reference. The axial actuator coupling force in stimulation of stapes and RW was adjusted to ~5 mN. The Bell prosthesis and Omega/Aerial prosthesis stimulation generated similar mean eq. SPLs (Bell: 127.5-141.8 eq. dB SPL; Omega/Aerial: 123.6-143.9 eq. dB SPL), being significantly more efficient than K-piston perilymph stimulation (108.6-131.6 eq. dB SPL) and RW stimulation (108.3-128.2 eq. dB SPL). Our results demonstrate that SH, SFP and RW are adequate alternative stimulation sites for the Codacs actuator using coupling prostheses and an axial coupling force of ~5 mN. Based on the eq. SPLs, all investigated methods were adequate for in vivo hearing aid applications, provided that experimental conditions including constant coupling force will be implemented.

Sfp1 and Rtg3 reciprocally modulate carbon source‐conditional stress adaptation in the pathogenic yeast Candida albicans

PubMed Central

Kastora, Stavroula L.; Herrero‐de‐Dios, Carmen; Avelar, Gabriela M.; Munro, Carol A.

2017-01-01

Summary The pathogenicity of the clinically important yeast, Candida albicans, is dependent on robust responses to host‐imposed stresses. These stress responses have generally been dissected in vitro at 30°C on artificial growth media that do not mimic host niches. Yet host inputs, such as changes in carbon source or temperature, are known to affect C. albicans stress adaptation. Therefore, we performed screens to identify novel regulators that promote stress resistance during growth on a physiologically relevant carboxylic acid and at elevated temperatures. These screens revealed that, under these ‘non‐standard’ growth conditions, numerous uncharacterised regulators are required for stress resistance in addition to the classical Hog1, Cap1 and Cta4 stress pathways. In particular, two transcription factors (Sfp1 and Rtg3) promote stress resistance in a reciprocal, carbon source‐conditional manner. SFP1 is induced in stressed glucose‐grown cells, whereas RTG3 is upregulated in stressed lactate‐grown cells. Rtg3 and Sfp1 regulate the expression of key stress genes such as CTA4, CAP1 and HOG1 in a carbon source‐dependent manner. These mechanisms underlie the stress sensitivity of C. albicans sfp1 cells during growth on glucose, and rtg3 cells on lactate. The data suggest that C. albicans exploits environmentally contingent regulatory mechanisms to retain stress resistance during host colonisation. PMID:28574606

Malnourished children and supplementary feeding during the war emergency in Guinea-Bissau in 1998-1999.

PubMed

Nielsen, Jens; Valentiner-Branth, Palle; Martins, Cesario; Cabral, Fernando; Aaby, Peter

2004-10-01

Supplementary feeding programs (SFPs) are intended to mitigate the deterioration of nutritional status and the increase in mortality among malnourished children. We investigated the effect of an SFP on malnourished children in Guinea-Bissau who were returning to their homes after having been displaced within the country because of war in 1998-1999. The effect of the war on the nutritional status of children aged 6-59 mo who were present in Bissau sometime from September 1998 to June 1999 was evaluated by comparing the mortality and the prevalence of malnutrition with the values expected had the war not occurred and by comparing the severity of malnutrition in malnourished children before and during the war. The quality of the SFP was also evaluated. Children with midupper arm circumference < 130 mm were provided weekly medical consultations and supplementary feeding until recovery. The degree of malnutrition did not increase during the war. The prevalence of malnutrition increased with the start of the war but then decreased. The mortality of malnourished children did not increase during the war. Seventy-four percent of the referred children received treatment; of those, 1% died, 67% recovered, and 32% abandoned treatment. Compliance was 89%. The recovery rate was 13.1. 1000(-1). d(-1), and the median time to recovery was 48 d. Better compliance was associated with shorter time to recovery. Our findings may be biased by changes in the cultural and socioeconomic background of the malnourished children. However, 3 different analyses indicated a beneficial effect of the SFP. Thus, the home-based SFP probably prevented nutritional deterioration during the war in Guinea-Bissau.

The Codacs™ Direct Acoustic Cochlear Implant Actuator: Exploring Alternative Stimulation Sites and Their Stimulation Efficiency

PubMed Central

Grossöhmichen, Martin; Salcher, Rolf; Kreipe, Hans-Heinrich; Lenarz, Thomas; Maier, Hannes

2015-01-01

This work assesses the efficiency of the Codacs system actuator (Cochlear Ltd., Sydney Australia) in different inner ear stimulation modalities. Originally the actuator was intended for direct perilymph stimulation after stapedotomy using a piston prosthesis. A possible alternative application is the stimulation of middle ear structures or the round window (RW). Here the perilymph stimulation with a K-piston through a stapes footplate (SFP) fenestration (N = 10) as well as stimulation of the stapes head (SH) with a Bell prosthesis (N = 9), SFP stimulation with an Omega/Aerial prosthesis (N = 8) and reverse RW stimulation (N = 10) were performed in cadaveric human temporal bones (TBs). Codacs actuator output is expressed as equivalent sound pressure level (eq. SPL) using RW and SFP displacement responses, measured by Laser Doppler velocimetry as reference. The axial actuator coupling force in stimulation of stapes and RW was adjusted to ~ 5 mN. The Bell prosthesis and Omega/Aerial prosthesis stimulation generated similar mean eq. SPLs (Bell: 127.5–141.8 eq. dB SPL; Omega/Aerial: 123.6–143.9 eq. dB SPL), being significantly more efficient than K-piston perilymph stimulation (108.6–131.6 eq. dB SPL) and RW stimulation (108.3–128.2 eq. dB SPL). Our results demonstrate that SH, SFP and RW are adequate alternative stimulation sites for the Codacs actuator using coupling prostheses and an axial coupling force of ~ 5 mN. Based on the eq. SPLs, all investigated methods were adequate for in vivo hearing aid applications, provided that experimental conditions including constant coupling force will be implemented. PMID:25785860

Family Skills Training for Parents and Children. Juvenile Justice Bulletin.

ERIC Educational Resources Information Center

Kumpfer, Karol L.; Tait, Connie M.

Originally designed as a drug abuse prevention program for drug-abusing parents and their children, the Strengthening Families Program (SFP) has developed into a family-change program. Presented in 14 2-hour-long, consecutive weekly sessions, SFP has two versions: for elementary school children and their parents and for parents and youth 10-14…

Performance of Single Friction Pendulum bearing for isolated buildings subjected to seismic actions in Vietnam

NASA Astrophysics Data System (ADS)

Nguyen, N. V.; Nguyen, C. H.; Hoang, H. P.; Huong, K. T.

2018-04-01

Using structural control technology in earthquake resistant design of buildings in Vietnam is very limited. In this paper, a performance evaluation of using Single Friction Pendulum (SFP) bearing for seismically isolated buildings with earthquake conditions in Vietnam is presented. A two-dimensional (2-D) model of the 5-storey building subjected to earthquakes is analyzed in time domain. Accordingly, the model is analyzed for 2 cases: with and without SFP bearing. The ground acceleration data is selected and scaled to suit the design acceleration in Hanoi followed by the Standard TCVN 9386:2012. It is shown that the seismically isolated buildings gets the performance objectives while achieving an 91% reduction in the base shear, a significant decrease in the inter-story drift and absolute acceleration of each story.

Maternal sensitivity and infant autonomic and endocrine stress responses.

PubMed

Bosquet Enlow, Michelle; King, Lucy; Schreier, Hannah Mc; Howard, Jamie M; Rosenfield, David; Ritz, Thomas; Wright, Rosalind J

2014-07-01

Early environmental exposures may help shape the development of the autonomic nervous system (ANS) and hypothalamic-pituitary-adrenal (HPA) axis, influencing vulnerability for health problems across the lifespan. Little is known about the role of maternal sensitivity in influencing the development of the ANS in early life. To examine associations among maternal sensitivity and infant behavioral distress and ANS and HPA axis reactivity to the Repeated Still-Face Paradigm (SFP-R), a dyadic stress task. Observational repeated measures study. Thirty-five urban, sociodemographically diverse mothers and their 6-month-old infants. Changes in infant affective distress, heart rate, respiratory sinus arrhythmia (RSA), and T-wave amplitude (TWA) across episodes of the SFP-R were assessed. A measure of cortisol output (area under the curve) in the hour following cessation of the SFP-R was also obtained. Greater maternal insensitivity was associated with greater infant sympathetic activation (TWA) during periods of stress and tended to be associated with greater cortisol output following the SFP-R. There was also evidence for greater affective distress and less parasympathetic activation (RSA) during the SFP-R among infants of predominantly insensitive mothers. Caregiving quality in early life may influence the responsiveness of the sympathetic and parasympathetic branches of the ANS as well as the HPA axis. Consideration of the ANS and HPA axis systems together provides a fuller representation of adaptive versus maladaptive stress responses. The findings highlight the importance of supporting high quality caregiving in the early years of life, which is likely to promote later health. Copyright © 2014 Elsevier Ltd. All rights reserved.

Sulforaphane Inhibits Mitochondrial Permeability Transition and Oxidative Stress

PubMed Central

Greco, Tiffany; Shafer, Jonathan; Fiskum, Gary

2012-01-01

Exposure of mitochondria to oxidative stress and elevated Ca2+ promotes opening of the mitochondrial permeability transition pore (PTP), resulting in membrane depolarization, uncoupling of oxidative phosphorylation, and potentially cell death. This study tested the hypothesis that treatment of rats with sulforaphane (SFP), an activator of the Nrf2 pathway of antioxidant gene expression, increases the resistance of liver mitochondria to redox-regulated PTP opening and elevates mitochondrial levels of antioxidants. Rats were injected with SFP or drug vehicle and liver mitochondria were isolated 40 hr later. Respiring mitochondria actively accumulated added Ca2+, which was then released through PTP opening induced by agents that either cause an oxidized shift in the mitochondrial redox state or that directly oxidize protein thiol groups. SFP treatment of rats inhibited the rate of pro-oxidant-induced mitochondrial Ca2+ release and increased expression of the glutathione peroxidase/reductase system, thioredoxin, and malic enzyme. These results are the first to demonstrate that SFP treatment of animals increases liver mitochondrial antioxidant defenses and inhibits redox-sensitive PTP opening. This novel form of preconditioning could protect against a variety of pathologies that include oxidative stress and mitochondrial dysfunction in their etiologies. PMID:21986339

Preventing substance misuse: study protocol for a randomised controlled trial of the Strengthening Families Programme 10–14 UK (SFP 10–14 UK)

PubMed Central

2014-01-01

Background Prevention of alcohol, drug and tobacco misuse by young people is a key public health priority. There is a need to develop the evidence base through rigorous evaluations of innovative approaches to substance misuse prevention. The Strengthening Families Programme 10–14 is a universal family-based alcohol, drugs and tobacco prevention programme, which has achieved promising results in US trials, and which now requires cross-cultural assessment. This paper therefore describes the protocol for a randomised controlled trial of the UK version of the Strengthening Families Programme 10–14 (SFP 10–14 UK). Methods/Design The trial comprises a pragmatic cluster randomised controlled effectiveness trial with families as the unit of randomisation, with embedded process and economic evaluations. Participating families will be randomised to one of two treatment groups - usual care with full access to existing services (control group), or usual care plus SFP 10–14 UK (intervention group). The trial has two primary outcomes - the number of occasions that young people report having drunk alcohol in the last 30 days, and drunkenness during the last 30 days, both dichotomised as ‘never’ and ‘1-2 times or more’. The main follow-up is at 2 years past baseline, and short-term and intermediate outcomes are also measured at 9 and 15 months. Discussion The results from this trial will provide evidence on the effectiveness and cost-effectiveness of an innovative universal family-based substance misuse prevention programme in a UK context. Trial registration Current Controlled Trials ISRCTN63550893. PMID:24438460

Pilot Study to Gauge Acceptability of a Mindfulness-Based, Family-Focused Preventive Intervention

ERIC Educational Resources Information Center

Duncan, Larissa G.; Coatsworth, J. Douglas; Greenberg, Mark T.

2009-01-01

The purpose of the present study was to conduct a test of acceptability of a new model for family-focused drug prevention programs for families of early adolescents. An existing evidence-based behavioral intervention, the Strengthening Families Program: For Parents and Youth 10-14 (SFP), was adapted to include concepts and activities related to…

Investigation of Zircaloy-2 oxidation model for SFP accident analysis

NASA Astrophysics Data System (ADS)

Nemoto, Yoshiyuki; Kaji, Yoshiyuki; Ogawa, Chihiro; Kondo, Keietsu; Nakashima, Kazuo; Kanazawa, Toru; Tojo, Masayuki

2017-05-01

The authors previously conducted thermogravimetric analyses on Zircaloy-2 in air. By using the thermogravimetric data, an oxidation model was constructed in this study so that it can be applied for the modeling of cladding degradation in spent fuel pool (SFP) severe accident condition. For its validation, oxidation tests of long cladding tube were conducted, and computational fluid dynamics analyses using the constructed oxidation model were proceeded to simulate the experiments. In the oxidation tests, high temperature thermal gradient along the cladding axis was applied and air flow rates in testing chamber were controlled to simulate hypothetical SFP accidents. The analytical outputs successfully reproduced the growth of oxide film and porous oxide layer on the claddings in oxidation tests, and validity of the oxidation model was proved. Influence of air flow rate for the oxidation behavior was thought negligible in the conditions investigated in this study.

Effectiveness of a Culturally Adapted Strengthening Families Program 12-16-Years for High-Risk Irish Families

ERIC Educational Resources Information Center

Kumpfer, Karol L.; Xie, Jing; O'Driscoll, Robert

2012-01-01

Background: Evidence-based programs (EBPs) targeting effective family skills are the most cost effective for improving adolescent behavioural health. Cochrane Reviews have found the "Strengthening Families Program" (SFP) to be the most effective substance abuse prevention intervention. Standardized cultural adaptation processes resulted…

MELCOR model for an experimental 17x17 spent fuel PWR assembly.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardoni, Jeffrey

2010-11-01

A MELCOR model has been developed to simulate a pressurized water reactor (PWR) 17 x 17 assembly in a spent fuel pool rack cell undergoing severe accident conditions. To the extent possible, the MELCOR model reflects the actual geometry, materials, and masses present in the experimental arrangement for the Sandia Fuel Project (SFP). The report presents an overview of the SFP experimental arrangement, the MELCOR model specifications, demonstration calculation results, and the input model listing.

The Strengthening Families Program 10-14: influence on parent and youth problem-solving skill.

PubMed

Semeniuk, Y; Brown, R L; Riesch, S K; Zywicki, M; Hopper, J; Henriques, J B

2010-06-01

The aim of this paper is to report the results of a preliminary examination of the efficacy of the Strengthening Families Program (SFP) 10-14 in improving parent and youth problem-solving skill. The Hypotheses in this paper include: (1) youth and parents who participated in SFP would have lower mean scores immediately (T2) and 6 months (T3) post intervention on indicators of hostile and negative problem-solving strategies; (2) higher mean scores on positive problem-solving strategies; and (3) youth who participated in SFP would have higher mean scores at T2 and at T3 on indicators of individual problem solving and problem-solving efficacy than youth in the comparison group. The dyads were recruited from elementary schools that had been stratified for race and assigned randomly to intervention or comparison conditions. Mean age of youth was 11 years (SD = 1.04). Fifty-seven dyads (34-intervention&23-control) were videotaped discussing a frequently occurring problem. The videotapes were analysed using the Iowa Family Interaction Rating Scale (IFIRS) and data were analysed using Dyadic Assessment Intervention Model. Most mean scores on the IFIRS did not change. One score changed as predicted: youth hostility decreased at T3. Two scores changed contrary to prediction: parent hostility increased T3 and parent positive problem solving decreased at T2. SFP demonstrated questionable efficacy for problem-solving skill in this study.

Expression of Staphylococcal Enterotoxins under Stress Encountered during Food Production and Preservation.

PubMed

Schelin, Jenny; Susilo, Yusak Budi; Johler, Sophia

2017-12-15

Staphylococcal food poisoning (SFP) is the most prevalent cause of food-borne intoxications worldwide. Consumption of enterotoxins preformed in food causes violent vomiting and can be fatal in children and the elderly. While being repressed by competing bacteria in most matrices, Staphylococcus aureus benefits from crucial competitive advantages in foods with high osmolarity or low pH. During recent years, the long-standing belief in the feasibility of assessing SFP risk based on colony-forming units of S. aureus present in food products has been disproven. Instead, researchers and food business operators are acutely aware of the imminent threat arising from unforeseeable enterotoxin production under stress conditions. This paradigm shift led to a variety of new publications enabling an improved understanding of enterotoxin expression under stress conditions encountered in food. The wealth of data provided by these studies is extremely diverse, as it is based on different methodological approaches, staphylococcal strains, stressors, and enterotoxins. Therefore, in this review, we aggregated and critically evaluated the complex findings of these studies, to provide readers with a current overview of the state of research in the field.

Three forms of assessment of prior knowledge, and improved performance following an enrichment programme, of English second language biology students within the context of a marine theme

NASA Astrophysics Data System (ADS)

Feltham, Nicola F.; Downs, Colleen T.

2002-02-01

The Science Foundation Programme (SFP) was launched in 1991 at the University of Natal, Pietermaritzburg, South Africa in an attempt to equip a selected number of matriculants from historically disadvantaged schools with the skills, resources and self-confidence needed to embark on their tertiary studies. Previous research within the SFP biology component suggests that a major contributor to poor achievement and low retention rates among English second language (ESL) students in the Life Sciences is the inadequate background knowledge in natural history. In this study, SFP student background knowledge was assessed along a continuum of language dependency using a set of three probes. Improved student performance in each of the respective assessments examined the extent to which a sound natural history background facilitated meaningful learning relative to ESL proficiency. Student profiles and attitudes to biology were also examined. Results indicated that students did not perceive language to be a problem in biology. However, analysis of the student performance in the assessment probes indicated that, although the marine course provided the students with the background knowledge that they were initially lacking, they continued to perform better in the drawing and MCQ tools in the post-tests, suggesting that it is their inability to express themselves in the written form that hampers their development. These results have implications for curriculum development within the constructivist framework of the SFP.

Special Forest Products on the Green Mountain and Finger Lakes National Forests: a research-based approach to management

Treesearch

Marla R. Emery; Clare Ginger

2014-01-01

Special forest products (SFPs) are gathered from more than 200 vascular and fungal species on the Green Mountain National Forest (GMNF) and Finger Lakes National Forest (FLNF). This report documents those SFPs and proposes an approach to managing them in the context of legislation directing the U.S. Forest Service to institute a program of active SFP management. Based...

Analysis of the structural organization and thermal stability of two spermadhesins. Calorimetric, circular dichroic and Fourier-transform infrared spectroscopic studies.

PubMed

Menéndez, M; Gasset, M; Laynez, J; López-Zumel, C; Usobiaga, P; Töpfer-Petersen, E; Calvete, J J

1995-12-15

The CUB domain is a widespread 110-amino-acid module found in functionally diverse, often developmentally regulated proteins, for which an antiparallel beta-barrel topology similar to that in immunoglobulin V domains has been predicted. Spermadhesins have been proposed as a subgroup of this protein family built up by a single CUB domain architecture. To test the proposed structural model, we have analyzed the structural organization of two members of the spermadhesin protein family, porcine seminal plasma proteins I/II (PSP-I/PSP-II) heterodimer and bovine acidic seminal fluid protein (aSFP) homodimer, using differential scanning calorimetry, far-ultraviolet circular dichroism and Fourier-transform infrared spectroscopy. Thermal unfolding of PSP-I/PSP-II and aSFP were irreversible and followed a one-step process with transition temperatures (Tm) of 60.5 degrees C and 78.6 degrees C, respectively. The calorimetric enthalpy changes (delta Hcat) of thermal denaturation were 439 kJ/mol for PSP-I/PSP-II and 660 kJ/mol for aSFP dimer. Analysis of the calorimetric curves of PSP-I/PSP-II showed that the entire dimer constituted the cooperative unfolding unit. Fourier-transform infrared spectroscopy and deconvolution of circular dichroic spectra using a convex constraint analysis indicated that beta-structure and turns are the major structural element of both PSP-I/PSP-II (53% of beta-sheet, 21% of turns) and aSFP (44% of beta-sheet, 36% of turns), and that the porcine and the bovine proteins contain little, if any, alpha-helical structure. Taken together, our results indicate that the porcine and the bovine spermadhesin molecules are probably all-beta-structure proteins, and would support a beta-barrel topology like that predicted for the CUB domain. Other beta-structure folds, such as the Greek-key pattern characteristic of many carbohydrate-binding protein domains cannot be eliminated. Finally, the same combination of biophysical techniques was used to characterize the residual secondary structure of thermally denatured forms of PSP-I/PSP-II and aSFP, and to emphasize the aggregation tendency of these forms.

[Polymorphism and structure of the population of Proteocephalus longicollis Zeder, 1800 (Cestoda: Proteocephalidae) in the vendace Coregonus albula L].

PubMed

Anikieva, L V; Kharin, V N; Spektor, E N

2004-01-01

Polymorphism and phenotypic diversity of a hostal ecoform of Proteocephalus longicollis from its typical host, the vendace, Coregonus albula L., were studied. A complex phenotypic structure of the parasite population and presence of morphologically different groupings were revealed. We distinguished four groupings based on the external characters and three groupings based on the feed and reproduction features; among latter groupings one has very specific variations of features. We conclude that P. longicollis has high intraspecific and intrapopulation heterogeneity, and the host plays a stabilising role in the parasite species formation.

Effect of filter designs on hydraulic properties and well efficiency.

PubMed

Kim, Byung-Woo

2014-09-01

To analyze the effect of filter pack arrangement on the hydraulic properties and the well efficiency of a well design, a step drawdown was conducted in a sand-filled tank model. Prior to the test, a single filter pack (SFP), granule only, and two dual filter packs (DFPs), type A (granule-pebble) and type B (pebble-granule), were designed to surround the well screen. The hydraulic properties and well efficiencies related to the filter packs were evaluated using the Hazen's, Eden-Hazel's, Jacob's, and Labadie-Helweg's methods. The results showed that the hydraulic properties and well efficiency of the DFPs were higher than those of a SFP, and the clogging effect and wellhead loss related to the aquifer material were the lowest owing to the grain size and the arrangement of the filter pack. The hydraulic conductivity of the DFPs types A and B was about 1.41 and 6.43 times that of a SFP, respectively. In addition, the well efficiency of the DFPs types A and B was about 1.38 and 1.60 times that of the SFP, respectively. In this study, hydraulic property and well efficiency changes were observed according to the variety of the filter pack used. The results differed from the predictions of previous studies on the grain-size ratio. Proper pack-aquifer ratios and filter pack arrangements are primary factors in the construction of efficient water wells, as is the grain ratio, intrinsic permeability (k), and hydraulic conductivity (K) between the grains of the filter packs and the grains of the aquifer. © 2014, National Ground Water Association.

Characterization of thermal-hydraulic and ignition phenomena in prototypic, full-length boiling water reactor spent fuel pool assemblies after a complete loss-of-coolant accident.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindgren, Eric Richard; Durbin, Samuel G

2007-04-01

The objective of this project was to provide basic thermal-hydraulic data associated with a SFP complete loss-of-coolant accident. The accident conditions of interest for the SFP were simulated in a full-scale prototypic fashion (electrically-heated, prototypic assemblies in a prototypic SFP rack) so that the experimental results closely represent actual fuel assembly responses. A major impetus for this work was to facilitate code validation (primarily MELCOR) and reduce questions associated with interpretation of the experimental results. It was necessary to simulate a cluster of assemblies to represent a higher decay (younger) assembly surrounded by older, lower-power assemblies. Specifically, this program providedmore » data and analysis confirming: (1) MELCOR modeling of inter-assembly radiant heat transfer, (2) flow resistance modeling and the natural convective flow induced in a fuel assembly as it heats up in air, (3) the potential for and nature of thermal transient (i.e., Zircaloy fire) propagation, and (4) mitigation strategies concerning fuel assembly management.« less

Are physicians aware of their role in tobacco control? A conference-based survey in Portugal.

PubMed

Ravara, Sofia B; Castelo-Branco, Miguel; Aguiar, Pedro; Calheiros, Jose M

2014-09-20

The crucial role of physicians in tobacco control (TC) is widely recognized. In 2008, Portugal implemented a non-comprehensive smoke-free policy (SFP). In 2009, a conference-survey was carried out to explore Portuguese physicians' engagement in tobacco control, by evaluating the following: 1) attendance at TC training and awareness of training needs; 2) participation in TC activities; 3) attitudes and beliefs regarding SFPs. Questionnaire-based cross-sectional study conducted during two major national medical conferences targeting GPs, hospitalists, and students/recent graduates. Descriptive analysis and logistic regression were performed. Response rate was 63.7% (605/950). Of the 605 participants, 58.3% were GPs, 32.4% hospitalists, 9.3% others; 62.6% were female; mean age was 39.0 ± 12.9 years. Smoking prevalence was 29.2% (95% CI: 23.3-35.1) in males; 15.8% (95% CI: 12.1-19.5) in females, p < 0.001. While the overwhelming majority of physicians strongly agreed that second-hand smoke (SHS) endangers health, awareness of SFP benefits and TC law was limited, p < 0.001. A significant minority (35.5%) believed that SHS can be eliminated by ventilation systems. Most physicians lacked training; only a minority (9.0%) participated regularly in TC. Training was the most consistent predictor of participation in TC. General agreement with SFP was high; but significantly lower for indoor leisure settings, outdoors bans in healthcare/schools settings and smoking restrictions in the home/car, p < 0.001. Smoking behaviour strongly predicted support for smoking restrictions in restaurants and bars/discos, healthcare outdoors and private settings. The findings suggest that Portuguese physicians are not aware of their role in tobacco control. Poor engagement of physicians in TC may contribute to the current lack of comprehensive policies in Portugal and Europe and undermine social norm change. Medical and professional continuing education on tobacco control should be made top priorities.

Performance of UNHCR nutrition programs in post-emergency refugee camps

PubMed Central

2011-01-01

Background The United Nations High Commissioner for Refugees (UNHCR) launched a health information system (HIS) in 2005 to enhance quality and consistency of routine health information available in post-emergency refugee camps. This paper reviews nutrition indicators and examines their application for monitoring and evaluating the performance of UNHCR nutrition programs in more than 90 refugee camps in 18 countries. Methods The HIS is a primary source of feeding program data which is collected using standardized case definitions and reporting formats across refugee camps in multiple settings. Data was aggregated across time periods and within and across countries for analysis. Basic descriptive statistics were then compared to UNHCR program performance standards. Results Camp populations covered by the HIS ranged from 192,000 to 219,000 between 2007 and mid-2009; 87% of under five children covered by the HIS were in Africa and 13% in Asia. Average moderate acute malnutrition (MAM) and severe acute malnutrition (SAM) rates reported in 74 of 81 camps for the 2007-2009 time periods were 7.0% and 1.6%, respectively. The supplementary feeding program (SFP) admission rate was 151/1000/yr with 93% of SFP admissions occurring in Africa. SFP performance consistently exceeded all UNHCR standards with the exception of length of enrollment. Average length of SFP enrollment was 12 weeks in Africa and 22 weeks in Asia as compared to the UNHCR standard of < 8 weeks. The therapeutic feeding program (TFP) admission was 22/1000/yr with 95% of TFP admissions in Africa. TFP performance met UNHCR standards with the exception of daily weight gain. Conclusions Inclusion of children identified as moderately and severely wasted in the HIS would allow UNHCR to better track and respond to changes in nutrition status. Improved growth monitoring coverage or active malnutrition surveillance would increase UNHCR's ability to identify and treat cases of acute malnutrition. Expansion of nutrition reporting to address the transition to community-based therapeutic care is essential for adequate performance monitoring in the future. In terms of program priorities, a focus on camps and countries with large refugee populations and high feeding program enrollment rates would have the greatest impact in terms of absolute reductions in the incidence and prevalence of malnutrition. PMID:22029657

Adherence to the Spanish dietary guidelines and its association with obesity in the European Prospective Investigation into Cancer and Nutrition (EPIC)-Granada study.

PubMed

Molina-Montes, Esther; Uzhova, Irina; Molina-Portillo, Elena; Huerta, José-María; Buckland, Genevieve; Amiano, Pilar; Menéndez, Virginia; Barricarte, Aurelio; González, Carlos A; Sánchez, María-José

2014-11-01

Dietary guidelines are intended to prevent chronic diseases and obesity. The aim of the present study was to develop a diet quality index based on the Spanish Food Pyramid (SFP) and to further explore its association with obesity in the European Prospective Investigation into Cancer and Nutrition (EPIC)-Granada study. Cross-sectional study. The SFP score considered recommendations given for twelve food groups, and for physical activity and alcohol consumption. Obesity was defined as BMI over 30 kg/m2 and abdominal obesity as waist circumference larger than 102 cm (men) and 88 cm (women). Logistic regression was conducted to estimate odds ratios of obesity by quintiles and by 10-point increment in adherence to the score, controlling for potential confounders. EPIC-Granada study. Participants (n 6717) aged 35-69 years (77 % women). A 10-point increase in adherence to the SFP score was associated with a 14 % (OR=0·86; 95 % CI 0·79, 0·94) lower odds of obesity in men (P interaction by sex=0·02). The odds of abdominal obesity decreased globally by 12 % (OR=0·88; 95 % CI 0·84, 0·93) per 10-point increase in adherence to this score. The effect of higher adherence to the score on abdominal obesity was stronger in physically inactive men and women (ORper 10-point increase=0·79; 95 % CI 0·68, 0·92 and ORper 10-point increase=0·89; 95 % CI 0·84, 0·95, respectively). These findings support that the Spanish dietary guidelines might be an effective tool for obesity prevention. However, prospective studies investigating this association are warranted.

[Sardine purified proteins improve blood pressure, glycemic control, anti-atherogenic metabolic pathways and antioxidant capacity in obese rats].

PubMed

Affane, F; Bensalah, F; Harrat, N I; Chekkal, H; Louala, S; Lamri-Senhadji, M Y

2018-05-09

The effects of sardine by-products (SBy-P) and fillet proteins (SF-P) were compared to casein (Cas) ; these effects were assessed on blood pressure, glycemic control, reverse cholesterol transport, lipid peroxidation and total antioxidant capacity in obese rats. Eighteen male Wistar rats were subjected for three months, to a high-fat diet. The obese rats were divided into three groups and consumed the same high-fat diet for 28 days after addition of either, 20% SBy-P, SF-P or Cas. The sardine proteins (SBy-P and SF-P) compared respectively to Cas, reduced diastolic (-14%, -11% P<0.05) and systolic pressures (-12%, -8% P<0.05), blood glucose (-24%, -21% P<0.05), glycated hemoglobin (-28%, -21% P<0.05), insulinemia (-29%, -18% P<0.05) and HOMA-IR index (-29%, -18% P<0.05). They improve the reverse cholesterol transport by increasing the lecithin: cholesterol acyltransferase (LCAT) activity (+43%, +30% P<0.05) and high-density lipoproteins in cholesterol esters (+108%, +88% P<0.05), and decreasing the atherogenicity ratios and membrane fluidity (P<0.05). Furthermore, SBy-P and SF-P induced a reduction of reactive thiobarbituric acid substances concentrations in heart (-45%, -25% P<0.05), aorta (-62%, -41% P<0.05), liver (-40%, -21% P<0.05) and adipose tissue (-50%, -37% P<0.05) with an improvement in antioxidant capacity. Sardine proteins, in particular those extracted from by-products, because of their hypotensive, hypoglycemic, anti-atherogenic and antioxidant properties, may have protective effects against the cardiovascular risk associated with obesity. Copyright © 2018. Published by Elsevier SAS.

Evaluation of a Swedish version of the Strengthening Families Programme.

PubMed

Skärstrand, Eva; Sundell, Knut; Andréasson, Sven

2014-08-01

Adolescents' alcohol consumption is a public health concern in Sweden as well as in many other countries. Underage drinking is associated with increased risks of alcohol-related injuries, risky sexual behaviours and dependence later in life. Different strategies have been used in the effort to prevent this behaviour, and to postpone the onset of alcohol. The Strengthening Families Programme 10-14 (SFP 10-14) from the USA has been highlighted as one of the more effective prevention programmes. The aim of the present article was to evaluate the effectiveness of a culturally adapted Swedish version of the SFP 10-14. This was a cluster randomized controlled trial including 587 sixth-grade students (age 12) and their parents in 19 elementary schools in Stockholm. Schools were randomly assigned to either control (9 schools, 216 students) or to the family skills training intervention (10 schools, 371 students). The SFP Swedish version consisted of two parts with seven and five sessions, respectively, held separately for youths and parents except two joint family sessions. Measures of students' self-reported episodes of drunkenness, smoking, illicit drug use and other norm-breaking behaviours were collected at baseline (March 2003) and at three subsequent yearly surveys. Data were analysed using multilevel models with an intention-to-treat approach. No preventive effects were found for smoking, alcohol and illicit drug use and other norm-breaking behaviours, nor did moderators affect the outcome. The Swedish version of the SFP 10-14 was not effective in preventing youths' substance use in a Swedish context. © The Author 2013. Published by Oxford University Press on behalf of the European Public Health Association. All rights reserved.

Templated sequence insertion polymorphisms in the human genome

NASA Astrophysics Data System (ADS)

Onozawa, Masahiro; Aplan, Peter

2016-11-01

Templated Sequence Insertion Polymorphism (TSIP) is a recently described form of polymorphism recognized in the human genome, in which a sequence that is templated from a distant genomic region is inserted into the genome, seemingly at random. TSIPs can be grouped into two classes based on nucleotide sequence features at the insertion junctions; Class 1 TSIPs show features of insertions that are mediated via the LINE-1 ORF2 protein, including 1) target-site duplication (TSD), 2) polyadenylation 10-30 nucleotides downstream of a “cryptic” polyadenylation signal, and 3) preference for insertion at a 5’-TTTT/A-3’ sequence. In contrast, class 2 TSIPs show features consistent with repair of a DNA double-strand break via insertion of a DNA “patch” that is derived from a distant genomic region. Survey of a large number of normal human volunteers demonstrates that most individuals have 25-30 TSIPs, and that these TSIPs track with specific geographic regions. Similar to other forms of human polymorphism, we suspect that these TSIPs may be important for the generation of human diversity and genetic diseases.

Twinning of cubic diamond explains reported nanodiamond polymorphs

NASA Astrophysics Data System (ADS)

Németh, Péter; Garvie, Laurence A. J.; Buseck, Peter R.

2015-12-01

The unusual physical properties and formation conditions attributed to h-, i-, m-, and n-nanodiamond polymorphs has resulted in their receiving much attention in the materials and planetary science literature. Their identification is based on diffraction features that are absent in ordinary cubic (c-) diamond (space group: Fd-3m). We show, using ultra-high-resolution transmission electron microscope (HRTEM) images of natural and synthetic nanodiamonds, that the diffraction features attributed to the reported polymorphs are consistent with c-diamond containing abundant defects. Combinations of {113} reflection and <011> rotation twins produce HRTEM images and d-spacings that match those attributed to h-, i-, and m-diamond. The diagnostic features of n-diamond in TEM images can arise from thickness effects of c-diamonds. Our data and interpretations strongly suggest that the reported nanodiamond polymorphs are in fact twinned c-diamond. We also report a new type of twin (<11> rotational), which can give rise to grains with dodecagonal symmetry. Our results show that twins are widespread in diamond nanocrystals. A high density of twins could strongly influence their applications.

Intra-procedural Path-insensitve Grams (I-GRAMS) and Disassembly Based Features for Packer Tool Classification and Detection

DTIC Science & Technology

2012-06-14

executable file is packed is a critical step in software security. This research uses machine learning methods to build the Polymorphic and Non-Polymorphic...Packer Detection (PNPD) system that detects whether an executable is packed by either ASPack, UPX, Metasploit’s polymorphic msfencode, or is packed in...detect packed executables used in experiments. Overall, it is discovered i-grams provide the best results with accuracies above 99.5%, average true

Strengthening Family Practices for Latino Families.

PubMed

Chartier, Karen G; Negroni, Lirio K; Hesselbrock, Michie N

2010-01-01

The study examined the effectiveness of a culturally-adapted Strengthening Families Program (SFP) for Latinos to reduce risks for alcohol and drug use in children. Latino families, predominantly Puerto Rican, with a 9-12 year old child and a parent(s) with a substance abuse problem participated in the study. Pre- and post-tests were conducted with each family. Parental stress, parent-child dysfunctional relations, and child behavior problems were reduced in the families receiving the intervention; family hardiness and family attachment were improved. Findings contribute to the validation of the SFP with Latinos, and can be used to inform social work practice with Puerto Rican families.

Spontaneous fungal peritonitis: Epidemiology, current evidence and future prospective.

PubMed

Fiore, Marco; Leone, Sebastiano

2016-09-14

Spontaneous bacterial peritonitis is a complication of ascitic patients with end-stage liver disease (ESLD); spontaneous fungal peritonitis (SFP) is a complication of ESLD less known and described. ESLD is associated to immunodepression and the resulting increased susceptibility to infections. Recent perspectives of the management of the critically ill patient with ESLD do not specify the rate of isolation of fungi in critically ill patients, not even the antifungals used for the prophylaxis, neither optimal treatment. We reviewed, in order to focus the epidemiology, characteristics, and, considering the high mortality rate of SFP, the use of optimal empirical antifungal therapy the current literature.

Gene expression changes in male accessory glands during ageing are accompanied by reproductive decline in Drosophila melanogaster.

PubMed

Koppik, Mareike; Fricke, Claudia

2017-12-01

Senescence is accompanied by loss of reproductive functions. Here, we studied reproductive ageing in Drosophila melanogaster males and asked whether the expected decline in male reproductive success is due to diminished functionality of the male accessory gland (AG). The male AG produces the majority of seminal fluid proteins (SFPs) transferred to the female at mating. SFPs induce female postmating changes and are key to male reproductive success. We measured age-dependent gene expression changes for five representative SFP genes in males from four different age groups ranging from 1 to 6 weeks after eclosion. Simultaneously, we also measured male reproductive success in postmating traits mediated by transfer of these five SFPs. We found a decreased in male SFP gene expression with advancing age and an accompanying decline in male postmating success. Hence, male reproductive senescence is associated with a decline in functionality of the male AG. While overall individual SFP genes decreased in expression, our results point towards the idea that the composition of an ejaculate might change with male age as the rate of change was variable for those five genes. © 2017 John Wiley & Sons Ltd.

Preparation of low molecular weight Sargassum fusiforme polysaccharide and its anticoagulant activity

NASA Astrophysics Data System (ADS)

Sun, Yuhao; Chen, Xiaolin; Liu, Song; Yu, Huahua; Li, Rongfeng; Wang, Xueqin; Qin, Yukun; Li, Pengcheng

2017-10-01

Heparin has been used as an anticoagulant drug for many years, but it has significant side effects. In the search for good substitutes, low molecular weight (MW) polysaccharides from Sargassum fusiforme have been examined and confirmed to possess biological activities. Here, S. fusiforme polysaccharides (SFP) were extracted and subjected to a hydrogen peroxide (H2O2) oxidation method for the preparation of low-MW SFP (LSFP). The effects of temperature, pH, and H2O2 concentration on the degradation process were also examined. Several LSFP of 36, 9, 5.7, and 2.7 kDa were obtained under different conditions, and their anticoagulant activities studied in vitro. The results showed that SFP and LSFP prolonged activated partial thromboplastin (APTT), prothrombin (PT) and thrombin times (TT) significantly, indicating that these low MW polysaccharides possessed anticoagulant activity in the intrinsic, extrinsic, and common coagulation pathways. As these effects were related to the MW of the polysaccharides in APTT and TT but not in PT, the contents of the monosaccharide fucose and sulfate and the polysaccharide MW could have exerted combined effects. The details of this mechanism require further verification.

The C-C motif chemokine ligands CCL5, CCL11, and CCL24 induce the migration of circulating fibrocytes from patients with severe asthma.

PubMed

Isgrò, M; Bianchetti, L; Marini, M A; Bellini, A; Schmidt, M; Mattoli, S

2013-07-01

The C-C motif chemokine ligand 5 (CCL5), CCL11, and CCL24 are involved in the pathogenesis of asthma, and their function is mainly associated with the airway recruitment of eosinophils. This study tested their ability to induce the migration of circulating fibrocytes, which may contribute to the development of irreversible airflow obstruction in severe asthma. The sputum fluid phase (SFP) from patients with severe/treatment-refractory asthma (PwSA) contained elevated concentrations of CCL5, CCL11, and CCL24 in comparison with the SFP from patients with non-severe/treatment-responsive asthma (PwNSA). The circulating fibrocytes from PwSA expressed the receptors for these chemokines at increased levels and migrated in response to recombinant CCL5, CCL11, and CCL24. The SFP from PwSA induced the migration of autologous fibrocytes, and its activity was significantly attenuated by neutralization of endogenous CCL5, CCL11, and CCL24. These findings suggest that CCL5, CCL11, and CCL24 may contribute to the airway recruitment of fibrocytes in severe asthma.

Multiple streams approach to tobacco control policymaking in a tobacco-growing state.

PubMed

Mamudu, Hadii M; Dadkar, Sumati; Veeranki, Sreenivas P; He, Yi; Barnes, Richard; Glantz, Stanton A

2014-08-01

Smokefree policies (SFPs) have diffused throughout the US and worldwide. However, the development of SFPs in the difficult policy environment of tobacco-producing states and economies worldwide has not been well-explored. In 2007, Tennessee, the third largest tobacco producer in the US, enacted the Non-Smoker Protection Act (NSPA). This study utilizes the multiple streams model to provide understanding of why and how this policy was developed by triangulating interviews with key stakeholders and legislative debates with archival documents. In June 2006, the Governor unexpectedly announced support for SFP, which created a window of opportunity for policy change. The Campaign for Healthy and Responsible Tennessee, a health coalition, seized this opportunity and worked with the administration and the Tennessee Restaurant Association to negotiate a comprehensive SFP, however, a weaker bill was used by the legislative leadership to develop the NSPA. Although the Governor and the Tennessee Restaurant Association's support generated an environment for 100% SFP, health groups did not fully capitalize on this environmental change and settled for a weak policy with several exemptions. This study suggests the importance for proponents of policy change to understand changes in their environment and be willing and able to capitalize on these changes.

Optical Sensing Device Containing Fiber Bragg Gratings

DTIC Science & Technology

2000-08-01

Fabry - Perot (SFP) filter-based interrogation (Kersey et al. Opt. Lett.. 18, 1370-2. 1993), tunable acousto-optic filter inteiTOgation (Geiger et al...a tunable Fabry - Perot filter, and a tunable acousto-optical filter. Alternatively, scanning filter 28 can be omitted in device 10 of the present...invention when broadband light source 20 is a tunable broadband light source. More preferably, scanning filter 28 is a tunable Fabry - Perot filter

Multiple Streams Approach to Tobacco Control Policymaking in a Tobacco-Growing State

PubMed Central

Mamudu, Hadii M.; Dadkar, Sumati; Veeranki, Sreenivas P.; He, Yi; Barnes, Richard; Glantz, Stanton A.

2014-01-01

Smokefree policies (SFPs) have diffused throughout the US and worldwide. However, the development of SFPs in the difficult policy environment of tobacco-producing states and economies worldwide has not been well-explored. In 2007, Tennessee, the third largest tobacco producer in the US, enacted the Non-Smoker Protection Act (NSPA). This study utilizes the multiple streams model to provide understanding of why and how this policy was developed by triangulating interviews with key stakeholders and legislative debates with archival documents. In June 2006, the Governor unexpectedly announced support for SFP, which created a window of opportunity for policy change. The Campaign for Healthy and Responsible Tennessee, a health coalition, seized this opportunity and worked with the administration and the Tennessee Restaurant Association to negotiate a comprehensive SFP, however, a weaker bill was used by the legislative leadership to develop the NSPA. Although the Governor and the Tennessee Restaurant Association’s support generated an environment for 100 % SFP, health groups did not fully capitalize on this environmental change and settled for a weak policy with several exemptions. This study suggests the importance for proponents of policy change to understand changes in their environment and be willing and able to capitalize on these changes. PMID:24370600

Gas emission from the UO2 samples, containing fission products and burnable absorber

NASA Astrophysics Data System (ADS)

Kopytin, V. P.; Baranov, V. G.; Burlakova, M. A.; Tenishev, A. V.; Kuzmin, R. S.; Pokrovskiy, S. A.; Mikhalchik, V. V.

2016-04-01

The process gas released from the fuel pellets of uranium fuel during fuel burn-up reduces the thermal conductivity of the rod-shell gap, enhances hydrogen embrittlement of the cladding material, causes it's carbonization, as well as transport processes in the fuel. In this study a technique of investigating the thermal desorption of gases from the UO2 fuel material were perfected in the temperature range 300-2000 K for uniform sample heating rate of 15 K/min in vacuum. The characteristic kinetic dependences are acquired for the gas emission from UO2 samples, containing simulators of fission products (SFP) and the burnable neutron absorber (BNA). Depending on the amount of SFP and BNA contained in the sample thermal desorption gas spectra (TDGS) vary. The composition of emitted gas varies, as well as the number of peaks in the TDGS and the peaks shift to higher temperatures. This indicates that introduction of SFPs and BNA alters the sample material structure and cause the creation of so- called traps which have different bonding energies to the gases. The traps can be a grid of dislocations, voids, and contained in the UO2 matrix SFP and BNA. Similar processes will occur in the fuel pellets in the real conditions of the Nuclear Power Plant as well.

Novel Solvent-free Perovskite Deposition in Fabrication of Normal and Inverted Architectures of Perovskite Solar Cells

PubMed Central

Nejand, Bahram Abdollahi; Gharibzadeh, Saba; Ahmadi, Vahid; Shahverdi, H. Reza

2016-01-01

We introduced a new approach to deposit perovskite layer with no need for dissolving perovskite precursors. Deposition of Solution-free perovskite (SFP) layer is a key method for deposition of perovskite layer on the hole or electron transport layers that are strongly sensitive to perovskite precursors. Using deposition of SFP layer in the perovskite solar cells would extend possibility of using many electron and hole transport materials in both normal and invert architectures of perovskite solar cells. In the present work, we synthesized crystalline perovskite powder followed by successful deposition on TiO2 and cuprous iodide as the non-sensitve and sensitive charge transport layers to PbI2 and CH3NH3I solution in DMF. The post compressing step enhanced the efficiency of the devices by increasing the interface area between perovskite and charge transport layers. The 9.07% and 7.71% cell efficiencies of the device prepared by SFP layer was achieved in respective normal (using TiO2 as a deposition substrate) and inverted structure (using CuI as deposition substrate) of perovskite solar cell. This method can be efficient in large-scale and low cost fabrication of new generation perovskite solar cells. PMID:27640991

The rate of metabolism as a factor determining longevity of the Saccharomyces cerevisiae yeast.

PubMed

Molon, Mateusz; Szajwaj, Monika; Tchorzewski, Marek; Skoczowski, Andrzej; Niewiadomska, Ewa; Zadrag-Tecza, Renata

2016-02-01

Despite many controversies, the yeast Saccharomyces cerevisiae continues to be used as a model organism for the study of aging. Numerous theories and hypotheses have been created for several decades, yet basic mechanisms of aging have remained unclear. Therefore, the principal aim of this work is to propose a possible mechanism leading to increased longevity in yeast. In this paper, we suggest for the first time that there is a link between decreased metabolic activity, fertility and longevity expressed as time of life in yeast. Determination of reproductive potential and total lifespan with the use of fob1Δ and sfp1Δ mutants allows us to compare the "longevity" presented as the number of produced daughters with the longevity expressed as the time of life. The results of analyses presented in this paper suggest the need for a change in the definition of longevity of yeast by taking into consideration the time parameter. The mutants that have been described as "long-lived" in the literature, such as the fob1Δ mutant, have an increased reproductive potential but live no longer than their standard counterparts. On the other hand, the sfp1Δ mutant and the wild-type strain produce a similar number of daughter cells, but the former lives much longer. Our results demonstrate a correlation between the decreased efficiency of the translational apparatus and the longevity of the sfp1Δ mutant. We suggest that a possible factor regulating the lifespan is the rate of cell metabolism. To measure the basic metabolism of the yeast cells, we used the isothermal microcalorimetry method. In the case of sfp1Δ, the flow of energy, ATP concentration, polysome profile and translational fitness are significantly lower in comparison with the wild-type strain and the fob1Δ mutant.

Molecular and biochemical characterization of Iranian surfactin-producing Bacillus subtilis isolates and evaluation of their biocontrol potential against Aspergillus flavus and Colletotrichum gloeosporioides.

PubMed

Mohammadipour, Matin; Mousivand, Maryam; Salehi Jouzani, Gholamreza; Abbasalizadeh, Saeed

2009-04-01

The characterization of surfactin-producing Bacillus subtilis isolates collected from different ecological zones of Iran is presented. Characterization was performed using blood agar, PCR, drop-collapse, and reverse-phase high-performance liquid chromatography (HPLC) analyses, and the isolates' biocontrol effects against the aflatoxin-producing agent Aspergillus flavus and the citrus antracnosis agent Colletotrichum gloeosporioides were studied. In total, 290 B. subtilis isolates were isolated from phylosphere and rhizosphere samples collected from fields and gardens of 5 provinces of Iran. Blood agar assays showed that 185 isolates produced different biosurfactants. Isolates containing the sfp gene, coding for surfactin, were detected using the PCR method. It was found that 14 different isolates contained the sfp gene. Drop-collapse assays, which detect isolates with high production of surfactin, showed that 7 isolates produced high levels of surfactin. It was found from HPLC analysis that the isolates containin the sfp gene produced between 55 and 1610 mg of surfactin per litre of broth medium. Four isolates, named BS119m, BS116l, N3dn, and BS113c, produced more than 1000 mg of surfactin per litre of broth. The highest surfactin production level was observed for isolate BS119m (1610 mg/L). The antagonistic potential of the sfp gene-containing isolates was determined using dual culture and chloroform vapour methods. Our bioassay results indicated that isolate BS119m showed high inhibitory effects against A. flavus (100%) and C. gloeosporioides (88%). Furthermore, the effect of purified surfactin on the growth of A. flavus was evaluated. Mycelia growth was considerably reduced with increasing concentration of surfactin, and 36%, 54%, 84%, and 100% inhibitions of mycelia growth were, respectively, observed at 20, 40, 80, and 160 mg/L after 7 days of incubation.

Identification of hallucinogenic fungi from the genera Psilocybe and Panaeolus by amplified fragment length polymorphism.

PubMed

Lee, J C; Cole, M; Linacre, A

2000-05-01

Unambiguous identification of the hallucinogenic fungi of the genera Psilocybe and Panaeolus is required by national and international drug control legislation. We report on a DNA-based test using the technique of amplified fragment length polymorphism (AFLP). AFLP can differentiate species of the two genera Psilocybe and Panaeolus by using different primer sets. The identification of hallucinogenic fungi using a DNA-based test, which can be used in conjunction with morphological features, will assist in forensic investigations.

Methicillin-resistant Staphylococcus aureus: a controversial food-borne pathogen.

PubMed

Sergelidis, D; Angelidis, A S

2017-06-01

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of severe healthcare-associated (HA) infections. Although during the last decade the incidence of HA invasive infections has dropped, the incidence of community-associated MRSA (CA-MRSA) infections has risen among the general population. Moreover, CA-MRSA, livestock-associated MRSA (LA-MRSA) and HA-MRSA (HA-MRSA) can be found in foods intended for human consumption. Several studies from different geographical areas have reported the presence of enterotoxin genes in several MRSA food isolates. Molecular typing studies have revealed genetic relatedness of these enterotoxigenic isolates with isolates incriminated in human infections. The contamination sources for foods, especially animal-origin foods, may be livestock as well as humans involved in animal husbandry and food-processing. Under favourable environmental conditions for growth and enterotoxin production, enterotoxigenic S. aureus isolates present in foods can cause staphylococcal food poisoning (SFP), irrespective of the contamination origin. Owing to the typically moderate clinical manifestations of SFP, the S. aureus strains responsible for SFP (cases or outbreaks) are frequently either not identified or not further characterized. Antimicrobial susceptibility testing is rarely performed, because administration of antimicrobial therapy is not required in the vast majority of cases. Staphylococcal food poisoning is the result of consumption of foods with preformed enterotoxins. Hence, similar to methicillin-sensitive enterotoxigenic S. aureus, enterotoxigenic MRSA can also act as food-borne pathogens upon favourable conditions for growth and enterotoxin production. The severity of the intoxication is not related to the antimicrobial resistance profile of the causative S. aureus strain and therefore MRSA food-borne outbreaks are not expected to be more severe. This review evaluates the potential of methicillin-resistant Staphylococcus aureus (MRSA) as food-borne pathogens based on the current knowledge about the epidemiology of MRSA, their prevalence in livestock, foods of animal origin and humans, and their ability to produce enterotoxins. © 2017 The Society for Applied Microbiology.

On-chip optical phase locking of single growth monolithically integrated Slotted Fabry Perot lasers.

PubMed

Morrissey, P E; Cotter, W; Goulding, D; Kelleher, B; Osborne, S; Yang, H; O'Callaghan, J; Roycroft, B; Corbett, B; Peters, F H

2013-07-15

This work investigates the optical phase locking performance of Slotted Fabry Perot (SFP) lasers and develops an integrated variable phase locked system on chip for the first time to our knowledge using these lasers. Stable phase locking is demonstrated between two SFP lasers coupled on chip via a variable gain waveguide section. The two lasers are biased differently, one just above the threshold current of the device with the other at three times this value. The coupling between the lasers can be controlled using the variable gain section which can act as a variable optical attenuator or amplifier depending on bias. Using this, the width of the stable phase locking region on chip is shown to be variable.

Proposals for Solutions to Problems Related to the Use of F-34 (SFP) and High Sulphur Diesel on Ground Equipment Using Advanced Reduction Emission Technologies (Propositions de solutions aux problemes lies a l’utilisation de F-34 (SFP) et de diesel a haute teneur en soufre pour le materiel terrestre disposant de technologies avancees de reduction des emissions)

DTIC Science & Technology

2008-09-01

In a two - stage process the urea decomposes to ammonia (NH3) which then reacts with the nitrogen oxides (NOx) and leads to formation of nitrogen and...Sulphur Fuel (HSF) is a potential problem to NATO forces when vehicles and equipment are fitted with advanced emission reduction devices that require Low...worldwide available, standard fuel (F-34) and equipment capable of using such high sulphur fuels (HSF). Recommendations • Future equipment fitted with

Molecular mechanisms of ribosomal protein gene coregulation

PubMed Central

Reja, Rohit; Vinayachandran, Vinesh; Ghosh, Sujana; Pugh, B. Franklin

2015-01-01

The 137 ribosomal protein genes (RPGs) of Saccharomyces provide a model for gene coregulation. We examined the positional and functional organization of their regulators (Rap1 [repressor activator protein 1], Fhl1, Ifh1, Sfp1, and Hmo1), the transcription machinery (TFIIB, TFIID, and RNA polymerase II), and chromatin at near-base-pair resolution using ChIP-exo, as RPGs are coordinately reprogrammed. Where Hmo1 is enriched, Fhl1, Ifh1, Sfp1, and Hmo1 cross-linked broadly to promoter DNA in an RPG-specific manner and demarcated by general minor groove widening. Importantly, Hmo1 extended 20–50 base pairs (bp) downstream from Fhl1. Upon RPG repression, Fhl1 remained in place. Hmo1 dissociated, which was coupled to an upstream shift of the +1 nucleosome, as reflected by the Hmo1 extension and core promoter region. Fhl1 and Hmo1 may create two regulatable and positionally distinct barriers, against which chromatin remodelers position the +1 nucleosome into either an activating or a repressive state. Consistent with in vitro studies, we found that specific TFIID subunits, in addition to cross-linking at the core promoter, made precise cross-links at Rap1 sites, which we interpret to reflect native Rap1–TFIID interactions. Our findings suggest how sequence-specific DNA binding regulates nucleosome positioning and transcription complex assembly >300 bp away and how coregulation coevolved with coding sequences. PMID:26385964

Potential of Visible and Near Infrared Spectroscopy and Pattern Recognition for Rapid Quantification of Notoginseng Powder with Adulterants

PubMed Central

Nie, Pengcheng; Wu, Di; Sun, Da-Wen; Cao, Fang; Bao, Yidan; He, Yong

2013-01-01

Notoginseng is a classical traditional Chinese medical herb, which is of high economic and medical value. Notoginseng powder (NP) could be easily adulterated with Sophora flavescens powder (SFP) or corn flour (CF), because of their similar tastes and appearances and much lower cost for these adulterants. The objective of this study is to quantify the NP content in adulterated NP by using a rapid and non-destructive visible and near infrared (Vis-NIR) spectroscopy method. Three wavelength ranges of visible spectra, short-wave near infrared spectra (SNIR) and long-wave near infrared spectra (LNIR) were separately used to establish the model based on two calibration methods of partial least square regression (PLSR) and least-squares support vector machines (LS-SVM), respectively. Competitive adaptive reweighted sampling (CARS) was conducted to identify the most important wavelengths/variables that had the greatest influence on the adulterant quantification throughout the whole wavelength range. The CARS-PLSR models based on LNIR were determined as the best models for the quantification of NP adulterated with SFP, CF, and their mixtures, in which the rP values were 0.940, 0.939, and 0.867 for the three models respectively. The research demonstrated the potential of the Vis-NIR spectroscopy technique for the rapid and non-destructive quantification of NP containing adulterants. PMID:24129019

MELCOR Model of the Spent Fuel Pool of Fukushima Dai-ichi Unit 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carbajo, Juan J

2012-01-01

Unit 4 of the Fukushima Dai-ichi Nuclear Power Plant suffered a hydrogen explosion at 6:00 am on March 15, 2011, exactly 3.64 days after the earthquake hit the plant and the off-site power was lost. The earthquake occurred on March 11 at 2:47 pm. Since the reactor of this Unit 4 was defueled on November 29, 2010, and all its fuel was stored in the spent fuel pool (SFP4), it was first believed that the explosion was caused by hydrogen generated by the spent fuel, in particular, by the recently discharged core. The hypothetical scenario was: power was lost, coolingmore » to the SFP4 water was lost, pool water heated/boiled, water level decreased, fuel was uncovered, hot Zircaloy reacted with steam, hydrogen was generated and accumulated above the pool, and the explosion occurred. Recent analyses of the radioisotopes present in the water of the SFP4 and underwater video indicated that this scenario did not occur - the fuel in this pool was not damaged and was never uncovered the hydrogen of the explosion was apparently generated in Unit 3 and transported through exhaust ducts that shared the same chimney with Unit 4. This paper will try to answer the following questions: Could that hypothetical scenario in the SFP4 had occurred? Could the spent fuel in the SPF4 generate enough hydrogen to produce the explosion that occurred 3.64 days after the earthquake? Given the magnitude of the explosion, it was estimated that at least 150 kg of hydrogen had to be generated. As part of the investigations of this accident, MELCOR models of the SFP4 were prepared and a series of calculations were completed. The latest version of MELCOR, version 2.1 (Ref. 1), was employed in these calculations. The spent fuel pool option for BWR fuel was selected in MELCOR. The MELCOR model of the SFP4 consists of a total of 1535 fuel assemblies out of which 548 assemblies are from the core defueled on Nov. 29, 2010, 783 assemblies are older assemblies, and 204 are new/fresh assemblies. The total decay heat of the fuel in the pool was, at the time of the accident, 2.284 MWt, of which 1.872 MWt were from the 548 assemblies of the last core discharged and 0.412 MWt were from the older 783 assemblies. These decay heat values were calculated at Oak Ridge National Laboratory using the ORIGEN2.2 code (Ref. 2) - they agree with values reported elsewhere (Ref. 3). The pool dimensions are 9.9 m x 12.2 m x 11.8 m (height), and with the water level at 11.5 m, the pool volume is 1389 m3, of which only 1240 m3 is water, as some volume is taken by the fuel and by the fuel racks. The initial water temperature of the SFP4 was assumed to be 301 K. The fuel racks are made of an aluminum alloy but are modeled in MELCOR with stainless steel and B4C. MELCOR calculations were completed for different initial water levels: 11.5 m (pool almost full, water is only 0.3 m below the top rim), 4.4577 m (top of the racks), 4.2 m, and 4.026 m (top of the active fuel). A calculation was also completed for a rapid loss of water due to a leak at the bottom of the pool, with the fuel rapidly uncovered and oxidized in air. Results of these calculations are shown in the enclosed Table I. The calculation with the initial water level at 11.5 m (full pool) takes 11 days for the water to boil down to the top of the fuel racks, 11.5 days for the fuel to be uncovered, 14.65 days to generate 150 kg of hydrogen and 19 days for the pool to be completely dry. The calculation with the initial water level at 4.4577 m, takes 1.1 days to uncover the fuel and 4.17 days to generate 150 kg of hydrogen. The calculation with the initial water level at 4.02 m takes 3.63 days to generate 150 kg of hydrogen this is exactly the time when the actual explosion occurred in Unit 4. Finally, fuel oxidation in air after the pool drained the water in 20 minutes, generates only 10 kg of hydrogen this is because very little steam is available and Zircaloy (Zr) oxidation with the oxygen of the air does not generate hydrogen. MELCOR calculated water levels and hydrogen generated in the SFP4 as a function of time for initial water levels of 4.457 m, 4.2 m and 4.02 m are shown in Figs. 1 and 2. Water levels increase at the beginning due to the expansion of the water during the heat-up from 301 K to 373 K. Boiling occurs after the water temperature reaches 373 K. The total amount of hydrogen generated is ~2000 kg, this amount includes hydrogen generated from Zr, which is the largest amount (~1580 kg), from stainless steel (~360 kg), and from B4C (~60 kg). In theory, it is possible to generate up to 3.4 kg of hydrogen per assembly (from oxidation of Zr in the fuel cladding and box), or a total of 4,525 kg from the hot 1331 assemblies stored in the SFP4. The hydrogen generated from oxidation of steel and B4C will be additional. So the answers to the questions are YES according to these MELCOR calculations, enough hydrogen (150 kg) could be generated in the SFP4 3.64 days after the earthquake to produce ...« less

Staphylococcal food poisoning caused by Staphylococcus argenteus harboring staphylococcal enterotoxin genes.

PubMed

Wakabayashi, Yuki; Umeda, Kaoru; Yonogi, Shinya; Nakamura, Hiromi; Yamamoto, Kaori; Kumeda, Yuko; Kawatsu, Kentaro

2018-01-16

Staphylococcal food poisoning (SFP) is caused by staphylococcal enterotoxins (SEs) preformed in food materials. SE genes are encoded on mobile genetic elements and are widely found across Staphylococcus species including S. argenteus, although most SFP cases are caused by S. aureus. S. argenteus, recently discriminated from S. aureus as a novel species, are non-pigmented staphylococci phenotypically related to S. aureus. In 2014 and 2015, two independent food poisoning cases occurred in Osaka, Japan, in which non-pigmented staphylococci were predominantly isolated. Several enterotoxin genes (seb, seg, sei, sem, sen, seo, and selu2) were found in their genome and the production of SEB was confirmed by reverse passive agglutination tests. The non-pigmented isolates from patients, food handlers, food, and cooking utensils all produced the same pulsed-field gel electrophoresis pattern. These non-pigmented isolates were coagulase-positive and biochemically identical to S. aureus. We performed further genetic analysis using nucA sequencing and multi-locus sequence typing, and identified these isolates as S. argenteus. We also found that seb was encoded on the Staphylococcus aureus pathogenicity island, while seg, sei, sem, sen, seo, and selu2 were encoded on the enterotoxin gene cluster. From these results, we concluded that the two food poisoning outbreaks were SFP cases caused by S. argenteus harboring SE genes. Copyright © 2017 Elsevier B.V. All rights reserved.

[Screening for the risk of allergy and prevention in French maternity units: A survey].

PubMed

Chouraqui, J-P; Simeoni, U; Tohier, C; Nguyen, F; Kempf, C; Beck, L; Lachambre, E

2015-09-01

Allergy has been on the rise for half a century and concerns nearly 30% of children; it has now become a real public health problem. The guidelines on prevention of allergy set up by the French Society of Paediatrics (SFP) and the European Society of Paediatric Allergology and Clinical Immunology (ESPACI) are based on screening children at risk through a systematic search of the family history and recommend, for children at risk, exclusive breastfeeding whenever possible or otherwise utilization of hypoallergenic infant formula, which has demonstrated efficacy. The AllerNaiss practice survey assessed the modes of screening and prevention of allergy in French maternity units in 2012. The SFP guidelines are known by 82% of the maternity units that took part in the survey, and the ESPACI guidelines by 55% of them. A screening strategy is in place in 59% of the participating maternity wards, based on local consensus for 36% of them, 13% of the units having a written screening procedure. Screening is based on the search for a history of allergy in first-degree relatives (99%) during pregnancy (51%), in the delivery room (50%), and after delivery (89%). A mode of prevention of the risk of allergy exists in 62% of the maternity units, most often in writing (49%). A hypoallergenic infant formula is prescribed for non-breastfed children in 90% of the units. The survey shows that there is a real need for formalization of allergy risk screening and prevention of allergy in newborns in French maternity units. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Molecular mechanisms of ribosomal protein gene coregulation.

PubMed

Reja, Rohit; Vinayachandran, Vinesh; Ghosh, Sujana; Pugh, B Franklin

2015-09-15

The 137 ribosomal protein genes (RPGs) of Saccharomyces provide a model for gene coregulation. We examined the positional and functional organization of their regulators (Rap1 [repressor activator protein 1], Fhl1, Ifh1, Sfp1, and Hmo1), the transcription machinery (TFIIB, TFIID, and RNA polymerase II), and chromatin at near-base-pair resolution using ChIP-exo, as RPGs are coordinately reprogrammed. Where Hmo1 is enriched, Fhl1, Ifh1, Sfp1, and Hmo1 cross-linked broadly to promoter DNA in an RPG-specific manner and demarcated by general minor groove widening. Importantly, Hmo1 extended 20-50 base pairs (bp) downstream from Fhl1. Upon RPG repression, Fhl1 remained in place. Hmo1 dissociated, which was coupled to an upstream shift of the +1 nucleosome, as reflected by the Hmo1 extension and core promoter region. Fhl1 and Hmo1 may create two regulatable and positionally distinct barriers, against which chromatin remodelers position the +1 nucleosome into either an activating or a repressive state. Consistent with in vitro studies, we found that specific TFIID subunits, in addition to cross-linking at the core promoter, made precise cross-links at Rap1 sites, which we interpret to reflect native Rap1-TFIID interactions. Our findings suggest how sequence-specific DNA binding regulates nucleosome positioning and transcription complex assembly >300 bp away and how coregulation coevolved with coding sequences. © 2015 Reja et al.; Published by Cold Spring Harbor Laboratory Press.

[Social marketing and public policies for health: campaign to promote smoke-free spaces in Mexico].

PubMed

Villalobos, Víctor; Ramírez, Olivia Ortiz; Thrasher, James F; Santillán, Edna Arillo; Hernández, Rosaura Pérez; Cedillo, Claudia; González, Wendy

2010-01-01

"Porque todos respiramos lo mismo" is a mass media campaign to promote smoke-free places (SFP). The development stages were: strategic planning; formative research; message development; media plan; and impact evaluation. Development involved formation of a coalition of key actors in various sectors. The target population was smokers and nonsmokers, with the aim of changing social norms around SFP. Nonsmokers were targeted because they comprised the majority and were most likely to appreciate the benefits of SFPs. Campaign materials were aired on television, radio, print and on billboards. One key limitation was the lack of evidence for previous campaigns, which increased the importance of formative research and of including a rigorous evaluation for this one. The campaign evaluation indicates a significant impact, which suggests that future campaigns use similar strategies in their development.

Maternal Posttraumatic Stress Symptoms and Infant Emotional Reactivity and Emotion Regulation

PubMed Central

Enlow, Michelle Bosquet; Kitts, Robert L.; Blood, Emily; Bizarro, Andrea; Hofmeister, Michelle; Wright, Rosalind J.

2011-01-01

The current study examined associations between maternal posttraumatic stress disorder (PTSD) symptoms and infant emotional reactivity and emotion regulation during the first year of life in a primarily low-income, urban, ethnic/racial minority sample of 52 mother-infant dyads. Mothers completed questionnaires assessing their own trauma exposure history and current PTSD and depressive symptoms and their infants’ temperament when the infants were 6 months old. Dyads participated in the repeated Still-Face Paradigm (SFP-R) when the infants were 6 months old, and infant affective states were coded for each SFP-R episode. Mothers completed questionnaires assessing infant trauma exposure history and infant current emotional and behavioral symptoms when the infants were 13 months old. Maternal PTSD symptoms predicted infants’ emotion regulation at 6 months as assessed by (a) infant ability to recover from distress during the SFP-R and (b) maternal report of infant rate of recovery from distress/arousal in daily life. Maternal PTSD symptoms also predicted maternal report of infant externalizing, internalizing, and dysregulation symptoms at 13 months. Maternal PTSD was not associated with measures of infant emotional reactivity. Neither maternal depressive symptoms nor infant direct exposure to trauma accounted for the associations between maternal PTSD symptoms and infant outcomes. These findings suggest that maternal PTSD is associated with offspring emotion regulation difficulties as early as infancy. Such difficulties may contribute to increased risk of mental health problems among children of mothers with PTSD. PMID:21862136

Separated fringe packet observations with the Chara Array. II. ω Andromeda, HD 178911, and ξ Cephei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farrington, C. D.; Ten Brummelaar, T. A.; Turner, N. H.

When observed with optical long-baseline interferometers, components of a binary star that are sufficiently separated produce their own interferometric fringe packets; these are referred to as separated fringe packet (SFP) binaries. These SFP binaries can overlap in angular separation with the regime of systems resolvable by speckle interferometry at single, large-aperture telescopes and can provide additional measurements for preliminary orbits lacking good phase coverage, help constrain elements of already established orbits, and locate new binaries in the undersampled regime between the bounds of spectroscopic surveys and speckle interferometry. In this process, a visibility calibration star is not needed, and themore » SFPs can provide an accurate vector separation. In this paper, we apply the SFP approach to ω Andromeda, HD 178911, and ξ Cephei with the CLIMB three-beam combiner at the CHARA Array. For these systems we determine component masses and parallax of 0.963 ± 0.049 M {sub ☉} and 0.860 ± 0.051 M {sub ☉} and 39.54 ± 1.85 mas for ω Andromeda, for HD 178911 of 0.802 ± 0.055 M {sub ☉} and 0.622 ± 0.053 M {sub ☉} with 28.26 ± 1.70 mas, and masses of 1.045 ± 0.031 M {sub ☉} and 0.408 ± 0.066 M {sub ☉} and 38.10 ± 2.81 mas for ξ Cephei.« less

Hypothesis: SLC12A3 Polymorphism modifies thiazide hypersensitivity of antenatal Bartter syndrome to thiazide resistance.

PubMed

Mammen, Cherry; Rupps, Rosemarie; Trnka, Peter; Boerkoel, Cornelius F

2012-02-01

We report a 5-year-old boy with thiazide-resistant Bartter syndrome. This is highly unusual since thiazide hypersensitivity is a common diagnostic finding in Bartter syndrome patients. Subsequent molecular testing identified compound heterozygosity for two novel mutations in KCNJ1, (c.556A > G and c.683G > A) which is associated with Bartter syndrome, and a paternally inherited polymorphism in SLC12A3 (c.791G > C). Mutations in SLC12A3 cause the thiazide-resistant tubulopathy Gitelman syndrome. Based on published studies of this polymorphism in SLC12A3 and the features of the proband's father, we postulate that this polymorphism modifies the phenotype of Bartter syndrome in the proband to thiazide resistance. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Association of Calpain (CAPN) 10 (UCSNP-43, rs3792267) gene polymorphism with elevated serum androgens in young women with the most severe phenotype of polycystic ovary syndrome (PCOS).

PubMed

Anastasia, Karela; Koika, Vasiliki; Roupas, Nikolaos D; Armeni, Anastasia; Marioli, Dimitra; Panidis, Dimitrios; George, Adonakis; Georgopoulos, Neoklis A

2015-01-01

To highlight a possible association of Calpain (CAPN 10) gene UCSNP-43 polymorphism with hormonal and metabolic traits of young women with different phenotypes of polycystic ovary syndrome (PCOS). PCOS women were genotyped for the CAPN 10 gene UCSNP-43 polymorphism. A comparison of clinical and biochemical features of women with PCOS stratified on the basis of the CAPN 10 gene UCSNP-43 variants was assessed. Anthropometric, hormonal and biochemical measurements were carried out in 668 PCOS women and 200 healthy controls. Subjects were also genotyped for the CAPN 10 gene UCSNP-43 polymorphism. The genotype frequency distributions between groups and controls were compared using the chi-square test. The association of the polymorphism with the clinical and biochemical features of the study cohort was estimated as well. No association of the frequency of CAPN 10 gene UCSNP-43 polymorphism with PCOS was detected. No association of the polymorphism with the anthropometric, biochemical and hormonal features was detected both in PCOS and control women. The polymorphism was associated with serum Δ4 androstenedione (p = 0.018), as well as with 17-OH progesterone (17-hydroxyprogesterone) among women with PCOS phenotype A (p = 0.012). CAPN 10 gene polymorphism UCSNP-43 is deprived of a metabolic contribution to cardiovascular disease (CVD). However, due to its association with androgen excess in phenotype A, CAPN 10 gene polymorphism UCSNP-43 could be used as a genetic marker for CVD in young PCOS women.

Hypolipidemic, antioxidant and antiatherogenic property of sardine by-products proteins in high-fat diet induced obese rats.

PubMed

Affane, Fouad; Louala, Sabrine; El Imane Harrat, Nour; Bensalah, Fatima; Chekkal, Hadjera; Allaoui, Amine; Lamri-Senhadji, Myriem

2018-04-15

Fish by-products valorization on account of their richness in bioactive compounds may represent a better alternative to marine products with a view to economic profitability and sustainable development. In this study, we compared the effect of sardine by-product proteins (SBy-P), with those of the fillets (SF-P) or casein (Cas), on growth parameters, serum leptin level, lipids disorders, lipid peroxidation and reverse cholesterol transport, in diet-induced obese rats. Obesity was induced by feeding rats a high-fat diet (20% sheep fat), during 12 weeks. At body weight (BW) of 400 ± 20 g, eighteen obese rats were divided into three homogenous groups and continue to consume the high-fat diet for 4 weeks containing either, 20% SBy-P, SF-P or Cas. The results showed that SBy-P, compared to SF-P and Cas, efficiently reduced food intake (FI), BW gain and serum leptin level, and improved blood lipids levels and reverse cholesterol transport by reducing total cholesterol (TC), triacylglycerols (TG) and low-density lipoprotein cholesterol (LDL-HDL 1 -C) serum levels, increasing the level of high-density lipoprotein cholesterol (HDL 2 -C and HDL 3 -C), and enhancing lecithin: cholesterol acyltransferase (LCAT) activity. Furthermore, they attenuated lipid peroxidation by increasing atheroprotective activity of the paraoxonase-1 (PON-1). Sardine by-product proteins due to their richness in certain essential amino acids, highlight weight-loss, lipid-lowering, antioxidant and anti-atherogenic potentials, contributing to the improvement of the complications associated with obesity. Copyright © 2018 Elsevier Inc. All rights reserved.

Sequence-Independent Cloning and Post-Translational Modification of Repetitive Protein Polymers through Sortase and Sfp-Mediated Enzymatic Ligation.

PubMed

Ott, Wolfgang; Nicolaus, Thomas; Gaub, Hermann E; Nash, Michael A

2016-04-11

Repetitive protein-based polymers are important for many applications in biotechnology and biomaterials development. Here we describe the sequential additive ligation of highly repetitive DNA sequences, their assembly into genes encoding protein-polymers with precisely tunable lengths and compositions, and their end-specific post-translational modification with organic dyes and fluorescent protein domains. Our new Golden Gate-based cloning approach relies on incorporation of only type IIS BsaI restriction enzyme recognition sites using PCR, which allowed us to install ybbR-peptide tags, Sortase c-tags, and cysteine residues onto either end of the repetitive gene polymers without leaving residual cloning scars. The assembled genes were expressed in Escherichia coli and purified using inverse transition cycling (ITC). Characterization by cloud point spectrophotometry, and denaturing polyacrylamide gel electrophoresis with fluorescence detection confirmed successful phosphopantetheinyl transferase (Sfp)-mediated post-translational N-terminal labeling of the protein-polymers with a coenzyme A-647 dye (CoA-647) and simultaneous sortase-mediated C-terminal labeling with a GFP domain containing an N-terminal GG-motif in a one-pot reaction. In a further demonstration, we installed an N-terminal cysteine residue into an elastin-like polypeptide (ELP) that was subsequently conjugated to a single chain poly(ethylene glycol)-maleimide (PEG-maleimide) synthetic polymer, noticeably shifting the ELP cloud point. The ability to straightforwardly assemble repetitive DNA sequences encoding ELPs of precisely tunable length and to post-translationally modify them specifically at the N- and C- termini provides a versatile platform for the design and production of multifunctional smart protein-polymeric materials.

Facing the rain after the phase out: Performance evaluation of alternative fluorinated and non-fluorinated durable water repellents for outdoor fabrics.

PubMed

Schellenberger, S; Gillgard, P; Stare, A; Hanning, A; Levenstam, O; Roos, S; Cousins, I T

2018-02-01

Fluorinated durable water repellent (DWR) agents are used to obtain water and stain repellent textiles. Due to the on-going phase-out of DWRs based on side-chain fluorinated polymers (SFP) with "long" perfluoroalkyl chains, the textile industry lacks suitable alternatives with comparable material characteristics. The constant development and optimization of SFPs for textile applications initiated more than half a century ago has resulted in a robust and very efficient DWR-technology and textiles with exceptional hydro- and oleo-phobic properties. The industry is now in the predicament that the long-chain SFPs with the best technical performance have undesirable toxicological and environmental behaviour. This study provides a comprehensive overview of the technical performance of presently available fluorinated and non-fluorinated DWRs as part of a chemical alternatives assessment (CAA). The results are based on a study with synthetic outdoor fabrics treated with alternative DWRs and tested for repellency using industrial standard and complementary methods. Using this approach, the complex structure-property relationships of DWR-polymers could be explained on a molecular level. Both short-chain SFPs and non-fluorinated DWRs showed excellent water repellency and durability in some cases while short-chain SFPs were the more robust of the alternatives to long-chain SFPs. A strong decline in oil repellency and durability with perfluoroalkyl chain length was shown for SFP DWRs. Non-fluorinated alternatives were unable to repel oil, which might limit their potential for substitution in textile application that require repellency towards non-polar liquids. Copyright © 2017. Published by Elsevier Ltd.

Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster

PubMed Central

Edwards, Stefan M.; Sørensen, Izel F.; Sarup, Pernille; Mackay, Trudy F. C.; Sørensen, Peter

2016-01-01

Predicting individual quantitative trait phenotypes from high-resolution genomic polymorphism data is important for personalized medicine in humans, plant and animal breeding, and adaptive evolution. However, this is difficult for populations of unrelated individuals when the number of causal variants is low relative to the total number of polymorphisms and causal variants individually have small effects on the traits. We hypothesized that mapping molecular polymorphisms to genomic features such as genes and their gene ontology categories could increase the accuracy of genomic prediction models. We developed a genomic feature best linear unbiased prediction (GFBLUP) model that implements this strategy and applied it to three quantitative traits (startle response, starvation resistance, and chill coma recovery) in the unrelated, sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel. Our results indicate that subsetting markers based on genomic features increases the predictive ability relative to the standard genomic best linear unbiased prediction (GBLUP) model. Both models use all markers, but GFBLUP allows differential weighting of the individual genetic marker relationships, whereas GBLUP weighs the genetic marker relationships equally. Simulation studies show that it is possible to further increase the accuracy of genomic prediction for complex traits using this model, provided the genomic features are enriched for causal variants. Our GFBLUP model using prior information on genomic features enriched for causal variants can increase the accuracy of genomic predictions in populations of unrelated individuals and provides a formal statistical framework for leveraging and evaluating information across multiple experimental studies to provide novel insights into the genetic architecture of complex traits. PMID:27235308

In situ 3D topographic and shape analysis by synchrotron radiation X-ray microtomography for crystal form identification in polymorphic mixtures

PubMed Central

Yin, Xian-Zhen; Xiao, Ti-Qiao; Nangia, Ashwini; Yang, Shuo; Lu, Xiao-Long; Li, Hai-Yan; Shao, Qun; He, You; York, Peter; Zhang, Ji-Wen

2016-01-01

Polymorphism denotes the existence of more than one crystal structure of a substance, and great practical and theoretical interest for the chemical and pharmaceutical industries. In many cases, it is challenging to produce a pure crystal form and establish a sensitive detection method for the identification of crystal form in a mixture of polymorphs. In this study, an accurate and sensitive method based on synchrotron radiation X-ray computed microtomography (SR-μCT) was devised to identify the polymorphs of clopidogrel bisulphate (CLP). After 3D reconstruction, crystal particles were extracted and dozens of structural parameters were calculated. Whilst, the particle shapes of the two crystal forms were all irregular, the surface of CLP II was found to be rougher than CLP I. In order to classify the crystal form based on the quantitative morphological property of particles, Volume Bias Percentage based on Surface Smoothing (VBP) was defined and a new method based on VBP was successfully developed, with a total matching rate of 99.91% for 4544 particles and a lowest detectable limit of 1%. More important for the mixtures in solid pharmaceutical formulations, the interference of excipients can be avoided, a feature cannot achieved by other available analytical methods. PMID:27097672

Development of GaInNAs-based 1.3-μm VCSEL

NASA Astrophysics Data System (ADS)

Ramakrishnan, Arun; Ebbinghaus, G.; Lima, A.; Supper, D.; Kristen, Guenter; Popp, M.; Degen, C.; Althaus, H.-L.; Killer, T.; Scholz, R.; Melinde, M.; Sauter, M.; Weigert, M.; Riechert, Henning; Steinle, Gunther

2003-12-01

In this paper the realization, development and production of 1.3μm vertical cavity surface emitting lasers (VCSEL) with datacom suitable performance are presented. These low cost laser diodes are well suited for optical interconnect applications for LAN and MAN with transmission distances up to 15 km. The possibilities as well as the advantages and limits of shifting the wavelength from commercially available VCSEL emitting at 850nm to 1300nm are discussed. 1300nm VCSELs in a low cost SMD plastic package assembled into an intelligent SFP-module developed by Infineon Technologies are demonstrated.

Landscape of Insertion Polymorphisms in the Human Genome

PubMed Central

Onozawa, Masahiro; Goldberg, Liat; Aplan, Peter D.

2015-01-01

Nucleotide substitutions, small (<50 bp) insertions or deletions (indels), and large (>50 bp) deletions are well-known causes of genetic variation within the human genome. We recently reported a previously unrecognized form of polymorphic insertions, termed templated sequence insertion polymorphism (TSIP), in which the inserted sequence was templated from a distant genomic region, and was inserted in the genome through reverse transcription of an RNA intermediate. TSIPs can be grouped into two classes based on nucleotide sequence features at the insertion junctions; class 1 TSIPs show target site duplication, polyadenylation, and preference for insertion at a 5′-TTTT/A-3′ sequence, suggesting a LINE-1 based insertion mechanism, whereas class 2 TSIPs show features consistent with repair of a DNA double strand break by nonhomologous end joining. To gain a more complete picture of TSIPs throughout the human population, we evaluated whole-genome sequence from 52 individuals, and identified 171 TSIPs. Most individuals had 25–30 TSIPs, and common (present in >20% of individuals) TSIPs were found in individuals throughout the world, whereas rare TSIPs tended to cluster in specific geographic regions. The number of rare TSIPs was greater than the number of common TSIPs, suggesting that TSIP generation is an ongoing process. Intriguingly, mitochondrial sequences were a frequent template for class 2 insertions, used more commonly than any nuclear chromosome. Similar to single nucleotide polymorphisms and indels, we suspect that these TSIPs may be important for the generation of human diversity and genetic diseases, and can be useful in tracking historical migration of populations. PMID:25745018

An Sfp-type PPTase and associated polyketide and nonribosomal peptide synthases in Agrobacterium vitis are essential for induction of tobacco hypersensitive response and grape necrosis.

PubMed

Zheng, Desen; Burr, Thomas J

2013-07-01

An Sfp-type phosphopantetheinyl transferase (PPTase) encoding gene F-avi5813 in Agrobacterium vitis F2/5 was found to be required for the induction of a tobacco hypersensitive response (HR) and grape necrosis. Sfp-type PPTases are post-translation modification enzymes that activate acyl-carry protein (ACP) domains in polyketide synthases (PKS) and peptidyl-carrier protein (PCP) domains of nonribosomal peptide synthases (NRPS). Mutagenesis of PKS and NRPS genes in A. vitis led to the identification of a PKS gene (F-avi4330) and NRPS gene (F-avi3342) that are both required for HR and necrosis. The gene immediately downstream of F-avi4330 (F-avi4329) encoding a predicted aminotransferase was also found to be required for HR and necrosis. Regulation of F-avi4330 and F-avi3342 by quorum-sensing genes avhR, aviR, and avsR and by a lysR-type regulator, lhnR, was investigated. It was determined that F-avi4330 expression is positively regulated by avhR, aviR, and lhnR and negatively regulated by avsR. F-avi3342 was found to be positively regulated by avhR, aviR, and avsR and negatively regulated by lhnR. Our results suggest that a putative hybrid peptide-polyketide metabolite synthesized by F-avi4330 and F-avi3342 is associated with induction of tobacco HR and grape necrosis. This is the first report that demonstrates that NRPS and PKS play essential roles in conferring the unique ability of A. vitis to elicit a non-host-specific HR and host-specific necrosis.

Predictive performance of four frailty measures in an older Australian population

PubMed Central

Widagdo, Imaina S.; Pratt, Nicole; Russell, Mary; Roughead, Elizabeth E.

2015-01-01

Background: there are several different frailty measures available for identifying the frail elderly. However, their predictive performance in an Australian population has not been examined. Objective: to examine the predictive performance of four internationally validated frailty measures in an older Australian population. Methods: a retrospective study in the Australian Longitudinal Study of Ageing (ALSA) with 2,087 participants. Frailty was measured at baseline using frailty phenotype (FP), simplified frailty phenotype (SFP), frailty index (FI) and prognostic frailty score (PFS). Odds ratios (OR) were calculated to measure the association between frailty and outcomes at Wave 3 including mortality, hospitalisation, nursing home admission, fall and a combination of all outcomes. Predictive performance was measured by assessing sensitivity, specificity, positive and negative predictive values (PPV and NPV) and likelihood ratio (LR). Area under the curve (AUC) of dichotomised and the multilevel or continuous model of the measures was examined. Results: prevalence of frailty varied from 2% up to 49% between the measures. Frailty was significantly associated with an increased risk of any outcome, OR (95% confidence interval) for FP: 1.9 (1.4–2.8), SFP: 3.6 (1.5–8.8), FI: 3.4 (2.7–4.3) and PFS: 2.3 (1.8–2.8). PFS had high sensitivity across all outcomes (sensitivity: 55.2–77.1%). The PPV for any outcome was highest for SFP and FI (70.8 and 69.7%, respectively). Only FI had acceptable accuracy in predicting outcomes, AUC: 0.59–0.70. Conclusions: being identified as frail by any of the four measures was associated with an increased risk of outcomes; however, their predictive accuracy varied. PMID:26504118

Storage Time and Temperature Effects on Histamine Production in Tuna Salad Preparations.

PubMed

McCarthy, Susan; Bjornsdottir-Butler, Kristin; Benner, Ronald

2015-07-01

Scombrotoxin fish poisoning (SFP), also known as histamine (Hst) poisoning, has been associated with consumption of scombroid-type fish, including tuna and tuna fish products. Preparation of commercial tuna salad contaminated with Hstproducing bacteria (HPB), combined with time-temperature abuse, can present a food safety hazard. A potential source of HPB is raw ingredients, such as celery and onions. The objectives of this study were to determine whether raw ingredients can be a source of HPB and to ascertain the effects of storage time (up to 4 days or 4 weeks) and temperature (4, 10, 18, 25, 30°C) on growth and Hst production by high-HPB (>1,000 ppm of Hst) in tuna salad preparations. Pantoea-Erwinia, Erwinia persicinus, Erwinia spp., and Enterobacter pyrinus isolated from celery in this study were used to inoculate tuna salad and tuna salad with celery or onion. HPB numbers were 0.7 to 4.3 log most probable number per g higher in the presence of celery or onion versus plain tuna salad (3:1 tuna:mayonnaise). E. pyrinus-inoculated plain tuna salad and tuna salad with celery and onion had >500 ppm of Hst after 2 days at 30°C and 4 days at 25°C. E. pyrinus-inoculated salad with celery and onion had >500 ppm of Hst after 4 days at 18°C and 2 weeks at 10°C. Raw celery can introduce HPB into tuna salad, which can cause SFP if the product is time-temperature abused. Tuna salad products must be refrigerated at ≤4°C to prevent growth and Hst production by the HPB used in this study, to protect consumers from potential SFP.

Assessment of toxic impact of metals on proline, antioxidant enzymes, and biological characteristics of Pseudomonas aeruginosa inoculated Cicer arietinum grown in chromium and nickel-stressed sandy clay loam soils.

PubMed

Saif, Saima; Khan, Mohammad Saghir

2018-04-17

Considering the heavy metal risk to soil microbiota and agro-ecosystems, the study was designed to determine metal toxicity to bacteria and to find metal tolerant bacteria carrying multifarious plant growth promoting activities and to assess their impact on chickpea cultivated in stressed soils. Metal tolerant strain SFP1 recognized as Pseudomonas aeruginosa employing 16S rRNA gene sequence determination showed maximum tolerance to Cr (400 μg/ml) and Ni (800 μg/ml) and produced variable amounts of indole acetic acid, HCN, NH 3 , and ACC deaminase and could solubilize insoluble phosphates even under Cr (VI) and Ni stress. Metal tolerant P. aeruginosa reduced toxicity of Cr (VI) and Ni and concomitantly enhanced the performance of chickpea grown under stressed and conventional soils. At 144 mg Cr kg -1 , the measured parameters of a bacterial strain was significantly enhanced, but it was lower compared to those recorded at 660 mg Ni kg -1 . The strain SFP1 demonstrated maximum increase in seed yield (81%) and grain protein (16%) at 660 mg Ni kg -1 over uninoculated and untreated control. Stressed plants had more proline, antioxidant enzymes, and metal concentrations in plant tissues. P. aeruginosa, however, remarkably declined the level of stress markers (proline and APX, SOD, CAT, and GR), as well as with Cr (VI) and Ni uptake by chickpea. Conclusively, P. aeruginosa strain SFP1 due to its dual metal tolerant ability, capacity to secrete plant growth promoting regulators even under metal stress and potential to mitigate metal toxicity, could be developed as microbial inoculant for enhancing chickpea production in Cr and Ni contaminated soils.

Alfalfa Biomass Germplasms: SFP Detection and Transcriptome Analysis

USDA-ARS?s Scientific Manuscript database

Advances in alfalfa [Medicago sativa (L.) subsp. sativa] breeding, molecular genetics, and genomics have been slow because this crop is an allogamous autotetraploid (2n = 4x = 32) with complex polysomic inheritance. Increasing cellulose and decreasing lignin in alfalfa stem cell walls would improve ...

Averrhoa carambola L. peel extract suppresses adipocyte differentiation in 3T3-L1 cells.

PubMed

Rashid, Asyifah Mohamed; Lu, Kaihui; Yip, Yew Mun; Zhang, Dawei

2016-02-01

Obesity is associated with an increased risk of many chronic diseases. Recently, a growing body of evidence has shown that phytochemicals may inhibit adipogenesis and obesity. In this study, we report for the first time, the ability of Averrhoa carambola L. peel extract commonly known as star fruit (SFP) to effectively suppress adipocyte differentiation in 3T3-L1 preadipocytes and therefore, address it as a potential candidate to treat obesity and its related diseases. (-)-Epicatechin was identified as a bioactive compound likely responsible for this suppression. As the genetic expression studies revealed that the adipogenic activity of SFP extract was due to the simultaneous downregulation of the C/EBPα and PPARγ as well as the upregulation of PPARα receptor genes, a detailed computational docking study was also elucidated to reveal the likely binding mode of (-)-epicatechin to the receptor of interest, accounting for the likely mechanism that results in the overall suppression of adipocyte differentiation.

A Single-Stranded DNA Aptamer That Selectively Binds to Staphylococcus aureus Enterotoxin B

PubMed Central

DeGrasse, Jeffrey A.

2012-01-01

The bacterium Staphylococcus aureus is a common foodborne pathogen capable of secreting a cocktail of small, stable, and strain-specific, staphylococcal enterotoxins (SEs). Staphylococcal food poisoning (SFP) results when improperly handled food contaminated with SEs is consumed. Gastrointestinal symptoms of SFP include emesis, diarrhea and severe abdominal pain, which manifest within hours of ingesting contaminated food. Immuno-affinity based methods directly detect, identify, and quantify several SEs within a food or clinical sample. However, the success of these assays depends upon the availability of a monoclonal antibody, the development of which is non-trivial and costly. The current scope of the available immuno-affinity based methods is limited to the classical SEs and does not encompass all of the known or emergent SEs. In contrast to antibodies, aptamers are short nucleic acids that exhibit high affinity and specificity for their targets without the high-costs and ethical concerns of animal husbandry. Further, researchers may choose to freely distribute aptamers and develop assays without the proprietary issues that increase the per-sample cost of immuno-affinity assays. This study describes a novel aptamer, selected in vitro, with affinity to staphylococcal enterotoxin B (SEB) that may be used in lieu of antibodies in SE detection assays. The aptamer, designated APTSEB1, successfully isolates SEB from a complex mixture of SEs with extremely high discrimination. This work sets the foundation for future aptamer and assay development towards the entire family of SEs. The rapid, robust, and low-cost identification and quantification of all of the SEs in S. aureus contaminated food is essential for food safety and epidemiological efforts. An in vitro generated library of SE aptamers could potentially allow for the comprehensive and cost-effective analysis of food samples that immuno-affinity assays currently cannot provide. PMID:22438927

A single-stranded DNA aptamer that selectively binds to Staphylococcus aureus enterotoxin B.

PubMed

DeGrasse, Jeffrey A

2012-01-01

The bacterium Staphylococcus aureus is a common foodborne pathogen capable of secreting a cocktail of small, stable, and strain-specific, staphylococcal enterotoxins (SEs). Staphylococcal food poisoning (SFP) results when improperly handled food contaminated with SEs is consumed. Gastrointestinal symptoms of SFP include emesis, diarrhea and severe abdominal pain, which manifest within hours of ingesting contaminated food. Immuno-affinity based methods directly detect, identify, and quantify several SEs within a food or clinical sample. However, the success of these assays depends upon the availability of a monoclonal antibody, the development of which is non-trivial and costly. The current scope of the available immuno-affinity based methods is limited to the classical SEs and does not encompass all of the known or emergent SEs. In contrast to antibodies, aptamers are short nucleic acids that exhibit high affinity and specificity for their targets without the high-costs and ethical concerns of animal husbandry. Further, researchers may choose to freely distribute aptamers and develop assays without the proprietary issues that increase the per-sample cost of immuno-affinity assays. This study describes a novel aptamer, selected in vitro, with affinity to staphylococcal enterotoxin B (SEB) that may be used in lieu of antibodies in SE detection assays. The aptamer, designated APT(SEB1), successfully isolates SEB from a complex mixture of SEs with extremely high discrimination. This work sets the foundation for future aptamer and assay development towards the entire family of SEs. The rapid, robust, and low-cost identification and quantification of all of the SEs in S. aureus contaminated food is essential for food safety and epidemiological efforts. An in vitro generated library of SE aptamers could potentially allow for the comprehensive and cost-effective analysis of food samples that immuno-affinity assays currently cannot provide.

Structural analysis of oligomeric and protofibrillar Aβ amyloid pair structures considering F20L mutation effects using molecular dynamics simulations.

PubMed

Lee, Myeongsang; Chang, Hyun Joon; Baek, Inchul; Na, Sungsoo

2017-04-01

Aβ amyloid proteins are involved in neuro-degenerative diseases such as Alzheimer's, Parkinson's, and so forth. Because of its structurally stable feature under physiological conditions, Aβ amyloid protein disrupts the normal cell function. Because of these concerns, understanding the structural feature of Aβ amyloid protein in detail is crucial. There have been some efforts on lowering the structural stabilities of Aβ amyloid fibrils by decreasing the aromatic residues characteristic and hydrophobic effect. Yet, there is a lack of understanding of Aβ amyloid pair structures considering those effects. In this study, we provide the structural characteristics of wildtype (WT) and phenylalanine residue mutation to leucine (F20L) Aβ amyloid pair structures using molecular dynamics simulation in detail. We also considered the polymorphic feature of F20L and WT Aβ pair amyloids based on the facing β-strand directions between the amyloid pairs. As a result, we were able to observe the varying effects of mutation, polymorphism, and protofibril lengths on the structural stability of pair amyloids. Furthermore, we have also found that opposite structural stability exists on a certain polymorphic Aβ pair amyloids depending on its oligomeric or protofibrillar state, which can be helpful for understanding the amyloid growth mechanism via repetitive fragmentation and elongation mechanism. Proteins 2017; 85:580-592. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Development and Assessment of CFD Models Including a Supplemental Program Code for Analyzing Buoyancy-Driven Flows Through BWR Fuel Assemblies in SFP Complete LOCA Scenarios

NASA Astrophysics Data System (ADS)

Artnak, Edward Joseph, III

This work seeks to illustrate the potential benefits afforded by implementing aspects of fluid dynamics, especially the latest computational fluid dynamics (CFD) modeling approach, through numerical experimentation and the traditional discipline of physical experimentation to improve the calibration of the severe reactor accident analysis code, MELCOR, in one of several spent fuel pool (SFP) complete loss-ofcoolant accident (LOCA) scenarios. While the scope of experimental work performed by Sandia National Laboratories (SNL) extends well beyond that which is reasonably addressed by our allotted resources and computational time in accordance with initial project allocations to complete the report, these simulated case trials produced a significant array of supplementary high-fidelity solutions and hydraulic flow-field data in support of SNL research objectives. Results contained herein show FLUENT CFD model representations of a 9x9 BWR fuel assembly in conditions corresponding to a complete loss-of-coolant accident scenario. In addition to the CFD model developments, a MATLAB based controlvolume model was constructed to independently assess the 9x9 BWR fuel assembly under similar accident scenarios. The data produced from this work show that FLUENT CFD models are capable of resolving complex flow fields within a BWR fuel assembly in the realm of buoyancy-induced mass flow rates and that characteristic hydraulic parameters from such CFD simulations (or physical experiments) are reasonably employed in corresponding constitutive correlations for developing simplified numerical models of comparable solution accuracy.

Insertion and deletion polymorphisms of the ancient AluS family in the human genome.

PubMed

Kryatova, Maria S; Steranka, Jared P; Burns, Kathleen H; Payer, Lindsay M

2017-01-01

Polymorphic Alu elements account for 17% of structural variants in the human genome. The majority of these belong to the youngest AluY subfamilies, and most structural variant discovery efforts have focused on identifying Alu polymorphisms from these currently retrotranspositionally active subfamilies. In this report we analyze polymorphisms from the evolutionarily older AluS subfamily, whose peak activity was tens of millions of years ago. We annotate the AluS polymorphisms, assess their likely mechanism of origin, and evaluate their contribution to structural variation in the human genome. Of 52 previously reported polymorphic AluS elements ascertained for this study, 48 were confirmed to belong to the AluS subfamily using high stringency subfamily classification criteria. Of these, the majority (77%, 37/48) appear to be deletion polymorphisms. Two polymorphic AluS elements (4%) have features of non-classical Alu insertions and one polymorphic AluS element (2%) likely inserted by a mechanism involving internal priming. Seven AluS polymorphisms (15%) appear to have arisen by the classical target-primed reverse transcription (TPRT) retrotransposition mechanism. These seven TPRT products are 3' intact with 3' poly-A tails, and are flanked by target site duplications; L1 ORF2p endonuclease cleavage sites were also observed, providing additional evidence that these are L1 ORF2p endonuclease-mediated TPRT insertions. Further sequence analysis showed strong conservation of both the RNA polymerase III promoter and SRP9/14 binding sites, important for mediating transcription and interaction with retrotransposition machinery, respectively. This conservation of functional features implies that some of these are fairly recent insertions since they have not diverged significantly from their respective retrotranspositionally competent source elements. Of the polymorphic AluS elements evaluated in this report, 15% (7/48) have features consistent with TPRT-mediated insertion, thus suggesting that some AluS elements have been more active recently than previously thought, or that fixation of AluS insertion alleles remains incomplete. These data expand the potential significance of polymorphic AluS elements in contributing to structural variation in the human genome. Future discovery efforts focusing on polymorphic AluS elements are likely to identify more such polymorphisms, and approaches tailored to identify deletion alleles may be warranted.

Size-dependent pressure-induced amorphization: a thermodynamic panorama.

PubMed

Machon, Denis; Mélinon, Patrice

2015-01-14

Below a critical particle size, some pressurized compounds (e.g. TiO2, Y2O3, PbTe) undergo a crystal-to-amorphous transformation instead of a polymorphic transition. This effect reflects the greater propensity of nanomaterials for amorphization. In this work, a panorama of thermodynamic interpretations is given: first, a descriptive analysis based on the energy landscape concept gives a general comprehension of the balance between thermodynamics and kinetics to obtain an amorphous state. Then, a formal approach based on Gibbs energy to describe the thermodynamics and phase transitions in nanoparticles gives a basic explanation of size-dependent pressure-induced amorphization. The features of this transformation (amorphization occurs at pressures lower than the polymorphic transition pressure!) and the nanostructuration can be explained in an elaborated model based on the Ginzburg-Landau theory of phase transition and on percolation theory. It is shown that the crossover between polymorphic transition and amorphization is highly dependent on the defect density and interfacial energy, i.e., on the synthesis process. Their behavior at high pressure is a quality control test for the nanoparticles.

FSR: feature set reduction for scalable and accurate multi-class cancer subtype classification based on copy number.

PubMed

Wong, Gerard; Leckie, Christopher; Kowalczyk, Adam

2012-01-15

Feature selection is a key concept in machine learning for microarray datasets, where features represented by probesets are typically several orders of magnitude larger than the available sample size. Computational tractability is a key challenge for feature selection algorithms in handling very high-dimensional datasets beyond a hundred thousand features, such as in datasets produced on single nucleotide polymorphism microarrays. In this article, we present a novel feature set reduction approach that enables scalable feature selection on datasets with hundreds of thousands of features and beyond. Our approach enables more efficient handling of higher resolution datasets to achieve better disease subtype classification of samples for potentially more accurate diagnosis and prognosis, which allows clinicians to make more informed decisions in regards to patient treatment options. We applied our feature set reduction approach to several publicly available cancer single nucleotide polymorphism (SNP) array datasets and evaluated its performance in terms of its multiclass predictive classification accuracy over different cancer subtypes, its speedup in execution as well as its scalability with respect to sample size and array resolution. Feature Set Reduction (FSR) was able to reduce the dimensions of an SNP array dataset by more than two orders of magnitude while achieving at least equal, and in most cases superior predictive classification performance over that achieved on features selected by existing feature selection methods alone. An examination of the biological relevance of frequently selected features from FSR-reduced feature sets revealed strong enrichment in association with cancer. FSR was implemented in MATLAB R2010b and is available at http://ww2.cs.mu.oz.au/~gwong/FSR.

Global image analysis to determine suitability for text-based image personalization

NASA Astrophysics Data System (ADS)

Ding, Hengzhou; Bala, Raja; Fan, Zhigang; Bouman, Charles A.; Allebach, Jan P.

2012-03-01

Lately, image personalization is becoming an interesting topic. Images with variable elements such as text usually appear much more appealing to the recipients. In this paper, we describe a method to pre-analyze the image and automatically suggest to the user the most suitable regions within an image for text-based personalization. The method is based on input gathered from experiments conducted with professional designers. It has been observed that regions that are spatially smooth and regions with existing text (e.g. signage, banners, etc.) are the best candidates for personalization. This gives rise to two sets of corresponding algorithms: one for identifying smooth areas, and one for locating text regions. Furthermore, based on the smooth and text regions found in the image, we derive an overall metric to rate the image in terms of its suitability for personalization (SFP).

Sequence-Based Prioritization of Nonsynonymous Single-Nucleotide Polymorphisms for the Study of Disease Mutations

PubMed Central

Jiang, Rui ; Yang, Hua ; Zhou, Linqi ; Kuo, C.-C. Jay ; Sun, Fengzhu ; Chen, Ting 

2007-01-01

The increasing demand for the identification of genetic variation responsible for common diseases has translated into a need for sophisticated methods for effectively prioritizing mutations occurring in disease-associated genetic regions. In this article, we prioritize candidate nonsynonymous single-nucleotide polymorphisms (nsSNPs) through a bioinformatics approach that takes advantages of a set of improved numeric features derived from protein-sequence information and a new statistical learning model called “multiple selection rule voting” (MSRV). The sequence-based features can maximize the scope of applications of our approach, and the MSRV model can capture subtle characteristics of individual mutations. Systematic validation of the approach demonstrates that this approach is capable of prioritizing causal mutations for both simple monogenic diseases and complex polygenic diseases. Further studies of familial Alzheimer diseases and diabetes show that the approach can enrich mutations underlying these polygenic diseases among the top of candidate mutations. Application of this approach to unclassified mutations suggests that there are 10 suspicious mutations likely to cause diseases, and there is strong support for this in the literature. PMID:17668383

Differentiation of animal fats from different origins: use of polymorphic features detected by Raman spectroscopy.

PubMed

Motoyama, Michiyo; Ando, Masahiro; Sasaki, Keisuke; Hamaguchi, Hiro-O

2010-11-01

Food safety requires the development of reliable techniques that ensure the origin of animal fats. In the present work, we try to verify the efficacy of using the polymorphic features of fats for discriminating animal-fat origins. We use Raman spectroscopy to collect the structural information of fat crystals. It is shown that a single Raman band at 1417 cm(-1) successfully differentiates pork fats from beef fats. This band is known to be characteristic of the β'-polymorph of fats. Pork fats show this band because they contain the β'-polymorph after rapid cooling to 0 °C. In beef-pork-fat mixtures, this band is not detected even in the presence of 50% pork fat; an addition of beef fat to pork fat is likely to produce a mixed fat with a completely different polymorphic behavior. This method seems to have the potential to detect beef products contaminated with pork-adipose tissue.

Clinical features of Bim deletion polymorphism and its relation with crizotinib primary resistance in Chinese patients with ALK/ROS1 fusion-positive non-small cell lung cancer.

PubMed

Zhang, Limin; Jiang, Tao; Li, Xuefei; Wang, Yan; Zhao, Chao; Zhao, Sha; Xi, Lei; Zhang, Shijia; Liu, Xiaozhen; Jia, Yijun; Yang, Hui; Shi, Jinpeng; Su, Chunxia; Ren, Shengxiang; Zhou, Caicun

2017-08-01

The authors' previous study demonstrated that the B-cell chronic lymphocytic leukemia/lymphoma (Bcl-2)-like 11 (BCL2L11) (Bim) deletion polymorphism was associated with poor clinical response to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors in patients with non-small cell lung cancer (NSCLC) with EGFR mutations. The objective of the current study was to investigate the impact of the Bim deletion polymorphism among patients with anaplastic lymphoma kinase (ALK)-positive or ROS proto-oncogene 1, receptor tyrosine kinase (ROS1)-positive NSCLC who were treated with crizotinib. A total of 55 patients with ALK-positive NSCLC and 14 patients with ROS1-positive NSCLC who were treated with crizotinib were enrolled into the current study. The Bim deletion polymorphism was analyzed by polymerase chain reaction. The clinical features of the Bim deletion polymorphism and its impact on the effect of crizotinib were investigated. The Bim deletion polymorphism was present in 9 of 69 patients with ALK-positive or ROS1-positive NSCLC (13.0%). There were no differences noted with regard to clinicopathological features between patients with and without the Bim deletion polymorphism. Patients with the Bim deletion polymorphism had a significantly shorter progression-free survival (PFS) and lower objective response rate compared with those without (median PFS, 182 days vs 377 days [P = .008]) (objective response rate, 44.4% vs 81.7% [P =.041]) in all populations. The significant difference in PFS was observed in patients with ALK-positive NSCLC (83 days vs 305 days [P =.0304]) compared with those with ROS1-positive NSCLC (218 days vs not reached [P =.082]). Multivariate analysis indicated that the Bim deletion polymorphism was an independent predictive factor for patients with ALK-positive NSCLC who were treated with crizotinib (hazard ratio, 4.786 [P =.006]). The Bim deletion polymorphism was found to be associated with poor clinical response to crizotinib in patients with ALK fusion-positive NSCLC. Cancer 2017;123:2927-35. © 2017 American Cancer Society. © 2017 American Cancer Society.

77 FR 59186 - Clean Air Act Operating Permit Program; Petition for Objection to State Operating Permit for...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-26

... ENVIRONMENTAL PROTECTION AGENCY [Petition IV-2011-1; FRL-9734-2] Clean Air Act Operating Permit Program; Petition for Objection to State Operating Permit for Tennessee Valley Authority's Shawnee Fossil... Valley Authority for its Shawnee Fossil Plant (SFP) facility located in West Paducah, Kentucky. This...

Social values of specialty forest products to rural communities

Treesearch

Marla R. Emery

1999-01-01

Rural communities have long been known for their cultural distinctiveness, independent spirits, and, unfortunately, comparatively high poverty rates. A look at the promotion of Specialty Forest Products (SFP) as a rural development strategy against the backdrop of larger social trends such as welfare reform and economic restructuring suggests the need to ask hard...

Malnutrition, School Feeding and Educational Performance. Notes, Comments...No. 186 = Malnutrition, alimentation scolaire et resultats educatifs.

ERIC Educational Resources Information Center

Levinger, Beryl

Studies reviewed in this paper analyze the relationship between School Feeding Programme (SFP) participation and cognitive development in both developing and industralized countries. Contents concern: (1) the relationship betweeen diet and cognitive development; (2) limitations of intelligence quotient tests and the need for more adequate…

78 FR 38078 - Biweekly Notice; Applications and Amendments to Facility Operating Licenses and Combined Licenses...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-25

... SFP Purification Loop and recirculation and purification of the RWST water using the BARS is not... revise the minimum volume and low level setpoint on the Refueling Water Storage Tank. Because the... proposed change would revise Technical Specification 3.5.4, ``Refueling Water Storage Tank (RWST)'' such...

Strengthening Family Practices for Latino Families

ERIC Educational Resources Information Center

Chartier, Karen G.; Negroni, Lirio K.; Hesselbrock, Michie N.

2010-01-01

This study examined the effectiveness of a culturally adapted Strengthening Families Program (SFP) for Latinos to reduce risks for alcohol and drug use in children. Latino families, predominantly Puerto Rican, with a 9- to 12-year-old child and a parent(s) with a substance abuse problem participated in the study. Pre- and post-tests were conducted…

77 FR 48556 - Applications and Amendments to Facility Operating Licenses and Combined Licenses Involving...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-14

... would use a combination of partial credit for soluble boron, Boral\\TM\\ for Region 1, burnup, rod cluster... storage racks or the new fuel handling processes. Operation of the SFP utilizes soluble boron; crediting this boron for criticality control does not change the probability of any accident. The proposed...

Analysis of gamma ray dose for dried up pond storing low enriched UO2 fuel

NASA Astrophysics Data System (ADS)

Nauchi, Yasushi; Suzuki, Motomu

2017-09-01

Gamma ray dose is calculated for loss of coolant accident in spent fuel pond (SFP) storing irradiated fuels used in light water reactors. Influence of modelling of fuel assemblies, source distributions, and loading fraction of fuel assemblies in the fuel rack on the dose are investigated.

Barriers and Opportunities Related to Whole Grain Foods in Minnesota School Foodservice

ERIC Educational Resources Information Center

Hesse, David; Braun, Curtis; Dostal, Allison; Jeffery, Robert; Marquart, Len

2009-01-01

Purpose/Objectives: The purpose of this research was to identify barriers and opportunities associated with the introduction of whole grain foods into school cafeterias. The primary objective was to elicit input from school foodservice personnel (SFP) regarding their experiences in ordering, purchasing, preparing, and serving whole grain foods in…

The dynamic still-face effect: do infants decrease bidding over time when parents are not responsive?

PubMed

Ekas, Naomi V; Haltigan, John D; Messinger, Daniel S

2013-06-01

The still-face paradigm (SFP) was designed to assess infant expectations that parents will respond to infant communicative signals. During the still-face (SF) episode, the parent ceases interaction and maintains a neutral expression. Original, qualitative descriptions of infant behavior suggested changes within the SF episode: infants decrease bidding and disengage from their impassive parent. Research has documented changes in mean levels of infant behavior between episodes of the SFP. The hypothesis that infant behavior changes within the SF episode has not been empirically tested. In this study, hierarchical linear modeling indicated that infant gazing at the parent, smiling, and social bidding (smiling while gazing at the parent) decreased with time in the SF episode, while infant cry-face expressions increased. Changes in infant behaviors within the SF episode were associated with infant attachment and infant internalizing problems. The dynamic still-face effect quantifies infant initiation of interaction in the face of parental unresponsiveness and is a potential predictor of individual differences in development. PsycINFO Database Record (c) 2013 APA, all rights reserved

Gas chromatographic quantitation of underivatized amines in the determination of their octanol-0.1 M sodium hydroxide partition coefficients by the shake-flask method.

PubMed

Grunewald, G L; Pleiss, M A; Gatchell, C L; Pazhenchevsky, R; Rafferty, M F

1984-06-01

The use of gas chromatography (GC) for the determination of 0.1 M sodium hydroxide-octanol partition coefficients (log P) for a wide variety of ethylamines is demonstrated. The conventional shake-flask procedure (SFP) is utilized, with the addition of an internal reference, which is cleanly separated from the desired solute and solvents on a 10% Apiezon L, 2% potassium hydroxide on 80-100 mesh Chromosorb W AW column. The partitioned solute is extracted from the aqueous phase with chloroform and analyzed by GC. The method provides an accurate and highly reproducible means of determining log P values, as demonstrated by the low relative standard errors. The technique is both rapid and extremely versatile. The use of the internal standard method of analysis introduces consistency, since variables like the exact weight of solute are not necessary (unlike the traditional SFP) and the volume of sample injected is not critical. The technique is readily accessible to microgram quantities of solutes, making it ideal for a wide range of volatile, amine-bearing compounds.

Feature-based classification of amino acid substitutions outside conserved functional protein domains.

PubMed

Gemovic, Branislava; Perovic, Vladimir; Glisic, Sanja; Veljkovic, Nevena

2013-01-01

There are more than 500 amino acid substitutions in each human genome, and bioinformatics tools irreplaceably contribute to determination of their functional effects. We have developed feature-based algorithm for the detection of mutations outside conserved functional domains (CFDs) and compared its classification efficacy with the most commonly used phylogeny-based tools, PolyPhen-2 and SIFT. The new algorithm is based on the informational spectrum method (ISM), a feature-based technique, and statistical analysis. Our dataset contained neutral polymorphisms and mutations associated with myeloid malignancies from epigenetic regulators ASXL1, DNMT3A, EZH2, and TET2. PolyPhen-2 and SIFT had significantly lower accuracies in predicting the effects of amino acid substitutions outside CFDs than expected, with especially low sensitivity. On the other hand, only ISM algorithm showed statistically significant classification of these sequences. It outperformed PolyPhen-2 and SIFT by 15% and 13%, respectively. These results suggest that feature-based methods, like ISM, are more suitable for the classification of amino acid substitutions outside CFDs than phylogeny-based tools.

Analysis of the VIDAS® Staph Enterotoxin III (SET3) for Detection of Staphylococcal Enterotoxins G, H, and I in Foods.

PubMed

Hait, Jennifer M; Nguyen, Angela T; Tallent, Sandra M

2018-04-20

Background : Staphylococcal food poisoning (SFP) frequently causes illnesses worldwide. SFP occurs from the ingestion of staphylococcal enterotoxins (SEs) preformed in foods by enterotoxigenic strains of Staphylococcus species, primarily S. aureus . SEG, SEH, and SEI induce emesis and have been implicated in outbreaks. Immunological-based methods are deemed the most practical methods for the routine analysis of SEs in foods given their ease of use, sensitivity, specificity, and commercial availability. These kits are routinely used to test for SEA-SEE. However, only recently has a kit been developed to detect SEG, SEH, and SEI. Objective: Our research examined the performance of the novel VIDAS ® Staph Enterotoxin III (SET3) for the detection of staphylococcal enterotoxins SEG, SEH, and SEI in foods. Methods : Here we assess the sensitivity and specificity of SET3 using duplicate test portions of six foods at varying concentrations of inclusivity and exclusivity inocula: pure SEG, SEH, SEI, S. aureus strain extracts positive for seg, seh , and sei , as well as SEA, SEB, SEC, SED, and SEE. Results : The overall detection limit was less than 2.09 ng/mL for foods inoculated with SEG, SEH, and SEI, with no cross reactivity observed. Highlights : Integrating concurrent testing to detect the presence of SEA-SEE and SEG-SEI utilizing the SET3 along with the VIDAS SET2, Ridascreen ® SET total, or other comparable kits will be instrumental for the future food assessments in our laboratory and may become the new standard for SE analysis of foods.

Brain monoamine levels and behaviour of young and adult chickens genetically selected on feather pecking.

PubMed

Kops, M S; Kjaer, J B; Güntürkün, O; Westphal, K G C; Korte-Bouws, G A H; Olivier, B; Korte, S M; Bolhuis, J E

2017-06-01

Severe feather pecking (SFP) in chickens is a detrimental behaviour with possibly neurochemical deficits at its base. Recent neurological studies depicted conflicting results on the role of serotonin (5-hydroxytryptamine, 5-HT) and dopamine (DA) in the development and display of feather pecking. We studied brain monoamine levels and behaviour in domestic chickens divergently genetically selected on feather pecking behaviour, the Low Feather Pecking (LFP) and High Feather Pecking (HFP) lines, both at a young age and when adult, to elucidate the role of 5-HT and DA in feather pecking. Also pecking behaviour and the behavioural response to challenging test situations was determined. At 8 weeks of age, HFP had lower 5-HT and DA turnover in several brain areas than LFP, whereas these differences had disappeared or were even reversed at 25 weeks of age. Line differences in central monoamine activity were found both in emotion-regulating and motor-regulating areas. As expected from previous generations, HFP exceeded LFP in most types of pecking at other birds, including severe feather pecking. Furthermore, HFP responded more actively in most behavioural tests conducted, and seem more impulsive or (hyper)active in their way of coping with challenges. This paper shows different developmental trajectories of the neurochemical systems (5-HT and DA) for chickens divergently selected on feather pecking behaviour, and a remarkable reversion of differences in monoamine activity at a later stage of life. Whether this is a cause or consequence of SFP needs further investigation. Copyright © 2017 Elsevier B.V. All rights reserved.

Positive Regulation of Staphylococcal Enterotoxin H by Rot (Repressor of Toxin) Protein and Its Importance in Clonal Complex 81 Subtype 1 Lineage-Related Food Poisoning

PubMed Central

Sato'o, Yusuke; Hisatsune, Junzo; Nagasako, Yuria; Ono, Hisaya K.; Omoe, Katsuhiko

2015-01-01

We previously demonstrated the clonal complex 81 (CC81) subtype 1 lineage is the major staphylococcal food poisoning (SFP)-associated lineage in Japan (Y. Sato'o et al., J Clin Microbiol 52:2637–2640, 2014, http://dx.doi.org/10.1128/JCM.00661-14). Strains of this lineage produce staphylococcal enterotoxin H (SEH) in addition to SEA. However, an evaluation of the risk for the recently reported SEH has not been sufficiently conducted. We first searched for staphylococcal enterotoxin (SE) genes and SE proteins in milk samples that caused a large SFP outbreak in Japan. Only SEA and SEH were detected, while there were several SE genes detected in the samples. We next designed an experimental model using a meat product to assess the productivity of SEs and found that only SEA and SEH were detectably produced in situ. Therefore, we investigated the regulation of SEH production using a CC81 subtype 1 isolate. Through mutant analysis of global regulators, we found the repressor of toxin (Rot) functioned oppositely as a stimulator of SEH production. SEA production was not affected by Rot. seh mRNA expression correlated with rot both in media and on the meat product, and the Rot protein was shown to directly bind to the seh promoter. The seh promoter sequence was predicted to form a loop structure and to hide the RNA polymerase binding sequences. We propose Rot binds to the promoter sequence of seh and unfolds the secondary structure that may lead the RNA polymerase to bind the promoter, and then seh mRNA transcription begins. This alternative Rot regulation for SEH may contribute to sufficient toxin production by the CC81 subtype 1 lineage in foods to induce SFP. PMID:26341202

Positive Regulation of Staphylococcal Enterotoxin H by Rot (Repressor of Toxin) Protein and Its Importance in Clonal Complex 81 Subtype 1 Lineage-Related Food Poisoning.

PubMed

Sato'o, Yusuke; Hisatsune, Junzo; Nagasako, Yuria; Ono, Hisaya K; Omoe, Katsuhiko; Sugai, Motoyuki

2015-11-01

We previously demonstrated the clonal complex 81 (CC81) subtype 1 lineage is the major staphylococcal food poisoning (SFP)-associated lineage in Japan (Y. Sato'o et al., J Clin Microbiol 52:2637-2640, 2014, http://dx.doi.org/10.1128/JCM.00661-14). Strains of this lineage produce staphylococcal enterotoxin H (SEH) in addition to SEA. However, an evaluation of the risk for the recently reported SEH has not been sufficiently conducted. We first searched for staphylococcal enterotoxin (SE) genes and SE proteins in milk samples that caused a large SFP outbreak in Japan. Only SEA and SEH were detected, while there were several SE genes detected in the samples. We next designed an experimental model using a meat product to assess the productivity of SEs and found that only SEA and SEH were detectably produced in situ. Therefore, we investigated the regulation of SEH production using a CC81 subtype 1 isolate. Through mutant analysis of global regulators, we found the repressor of toxin (Rot) functioned oppositely as a stimulator of SEH production. SEA production was not affected by Rot. seh mRNA expression correlated with rot both in media and on the meat product, and the Rot protein was shown to directly bind to the seh promoter. The seh promoter sequence was predicted to form a loop structure and to hide the RNA polymerase binding sequences. We propose Rot binds to the promoter sequence of seh and unfolds the secondary structure that may lead the RNA polymerase to bind the promoter, and then seh mRNA transcription begins. This alternative Rot regulation for SEH may contribute to sufficient toxin production by the CC81 subtype 1 lineage in foods to induce SFP. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Individual Consistency of Feather Pecking Behavior in Laying Hens: Once a Feather Pecker Always a Feather Pecker?

PubMed Central

Daigle, Courtney L.; Rodenburg, T. Bas; Bolhuis, J. Elizabeth; Swanson, Janice C.; Siegford, Janice M.

2015-01-01

The pecking behavior [severe feather, gentle feather, and aggressive pecks (AP)] of individual White Shaver non-cage laying hens (n = 300) was examined at 21, 24, 27, 32, and 37 weeks. Hens were housed in 30 groups of 10 hens each and on 3 cm litter with access to a feeder, perch, and two nest boxes. The number of severe feather pecks given (SFPG) and received (SFPR) was used to categorize hens as feather peckers (P), victims (V), neutrals (N), or feather pecker-victims (PV) at each age. Hens categorized as PV exhibited pecking behaviors similar to P and received pecks similar to V. SFP given were correlated with APs given, but not with gentle feather pecks (GFP) given throughout the study. State-transition plot maps illustrated that 22.5% of P remained P, while 44% of PV remained PV throughout the duration of the study. Lifetime behavioral categories identified hens as a consistent feather pecker (5%), consistent neutral (3.9%), consistent victim (7.9%), consistent feather pecker-victim (29.4%), or inconsistent (53.8%) in their behavioral patterns throughout their life. Consistent feather peckers performed more SFP than hens of other categories, and consistent neutral hens received fewer GFP than consistent feather PV. No differences in corticosterone or whole blood serotonin levels were observed among the categories. Approximately, half of the population was classified as a feather pecker at least once during the study, while the remainder was never categorized as a feather pecker. Therefore, even if the development and cause of feather pecking may be multifactorial, once the behavior has been developed, some hens may persist in feather pecking. However, as some hens were observed to never receive or perform SFP, emphasis should be made to select for these hens in future breeding practices. PMID:26664935

An application of Extended Normalisation Process Theory in a randomised controlled trial of a complex social intervention: Process evaluation of the Strengthening Families Programme (10-14) in Wales, UK.

PubMed

Segrott, Jeremy; Murphy, Simon; Rothwell, Heather; Scourfield, Jonathan; Foxcroft, David; Gillespie, David; Holliday, Jo; Hood, Kerenza; Hurlow, Claire; Morgan-Trimmer, Sarah; Phillips, Ceri; Reed, Hayley; Roberts, Zoe; Moore, Laurence

2017-12-01

Process evaluations generate important data on the extent to which interventions are delivered as intended. However, the tendency to focus only on assessment of pre-specified structural aspects of fidelity has been criticised for paying insufficient attention to implementation processes and how intervention-context interactions influence programme delivery. This paper reports findings from a process evaluation nested within a randomised controlled trial of the Strengthening Families Programme 10-14 (SFP 10-14) in Wales, UK. It uses Extended Normalisation Process Theory to theorise how interaction between SFP 10-14 and local delivery systems - particularly practitioner commitment/capability and organisational capacity - influenced delivery of intended programme activities: fidelity (adherence to SFP 10-14 content and implementation requirements); dose delivered; dose received (participant engagement); participant recruitment and reach (intervention attendance). A mixed methods design was utilised. Fidelity assessment sheets (completed by practitioners), structured observation by researchers, and routine data were used to assess: adherence to programme content; staffing numbers and consistency; recruitment/retention; and group size and composition. Interviews with practitioners explored implementation processes and context. Adherence to programme content was high - with some variation, linked to practitioner commitment to, and understanding of, the intervention's content and mechanisms. Variation in adherence rates was associated with the extent to which multi-agency delivery team planning meetings were held. Recruitment challenges meant that targets for group size/composition were not always met, but did not affect adherence levels or family engagement. Targets for staffing numbers and consistency were achieved, though capacity within multi-agency networks reduced over time. Extended Normalisation Process Theory provided a useful framework for assessing implementation and explaining variation by examining intervention-context interactions. Findings highlight the need for process evaluations to consider both the structural and process components of implementation to explain whether programme activities are delivered as intended and why.

[Features of allele polymorphism of genes involved in homocysteine and folate metabolism in patients with atherosclerosis of the lower extremity arteries].

PubMed

Klenkova, N A; Kapustin, S I; Saltykova, N B; Shmeleva, V M; Blinov, M N

2009-01-01

Under study were features of allele polymorphism of genes of methylenetetrahydrofolate reductase (MTHFR C677T and A1298C), methionine synthase (MS A 2756G), methionine synthase reductase (MTRR A66G) and methylenetetrahydrofolate dehydrogenase (MTHFD G1958A) in patients with atherosclerosis of the lower extremity arteries (ALEA). Patients with hyperhomocysteinemia (HHcy) had statistically significant increase of allele MTHFR 677T and MTRR 66GG as compared both with the control group and with the group of patients without HHcy. It suggests that polymorphism of genes involved in homocystein and folate metabolism might affect the risk of HHcy in patients with ALEA.

Identification of copper phthalocyanine blue polymorphs in unaged and aged paint systems by means of micro-Raman spectroscopy and Random Forest.

PubMed

Anghelone, Marta; Jembrih-Simbürger, Dubravka; Schreiner, Manfred

2015-10-05

Copper phthalocyanine (CuPc) blues (PB15) are largely used in art and industry as pigments. In these fields mainly three different polymorphic modifications of PB15 are employed: alpha, beta and epsilon. Differentiating among these CuPc forms can give important information for developing conservation strategy and can help in relative dating, since each form was introduced in the market in different time periods. This study focuses on the classification of Raman spectra measured using 532 nm excitation wavelength on: (i) dry pigment powders, (ii) unaged mock-ups of self-made paints, (iii) unaged commercial paints, and (iv) paints subjected to accelerated UV ageing. The ratios among integrated Raman bands are taken in consideration as features to perform Random Forest (RF). Features selection based on Gini Contrast score was carried out on the measured dataset to determine the Raman bands ratios with higher predictive power. These were used as polymorphic markers, in order to establish an easy and accessible method for the identification. Three different ratios and the presence of a characteristic vibrational band allowed the identification of the crystal modification in pigments powder as well as in unaged and aged paint films. Copyright © 2015 Elsevier B.V. All rights reserved.

78 FR 70589 - Biweekly Notice; Applications and Amendments to Facility Operating Licenses and Combined Licenses...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-26

... the NRC's E-Filing system does not support unlisted software, and the NRC Meta System Help Desk will... Osmosis (RO) system borated water storage tank suction connections. Basis for proposed no significant... requirement. For the SFP, the suction to the RO system is above the required TS water level, therefore, the...

75 FR 77906 - Biweekly Notice; Applications and Amendments to Facility Operating Licenses Involving No...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-14

... level be raised to support SSF RC Makeup System operability. Thus, the SFP water level will not be..., but should note that the NRC's E-Filing system does not support unlisted software, and the NRC Meta... a reverse osmosis system during normal plant operation to remove silica from borated water storage...

Alternative Fuels Data Center: Maps and Data

Science.gov Websites

fleet type from 1992-2014 Last update August 2016 View Graph Graph Download Data Generated_thumb20160830 Trend of S&FP AFV acquisitions by fuel type from 1992-2015 Last update August 2016 View Graph Graph transactions from 1997-2014 Last update August 2016 View Graph Graph Download Data Biofuelsatlas BioFuels Atlas

Alternative Fuels Data Center: Maps and Data

Science.gov Websites

-1paywcu Last update August 2014 View Graph Graph Download Data State & Alt Fuel Providers -kgi9ks Trend of S&FP AFV acquisitions by fleet type from 1992-2014 Last update August 2016 View Graph -2015 Last update August 2016 View Graph Graph Download Data Generated_thumb20160907-12999-119sgvk

76 FR 40628 - Groundfish Fisheries of the EEZ Off Alaska; Pacific Halibut Fisheries; CDQ Program; Bering Sea...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-11

..., business telephone number, e-mail address, port of landing, operation type (for catcher/processors.../processor, the at-sea operation type is pre-filled automatically. (3) If an SFP and crab delivery is... Registered Crab Receiver record in eLandings the region in which the stationary floating processor is located...

75 FR 9445 - Notice; Applications and Amendments to Facility Operating Licenses Involving Proposed No...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-02

... evaluated the effects of these ITAs on post- irradiation conditions. The additional heat from the Co-60 decay is insignificant when compared to the total heat from a normal refueling discharge. The small amount of extra heat added by the cobalt isotope rods poses no additional risk of spent fuel pool (SFP...

The Dynamic Still-Face Effect: Do Infants Decrease Bidding over Time when Parents Are Not Responsive?

ERIC Educational Resources Information Center

Ekas, Naomi V.; Haltigan, John D.; Messinger, Daniel S.

2013-01-01

The still-face paradigm (SFP) was designed to assess infant expectations that parents will respond to infant communicative signals. During the still-face (SF) episode, the parent ceases interaction and maintains a neutral expression. Original, qualitative descriptions of infant behavior suggested changes within the SF episode: infants decrease…

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

PubMed Central

2012-01-01

Background High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). Results We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. Conclusion By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously. PMID:22583801

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.).

PubMed

Stoffel, Kevin; van Leeuwen, Hans; Kozik, Alexander; Caldwell, David; Ashrafi, Hamid; Cui, Xinping; Tan, Xiaoping; Hill, Theresa; Reyes-Chin-Wo, Sebastian; Truco, Maria-Jose; Michelmore, Richard W; Van Deynze, Allen

2012-05-14

High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.

Navigating at Will on the Water Phase Diagram

NASA Astrophysics Data System (ADS)

Pipolo, S.; Salanne, M.; Ferlat, G.; Klotz, S.; Saitta, A. M.; Pietrucci, F.

2017-12-01

Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in the topology of the interatomic network, we are able to systematically track transitions among liquid, amorphous, and crystalline forms throughout the whole phase diagram of water, including the nucleation of crystals above and below the melting point. Our approach, based on molecular dynamics and enhanced sampling or free energy calculation techniques, is not specific to water and could be applied to very different structural phase transitions, paving the way towards the prediction of kinetic routes connecting polymorphic structures in a range of materials.

[Genetic polymorphism of Gentiana lutea L. (Gentianaceae) populations from Chornohora Ridge of Ukrainian Carpathians].

PubMed

Mosula, M Z; Konvaliuk, I I; Mel'nyk, V M; Drobyk, N M; Tsaryk, I V; Nesteruk, Iu I; Kunakh, V A

2014-01-01

The features of genetic structure and level of diversity were investigated for G. lutea populations from Chornohora Ridge of Ukrainian Carpathians using RAPD- and ISSR-PCR. We have shown a high level of genetic diversity for investigated populations. The differences between populations account for 59-72% of the total genetic variation, whereas intrapopulation polymorphism makes up 28-41%. The relationships among genetic variability level and ecological-geographical conditions as well as biological features of the species were assumed to be possible. The obtained results indicate the genetic isolation of G. lutea Chornohora populations from Ukrainian Carpathians. Pozhyzhevska agropopulation was characterized by a high level of polymorphism that means the possibility to use artificial plantings of the investigated species for its conservation.

Overcoming Malnutrition: Putting Federal Programs to Work. A Report on the First National WIC Symposium.

ERIC Educational Resources Information Center

Fleming, Virginia; And Others

This report describes the proceedings of a symposium on the Special Supplemental Food Program for Women, Infants and Children (WIC) and the Commodity Supplemental Food Program (SFP), held in January, 1977. The symposium was intended to bring together a variety of individuals concerned with providing adequate nutrition and health care to low-income…

Alternative Fuels Data Center: Maps and Data

Science.gov Websites

acquisitions by fleet type from 1992-2014 Last update August 2016 View Graph Graph Download Data -m8i0e0 Trend of S&FP AFV acquisitions by fuel type from 1992-2015 Last update August 2016 View Graph transactions from 1997-2014 Last update August 2016 View Graph Graph Download Data Generated_thumb20160907

Sexual imprinting on continuous variation: do female zebra finches prefer or avoid unfamiliar sons of their foster parents?

PubMed

Schielzeth, H; Burger, C; Bolund, E; Forstmeier, W

2008-09-01

Sexual imprinting on discrete variation that serves the identification of species, morphs or sexes is well documented. By contrast, sexual imprinting on continuous variation leading to individual differences in mating preferences within a single species, morph and sex has been studied only once (in humans). We measured female preferences in a captive population of wild-type zebra finches. Individual cross-fostering ensured that all subjects grew up with unrelated foster parents and nest mates. Females from two cohorts (N = 113) were given a simultaneous choice between (two or four) unfamiliar males, one of which was a genetic son of their foster parents (SFP). We found no significant overall preference for the SFP (combined effect size d = 0.14 +/- 0.15). Additionally, we tested if foster parent traits could potentially explain between-female variation in preferences. However, neither the effectiveness of cooperation between the parents nor male contribution to parental care affected female preferences for the son of the foster father. We conclude that at least in zebra finches sexual imprinting is not a major source of between-individual variation in mating preferences.

Legionella shows a diverse secondary metabolism dependent on a broad spectrum Sfp-type phosphopantetheinyl transferase.

PubMed

Tobias, Nicholas J; Ahrendt, Tilman; Schell, Ursula; Miltenberger, Melissa; Hilbi, Hubert; Bode, Helge B

2016-01-01

Several members of the genus Legionella cause Legionnaires' disease, a potentially debilitating form of pneumonia. Studies frequently focus on the abundant number of virulence factors present in this genus. However, what is often overlooked is the role of secondary metabolites from Legionella . Following whole genome sequencing, we assembled and annotated the Legionella parisiensis DSM 19216 genome. Together with 14 other members of the Legionella , we performed comparative genomics and analysed the secondary metabolite potential of each strain. We found that Legionella contains a huge variety of biosynthetic gene clusters (BGCs) that are potentially making a significant number of novel natural products with undefined function. Surprisingly, only a single Sfp-like phosphopantetheinyl transferase is found in all Legionella strains analyzed that might be responsible for the activation of all carrier proteins in primary (fatty acid biosynthesis) and secondary metabolism (polyketide and non-ribosomal peptide synthesis). Using conserved active site motifs, we predict some novel compounds that are probably involved in cell-cell communication, differing to known communication systems. We identify several gene clusters, which may represent novel signaling mechanisms and demonstrate the natural product potential of Legionella .

Analysis of vitamin D receptor gene polymorphisms in patients with chronic periodontitis.

PubMed

Gunes, Sezgin; Sumer, A Pinar; Keles, Gonca Cayir; Kara, Nurten; Koprulu, Hulya; Bagci, Hasan; Bek, Yuksel

2008-01-01

Genetic polymorphisms in the vitamin D receptor (VDR) gene are related to bone mineral density, bone turnover, and diseases with bone loss. Alveolar bone loss is a key feature in periodontitis. The aim of this study was to determine whether severe generalized chronic periodontitis (CP) in a Turkish population was associated with polymorphisms in the VDR gene. Samples of venous blood and DNA were obtained from 72 patients with severe generalized chronic periodontitis and 102 healthy controls. The polymorphic regions were amplified using PCR followed by digestion with restriction enzymes BsmI A/G(rs1544410), ApaI G/T(rs11168271), TaqI T/C(rs731236), and analyzed electrophoretically. Genotype and allele frequencies were calculated. There were no statistically significant differences in the frequencies of VDR BsmI, ApaI, TaqI genotypes between the CP patients and healthy controls. The GTT haplotype, constructed from the three adjacent restriction fragment length polymorphisms was found to be over-represented among CP cases. This corresponded an OR of 2.4 (95% confidence interval, 1.12-5.18) for heterozygous carriers and 2.27 (95% confidence interval, 0.95-5.4) for homozygous carrier of the risk haplotype. The present findings indicated that BsmI, ApaI, TaqI polymorphisms of the VDR gene were not associated with the severe generalized CP in the studied Turkish patients. Moreover, the VDR genotypes based on haplotype analysis may be associated with chronic periodontitis. In the future, diagnostic periodontal risk assessments like polymorphisms may be useful in detection of individuals susceptible for periodontitis.

H-type bovine spongiform encephalopathy associated with E211K prion protein polymorphism: clinical and pathologic features in wild-type and E211K cattle following intracranial inoculation

USDA-ARS?s Scientific Manuscript database

In 2006 an H-type bovine spongiform encephalopathy (BSE) case was reported in an animal with an unusual polymorphism (E211K) in the prion protein gene. Although the prevalence of this polymorphism is low, cattle carrying the K211 allele are predisposed to rapid onset of H-type BSE when exposed. The ...

Correlations Between COL2A and Aggrecan Genetic Polymorphisms and the Risk and Clinicopathological Features of Intervertebral Disc Degeneration in a Chinese Han Population: A Case-Control Study.

PubMed

Deng, Yu; Tan, Xin-Ti; Wu, Qiang; Wang, Xin

2017-02-01

This case-control study was designed to evaluate the association of three COL2A1 single nucleotide polymorphism (SNPs) (rs1793953, rs2276454, and rs1793937) and Aggrecan variable number of tandem repeat (VNTR) polymorphisms with the risk and clinicopathological features of intervertebral disc degeneration (IVDD) in a Chinese Han population. Data from 295 IVDD patients (case group) and 324 healthy volunteers (control group) were collected between January 2012 and December 2014. Magnetic resonance examinations were conducted on all included subjects. The frequency distributions of the COL2A1 and Aggrecan polymorphisms were detected using direct sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, respectively. The genotype and allele frequencies of the COL2A1 genetic polymorphisms (rs1793953 and rs2276454) and the Aggrecan VNTR polymorphisms differed significantly between the case group and the control group (all p < 0.05). The haplotype analysis indicated that the frequencies of ACGL (L, long) and GTCL haplotypes were lower in the case group than in the control group (both p < 0.05). In the case group, the genotype and allele frequencies of the COL2A1 genes, rs1793953 and rs2276454, and Aggrecan VNTR significantly differed in terms of Pfirrmann grades III, IV, and V (all p < 0.05). Personal history of spine sprain or crush injury, history of IVDD in a first-degree relative, and COL2A1 rs2276454 and Aggrecan VNTR presence may be independent risk factors of IVDD (all p < 0.05, odds ratio [OR] >1), whereas tea drinking habit, part-time sports participation, and COL2A1 rs1793953 presence may be protective factors of IVDD (all p < 0.05, OR <1). Our study provides evidence that COL2A1 and Aggrecan genetic polymorphisms may be correlated with the risk and clinicopathological features of IVDD in a Chinese Han population, and ACGL and GTCL haplotypes may be protective factors of IVDD.

Different frequencies and effects of ABCB1 T3435C polymorphism on clinical and laboratory features of B cell chronic lymphocytic leukemia in Kurdish patients.

PubMed

Maroofi, Farzad; Amini, Sabrieh; Roshani, Daem; Ghaderi, Bayazid; Abdi, Mohammad

2015-04-01

Finding the effects of gene polymorphism on cancer pathogenesis is very desirable. The ATP-binding cassette is involved in drug metabolism, and the polymorphism of this gene may be an important risk factor in B cell chronic lymphocytic leukemia (B-CLL) or progression and/or response to chemotherapy agents. For the first time, the present study was aimed to evaluate the probable effects of ABCB1 T3435C polymorphism on clinical and laboratory features of Kurdish patients with B-CLL. This descriptive analytical case-control study was performed on 50 B-CLL patients and 100 healthy subjects. Serum levels of beta-2-microglobulin (B2M) and lactate dehydrogenase (LDH) and blood WBC, RBC, Plt and ESR were measured. The T3435C polymorphism of the ABCB1 gene was determined by PCR-RFLP. Concentration of serum and blood markers was significantly higher in the malignant group than in the benign subjects. The CC genotype had the highest frequency (66%) in the patient groups. There are no significant differences between the genotypes and type of treatment. Our results demonstrate the high frequency of C allele of ABCB1 T3435C in B-CLL patients with Kurdish ethnicity. We also show that this polymorphism has a significant risk factor in B-CLL. However, the effect of this polymorphism on clinical and laboratory characteristics of B-CLL patients was not significant.

A novel MALDI–TOF based methodology for genotyping single nucleotide polymorphisms

PubMed Central

Blondal, Thorarinn; Waage, Benedikt G.; Smarason, Sigurdur V.; Jonsson, Frosti; Fjalldal, Sigridur B.; Stefansson, Kari; Gulcher, Jeffery; Smith, Albert V.

2003-01-01

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

Two new phoretomorphic Siteroptes from galleries of the southern pine beetle

Treesearch

Robert L. Smiley; John C. Moser

1976-01-01

This paper provides taxonomic descriptions of two pyemotid mite species displaying polymorphic features discovered by Moser & Cross(1975). Polymorphism in the Acarina was first noted by Canestrini in 1888 for Rhizoglyphus echinopus (Fumouze & Robin). He associated the heteromorphic male with the normal homeomorphicm ale of this species....

Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.

PubMed

Feuk, Lars; MacDonald, Jeffrey R; Tang, Terence; Carson, Andrew R; Li, Martin; Rao, Girish; Khaja, Razi; Scherer, Stephen W

2005-10-01

With a draft genome-sequence assembly for the chimpanzee available, it is now possible to perform genome-wide analyses to identify, at a submicroscopic level, structural rearrangements that have occurred between chimpanzees and humans. The goal of this study was to investigate chromosomal regions that are inverted between the chimpanzee and human genomes. Using the net alignments for the builds of the human and chimpanzee genome assemblies, we identified a total of 1,576 putative regions of inverted orientation, covering more than 154 mega-bases of DNA. The DNA segments are distributed throughout the genome and range from 23 base pairs to 62 mega-bases in length. For the 66 inversions more than 25 kilobases (kb) in length, 75% were flanked on one or both sides by (often unrelated) segmental duplications. Using PCR and fluorescence in situ hybridization we experimentally validated 23 of 27 (85%) semi-randomly chosen regions; the largest novel inversion confirmed was 4.3 mega-bases at human Chromosome 7p14. Gorilla was used as an out-group to assign ancestral status to the variants. All experimentally validated inversion regions were then assayed against a panel of human samples and three of the 23 (13%) regions were found to be polymorphic in the human genome. These polymorphic inversions include 730 kb (at 7p22), 13 kb (at 7q11), and 1 kb (at 16q24) fragments with a 5%, 30%, and 48% minor allele frequency, respectively. Our results suggest that inversions are an important source of variation in primate genome evolution. The finding of at least three novel inversion polymorphisms in humans indicates this type of structural variation may be a more common feature of our genome than previously realized.

CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences.

PubMed

Chou, A; Burke, J

1999-05-01

DNA sequence clustering has become a valuable method in support of gene discovery and gene expression analysis. Our interest lies in leveraging the sequence diversity within clusters of expressed sequence tags (ESTs) to model gene structure for the study of gene variants that arise from, among other things, alternative mRNA splicing, polymorphism, and divergence after gene duplication, fusion, and translocation events. In previous work, CRAW was developed to discover gene variants from assembled clusters of ESTs. Most importantly, novel gene features (the differing units between gene variants, for example alternative exons, polymorphisms, transposable elements, etc.) that are specialized to tissue, disease, population, or developmental states can be identified when these tools collate DNA source information with gene variant discrimination. While the goal is complete automation of novel feature and gene variant detection, current methods are far from perfect and hence the development of effective tools for visualization and exploratory data analysis are of paramount importance in the process of sifting through candidate genes and validating targets. We present CRAWview, a Java based visualization extension to CRAW. Features that vary between gene forms are displayed using an automatically generated color coded index. The reporting format of CRAWview gives a brief, high level summary report to display overlap and divergence within clusters of sequences as well as the ability to 'drill down' and see detailed information concerning regions of interest. Additionally, the alignment viewing and editing capabilities of CRAWview make it possible to interactively correct frame-shifts and otherwise edit cluster assemblies. We have implemented CRAWview as a Java application across windows NT/95 and UNIX platforms. A beta version of CRAWview will be freely available to academic users from Pangea Systems (http://www.pangeasystems.com). Contact :

Community-level physiological profiles of bacteria and fungi: Plate type and incubation temperature influences on contrasting soils

Treesearch

Aimee T. Classen; Sarah I. Boyle; Kristin E. Haskins; Steven T. Overby; Stephen C. Hart

2003-01-01

Temperature sensitivity of community-level physiological profiles (CLPPs) was examined for two semiarid soils from the southwestern United States using five different C-substrate profile microtiter plates (Biolog GN2, GP2, ECO, SFN2, and SFP2) incubated at five different temperature regimes.The CLPPs produced from all plate types were relatively unaffected by these...

Lessons Learnt from Applying Action Research to Support Strategy Formation Processes in Long-Term Care Networks

ERIC Educational Resources Information Center

Cramer, Hendrik; Dewulf, Geert; Voordijk, Hans

2015-01-01

This study demonstrates how action research (AR) that is aimed at scaling-up experiments can be applied to support a strategy formation process (SFP) in a subsidized long-term care network. Previous research has developed numerous AR frameworks to support experiments in various domains, but has failed to explain how to apply AR and action learning…

A U.S. Forest Service special forest products appraisal system: background, methods, and assessment.

Treesearch

Jerry Smith; Lisa K. Crone; Susan J. Alexander

2010-01-01

Increasing concern over the management and harvest of special forest products (SFP) from national forest lands has led to the development of new Forest Service policy directives. In this paper, we present a brief history of SFPs in the Western United States, highlighting the issues that necessitated new management direction. The new policy directives that led to the...

The (Re)Construction of a Philosophical and Pedagogical Position for the Foundation Programme at UKZN with Particular Reference to the Biology Module

ERIC Educational Resources Information Center

Kirby, N. F.; Dempster, E. R.

2011-01-01

The Centre for Science Access Foundation Programme at the University of KwaZulu-Natal provides alternative access to tertiary science studies to educationally disadvantaged students. The philosophical basis for this Programme is that of constructivism, as adopted by the original Science Foundation Programme (SFP) which was initiated in 1991 on the…

Farm Diversification, Tenancy and CAP Reform: Results from a Survey of Tenant Farmers in England

ERIC Educational Resources Information Center

Maye, Damian; Ilbery, Brian; Watts, David

2009-01-01

Little work has considered explicitly the role of farm tenancy in influencing the uptake (or not) of diversification activities. The need to examine this link has been heightened because of the 2003 CAP reforms and the decision to tie Single Farm Payment (SFP) entitlement to the land rather than what is produced on that land. The main objective of…

Effect of a package of health and nutrition services on sustained recovery in children after moderate acute malnutrition and factors related to sustaining recovery: a cluster-randomized trial.

PubMed

Stobaugh, Heather C; Bollinger, Lucy B; Adams, Sara E; Crocker, Audrey H; Grise, Jennifer B; Kennedy, Julie A; Thakwalakwa, Chrissie; Maleta, Kenneth M; Dietzen, Dennis J; Manary, Mark J; Trehan, Indi

2017-08-01

Background: Children who recover from moderate acute malnutrition (MAM) have high rates of relapse in the year after nutritional recovery. Interventions to decrease these adverse outcomes are needed to maximize the overall effectiveness of supplemental feeding programs (SFPs). Objective: We evaluated the effectiveness of a package of health and nutrition interventions on improving the proportion of children who sustained recovery for 1 y after MAM treatment. We further explored factors related to sustained recovery. Design: We conducted a cluster-randomized clinical effectiveness trial involving rural Malawian children aged 6-62 mo who were enrolled on discharge from an SFP for MAM. We enrolled 718 children at 10 control sites and 769 children at 11 intervention sites. In addition to routine health and nutrition counseling, the intervention group received a package of health and nutrition interventions that consisted of a lipid nutrient supplement, deworming medication, zinc supplementation, a bed net, and malaria chemoprophylaxis. A survival analysis was used to determine the effectiveness of the intervention as well as to identify factors associated with sustained recovery. Results: Of 1383 children who returned for the full 12-mo follow-up period, 407 children (56%) and 347 children (53%) sustained recovery in the intervention and control groups, respectively. There was no significant difference in relapse-free survival curves between the treatment and control groups ( P = 0.380; log-rank test). The risk factors for relapse or death after initial recovery were a smaller midupper arm circumference on SFP admission ( P = 0.01) and discharge ( P < 0.001), a lower weight-for-height z score on discharge ( P < 0.01), and the receipt of ready-to-use supplementary food as opposed to ready-to-use therapeutic food during treatment ( P < 0.05). Conclusion: The provision of a package of health and nutrition services in addition to traditional SFP treatment has no significant effect on improving sustained recovery in children after treatment of MAM. This trial was registered at clinicaltrials.gov as NCT02351687. © 2017 American Society for Nutrition.

Pathological Roles of Interleukin-22 in the Development of Recurrent Hepatitis C after Liver Transplantation

PubMed Central

Li, Jin; Cheung, Eddie; Li, Hanwei; Zhao, Jingmin; Liu, Hongling; Liu, Zhenwen; Zhang, Min

2016-01-01

Objective The aim of this study was to longitudinally evaluate and analyze the role of interleukin-22-producing CD4 positive cells (IL-22) in the pathogenesis of Hepatitis C Virus recurrence after Orthotopic Liver Transplantation (HCV-OLT). Methods 15 HCV-OLT, 15 age- and gender- matched non-HCV post-OLT (OLT) and 15 hepatitis C virus infected (HCV) patients were enrolled into our study from the liver transplantation and research center at Beijing 302 Hospital. We determined the frequencies of IL-22 using flow cytometry and expression of IL-22 mRNA using PCR in peripheral blood and liver tissue. We also divided HCV-OLT patients into rapid fibrosis progression (RFP) and slow fibrosis progression (SFP), examined IL-22 cells and analyzed the correlations between IL-22 frequencies and liver injury, fibrosis and clinical parameters. Moreover, we investigated the role of IL-22 in Human Hepatic Stellate Cells (HSCs). Results The levels of serum IL-22, frequencies of IL-22 producing cells in peripheral blood mononuclear cells, and expression of IL-22 mRNA and protein in the liver in the HCV-OLT group were significantly higher than that in the HCV and OLT groups. Furthermore, eight (53.3%) patients developed RFP after two years; another three patients were diagnosed liver cirrhosis. The frequencies of IL-22 were much higher in RFP compared with SFP, while no significant difference existed between OLT and SFP. Intrahepatic IL-22 positive cells were located in fibrotic areas and significantly correlated with α-smooth muscle actin (α-SMA) and fibrosis staging scores, not with grading scores and HCRVNA. In vitro, IL-22 administration prevented HSCs apoptosis, promoted HSCs proliferation and activation, up-regulated the expression of HSC-sourced growth factors including α-SMA, TGF-β and TIMP-1, and increased the production of liver fibrosis markers including laminin, hyaluronic acid and collagen type IV. Conclusion Peripheral and intrahepatic IL-22 is up-regulated and plays a pathological role in exacerbating liver fibrosis by activating HSCs in HCV-OLT patients, which may predict RFP and serve as an attractive target for anti-fibrotic therapy. PMID:27123854

Spectral characteristics of the iron oxides with application to the Martian bright region mineralogy

NASA Technical Reports Server (NTRS)

Sherman, D. M.; Burns, R. G.; Mee Burns, V.

1982-01-01

Reflectance spectra of eight polymorphs of FeOOH and Fe2O3 are determined in order to clarify the nature and significance of the iron oxide mineralogy on Mars. The effect of other components that might interfere with iron oxide absorption features is qualitatively constrained through the use of the Kebulka-Munk theory. It is found that the effect of temperature complicates the identification of a given Fe(3+) phase based on the position of the 6A1-4T1 absorption feature. While the Fe(3+) crystal field transitions are spin forbidden, most of the iron oxide polymorphs exhibit anomalously intense crystal field absorption features due to magnetic coupling between adjacent FeO6 octahedra. It is suggested that the resulting deviations from observed remotely sensed reflectance spectra of Mars may provide a basis for the exclusion of many iron oxide phases as significant components of the Martian Fe(3+) mineralogy. A comparison of these results with the visible region spectra of Martian bright regions indicates that the predominant Fe(3+)-bearing phase may be a magnetically disordered material, such as amorphous gels, some ferric sulphates, and other minerals in which Fe(3+) ions in the crystal structure are not magnetically coupled.

On-line fission products measurements during a PWR severe accident: the French DECA-PF project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ducros, G.; Allinei, P.G.; Roure, C.

Following the Fukushima accident, a lot of recommendations was drawn by international organizations (IAEA, OECD, NUGENIA network...) in order to improve the safety in such accidental conditions and mitigate their consequences. One of these recommendations was to improve the robustness of the instrumentation, which was dramatically lacking at Fukushima, as well as to better determine the Source Term involved in nuclear accident. The DECA-PF project (Diagnosis of a degraded reactor core through Fission Product measurements) was elaborated in this context and selected as one of 21 collaborative R and D projects in the field of nuclear safety and radioprotection, fundedmore » in May 2013 by the French National Research Agency. Over the months following the Fukushima accident, a CEA crisis team was held in order to analyze on-line the situation taking into account the data delivered by TEPCO and other organizations. Despite the difficulties encountered concerning the reliability of these data, the work performed showed the high capacity of Fission Products (FP) measurements to get a diagnosis relative to the status of the reactors and the spent fuel pools (SFP). Based on these FP measurements, it was possible to conclude that the main origin of the releases was coming from the cores and not from the SFP, in particular for SFP-4 which was of high concern, and that the degradation level of the reactors was very large, including probably an extensive core melting. To improve the reliability of this kind of diagnosis, the necessity to get such measurements as soon as possible after the accident and as near as possible from the reactor was stressed. In this way the present DECA-PF project intends to develop a new and innovative instrumentation taking into account the design of the French nuclear power plants on which sand bed filters have been implemented for severe accident management. Three complementary techniques, devoted to measure the FP release on-line, are being studied: - Gamma spectrometry, with an industrial objective to build a prototype aimed at improving the capacity of the present radiation monitoring system, - Gas chromatography, for the quantification of the fission gases (Xe, Kr) as well as potential carbon oxides produced in case of Molten Corium Concrete Interaction, - Optical absorption spectroscopy, the objective of this most innovative technique being to quantify the tetra-oxide of ruthenium, which could be produced in case of lower head failure, and the gaseous forms of iodine (molecular and organic) released in the environment. A global description and the present status of this project is presented, focusing on the Source Term establishment at the outlet stack of the sand bed filters and on the perspectives of implementation of the on-line gamma spectrometry equipment. (authors)« less

Association of Genetic Polymorphisms in TNF and MIF Gene with the Risk of Primary Dysmenorrhea.

PubMed

Dogru, Hatice Yilmaz; Ozsoy, Asker Zeki; Karakus, Nevin; Delibas, Ilhan Bahri; Isguder, Cigdem Kunt; Yigit, Serbulent

2016-08-01

Primary dysmenorrhea, which affects 90 % of adolescent girls and more than 50 % of menstruating women worldwide, is characterized by recurrent pain during menses in the absence of a detectable organic disease. The aim of this study is to assess the association between MIF -173 and TNF -308 genetic polymorphisms and the clinical features of primary dysmenorrhea. The study population comprised 154 unrelated female patients with clinical diagnosis of dysmenorrhea, and a total of 144 control subjects were recruited consecutively. The MIF -173G > C promoter polymorphism (rs755622) and TNF gene -308G > A (rs1800629) polymorphism were analyzed by polymerase chain reaction-based restriction fragment length polymorphism assay. Two fragments (268 and 97 bp) were seen when the G allele was present at position -173, and three fragments (206, 97, and 62 bp) were observed when the C allele was present. Two fragments (87 and 20 bp) were seen when G allele was present at position -308. There were statistically significant associations between age at menarche and history of back pain among dysmenorrhea patients and MIF gene -173G > C polymorphism (p = 0.003 and p = 0.042, respectively). The genotype and allele frequencies of -308G > A polymorphism showed statistically significant differences between dysmenorrhea patients and controls (p = 0.023 and p = 0.009, respectively). A high association was also observed when the patients were compared with the controls according to the GG genotype versus GA+AA genotypes (p = 0.009). The present study showed that the TNF-α -308 GG genotype may be a useful tool to predict the susceptibility of dysmenorrhea.

The AP1000{sup R} nuclear power plant innovative features for extended station blackout mitigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vereb, F.; Winters, J.; Schulz, T.

2012-07-01

Station Blackout (SBO) is defined as 'a condition wherein a nuclear power plant sustains a loss of all offsite electric power system concurrent with turbine trip and unavailability of all onsite emergency alternating current (AC) power system. Station blackout does not include the loss of available AC power to buses fed by station batteries through inverters or by alternate AC sources as defined in this section, nor does it assume a concurrent single failure or design basis accident...' in accordance with Reference 1. In this paper, the innovative features of the AP1000 plant design are described with their operation inmore » the scenario of an extended station blackout event. General operation of the passive safety systems are described as well as the unique features which allow the AP1000 plant to cope for at least 7 days during station blackout. Points of emphasis will include: - Passive safety system operation during SBO - 'Fail-safe' nature of key passive safety system valves; automatically places the valve in a conservatively safe alignment even in case of multiple failures in all power supply systems, including normal AC and battery backup - Passive Spent Fuel Pool cooling and makeup water supply during SBO - Robustness of AP1000 plant due to the location of key systems, structures and components required for Safe Shutdown - Diverse means of supplying makeup water to the Passive Containment Cooling System (PCS) and the Spent Fuel Pool (SFP) through use of an engineered, safety-related piping interface and portable equipment, as well as with permanently installed onsite ancillary equipment. (authors)« less

Fluctuation Induced Almost Invariant Sets

DTIC Science & Technology

2006-12-28

Planck) for the probability density function [15], discrete dynamical systems benefit from using the Frobenius - Perron operator (FP) formalism [12] to...from epidemiology. Conclusions are summarized in Section 4. II. GENERAL THEORY A. Stochastic Frobenius - Perron operator We define the Frobenius - Perron ...function ν(x). The stochastic Frobenius - 3 Perron (SFP) operator is defined to be PF [ρ(x)] = ∫ M ν(x− F (y))ρ(y)dy. (4) For our applications, we will

The Seminal fluid proteome of the polyandrous Red junglefowl offers insights into the molecular basis of fertility, reproductive ageing and domestication

PubMed Central

Borziak, Kirill; Álvarez-Fernández, Aitor; L. Karr, Timothy; Pizzari, Tommaso; Dorus, Steve

2016-01-01

Seminal fluid proteins (SFPs) are emerging as fundamental contributors to sexual selection given their role in post-mating reproductive events, particularly in polyandrous species where the ejaculates of different males compete for fertilisation. SFP identification however remains taxonomically limited and little is known about avian SFPs, despite extensive work on sexual selection in birds. We characterize the SF proteome of the polyandrous Red junglefowl, Gallus gallus, the wild species that gave rise to the domestic chicken. We identify 1,141 SFPs, including proteins involved in immunity and antimicrobial defences, sperm maturation, and fertilisation, revealing a functionally complex SF proteome. This includes a predominant contribution of blood plasma proteins that is conserved with human SF. By comparing the proteome of young and old males with fast or slow sperm velocity in a balanced design, we identify proteins associated with ageing and sperm velocity, and show that old males that retain high sperm velocity have distinct proteome characteristics. SFP comparisons with domestic chickens revealed both qualitative and quantitative differences likely associated with domestication and artificial selection. Collectively, these results shed light onto the functional complexity of avian SF, and provide a platform for molecular studies of fertility, reproductive ageing, and domestication. PMID:27804984

More than anticipated - production of antibiotics and other secondary metabolites by Bacillus amyloliquefaciens FZB42.

PubMed

Chen, Xiao-Hua; Koumoutsi, Alexandra; Scholz, Romy; Borriss, Rainer

2009-01-01

The genome of environmental Bacillus amyloliquefaciens FZB42 harbors numerous gene clusters involved in synthesis of antifungal and antibacterial acting secondary metabolites. Five gene clusters, srf, bmy, fen, nrs, dhb, covering altogether 137 kb, direct non-ribosomal synthesis of the cyclic lipopeptides surfactin, bacillomycin, fengycin, an unknown peptide, and the iron siderophore bacillibactin. Bacillomycin and fengycin were shown to act against phytopathogenic fungi in a synergistic manner. Three gene clusters, mln, bae, and dif, with a total length of 199 kb were shown to direct synthesis of the antibacterial acting polyketides macrolactin, bacillaene, and difficidin. Both, non-ribosomal synthesis of cyclic lipopeptides and synthesis of polyketides are dependent on the presence of a functional sfp gene product, 4'-phosphopantetheinyl transferase, as evidenced by knockout mutation of the sfp gene resulting in complete absence of all those eight compounds. In addition, here we present evidence that a gene cluster encoding enzymes involved in synthesis and export of the antibacterial acting dipeptide bacilysin is also functional in FZB42. In summary, environmental FZB42 devoted about 340 kb, corresponding to 8.5% of its total genetic capacity, to synthesis of secondary metabolites useful to cope with other competing microorganisms present in the plant rhizosphere. Copyright (c) 2008 S. Karger AG, Basel.

Early maladaptive schemas and aggressive sexual behavior: a preliminary study with male college students.

PubMed

Sigre-Leirós, Vera Lúcia; Carvalho, Joana; Nobre, Pedro

2013-07-01

The influence of adverse early attachment experiences on the development of aggressive sexual behavior has been demonstrated. Nonetheless, there is a gap in the literature regarding the conceptualization of this behavior according to developmental psychopathology models. The purpose of the present study was to investigate a potential association between Early Maladaptive Schemas (EMSs) and aggressive sexual behavior. A total of 166 male college students participated in the study. Participants were divided into two comparative groups according to data from the Sexual Experiences Survey-Short Form Perpetration (SES-SFP): Group of individuals with history of aggressive sexual behavior (N = 37) and Group of individuals without history of aggressive sexual behavior (N = 129). Aggressive sexual behavior was measured by the SES-SFP, and EMSs were measured by the Young Schema Questionnaire (YSQ-S3). Results showed that students who have committed any form of sexually aggressive behavior exhibited significantly higher levels of EMSs from the Disconnection and Rejection domain (namely, Mistrust/Abuse schema), from the Impaired Autonomy and Performance domain (namely, Dependence/Incompetence schema), and from the Overvigilance and Inhibition domain (namely, Negativity/Pessimism schema). These preliminary findings suggest that the EMSs were associated with aggressive sexual behavior, but further investigation is warranted. © 2012 International Society for Sexual Medicine.

The Seminal fluid proteome of the polyandrous Red junglefowl offers insights into the molecular basis of fertility, reproductive ageing and domestication.

PubMed

Borziak, Kirill; Álvarez-Fernández, Aitor; L Karr, Timothy; Pizzari, Tommaso; Dorus, Steve

2016-11-02

Seminal fluid proteins (SFPs) are emerging as fundamental contributors to sexual selection given their role in post-mating reproductive events, particularly in polyandrous species where the ejaculates of different males compete for fertilisation. SFP identification however remains taxonomically limited and little is known about avian SFPs, despite extensive work on sexual selection in birds. We characterize the SF proteome of the polyandrous Red junglefowl, Gallus gallus, the wild species that gave rise to the domestic chicken. We identify 1,141 SFPs, including proteins involved in immunity and antimicrobial defences, sperm maturation, and fertilisation, revealing a functionally complex SF proteome. This includes a predominant contribution of blood plasma proteins that is conserved with human SF. By comparing the proteome of young and old males with fast or slow sperm velocity in a balanced design, we identify proteins associated with ageing and sperm velocity, and show that old males that retain high sperm velocity have distinct proteome characteristics. SFP comparisons with domestic chickens revealed both qualitative and quantitative differences likely associated with domestication and artificial selection. Collectively, these results shed light onto the functional complexity of avian SF, and provide a platform for molecular studies of fertility, reproductive ageing, and domestication.

The TNF-α -308 polymorphism may affect the severity of Crohn's disease

PubMed Central

Santana, Genoile; Bendicho, Maria Teresita; Santana, Tamara Celi; dos Reis, Lidiane Bianca; Lemaire, Denise; Lyra, André Castro

2011-01-01

OBJECTIVE: The goal of this project was to analyze the association between Crohn's disease, its clinical features, and the tumor necrosis factor alpha (TNF-α) -308 polymorphism. METHODS: This is a case-control and cross-sectional study that enrolled 91 patients with Crohn's disease and 91 controls. Patients with Crohn's disease were characterized according to the Montreal Classification, along with their clinical and surgical treatment history. Analysis of the TNF-α -308 polymorphism was performed using a commercial kit. A stratified analysis was applied using an OR (odds ratio) with a 95% confidence interval. The chi-square and Fisher's exact tests were utilized for analysis of the association between the polymorphism and the clinical features of Crohn's disease. RESULTS: The low producer predicted phenotype was present in 76.9% of Crohn's disease cases and 75.8% of controls (OR 0.94 [0.45-1.97]). The TNF2 allele and the high producer predicted phenotype were more frequent among patients with Crohn's disease penetrating behavior (p = 0.004). The TNF2 allele and the high producer predicted phenotype were also associated with a history of colectomy (p = 0.02), and the TNF2 allele was associated with small bowel resection (p = 0.03). CONCLUSIONS: The TNF-α -308 polymorphism appears to affect the severity of the disease. However, TNF-α -308 polymorphism does not appear to be important for the susceptibility in the development of Crohn's disease. PMID:21915486

Polymorphism of SMAD7 gene (rs2337104) and risk of colorectal cancer in an Iranian population: a case-control study

PubMed Central

Akbari, Zahra; Safari-Alighiarloo, Nahid; Taleghani, Mohammad Yaghoob; Mirfakhar, Farzaneh Sadat; Asadzadeh Aghdaei, Hamid; Vahedi, Mohsen; Irani Shemirani, Atena; Nazemalhosseini-Mojarad, Ehsan; Zali, Mohammad Reza

2014-01-01

Aim: The purpose of this study was to evaluate the influence of intronic polymorphism of the SMAD7 (Mothers Against Decantaplegic Homolog 7) gene (rs2337104) on the risk of colorectal cancer (CRC) and clinicopathological features in an Iranian population. Background: SMAD7 has been identified as an antagonist of transforming growth factor beta (TGF-b)-mediating fibrosis, carcinogenesis, and inflammation. Regarding to the recent genome-wide scan, a risk locus for colorectal cancer at 18q21 has been found, which maps to the SMAD7 gene. Patients and methods: This case-control study was performed on 109 CRC patients and 109 healthy controls recruited in Taleghani Hospital. The genotyping of all samples were done by TaqMan assay via an ABI 7500 Real Time PCR System (Applied Biosystems) with DNA from peripheral blood. The association of this polymorphism with the risk of CRC and clinicopathological features was investigated. Results: Our results indicated that there were no significant association between genotypic and allelic frequencies of SMAD7 polymorphism (rs2337104) and CRC risk in our population. Although the T allele is the most frequent one in this population and its frequency was 86.7% in patients compared with 91.7% in controls (OR=1.705, 95% CI= 0.916–3.172). Also, the SMAD7 genotypes were not associated with any clinicopathological characteristics in CRC patients (P>0.05). Conclusion: For the first time, this study results revealed that this SMAD7 polymorphism couldn’t be a potential risk factor for CRC or a prognostic biomarker for prediction of clinicopathological features in an Iranian population. A large-scale case-control study is needed to validate our results. PMID:25289133

FcγRIIa and FcγRIIIb polymorphisms and associations with clinical manifestations in systemic lupus erythematosus patients.

PubMed

Vigato-Ferreira, Isabel Cristina Costa; Toller-Kawahisa, Juliana Escher; Pancoto, João Alexandre Trés; Mendes-Junior, Celso Teixeira; Martinez, Edson Zangiacomi; Donadi, Eduardo Antônio; Louzada-Júnior, Paulo; Del Lama, José Eduardo Cavalcanti; Marzocchi-Machado, Cleni Mara

2014-11-01

In this study, we aimed to investigate whether the distribution of the FcγRIIa and FcγRIIIb polymorphisms determines susceptibility to systemic lupus erythematosus (SLE) and acts as predictors of SLE clinical manifestations in the Brazilian patients. A total of 157 patients that fulfilled the American College of Rheumatology classification criteria for SLE and 160 healthy volunteers were included in this study. FCGR2A and FCGR3B genotypes were determined by polymerase chain reaction-based allotyping methods with allele-specific primers; the clinical features were obtained from the patients' official medical records. In the case of FcγRIIa polymorphism, it was observed association of the allele FCGR2A-R-131 (p = 0.02, odds ratio (OR)=1.44) and genotype RR-131 (p = 0.03, OR = 2.09) with SLE. These associations were higher with allele (p < 0.01, OR = 1.67) as well genotype (p = 0.01, OR = 2.85) when lupus nephritis was considered. In contrast, the allele FCGR2A-H-131 was associated with susceptibility to arthritis and anti-DNA antibodies (p = 0.05 for both). As for FcγRIIIb polymorphism, skewing did not differ significantly between patients and controls, however the genotype FCGR3B*02*02 was associated with susceptibility to arthritis (p = 0.02) and malar rash (p = 0.03), but no association with nephritis was found. The results demonstrate that FcγRIIa polymorphism is associated with susceptibility to SLE in Brazilian patients, whereas for FcγRIIIb polymorphism no association was found. However, notably, both polymorphisms present allelic variants that influence the clinical manifestations and may contribute to the pathogenesis of the disease. In addition, to our knowledge, this is the first study considering the frequency of FcγRIIIb polymorphism in Brazilian SLE patients.

Strengthening Incarcerated Families: Evaluating a Pilot Program for Children of Incarcerated Parents and Their Caregivers

PubMed Central

Miller, Alison L.; Perryman, Jamie; Markovitz, Lara; Franzen, Susan; Cochran, Shirley; Brown, Shavonnea

2013-01-01

Parental incarceration can be devastating for families. Children may experience difficulties, and the stress on caregivers who take on unexpected childrearing is high. We implemented and evaluated a family-level intervention with caregivers and children experiencing parental (typically maternal) incarceration, in a community setting. We partnered with a community-based organization serving families with an incarcerated parent to conduct a pilot trial of the Strengthening Families Program (SFP). Process evaluation indicated high implementation fidelity, satisfaction, engagement, and attendance. Outcome evaluation results indicated positive changes in family-level functioning, caregivers’ positive parenting, and caregiver depression symptoms from pre- to post-intervention, with some changes retained at follow-up 4 months later. Implications for preventive interventions with children of incarcerated parents, and their caregivers, are discussed. PMID:24353363

Strengthening Incarcerated Families: Evaluating a Pilot Program for Children of Incarcerated Parents and Their Caregivers.

PubMed

Miller, Alison L; Perryman, Jamie; Markovitz, Lara; Franzen, Susan; Cochran, Shirley; Brown, Shavonnea

2013-10-01

Parental incarceration can be devastating for families. Children may experience difficulties, and the stress on caregivers who take on unexpected childrearing is high. We implemented and evaluated a family-level intervention with caregivers and children experiencing parental (typically maternal) incarceration, in a community setting. We partnered with a community-based organization serving families with an incarcerated parent to conduct a pilot trial of the Strengthening Families Program (SFP). Process evaluation indicated high implementation fidelity, satisfaction, engagement, and attendance. Outcome evaluation results indicated positive changes in family-level functioning, caregivers' positive parenting, and caregiver depression symptoms from pre- to post-intervention, with some changes retained at follow-up 4 months later. Implications for preventive interventions with children of incarcerated parents, and their caregivers, are discussed.

Classical phenotype of Laron syndrome in a girl with a heterozygous mutation and heterozygous polymorphism of the growth hormone receptor gene.

PubMed

Shevah, Orit; Galli-Tsinopoulou, Assimina; Rubinstein, Menachem; Nousia-Arvanitakis, Sanda; Laron, Zvi

2004-03-01

We describe here a 19 month-old girl with classical Laron syndrome (LS). Molecular analysis of the GH receptor gene in the patient and her parents was performed. The patient was found to be heterozygous for a mutation in exon 4 (R43X) and heterozygous for a polymorphism in exon 6 (Gly168Gly). Her mother was also heterozygous for R43X but homozygous for the polymorphism. In the father, a heterozygous polymorphism was found. Contrary to previous assumptions that only homozygous patients express the typical phenotype, this patient shows all the classical features of LS, despite being a heterozygote for a pathological defect.

Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions.

PubMed

Harpke, Doerte; Peterson, Angela

2008-05-01

The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, ITS2) represents the most widely applied nuclear marker in eukaryotic phylogenetics. Although this region has been assumed to evolve in concert, the number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenes has risen. The 5.8S rDNA is the most important diagnostic marker for functionality of the ITS region. In Mammillaria, intra-individual 5.8S rDNA polymorphisms of up to 36% and up to nine different types have been found. Twenty-eight of 30 cloned genomic Mammillaria sequences were identified as putative pseudogenes. For the identification of pseudogenic ITS regions, in addition to formal tests based on substitution rates, we attempted to focus on functional features of the 5.8S rDNA (5.8S motif, secondary structure). The importance of functional data for the identification of pseudogenes is outlined and discussed. The identification of pseudogenes is essential, because they may cause erroneous phylogenies and taxonomic problems.

The Role of −786T/C Polymorphism in the Endothelial Nitric Oxide Synthase Gene in Males with Clinical and Biochemical Features of the Metabolic Syndrome

PubMed Central

Misiak, Blazej; Krolik, Marta; Kukowka, Anna; Lewera, Anna; Leszczynski, Przemyslaw; Stankiewicz-Olczyk, Joanna; Slezak, Ryszard

2011-01-01

Background. Extensive evidence, arising from models of endothelial nitric oxide synthase gene (NOS3)-knockout mice supports the role of endothelial malfunction in the pathogenesis of the metabolic syndrome (MS). Aims. The aim of this study was to evaluate the role of −786T/C polymorphism in the etiology of MS and assess previously reported interaction with cigarette smoking. Methods. Based on International Diabetes Federation 2005 criteria, we recruited randomly 152 subjects with MS and 75 subjects without MS. Results. Allelic and genotype frequencies did not differ significantly between both groups. Total cholesterol level (CHOLT) and intima-media thickness of carotid arteries were significantly higher in −786CC homozygotes, in comparison with −786TC and −786TT patients. Regarding current smoking status, −786C allele was associated with higher CHOLT than −786T allele. Conclusion. Our study indicates the putative role of −786T/C polymorphism in the development of hypercholesterolemia, in patients with MS, which might be enhanced by cigarette smoking. PMID:22164159

The Role of -786T/C Polymorphism in the Endothelial Nitric Oxide Synthase Gene in Males with Clinical and Biochemical Features of the Metabolic Syndrome.

PubMed

Misiak, Blazej; Krolik, Marta; Kukowka, Anna; Lewera, Anna; Leszczynski, Przemyslaw; Stankiewicz-Olczyk, Joanna; Slezak, Ryszard

2011-01-01

Background. Extensive evidence, arising from models of endothelial nitric oxide synthase gene (NOS3)-knockout mice supports the role of endothelial malfunction in the pathogenesis of the metabolic syndrome (MS). Aims. The aim of this study was to evaluate the role of -786T/C polymorphism in the etiology of MS and assess previously reported interaction with cigarette smoking. Methods. Based on International Diabetes Federation 2005 criteria, we recruited randomly 152 subjects with MS and 75 subjects without MS. Results. Allelic and genotype frequencies did not differ significantly between both groups. Total cholesterol level (CHOLT) and intima-media thickness of carotid arteries were significantly higher in -786CC homozygotes, in comparison with -786TC and -786TT patients. Regarding current smoking status, -786C allele was associated with higher CHOLT than -786T allele. Conclusion. Our study indicates the putative role of -786T/C polymorphism in the development of hypercholesterolemia, in patients with MS, which might be enhanced by cigarette smoking.

A comparative study of two polymorphs of L-aspartic acid hydrochloride.

PubMed

Benali-Cherif, Rim; Takouachet, Radhwane; Bendeif, El-Eulmi; Benali-Cherif, Nourredine

2014-07-01

Two polymorphs of L-aspartic acid hydrochloride, C4H8NO4(+)·Cl(-), were obtained from the same aqueous solution. Their crystal structures have been determined from single-crystal data collected at 100 K. The crystal structures revealed three- and two-dimensional hydrogen-bonding networks for the triclinic and orthorhombic polymorphs, respectively. The cations and anions are connected to one another via N-H···Cl and O-H···Cl interactions and form alternating cation-anion layer-like structures. The two polymorphs share common structural features; however, the conformations of the L-aspartate cations and the crystal packings are different. Furthermore, the molecular packing of the orthorhombic polymorph contains more interesting interactions which seems to be a favourable factor for more efficient charge transfer within the crystal.

Mutation covariation of HIV-1 CRF07_BC reverse transcriptase during antiretroviral therapy.

PubMed

Li, Zhenpeng; Huang, Yang; Ouyang, Yabo; Xing, Hui; Liao, Lingjie; Jiang, Shibo; Shao, Yiming; Ma, Liying

2013-11-01

To understand the effect of HIV-1 drug resistance mutations in the context of antiretroviral therapy (ART), we compared the prevalence of protease (PR) and reverse transcriptase (RT) mutations in HIV-1 CRF07_BC sequences from blood samples of treatment-naive and ART-treated patients. Mutation covariation in the RT and PR of HIV-1 CRF07_BC viruses from 542 treatment-naive patients and 261 patients treated with lamivudine/zidovudine/nevirapine or lamivudine/zidovudine/efavirenz was analysed. Stratified networks were used to display the mutation covariation. Based on the comparison between treatment-naive and ART-treated patients, three types of featured mutations for RT and PR were initially identified: treatment-associated mutations, treatment-agonistic mutations and overlapping polymorphisms. Twelve significant covariation pairs were found between five treatment-associated mutations (K103N, M184V, Q197K, G190A and Y181C) and nine overlapping polymorphisms (A36E, D39N, Y121H, D123E, R135I, T200A, R277K, L283I and D291E). Meanwhile, three covariation pairs between three treatment-associated mutations (I132L and M184V for RT and I15V for PR) and three overlapping polymorphisms (L10I, L36M and A71V) for PR were also detected. Finally, the overlapping polymorphisms for RT and PR were both found to have significant correlations with treatment-associated mutations, indicating a possible association between polymorphisms and drug resistance. When compared with HIV-1 subtype B under the same regimens as CRF07_BC, the mutation covariations of CRF07_BC showed a distinct pattern of RT and PR mutation covariation. The role of polymorphisms in the development of drug resistance has been widely reported. Here, we found a significant correlation between overlapping polymorphisms for RT and PR and treatment-associated mutations, indicating that polymorphisms exert a global influence on treatment-associated mutations. Polymorphism mutations might therefore be considered before initiating ART to improve the efficacy of drug combinations.

Integrating Genetic, Neuropsychological and Neuroimaging Data to Model Early-Onset Obsessive Compulsive Disorder Severity

PubMed Central

Mas, Sergi; Gassó, Patricia; Morer, Astrid; Calvo, Anna; Bargalló, Nuria; Lafuente, Amalia; Lázaro, Luisa

2016-01-01

We propose an integrative approach that combines structural magnetic resonance imaging data (MRI), diffusion tensor imaging data (DTI), neuropsychological data, and genetic data to predict early-onset obsessive compulsive disorder (OCD) severity. From a cohort of 87 patients, 56 with complete information were used in the present analysis. First, we performed a multivariate genetic association analysis of OCD severity with 266 genetic polymorphisms. This association analysis was used to select and prioritize the SNPs that would be included in the model. Second, we split the sample into a training set (N = 38) and a validation set (N = 18). Third, entropy-based measures of information gain were used for feature selection with the training subset. Fourth, the selected features were fed into two supervised methods of class prediction based on machine learning, using the leave-one-out procedure with the training set. Finally, the resulting model was validated with the validation set. Nine variables were used for the creation of the OCD severity predictor, including six genetic polymorphisms and three variables from the neuropsychological data. The developed model classified child and adolescent patients with OCD by disease severity with an accuracy of 0.90 in the testing set and 0.70 in the validation sample. Above its clinical applicability, the combination of particular neuropsychological, neuroimaging, and genetic characteristics could enhance our understanding of the neurobiological basis of the disorder. PMID:27093171

Electron petrography of silica polymorphs associated with pseudotachylite, Vredefort structure, South Africa

NASA Technical Reports Server (NTRS)

White, J. C.

1992-01-01

High-pressure silica polymorphs (coesite and stishovite) were described from the Vredefort structure in association with pseudotachylite veinlets. In addition to the fundamental significance of the polymorphs to genetic interpretations of the structure, it was additionally argued that the type of pseudotachylite with which they occur forms during the compressional phase of the shock process, while the larger, classic pseudotachylite occurrences are barren of polymorphs and formed during passage of the rarefaction wave. This identification of temporal relationships among transient shock features at a regional scale is similar to observations from the Manicouagan structure, Quebec, where texturally distinct diaplectic plagioclase glasses formed during both compressional and decompressional phases of the shock process. The clarification of such relationships impinges directly on interpretations of natural shock processes and the identification of high probability targets for polymorph searches. Detailed analytical scanning (SEM) and transmission electron microscopy (TEM) were utilized to further establish the nature of both the pseudotachylite and the silica polymorph occurrences in the Vredefort rocks. The results of this investigation are discussed.

Comparisons of stemflow and its bio-/abiotic influential factors between two xerophytic shrub species

NASA Astrophysics Data System (ADS)

Yuan, Chuan; Gao, Guangyao; Fu, Bojie

2017-03-01

Stemflow transports nutrient-enriched precipitation to the rhizosphere and functions as an efficient terrestrial flux in water-stressed ecosystems. However, its ecological significance has generally been underestimated because it is relatively limited in amount, and the biotic mechanisms that affect it have not been thoroughly studied at the leaf scale. This study was conducted during the 2014 and 2015 rainy seasons at the northern Loess Plateau of China. We measured the branch stemflow volume (SFb), shrub stemflow equivalent water depth (SFd), stemflow percentage of incident precipitation (SF %), stemflow productivity (SFP), funnelling ratio (FR), the meteorological characteristics and the plant traits of branches and leaves of C. korshinskii and S. psammophila. This study evaluated stemflow efficiency for the first time with the combined results of SFP and FR, and sought to determine the inter- and intra-specific differences of stemflow yield and efficiency between the two species, as well as the specific bio-/abiotic mechanisms that affected stemflow. The results indicated that C. korshinskii had a greater stemflow yield and efficiency at all precipitation levels than that of S. psammophila. The largest inter-specific difference generally occurred at the 5-10 mm branches during rains of ≤ 2 mm. Precipitation amount was the most influential meteorological characteristic that affected stemflow yield and efficiency in these two endemic shrub species. Branch angle was the most influential plant trait on FR. For SFb, stem biomass and leaf biomass were the most influential plant traits for C. korshinskii and S. psammophila, respectively. For SFP of these two shrub species, leaf traits (the individual leaf area) and branch traits (branch size and biomass allocation pattern) had a great influence during lighter rains ≤ 10 mm and heavier rains > 15 mm, respectively. The lower precipitation threshold to start stemflow allowed C. korshinskii (0.9 mm vs. 2.1 mm for S. psammophila) to employ more rains to harvest water via stemflow. The beneficial leaf traits (e.g., leaf shape, arrangement, area, amount) might partly explain the greater stemflow production of C. korshinskii. Comparison of SFb between the foliated and manually defoliated shrubs during the 2015 rainy season indicated that the newly exposed branch surface at the defoliated period and the resulting rainfall intercepting effects might be an important mechanism affecting stemflow in the dormant season.

Further exploration of the conformational space of α-synuclein fibrils: solid-state NMR assignment of a high-pH polymorph.

PubMed

Verasdonck, Joeri; Bousset, Luc; Gath, Julia; Melki, Ronald; Böckmann, Anja; Meier, Beat H

2016-04-01

Polymorphism is a common and important phenomenon for protein fibrils which has been linked to the appearance of strains in prion and other neurodegenerative diseases. Parkinson disease is a frequently occurring neurodegenerative pathology, tightly associated with the formation of Lewy bodies. These deposits mainly consist of α-synuclein in fibrillar, β-sheet-rich form. α-synuclein is known to form numerous different polymorphs, which show distinct structural features. Here, we describe the chemical shift assignments, and derive the secondary structure, of a polymorph that was fibrillized at higher-than-physiological pH conditions. The fibrillar core contains residues 40-95, with both the C- and N-terminus not showing any ordered, rigid parts. The chemical shifts are similar to those recorded previously for an assigned polymorph that was fibrillized at neutral pH.

Molecular mechanisms for protein-encoded inheritance

PubMed Central

Wiltzius, Jed J. W.; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R.; Apostol, Marcin I.; Goldschmidt, Lukasz; Soriaga, Angela B.; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David

2013-01-01

Strains are phenotypic variants, encoded by nucleic acid sequences in chromosomal inheritance and by protein “conformations” in prion inheritance and transmission. But how is a protein “conformation” stable enough to endure transmission between cells or organisms? Here new polymorphic crystal structures of segments of prion and other amyloid proteins offer structural mechanisms for prion strains. In packing polymorphism, prion strains are encoded by alternative packings (polymorphs) of β-sheets formed by the same segment of a protein; in a second mechanism, segmental polymorphism, prion strains are encoded by distinct β-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring “conformations,” capable of encoding strains. These molecular mechanisms for transfer of information into prion strains share features with the familiar mechanism for transfer of information by nucleic acid inheritance, including sequence specificity and recognition by non-covalent bonds. PMID:19684598

Molecular-genetic correlates of infant attachment: A cautionary tale

PubMed Central

Booth-Laforce, Cathryn; Belsky, Jay; Burt, Keith B.; Groh, Ashley M.

2014-01-01

This paper advises caution in relation to the increasing interest in molecular-genetic association studies in developmental psychology based on a set of empirical examples from the NICHD Study of Early Child Care and Youth Development (SECCYD) that highlight the fragility of effects reported in the literature on the molecular-genetic correlates of infant attachment. Specifically, this paper updates and provides three extensions to results reported in Luijk et al. (2011), which recently failed to replicate evidence from smaller-sample studies that a set of dopaminergic, serotonergic, and oxytonergic markers are significantly associated with infant attachment security or disorganization. First, we report here that the average effect of “usual suspect” polymorphisms on infant attachment security and disorganization in the SECCYD is approximately zero. Second, because Luijk et al. (2011) reported data based exclusively on the White infants in the SECCYD, this paper reveals that the average effect of polymorphisms featured in this literature is also of trivial magnitude in the non-White sub-sample (cf. Chen, Barth, Johnson, Gotlib, & Johnson, 2011). Third, this paper attempts, but fails, to replicate a recent finding by Raby et al. (2012) suggesting that, although molecular-genetic polymorphisms might not be implicated in security versus insecurity, the serotonin transporter gene contributes to variation in emotional distress during the Strange Situation Procedure. Implications for future research on the genetics of developmental phenotypes in general and attachment in particular are discussed, with a focus on statistical power and model-based theory testing. PMID:23421800

Bacilysin from Bacillus amyloliquefaciens FZB42 Has Specific Bactericidal Activity against Harmful Algal Bloom Species

PubMed Central

Wu, Liming; Wu, Huijun; Chen, Lina; Xie, Shanshan; Zang, Haoyu; Borriss, Rainer

2014-01-01

Harmful algal blooms, caused by massive and exceptional overgrowth of microalgae and cyanobacteria, are a serious environmental problem worldwide. In the present study, we looked for Bacillus strains with sufficiently strong anticyanobacterial activity to be used as biocontrol agents. Among 24 strains, Bacillus amyloliquefaciens FZB42 showed the strongest bactericidal activity against Microcystis aeruginosa, with a kill rate of 98.78%. The synthesis of the anticyanobacterial substance did not depend on Sfp, an enzyme that catalyzes a necessary processing step in the nonribosomal synthesis of lipopeptides and polyketides, but was associated with the aro gene cluster that is involved in the synthesis of the sfp-independent antibiotic bacilysin. Disruption of bacB, the gene in the cluster responsible for synthesizing bacilysin, or supplementation with the antagonist N-acetylglucosamine abolished the inhibitory effect, but this was restored when bacilysin synthesis was complemented. Bacilysin caused apparent changes in the algal cell wall and cell organelle membranes, and this resulted in cell lysis. Meanwhile, there was downregulated expression of glmS, psbA1, mcyB, and ftsZ—genes involved in peptidoglycan synthesis, photosynthesis, microcystin synthesis, and cell division, respectively. In addition, bacilysin suppressed the growth of other harmful algal species. In summary, bacilysin produced by B. amyloliquefaciens FZB42 has anticyanobacterial activity and thus could be developed as a biocontrol agent to mitigate the effects of harmful algal blooms. PMID:25261512

Study of Lateral Misalignment Tolerance of a Symmetric Free-Space Optical Link for Intra International Space Station Communication

NASA Technical Reports Server (NTRS)

Tedder, Sarah A.; Schoenholz, Bryan; Suddath, Shannon N.

2016-01-01

This paper describes the study of lateral misalignment tolerance of a symmetric high-rate free-space optical link (FSOL) for use between International Space Station (ISS) payload sites and the main cabin. The link will enable gigabit per second (Gbps) transmission of data, which is up to three orders of magnitude greater than the current capabilities. This application includes 10-20 meter links and requires minimum size, weight, and power (SWaP). The optical power must not present an eye hazard and must be easily integrated into the existing ISS infrastructure. On the ISS, rapid thermal changes and astronaut movement will cause flexure of the structure which will potentially misalign the free space transmit and receive optics 9 cm laterally and 0.2 degrees angularly. If this misalignment is not accounted for, a loss of the link or degradation of link performance will occur. Power measurements were collected to better understand the effect of various system design parameters on lateral misalignment. Parameters that were varied include: the type of small form pluggable (SFP) transceivers, type of fiber, and transmitted power level. A potential solution was identified that can reach the lateral misalignment tolerance (decenter span) required to create an FSOL on the ISS by using 105 m core fibers, a duplex SFP, two channels of light, and two fiber amplifiers.

HLA-G Haplotypes Are Differentially Associated with Asthmatic Features.

PubMed

Ribeyre, Camille; Carlini, Federico; René, Céline; Jordier, François; Picard, Christophe; Chiaroni, Jacques; Abi-Rached, Laurent; Gouret, Philippe; Marin, Grégory; Molinari, Nicolas; Chanez, Pascal; Paganini, Julien; Gras, Delphine; Di Cristofaro, Julie

2018-01-01

Human leukocyte antigen (HLA)-G, a HLA class Ib molecule, interacts with receptors on lymphocytes such as T cells, B cells, and natural killer cells to influence immune responses. Unlike classical HLA molecules, HLA-G expression is not found on all somatic cells, but restricted to tissue sites, including human bronchial epithelium cells (HBEC). Individual variation in HLA-G expression is linked to its genetic polymorphism and has been associated with many pathological situations such as asthma, which is characterized by epithelium abnormalities and inflammatory cell activation. Studies reported both higher and equivalent soluble HLA-G (sHLA-G) expression in different cohorts of asthmatic patients. In particular, we recently described impaired local expression of HLA-G and abnormal profiles for alternatively spliced isoforms in HBEC from asthmatic patients. sHLA-G dosage is challenging because of its many levels of polymorphism (dimerization, association with β2-microglobulin, and alternative splicing), thus many clinical studies focused on HLA-G single-nucleotide polymorphisms as predictive biomarkers, but few analyzed HLA-G haplotypes. Here, we aimed to characterize HLA-G haplotypes and describe their association with asthmatic clinical features and sHLA-G peripheral expression and to describe variations in transcription factor (TF) binding sites and alternative splicing sites. HLA - G haplotypes were differentially distributed in 330 healthy and 580 asthmatic individuals. Furthermore, HLA-G haplotypes were associated with asthmatic clinical features showed. However, we did not confirm an association between sHLA-G and genetic, biological, or clinical parameters. HLA-G haplotypes were phylogenetically split into distinct groups, with each group displaying particular variations in TF binding or RNA splicing sites that could reflect differential HLA-G qualitative or quantitative expression, with tissue-dependent specificities. Our results, based on a multicenter cohort, thus support the pertinence of HLA-G haplotypes as predictive genetic markers for asthma.

HLA-G Haplotypes Are Differentially Associated with Asthmatic Features

PubMed Central

Ribeyre, Camille; Carlini, Federico; René, Céline; Jordier, François; Picard, Christophe; Chiaroni, Jacques; Abi-Rached, Laurent; Gouret, Philippe; Marin, Grégory; Molinari, Nicolas; Chanez, Pascal; Paganini, Julien; Gras, Delphine; Di Cristofaro, Julie

2018-01-01

Human leukocyte antigen (HLA)-G, a HLA class Ib molecule, interacts with receptors on lymphocytes such as T cells, B cells, and natural killer cells to influence immune responses. Unlike classical HLA molecules, HLA-G expression is not found on all somatic cells, but restricted to tissue sites, including human bronchial epithelium cells (HBEC). Individual variation in HLA-G expression is linked to its genetic polymorphism and has been associated with many pathological situations such as asthma, which is characterized by epithelium abnormalities and inflammatory cell activation. Studies reported both higher and equivalent soluble HLA-G (sHLA-G) expression in different cohorts of asthmatic patients. In particular, we recently described impaired local expression of HLA-G and abnormal profiles for alternatively spliced isoforms in HBEC from asthmatic patients. sHLA-G dosage is challenging because of its many levels of polymorphism (dimerization, association with β2-microglobulin, and alternative splicing), thus many clinical studies focused on HLA-G single-nucleotide polymorphisms as predictive biomarkers, but few analyzed HLA-G haplotypes. Here, we aimed to characterize HLA-G haplotypes and describe their association with asthmatic clinical features and sHLA-G peripheral expression and to describe variations in transcription factor (TF) binding sites and alternative splicing sites. HLA-G haplotypes were differentially distributed in 330 healthy and 580 asthmatic individuals. Furthermore, HLA-G haplotypes were associated with asthmatic clinical features showed. However, we did not confirm an association between sHLA-G and genetic, biological, or clinical parameters. HLA-G haplotypes were phylogenetically split into distinct groups, with each group displaying particular variations in TF binding or RNA splicing sites that could reflect differential HLA-G qualitative or quantitative expression, with tissue-dependent specificities. Our results, based on a multicenter cohort, thus support the pertinence of HLA-G haplotypes as predictive genetic markers for asthma. PMID:29527207

Association of GSK3beta polymorphisms with brain structural changes in major depressive disorder.

PubMed

Inkster, Becky; Nichols, Thomas E; Saemann, Philipp G; Auer, Dorothee P; Holsboer, Florian; Muglia, Pierandrea; Matthews, Paul M

2009-07-01

Indirect evidence suggests that the glycogen synthase kinase-3beta (GSK3beta) gene might be implicated in major depressive disorder (MDD). We evaluated 15 GSK3beta single-nucleotide polymorphisms (SNPs) to test for associations with regional gray matter (GM) volume differences in patients with recurrent MDD. We then used the defined regions of interest based on significant associations to test for MDD x genotype interactions by including a matched control group without any psychiatric disorder, including MDD. General linear model with nonstationary cluster-based inference. Munich, Germany. Patients with recurrent MDD (n = 134) and age-, sex-, and ethnicity-matched healthy controls (n = 143). Associations between GSK3beta polymorphisms and regional GM volume differences. Variation in GM volume was associated with GSK3beta polymorphisms; the most significant associations were found for rs6438552, a putative functional intronic SNP that showed 3 significant GM clusters in the right and left superior temporal gyri and the right hippocampus (P < .001, P = .02, and P = .02, respectively, corrected for multiple comparisons across the whole brain). Similar results were obtained with rs12630592, an SNP in high linkage disequilibrium. A significant SNP x MDD status interaction was observed for the effect on GM volumes in the right hippocampus and superior temporal gyri (P < .001 and P = .01, corrected, respectively). The GSK3beta gene may have a role in determining regional GM volume differences of the right hippocampus and bilateral superior temporal gyri. The association between genotype and brain structure was specific to the patients with MDD, suggesting that GSK3beta genotypes might interact with MDD status. We speculate that this is a consequence of regional neocortical, glial, or neuronal growth or survival. In considering core cognitive features of MDD, the association of GSK3beta polymorphisms with structural variation in the temporal lobe and hippocampus is of particular interest in the context of other evidence for structural and functional abnormalities in the hippocampi of patients with MDD.

[About the signs of malignant pheochromocytoma].

PubMed

Simonenko, V B; Makanin, M A; Dulin, P A; Vasilchenko, M I; Lesovik, V S

2012-01-01

Morphological criteria for malignant pheochromocytoma remain to be developed According to the WHO recommendations, the sole absolute criteria is the presence of metastases in the organs normally containing no chromaffin tissue. Such signs as cellular and nuclear polymorphism, mytotic activity, vascular invasion, capsular ingrowth are not sufficient to describe a pheochromocytoma as malignant. It is equally dfficult to differentiate between malignant and benign tumours based on histological data since histologically mature neoplasms can produce metastases. Based on the results of original studies, the authors believe that such histological features as vascular and capsular invasion do not necessarily suggest unfavourable prognosis. Therefore, the conclusion of malignancy based on such features can not be regarded as absolute. Probably such neoplasms should be called "pheochromocytomas with morphological signs of malignant growths". They should be referred to the tumours with uncertain malignancy potential based on the known discrepancy between morphological structure and biological activity of neoplasms. Comparative studies of clinical and morphological features of pheochromocytomas showed that their histological type (alveolar; solid, dyscomplexed, trabecular) and morphological signs of malignant growth influence both the clinical picture and arterial hypertension. There are no significant relationship between the above morphological signs, timour mass and clinical manifestations of pheochromocytomas.

Evaluation of glucose metabolism and reproductive hormones in polycystic ovary syndrome on the basis of peroxisome proliferator-activated receptor (PPAR)-gamma2 Pro12Ala genotype.

PubMed

Tok, E C; Aktas, A; Ertunc, D; Erdal, E M; Dilek, S

2005-06-01

Peroxisome proliferator-activated receptor (PPAR)-gamma2 Pro12Ala polymorphism has been suggested as a protective factor for polycystic ovary syndrome (PCOS). In this study, we aimed to investigate metabolic features and reproductive hormones in women with PCOS and compare these features with control women on the basis of Pro12Ala genotype. This study involved 60 randomly selected women with PCOS and 60 controls. Main outcome measures were anthropometric measures, variables of glucose metabolism and reproductive hormones. All the patients were genotyped for Pro12Ala variant of PPAR-gamma2 gene. Patients with Pro12Ala polymorphism were more obese in both groups. Furthermore, they had lower fasting insulin levels, were less insulin-resistant and were less glucose-intolerant as demonstrated by 2 h glucose concentrations. However, there was no difference in reproductive hormone levels on the basis of Pro12Ala genotype. Both control women and women with PCOS had significant differences in glucose metabolism on the basis of PPAR-gamma2 Pro12Ala polymorphism. Pro12Ala variant may break the process that leads to PCOS in susceptible women, instead of being a direct causal relationship between Pro12Ala polymorphism and PCOS.

Development of ROACH firmware for microwave multiplexed X-ray TES microcalorimeters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madden, T. J.; Cecil, T. W.; Gades, L. M.

We are developing room temperature electronics based upon the ROACH platform for reading out microwave multiplexed X-ray TES. ROACH is an open-source hardware and software platform featuring a large Xilinx Field Programmable Gate Array (FPGA), Power PC processor, several 10GB Ethernet SFP+ interfaces, and a collection of daughter boards for analog signal generation and acquisition. The combination of a ROACH board, ADC/DAC conversion daughter boards, and hardware for RF mixing allows for the generation and capture of multiple RF tones for reading out microwave multiplexed x-ray TES microcalorimeters. The FPGA is used to generate multiple tones in base band, frommore » 10MHz to 250MHz, which are subsequently mixed to RF in the multiple GHz range and sent through the microwave multiplexer. The tones are generated in the FPGA by storing a large lookup table in Quad Data Rate (QDR) SRAM modules and playing out the waveform to a DAC board. Once the signal has been modulated to RF, passed through the microwave multiplexer, and has been modulated back to base band, the signal is digitized by an ADC board. The tones are modulated to 0Hz by using a FPGA circuit consisting of a polyphase filter bank, several Xilinx FFT blocks, Xilinx CORDIC blocks (for converting to magnitude and phase), and special phase accumulator circuit for mixing to exactly 0Hz. Upwards of 256 channels can be simultaneously captured and written into a bank of 256 First-In-First-Out (FIFO) memories, with each FIFO corresponding to a channel. Individual channel data can be further processed in the FPGA before being streamed through a 10GB Ethernet fiber-optic interface to a Linux system. The Linux system runs software written in Python and QT C++ for controlling the ROACH system, capturing data, and processing data.« less

Soil cover patterns and SOC dynamics impacts on the soil processes, land management and ecosystem services in Central Region of Russia

NASA Astrophysics Data System (ADS)

Vasenev, Ivan; Chernikov, Vladimir; Yashin, Ivan; Geraskin, Mikhail; Morev, Dmitriy

2014-05-01

In the Central Region of Russia (CRR) the soil cover patterns usually play the very important role in the soil forming and degradation processes (SFP & SDP) potential and current rates, soil organic carbon (SOC) dynamics and pools, greenhouse gases (GHG) emissions and soluble SOC fluxes that we need take into attention for better assessment of the natural and especially man-changed ecosystems' services and for best land-use practices development. Central Region of Russia is the biggest one in RF according to its population and role in the economy. CRR is characterized by high spatial variability of soil cover due to as original landscape heterogeneity as complicated history of land-use practices during last 700 years. Our long-term researches include the wide zonal-provincial set of representative ecosystems and soil cover patterns with different types and history of land-use (forest, meadow-steppe and agricultural ones) from middle-taiga to steppe zones with different level of continentality. The carried out more than 30-years region- and local-scale researches of representative natural and rural landscapes in Tver', Yaroslavl', Kaluga, Moscow, Vladimir, Saransk (Mordovia), Kursk, Orel, Tambov, Voronezh and Saratov oblasts give us the interregional multi-factorial matrix of elementary soil cover patterns (ESCP) with different soil forming and degradation processes rates and soil organic carbon dynamics due to regionally specific soil-geomorphologic features, environmental and dominated microclimate conditions, land-use current practices and history. The validation and ranging of the limiting factors of SFP and SDP develop¬ment, soil carbon dynamics and sequestration potential, ecosystem (agroecosystem) principal services, land functional qualities and agroecological state have been done for dominating and most dynamical components of ESCP regional-typological forms - with application of SOC structure analysis, regional and local GIS, soil spatial patterns detail mapping, traditional regression kriging, correlation tree models and DSS adapted to concrete region and agrolandscape conditions. The outcomes of statistical process modeling show the essential amplification of erosion, dehumification, CO2, CH4 and N2O emission, soluble SOC fluxes, acidification or alkalization, disaggregation and overcompaction processes due to violation of environmentally sound land-use systems and traditional balances of organic matter, nutrients, Ca and Na in agrolandscapes. Due to long-term intensive and out-of-balance land-use practices the most zonal soils and soil cover pattern essentially lost not only their unique natural features (humus horizons depth till 1 m and more in case of Chernozems, 2-6 % of SOC and favorable agrophysical features), but ecosystem services and ecological functions including terrestrial ecosystem carbon balance and the GHG fluxes control. Key-site monitoring results and regional generalized data showed 1-1.5% SOC lost during last 50 years period and active processes of CO2 emission and humus profile eluvial-illuvial redistribution too. A drop of Corg content below threshold "humus limiting content" values (for different soils they vary from 1 to 3-4% of SOC) considerably reduces effectiveness of used fertilizers and possibility of sustai¬nable agronomy here. Forest-steppe Chernozems are usually characterized by higher stability than steppe ones. The ratio between erosive and biological losses in humus supplies can be ten-tatively estimated as fifty-fifty with strong spatial variability due to slope and land-use parameters. These processes have essentially different sets of environmental consequences and ecosystem services that we need to understand in frame of environmental and agroecological problems development prediction.

Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip

PubMed Central

Hill, Theresa A.; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W.; Van Deynze, Allen

2013-01-01

The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum. PMID:23409153

Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

PubMed

Hill, Theresa A; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W; Van Deynze, Allen

2013-01-01

The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum.

Association of insertion-deletions polymorphisms with colorectal cancer risk and clinical features.

PubMed

Marques, Diego; Ferreira-Costa, Layse Raynara; Ferreira-Costa, Lorenna Larissa; Correa, Romualdo da Silva; Borges, Aline Maciel Pinheiro; Ito, Fernanda Ribeiro; Ramos, Carlos Cesar de Oliveira; Bortolin, Raul Hernandes; Luchessi, André Ducati; Ribeiro-Dos-Santos, Ândrea; Santos, Sidney; Silbiger, Vivian Nogueira

2017-10-07

To investigate the association between 16 insertion-deletions (INDEL) polymorphisms, colorectal cancer (CRC) risk and clinical features in an admixed population. One hundred and forty patients with CRC and 140 cancer-free subjects were examined. Genomic DNA was extracted from peripheral blood samples. Polymorphisms and genomic ancestry distribution were assayed by Multiplex-PCR reaction, separated by capillary electrophoresis on the ABI 3130 Genetic Analyzer instrument and analyzed on GeneMapper ID v3.2. Clinicopathological data were obtained by consulting the patients' clinical charts, intra-operative documentation, and pathology scoring. Logistic regression analysis showed that polymorphism variations in IL4 gene was associated with increased CRC risk, while TYMS and UCP2 genes were associated with decreased risk. Reference to anatomical localization of tumor Del allele of NFKB1 and CASP8 were associated with more colon related incidents than rectosigmoid. In relation to the INDEL association with tumor node metastasis (TNM) stage risk, the Ins alleles of ACE , HLAG and TP53 (6 bp INDEL) were associated with higher TNM stage. Furthermore, regarding INDEL association with relapse risk, the Ins alleles of ACE , HLAG , and UGT1A1 were associated with early relapse risk, as well as the Del allele of TYMS . Regarding INDEL association with death risk before 10 years, the Ins allele of SGSM3 and UGT1A1 were associated with death risk. The INDEL variations in ACE , UCP2 , TYMS , IL4 , NFKB1 , CASP8 , TP53 , HLAG , UGT1A1 , and SGSM3 were associated with CRC risk and clinical features in an admixed population. These data suggest that this cancer panel might be useful as a complementary tool for better clinical management, and more studies need to be conducted to confirm these findings.

A characteristic of polymorphic membrane protein F of Chlamydia trachomatis isolated from male urogenital tracts in Japan.

PubMed

Yamazaki, Tomohiro; Matsuo, Junji; Takahashi, Satoshi; Kumagai, Shouta; Shimoda, Tomoko; Abe, Kiyotaka; Minami, Kunihiro; Yamaguchi, Hiroyuki

2015-12-01

Although sexually transmitted disease due to Chlamydia trachomatis occurs similarly in both men and women, the female urogenital tract differs from that of males anatomically and physiologically, possibly leading to specific polymorphisms of the bacterial surface molecules. In the present study, we therefore characterized polymorphic features in a high-definition phylogenetic marker, polymorphic outer membrane protein (Pmp) F of C. trachomatis strains isolated from male urogenital tracts in Japan (Category: Japan-males, n = 12), when compared with those isolated from female cervical ducts in Japan (Category: Japan-females, n = 11), female cervical ducts in the other country (Category: Ref-females, n = 12) or homosexual male rectums in the other country (Category: Ref-males, n = 7), by general bioinformatics analysis tool with MAFFT software. As a result, phylogenetic reconstruction of the PmpF amino acid sequences showing three distinct clusters revealed that the Japan-males were limited into cluster 1 and 2, although there were only four clusters even though including an outgroup. Meanwhile, the phylogenetic distance values of PmpF passenger domain without hinge region, but not its full-length sequence, showed that the Japan-males were more stable and displayed less diversity when compared with the other categories, supported by the sequence conservation features. Thus, PmpF passenger domain is a useful phylogenetic maker, and the phylogenic features indicate that C. trachomatis strains isolated from male urogenital tracts in Japan may be unique, suggesting an adaptation depending on selective pressure, such as the presence or absence of microbial flora, furthermore possibly connecting to sexual differentiation. Copyright © 2015 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

TP53 PIN3 and PEX4 polymorphisms and infertility associated with endometriosis or with post-in vitro fertilization implantation failure

PubMed Central

Paskulin, D D; Cunha-Filho, J S L; Souza, C A B; Bortolini, M C; Hainaut, P; Ashton-Prolla, P

2012-01-01

p53 has a crucial role in human fertility by regulating the expression of leukemia inhibitory factor (LIF), a secreted cytokine critical for blastocyst implantation. To examine whether TP53 polymorphisms may be involved with in vitro fertilization (IVF) failure and endometriosis (END), we have assessed the associations between TP53 polymorphism in intron 2 (PIN2; G/C, intron 2), PIN3 (one (N, non-duplicated) or two (D, duplicated) repeats of a 16-bp motif, intron 3) and polymorphism in exon 4 (PEX4; C/G, p.P72R, exon 4) in 98 women with END and 115 women with post-IVF failure. In addition, 134 fertile women and 300 women unselected with respect to fertility-related features were assessed. TP53 polymorphisms and haplotypes were identified by amplification refractory mutation system polymerase chain reaction. TP53 PIN3 and PEX4 were associated with both END (P=0.042 and P=0.007, respectively) and IVF (P=0.004 and P=0.009, respectively) when compared with women both selected and unselected for fertility-related features. Haplotypes D-C and N-C were related to higher risk for END (P=0.002, P=0.001, respectively) and failure of IVF (P=0.018 and P=0.002, respectively) when compared with the Fertile group. These results support that specific TP53 haplotypes are associated with an increased risk of END-associated infertility and with post-IVF failure. PMID:23013791

Identifying disease polymorphisms from case-control genetic association data.

PubMed

Park, L

2010-12-01

In case-control association studies, it is typical to observe several associated polymorphisms in a gene region. Often the most significantly associated polymorphism is considered to be the disease polymorphism; however, it is not clear whether it is the disease polymorphism or there is more than one disease polymorphism in the gene region. Currently, there is no method that can handle these problems based on the linkage disequilibrium (LD) relationship between polymorphisms. To distinguish real disease polymorphisms from markers in LD, a method that can detect disease polymorphisms in a gene region has been developed. Relying on the LD between polymorphisms in controls, the proposed method utilizes model-based likelihood ratio tests to find disease polymorphisms. This method shows reliable Type I and Type II error rates when sample sizes are large enough, and works better with re-sequenced data. Applying this method to fine mapping using re-sequencing or dense genotyping data would provide important information regarding the genetic architecture of complex traits.

Prediction of phenotypes of missense mutations in human proteins from biological assemblies.

PubMed

Wei, Qiong; Xu, Qifang; Dunbrack, Roland L

2013-02-01

Single nucleotide polymorphisms (SNPs) are the most frequent variation in the human genome. Nonsynonymous SNPs that lead to missense mutations can be neutral or deleterious, and several computational methods have been presented that predict the phenotype of human missense mutations. These methods use sequence-based and structure-based features in various combinations, relying on different statistical distributions of these features for deleterious and neutral mutations. One structure-based feature that has not been studied significantly is the accessible surface area within biologically relevant oligomeric assemblies. These assemblies are different from the crystallographic asymmetric unit for more than half of X-ray crystal structures. We find that mutations in the core of proteins or in the interfaces in biological assemblies are significantly more likely to be disease-associated than those on the surface of the biological assemblies. For structures with more than one protein in the biological assembly (whether the same sequence or different), we find the accessible surface area from biological assemblies provides a statistically significant improvement in prediction over the accessible surface area of monomers from protein crystal structures (P = 6e-5). When adding this information to sequence-based features such as the difference between wildtype and mutant position-specific profile scores, the improvement from biological assemblies is statistically significant but much smaller (P = 0.018). Combining this information with sequence-based features in a support vector machine leads to 82% accuracy on a balanced dataset of 50% disease-associated mutations from SwissVar and 50% neutral mutations from human/primate sequence differences in orthologous proteins. Copyright © 2012 Wiley Periodicals, Inc.

Lessons from the canine Oxtr gene: populations, variants and functional aspects.

PubMed

Bence, M; Marx, P; Szantai, E; Kubinyi, E; Ronai, Z; Banlaki, Z

2017-04-01

Oxytocin receptor (OXTR) acts as a key behavioral modulator of the central nervous system, affecting social behavior, stress, affiliation and cognitive functions. Variants of the Oxtr gene are known to influence behavior both in animals and humans; however, canine Oxtr polymorphisms are less characterized in terms of possible relevance to function, selection criteria in breeding and domestication. In this report, we provide a detailed characterization of common variants of the canine Oxtr gene. In particular (1) novel polymorphisms were identified by direct sequencing of wolf and dog samples, (2) allelic distributions and pairwise linkage disequilibrium patterns of several canine populations were compared, (3) neighbor joining (NJ) tree based on common single nucleotide polymorphisms (SNPs) was constructed, (4) mRNA expression features were assessed, (5) a novel splice variant was detected and (6) in vitro functional assays were performed. Results indicate marked differences regarding Oxtr variations between purebred dogs of different breeds, free-ranging dog populations, wolf subspecies and golden jackals. This, together with existence of explicitly dog-specific alleles and data obtained from the NJ tree implies that Oxtr could indeed have been a target gene during domestication and selection for human preferred aspects of temperament and social behavior. This assumption is further supported by the present observations on gene expression patterns within the brain and luciferase reporter experiments, providing a molecular level link between certain canine Oxtr polymorphisms and differences in nervous system function and behavior. © 2016 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Epidermal growth factor receptor gene polymorphisms are associated with prognostic features of breast cancer

PubMed Central

2014-01-01

Background The epidermal growth factor receptor (EGFR) is differently expressed in breast cancer, and its presence may favor cancer progression. We hypothesized that two EGFR functional polymorphisms, a (CA)n repeat in intron 1, and a single nucleotide polymorphism, R497K, may affect EGFR expression and breast cancer clinical profile. Methods The study population consisted of 508 Brazilian women with unilateral breast cancer, and no distant metastases. Patients were genotyped for the (CA)n and R497K polymorphisms, and the associations between (CA)n polymorphism and EGFR transcript levels (n = 129), or between either polymorphism and histopathological features (n = 505) were evaluated. The REMARK criteria of tumor marker evaluation were followed. Results (CA)n lengths ranged from 14 to 24 repeats, comprehending 11 alleles and 37 genotypes. The most frequent allele was (CA)16 (0.43; 95% CI = 0.40–0.46), which was set as the cut-off length to define the Short allele. Variant (CA)n genotypes had no significant effect in tumoral EGFR mRNA levels, but patients with two (CA)n Long alleles showed lower chances of being negative for progesterone receptor (ORadjusted = 0.42; 95% CI = 0.19–0.91). The evaluation of R497K polymorphism indicated a frequency of 0.21 (95% CI = 0.19 – 0.24) for the variant (Lys) allele. Patients with variant R497K genotypes presented lower proportion of worse lymph node status (pN2 or pN3) when compared to the reference genotype Arg/Arg (ORadjusted = 0.32; 95% CI = 0.17–0.59), which resulted in lower tumor staging (ORadjusted = 0.34; 95% CI = 0.19-0.63), and lower estimated recurrence risk (OR = 0.50; 95% CI = 0.30-0.81). The combined presence of both EGFR polymorphisms (Lys allele of R497K and Long/Long (CA)n) resulted in lower TNM status (ORadjusted = 0.22; 95% CI = 0.07-0.75) and lower ERR (OR = 0.25; 95% CI = 0.09-0.71). When tumors were stratified according to biological classification, the favorable effects of variant EGFR polymorphisms were preserved for luminal A tumors, but not for other subtypes. Conclusions The data suggest that the presence of the variant forms of EGFR polymorphisms may lead to better prognosis in breast cancer, especially in patients with luminal A tumors. PMID:24629097

IL23R +2199A/C polymorphism is associated with decreased risk of certain subtypes of gastric cancer in Chinese: a case-control study.

PubMed

Chen, Bin; Zeng, Zhirong; Xu, Lixia; Wu, Xiaoqin; Yu, Jun; Xue, Ling; Hao, Yuantao; Wang, Yiming; Sung, Joseph J Y; Chen, Minhu; Hu, Pinjin

2011-04-01

Today, the causal relationship between inflammation and gastric cancer is more widely accepted. Genetic variations in inflammation-related genes especially cytokines and their receptors, were thought to partly determine the outcome of Helicobacter pylori (H. pylori) infection and progression of gastric lesions. Interleukin 23 receptor (IL23R), as a key cytokine receptor gene in the important inflammatory IL-17/IL-23 axis, may contribute to gastric cancer predisposition. Up till now, the associations of IL23R gene polymorphisms with subtypes of gastric cancer are largely unknown. We investigated whether the association between IL23R +2199 rs10889677 and gastric cancer risk varies by clinical characteristics and the prognostic value of the polymorphism in a case-control study. A population-based case-control study was conducted in Guangdong. 1010 gastric cancer patients and 800 healthy controls were enrolled. Polymorphism in IL23R was analyzed by PCR-RFLP. Compared with AA, CC carriers of IL23R +2199 polymorphism were associated with protection against gastric cancer (OR=0.47, 95% CI=0.31-0.71). In stratified analyses, CC genotype was significantly associated with decreased risk of intestinal type (OR=0.44, 95% CI=0.27-0.70), but not with diffuse or mix type of gastric cancer. CC genotype was found to be associated with poorly differentiated (OR=0.43, 95% CI=0.26-0.70), but not with moderately or well differentiated gastric cancer. Multivariate analysis showed IL23R +2199A/C variant was not an independent prognostic factor for gastric cancer patients. IL23R polymorphism influences certain subtypes of gastric cancer according to clinical and pathological features. Understanding the etiologic heterogeneity of gastric cancer may result in improvements in controlling this disorder. Copyright © 2010 Elsevier Ltd. All rights reserved.

Crystallization of D-mannitol in binary mixtures with NaCl: phase diagram and polymorphism.

PubMed

Telang, Chitra; Suryanarayanan, Raj; Yu, Lian

2003-12-01

To study the crystallization, polymorphism, and phase behavior of D-mannitol in binary mixtures with NaCl to better understand their interactions in frozen aqueous solutions. Differential scanning calorimetry, hot-stage microscopy, Raman microscopy, and variable-temperature X-ray diffractometry were used to characterize D-mannitol-NaCl mixtures. NaCl and D-mannitol exhibited significant melt miscibility (up to 7.5% w/w or 0.20 mole fraction of NaCl) and a eutectic phase diagram (eutectic composition 7.5% w/w NaCl; eutectic temperature 150 degrees C for the alpha and beta polymorphs of D-mannitol and 139 degrees C for the delta). The presence of NaCl did not prevent mannitol from crystallizing but, depending on sample size, affected the polymorph crystallized: below 10 mg, delta was obtained; above 100 mg, alpha was obtained. Pure mannitol crystallized under the same conditions first as the delta polymorph and then as the a polymorph, with the latter nucleating on the former. KCl showed similar eutectic points and melt miscibility with D-mannitol as NaCl. LiCl yielded lower eutectic melting points, inhibited the crystallization of D-mannitol during cooling, and enabled the observation of its glass transition. Despite their structural dissimilarity, significant melt miscibility exists between D-mannitol and NaCl. Their phase diagram has been determined and features polymorph-dependent eutectic points. NaCl influences the polymorphic behavior of mannitol, and the effect is linked to the crystallization of mannitol in two polymorphic stages.

First principles and experimental study of the electronic structure and phase stability of bulk thallium bromide

NASA Astrophysics Data System (ADS)

Smith, Holland M.; Zhou, Yuzhi; Ciampi, Guido; Kim, Hadong; Cirignano, Leonard J.; Shah, Kanai S.; Haller, E. E.; Chrzan, D. C.

2013-08-01

We apply state-of-art first principle calculations to study the polymorphism and electronic structure of three previously reported phases of TlBr. The calculated band structures of NaCl-structure phase and orthorhombic-structure phase have different features than that of commonly observed CsCl-structure phase. We further interpret photoluminescence spectra based on our calculations. Several peaks close to calculated band gap values of the NaCl-structure phase and the orthorhombic-structure phase are found in unpolished TlBr samples.

New data from basal Australian songbird lineages show that complex structure of MHC class II β genes has early evolutionary origins within passerines.

PubMed

Balasubramaniam, Shandiya; Bray, Rebecca D; Mulder, Raoul A; Sunnucks, Paul; Pavlova, Alexandra; Melville, Jane

2016-05-21

The major histocompatibility complex (MHC) plays a crucial role in the adaptive immune system and has been extensively studied across vertebrate taxa. Although the function of MHC genes appears to be conserved across taxa, there is great variation in the number and organisation of these genes. Among avian species, for instance, there are notable differences in MHC structure between passerine and non-passerine lineages: passerines typically have a high number of highly polymorphic MHC paralogs whereas non-passerines have fewer loci and lower levels of polymorphism. Although the occurrence of highly polymorphic MHC paralogs in passerines is well documented, their evolutionary origins are relatively unexplored. The majority of studies have focussed on the more derived passerine lineages and there is very little empirical information on the diversity of the MHC in basal passerine lineages. We undertook a study of MHC diversity and evolutionary relationships across seven species from four families (Climacteridae, Maluridae, Pardalotidae, Meliphagidae) that comprise a prominent component of the basal passerine lineages. We aimed to determine if highly polymorphic MHC paralogs have an early evolutionary origin within passerines or are a more derived feature of the infraorder Passerida. We identified 177 alleles of the MHC class II β exon 2 in seven basal passerine species, with variation in numbers of alleles across individuals and species. Overall, we found evidence of multiple gene loci, pseudoalleles, trans-species polymorphism and high allelic diversity in these basal lineages. Phylogenetic reconstruction of avian lineages based on MHC class II β exon 2 sequences strongly supported the monophyletic grouping of basal and derived passerine species. Our study provides evidence of a large number of highly polymorphic MHC paralogs in seven basal passerine species, with strong similarities to the MHC described in more derived passerine lineages rather than the simpler MHC in non-passerine lineages. These findings indicate an early evolutionary origin of highly polymorphic MHC paralogs in passerines and shed light on the evolutionary forces shaping the avian MHC.

New Insights into the Diverse Electronic Phases of a Novel Vanadium Dioxide Polymorph: A Terahertz Spectroscopy Study

PubMed Central

Lourembam, James; Srivastava, Amar; La-o-vorakiat, Chan; Rotella, H.; Venkatesan, T.; Chia, Elbert E. M.

2015-01-01

A remarkable feature of vanadium dioxide is that it can be synthesized in a number of polymorphs. The conductivity mechanism in the metastable layered polymorph VO2(B) thin films has been investigated by terahertz time-domain spectroscopy (THz-TDS). In VO2(B), a critical temperature of 240 K marks the appearance of a non-zero Drude term in the observed complex conductivity, indicating the evolution from a pure insulating state towards a metallic state. In contrast, the THz conductivity of the well-known VO2(M1) is well fitted only by a modification of the Drude model to include backscattering. We also identified two different THz conductivity regimes separated by temperature in these two polymorphs. The electronic phase diagram is constructed, revealing that the width and onset of the metal-insulator transition in the B phase develop differently from the M1 phase. PMID:25777320

Analysis of genetic diversity in pigeon pea germplasm using retrotransposon-based molecular markers.

PubMed

Maneesha; Upadhyaya, Kailash C

2017-09-01

Pigeon pea (Cajanus cajan), an important legume crop is predominantly cultivated in tropical and subtropical regions of Asia and Africa. It is normally considered to have a low degree of genetic diversity, an impediment in undertaking crop improvement programmes.We have analysed genetic polymorphism of domesticated pigeon pea germplasm (47 accessions) across the world using earlier characterized panzee retrotransposon-based molecularmarkers. Itwas conjectured that since retrotransposons are interspersed throughout the genome, retroelements-based markers would be able to uncover polymorphism possibly inherent in the diversity of retroelement sequences. Two PCR-based techniques, sequence-specific amplified polymorphism (SSAP) and retrotransposon microsatellite amplified polymorphism (REMAP) were utilized for the analyses.We show that a considerable degree of polymorphism could be detected using these techniques. Three primer combinations in SSAP generated 297 amplified products across 47 accessions with an average of 99 amplicons per assay. Degree of polymorphism varied from 84-95%. In the REMAP assays, the number of amplicons was much less but up to 73% polymorphism could be detected. On the basis of similarity coefficients, dendrograms were constructed. The results demonstrate that the retrotransposon-based markers could serve as a better alternative for the assessment of genetic diversity in crops with apparent low genetic base.

Diversity Arrays Technology (DArT) for whole-genome profiling of barley

PubMed Central

Wenzl, Peter; Carling, Jason; Kudrna, David; Jaccoud, Damian; Huttner, Eric; Kleinhofs, Andris; Kilian, Andrzej

2004-01-01

Diversity Arrays Technology (DArT) can detect and type DNA variation at several hundred genomic loci in parallel without relying on sequence information. Here we show that it can be effectively applied to genetic mapping and diversity analyses of barley, a species with a 5,000-Mbp genome. We tested several complexity reduction methods and selected two that generated the most polymorphic genomic representations. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 98.0% and a scoring reproducibility of at least 99.8%. The fingerprints grouped barley lines according to known genetic relationships. To validate the Mendelian behavior of DArT markers, we constructed a genetic map for a cross between cultivars Steptoe and Morex. Nearly all polymorphic array features could be incorporated into one of seven linkage groups (98.8%). The resulting map comprised ≈385 unique DArT markers and spanned 1,137 centimorgans. A comparison with the restriction fragment length polymorphism-based framework map indicated that the quality of the DArT map was equivalent, if not superior, to that of the framework map. These results highlight the potential of DArT as a generic technique for genome profiling in the context of molecular breeding and genomics. PMID:15192146

Polymorphous computing fabric

DOEpatents

Wolinski, Christophe Czeslaw [Los Alamos, NM; Gokhale, Maya B [Los Alamos, NM; McCabe, Kevin Peter [Los Alamos, NM

2011-01-18

Fabric-based computing systems and methods are disclosed. A fabric-based computing system can include a polymorphous computing fabric that can be customized on a per application basis and a host processor in communication with said polymorphous computing fabric. The polymorphous computing fabric includes a cellular architecture that can be highly parameterized to enable a customized synthesis of fabric instances for a variety of enhanced application performances thereof. A global memory concept can also be included that provides the host processor random access to all variables and instructions associated with the polymorphous computing fabric.

Polymorphism at the ref(2)P locus in Drosophila melanogaster: preliminary experiments concerning the selection mechanisms involved in its maintenance.

PubMed

Fleuriet, A

1981-02-01

It has been shown previously that a polymorphism for two alleles of the ref(2)P locus is a regular feature of French natural populations of Drosophila melanogaster and that this is maintained in laboratory populations raised in cages. In this paper, an experimental population and egg-collection experiments are reported. Differential survival of the three genotypes would be the main factor leading to the equilibrium frequencies, working only in drastic conditions of larval competition.

Heterogeneous Amyloid β-Sheet Polymorphs Identified on Hydrogen Bond Promoting Surfaces Using 2D SFG Spectroscopy.

PubMed

Ho, Jia-Jung; Ghosh, Ayanjeet; Zhang, Tianqi O; Zanni, Martin T

2018-02-08

Two-dimensional sum-frequency generation spectroscopy (2D SFG) is used to study the structures of the pentapeptide FGAIL on hydrogen bond promoting surfaces. FGAIL is the most amyloidogenic portion of the human islet amyloid polypeptide (hIAPP or amylin). In the presence of a pure gold surface, FGAIL does not form ordered structures. When the gold is coated with a self-assembled monolayer of mercaptobenzoic acid (MBA), 2D SFG spectra reveal features associated with β-sheets. Also observed are cross peaks between the FGAIL peptides and the carboxylic acid groups of the MBA monolayer, indicating that the peptides are in close contact with the surface headgroups. In the second set of samples, FGAIL peptides chemically ligated to the MBA monolayer also exhibited β-sheet features but with a much simpler spectrum. From simulations of the experiments, we conclude that the hydrogen bond promoting surface catalyzes the formation of both parallel and antiparallel β-sheet structures with several different orientations. When ligated, parallel sheets with only a single orientation are the primary structure. Thus, this hydrogen bond promoting surface creates a heterogeneous distribution of polymorph structures, consistent with a concentration effect that allows nucleation of many different amyloid seeding structures. A single well-defined seed favors one polymorph over the others, showing that the concentrating influence of a membrane can be counterbalanced by factors that favor directed fiber growth. These experiments lay the foundation for the measurement and interpretation of β-sheet structures with heterodyne-detected 2D SFG spectroscopy. The results of this model system suggest that a heterogeneous distribution of polymorphs found in nature are an indication of nonselective amyloid aggregation whereas a narrow distribution of polymorph structures is consistent with a specific protein or lipid interaction that directs fiber growth.

TNFalpha and IL-10 gene polymorphisms in inflammatory bowel disease. Association of -1082 AA low producer IL-10 genotype with steroid dependency.

PubMed

Castro-Santos, Patricia; Suarez, Ana; López-Rivas, Laureano; Mozo, Lourdes; Gutierrez, Carmen

2006-05-01

An altered production of cytokines underlies inflammatory bowel disease (IBD) susceptibility. Various polymorphisms at the IL-10 and TNFalpha gene promoters control cytokine production levels. The influence of these polymorphisms on susceptibility to ulcerative colitis (UC) and Crohn's disease (CD) and their association with clinical features were analyzed. Genetic polymorphisms of TNFalpha (-308 G/A) and IL-10 (-1082 G/A, -812 C/T, and -592 C/A) were determined using the LightCycler system with hybridization probes matched with one sequence variant. The study population included 99 UC patients, 146 CD patients, and 343 matched controls. We did not find association between TNFalpha or IL-10 gene polymorphisms and UC or CD susceptibility, though a slight influence of -1082*G allele in UC appearance was observed. In a stratified analysis, a highly significant association between the -1082 AA IL-10 genotype and the steroid dependency was observed in IBD (p < 0.0001), contributing both UC (p = 0.004) and CD (p = 0.003) to this association. In contrast, TNFalpha genotypes did not influence steroid dependency in IBD. Further, the contribution of cytokine genotypes and of clinical features to the appearance of steroid-dependent status (dependent variable) was studied by multivariate analysis. The steroid-dependent phenotype correlated in UC with extensive disease (p = 0.010) and with the low producer -1082 AA IL-10 genotype (p = 0.002) and in CD with penetrating disease (p = 0.010), arthritis (p = 0.011), and the -1082 AA IL-10 genotype (p = 0.006). The main conclusion is that carriage of the -1082 AA IL-10 genotype (low producer) is a relevant risk factor for developing steroid-dependent IBD.

Association of PDCD1 polymorphism to systemic lupus erythematosus and rheumatoid arthritis susceptibility.

PubMed

do Canto, Luisa Matos; Farias, Ticiana Della Justina; Medeiros, Mayara Delagnelo; Coêlho, Cíntia Callegari; Sereia, Aline Fernanda Rodrigues; de Carlos Back, Lia Kubelka Fernandes; de Mello, Filipe Martins; Zimmermann, Adriana Fontes; Pereira, Ivânio Alves; de Souza, Ilíada Rainha

This study aims to analyze the relationship of programmed cell death 1 (PDCD1) gene polymorphism (PD1.3G/A - rs11568821) with features of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) in a Southern Brazilian population. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed in 95 SLE and 87 RA patients and 128 control group individuals from Santa Catarina, Southern Brazil. The Hardy-Weinberg equilibrium (HWE) test, and odds ratio (OR) were analyzed, considering CI 95% and p≤0.05. The PD1.3A allele frequencies were 0.095 (SLE), 0.115 (RA) and 0.078 (controls). The genotypes of the control group were in HWE, while those of SLE and RA patients were not. However, we found no association between PD1.3 polymorphism and the SLE or RA susceptibility, nor clinical or epidemiological data. There was no significant association between PD1.3 polymorphism and SLE or RA susceptibility in this Southern Brazilian population. Copyright © 2015 Elsevier Editora Ltda. All rights reserved.

Association of PDCD1 polymorphism to Systemic Lupus Erythematosus and Rheumatoid Arthritis susceptibility.

PubMed

Canto, Luisa Matos do; Farias, Ticiana Della Justina; Medeiros, Mayara Delagnelo; Coêlho, Cíntia Callegari; Sereia, Aline Fernanda Rodrigues; Back, Lia Kubelka Fernandes de Carlos; Mello, Filipe Martins de; Zimmermann, Adriana Fontes; Pereira, Ivânio Alves; Souza, Ilíada Rainha de

2015-07-17

This study aims to analyze the relationship of programmed cell death 1 (PDCD1) gene polymorphism (PD1.3G/A - rs11568821) with features of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) in a Southern Brazilian population. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) was performed in 95 SLE and 87 RA patients and 128 control group individuals from Santa Catarina, Southern Brazil. The Hardy-Weinberg Equilibrium (HWE) test, and odds ratio (OR) were analyzed, considering CI 95% and p≤0.05. The PD1.3A allele frequencies were 0.095 (SLE), 0.115 (RA) and 0.078 (controls). The genotypes of the control group were in HWE, while those of SLE and RA patients were not. However, we found no association between PD1.3 polymorphism and the SLE or RA susceptibility, nor clinical or epidemiological data. There was no significant association between PD1.3 polymorphism and SLE or RA susceptibility in this Southern Brazilian population. Copyright © 2015 Elsevier Editora Ltda. All rights reserved.

Functional Interaction of the Ankylosing Spondylitis-associated Endoplasmic Reticulum Aminopeptidase 1 Polymorphism and HLA-B27 in Vivo*

PubMed Central

García-Medel, Noel; Sanz-Bravo, Alejandro; Van Nguyen, Dung; Galocha, Begoña; Gómez-Molina, Patricia; Martín-Esteban, Adrián; Alvarez-Navarro, Carlos; de Castro, José A. López

2012-01-01

The association of ERAP1 with ankylosing spondylitis (AS)1 among HLA-B27-positive individuals suggests that ERAP1 polymorphism may affect pathogenesis by altering peptide-dependent features of the HLA-B27 molecule. Comparisons of HLA-B*27:04-bound peptidomes from cells expressing different natural variants of ERAP1 revealed significant differences in the size, length, and amount of many ligands, as well as in HLA-B27 stability. Peptide analyses suggested that the mechanism of ERAP1/HLA-B27 interaction is a variant-dependent alteration in the balance between epitope generation and destruction determined by the susceptibility of N-terminal flanking and P1 residues to trimming. ERAP1 polymorphism associated with AS susceptibility ensured efficient peptide trimming and high HLA-B27 stability. Protective polymorphism resulted in diminished ERAP1 activity, less efficient trimming, suboptimal HLA-B27 peptidomes, and decreased molecular stability. This study demonstrates that natural ERAP1 polymorphism affects HLA-B27 antigen presentation and stability in vivo and proposes a mechanism for the interaction between these molecules in AS. PMID:22918227

A triclinic polymorph of tri­cyclo­hexyl­phosphane sulfide: crystal structure and Hirshfeld surface analysis

PubMed Central

Tan, Yi Jiun; Yeo, Chien Ing; Halcovitch, Nathan R.; Jotani, Mukesh M.

2017-01-01

The title compound, (C6H11)3PS (systematic name: tri­cyclo­hexyl-λ5-phosphane­thione), is a triclinic (P-1, Z′ = 1) polymorph of the previously reported ortho­rhom­bic form (Pnma, Z′ = 1/2) [Kerr et al. (1977 ▸). Can. J. Chem. 55, 3081–3085; Reibenspies et al. (1996 ▸). Z. Kristallogr. 211, 400]. While conformational differences exist between the non-symmetric mol­ecule in the triclinic polymorph, cf. the mirror-symmetric mol­ecule in the ortho­rhom­bic form, these differences are not chemically significant. The major feature of the mol­ecular packing in the triclinic polymorph is the formation of linear chains along the a axis sustained by methine-C—H⋯S(thione) inter­actions. The chains pack with no directional inter­actions between them. The analysis of the Hirshfeld surface for both polymorphs indicates a high degree of similarity, being dominated by H⋯H (ca 90%) and S⋯H/H⋯S contacts. PMID:28435705

The long-term evolution of multilocus traits under frequency-dependent disruptive selection.

PubMed

van Doorn, G Sander; Dieckmann, Ulf

2006-11-01

Frequency-dependent disruptive selection is widely recognized as an important source of genetic variation. Its evolutionary consequences have been extensively studied using phenotypic evolutionary models, based on quantitative genetics, game theory, or adaptive dynamics. However, the genetic assumptions underlying these approaches are highly idealized and, even worse, predict different consequences of frequency-dependent disruptive selection. Population genetic models, by contrast, enable genotypic evolutionary models, but traditionally assume constant fitness values. Only a minority of these models thus addresses frequency-dependent selection, and only a few of these do so in a multilocus context. An inherent limitation of these remaining studies is that they only investigate the short-term maintenance of genetic variation. Consequently, the long-term evolution of multilocus characters under frequency-dependent disruptive selection remains poorly understood. We aim to bridge this gap between phenotypic and genotypic models by studying a multilocus version of Levene's soft-selection model. Individual-based simulations and deterministic approximations based on adaptive dynamics theory provide insights into the underlying evolutionary dynamics. Our analysis uncovers a general pattern of polymorphism formation and collapse, likely to apply to a wide variety of genetic systems: after convergence to a fitness minimum and the subsequent establishment of genetic polymorphism at multiple loci, genetic variation becomes increasingly concentrated on a few loci, until eventually only a single polymorphic locus remains. This evolutionary process combines features observed in quantitative genetics and adaptive dynamics models, and it can be explained as a consequence of changes in the selection regime that are inherent to frequency-dependent disruptive selection. Our findings demonstrate that the potential of frequency-dependent disruptive selection to maintain polygenic variation is considerably smaller than previously expected.

Comparison of macro and micro Raman measurement for reliable quantitative analysis of pharmaceutical polymorphs.

PubMed

Paiva, Eduardo M; da Silva, Vitor H; Poppi, Ronei J; Pereira, Claudete F; Rohwedder, Jarbas J R

2018-05-12

This work reports on the use of micro- and macro-Raman measurements for quantification of mebendazole (MBZ) polymorphs A, B, and C in mixtures. Three Raman spectrophotometers were studied with a laser spot size of 3, 80 and 100 μm and spectral resolutions of 3.9, 9 and 4 cm -1 , respectively. The samples studied were ternary mixtures varying the MBZ polymorphs A and C from 0 to 100% and polymorph B from 0 to 30%. Partial Least Squares (PLS) regression models were developed using the pre-processing spectra (2nd derivative) of the ternary mixtures. The best performance was obtained when the macro-Raman configuration was applied, obtaining RMSEP values of 1.68%, 1.24% and 2.03% w/w for polymorphs A, B, and C, respectively. In general, micro-Raman presented worst results for MBZ polymorphs prediction because the spectra obtained with this configuration does not represent the bulk proportion of mixtures, which have different particle morphologies and sizes. In addition, the influence of these particle features on micro-Raman measurements was also studied. Finally, the results demonstrated that reliable analytical quantifying of MBZ polymorphs can be reached using a laser with wider area illuminated, thus enabling acquisition of more reproductive and representative spectra of the mixtures. Copyright © 2018 Elsevier B.V. All rights reserved.

Inherited Variation in Cytokine, Acute Phase Response, and Calcium Metabolism Genes Affects Susceptibility to Infective Endocarditis

PubMed Central

Rutkovskaya, Natalia V.; Kondyukova, Natalia V.; Odarenko, Yuri N.; Kazachek, Yana V.; Tsepokina, Anna V.; Barbarash, Leonid S.

2017-01-01

Infective endocarditis (IE) is a septic inflammation of the endocardium. Recognition of microbial patterns, cytokine and acute phase responses, hemostasis features, and alterations in plasma lipid and calcium profile all have been reported to affect pathogenesis and clinical course of IE. Having recruited 123 patients with IE and 300 age-, sex-, and ethnicity-matched healthy blood donors, we profiled their genomic DNA for 35 functionally significant polymorphisms within the 22 selected genes involved in the abovementioned pathways, with the further genetic association analysis. We found that the G/A genotype of the rs1143634 polymorphism within the IL1B gene, the G/T genotype of the rs3212227 polymorphism within the IL12B gene, the A/G genotype of the rs1130864 polymorphism within the CRP gene, and the G allele of the rs1801197 polymorphism within the CALCR gene were associated with a decreased risk of IE whereas the T/T genotype of the rs1205 polymorphism within the CRP gene was associated with a higher risk of IE. Furthermore, heterozygous genotypes of the rs1143634 and rs3212227 polymorphisms were associated with the higher plasma levels of IL-1β and IL-12, respectively. Our results indicate that inherited variation in the cytokine, acute phase response, and calcium metabolism pathways may be linked to IE. PMID:28659664

Recipient But Not Donor Adiponectin Polymorphisms Are Associated With Early Posttransplant Hepatic Steatosis in Patients Transplanted for Non-Nonalcoholic Fatty Liver Disease Indications.

PubMed

John, Binu V; Aiken, Taylor; Garber, Ari; Thomas, Dawn; Lopez, Rocio; Patil, Deepa; Konjeti, Venkata Rajesh; Fung, John J; McCollough, Arthur J; Askar, Medhat

2018-06-01

De novo steatosis after liver transplant is common and can occur in up to one-third of patients who are transplanted for liver disease other than for nonalcoholic fatty liver disease. Genetic factors may influence posttransplant steatosis; in a posttransplant setting, donor or recipient genetic factors could also play roles. Genetic polymorphisms in the adiponectin gene have been associated with metabolic syndrome in the pretransplant setting. We aimed to assess the association between donor and recipient adiponectin polymorphisms and early posttransplant hepatic steatosis identified on liver biopsies. Clinical data were collected for 302 liver transplant patients who underwent protocol biopsies for hepatitis C. Of these, 111 patients had available biopsies and donor/recipient DNA. Patients with grade 1 steatosis or greater (35% of patients) were compared with patients without posttransplant steatosis with respect to clinical features and donor/recipient adiponectin polymorphism genotypes. Patients who developed posttransplant steatosis and those without steatosis were similar with respect to individual components of metabolic syndrome. The adiponectin polymorphisms rs1501299 G/G and rs17300539 G/G genotypes in recipients were associated with early posttransplant graft steatosis. We found no associations between graft steatosis and donor adiponectin polymorphisms. Genetic polymorphisms in the adiponectin gene of recipients (but not donors) are associated with early de novo posttransplant hepatic steatosis, independent of components of metabolic syndrome.

Correlation between facial morphology and gene polymorphisms in the Uygur youth population.

PubMed

He, Huiyu; Mi, Xue; Zhang, Jiayu; Zhang, Qin; Yao, Yuan; Zhang, Xu; Xiao, Feng; Zhao, Chunping; Zheng, Shutao

2017-04-25

Human facial morphology varies considerably among individuals and can be influenced by gene polymorphisms. We explored the effects of single nucleotide polymorphisms (SNPs) on facial features in the Uygur youth population of the Kashi area in Xinjiang, China. Saliva samples were collected from 578 volunteers, and 10 SNPs previously associated with variations in facial physiognomy were genotyped. In parallel, 3D images of the subjects' faces were obtained using grating facial scanning technology. After delimitation of 15 salient landmarks, the correlation between SNPs and the distances between facial landmark pairs was assessed. Analysis of variance revealed that ENPP1 rs7754561 polymorphism was significantly associated with RAla-RLipCn and RLipCn-Sbn linear distances (p = 0.044 and p = 0.012, respectively) as well as RLipCn-Stm curve distance (p = 0.042). The GHR rs6180 polymorphism correlated with RLipCn-Stm linear distance (p = 0.04), while the GHR rs6184 polymorphism correlated with RLipCn-ULipP curve distance (p = 0.047). The FGFR1 rs4647905 polymorphism was associated with LLipCn-Nsn linear distance (p = 0.042). These results reveal that ENPP1 and FGFR1 influence lower anterior face height, the distance from the upper lip to the nasal floor, and lip shape. FGFR1 also influences the lower anterior face height, while GHR is associated with the length and width of the lip.

Distribution of putative adhesins in different seropathotypes of Shiga toxin-producing Escherichia coli.

PubMed

Toma, Claudia; Martínez Espinosa, Estela; Song, Tianyan; Miliwebsky, Elizabeth; Chinen, Isabel; Iyoda, Sunao; Iwanaga, Masaaki; Rivas, Marta

2004-11-01

The distribution of eight putative adhesins that are not encoded in the locus for enterocyte effacement (LEE) in 139 Shiga toxin-producing Escherichia coli (STEC) of different serotypes was investigated by PCR. Five of the adhesins (Iha, Efa1, LPF(O157/OI-141), LPF(O157/OI-154), and LPF(O113)) are encoded in regions corresponding to genomic O islands of E. coli EDL933, while the other three adhesins have been reported to be encoded in the STEC megaplasmid of various serotypes (ToxB [O157:H7], Saa [O113:H21], and Sfp [O157:NM]). STEC strains were isolated from humans (n = 54), animals (n = 52), and food (n = 33). They were classified into five seropathotypes (A through E) based on the reported occurrence of STEC serotypes in human disease, in outbreaks, and in the hemolytic-uremic syndrome (M. A. Karmali, M. Mascarenhas, S. Shen, K. Ziebell, S. Johnson, R. Reid-Smith, J. Isaac-Renton, C. Clark, K. Rahn, and J. B. Kaper, J. Clin. Microbiol. 41:4930-4940, 2003). The most prevalent adhesin was that encoded by the iha gene (91%; 127 of 139 strains), which was distributed in all seropathotypes. toxB and efa1 were present mainly in strains of seropathotypes A and B, which were LEE positive. saa was present only in strains of seropathotypes C, D, and E, which were LEE negative. Two fimbrial genes, lpfA(O157/OI-141) and lpfA(O157/OI-154), were strongly associated with seropathotype A. The fimbrial gene lpfA(O113) was present in all seropathotypes except for seropathotype A, while sfpA was not present in any of the strains studied. The distribution of STEC adhesins depends mainly on serotypes and not on the source of isolation. Seropathotype A, which is associated with severe disease and frequently is involved in outbreaks, possesses a unique adhesin profile which is not present in the other seropathotypes. The wide distribution of iha in STEC strains suggested that it could be a candidate for vaccine development.

Integrated Cox's model for predicting survival time of glioblastoma multiforme.

PubMed

Ai, Zhibing; Li, Longti; Fu, Rui; Lu, Jing-Min; He, Jing-Dong; Li, Sen

2017-04-01

Glioblastoma multiforme is the most common primary brain tumor and is highly lethal. This study aims to figure out signatures for predicting the survival time of patients with glioblastoma multiforme. Clinical information, messenger RNA expression, microRNA expression, and single-nucleotide polymorphism array data of patients with glioblastoma multiforme were retrieved from The Cancer Genome Atlas. Patients were separated into two groups by using 1 year as a cutoff, and a logistic regression model was used to figure out any variables that can predict whether the patient was able to live longer than 1 year. Furthermore, Cox's model was used to find out features that were correlated with the survival time. Finally, a Cox model integrated the significant clinical variables, messenger RNA expression, microRNA expression, and single-nucleotide polymorphism was built. Although the classification method failed, signatures of clinical features, messenger RNA expression levels, and microRNA expression levels were figured out by using Cox's model. However, no single-nucleotide polymorphisms related to prognosis were found. The selected clinical features were age at initial diagnosis, Karnofsky score, and race, all of which had been suggested to correlate with survival time. Both of the two significant microRNAs, microRNA-221 and microRNA-222, were targeted to p27 Kip1 protein, which implied the important role of p27 Kip1 on the prognosis of glioblastoma multiforme patients. Our results suggested that survival modeling was more suitable than classification to figure out prognostic biomarkers for patients with glioblastoma multiforme. An integrated model containing clinical features, messenger RNA levels, and microRNA expression levels was built, which has the potential to be used in clinics and thus to improve the survival status of glioblastoma multiforme patients.

Evolutionary Determinants of Morphological Polymorphism in Colonial Animals.

PubMed

Simpson, Carl; Jackson, Jeremy B C; Herrera-Cubilla, Amalia

2017-07-01

Colonial animals commonly exhibit morphologically polymorphic modular units that are phenotypically distinct and specialize in specific functional tasks. But how and why these polymorphic modules have evolved is poorly understood. Across colonial invertebrates, there is wide variation in the degree of polymorphism, from none in colonial ascidians to extreme polymorphism in siphonophores, such as the Portuguese man-of-war. Bryozoa are a phylum of exclusively colonial invertebrates that uniquely exhibit almost the entire range of polymorphism, from monomorphic species to others that rival siphonophores in their polymorphic complexity. Previous approaches to understanding the evolution of polymorphism have been based on analyses of (1) the functional role of polymorphs or (2) presumed evolutionary costs and benefits based on evolutionary theory that postulates polymorphism should be evolutionarily sustainable only in more stable environments because polymorphism commonly leads to the loss of feeding and sexual competence. Here we use bryozoans from opposite shores of the Isthmus of Panama to revisit the environmental hypothesis by comparison of faunas from distinct oceanographic provinces that differ greatly in environmental variability, and we then examine the correlations between the extent of polymorphism in relation to patterns of ecological succession and variation in life histories. We find no support for the environmental hypothesis. Distributions of the incidence of polymorphism in the oceanographically unstable Eastern Pacific are indistinguishable from those in the more stable Caribbean. In contrast, the temporal position of species in a successional sequence is collinear with the degree of polymorphism because species with fewer types of polymorphs are competitively replaced by species with higher numbers of polymorphs on the same substrata. Competitively dominant species also exhibit patterns of growth that increase their competitive ability. The association between degrees of polymorphism and variations in life histories is fundamental to understanding of the macroevolution of polymorphism.

Characterization of polymorphic states in energetic samples of 1,3,5-trinitro-1,3,5-triazine (RDX) fabricated using drop-on-demand inkjet technology.

PubMed

Emmons, Erik D; Farrell, Mikella E; Holthoff, Ellen L; Tripathi, Ashish; Green, Norman; Moon, Raphael P; Guicheteau, Jason A; Christesen, Steven D; Pellegrino, Paul M; Fountain, Augustus W

2012-06-01

The United States Army and the first responder community are evaluating optical detection systems for the trace detection of hazardous energetic materials. Fielded detection systems must be evaluated with the appropriate material concentrations to accurately identify the residue in theater. Trace levels of energetic materials have been observed in mutable polymorphic phases and, therefore, the systems being evaluated must be able to detect and accurately identify variant sample phases observed in spectral data. In this work, we report on the novel application of drop-on-demand technology for the fabrication of standardized trace 1,3,5-trinitro-1,3,5-triazine (RDX) samples. The drop-on-demand sample fabrication technique is compared both visually and spectrally to the more commonly used drop-and-dry technique. As the drop-on-demand technique allows for the fabrication of trace level hazard materials, concerted efforts focused on characterization of the polymorphic phase changes observed with low concentrations of RDX commonly used in drop-on-demand processing. This information is important when evaluating optical detection technologies using samples prepared with a drop-on-demand inkjet system, as the technology may be "trained" to detect the common bulk α phase of the explosive based on its spectral features but fall short in positively detecting a trace quantity of RDX (β-phase). We report the polymorphic shifts observed between α- and β-phases of this energetic material and discuss the conditions leading to the favoring of one phase over the other.

The impact of ACE gene polymorphism on the incidence and phenotype of sarcoidosis in rural and urban settings.

PubMed

Kieszko, Robert; Krawczyk, Paweł; Powrózek, Tomasz; Szudy-Szczyrek, Aneta; Szczyrek, Michał; Homa, Iwona; Daniluk, Jadwiga; Milanowski, Janusz

2016-12-01

Sarcoidosis is a multisystem granulomatous disease of unknown etiology. Current theory on the etiology of this disease involves participation of genetic factors and unknown antigens present in the patients' environment. The aim of the study was to evaluate the prevalence of different polymorphic forms of the ACE gene in healthy individuals and sarcoidosis patients, and to estimate the risk of sarcoidosis in carriers of different ACE genotypes living in rural and urban settings. The study group included 180 patients with pulmonary sarcoidosis. Assessment of the disease was based on clinical features, laboratory and imaging examinations, as well as bronchoscopy with bronchoalveolar lavage (BAL). ACE gene polymorphism was examined in DNA isolated from peripheral blood or BAL fluid (BALF) leukocytes. Incidence of sarcoidosis was not influenced by gender, age or place of residence of the patients. There were no differences in the frequency of particular genotypes in patients with sarcoidosis and in healthy individuals. The risk of disease did not depend on the ACE gene polymorphism. There were no differences in the frequencies of the different genotypes and alleles of the ACE gene in patients with sarcoidosis divided by gender, age and place of residence or by clinical manifestation of sarcoidosis. Our results do not support the previous concept which suggested a higher incidence of sarcoidosis in individuals living in rural areas and in carriers of selected ACE genotypes. It is possible that this is related to the changing environment of rural areas, increasing urbanization and pollution.

Effect of cyclin [corrected] D1 (CCND1) gene polymorphism on tumor formation and behavior in patients with prolactinoma.

PubMed

Cander, Soner; Ertürk, Erdinç; Karkucak, Mutlu; Oz Gül, Ozen; Görükmez, Orhan; Yakut, Tahsin; Unal, Oğuz Kaan; Ersoy, Canan; Tuncel, Ercan; Imamoğlu, Sazi

2012-11-01

The objective of this study was to investigate the effect of G870A gene polymorphism of CCND1 on the formation and behavioral features of prolactinomas. One hundred and thirteen patients with prolactinoma and 108 age and gender matched control were included in the study. The patients were divided into two groups as noninvasive and invasive tumors. CCND1 G870A gene polymorphism was compared in patients/control and invasive/noninvasive groups. A and G allele frequencies were found as 41.7% and 58.3% in the controls, and 61.1% and 38.9% in the patients (p<0.01). Rates of G/G, G/A and A/A genotypes were found as 11.8%, 55.9% and 32.4% in the noninvasive group, and 15.6%, 44.4% and 40.0% in the invasive group, respectively. Differences between patient and control groups were significant but were not between invasive and noninvasive groups in terms of the allele frequencies and genotype distribution. Mean tumor size and serum levels of prolactin at the time of diagnosis and change in these values after the treatment were not found statistically significant in genotype subgroups. CCND1 G870A gene polymorphism may be an important factor in the early stages of the tumor formation. However, it did not affect the features of the tumor. Copyright © 2012 Elsevier B.V. All rights reserved.

[Association of I/D and -786 Polymorphisms of ACE and NOS3 Genes With Features of the Course of Ischemic Heart Disease and Diabetes Mellitus Type 2].

PubMed

Afanasiev, S A; Muslimova, E F; Rebrov, T Y; Sergienko, T N; Repin, A N

2016-09-01

to study relationship of ACE insertion-deletion (I/D) polymorphism and NOS3 T-786C polymorphism with characteristics of the course of ischemic heart disease (IHD) at the background of diabetes mellitus. Were examined 114 patients with IHD, 29.8% of patients had type 2 diabetes mellitus. ACE and NOS3 polymorphisms were determined by allele-specific polymerase chain reaction with primers by "Lytech". Patients with combined pathology belonged to older age group, had increased frequency of obesity and predominance of functional class II chronic heart failure. In this group we detected association of D allele of the ACE gene with higher frequency of dyslipidemia and obesity. Among patients with IHD without diabetes we observed associations of ACE I/D and NOS3 T-786C polymorphisms (close and moderate, respectively) with severity of effort angina. We also found that frequency of dyslipidemia among carriers of II and TT genotypes was lower than among carriers of other genotypes. Presence of type 2 diabetes as background pathology leads to a change of character of association of ACE I/D and NOS3 T-786C polymorphisms with clinical characteristics of patients with IHD.

Association of insertion-deletions polymorphisms with colorectal cancer risk and clinical features

PubMed Central

Marques, Diego; Ferreira-Costa, Layse Raynara; Ferreira-Costa, Lorenna Larissa; Correa, Romualdo da Silva; Borges, Aline Maciel Pinheiro; Ito, Fernanda Ribeiro; Ramos, Carlos Cesar de Oliveira; Bortolin, Raul Hernandes; Luchessi, André Ducati; Ribeiro-dos-Santos, Ândrea; Santos, Sidney; Silbiger, Vivian Nogueira

2017-01-01

AIM To investigate the association between 16 insertion-deletions (INDEL) polymorphisms, colorectal cancer (CRC) risk and clinical features in an admixed population. METHODS One hundred and forty patients with CRC and 140 cancer-free subjects were examined. Genomic DNA was extracted from peripheral blood samples. Polymorphisms and genomic ancestry distribution were assayed by Multiplex-PCR reaction, separated by capillary electrophoresis on the ABI 3130 Genetic Analyzer instrument and analyzed on GeneMapper ID v3.2. Clinicopathological data were obtained by consulting the patients’ clinical charts, intra-operative documentation, and pathology scoring. RESULTS Logistic regression analysis showed that polymorphism variations in IL4 gene was associated with increased CRC risk, while TYMS and UCP2 genes were associated with decreased risk. Reference to anatomical localization of tumor Del allele of NFKB1 and CASP8 were associated with more colon related incidents than rectosigmoid. In relation to the INDEL association with tumor node metastasis (TNM) stage risk, the Ins alleles of ACE, HLAG and TP53 (6 bp INDEL) were associated with higher TNM stage. Furthermore, regarding INDEL association with relapse risk, the Ins alleles of ACE, HLAG, and UGT1A1 were associated with early relapse risk, as well as the Del allele of TYMS. Regarding INDEL association with death risk before 10 years, the Ins allele of SGSM3 and UGT1A1 were associated with death risk. CONCLUSION The INDEL variations in ACE, UCP2, TYMS, IL4, NFKB1, CASP8, TP53, HLAG, UGT1A1, and SGSM3 were associated with CRC risk and clinical features in an admixed population. These data suggest that this cancer panel might be useful as a complementary tool for better clinical management, and more studies need to be conducted to confirm these findings. PMID:29085228

Selected gene polymorphisms effect on skin and hair pigmentation in Polish children at the prepubertal age.

PubMed

Sitek, Aneta; Rosset, Iwona; Żądzińska, Elżbieta; Siewierska-Górska, Anna; Pietrowska, Edyta; Strapagiel, Dominik

2016-11-01

Background : Human pigmentation, similarly as many other biological features, changes in the course of post-natal ontogenesis, while in case of hair, pigmentation changes are more distinctive than in the skin or the iris. It is therefore extremely important to identify the genes, involved in the constitution of human pigmentation features at various stages of ontogenesis. Results of this type of analyses are of high practical significance in forensic study because they enable to create mathematical tools, allowing for prediction of the pigmentation phenotype, based on DNA studies. Aim : The objective of the investigation was finding out whether the genes, associated with pigmentation of adult subjects, differentiated in any way the newly forming pigmentation phenotype in Polish prepubertal children. Material and methods : The study encompassed Polish children, aged 7 to 10 years, without any abnormalities in skin or hair pigmentation. A total of 245 children were examined. Constitutive skin pigmentation according to skin melanin index (SMI) was evaluated, using a dermaspectrometer, and classified into three groups based on the reference values of 25 and 75 percentile for Polish children. Hair colors were evaluated by means of the descriptive Fischer-Saller scale and classified by a division of color variants (as accepted in that scale) (light blonde, blonde, dark blonde, brown and dark brown). In saliva samples, collected from the children, five (5) single nucleotide polymorphisms were identified: SNPs : rs1800401 ( OCA2 -15q11.2-q12), rs35264875 ( TPCN2 -11q13.3), rs16891982 ( SLC45A2 -5p13.2), rs12913832 ( HERC2 -15q13) and rs1805007 ( MC1R -16q24.3). An association between each allele of verified genotype and skin and hair color phenotypes was assessed, using the z-statistic and associated p -value. The quality of classifiers was evaluated by 10-fold stratified cross-validation and was characterized by the area under the receiver operating characteristic curve (AUC). Results : Light skin pigmentation phenotype (SMI<25 percentile) was associated with rs1805007 ( MC1R ) (allelic OR=3.95; 95% Cl:1.20-12.99; p =0.0235), while the dark shade of the skin (SMI>75 percentile) with rs16891982 ( SLC45A2 ) (allelic OR =14.37; 95% Cl: 1.78-115.88; p =0.0123). The probability of dark hair (brown and dark brown) in childhood was increased by T rs12913832 allele ( HERC2 ) (OR=3.63); 95% Cl: 2.25-5.85; p < 0.0001) and dependent on it - rs1800401 ( OCA2 ) (OR=6.31; 95% Cl: 1.74-22.91; p =0.0051). Other SNPs were not significantly associated with skin and hair color but improved prediction of these features. Conclusions : From the five gene polymorphisms analysed in Polish children the strongest correlation with hair color has the rs12913832 ( HERC2 ) and with skin color - rs16891982 ( SLC45A2 ). Therefore, the above-mentioned polymorphisms may be used as components of potential models, used to predict pigmentation features in European origin children in prepubertal age. To improve predictive value of the potential scoring model for hair color, the following should be additionally included: rs1800401 ( OCA2 ), rs35264875 ( TPCN2 ) and rs1805007 ( MC1R ), while for skin color: rs12913832 ( HERC2 ) and rs1805007 ( MC1R ).

Conformational dimorphism in o-nitrobenzoic acid: alternative ways to avoid the O...O clash.

PubMed

Ibragimov, Aziz; Ashurov, Jamshid; Ibragimov, Bakhtiyar; Wang, Ai; Mouhib, Halima; Englert, Ulli

2016-07-01

Polymorphism is a challenging phenomenon and the competitive packing alternatives which are characteristic for polymorphs may be encountered for essentially rigid molecules. A second crystal form of the well known compound o-nitrobenzoic acid, C7H5NO4, an important intermediate in the production of dyes, pharmaceuticals and agrochemicals, is described. Although obtained serendipitously, its intra- and intermolecular features match expectations from database searches and theoretical calculations. O-H...O hydrogen-bonded carboxylic acid dimers represent the building blocks in both polymorphs. For steric reasons and in agreement with a calculated potential energy surface, the carboxylic acid and nitro groups cannot simultaneously be coplanar with the benzene ring but have to tilt. In the well established crystal form, this out-of-plane torsion is more pronounced for the nitro substituent. In contrast, the new polymorph is characterized by a major tilt of the carboxylic acid group. The molecules in both alternative crystal forms achieve a similar compromise with respect to acceptable intramolecular O...O contacts.

DNApod: DNA polymorphism annotation database from next-generation sequence read archives.

PubMed

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information.

DNApod: DNA polymorphism annotation database from next-generation sequence read archives

PubMed Central

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information. PMID:28234924

Mass and charge distributions of amyloid fibers involved in neurodegenerative diseases: mapping heterogeneity and polymorphism† †Electronic supplementary information (ESI) available: Experimental section and supplementary figures. See DOI: 10.1039/c7sc04542e

PubMed Central

Pansieri, Jonathan; Halim, Mohammad A.; Vendrely, Charlotte; Dumoulin, Mireille; Legrand, François; Sallanon, Marcelle Moulin; Chierici, Sabine; Denti, Simona; Dagany, Xavier; Dugourd, Philippe; Marquette, Christel

2018-01-01

Heterogeneity and polymorphism are generic features of amyloid fibers with some important effects on the related disease development. We report here the characterization, by charge detection mass spectrometry, of amyloid fibers made of three polypeptides involved in neurodegenerative diseases: Aβ1–42 peptide, tau and α-synuclein. Beside the mass of individual fibers, this technique enables to characterize the heterogeneity and the polymorphism of the population. In the case of Aβ1–42 peptide and tau protein, several coexisting species could be distinguished and characterized. In the case of α-synuclein, we show how the polymorphism affects the mass and charge distributions. PMID:29732065

Polymorphism at the REF(2)P Locus in DROSOPHILA MELANOGASTER: Preliminary Experiments concerning the Selection Mechanisms Involved in Its Maintenance

PubMed Central

Fleuriet, Annie

1981-01-01

It has been shown previously that a polymorphism for two alleles of the ref(2)P locus is a regular feature of French natural populations of Drosophila melanogaster and that this is maintained in laboratory populations raised in cages. In this paper, an experimental population and egg-collection experiments are reported. Differential survival of the three genotypes would be the main factor leading to the equilibrium frequencies, working only in drastic conditions of larval competition. PMID:6791986

PREMIX: PRivacy-preserving EstiMation of Individual admiXture.

PubMed

Chen, Feng; Dow, Michelle; Ding, Sijie; Lu, Yao; Jiang, Xiaoqian; Tang, Hua; Wang, Shuang

2016-01-01

In this paper we proposed a framework: PRivacy-preserving EstiMation of Individual admiXture (PREMIX) using Intel software guard extensions (SGX). SGX is a suite of software and hardware architectures to enable efficient and secure computation over confidential data. PREMIX enables multiple sites to securely collaborate on estimating individual admixture within a secure enclave inside Intel SGX. We implemented a feature selection module to identify most discriminative Single Nucleotide Polymorphism (SNP) based on informativeness and an Expectation Maximization (EM)-based Maximum Likelihood estimator to identify the individual admixture. Experimental results based on both simulation and 1000 genome data demonstrated the efficiency and accuracy of the proposed framework. PREMIX ensures a high level of security as all operations on sensitive genomic data are conducted within a secure enclave using SGX.

Polymorphic Imprinting of SLC38A4 Gene in Bovine Placenta.

PubMed

Xu, Da; Zhang, Cui; Li, Junliang; Wang, Guannan; Chen, Weina; Li, Dongjie; Li, Shijie

2018-05-21

Imprinted genes are characterized by monoallelic expression that is dependent on parental origin. Comparative analysis of imprinted genes between species is a powerful tool for understanding the biological significance of genomic imprinting. The slc38a4 gene encodes a neutral amino acid transporter and is identified as imprinted in mice. In this study, the imprinting status of SLC38A4 was assessed in bovine adult tissues and placenta using a polymorphism-based approach. Results indicate that SLC38A4 is not imprinted in eight adult bovine tissues including heart, liver, spleen, lung, kidney, muscle, fat, and brain. It was interesting to note that SLC38A4 showed polymorphic status in five heterogeneous placentas, with three exhibiting paternal monoallelic expression and two exhibiting biallelic expression. Monoallelic expression of imprinted genes is generally associated with allele-specific differentially methylation regions (DMRs) of CpG islands (CGIs)-encompassed promoter; therefore, the DNA methylation statuses of three CGIs in the SLC38A4 promoter and exon 1 region were tested in three placentas (two exhibiting paternal monoallelic and one showing biallelic expression of SLC38A4) and their corresponding paternal sperms. Unexpectedly, extreme hypomethylation (< 3%) of the DNA was observed in all the three detected placentas and their corresponding paternal sperms. The absence of DMR in bovine SLC38A4 promoter region implied that DNA methylation of these three CGIs does not directly or indirectly affect the polymorphic imprinting of SLC38A4 in bovine placenta. This suggested other epigenetic features other than DNA methylation are needed in regulating the imprinting of bovine SLC38A4, which is different from that of mouse with respect to a DMR existence at the mouse's slc38a4 promoter region. Although further work is needed, this first characterization of polymorphic imprinting status of SLC38A4 in cattle placenta provides valuable information on investigating the genomic imprinting phenomenon itself.

Association of Ring Finger Protein 213 Gene P.R4810k Polymorphism with Intracranial Major Artery Stenosis/Occlusion.

PubMed

Zhang, Qian; Yu, Lebao; Ge, Peicong; Ma, Yonggang; Zhang, Dong; Zhang, Yan; Wang, Rong; Wang, Shuo; Zhao, Yuanli; Cao, Yong; Liu, Xingju; Deng, Xiaofeng; Zhao, Jizong

2018-06-01

Intracranial major artery stenosis/occlusion (ICASO) is a common cause of ischemic stroke worldwide. A number of studies have assessed the association of the p.R4810K polymorphism in the ring finger protein 213 (RNF213) gene with ICASO, but the results have not been entirely consistent. We conducted a case-control study to estimate the association between the p.R4810K polymorphism and the risk of ICASO in a Chinese population. A total of 124 patients and 230 controls were enrolled. Moreover, a meta-analysis was performed to evaluate this association in the East Asian populations. In our case-control study, the frequencies of the G/A genotype of p.R4810K were significantly higher in the ICASO patients than in the control group (4.03% versus .43%, P = .021, respectively). Moreover, in the meta-analysis, we assessed 7 case-control studies that included 1239 patients and 1377 controls. The pooled odds ratios (ORs) indicated significant association between the p.R4810K polymorphism and the ICASO risk in the dominant model (OR = 9.37, 95% confidence interval: 4.61-19.02, P = .000), the heterozygote comparison (OR = 8.97, 95% CI: 4.41-18.25, P = .000), and the allele comparison (OR = 9.50, 95% confidence interval: 4.71-19.19, P = .000) in the East Asian populations. Subgroup analysis based on ethnicity revealed that the risks in the Japanese and the Korean populations were higher than that in the Chinese population. The p.R4810K polymorphism was associated with an increased risk of ICASO in the East Asian populations. Further studies on the function of the RNF213 protein and the clinical features of this subtype of ICASO are needed. Copyright © 2018 National Stroke Association. Published by Elsevier Inc. All rights reserved.

On the importance of balancing selection in plants

PubMed Central

Delph, Lynda F.; Kelly, John K.

2013-01-01

Summary Balancing selection refers to a variety of selective regimes that maintain advantageous genetic diversity within populations. We review the history of the ideas regarding the types of selection that maintain such polymorphism in flowering plants, notably heterozygote advantage, negative frequency-dependent selection, and spatial heterogeneity. One shared feature of these mechanisms is that whether an allele is beneficial or detrimental is conditional on its frequency in the population. We highlight examples of balancing selection on a variety of discrete traits. These include the well-referenced case of self-incompatibility and recent evidence from species with nuclear-cytoplasmic gynodioecy, both of which exhibit trans-specific polymorphism, a hallmark of balancing selection. We also discuss and give examples of how spatial heterogeneity in particular, which is often thought unlikely to allow protected polymorphism, can maintain genetic variation in plants (which are rooted in place) as a result of microhabitat selection. Lastly, we discuss limitations of the protected polymorphism concept for quantitative traits, where selection can inflate the genetic variance without maintaining specific alleles indefinitely. We conclude that while discrete-morph variation provides the most unambiguous cases of protected polymorphism, they represent only a fraction of the balancing selection at work in plants. PMID:23952298

How social learning adds up to a culture: from birdsong to human public opinion

PubMed Central

Feher, Olga; Fimiarz, Daniel; Conley, Dalton

2017-01-01

ABSTRACT Distributed social learning may occur at many temporal and spatial scales, but it rarely adds up to a stable culture. Cultures vary in stability and diversity (polymorphism), ranging from chaotic or drifting cultures, through cumulative polymorphic cultures, to stable monolithic cultures with high conformity levels. What features can sustain polymorphism, preventing cultures from collapsing into either chaotic or highly conforming states? We investigate this question by integrating studies across two quite separate disciplines: the emergence of song cultures in birds, and the spread of public opinion and social conventions in humans. In songbirds, the learning process has been studied in great detail, while in human studies the structure of social networks has been experimentally manipulated on large scales. In both cases, the manner in which communication signals are compressed and filtered – either during learning or while traveling through the social network – can affect culture polymorphism and stability. We suggest a simple mechanism of a shifting balance between converging and diverging social forces to explain these effects. Understanding social forces that shape cultural evolution might be useful for designing agile communication systems, which are stable and polymorphic enough to promote gradual changes in institutional behavior. PMID:28057835

Fluorescent techniques for discovery and characterization of phosphopantetheinyl transferase inhibitors

PubMed Central

Kosa, Nicolas M.; Foley, Timothy L.; Burkart, Michael D.

2016-01-01

Phosphopantetheinyl transferase (E.C. 2.7.8.-) activates biosynthetic pathways that synthesize both primary and secondary metabolites in bacteria. Inhibitors of these enzymes have the potential to serve as antibiotic compounds that function through a unique mode of action and possess clinical utility. Here we report a direct and continuous assay for this enzyme class based upon monitoring polarization of a fluorescent phosphopantetheine analog as it is transferred from a low molecular weight coenzyme A substrate to higher molecular weight protein acceptor. We demonstrate the utility of this method for the biochemical characterization of phosphopantetheinyl transferase Sfp, a canonical representative from this class. We also establish the portability of this technique to other homologs by adapting the assay to function with the human phosphopantetheinyl transferase, a target for which a microplate detection method does not currently exist. Comparison of these targets provides a basis to predict therapeutic index of inhibitor candidates and offers a valuable characterization of enzyme activity. PMID:24192555

DNA octaplex formation with an I-motif of water-mediated A-quartets: reinterpretation of the crystal structure of d(GCGAAAGC).

PubMed

Sato, Yoshiteru; Mitomi, Kenta; Sunami, Tomoko; Kondo, Jiro; Takénaka, Akio

2006-12-01

The crystal structure of the tetragonal form of d(gcGAAAgc) has been revised and reasonably refined including the disordered residues. The two DNA strands form a base-intercalated duplex, and the four duplexes are assembled according to the crystallographic 222 symmetry to form an octaplex. In the central region, the eight strands are associated by I-motif of double A-quartets. Furthermore, eight hydrated-magnesium cations link the four duplexes to support the octaplex formation. Based on these structural features, a proposal that folding of d(GAAA)n, found in the non-coding region of genomes, into an octaplex can induce slippage during replication to facilitate length polymorphism is presented.

Widespread Impact of HLA Restriction on Immune Control and Escape Pathways of HIV-1

PubMed Central

Listgarten, Jennifer; Pfeifer, Nico; Tan, Vincent; Kadie, Carl; Walker, Bruce D.; Ndung'u, Thumbi; Shapiro, Roger; Frater, John; Brumme, Zabrina L.; Goulder, Philip J. R.; Heckerman, David

2012-01-01

The promiscuous presentation of epitopes by similar HLA class I alleles holds promise for a universal T-cell-based HIV-1 vaccine. However, in some instances, cytotoxic T lymphocytes (CTL) restricted by HLA alleles with similar or identical binding motifs are known to target epitopes at different frequencies, with different functional avidities and with different apparent clinical outcomes. Such differences may be illuminated by the association of similar HLA alleles with distinctive escape pathways. Using a novel computational method featuring phylogenetically corrected odds ratios, we systematically analyzed differential patterns of immune escape across all optimally defined epitopes in Gag, Pol, and Nef in 2,126 HIV-1 clade C-infected adults. Overall, we identified 301 polymorphisms in 90 epitopes associated with HLA alleles belonging to shared supertypes. We detected differential escape in 37 of 38 epitopes restricted by more than one allele, which included 278 instances of differential escape at the polymorphism level. The majority (66 to 97%) of these resulted from the selection of unique HLA-specific polymorphisms rather than differential epitope targeting rates, as confirmed by gamma interferon (IFN-γ) enzyme-linked immunosorbent spot assay (ELISPOT) data. Discordant associations between HLA alleles and viral load were frequently observed between allele pairs that selected for differential escape. Furthermore, the total number of associated polymorphisms strongly correlated with average viral load. These studies confirm that differential escape is a widespread phenomenon and may be the norm when two alleles present the same epitope. Given the clinical correlates of immune escape, such heterogeneity suggests that certain epitopes will lead to discordant outcomes if applied universally in a vaccine. PMID:22379086

[Effect of TNF-alpha gene polymorphism on outcome of thalidomide-based regimens for multiple myeloma].

PubMed

DU, Juan; Yuan, Zhen-Gang; Zhang, Chun-Yang; Fu, Wei-Jun; Jiang, Hua; Chen, Bao-An; Hou, Jian

2009-10-01

To evaluate the effect of polymorphism at the -238 and -308 position of the TNF-alpha promotor region on the clinical outcome of thalidomide (Thal)-based regimens for the treatment of multiple myeloma (MM). The polymorphism at the -238 and -308 position of the TNF-alpha promotor region of 168 MM patients treated with Thal-based regimens were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Genotypes were tested for association with overall response by logistic regression, and survival was evaluated by univariate and multivariate analysis. In TNF-alpha -238 position, 11 (6.5%) patients had GA genotype and 1 (0.6%) AA genotype. In TNF-alpha -308 position, 19 (11.3%) had GA genotype and 1 (0.6%) AA genotype. In univariate analysis, the TNF-alpha -238 GA + AA genotypes were associated with a significantly prolonged progression free survival (PFS) (P = 0.017), and a better overall survival (OS) (P = 0.150). Multivariate COX regression analysis showed that TNF-alpha -238 polymorphic status was an independent prognostic factor for prolonged PFS (P = 0.049). The TNF-alpha -238 polymorphic status is associated with a favorable clinical outcome in MM patients treated with thalidomide-based regimen. The polymorphism status of TNF-alpha gene might be of promise for developing a more informative stratification system for MM.

Polymorphism of a new Mannich base - [-4-methyl-2-((4-(4-nitrophenyl)piperazin-1-yl)methyl)phenol

NASA Astrophysics Data System (ADS)

Ayeni, Ayowole O.; Watkins, Gareth M.; Hosten, Eric C.

2018-05-01

Two polymorphs (forms I and II) of a new Mannich base 4-methyl-2-((4-(4-nitrophenyl)piperazin-1-yl)methyl)phenol have been isolated and characterized by single crystal and powder (experimental and theoretical) X-ray diffraction, thermal analysis (differential scanning calorimetry), Fourier transform infrared spectroscopy. 1H and 13C nuclear magnetic resonance spectroscopy was employed in characterising the new Mannich base. Single crystal X-ray diffraction revealed that the two polymorphs contain different conformers of the Mannich base whose hydrogen bonding schemes and packing arrangements in their respective crystals are different. Thermal analysis led to the conclusion that the two polymorphs are enantiotropically related, with a transition temperature of 138.5 °C.

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

PubMed Central

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

2013-01-01

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

PubMed

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W

2013-04-09

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F 7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. Copyright © 2013 Truco et al.

Evaluation of genetic diversity in Chinese kale (Brassica oleracea L. var. alboglabra Bailey) by using rapid amplified polymorphic DNA and sequence-related amplified polymorphism markers.

PubMed

Zhang, J; Zhang, L G

2014-02-14

Chinese kale is an original Chinese vegetable of the Cruciferae family. To select suitable parents for hybrid breeding, we thoroughly analyzed the genetic diversity of Chinese kale. Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) molecular markers were used to evaluate the genetic diversity across 21 Chinese kale accessions from AVRDC and Guangzhou in China. A total of 104 bands were detected by 11 RAPD primers, of which 66 (63.5%) were polymorphic, and 229 polymorphic bands (68.4%) were observed in 335 bands amplified by 17 SRAP primer combinations. The dendrogram showed the grouping of the 21 accessions into 4 main clusters based on RAPD data, and into 6 clusters based on SRAP and combined data (RAPD + SRAP). The clustering of accessions based on SRAP data was consistent with petal colors. The Mantel test indicated a poor fit for the RAPD and SRAP data (r = 0.16). These results have an important implication for Chinese kale germplasm characterization and improvement.

Inaccurate Color Discrimination by Pollinators Promotes Evolution of Discrete Color Polymorphism in Food-Deceptive Flowers.

PubMed

Kagawa, Kotaro; Takimoto, Gaku

2016-02-01

Many plant species employing a food-deceptive pollination strategy show discrete or continuous floral polymorphism within their populations. Previous studies have suggested that negative frequency-dependent selection (NFDS) caused by the learning behavior of pollinators was responsible for the maintenance of floral polymorphism. However, NFDS alone does not explain why and when discrete or continuous polymorphism evolves. In this study, we use an evolutionary simulation model to propose that inaccurate discrimination of flower colors by pollinators results in evolution of discrete flower color polymorphism. Simulations showed that associative learning based on inaccurate discrimination in pollinators caused disruptive selection of flower colors. The degree of inaccuracy determined the number of discrete flower colors that evolved. Our results suggest that animal behavior based on inaccurate discrimination may be a general cause of disruptive selection that promotes discrete trait polymorphism.

Enhancing the Thermotolerance of Entomopathogenic Isaria fumosorosea SFP-198 Conidial Powder by Controlling the Moisture Content Using Drying and Adjuvants

PubMed Central

Lee, Se Jin; Lee, Hyang Burm

2014-01-01

Entomopathogenic fungi are promising pest-control agents but their industrial applicability is limited by their thermosusceptibility. With an aim to increase the thermotolerance of Isaria fumosorosea SFP-198, moisture absorbents were added to dried conidial powder, and the relationship between its water potential and thermotolerance was investigated. Mycotized rice grains were dried at 10℃, 20℃, 30℃, and 40℃ and the drying effect of each temperature for 24, 48, 96, and 140 hr was determined. Drying for 48 hr at 10℃ and 20℃ reduced the moisture content to < 5% without any significant loss of conidial thermotolerance, but drying at 30℃ and 40℃ reduced both moisture content and conidial thermotolerance. To maintain thermotolerance during storage, moisture absorbents, such as calcium chloride, silica gel, magnesium sulfate, white carbon, and sodium sulfate were individually added to previously dried-conidial powder at 10% (w/w). These mixtures was then stored at room temperature for 30 days and subjected to 50℃ for 2 hr. The white carbon mixture had the highest conidial thermotolerance, followed by silica gel, magnesium sulfate, and then the other absorbents. A significant correlation between the water potential and conidial thermotolerance was observed in all conidia-absorbent mixtures tested in this study (r = -0.945). Conidial thermotolerance in wet conditions was evaluated by adding moisturized white carbon (0~20% H2O) to conidia to mimic wet conditions. Notably, the conidia still maintained their thermotolerance under these conditions. Thus, it is evident that conidial thermotolerance can be maintained by drying mycotized rice grains at low temperatures and adding a moisture absorbent, such as white carbon. PMID:24808736

Correlation of interactions between NOS3 polymorphisms and oxygen therapy with retinopathy of prematurity susceptibility

PubMed Central

Yu, Chunhong; Yi, Jinglin; Yin, Xiaolong; Deng, Yan; Liao, Yujun; Li, Xiaobing

2015-01-01

Aim: This study was aimed to detect the correlation of nitric oxide synthase 3 (NOS3) gene polymorphisms (T-786C and G894T) and retinopathy of prematurity (ROP) susceptibility. Interaction between NOS3 gene polymorphisms and the duration of oxygen therapy was also explored in ROP babies. Methods: Genotypes of NOS3 gene polymorphisms were genotyped by MassArray method. Hardy-Weinberg equilibrium (HWE) was used to calculate the representativeness of the cases and controls. Crossover analysis was utilized to explore the gene environment interactions. Relative risk of ROP was presented by odds ratios (ORs) with corresponding 95% confidence intervals (95% CIs). Results: Among the subject features, oxygen therapy had obvious difference between case and control groups (P<0.05). There existed significant association between-786C allele and ROP susceptibility (P=0.049, OR=0.669, 95% CI=0.447-0.999). Genotypes of T-786C polymorphism and genotypes and alleles of G894T polymorphism did not related to the susceptibility of ROP. Interactions were existed between NOS3 gene polymorphisms and oxygen therapy duration. When the duration of oxygen therapy was less than 17 days, both -786CC genotype and 894GT genotype were correlated with ROP susceptibility (P=0.020, OR=0.115, 95% CI=0.014-0.960; P=0.011, OR=0.294, 95% CI=0.100-0.784). Conclusion: -786C allele might have a protective effect for ROP. Interactions of -786CC and 894GT genotype with oxygen therapy duration (less than 17 days) were both protection factors of ROP. PMID:26823875

DNA repair polymorphisms in B-cell chronic lymphocytic leukemia in sufferers of Chernobyl Nuclear Power Plant accident.

PubMed

Abramenko, Iryna; Bilous, Nadiia; Chumak, Anatolyi; Kostin, Alexey; Martina, Zoya; Dyagil, Iryna

2012-01-01

An association between DNA repair gene polymorphisms, environmental factors, and development of some types of cancer has been suggested by several studies. Chronic lymphocytic leukemia (CLL) is the most common form of leukemia in the clean-up workers of the Chernobyl Nuclear Power Plant (NPP) accident and it has some specific features. Therefore, we have studied the possible differences in DNA repair gene polymorphisms in CLL patients depending on ionizing radiation (IR) exposure history and their clinical characterictics. Arg399Gln XRCC1, Thr241Met XRCC3, and Lys751Gln XPD polymorphisms were studied in 64 CLL patients, exposed to IR due to the Chernobyl NPP accident, 114 IR-non-exposed CLL patients, and 103 sex- and age-matched IR-exposed controls using polymerase chain reaction-restriction fragment-length polymorphism analysis. All investigated polymorphisms were equally distributed between two groups of CLL patients and IR-exposed controls, except that that there was a significant reduction of the common homozygous Lys/Lys XPD genotype among IR-exposed CLL patients (23.7%) compared with IR-exposed controls (45.6%), OR = 0.37; 95% CI = 0.18-0.75; (P = 0.005). The number of IR-non-exposed CLL patients (37.4%) with the Lys/Lys XPD genotype was also decreased compared to IR-exposed controls, although this difference was not significant (P = 0.223). These preliminary data suggest a possible modifying role of Lys751Gln XPD polymorphism for the development of CLL, expecially in radiation-exposed persons.

Polymorphisms of cytochrome b gene in Leishmania parasites and their relation to types of cutaneous leishmaniasis lesions in Pakistan.

PubMed

Myint, Chomar Kaung; Asato, Yutaka; Yamamoto, Yu-ichi; Kato, Hirotomo; Bhutto, Abdul M; Soomro, Farooq R; Memon, Muhamad Z; Matsumoto, Jun; Marco, Jorge D; Oshiro, Minoru; Katakura, Ken; Hashiguchi, Yoshihisa; Uezato, Hiroshi

2008-02-01

The exact species and/or strains of Leishmania parasites involved strongly influence the clinical and epidemiological features of leishmaniasis, and current knowledge of those influences and relationships is inadequate. We report that cytochrome b (cyt b) gene sequencing identified causal Leishmania parasites of 69 cutaneous leishmaniasis cases in Pakistan over a 3-year period. Of 21 cases in highland areas (Quetta city, Balochistan province), 16 (76.2%) were identified as Leishmania (L.) tropica and five (23.8%) as Leishmania (L.) major. Of 48 cases from lowland areas, cities/villages in Indus valley in Sindh and Balochistan provinces, 47 (97.9%) were identified as L. (L.) major and one (2.1%) as L. (L.) tropica. Statistical analysis (Fisher's exact test) revealed a significant difference (P < 0.0001) in the distribution of the two species by altitude; L. (L.) major is predominant in lowland and L. (L.) tropica at highland areas. The present result enriched our earlier finding, based on the first year's cultured parasite data, that only L. (L.) tropica was found in highland areas and only L. (L.) major in lowland areas. Among Leishmania samples analyzed, three types of cyt b polymorphism of L. (L.) major were found, including 45 (86.5%) cases of type I, six (11.5%) of type II and one (2%) of type III. We report for the first time on the presence of polymorphisms in L. (L.) major (types I, II and III) based on species identification using cyt b gene sequencing from clinical samples. Moreover, we found no correlation between clinical presentation (wet-, dry- and/or mixed-types of cutaneous lesions) and causal Leishmania parasites.

Upper lumbar disk herniations.

PubMed

Cedoz, M E; Larbre, J P; Lequin, C; Fischer, G; Llorca, G

1996-06-01

Specific features of upper lumbar disk herniations are reviewed based on data from the literature and from a retrospective study of 24 cases treated surgically between 1982 and 1994 (seven at L1-L2 and 17 at L2-L3). Clinical manifestations are polymorphic, misleading (abdominogenital pain suggestive of a visceral or psychogenic condition, meralgia paresthetica, isolated sciatica; femoral neuralgia is uncommon) and sometimes severe (five cases of cauda equina syndrome in our study group). The diagnostic usefulness of imaging studies (radiography, myelography, computed tomography, magnetic resonance imaging) and results of surgery are discussed. The risk of misdiagnosis and the encouraging results of surgery are emphasized.

Influence of Methylenetetrahydrofolate Reductase C677T Polymorphism on the Risk of Lung Cancer and the Clinical Response to Platinum-Based Chemotherapy for Advanced Non-Small Cell Lung Cancer: An Updated Meta-Analysis

PubMed Central

Zhu, Ning; Gong, Yi; He, Jian; Xia, Jingwen

2013-01-01

Purpose Methylenetetrahydrofolate reductase (MTHFR) has been implicated in lung cancer risk and response to platinum-based chemotherapy in advanced non-small cell lung cancer (NSCLC). However, the results are controversial. We performed meta-analysis to investigate the effect of MTHFR C677T polymorphism on lung cancer risk and response to platinum-based chemotherapy in advanced NSCLC. Materials and Methods The databases of PubMed, Ovid, Wanfang and Chinese Biomedicine were searched for eligible studies. Nineteen studies on MTHFR C677T polymorphism and lung cancer risk and three articles on C677T polymorphism and response to platinum-based chemotherapy in advanced NSCLC, were identified. Results The results indicated that the allelic contrast, homozygous contrast and recessive model of the MTHFR C677T polymorphism were associated significantly with increased lung cancer risk. In the subgroup analysis, the C677T polymorphism was significantly correlated with an increased risk of NSCLC, with the exception of the recessive model. The dominant model and the variant T allele showed a significant association with lung cancer susceptibility of ever smokers. Male TT homozygote carriers had a higher susceptibility, but the allelic contrast and homozygote model had a protective effect in females. No relationship was observed for SCLC in any comparison model. In addition, MTHFR 677TT homozygote carriers had a better response to platinum-based chemotherapy in advanced NSCLC in the recessive model. Conclusion The MTHFR C677T polymorphism might be a genetic marker for lung cancer risk or response to platinum-based chemotherapy in advanced NSCLC. However, our results require further verification. PMID:24142642

Report of Freshwater Mollusks Workshop 19-20 May 1981.

DTIC Science & Technology

1982-05-01

biomes . If discrete groups of individuals may be recognized on the basis of ERM features , and no intergrades occur even in areas of sympatry, it is...the Canadian Interior Basis," Malacologia, Vol 13, pp 1-509. 1979. "Polymorphism in Marine Mollusks and Biome Develop- ment," Smithsonian Contributions...includes data on range, life history, ecological requirements, and identifying features . c. Analyze techniques used to relocate or create habitat for

Genetic association analysis of inositol polyphosphate phosphatase‐like 1 (INPPL1, SHIP2) variants with essential hypertension

PubMed Central

Marçano, Ana Carolina Braga; Burke, Beverley; Gungadoo, Johannie; Wallace, Chris; Kaisaki, Pamela J; Woon, Peng Y; Farrall, Martin; Clayton, David; Brown, Morris; Dominiczak, Anna; Connell, John M; Webster, John; Lathrop, Mark; Caulfield, Mark; Samani, Nilesh; Gauguier, Dominique; Munroe, Patricia B

2007-01-01

Background Inositol polyphosphate phosphatase‐like 1 (INPPL1, SHIP2) is a negative regulator of insulin signalling and has previously been found to be associated with hypertension, obesity and type 2 diabetes in a cohort of families with diabetes in the UK presenting features of metabolic syndrome. In particular, a haplotype of three genetic polymorphisms (rs2276047, rs9886 and an insertion/deletion polymorphism in intron 1) was found to be strongly associated with increased susceptibility to hypertension. Objective and methods To assess if INPPL1 variants play a direct role in the development of essential hypertension, we genotyped the three previously associated INPPL1 polymorphisms in a cohort of 712 families with severe hypertension from the BRIGHT study transmission disequilibrium test cohort. Results We found no evidence of significant association between hypertension and any of the three INPPL1 polymorphisms or haplotypes (p>0.1). Conclusion These results suggest that INPPL1 variants may be involved in mechanisms causing hypertension in metabolic syndrome patients specifically. PMID:17557929

Genetic Polymorphism in Wine Yeasts: Mechanisms and Methods for Its Detection

PubMed Central

Guillamón, José M.; Barrio, Eladio

2017-01-01

The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking. Moreover, the availability of rapid and simple molecular techniques that show genetic polymorphisms at species and strain levels have enabled the study of yeast diversity during wine fermentation. This review will summarize the mechanisms involved in generating genetic polymorphisms in yeasts, the molecular methods used to unveil genetic variation, and the utility of these polymorphisms to differentiate strains, populations, and species in order to infer the evolutionary history and the adaptive evolution of wine yeasts, and to identify their influence on their biotechnological and sensorial properties. PMID:28522998

The BIM Deletion Polymorphism and its Clinical Implication in Patients with EGFR-Mutant Non-Small-Cell Lung Cancer Treated with EGFR Tyrosine Kinase Inhibitors.

PubMed

Lee, Ji Yun; Ku, Bo Mi; Lim, Sung Hee; Lee, Min-Young; Kim, Haesu; Kim, Moonjin; Kim, Sungmin; Jung, Hyun Ae; Sun, Jong-Mu; Ahn, Jin Seok; Park, Keunchil; Ahn, Myung-Ju

2015-06-01

A germline BIM deletion polymorphism has been proposed to predict poor treatment response to certain kinase inhibitors. The purpose of this study was to explore whether the BIM deletion polymorphism predicts treatment efficacy of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) in Korean patients with EGFR-mutant non-small-cell lung cancer (NSCLC). Peripheral blood samples from a total of 205 patients with EGFR-mutant NSCLC who were treated with EGFR TKIs between July 2008 and April 2013 were included. The incidence of BIM deletions in these samples was detected by polymerase chain reaction. We compared the clinical outcomes in patients with and without the polymorphism after treatment with EGFR TKIs (gefitinib or erlotinib). The BIM deletion polymorphism was present in 15.6% (32 of 205) of patients. One patient was homozygous for the deletion, and the remaining 31 had heterozygous deletions. The majority of patients were younger than 65 years (74%), female (68%), never smokers (76%), and had stage IV NSCLC (67%). There were no associations between the BIM deletion polymorphism and clinicopathological features including gender, age, smoking status, histology, stage, and number of metastasis sites. Patients with and without the BIM deletion polymorphism had similar objective response rates (91 vs. 84%, p = 0.585). Progression-free survival and overall survival did not differ significantly between patients with and without the BIM deletion polymorphism (median progression-free survival 12 vs. 11 months, p = 0.160; median overall survival 31 vs. 30 months, p = 0.452). Multivariate analysis identified significantly predictive markers for clinical outcomes of EGFR TKIs including Eastern Cooperative Oncology Group performance status 0-1, adenocarcinoma histology, recurrent disease, and EGFR mutation type. The results were validated in an independent cohort of 69 NSCLC patients. It remains to be determined whether the BIM deletion polymorphism provides intrinsic resistance or decreased sensitivity to EGFR TKIs in EGFR-mutant NSCLC patients.

A second ortho-rhom-bic polymorph of (Z)-3-(9-anthr-yl)-1-(2-thien-yl)prop-2-en-1-one.

PubMed

Chantrapromma, Suchada; Suwunwong, Thitipone; Boonnak, Nawong; Fun, Hoong-Kun

2010-01-09

The title heteroaryl chalcone, C(21)H(14)OS, is a second ortho-rhom-bic polymorph which crystallizes in the space group P2(1)2(1)2(1). The structure was previously reported [Fun et al. (2009 ▶). Acta Cryst. E65, o2168-o2169] in the space group Pna2(1). The bond distances and angles are similar in both structures. In contrast, the overall crystal packing is different from that in the first ortho-rhom-bic Pna2(1) polymorph in which mol-ecules were stacked into columns along the b axis and the thio-phene units of two adjacent columns were stacked in a head to tail fashion. In the present polymorph, mol-ecules are found to dimerize through a weak S⋯S inter-action [3.6513 (7) Å] and these dimers are arranged into sheets parallel to the bc plane. There are no classical hydrogen bonds in the packing which features short C⋯O [3.2832 (2)-3.6251 (9) Å], C⋯S [3.4879 (17)-3.6251 (19) Å] and S⋯O [2.9948 (16) Å] contacts, together with C-H⋯π inter-actions. Similar contacts were found in the other polymorph.

Association of XRCC1 Trp194 allele with risk of breast cancer, and Ki67 protein status in breast tumor tissues

PubMed Central

Jalali, Chiya; Ghaderi, Bayazid; Amini, Sabrieh; Abdi, Mohammad; Roshani, Daem

2016-01-01

Objectives: To evaluate the role of this polymorphism as a risk factor for breast cancer in Kurdish patients and to investigate the possible association between Arg194Trp x-ray repair cross-complementing group 1 (XRCC1) gene polymorphisms with clinical and histopathological outcomes of patients with breast cancer. Methods: A total of 100 breast cancer patients and 200 cancer-free controls in Kurdish population of Kurdistan state admitted to Tohid Hospital, Sanandaj, Kurdistan, Iran between January 2012 and May 2015 were enrolled in this cross-sectional study. Tissue expression of estrogen receptor (ER), progesteron receptor (PR), human epidermal growth factor receptor 2 (Her2/neu), and Ki67 were evaluated by immunohistochemistry (IHC). The Arg194Trp genotypes were determined by polymerase chain reaction- restriction fragment length polymorphism method. Results: Our data showed that the risk for breast cancer increased significantly among the Trp variant of XRCC1. Statistically significant association was found between codon 194 polymorphisms and tissue expression of Ki67. Conclusion: The Trp allele of codon 194 XRCC1 is a potential risk factor for breast cancer in Kurdish ethnicity. Furthermore, effect of this polymorphism on clinical and histological features of breast cancer was significant. PMID:27279507

Association between ghrelin gene variations, body mass index, and waist-to-hip ratio in patients with polycystic ovary syndrome.

PubMed

Xu, L; Shi, Y; Gu, J; Wang, Y; Wang, L; You, L; Qi, X; Ye, Y; Chen, Z

2014-03-01

To investigate the association between 2 single nucleotide polymorphisms (SNP501A/C and 604 G/A) in the promoter of the ghrelin gene and the hormonal and metabolic phenotypes of polycystic ovary syndrome (PCOS) in a Chinese population. 285 patients with PCOS and 260 healthy controls were selected for a prospective, case-control study at Shandong Provincial Hospital, Jinan, China. All subjects underwent genotype analysis of the 2 single nucleotide polymorphisms of the ghrelin gene. Measurements were also taken of blood lipids, glucose, and hormone levels, and calculations of body mass index (BMI) and waist-to-hip ratio (WHR) were performed to detect hormonal and metabolic phenotypes. No significant diff erences in polymorphism genotypes were found between PCOS patients and healthy controls. However, the frequency of the -501 A/C A allele was significantly higher in the PCOS group than in the control group. PCOS -501 A/C A carriers had significantly higher BMI and WHR than PCOS women with the CC genotype. -604 G/A polymorphisms were not associated with clinical or biochemical characteristics of PCOS. The -501 A/C polymorphism of the ghrelin gene is associated with metabolic features of PCOS in a Chinese population. © J. A. Barth Verlag in Georg Thieme Verlag KG Stuttgart · New York.

How social learning adds up to a culture: from birdsong to human public opinion.

PubMed

Tchernichovski, Ofer; Feher, Olga; Fimiarz, Daniel; Conley, Dalton

2017-01-01

Distributed social learning may occur at many temporal and spatial scales, but it rarely adds up to a stable culture. Cultures vary in stability and diversity (polymorphism), ranging from chaotic or drifting cultures, through cumulative polymorphic cultures, to stable monolithic cultures with high conformity levels. What features can sustain polymorphism, preventing cultures from collapsing into either chaotic or highly conforming states? We investigate this question by integrating studies across two quite separate disciplines: the emergence of song cultures in birds, and the spread of public opinion and social conventions in humans. In songbirds, the learning process has been studied in great detail, while in human studies the structure of social networks has been experimentally manipulated on large scales. In both cases, the manner in which communication signals are compressed and filtered - either during learning or while traveling through the social network - can affect culture polymorphism and stability. We suggest a simple mechanism of a shifting balance between converging and diverging social forces to explain these effects. Understanding social forces that shape cultural evolution might be useful for designing agile communication systems, which are stable and polymorphic enough to promote gradual changes in institutional behavior. © 2017. Published by The Company of Biologists Ltd.

Polymorphisms in the oxytocin receptor gene are associated with the development of psychopathy.

PubMed

Dadds, Mark R; Moul, Caroline; Cauchi, Avril; Dobson-Stone, Carol; Hawes, David J; Brennan, John; Urwin, Ruth; Ebstein, Richard E

2014-02-01

The co-occurrence of child conduct problems (CPs) and callous-unemotional (CU) traits confers risk for psychopathy. The oxytocin (OXT) system is a likely candidate for involvement in the development of psychopathy. We tested variations in the OXT receptor gene (OXTR) in CP children and adolescents with varying levels of CU traits. Two samples of Caucasian children, aged 4-16 years, who met DSM criteria for disruptive behavior problems and had no features of autism spectrum disorder, were stratified into low versus high CU traits. Measures were the frequencies of nine candidate OXTR polymorphisms (single nucleotide polymorphisms). In Sample 1, high CU traits were associated with single nucleotide polymorphism rs1042778 in the 3' untranslated region of OXTR and the CGCT haplotype of rs2268490, rs2254298, rs237889, and rs13316193. The association of rs1042778 was replicated in the second rural sample and held across gender and child versus adolescent age groups. We conclude that polymorphic variation of the OXTR characterizes children with high levels of CU traits and CPs. The results are consistent with a hypothesized role of OXT in the developmental antecedents of psychopathy, particularly the differential amygdala activation model of psychopathic traits, and add genetic evidence that high CU traits specify a distinct subgroup within CP children.

High-content tripartite split-GFP cell-based assays to screen for modulators of small GTPase activation

PubMed Central

Gence, Rémi; Bouchenot, Catherine; Lajoie-Mazenc, Isabelle

2018-01-01

ABSTRACT The human Ras superfamily of small GTPases controls essential cellular processes such as gene expression and cell proliferation. As their deregulation is widely associated with human cancer, small GTPases and their regulatory proteins have become increasingly attractive for the development of novel therapeutics. Classical methods to monitor GTPase activation include pulldown assays that limit the analysis of GTP-bound form of proteins from cell lysates. Alternatively, live-cell FRET biosensors may be used to study GTPase activation dynamics in response to stimuli, but these sensors often require further optimization for high-throughput applications. Here, we describe a cell-based approach that is suitable to monitor the modulation of small GTPase activity in a high-content analysis. The assay relies on a genetically encoded tripartite split-GFP (triSFP) system that we integrated in an optimized cellular model to monitor modulation of RhoA and RhoB GTPases. Our results indicate the robust response of the reporter, allowing the interrogation of inhibition and stimulation of Rho activity, and highlight potential applications of this method to discover novel modulators and regulators of small GTPases and related protein-binding domains. PMID:29192060

Feature co-localization landscape of the human genome

PubMed Central

Ng, Siu-Kin; Hu, Taobo; Long, Xi; Chan, Cheuk-Hin; Tsang, Shui-Ying; Xue, Hong

2016-01-01

Although feature co-localizations could serve as useful guide-posts to genome architecture, a comprehensive and quantitative feature co-localization map of the human genome has been lacking. Herein we show that, in contrast to the conventional bipartite division of genomic sequences into genic and inter-genic regions, pairwise co-localizations of forty-two genomic features in the twenty-two autosomes based on 50-kb to 2,000-kb sequence windows indicate a tripartite zonal architecture comprising Genic zones enriched with gene-related features and Alu-elements; Proximal zones enriched with MIR- and L2-elements, transcription-factor-binding-sites (TFBSs), and conserved-indels (CIDs); and Distal zones enriched with L1-elements. Co-localizations between single-nucleotide-polymorphisms (SNPs) and copy-number-variations (CNVs) reveal a fraction of sequence windows displaying steeply enhanced levels of SNPs, CNVs and recombination rates that point to active adaptive evolution in such pathways as immune response, sensory perceptions, and cognition. The strongest positive co-localization observed between TFBSs and CIDs suggests a regulatory role of CIDs in cooperation with TFBSs. The positive co-localizations of cancer somatic CNVs (CNVT) with all Proximal zone and most Genic zone features, in contrast to the distinctly more restricted co-localizations exhibited by germline CNVs (CNVG), reveal disparate distributions of CNVTs and CNVGs indicative of dissimilarity in their underlying mechanisms. PMID:26854351

AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation.

PubMed

Masso, Majid; Vaisman, Iosif I

2014-01-01

The AUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins upon single residue substitutions, developed by combining structure-based features with trained statistical learning models. Three of the predictors evaluate changes to protein stability upon mutation, each complementing a distinct experimental approach. Two additional classifiers are available, one for predicting activity changes due to residue replacements and the other for determining the disease potential of mutations associated with nonsynonymous single nucleotide polymorphisms (nsSNPs) in human proteins. These five command-line driven tools, as well as all the supporting programs, complement those that run our AUTO-MUTE web-based server. Nevertheless, all the codes have been rewritten and substantially altered for the new portable software, and they incorporate several new features based on user feedback. Included among these upgrades is the ability to perform three highly requested tasks: to run "big data" batch jobs; to generate predictions using modified protein data bank (PDB) structures, and unpublished personal models prepared using standard PDB file formatting; and to utilize NMR structure files that contain multiple models.

Are "functionally related polymorphisms" of renin-angiotensin-aldosterone system gene polymorphisms associated with hypertension?

PubMed

Hahntow, Ines N; Mairuhu, Gideon; van Valkengoed, Irene Gm; Koopmans, Richard P; Michel, Martin C

2010-06-02

Genotype-phenotype association studies are typically based upon polymorphisms or haplotypes comprised of multiple polymorphisms within a single gene. It has been proposed that combinations of polymorphisms in distinct genes, which functionally impact the same phenotype, may have stronger phenotype associations than those within a single gene. We have tested this hypothesis using genes encoding components of the renin-angiotensin-aldosterone system and the high blood pressure phenotype. Our analysis is based on 1379 participants of the cross-sectional SUNSET study randomly selected from the population register of Amsterdam. Each subject was genotyped for the angiotensinogen M235T, the angiotensin-converting enzyme insertion/deletion and the angiotensin II type 1 receptor A1166C polymorphism. The phenotype high blood pressure was defined either as a categorical variable comparing hypertension versus normotension as in most previous studies or as a continuous variable using systolic, diastolic and mean blood pressure in a multiple regression analysis with gender, ethnicity, age, body-mass-index and antihypertensive medication as covariates. Genotype-phenotype relationships were explored for each polymorphism in isolation and for double and triple polymorphism combinations. At the single polymorphism level, only the A allele of the angiotensin II type 1 receptor was associated with a high blood pressure phenotype. Using combinations of polymorphisms of two or all three genes did not yield stronger/more consistent associations. We conclude that combinations of physiologically related polymorphisms of multiple genes, at least with regard to the renin-angiotensin-aldosterone system and the hypertensive phenotype, do not necessarily offer additional benefit in analyzing genotype/phenotype associations.

Recent developments in the study of opioid receptors.

PubMed

Cox, Brian M

2013-04-01

It is now about 40 years since Avram Goldstein proposed the use of the stereoselectivity of opioid receptors to identify these receptors in neural membranes. In 2012, the crystal structures of the four members of the opioid receptor family were reported, providing a structural basis for understanding of critical features affecting the actions of opiate drugs. This minireview summarizes these recent developments in our understanding of opiate receptors. Receptor function is also influenced by amino acid substitutions in the protein sequence. Among opioid receptor genes, one polymorphism is much more frequent in human populations than the many others that have been found, but the functional significance of this single nucleotide polymorphism (SNP) has been unclear. Recent studies have shed new light on how this SNP might influence opioid receptor function. In this minireview, the functional significance of the most prevalent genetic polymorphism among the opioid receptor genes is also considered.

Micro-evolution in grasshoppers mediated by polymorphic Robertsonian translocations.

PubMed

Colombo, Pablo C

2013-01-01

This review focuses on grasshoppers that are polymorphic for Robertsonian translocations because in these organisms the clarity of meiotic figures allows the study of both chiasma distribution and the orientation of trivalents and multivalents in metaphase I. Only five species of such grasshoppers were found in the literature, and all of them were from the New World: Oedaleonotus enigma (Scudder) (Orthoptera: Acrididae), Leptysma argentina Bruner, Dichroplus pratensis Bruner, Sinipta dalmani Stål, and Cornops aquaticum Bruner. A general feature of these species (except O. enigma) is that fusion carriers suffer a marked reduction of proximal and interstitial (with respect to the centromere) chiasma frequency; this fact, along with the reduction in the number of linkage groups with the consequent loss of independent segregation, produces a marked decrease of recombination in fusion carriers. This reduction in recombination has led to the conclusion that Robertsonian polymorphic grasshopper species share some properties with inversion polymorphic species of Drosophila, such as the central-marginal pattern (marginal populations are monomorphic, central populations are highly polymorphic). This pattern might be present in D. pratensis, which is certainly the most complex Robertsonian polymorphism system in the present study. However, L. argentina and C. aquaticum do not display this pattern. This issue is open to further research. Since C. aquaticum is soon to be released in South Africa as a biological control, the latitudinal pattern found in South America may repeat there. This experiment's outcome is open and deserves to be followed.

No association of the Arg51Gln and Leu72Met polymorphisms of the ghrelin gene and polycystic ovary syndrome.

PubMed

Wang, Kehua; Wang, Leiguang; Zhao, Yueran; Shi, Yuhua; Wang, Laicheng; Chen, Zi-Jiang

2009-02-01

Ghrelin plays a role in regulating glucose metabolism and energy balance. Polymorphisms in preproghrelin and ghrelin gene could be responsible for obesity, insulin resistance and low ghrelin levels observed in some individuals. The objective of this study was to evaluate the influence of two single-nucleotide polymorphisms (SNPs) of ghrelin gene on the clinical, the hormonal and metabolic features in women with polycystic ovary syndrome (PCOS) in a Chinese population. A large sample of Chinese PCOS (n = 271) women and a control group (n = 296) of healthy women matched for age were studied. Hormone and metabolic profiles were measured and blood samples were collected for genotype and allelic frequency analysis. Non-synonymous SNPs in the coding region (exon 2) of the preproghrelin gene (Arg51Gln (346 G>A) and Leu72Met (408 C>A) were studied using PCR and restriction fragment length polymorphism analysis. The polymorphism Arg51Gln was not found in the cohorts studied. The distribution of Leu72Met was similar in PCOS group and in healthy controls. There was no significant difference in age, BMI, waist-hip-ratio and levels of FSH, LH, estradiol, testosterone and prolactin between PCOS patients with different genotypes, and the level of plasma glucose and insulin was also similar. No association was found between Leu72Met and Arg51Gln polymorphisms in the ghrelin gene and PCOS in Chinese population.

Genetic variation in exon 17 of INSR is associated with insulin resistance and hyperandrogenemia among lean Indian women with polycystic ovary syndrome.

PubMed

Mukherjee, Srabani; Shaikh, Nuzhat; Khavale, Sushma; Shinde, Gayatri; Meherji, Pervin; Shah, Nalini; Maitra, Anurupa

2009-05-01

Polycystic ovary syndrome (PCOS) is a multigenic disorder, and insulin resistance is one of its hallmark features. Polymorphisms in exon 17 of insulin receptor (INSR) gene are reported to be associated with PCOS. We investigated this association in Indian women and its putative relationship with PCOS associated traits, which has not been explored so far. In this case control study, the polymorphisms were investigated by direct sequencing in 180 women with PCOS and 144 age matched controls. Clinical, anthropometric, biochemical, and hormonal parameters were also estimated. The silent C/T polymorphism at His1058 in exon 17 of INSR was found to be present in our study population. The polymorphic genotype (CT+TT) was significantly associated with PCOS in lean women (chi(2)=8.493, df=1, P=0.004). It showed association with higher fasting insulin levels (P=0.02), homeostasis model assessment of insulin resistance (P=0.005), free androgen index (P=0.03), and lower quantitative insulin sensitivity check index (P=0.004) in lean PCOS women. No other novel or known polymorphism was identified in exon 17 in this cohort. The study shows significant association of C/T polymorphism at His1058 of INSR with PCOS in the lean rather than obese Indian women. Its association with indices of insulin resistance and hyperandrogenemia is also seen in the same group. The findings strengthen the concept that pathogenesis of PCOS is different in lean and obese women.

Genomic and genotyping characterization of haplotype-based polymorphic microsatellites in Prunus

USDA-ARS?s Scientific Manuscript database

Efficient utilization of microsatellites in genetic studies remains impeded largely due to the unknown status of their primer reliability, chromosomal location, and allele polymorphism. Discovery and characterization of microsatellite polymorphisms in a taxon will disclose the unknowns and gain new ...

Station Climatic Summaries, Latin America

DTIC Science & Technology

1990-06-01

GERONA, CUBA STATION 4: 782210 ICAO ID: MUNG LOCATION: 21 50’N, 82 47’W ELEVATION (FEET): 75 LST - GMT: -5 PREPARED BY: USAFETAC/ECR, MAR 1987 PERIOD...AUG SFP ocr Nt;V DEC ANN 00=02 [, sTr "• -€ -• : € : . : ’ " ’ 06-08 LST # # # 1 0 2 1 #i 1 1 1 2 1 09-1 [IST # 0 i 2 1 3 2 ! 1 # I 13 12-14 LST I # # 2...A N S STATIO .NAME ASU-N-CIU.N./.P.R.ES.- STR SSIR PARAG STATION MSC: 862180 LATITUDE/LOITITE: S 25 14 I 057 31 FIELD ELEVATION: 292 FEET CALL

Separated Fringe Packet Observations with the CHARA Array. II. Omega Andromeda, HD 178911, and Xi Cephei

DTIC Science & Technology

2014-07-31

Printed in the U.S.A. SEPARATED FRINGE PACKET OBSERVATIONS WITH THE CHARA ARRAY. II. ω ANDROMEDA , HD 178911, AND ξ CEPHEI C. D. Farrington1, T. A...calibration star is not needed, and the SFPs can provide an accurate vector separation. In this paper, we apply the SFP approach to ω Andromeda , HD 178911...and 0.860 ± 0.051M and 39.54 ± 1.85 mas for ω Andromeda , for HD 178911 of 0.802 ± 0.055M and 0.622 ± 0.053M with 28.26 ± 1.70 mas, and masses of

FIFS: A data mining method for informative marker selection in high dimensional population genomic data.

PubMed

Kavakiotis, Ioannis; Samaras, Patroklos; Triantafyllidis, Alexandros; Vlahavas, Ioannis

2017-11-01

Single Nucleotide Polymorphism (SNPs) are, nowadays, becoming the marker of choice for biological analyses involving a wide range of applications with great medical, biological, economic and environmental interest. Classification tasks i.e. the assignment of individuals to groups of origin based on their (multi-locus) genotypes, are performed in many fields such as forensic investigations, discrimination between wild and/or farmed populations and others. Τhese tasks, should be performed with a small number of loci, for computational as well as biological reasons. Thus, feature selection should precede classification tasks, especially for Single Nucleotide Polymorphism (SNP) datasets, where the number of features can amount to hundreds of thousands or millions. In this paper, we present a novel data mining approach, called FIFS - Frequent Item Feature Selection, based on the use of frequent items for selection of the most informative markers from population genomic data. It is a modular method, consisting of two main components. The first one identifies the most frequent and unique genotypes for each sampled population. The second one selects the most appropriate among them, in order to create the informative SNP subsets to be returned. The proposed method (FIFS) was tested on a real dataset, which comprised of a comprehensive coverage of pig breed types present in Britain. This dataset consisted of 446 individuals divided in 14 sub-populations, genotyped at 59,436 SNPs. Our method outperforms the state-of-the-art and baseline methods in every case. More specifically, our method surpassed the assignment accuracy threshold of 95% needing only half the number of SNPs selected by other methods (FIFS: 28 SNPs, Delta: 70 SNPs Pairwise FST: 70 SNPs, In: 100 SNPs.) CONCLUSION: Our approach successfully deals with the problem of informative marker selection in high dimensional genomic datasets. It offers better results compared to existing approaches and can aid biologists in selecting the most informative markers with maximum discrimination power for optimization of cost-effective panels with applications related to e.g. species identification, wildlife management, and forensics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sulcal Polymorphisms of the IFC and ACC Contribute to Inhibitory Control Variability in Children and Adults

PubMed Central

Linzarini, Adriano; Dollfus, Sonia; Etard, Olivier; Orliac, François; Houdé, Olivier

2018-01-01

Abstract Inhibitory control (IC) is a core executive function that enables humans to resist habits, temptations, or distractions. IC efficiency in childhood is a strong predictor of academic and professional success later in life. Based on analysis of the sulcal pattern, a qualitative feature of cortex anatomy determined during fetal life and stable during development, we searched for evidence that interindividual differences in IC partly trace back to prenatal processes. Using anatomical magnetic resonance imaging (MRI), we analyzed the sulcal pattern of two key regions of the IC neural network, the dorsal anterior cingulate cortex (ACC) and the inferior frontal cortex (IFC), which limits the inferior frontal gyrus. We found that the sulcal pattern asymmetry of both the ACC and IFC contributes to IC (Stroop score) in children and adults: participants with asymmetrical ACC or IFC sulcal patterns had better IC efficiency than participants with symmetrical ACC or IFC sulcal patterns. Such additive effects of IFC and ACC sulcal patterns on IC efficiency suggest that distinct early neurodevelopmental mechanisms targeting different brain regions likely contribute to IC efficiency. This view shares some analogies with the “common variant–small effect” model in genetics, which states that frequent genetic polymorphisms have small effects but collectively account for a large portion of the variance. Similarly, each sulcal polymorphism has a small but additive effect: IFC and ACC sulcal patterns, respectively, explained 3% and 14% of the variance of the Stroop interference scores. PMID:29527565

Sulcal Polymorphisms of the IFC and ACC Contribute to Inhibitory Control Variability in Children and Adults.

PubMed

Tissier, Cloélia; Linzarini, Adriano; Allaire-Duquette, Geneviève; Mevel, Katell; Poirel, Nicolas; Dollfus, Sonia; Etard, Olivier; Orliac, François; Peyrin, Carole; Charron, Sylvain; Raznahan, Armin; Houdé, Olivier; Borst, Grégoire; Cachia, Arnaud

2018-01-01

Inhibitory control (IC) is a core executive function that enables humans to resist habits, temptations, or distractions. IC efficiency in childhood is a strong predictor of academic and professional success later in life. Based on analysis of the sulcal pattern, a qualitative feature of cortex anatomy determined during fetal life and stable during development, we searched for evidence that interindividual differences in IC partly trace back to prenatal processes. Using anatomical magnetic resonance imaging (MRI), we analyzed the sulcal pattern of two key regions of the IC neural network, the dorsal anterior cingulate cortex (ACC) and the inferior frontal cortex (IFC), which limits the inferior frontal gyrus. We found that the sulcal pattern asymmetry of both the ACC and IFC contributes to IC (Stroop score) in children and adults: participants with asymmetrical ACC or IFC sulcal patterns had better IC efficiency than participants with symmetrical ACC or IFC sulcal patterns. Such additive effects of IFC and ACC sulcal patterns on IC efficiency suggest that distinct early neurodevelopmental mechanisms targeting different brain regions likely contribute to IC efficiency. This view shares some analogies with the "common variant-small effect" model in genetics, which states that frequent genetic polymorphisms have small effects but collectively account for a large portion of the variance. Similarly, each sulcal polymorphism has a small but additive effect: IFC and ACC sulcal patterns, respectively, explained 3% and 14% of the variance of the Stroop interference scores.

Biomarker sensing using nanostructured metal oxide sensors

NASA Astrophysics Data System (ADS)

Kalyanasundaram, Krithika

Resistive Chemical sensors are those gas sensitive materials, typically semiconducting metal oxides, that change their electrical properties in response to a change in the ambient. The key features of a chemosensor are sensitivity, selectivity, response time and sensor stability. The hypothesis of this work is that, since metal oxides are polymorphic compounds, the crystal structure of the specific polymorph determines the relative gas selectivity of the material; also that the morphology of the sensing element determines the gas sensitivity limit. This work focuses on the synthesis of nanostructured metal oxides for chemosensors used in selective 'biomarker' detection. Biomarkers are chemical compounds, products of human metabolism which act as specific disease markers. The biomarkers studied in this work include NO, isoprene, NH3, ethanol and acetone which can all be found in exhaled human breath and which allow the non-invasive detection of a range of diseases. Sensors based on three different metal oxides-MoO3, WO 3, and TiO2 were fabricated using sol-gel, electrospinning and spray pyrolysis techniques and tested both as single elements and in an array configuration (electronic nose). The effects of the processing method used, grain size and shape and crystal phase of the material produced, and temperature effects of postsynthesis processing and sensing have been evaluated. Structural characterization has been carried out using X-Ray Diffraction, Scanning and High Resolution Transmission Electron Microscopy, while spectroscopic measurements using XPS, Raman and In-situ FTIR provide valuable information about the surface-analyte interactions. This work has shown that the use of monoclinic polymorph of WO3 yields a selective response to NO, while the other phase of the same oxide give a non-selective chemical response. The orthorhombic phase of MoO 3 exhibits specificity to NH3. An explanation for the variable sensing properties is given based on the gas interactions with the given polymorph involving adsorption/reaction processes. Another major finding of this work is that there was orders of magnitude increase in gas sensitivity when high aspect ratio nanowires as opposed to nanoparticles of the same diameter were used.

The Gly972Arg polymorphism in insulin receptor substrate-1 is associated with decreased birth weight in a population-based sample of Brazilian newborns.

PubMed

Bezerra, Rosângela M N; de Castro, Vagner; Sales, Teresa; Passini, Renato; Marba, Sergio T M; Saad, Sara T O; Saad, Mario J A

2002-03-01

We studied the association between the Gly972Arg polymorphism in insulin receptor substrate-1 (IRS-1) and birth weight in a population-based sample of Brazilian newborns. We studied 194 newborn children with adequate gestational age to identify the association between the Gly972Arg polymorphism and birth weight using PCR-restriction fragment length polymorphism analysis. The data showed that the birth weight was lower in the newborns with the Gly972Arg polymorphism in IRS-1 compared with control subjects (3,141 +/- 31.8 vs. 3,373 +/- 80.3 g, P < 0.008). The results also showed that the frequency of this polymorphism was increased in newborns with a birth weight <3,000 g (P=0.041). These results suggest that the genotype Gly972Arg may influence birth weight, reinforcing the hypothesis that genetically determined insulin resistance and/or reduced insulin secretion can result in impaired insulin-mediated growth in the fetus.

Simultaneous imaging of fat crystallinity and crystal polymorphic types by Raman microspectroscopy.

PubMed

Motoyama, Michiyo; Ando, Masahiro; Sasaki, Keisuke; Nakajima, Ikuyo; Chikuni, Koichi; Aikawa, Katsuhiro; Hamaguchi, Hiro-O

2016-04-01

The crystalline states of fats, i.e., the crystallinity and crystal polymorphic types, strongly influence their physical properties in fat-based foods. Imaging of fat crystalline states has thus been a subject of abiding interest, but conventional techniques cannot image crystallinity and polymorphic types all at once. This article demonstrates a new technique using Raman microspectroscopy for simultaneously imaging the crystallinity and polymorphic types of fats. The crystallinity and β' crystal polymorph, which contribute to the hardness of fat-based food products, were quantitatively visualized in a model fat (porcine adipose tissue) by analyzing several key Raman bands. The emergence of the β crystal polymorph, which generally results in food product deterioration, was successfully imaged by analyzing the whole fingerprint regions of Raman spectra using multivariate curve resolution alternating least squares analysis. The results demonstrate that the crystalline states of fats can be nondestructively visualized and analyzed at the molecular level, in situ, without laborious sample pretreatments. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effect of supersaturation on L-glutamic acid polymorphs under droplet-based microchannels

NASA Astrophysics Data System (ADS)

Jiang, Nan; Wang, Zhanzhong; Dang, Leping; Wei, Hongyuan

2016-07-01

Supersaturation is an important controlling factor for crystallization process and polymorphism. Droplet-based microchannels and conventional crystallization were used to investigate polymorphs of L-gluatamic acid in this work. The results illustrate that it is easy to realize the accurate and rapid control of the crystallization temperature in the droplets, which is especially beneficial to heat and mass transfer during crystallization. It is also noted that higher degree of supersaturation favors the nucleation of α crystal form, while lower degree of supersaturation favors the nucleation of β crystal form under droplet-based microchannels for L-gluatamic acid. In addition, there is a different nucleation behavior to be found under droplet-based microchannels both for the β form and α form of L-glutamic acid. This new finding can provide important insight into the development and design of investigation meanings for drug polymorph.

Synthesis, characterization, crystal structure and DFT study of two new polymorphs of a Schiff base (E)-2-((2,6-dichlorobenzylidene)amino)benzonitrile

NASA Astrophysics Data System (ADS)

Benarous, N.; Cherouana, A.; Aubert, Emmanuel; Durand, Pierrick; Dahaoui, S.

2016-02-01

Two new polymorphs of Schiff base, (E)-2-((2,6-dichlorobenzylidene)amino)benzonitrile, were prepared from the condensation of 4-amino-benzonitrile and 2,6-dichlorobenzaldehyde. The two polymorphs crystallize in two different space groups: P21/c for polymorph (I) with volume 1264.23(2) Å3 and Pbca for polymorph (II) with volume 2469.3(2) Å3. The two polymorphs have been characterized by FT-IR and UV-VIS spectroscopy. The crystal structures of both compounds were determined by single X-ray analysis. The difference between the two polymorphs was observed at the angle between the two phenyl rings which is 4.81° for the first one and 82.27° for the second one. Both crystal structures are built on the basis of moderate and weak hydrogen bonds. Theoretical calculations on isolated molecules at the MP2 cc-pVDZ level show that the two polymorphs correspond to two molecular conformations that are within less than 1 kJ mol-1 and DFT periodic calculations indicate that (II) is more stable than (I) by 4.1 kJ mol-1 of formula unit. Additionally, we performed TD-DFT calculation for free ligands to support the experimental data.

QTL mapping of potato chip color and tuber traits within an autotetraploid family

USDA-ARS?s Scientific Manuscript database

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid crop species, and this presents challenges for traditional line development and molecular breeding. Recent availability of a single nucleotide polymorphism (SNP) array with 8303 features and software packages for linkag...

Structure-dependent vibrational dynamics of Mg(BH 4 ) 2 polymorphs probed with neutron vibrational spectroscopy and first-principles calculations

DOE PAGES

Dimitrievska, Mirjana; White, James L.; Zhou, Wei; ...

2016-08-19

We investigated the structure-dependent vibrational properties of different Mg(BH 4) 2 polymorphs (α, β, γ, and δ phases) with a combination of neutron vibrational spectroscopy (NVS) measurements and density functional theory (DFT) calculations, with emphasis placed on the effects of the local structure and orientation of the BH 4 - anions. DFT simulations closely match the neutron vibrational spectra. The main bands in the low-energy region (20–80 meV) are associated with the BH4 - librational modes. The features in the intermediate energy region (80–120 meV) are attributed to overtones and combination bands arising from the lower-energy modes. The features inmore » the high-energy region (120–200 meV) correspond to the BH 4 - symmetric and asymmetric bending vibrations, of which four peaks located at 140, 142, 160, and 172 meV are especially intense. There are noticeable intensity distribution variations in the vibrational bands for different polymorphs. We can explain these differences using the spatial distribution of BH 4 - anions within various structures. An example of the possible identification of products after the hydrogenation of MgB 2, using NVS measurements, is presented. Our results provide fundamental insights of benefit to researchers currently studying these promising hydrogen-storage materials.« less

Genomic signatures of selection at linked sites: unifying the disparity among species

PubMed Central

Cutter, Asher D.; Payseur, Bret A.

2014-01-01

Population genetics theory supplies powerful predictions about how natural selection interacts with genetic linkage to sculpt the genomic landscape of nucleotide polymorphism. Both the spread of beneficial mutations and removal of deleterious mutations act to depress polymorphism levels, especially in low-recombination regions. However, empiricists have documented extreme disparities among species. Here we characterize the dominant features that could drive variation in linked selection among species, including roles for selective sweeps being ‘hard’ or ‘soft’, and concealing by demography and genomic confounds. We advocate targeted studies of close relatives to unify our understanding of how selection and linkage interact to shape genome evolution. PMID:23478346

Sorbitol-Fermenting Enterohemorrhagic Escherichia coli O157:H− Isolates from Czech Patients with Novel Plasmid Composition Not Previously Seen in German Isolates

PubMed Central

Bauwens, Andreas; Marejková, Monika; Middendorf-Bauchart, Barbara; Prager, Rita; Kossow, Annelene; Zhang, Wenlan; Karch, Helge

2017-01-01

ABSTRACT Sorbitol-fermenting (SF) enterohemorrhagic Escherichia coli (EHEC) O157:H− strains, first identified in Germany, have emerged as important pathogens throughout Europe. Besides chromosomally encoded Shiga toxin 2a (the major virulence factor), several putative virulence loci, including the hly, etp, and sfp operons, encoding EHEC hemolysin, type II secretion system proteins, and Sfp fimbriae, respectively, are located on the 121-kb plasmid pSFO157 in German strains. Here we report novel SF EHEC O157:H− strains isolated from patients in the Czech Republic. These strains share the core genomes and chromosomal virulence loci encoding toxins (stx2a and the cdtV-ABC operon) and adhesins (eae-γ, efa1, lpfAO157OI-141, and lpfAO157OI-154) with German strains but differ essentially in their plasmids. In contrast to all previously detected SF EHEC O157:H− strains, the Czech strains carry two plasmids, of 79 kb and 86 kb. The 79-kb plasmid harbors the sfp operon, but neither of the plasmids contains the hly and etp operons. Sequence analyses demonstrated that the 79-kb plasmid (pSFO157 258/98-1) evolved from pSFO157 of German strains by deletion of a 41,534-bp region via homologous recombination, resulting in loss of the hly and etp operons. The 86-kb plasmid (pSFO157 258/98-2) displays 98% sequence similarity to a 92.7-kb plasmid of an extraintestinal pathogenic E. coli bloodstream isolate. Our finding of this novel plasmid composition in SF EHEC O157:H− strains extends the evolutionary history of EHEC O157 plasmids. Moreover, the unique molecular plasmid characteristics permit the identification of such strains, thereby facilitating further investigations of their geographic distribution, clinical significance, and epidemiology. IMPORTANCE Since their first identification in Germany in 1989, sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H− (nonmotile) strains have emerged as important causes of the life-threatening disease hemolytic-uremic syndrome in Europe. They account for 10 to 20% of sporadic cases of this disease and have caused several large outbreaks. The strains isolated throughout Europe share conserved chromosomal and plasmid characteristics. Here we identified novel sorbitol-fermenting enterohemorrhagic E. coli O157:H− patient isolates in the Czech Republic which differ from all such strains reported previously by their unique plasmid characteristics, including plasmid number, composition of plasmid-carried virulence genes, and plasmid origins. Our findings contribute substantially to understanding the evolution of E. coli O157 strains and their plasmids. In practical terms, they enable the identification of strains with these novel plasmid characteristics in patient stool samples and thus the investigation of their roles as human pathogens in other geographic areas. PMID:28970221

Sorbitol-Fermenting Enterohemorrhagic Escherichia coli O157:H- Isolates from Czech Patients with Novel Plasmid Composition Not Previously Seen in German Isolates.

PubMed

Bauwens, Andreas; Marejková, Monika; Middendorf-Bauchart, Barbara; Prager, Rita; Kossow, Annelene; Zhang, Wenlan; Karch, Helge; Mellmann, Alexander; Bielaszewska, Martina

2017-12-01

Sorbitol-fermenting (SF) enterohemorrhagic Escherichia coli (EHEC) O157:H - strains, first identified in Germany, have emerged as important pathogens throughout Europe. Besides chromosomally encoded Shiga toxin 2a (the major virulence factor), several putative virulence loci, including the hly , etp , and sfp operons, encoding EHEC hemolysin, type II secretion system proteins, and Sfp fimbriae, respectively, are located on the 121-kb plasmid pSFO157 in German strains. Here we report novel SF EHEC O157:H - strains isolated from patients in the Czech Republic. These strains share the core genomes and chromosomal virulence loci encoding toxins ( stx 2a and the cdtV -ABC operon) and adhesins ( eae -γ, efa1 , lpfA O157OI-141 , and lpfA O157OI-154 ) with German strains but differ essentially in their plasmids. In contrast to all previously detected SF EHEC O157:H - strains, the Czech strains carry two plasmids, of 79 kb and 86 kb. The 79-kb plasmid harbors the sfp operon, but neither of the plasmids contains the hly and etp operons. Sequence analyses demonstrated that the 79-kb plasmid (pSFO157 258/98-1) evolved from pSFO157 of German strains by deletion of a 41,534-bp region via homologous recombination, resulting in loss of the hly and etp operons. The 86-kb plasmid (pSFO157 258/98-2) displays 98% sequence similarity to a 92.7-kb plasmid of an extraintestinal pathogenic E. coli bloodstream isolate. Our finding of this novel plasmid composition in SF EHEC O157:H - strains extends the evolutionary history of EHEC O157 plasmids. Moreover, the unique molecular plasmid characteristics permit the identification of such strains, thereby facilitating further investigations of their geographic distribution, clinical significance, and epidemiology. IMPORTANCE Since their first identification in Germany in 1989, sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H - (nonmotile) strains have emerged as important causes of the life-threatening disease hemolytic-uremic syndrome in Europe. They account for 10 to 20% of sporadic cases of this disease and have caused several large outbreaks. The strains isolated throughout Europe share conserved chromosomal and plasmid characteristics. Here we identified novel sorbitol-fermenting enterohemorrhagic E. coli O157:H - patient isolates in the Czech Republic which differ from all such strains reported previously by their unique plasmid characteristics, including plasmid number, composition of plasmid-carried virulence genes, and plasmid origins. Our findings contribute substantially to understanding the evolution of E. coli O157 strains and their plasmids. In practical terms, they enable the identification of strains with these novel plasmid characteristics in patient stool samples and thus the investigation of their roles as human pathogens in other geographic areas. Copyright © 2017 American Society for Microbiology.

Dopamine D{sub 3} receptor gene: Organization transcript variants, and polymorphism associated with schizophrenia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Griffon, N.; Pilon, C.; Martres, M.P.

1996-02-16

DNA fragments from a genomic library were used to establish the partial structure of the human dopamine D{sub 3} receptor gene (DRD3). Its coding sequence contains 6 exons and stretches over 40,000 base pairs. The complete DRD3 transcript and three shorter variants, in which the second and/or third exon are deleted, were detected in similar proportions in brains from four controls and three psychiatric patients. The Msp I polymorphism was localized in the fifth intron of the gene, 40,000 base pairs downstream the Bal I polymorphism and a PCR-based method was developed for genotyping this polymorphism. The distributions of themore » Msp I and Bal I genotypes were not independent in 297 individuals ({chi}{sup 2} = 10.5, df = 4, P = 0.03), but only a weak association was found between allele 1 of the Bal I polymorphism and allele 2 of the Msp I polymorphism ({chi}{sup 2} = 3.99, df = 1, P = 0.04). The previously reported association between homozygosity at both alleles of the Bal I polymorphism and schizophrenia was presently maintained in an extended sample, comprising 119 DSM-III-R chronic schizophrenics and 85 controls ({chi}{sup 2}= 5.3, df = 1, P = 0.02) and found more important in males than in females. The presence of the Bal I allele 2 is associated with an early age at onset, particularly in males (df = 35, t value = 2.6, P = 0.014). In the same sample, allelic frequencies, genotype counts, and proportion of homozygotes for the Msp I polymorphism did not differ between schizophrenics and controls ({chi}{sup 2}= 0.06, df = 1, P = 0.80, {chi}{sup 2} = 0.22, df = 1, P = 0.90 and {chi}{sup 2} = 0.16, df = 1, P = 0.69, respectively). The large distance of the Msp I polymorphism from the Bal I polymorphism and its localization in the 3{prime} part of the gene may explain the discrepant results obtained with the two polymorphisms. 36 refs., 2 figs., 4 tabs.« less

Strong Impact of TGF-β1 Gene Polymorphisms on Breast Cancer Risk in Indian Women: A Case-Control and Population-Based Study

PubMed Central

Rajender, Singh; Tamang, Rakesh; Rajkumar, Raja; Saini, Karan Singh; Megu, Kaling; Goel, Madhu Mati; Surekha, Daminani; Rao, Digumarthi Raghunatha; Rao, Lakshmi; Ramachandra, Lingadakai; Kumar, Sandeep; Kumar, Surender; Vishnupriya, Satti; Satyamoorthy, Kapaettu; Negi, Mahendra Pal Singh; Thangaraj, Kumarasamy; Konwar, Rituraj

2013-01-01

Introduction TGF-β1 is a multi-functional cytokine that plays an important role in breast carcinogenesis. Critical role of TGF-β1 signaling in breast cancer progression is well documented. Some TGF-β1 polymorphisms influence its expression; however, their impact on breast cancer risk is not clear. Methods We analyzed 1222 samples in a candidate gene-based genetic association study on two distantly located and ethnically divergent case-control groups of Indian women, followed by a population-based genetic epidemiology study analyzing these polymorphisms in other Indian populations. The c.29C>T (Pro10Leu, rs1982073 or rs1800470) and c.74G>C (Arg25Pro, rs1800471) polymorphisms in the TGF-β1 gene were analyzed using direct DNA sequencing, and peripheral level of TGF-β1 were measured by ELISA. Results c.29C>T substitution increased breast cancer risk, irrespective of ethnicity and menopausal status. On the other hand, c.74G>C substitution reduced breast cancer risk significantly in the north Indian group (p = 0.0005) and only in the pre-menopausal women. The protective effect of c.74G>C polymorphism may be ethnicity-specific, as no association was seen in south Indian group. The polymorphic status of c.29C>T was comparable among Indo-Europeans, Dravidians, and Tibeto-Burmans. Interestingly, we found that Tibeto-Burmans lack polymorphism at c.74G>C locus as true for the Chinese populations. However, the Brahmins of Nepal (Indo-Europeans) showed polymorphism in 2.08% of alleles. Mean TGF-β1 was significantly elevated in patients in comparison to controls (p<0.001). Conclusion c.29C>T and c.74G>C polymorphisms in the TGF-β1 gene significantly affect breast cancer risk, which correlates with elevated TGF-β1 level in the patients. The c.29C>T locus is polymorphic across ethnically different populations, but c.74G>C locus is monomorphic in Tibeto-Burmans and polymorphic in other Indian populations. PMID:24146803

Decision Tree Algorithm-Generated Single-Nucleotide Polymorphism Barcodes of rbcL Genes for 38 Brassicaceae Species Tagging.

PubMed

Yang, Cheng-Hong; Wu, Kuo-Chuan; Chuang, Li-Yeh; Chang, Hsueh-Wei

2018-01-01

DNA barcode sequences are accumulating in large data sets. A barcode is generally a sequence larger than 1000 base pairs and generates a computational burden. Although the DNA barcode was originally envisioned as straightforward species tags, the identification usage of barcode sequences is rarely emphasized currently. Single-nucleotide polymorphism (SNP) association studies provide us an idea that the SNPs may be the ideal target of feature selection to discriminate between different species. We hypothesize that SNP-based barcodes may be more effective than the full length of DNA barcode sequences for species discrimination. To address this issue, we tested a r ibulose diphosphate carboxylase ( rbcL ) S NP b arcoding (RSB) strategy using a decision tree algorithm. After alignment and trimming, 31 SNPs were discovered in the rbcL sequences from 38 Brassicaceae plant species. In the decision tree construction, these SNPs were computed to set up the decision rule to assign the sequences into 2 groups level by level. After algorithm processing, 37 nodes and 31 loci were required for discriminating 38 species. Finally, the sequence tags consisting of 31 rbcL SNP barcodes were identified for discriminating 38 Brassicaceae species based on the decision tree-selected SNP pattern using RSB method. Taken together, this study provides the rational that the SNP aspect of DNA barcode for rbcL gene is a useful and effective sequence for tagging 38 Brassicaceae species.

1513A>C polymorphism in the P2X7 receptor gene in patients with papillary thyroid cancer: correlation with histological variants and clinical parameters.

PubMed

Dardano, Angela; Falzoni, Simonetta; Caraccio, Nadia; Polini, Antonio; Tognini, Sara; Solini, Anna; Berti, Piero; Di Virgilio, Francesco; Monzani, Fabio

2009-02-01

The modulation of the purinergic receptor P2X7 may be implicated in human carcinogenesis. The 1513A>C and 489C>T polymorphisms of P2X7R gene induce loss of function and gain of function, respectively. The aim of the study was to assess the frequency of both 1513A>C and 489C>T polymorphisms in patients with papillary thyroid carcinoma (PTC) and to evaluate the possible association with clinical and histological features. P2X7R analysis was performed in lymphocytes from 121 PTC patients (100 women, 21 men; aged 43.4 +/- 13.6 yr), 100 matched healthy subjects, and 80 patients with nodular goiter. The minor allele frequency for 1513A>C polymorphism in PTC patients with the classical variant was similar to controls (0.21 and 0.20, respectively), whereas it resulted in a significant increase in patients with the follicular variant (0.36; P = 0.01 vs. classical variant, and P = 0.005 vs. controls). In detail, 13.6% of patients with PTC follicular variant were homozygous for the 1513C allele, compared to 2.6% of patients with the classical variant and 2% of controls. Moreover, a positive relationship between 1513A>C polymorphism and either cancer diameter (Rho = 0.22; P = 0.02) or TNM stage (Rho = 0.38; P < 0.001) was found. No significant difference in the genotype frequency of 489C>T polymorphism between PTC patients and healthy controls was observed (0.42 and 0.47, respectively). Our data show, for the first time, a strong association between 1513A>C polymorphism of P2X7R gene and the follicular variant of PTC. Further studies are needed to confirm the possible role of this polymorphism as a novel clinical marker of PTC follicular variant and its usefulness in selecting patients with different clinical outcome.

A second ortho­rhom­bic polymorph of (Z)-3-(9-anthr­yl)-1-(2-thien­yl)prop-2-en-1-one1

PubMed Central

Chantrapromma, Suchada; Suwunwong, Thitipone; Boonnak, Nawong; Fun, Hoong-Kun

2010-01-01

The title heteroaryl chalcone, C21H14OS, is a second ortho­rhom­bic polymorph which crystallizes in the space group P212121. The structure was previously reported [Fun et al. (2009 ▶). Acta Cryst. E65, o2168-o2169] in the space group Pna21. The bond distances and angles are similar in both structures. In contrast, the overall crystal packing is different from that in the first ortho­rhom­bic Pna21 polymorph in which mol­ecules were stacked into columns along the b axis and the thio­phene units of two adjacent columns were stacked in a head to tail fashion. In the present polymorph, mol­ecules are found to dimerize through a weak S⋯S inter­action [3.6513 (7) Å] and these dimers are arranged into sheets parallel to the bc plane. There are no classical hydrogen bonds in the packing which features short C⋯O [3.2832 (2)–3.6251 (9) Å], C⋯S [3.4879 (17)–3.6251 (19) Å] and S⋯O [2.9948 (16) Å] contacts, together with C—H⋯π inter­actions. Similar contacts were found in the other polymorph. PMID:21579743

Maximal oxygen uptake is associated with allele -202 A of insulin-like growth factor binding protein-3 (IGFBP3) promoter polymorphism and (CA)n tandem repeats of insulin-like growth factor IGF1 in Caucasians from Poland.

PubMed

Gronek, Piotr; Holdys, Joanna; Kryściak, Jakub; Wieliński, Dariusz; Słomski, Ryszard

2014-01-01

Physical fitness is a trait determined by multiple genes, and its genetic basis is modified by numerous environmental factors. The present study examines the effects of the (CA)n tandem repeats polymorphism in IGFI gene and SNP Alw21I restriction site -202 A>C polymorphism in IGF1BP3 on VO2max--a physiological index of aerobic capacity of high heritability. The study sample consisted of 239 (154 male and 85 female) students of the University School of Physical Education in Poznań and athletes practicing various sports, including members of the Polish national team. An association was found between -202 A/C polymorphism of IGFBP3 gene with VO2max in men. Higher VO2max values were attained by men with CC genotype, especially male athletes practicing endurance sports and sports featuring energy metabolism of aerobic/anaerobic character. A statistically significant influence of allele 188 and genotype 188/188 of tandem repeats (CA)n polymorphism of IGF1 gene on VO2max was found in women. Also, lower values of maximal oxygen uptake were noted in individuals with allele 186 or genotype 186/186, and higher VO2max values in athletes with allele 194.

[Clustered regularly interspaced short palindromic repeats (CRISPR) site in Bacillus anthracis].

PubMed

Gao, Zhiqi; Wang, Dongshu; Feng, Erling; Wang, Bingxiang; Hui, Yiming; Han, Shaobo; Jiao, Lei; Liu, Xiankai; Wang, Hengliang

2014-11-04

To investigate the polymorphism of clustered regularly interspaced short palindromic repeats (CRISPR) in Bacillu santhracis and the application to molecular typing based on the polymorphism of CRISPR in B. anthracis. We downloaded the whole genome sequence of 6 B. anthracis strains and extracted the CRISPR sites. We designed the primers of CRISPR sites and amplified the CRISPR fragments in 193 B. anthracis strains by PCR and sequenced these fragments. In order to reveal the polymorphism of CRISPR in B. anthracis, wealigned all the extracted sequences and sequenced results by local blasting. At the same time, we also analyzed the CRISPR sites in B. cereus and B. thuringiensis. We did not find any polymorphism of CRISPR in B. anthracis. The molecular typing approach based on CRISPR polymorphism is not suitable for B. anthracis, but it is possible for us to distinguish B. anthracis from B. cereus and B. thuringiensis.

GESPA: classifying nsSNPs to predict disease association.

PubMed

Khurana, Jay K; Reeder, Jay E; Shrimpton, Antony E; Thakar, Juilee

2015-07-25

Non-synonymous single nucleotide polymorphisms (nsSNPs) are the most common DNA sequence variation associated with disease in humans. Thus determining the clinical significance of each nsSNP is of great importance. Potential detrimental nsSNPs may be identified by genetic association studies or by functional analysis in the laboratory, both of which are expensive and time consuming. Existing computational methods lack accuracy and features to facilitate nsSNP classification for clinical use. We developed the GESPA (GEnomic Single nucleotide Polymorphism Analyzer) program to predict the pathogenicity and disease phenotype of nsSNPs. GESPA is a user-friendly software package for classifying disease association of nsSNPs. It allows flexibility in acceptable input formats and predicts the pathogenicity of a given nsSNP by assessing the conservation of amino acids in orthologs and paralogs and supplementing this information with data from medical literature. The development and testing of GESPA was performed using the humsavar, ClinVar and humvar datasets. Additionally, GESPA also predicts the disease phenotype associated with a nsSNP with high accuracy, a feature unavailable in existing software. GESPA's overall accuracy exceeds existing computational methods for predicting nsSNP pathogenicity. The usability of GESPA is enhanced by fast SQL-based cloud storage and retrieval of data. GESPA is a novel bioinformatics tool to determine the pathogenicity and phenotypes of nsSNPs. We anticipate that GESPA will become a useful clinical framework for predicting the disease association of nsSNPs. The program, executable jar file, source code, GPL 3.0 license, user guide, and test data with instructions are available at http://sourceforge.net/projects/gespa.

Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance.

PubMed

Williamson, Scott; Fledel-Alon, Adi; Bustamante, Carlos D

2004-09-01

We develop a Poisson random-field model of polymorphism and divergence that allows arbitrary dominance relations in a diploid context. This model provides a maximum-likelihood framework for estimating both selection and dominance parameters of new mutations using information on the frequency spectrum of sequence polymorphisms. This is the first DNA sequence-based estimator of the dominance parameter. Our model also leads to a likelihood-ratio test for distinguishing nongenic from genic selection; simulations indicate that this test is quite powerful when a large number of segregating sites are available. We also use simulations to explore the bias in selection parameter estimates caused by unacknowledged dominance relations. When inference is based on the frequency spectrum of polymorphisms, genic selection estimates of the selection parameter can be very strongly biased even for minor deviations from the genic selection model. Surprisingly, however, when inference is based on polymorphism and divergence (McDonald-Kreitman) data, genic selection estimates of the selection parameter are nearly unbiased, even for completely dominant or recessive mutations. Further, we find that weak overdominant selection can increase, rather than decrease, the substitution rate relative to levels of polymorphism. This nonintuitive result has major implications for the interpretation of several popular tests of neutrality.

Association between Mitofusin 2 Gene Polymorphisms and Late-Onset Alzheimer's Disease in the Korean Population

PubMed Central

Kim, Young Jong; Park, Jin Kyung; Kang, Won Sub; Kim, Su Kang; Han, Changsu; Na, Hae Ri; Park, Hae Jeong; Kim, Jong Woo; Kim, Young Youl; Park, Moon Ho

2017-01-01

Objective Mitochondrial dysfunction is a prominent and early feature of Alzheimer's disease (AD). The morphologic changes observed in the AD brain could be caused by a failure of mitochondrial fusion mechanisms. The aim of this study was to investigate whether genetic polymorphisms of two genes involved in mitochondrial fusion mechanisms, optic atrophy 1 (OPA1) and mitofusin 2 (MFN2), were associated with AD in the Korean population by analyzing genotypes and allele frequencies. Methods One coding single nucleotide polymorphism (SNP) in the MFN2, rs1042837, and two coding SNPs in the OPA1, rs7624750 and rs9851685, were compared between 165 patients with AD (83 men and 82 women, mean age 72.3±4.41) and 186 healthy control subjects (82 men and 104 women, mean age 76.5±5.98). Results Among these three SNPs, rs1042837 showed statistically significant differences in allele frequency, and genotype frequency in the co-dominant 1 model and in the dominant model. Conclusion These results suggest that the rs1042837 polymorphism in MFN2 may be involved in the pathogenesis of AD. PMID:28096879

Angiotensin-converting enzyme (ACE) gene insertion/deletion polymorphism is not a risk factor for hypertension in SLE nephritis.

PubMed

Negi, Vir S; Devaraju, Panneer; Gulati, Reena

2015-09-01

SLE is a systemic autoimmune disease with high prevalence of hypertension. Around 40-75 % of SLE patients develop nephritis, a major cause of hypertension and mortality. Angiotensin-converting enzyme (ACE) maintains the blood pressure and blood volume homeostasis. An insertion/deletion (I/D) polymorphism in intron 16 of ACE gene was reported to influence the development of hypertension, nephritis, and cardiovascular diseases in different ethnic populations. Despite compelling evidence for the high prevalence of hypertension in individuals with SLE, underlying factors for its development are not well studied. With this background, we analyzed the influence of ACE insertion/deletion polymorphism on susceptibility to SLE, development of nephritis and hypertension, other clinical features and autoantibody phenotype in South Indian SLE patients. Three hundred patients with SLE and 460 age and sex similar ethnicity matched individuals were included as patients and healthy controls, respectively. The ACE gene insertion/deletion polymorphism was analyzed by PCR. Insertion (I) and deletion (D) alleles were observed to be equally distributed among patients (57 and 43 %) and controls (59 and 41 %), respectively. The mutant (D) allele did not confer significant risk for SLE (II vs. ID: p = 0.4, OR 1.15, 95 % CI 0.8-1.6; II vs. DD: p = 0.34, OR 1.22, 95 % CI 0.8-1.85). There was no association of the ACE genotype or the allele with development of lupus nephritis (II vs. ID: p = 0.19, OR 1.41, 95 % CI 0.84-2.36; II vs. DD: p = 0.41, OR 0.74, 95 % CI 0.38-1.41) or hypertension (II vs. ID: p = 0.85, OR 0.9, 95 % CI 0.43-1.8; II vs. DD: p = 0.66, OR 1.217, 95 % CI 0.5-2.8). The presence of mutant allele (D) was not found to influence any clinical features or autoantibody phenotype. The insertion/deletion polymorphism of the ACE gene is not a genetic risk factor for SLE and does not influence development of hypertension or lupus nephritis in South Indian Tamils.

Genetic variants of apolipoprotein A5 T-1131C and apolipoprotein E common polymorphisms and their relationship to features of metabolic syndrome in adult dyslipidemic patients.

PubMed

Novotny, Dalibor; Vaverkova, Helena; Karasek, David; Malina, Pavel

2014-08-01

The aim was to evaluate the relationships of the T-1131C (rs662799) polymorphism variants of apolipoprotein A5 (Apo A5) gene and variants of apolipoprotein E (Apo E) gene common polymorphism (rs429358, rs7412) to signs of metabolic syndrome (MetS). We examined 590 asymptomatic dyslipidemic patients divided into MetS+ (n=146) and MetS- (n=444) groups according to criteria of NCEP ATPIII Panel. We evaluated genotype frequencies and differences in MetS features between individual groups. Logistic regression analysis was used for the evaluation of Apo A5/Apo E variants as possible risk factors for MetS. We found no statistical differences between genotype and allele frequencies for both Apo A5 and Apo E polymorphisms between MetS+ and MetS- groups. In all subjects and MetS- group, we confirmed well-known association of the -1131C Apo A5 minor allele with elevated triglycerides (TG, p<0.001). The Apo E gene E2 and E4 variants were associated with higher levels of TG (p<0.01) in comparison to E33 common variant. However, no statistical differences were observed in MetS+ subjects, regardless of significantly higher TG levels in this group. Apo A5/Apo E variant analysis in all dyslipidemic patients revealed significant increase of TG levels in all subgroups in comparison to common -1131T/E3 variant carriers, the most in -1131C/E4 variant subgroup. Logistic regression analysis models showed no association of Apo A5, Apo E and all Apo A5/Apo E variants with metabolic syndrome, even after adjustment for age and sex. Our study refined the role of Apo A5 and Apo E genetic variants in the group of adult dyslipidemic patients. We demonstrate that except of TG, Apo A5 T-1131C (rs662799) and Apo E (rs429358, rs7412) polymorphisms have no remarkable effect on MetS characteristics. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Association between ADH1C and ALDH2 polymorphisms and alcoholism in a Turkish sample.

PubMed

Ayhan, Yavuz; Gürel, Şeref Can; Karaca, Özgür; Zoto, Teuta; Hayran, Mutlu; Babaoğlu, Melih; Yaşar, Ümit; Bozkurt, Atilla; Dilbaz, Nesrin; Uluğ, Berna Diclenur; Demir, Başaran

2015-04-01

Polymorphisms in the genes encoding alcohol metabolizing enzymes are associated with alcohol dependence. To evaluate the association between the alcohol dehydrogenase 1C (ADH1C) Ile350Val and aldehyde dehydrogenase 2 (ALDH2) Glu504Lys polymorphisms and alcohol dependence in a Turkish sample. 235 individuals (115 alcohol-dependent patients and 120 controls) were genotyped for ADH1C and ALDH2 with PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism). Association between the polymorphisms and family history, daily and maximum amount of alcohol consumed was investigated. The associations between alcohol dependence, severity of consumption and family history and the polymorphisms were analyzed by chi-square or Fisher's exact test where necessary. Relationship between genotypes and dependence related features was evaluated using analysis of variance (ANOVA). The -350Val allele for ADH1C (ADH1C*2) was increased in alcohol-dependent patients (P = 0.05). In individuals with a positive family history, the genotype distribution differed significantly (P = 0.031) and more patients carried the Val allele compared with controls (P = 0.025). Genotyping of 162 participants did not reveal the -504Lys allele in ALDH2. These findings suggest that ADH1C*2 is associated with alcohol dependence in the Turkish population displaying a dominant inheritance model. ADH1C*2 allele may contribute to the variance in heritability of alcohol dependence. The ALDH2 -504Lys/Lys or Glu/Lys genotypes were not present in alcohol-dependent patients, similar to that seen in European populations and in contrast to the findings in the Asian populations.

Polymorph-dependent titanium dioxide nanoparticle dissolution in acidic and alkali digestions

EPA Science Inventory

Multiple polymorphs (anatase, brookite and rutile) of titanium dioxide nanoparticles (TiO2-NPs) with variable structures were quantified in environmental matrices via microwave-based hydrofluoric (HF) and nitric (HNO3) mixed acid digestion and muffle furnace (MF)-based potassium ...

How and how much does RAD-seq bias genetic diversity estimates?

PubMed

Cariou, Marie; Duret, Laurent; Charlat, Sylvain

2016-11-08

RAD-seq is a powerful tool, increasingly used in population genomics. However, earlier studies have raised red flags regarding possible biases associated with this technique. In particular, polymorphism on restriction sites results in preferential sampling of closely related haplotypes, so that RAD data tends to underestimate genetic diversity. Here we (1) clarify the theoretical basis of this bias, highlighting the potential confounding effects of population structure and selection, (2) confront predictions to real data from in silico digestion of full genomes and (3) provide a proof of concept toward an ABC-based correction of the RAD-seq bias. Under a neutral and panmictic model, we confirm the previously established relationship between the true polymorphism and its RAD-based estimation, showing a more pronounced bias when polymorphism is high. Using more elaborate models, we show that selection, resulting in heterogeneous levels of polymorphism along the genome, exacerbates the bias and leads to a more pronounced underestimation. On the contrary, spatial genetic structure tends to reduce the bias. We confront the neutral and panmictic model to "ideal" empirical data (in silico RAD-sequencing) using full genomes from natural populations of the fruit fly Drosophila melanogaster and the fungus Shizophyllum commune, harbouring respectively moderate and high genetic diversity. In D. melanogaster, predictions fit the model, but the small difference between the true and RAD polymorphism makes this comparison insensitive to deviations from the model. In the highly polymorphic fungus, the model captures a large part of the bias but makes inaccurate predictions. Accordingly, ABC corrections based on this model improve the estimations, albeit with some imprecisions. The RAD-seq underestimation of genetic diversity associated with polymorphism in restriction sites becomes more pronounced when polymorphism is high. In practice, this means that in many systems where polymorphism does not exceed 2 %, the bias is of minor importance in the face of other sources of uncertainty, such as heterogeneous bases composition or technical artefacts. The neutral panmictic model provides a practical mean to correct the bias through ABC, albeit with some imprecisions. More elaborate ABC methods might integrate additional parameters, such as population structure and selection, but their opposite effects could hinder accurate corrections.

Chloroplast DNA polymorphism and evolutional relationships between Asian cultivated rice (Oryza sativa) and its wild relatives (O. rufipogon).

PubMed

Li, W J; Zhang, B; Huang, G W; Kang, G P; Liang, M Z; Chen, L B

2012-12-17

We analyzed chloroplast DNA (cpDNA) polymorphism and phylogenic relationships between 6 typical indica rice, 4 japonica rice, 8 javanica rice, and 12 Asian common wild rice (Oryza rufipogon) strains collected from different latitudes in China by comparing polymorphism at 9 highly variable regions. One hundred and forty-four polymorphic bases were detected. The O. rufipogon samples had 117 polymorphic bases, showing rich genetic diversity. One hundred and thirty-one bases at 13 sites were identified with indica/japonica characteristics; they showed differences between the indica and japonica subspecies at these sites. The javanica strains and japonica shared similar bases at these 131 polymorphic sites, suggesting that javanica is closely related to japonica. On the basis of length analyses of the open reading frame (ORF)100 and (ORF)29-tRNA-Cys(GCA) (TrnC(GCA)) fragments, the O. rufipogon strains were classified into indica/japonica subgroups, which was consistent with the results of the phylogenic tree assay based on concatenated datasets. These results indicated that differences in indica and japonica also exist in the cpDNA genome of the O. rufipogon strains. However, these differences demonstrated a certain degree of primitiveness and incompleteness, as an O. rufipogon line may show different indica/ japonica attributes at different sites. Consequently, O. rufipogon cannot be simply classified into the indica/japonica types as O. sativa. Our data support the hypothesis that Asian cultivated rice, O. indica and O. japonica, separately evolved from Asian common wild rice (O. rufipogon) strains, which have different indica-japonica differentiation trends.

A Genetic Linkage Map of Longleaf Pine (Pinus palustris Mill.) Based on Random Amplified Polymorphic DNAs

Treesearch

C.D. Nelson; Thomas L. Kubisiak; M. Stine; W.L. Nance

1994-01-01

Eight megagametophyte DNA samples from a single longleaf pine (Pinus palustris Mill.) tree were used to screen 576 oligonucleotide primers for random amplified polymorphic DNA (RAPD) fragments. Primers amplifying repeatable polymorphic fragments were further characterized within a sample of 72 megagametophytes from the same tree. Fragments...

ReadXplorer—visualization and analysis of mapped sequences

PubMed Central

Hilker, Rolf; Stadermann, Kai Bernd; Doppmeier, Daniel; Kalinowski, Jörn; Stoye, Jens; Straube, Jasmin; Winnebald, Jörn; Goesmann, Alexander

2014-01-01

Motivation: Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data. Results: ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions and displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion–insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets. Availability and implementation: ReadXplorer is available as open-source software at http://www.readxplorer.org along with a detailed manual. Contact: rhilker@mikrobio.med.uni-giessen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24790157

The modulator driven polymorphism of Zr(IV) based metal-organic frameworks

NASA Astrophysics Data System (ADS)

Drache, Franziska; Bon, Volodymyr; Senkovska, Irena; Getzschmann, Jürgen; Kaskel, Stefan

2017-01-01

The reaction of ZrCl4 and 2,5-thiophenedicarboxylic acid (H2tdc) in the presence of trifluoroacetic acid (Htfa) as modulator results in the formation of the new metal-organic framework (MOF) named DUT-126 (DUT = Dresden University of Technology). The nature and concentration of modulators are found to be decisive synthetic parameters affecting the topology of the formed product. DUT-126 (hbr) extends the series of polymorphs differing in topology, namely DUT-67 (reo), DUT-68 (bon) and DUT-69 (bct) to four, where DUT-67 and DUT-68 show the same eight-connected secondary building units as in DUT-126. In DUT-126, linker molecules have a peculiar orientation, resulting in hbr topology, which is described for the first time in this work for MOFs. DUT-126 contains three pore types, including two micropores surrounding mesoporous channels. DUT-126 is stable against hydrolysis and features permanent porosity with a specific surface area of 1297 m2 g-1 and a total pore volume of 0.48 cm3 g-1, calculated from the nitrogen physisorption isotherm measured at 77 K. This article is part of the themed issue 'Coordination polymers and metal-organic frameworks: materials by design'.

The impact of HIV-1 reverse transcriptase polymorphisms on responses to first-line nonnucleoside reverse transcriptase inhibitor-based therapy in HIV-1-infected adults.

PubMed

Mackie, Nicola E; Dunn, David T; Dolling, David; Garvey, Lucy; Harrison, Linda; Fearnhill, Esther; Tilston, Peter; Sabin, Caroline; Geretti, Anna M

2013-09-10

HIV-1 genetic variability may influence antiretroviral therapy (ART) outcomes. The study aim was to determine the impact of polymorphisms in regions known to harbor major nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations (codons 90-108, 135-138, 179-190, 225-348) on virologic responses to first-line NNRTI-based ART. Reverse transcriptase sequences from ART-naive individuals who commenced efavirenz (EFV) or nevirapine (NVP) with at least two nucleos(t)ide reverse transcriptase inhibitors (NRTIs) without major drug resistance mutations were analyzed. The impact of polymorphisms on week 4 viral load decrease and time to virologic failure was measured over a median 97 weeks. Among 4528 patients, most were infected with HIV-1 subtype B (67%) and commenced EFV-based ART (84%). Overall, 2598 (57%) had at least one polymorphism, most frequently at codons 90, 98, 101, 103, 106, 135, 138, 179, and 238. Virologic failure rates were increased in patients with two (n = 597) or more than two (n = 72) polymorphisms [adjusted hazard ratio 1.43; 95% confidence interval (CI) 1.07-1.92; P = 0.016]. Polymorphisms associated with virologic failure occurred at codons 90 (mostly V90I), 98 (mostly A98S), and 103 (mostly K103R), with adjusted hazard ratios of 1.78 (1.15-2.73; P = 0.009), 1.55 (1.16-2.08; P = 0.003), and 1.75 (1.00-3.05: P = 0.049), respectively. Polymorphisms at codon 179, especially V179D/E/T, predicted reduced week 4 responses (P = 0.001) but not virologic failure. The occurrence of multiple polymorphisms, though uncommon, was associated with a small increase in the risk of NNRTI treatment failure; significant effects were seen with polymorphisms at codon 90, 98, and 103. The mechanisms underlying the slower suppression seen with V179D/E/T deserve further investigation.

Serous cutaneous glands in new world hylid frogs: an ultrastructural study on skin poisons confirms phylogenetic relationships between Osteopilus septentrionalis and Phrynohyas venulosa.

PubMed

Delfino, Giovanni; Brizzi, Rossana; Nosi, Daniele; Terreni, Alessandro

2002-08-01

Transmission electron microscope investigations of the serous (poison) skin glands in the New World tree frogs Osteopilus septentrionalis and Phrynohyas venulosa revealed that they produce granules with closely similar substructures, namely, a dense cortex and pale medulla. In both species these features, that contrast the complex, sometimes repeating patterns described in other hylid frogs, derive from similar secretory and maturational processes starting from the Golgi phase of poison biosynthesis. Observations on secretory discharge showed that the two species share common release mechanisms, based on bulk discharge (holocrine) processes. Our data provide novel evidence of the extensive ultrastructural polymorphism of serous skin products in Hylidae and agree with phylogenies that regard this family as polyphyletic in origin. Assuming that ultrastructural features of cutaneous poison biosynthesis and maturation are adequate clues for tracking anuran phylogeny, the present findings also support a close relationship between Osteopilus and Phrynohyas taxa as previously suggested by osteological evidence. Copyright 2002 Wiley-Liss, Inc.

Hydration-induced crystalline transformation of starch polymer under ambient conditions.

PubMed

Qiao, Dongling; Zhang, Binjia; Huang, Jing; Xie, Fengwei; Wang, David K; Jiang, Fatang; Zhao, Siming; Zhu, Jie

2017-10-01

With synchrotron small/wide-angle X-ray scattering (SAXS/WAXS), we revealed that post-harvest hydration at ambient conditions can further alter the starch crystalline structure. The hydration process induced the alignment of starch helices into crystalline lamellae, irrespective of the starch type (A- or B-). In this process, non-crystalline helices were probably packed with water molecules to form new crystal units, thereby enhancing the overall concentration of starch crystallinity. In particular, a fraction of the monoclinic crystal units of the A-type starches encapsulated water molecules during hydration, leading to the outward movement of starch helices. Such movement resulted in the transformation of monoclinic units into hexagonal units, which was associated with the B-type crystallites. Hence, the hydration under ambient conditions could enhance the B-polymorphic features for both A-type and B-type starches. The new knowledge obtained here may guide the design of biopolymer-based liquid crystal materials with controlled lattice regularity and demanded features. Copyright © 2017 Elsevier B.V. All rights reserved.

A laboratory comparison of individual Targis/Vectris posts with standard fiberglass posts.

PubMed

Corsalini, Massimo; Genovese, Katia; Lamberti, Luciano; Pappalettere, Carmine; Carella, Mauro; Carossa, Stefano

2007-01-01

This article presents an in vitro analysis of a specific occlusal loading test on endodontically treated teeth restored with 2 different composite post materials. Individual, customized posts (IFPs) were compared to standard fiberglass posts (SFPs). The selected IFPs (standard cylindric Targis/Vectris posts) were compared to SFPs (Conic 6% Post, Ghimas). The posts were first subjected to a 3-point bending test to compare their flexural elastic properties. They were then used to restore 22 endodontically treated artificial maxillary central incisors and subjected to a specific occlusal loading simulation test. The loading test showed that IFP restorations performed better than SFP restorations. A clinical evaluation of this laboratory observation is suggested.

Monoclinic structures of niobium trisulfide

NASA Astrophysics Data System (ADS)

Bloodgood, Matthew A.; Wei, Pingrong; Aytan, Ece; Bozhilov, Krassimir N.; Balandin, Alexander A.; Salguero, Tina T.

2018-02-01

Two new polymorphs of niobium trisulfide are established by single crystal x-ray diffraction. NbS3-iv crystallizes in the monoclinic space group P21/c with lattice parameters a = 6.7515(5) Å, b = 4.9736(4) Å, c = 18.1315(13) Å, and β = 90.116(2)°. Its structure is based on chains of [NbS6] trigonal prisms containing Nb-Nb pairs with a bond length of 3.0448(8) Å; this pairing causes the chains to corrugate slightly along their axis, a feature also present in triclinic NbS3-i that leads to semiconductor properties. The stacking arrangement of chains is different in these polymorphs, however, with NbS3-i having an ABCDE repeating sequence of chain bilayers and NbS3-iv having an AB repeating sequence. HRTEM studies show the presence of topotactically-oriented intergrown zones and numerous dislocations, which result in mosaic structuring. A second new polymorph, NbS3-v, crystallizes in the monoclinic space group P21/m with lattice parameters a = 4.950(5) Å, b = 3.358(4) Å, c = 9.079(10) Å, β = 97.35(2)°. In contrast to NbS3-iv, NbS3-v maintains fixed a Nb-Nb bond distance of 3.358(4) Å along the chains, and it has an ABCDE repeating sequence of chain bilayers similar to NbS3-i. High resolution scanning transmission electron microscopy (HR-STEM) imaging of an exfoliated NbS3-v nanoribbon shows the continuous [NbS6] chains oriented along the b-axis. These results provide the first firmly established structural data for monoclinic NbS3. In addition, SEM images show the formation of NbS3 rings and cylinders, and a combination of powder x-ray diffraction and Raman spectroscopy provides a way to distinguish between NbS3 polymorphs.

Controlling the Immunological Crosstalk during Conception and Pregnancy: HLA-G in Reproduction

PubMed Central

Lynge Nilsson, Line; Djurisic, Snezana; Hviid, Thomas Vauvert F.

2014-01-01

In several years after its discovery in the placenta, the human leukocyte antigen (HLA) class Ib protein, HLA-G, was not given much attention, nor was it assigned great importance. As time has unraveled, HLA-G has proven to have distinctive functions and an unforeseen and possibly important role in reproduction. HLA-G is characterized mainly by its low polymorphism and restricted tissue distribution in non-pathological conditions. In fact, its expression pattern is primarily limited to extravillous cytotrophoblast cells at the maternal-fetal interface during pregnancy. Due to low polymorphism, almost the same protein is expressed by virtually all individuals. It is these unique features that make HLA-G differ from its highly polymorphic HLA class Ia counterparts, the HLA-A, -B, and -C molecules. Its function, seemingly diverse, is typically receptor-mediated, and involves interactions with a wide range of immune cells. As the expression of HLA-G primarily is limited to gestation, this has given rise to the hypothesis that HLA-G plays an important role in the immunological tolerance of the fetus by the mother. In keeping with this, it might not be surprising that polymorphisms in the HLA-G gene, and levels of HLA-G expression, have been linked to reproductive failure and pre-eclampsia. Based on recent studies, we speculate that HLA-G might be involved in mechanisms in reproductive immunology even before conception because HLA-G can be detected in the genital tract and in the blood of non-pregnant women, and is present in seminal fluid from men. In addition, HLA-G expression has been found in the pre-implanted embryo. Therefore, we propose that a combined contribution from the mother, the father, and the embryo/fetus is likely to be important. Furthermore, this review presents important aspects of HLA-G in relation to reproduction: from genetics to physiological effects, from pregnancy and pregnancy complications to a short discussion on future possible means of preventative measures and therapy. PMID:24860568

The CHRNA3 rs578776 Variant is Associated with an Intrinsic Reward Sensitivity Deficit in Smokers.

PubMed

Robinson, Jason D; Versace, Francesco; Lam, Cho Y; Minnix, Jennifer A; Engelmann, Jeffrey M; Cui, Yong; Karam-Hage, Maher; Shete, Sanjay S; Tomlinson, Gail E; Chen, Tina T-L; Wetter, David W; Green, Charles E; Cinciripini, Paul M

2013-01-01

A compromised brain reward system has been postulated as a key feature of drug dependence. We examined whether several polymorphisms of genes found to regulate nicotinic acetylcholine receptor (nAChR) and dopamine expression were related to an intrinsic reward sensitivity (IRS) deficit we previously identified among a subgroup of smokers using event-related potentials (ERPs). We examined genetic polymorphisms within the CHRNA5-A3-B4 gene cluster (CHRNA3 rs578776, CHRNA5 rs16969968, LOC123688 rs8034191, and CHRNA3 rs1051730), the ANKK1 gene (rs1800497), and the D2 dopamine receptor gene (DRD2 rs1079597, DRD2 rs1799732) from 104 smokers of European ancestry in a smoking cessation trial. Prior to treatment, we recorded ERPs evoked by emotional (both pleasant and unpleasant), neutral, and cigarette-related pictures. Smokers were assigned to two groups (IRS+/IRS-) based on the amplitude of the late positive potential (LPP) component to the pictures, a neural marker of motivational salience. Smokers (n = 42) with blunted brain responses to intrinsically rewarding (pleasant) pictures and enhanced responses to cigarette pictures were assigned to the IRS- group, while smokers (n = 62) with the opposite pattern of LPP responding were assigned to the IRS+ group. Carriers of the protective minor T allele (T/T, C/T) of the CHRNA3 rs578776 were less likely to be members of the IRS- group than those homozygous for the at-risk C allele (C/C). The CHRNA3 rs578776 polymorphism did not differ on questionnaires of nicotine dependence, depressed mood, or trait affective disposition and did not predict abstinence at 6 months after the quit date. These results suggest that polymorphisms of genes influencing nAChR expression are related to an endophenotype of reward sensitivity in smokers.

Lack of association between alpha2-macroglobulin polymorphisms and Alzheimer's disease.

PubMed

Wang, X; Luedecking, E K; Minster, R L; Ganguli, M; DeKosky, S T; Kamboh, M I

2001-02-01

This study was undertaken to investigate the role of two alpha2-macroglobulin (A2M) polymorphisms, an intronic 5-bp deletion and Ile1000Val, in the development of Alzheimer's disease (AD) and to evaluate the interaction between the apolipoprotein E (APOE) and A2M polymorphisms. The A2M polymorphisms were screened by using polymerase-chain-reaction-based assays in 555 white late-onset AD cases and 446 controls. The gentoype distributions of the 5-bp deletion and Ile1000Val polymorphisms were comparable between cases and controls (P = 0.158 and P = 0.148, respectively). Likewise, there was no significant difference in allele frequencies of each polymorphism among cases and controls (P = 0.361 and P = 0.062, respectively). The stratification of data by APOE*4 status also did not yield any significant association. In conclusion, we observed no association between either the intronic deletion polymorphism or the Ile1000Val polymorphism of A2M and AD in our case-control cohort.

The Genealogical Consequences of Fecundity Variance Polymorphism

PubMed Central

Taylor, Jesse E.

2009-01-01

The genealogical consequences of within-generation fecundity variance polymorphism are studied using coalescent processes structured by genetic backgrounds. I show that these processes have three distinctive features. The first is that the coalescent rates within backgrounds are not jointly proportional to the infinitesimal variance, but instead depend only on the frequencies and traits of genotypes containing each allele. Second, the coalescent processes at unlinked loci are correlated with the genealogy at the selected locus; i.e., fecundity variance polymorphism has a genomewide impact on genealogies. Third, in diploid models, there are infinitely many combinations of fecundity distributions that have the same diffusion approximation but distinct coalescent processes; i.e., in this class of models, ancestral processes and allele frequency dynamics are not in one-to-one correspondence. Similar properties are expected to hold in models that allow for heritable variation in other traits that affect the coalescent effective population size, such as sex ratio or fecundity and survival schedules. PMID:19433628

Ab initio random structure searching of organic molecular solids: assessment and validation against experimental data.

PubMed

Zilka, Miri; Dudenko, Dmytro V; Hughes, Colan E; Williams, P Andrew; Sturniolo, Simone; Franks, W Trent; Pickard, Chris J; Yates, Jonathan R; Harris, Kenneth D M; Brown, Steven P

2017-10-04

This paper explores the capability of using the DFT-D ab initio random structure searching (AIRSS) method to generate crystal structures of organic molecular materials, focusing on a system (m-aminobenzoic acid; m-ABA) that is known from experimental studies to exhibit abundant polymorphism. Within the structural constraints selected for the AIRSS calculations (specifically, centrosymmetric structures with Z = 4 for zwitterionic m-ABA molecules), the method is shown to successfully generate the two known polymorphs of m-ABA (form III and form IV) that have these structural features. We highlight various issues that are encountered in comparing crystal structures generated by AIRSS to experimental powder X-ray diffraction (XRD) data and solid-state magic-angle spinning (MAS) NMR data, demonstrating successful fitting for some of the lowest energy structures from the AIRSS calculations against experimental low-temperature powder XRD data for known polymorphs of m-ABA, and showing that comparison of computed and experimental solid-state NMR parameters allows different hydrogen-bonding motifs to be discriminated.

The Tubulin-Based-Polymorphism Method Provides a Simple and Effective Alternative to the Genomic Profiling of Grape

PubMed Central

Mastromauro, Francesco; Gianì, Silvia; Morello, Laura

2016-01-01

The TBP (Tubulin-Based-Polymorphism) method, based on a nuclear ILP (Intron-Length-Polymorphism) molecular marker, has been used for genotyping 37 accessions of the genus Vitis inclusive of different species, rootstocks, wild and cultivated subspecies. A distinct DNA barcode made up by a different number of amplicons, was attributed to each of the different accessions. TBP data were compared with those obtained, with the use of an internationally validated set of six SSR markers. Genetic relationships among the different accessions, dendrogram distributions, correlation values and polymorphic index values (PICs) were definitively comparable when not in favor of TBP. Such an experimental consistency is based upon a genomic organization of the multiple members of the β-tubulin gene family, the targets of TBP-mediated amplification, that is conserved in Vitis as in any other plant species. The TBP amplicons can actually be used as a useful source of sequence polymorphisms for generating primer pairs capable of identifying specific cultivars in a simple assay. An example for the identification of the ‘Sangiovese’ cv. is reported. More generally, these data are discussed in terms of the actual advantages that the introduction of the TBP method in the field of grape characterization and genotyping can provide. PMID:27643687

Polymorphism at the 3'-UTR of the thymidylate synthase gene: A potential predictor for outcomes in Caucasian patients with esophageal adenocarcinoma treated with preoperative chemoradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liao Zhongxing; Liu Hongji; Swisher, Stephen G.

2006-03-01

Purpose: To test the hypothesis that TS3'UTR polymorphisms predict outcomes in 146 Caucasian patients with esophageal adenocarcinoma treated with preoperative 5-fluorouracil-based chemoradiation. Methods and Materials: DNA was extracted from hematoxylin-and-eosin stained histologic slides of normal esophageal or gastric mucosa sections from paraffin blocks of esophagectomy specimens. Genotypes of the TS3'UTR polymorphism were determined by polymerase chain reaction for a 6-bp insertion. The genotype groups (0bp/0bp, 6bp/0bp, and 6bp/6bp) were compared for clinical features and overall survival, recurrence-free-survival, locoregional control (LRC), and distant metastasis control. Multivariable Cox regression analyses were performed to find independent predictors for the stated outcomes. Results: Theremore » was a trend of association between 6bp/6bp genotype and a decreased risk of local regional recurrence (hazards ratio = 0.211, 95% confidence interval = 0.041-1.095, p = 0.06) compared with other genotypes. There was a trend that patients with 6bp/6bp genotype had a higher 3-year probability of LRC compared with patients with the other two genotypes combined (p = 0.07); however, the difference was not statistically significant. Conclusions: The null hypotheses were not rejected in this study, probably owing to small sample size or the single gene examined. Prospective studies with adequate statistical power analyzing a family of genes involved in the 5-fluorouracil metabolism are needed to assess genetic determinants of treatment-related outcomes in esophageal adenocarcinoma.« less

Correlation of MSH3 polymorphisms with response and survival in advanced non-small cell lung cancer patients treated with first-line platinum-based chemotherapy.

PubMed

Xu, X-L; Yao, Y-L; Xu, W-Z; Feng, J-G; Mao, W-M

2015-04-15

Mismatch repair (MMR) genes, as well as the nucleotide excision repair genes, play an important role in removing cisplatin-DNA adducts, and the mutation of MMR genes in tumors can lead to a decreased response to platinum-based therapies. We examined MutS homolog 3 (MSH3), a mismatch repair gene, and whether polymorphisms of MSH3 were associated with response and survival in advanced non-small cell lung cancer (NCSLC) patients who were treated with platinum-based chemotherapy. The peripheral blood of 180 advanced NCSLC patients who were treated with first-line platinum-based chemotherapy was collected to determine the patients' genotypes of MSH3. The three genotypes of the MSH3 polymorphisms rs26279, rs1650697 and rs1105524 were investigated. A statistically significant association was observed between the polymorphism rs26279 (Ala1054Thr) and sensitivity to platinum-based chemotherapy (P = 0.014). A significant correlation was found between rs1105524 and progression-free survival (PFS), with the G/A and A/A genotypes (median survival time: 14.27 months; 95%CI = 9.80-18.75) suffering shorter survival than patients with the G/G genotype (median survival time: 26.37 months; 95%CI = 15.03-37.71) (P = 0.04). Our results showed that single nucleotide polymorphisms in MSH3 had an impact on the chemotherapy response and prognosis of advanced NCSLC patients who were treated with platinum-based chemotherapy.

Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites.

PubMed

Rogan, P K; Schneider, T D

1995-01-01

Predicting the effects of nucleotide substitutions in human splice sites has been based on analysis of consensus sequences. We used a graphic representation of sequence conservation and base frequency, the sequence logo, to demonstrate that a change in a splice acceptor of hMSH2 (a gene associated with familial nonpolyposis colon cancer) probably does not reduce splicing efficiency. This confirms a population genetic study that suggested that this substitution is a genetic polymorphism. The information theory-based sequence logo is quantitative and more sensitive than the corresponding splice acceptor consensus sequence for detection of true mutations. Information analysis may potentially be used to distinguish polymorphisms from mutations in other types of transcriptional, translational, or protein-coding motifs.

Influence of autoantibodies against AT1 receptor and AGTR1 polymorphisms on candesartan-based antihypertensive regimen: results from the study of optimal treatment in hypertensive patients with anti-AT1-receptor autoantibodies trial.

PubMed

Sun, Yanxiang; Liao, Yuhua; Yuan, Yong; Feng, Li; Ma, Shihui; Wei, Feng; Wang, Min; Zhu, Feng

2014-01-01

The autoantibodies against angiotensin AT1 receptors (AT1-AAs) in patients with essential hypertension exhibited an agonistic action like angiotensin II and maintained high blood pressure (BP). Angiotensin II receptor gene (AGTR1) polymorphisms were associated with BP response to RAS inhibition in the hypertensive population. Furthermore, the BP response to AT1 receptor blockers varied significantly among individuals with hypertension. We hypothesized that the polymorphisms of the AGTR1 and AT1-AAs might affect antihypertensive response to AT1 receptor blockers based in patients with primary hypertension. Patients who received a candesartan-based regimen came from the SOT-AT1 study (Study of Optimal Treatment in Hypertensive Patients with Anti-AT1-Receptor Autoantibodies). The established enzyme-labeled immunosorbent assay was used to detect AT1-AAs in the sera of the patients. Genotype 3 single nucleotide polymorphisms in AGTR1 gene was used by DNA sequencing. The correlations among AT1-AAs, AGTR1 gene polymorphisms or haplotypes, and the antihypertensive effect candesartan-based were analyzed using SPSS. The percentage of systolic BP reduction that was candesartan-based was greater in AT1-AA positive groups than in AT1-AA negative ones (21 ± 8 vs. 18 ± 9; P = .001). Meanwhile, systolic BP reduction that was candesartan-based was more significant in the group of rs5186 AC genotypes than AA homozygotes after adjusting for other confounding factors (37.55 ± 13.7 vs. 32.47 ± 17.27 mm Hg; adjusted P = .028). Furthermore, haplotypes (GCC) and (AAC) had impacts on the antihypertensive effect of candesartan therapy. The AT1-AAs, AGTR1 gene polymorphisms and haplotypes solely or jointly have influences on candesartan-based antihypertensive response in patients with primary hypertension. Copyright © 2014 American Society of Hypertension. Published by Elsevier Inc. All rights reserved.

Characterization of a highly polymorphic region 5′ to JH in the human immunoglobulin heavy chain

PubMed Central

Silva, Alcino J.; Johnson, John P.; White, Raymond L.

1987-01-01

A cloned DNA segment 1.25 kilobases (kb) upstream from the joining segments of the human heavy chain immunoglobulin gene revealed extensive polymorphic variation at this locus, and the polymorphic pattern was stably transmitted to the next generation. Genomic restriction analysis showed that the polymorphism was caused by insertions/deletions within an MspI/BamHI fragment. Sequencing of one allele, 848 base pairs (bp) long, revealed eleven 50-base-pair tandem repeats. A second allele, 648 bp long, was cloned from a human genomic cosmid library, sequenced, and found to contain four fewer repeats than the first allele. A survey of 186 chromosomes from unrelated individuals of primarily northern European descent revealed at least six alleles. Images PMID:2884636

Ethnicity and lipoprotein(a) polymorphism in Native Mexican populations.

PubMed

Cardoso-Saldaña, G; De La Peña-Díaz, A; Zamora-González, J; Gomez-Ortega, R; Posadas-Romero, C; Izaguirre-Avila, R; Malvido-Miranda, E; Morales-Anduaga, M E; Anglés-Cano, E

2006-01-01

Lp(a) is a lipoparticle of unknown function mainly present in primates and humans. It consists of a low-density lipoprotein and apo(a), a polymorphic glycoprotein. Apo(a) shares sequence homology and fibrin binding with plasminogen, inhibiting its fibrinolytic properties. Lp(a) is considered a link between atherosclerosis and thrombosis. Marked inter-ethnic differences in Lp(a) concentration related to the genetic polymorphism of apo(a) have been reported in several populations. The study examined the structural and functional features of Lp(a) in three Native Mexican populations (Mayos, Mazahuas and Mayas) and in Mestizo subjects. We determined the plasma concentration of Lp(a) by immunonephelometry, apo(a) isoforms by Western blot, Lp(a) fibrin binding by immuno-enzymatic assay and short tandem repeat (STR) polymorphic marker genetic analysis by capillary electrophoresis. Mestizos presented the less skewed distribution and the highest median Lp(a) concentration (13.25 mg dL(-1)) relative to Mazahuas (8.2 mg dL(-1)), Mayas (8.25 mg dL(-1)) and Mayos (6.5 mg dL(-1)). Phenotype distribution was different in Mayas and Mazahuas as compared with the Mestizo group. The higher Lp(a) fibrin-binding capacity was found in the Maya population. There was an inverse relationship between the size of apo(a) polymorphs and both Lp(a) levels and Lp(a) fibrin binding. There is evidence of significative differences in Lp(a) plasma concentration and phenotype distribution in the Native Mexican and the Mestizo group.

Ethnicity and lipoprotein(a) polymorphism in Native Mexican populations

PubMed Central

Cardoso-Saldaña, Guillermo; De La Peña-Díaz, Aurora; Zamora-González, José; Gomez-Ortega, Rocio; Posadas-Romero, Carlos; Izaguirre-Avila, Raul; Malvido-Miranda, Elsa; Morales-Anduaga, Maria Elena; Angles-Cano, Eduardo

2006-01-01

Background Lp(a) is a lipoparticle of unknown function mainly present in primates and humans. It consists of a low-density lipoprotein and apo(a), a polymorphic glycoprotein. Apo(a) shares sequence homology and fibrin-binding with plasminogen inhibiting its fibrinolytic properties. Lp(a) is considered a link between atherosclerosis and thrombosis. Marked inter-ethnic differences in Lp(a) concentration related to the genetic polymorphism of apo(a), have been reported in several populations. Aim To study the structural and functional features of Lp(a) in three Native Mexican populations (Mayos, Mazahuas and Mayas) and in Mestizo subjects. Methods We determined the plasma concentration of Lp(a) by immunonephelometry, apo(a) isoforms by Western blot, Lp(a) fibrin-binding by immuno-enzymatic assay and STR polymorphic markers genetic analysis by capillary electrophoresis. Results Mestizos presented the less skewed distribution and the highest median Lp(a) concentration (13.25 mg/dL) relative to Mazahuas (8.2 mg/dL), Mayas (8.25 mg/dL) and Mayos (6.5 mg/dL). Phenotype distribution was different in Mayas and Mazahuas as compared to the Mestizo group. The higher Lp(a) fibrin-binding capacity was found in the Maya population. There was an inverse relationship between the size of apo(a) polymorphs and both Lp(a) levels and Lp(a) fibrin binding. Conclusion There is evidence of significative differences in Lp(a) plasma concentration and phenotype distribution in Native Mexican and the Mestizo group. PMID:16684693

Homocysteine and the C677T Gene Polymorphism of Its Key Metabolic Enzyme MTHFR Are Risk Factors of Early Renal Damage in Hypertension in a Chinese Han Population.

PubMed

Yun, Lin; Xu, Rui; Li, Guohua; Yao, Yucai; Li, Jiamin; Cong, Dehong; Xu, Xingshun; Zhang, Lihua

2015-12-01

The combined hyperhomocysteinemia condition is a feature of the Chinese hypertensive population. This study used the case-control method to investigate the association between plasma homocysteine and the C677T gene polymorphism of its key metabolic enzyme, 5, 10-methylenetetrahydrofolate reductase (MTHFR), and early renal damage in a hypertensive Chinese Han population.A total of 379 adult essential hypertensive patients were selected as the study subjects. The personal information, clinical indicators, and the C677T gene polymorphism of MTHFR were texted. This study used the urine microalbumin/urine creatinine ratio (UACR) as a grouping basis: the hypertension without renal damage group (NRD group) and the hypertension combined with early renal damage group (ERD group).Early renal damage in the Chinese hypertensive population was associated with body weight, systolic pressure, diastolic pressure, urea nitrogen, serum creatinine, cystatin C, uric acid, aldosterone, and glomerular filtration rate. The homocysteine level and the UACR in the TT genotype group were higher than those in the CC genotype group. The binary logistic regression analysis results showed that after sex and age were adjusted, the MTHFR C677T gene polymorphism was correlated with early renal damage in hypertension in both the recessive model and in the additive model.Plasma homocysteine and the C677T gene polymorphism of its key metabolic enzyme MTHFR might be independent risk factors of early renal damage in the hypertensive Chinese Han population.

New frontiers in sport training: genetics and artistic gymnastics.

PubMed

Morucci, Gabriele; Punzi, Tiziana; Innocenti, Giovanni; Gulisano, Massimo; Ceroti, Marco; Pacini, Stefania

2014-02-01

The increasing understanding of the genetic influences in sport has prompted an association study between the athletic performances and the polymorphisms of the angiotensin-converting enzyme (ACE), the α-actinin-3 (ACTN3), and the vitamin D receptor genes. The details of these gene polymorphisms can provide useful information to improve and plan new modern training programs for elite athletes. Eighty Italian male high level gymnasts were trained and tested for gymnastic-specific exercises and tested in all the men's artistic gymnastic apparatus (floor, pommel horse, rings, vault, parallel bars, and horizontal bar), and then genotyped. The training parameters of volume, intensity, and density of each gymnast were periodically measured during the season in each apparatus from the tests performed, and the seasonal average values were calculated. Gene polymorphisms were determined by polymerase chain reaction restriction fragment length polymorphism assay and studied in association with the performance results. The performances of ACE II gymnasts were significantly lower than that of the ACE ID/DD gymnasts in the apparatus expressing power features, confirming the predisposition of these athletes toward power-oriented sport. Gymnasts with ACTN3 RR/RX genotypes did not show a predisposition to the power-oriented apparatus, having worse performances compared with that of the ACTN3 XX gymnasts. Similarly, gymnasts with ACE II + ACTN3 RR/RX combined genotypes showed lower performances in comparison with that of the other gymnasts. Vitamin D receptor polymorphisms showed no significant association with the athletic performances. Because ACE insertion/deletion (I/D) and ACTN3 R577X polymorphisms heavily affect the physical performance of elite male gymnasts, the Italian Gymnastic Federation trainers have started to customize the current high-level training programs.

Patterns of genetic diversity in the polymorphic ground snake (Sonora semiannulata).

PubMed

Cox, Christian L; Chippindale, Paul T

2014-08-01

We evaluated the genetic diversity of a snake species with color polymorphism to understand the evolutionary processes that drive genetic structure across a large geographic region. Specifically, we analyzed genetic structure of the highly polymorphic ground snake, Sonora semiannulata, (1) among populations, (2) among color morphs (3) at regional and local spatial scales, using an amplified fragment length polymorphism dataset and multiple population genetic analyses, including FST-based and clustering analytical techniques. Based upon these methods, we found that there was moderate to low genetic structure among populations. However, this diversity was not associated with geographic locality at either spatial scale. Similarly, we found no evidence for genetic divergence among color morphs at either spatial scale. These results suggest that despite dramatic color polymorphism, this phenotypic diversity is not a major driver of genetic diversity within or among populations of ground snakes. We suggest that there are two mechanisms that could explain existing genetic diversity in ground snakes: recent range expansion from a genetically diverse founder population and current or recent gene flow among populations. Our findings have further implications for the types of color polymorphism that may generate genetic diversity in snakes.

Impact of the 4G/5G polymorphism in the plasminogen activator inhibitor-1 gene on primary nephrotic syndrome.

PubMed

Luo, Yuezhong; Wang, Chao; Tu, Haitao

2014-03-01

The aim of the present study was to investigate whether the four guanosines (4G)/five guanosines (5G) polymorphism in the gene coding for plasminogen activator inhibitor-1 (PAI-1) affects the clinical features of primary nephrotic syndrome (PNS). A cohort of 200 biopsy-diagnosed PNS patients was studied, with 40 healthy subjects as controls. The PAI-1 gene polymorphism was detected by polymerase chain reaction and DNA sequencing. Associations between the PAI-1 4G/5G polymorphism and clinical features and pathological types of PNS were analyzed. The results indicated that the PAI-1 genotype distribution is significantly different between patients with PNS and healthy controls, with significantly higher numbers of the 4G/4G genotype and lower numbers of the 5G5G genotype detected in PNS patients compared to controls (both P<0.05). The frequency of the 4G allele was also significantly higher in PNS patients compared to healthy controls (P<0.01). Among the different pathological types of PNS, IgA nephropathy (IgAN) and membranous nephropathy (MN) were associated with significantly increased frequencies of the 4G/4G and 4G/5G genotypes, as well as of the 4G allele. The increased 4G frequency was also detected in patients with minimal change disease (MCD). Significantly increased international normalized ratio (INR) and prolonged activated partial thromboplastin time (APTT) were observed in 4G/4G compared to 5G/5G PNS subjects. The response to steroids was not significantly different among the three genotypes. In conclusion, the 4G allele of the PAI-1 gene appears to be associated with PNS, especially in MN and IgAN patients. These findings suggest that specific targeting may be required for the treatment of PNS patients with the 4G/4G genotype.

Distribution of HLA-DRB1 and HLA-DQB1 alleles in Lak population of Iran.

PubMed

Varzi, Ali Mohammad; Shahsavar, Farhad; Tarrahi, Mohammad Javad

2016-07-01

Human leukocyte antigen (HLA) genes are the most polymorphic loci in the human genome and encode the highly polymorphic molecules critically involved in immune responses. Anthropological studies based on highly polymorphic HLA genes provide useful information for bone marrow donor registry, forensic medicine, disease association studies, as well as designing peptide vaccines against tumors, and infectious or autoimmune diseases. The aim of this study was to determine the HLA-DRB1 and HLA-DQB1 allele frequencies in 100 unrelated Lak individuals from Lorestan province of Iran. Finally, we compared the results with those previously described in four other Iranian populations. Commercial HLA-Type kits were used for determination of the HLA-DRB1 and HLA-DQB1 allele frequencies. Differences between populations in the distribution of HLA-DRB1 and HLA-DQB1 alleles were estimated by χ2 test with Yate's correction and Fisher's exact test. The most frequent HLA-DRB1 alleles were (*)1103=4 (23%), (*)1502 (9.5%), (*)0701 (9%), (*)0301 (8.5%), (*)1101 (7.5%) and (*)1501 (6%) while HLA-DQB1(*)0301 (40%), (*)0201 (15%), (*)0502 (10.5%), (*)0303 (10%), (*)0602=3 (9.5%), and (*)0501 (7.5%) were the most frequent alleles in Lak population. HLA-DRB1(*)0409, (*)0804, (*)1102, (*)1112, (*)1405, and HLA-DQB1(*)0503, (*)0604 were the least observed frequencies in Lak population. Our results based on HLA-DRB1 and HLA-DQB1 allele frequencies showed that the Lak population possesses the previously reported general features of the Lur and Kurd populations but still with unique, decreased or increased frequencies of several alleles. In other words, the Lak population is close to Lurs Khorramabadi and Kurd but far from Lurs Kohkiloyeh/Boyerahmad and Bakhtiari. Copyright © 2016 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Analysis of Genetic Diversity and Structure Pattern of Indigofera Pseudotinctoria in Karst Habitats of the Wushan Mountains Using AFLP Markers.

PubMed

Fan, Yan; Zhang, Chenglin; Wu, Wendan; He, Wei; Zhang, Li; Ma, Xiao

2017-10-16

Indigofera pseudotinctoria Mats is an agronomically and economically important perennial legume shrub with a high forage yield, protein content and strong adaptability, which is subject to natural habitat fragmentation and serious human disturbance. Until now, our knowledge of the genetic relationships and intraspecific genetic diversity for its wild collections is still poor, especially at small spatial scales. Here amplified fragment length polymorphism (AFLP) technology was employed for analysis of genetic diversity, differentiation, and structure of 364 genotypes of I. pseudotinctoria from 15 natural locations in Wushan Montain, a highly structured mountain with typical karst landforms in Southwest China. We also tested whether eco-climate factors has affected genetic structure by correlating genetic diversity with habitat features. A total of 515 distinctly scoreable bands were generated, and 324 of them were polymorphic. The polymorphic information content (PIC) ranged from 0.694 to 0.890 with an average of 0.789 per primer pair. On species level, Nei's gene diversity ( H j ), the Bayesian genetic diversity index ( H B ) and the Shannon information index ( I ) were 0.2465, 0.2363 and 0.3772, respectively. The high differentiation among all sampling sites was detected ( F ST = 0.2217, G ST = 0.1746, G' ST = 0.2060, θ B = 0.1844), and instead, gene flow among accessions ( N m = 1.1819) was restricted. The population genetic structure resolved by the UPGMA tree, principal coordinate analysis, and Bayesian-based cluster analyses irrefutably grouped all accessions into two distinct clusters, i.e., lowland and highland groups. The population genetic structure resolved by the UPGMA tree, principal coordinate analysis, and Bayesian-based cluster analyses irrefutably grouped all accessions into two distinct clusters, i.e., lowland and highland groups. This structure pattern may indicate joint effects by the neutral evolution and natural selection. Restricted N m was observed across all accessions, and genetic barriers were detected between adjacent accessions due to specifically geographical landform.

Multilocus Sequence Typing and Virulence-Associated Gene Profile Analysis of Staphylococcus aureus Isolates From Retail Ready-to-Eat Food in China.

PubMed

Yang, Xiaojuan; Yu, Shubo; Wu, Qingping; Zhang, Jumei; Wu, Shi; Rong, Dongli

2018-01-01

The aim of this study was to characterize the subtypes and virulence profiles of 69 Staphylococcus aureus isolates obtained from retail ready-to-eat food in China. The isolates were analyzed using multilocus sequence typing (MLST) and polymerase chain reaction (PCR) analysis of important virulence factor genes, including the staphylococcal enterotoxin (SE) genes ( sea , seb , sec , sed , see , seg , seh , sei , sej ), the exfoliative toxin genes ( eta and etb ), the toxic shock syndrome toxin-1 gene ( tst ), and the Panton-Valentine leucocidin-encoding gene ( pvl ). The isolates encompassed 26 different sequence types (STs), including four new STs (ST3482, ST3484, ST3485, ST3504), clustered in three clonal complexes and 17 singletons. The most prevalent STs were ST1, ST6, and ST15, constituting 34.8% of all isolates. Most STs (15/26, 57.7%) detected have previously been associated with human infections. All 13 toxin genes examined were detected in the S. aureus isolates, with 84.1% of isolates containing toxin genes. The three most prevalent toxin genes were seb (36.2%), sea (33.3%), and seg (33.3%). The classical SE genes ( sea - see ), which contribute significantly to staphylococcal food poisoning (SFP), were detected in 72.5% of the S. aureus isolates. In addition, pvl , eta , etb , and tst were found in 11.6, 10.1, 10.1, and 7.2% of the S. aureus isolates, respectively. Strains ST6 carrying sea and ST1 harboring sec-seh enterotoxin profile, which are the two most common clones associated with SFP, were also frequently detected in the food samples in this study. This study indicates that these S. aureus isolates present in Chinese ready-to-eat food represents a potential public health risk. These data are valuable for epidemiological studies, risk management, and public health strategies.

Multilocus Sequence Typing and Virulence-Associated Gene Profile Analysis of Staphylococcus aureus Isolates From Retail Ready-to-Eat Food in China

PubMed Central

Yang, Xiaojuan; Yu, Shubo; Wu, Qingping; Zhang, Jumei; Wu, Shi; Rong, Dongli

2018-01-01

The aim of this study was to characterize the subtypes and virulence profiles of 69 Staphylococcus aureus isolates obtained from retail ready-to-eat food in China. The isolates were analyzed using multilocus sequence typing (MLST) and polymerase chain reaction (PCR) analysis of important virulence factor genes, including the staphylococcal enterotoxin (SE) genes (sea, seb, sec, sed, see, seg, seh, sei, sej), the exfoliative toxin genes (eta and etb), the toxic shock syndrome toxin-1 gene (tst), and the Panton-Valentine leucocidin-encoding gene (pvl). The isolates encompassed 26 different sequence types (STs), including four new STs (ST3482, ST3484, ST3485, ST3504), clustered in three clonal complexes and 17 singletons. The most prevalent STs were ST1, ST6, and ST15, constituting 34.8% of all isolates. Most STs (15/26, 57.7%) detected have previously been associated with human infections. All 13 toxin genes examined were detected in the S. aureus isolates, with 84.1% of isolates containing toxin genes. The three most prevalent toxin genes were seb (36.2%), sea (33.3%), and seg (33.3%). The classical SE genes (sea–see), which contribute significantly to staphylococcal food poisoning (SFP), were detected in 72.5% of the S. aureus isolates. In addition, pvl, eta, etb, and tst were found in 11.6, 10.1, 10.1, and 7.2% of the S. aureus isolates, respectively. Strains ST6 carrying sea and ST1 harboring sec-seh enterotoxin profile, which are the two most common clones associated with SFP, were also frequently detected in the food samples in this study. This study indicates that these S. aureus isolates present in Chinese ready-to-eat food represents a potential public health risk. These data are valuable for epidemiological studies, risk management, and public health strategies. PMID:29662467

Behavioral and facial thermal variations in 3-to 4-month-old infants during the Still-Face Paradigm

PubMed Central

Aureli, Tiziana; Grazia, Annalisa; Cardone, Daniela; Merla, Arcangelo

2015-01-01

Behavioral and facial thermal responses were recorded in twelve 3- to 4-month-old infants during the Still-Face Paradigm (SFP). As in the usual procedure, infants were observed in a three-step, face-to-face interaction: a normal interaction episode (3 min); the “still-face” episode in which the mother became unresponsive and assumed a neutral expression (1 min); a reunion episode in which the mother resumed the interaction (3 min). A fourth step that consisted of a toy play episode (5 min) was added for our own research interest. We coded the behavioral responses through the Infant and Caregiver Engagement Phases system, and recorded facial skin temperature via thermal infrared (IR) imaging. Comparing still-face episode to play episode, the infants’ communicative engagement decreased, their engagement with the environment increased, and no differences emerged in self-regulatory and protest behaviors. We also found that facial skin temperature increased. For the behavioral results, infants recognized the interruption of the interactional reciprocity caused by the still-face presentation, without showing upset behaviors. According to autonomic results, the parasympathetic system was more active than the sympathetic, as usually happens in aroused but not distressed situations. With respect to the debate about the causal factor of the still-face effect, thermal data were consistent with behavioral data in showing this effect as related to the infants’ expectations of the nature of the social interactions being violated. Moreover, as these are associated to the infants’ subsequent interest in the environment, they indicate the thermal IR imaging as a reliable technique for the detection of physiological variations not only in the emotional system, as indicated by research to date, but also in the attention system. Using this technique for the first time during the SFP allowed us to record autonomic data in a more ecological manner than in previous studies. PMID:26528229

Enhancing the biophysical properties of mRFP1 through incorporation of fluoroproline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deepankumar, Kanagavel; Nadarajan, Saravanan Prabhu; Ayyadurai, Niraikulam

2013-11-01

Graphical abstract: Enhancing the biophysical properties of mRFP1 through incorporation of (2S, 4R)-4-fluoroproline at proline residues after mutating non-permissive site Pro63 into Ala. -- Highlights: •We incorporate (4S)-FP into mRFP1 led to insoluble protein. •Whereas, incorporation of (4R)-FP resulted in soluble but lost its fluorescence. •mRFP1-P63A mutant accommodate (4R)-FP and gave soluble protein with fluorescence. •Moreover mRFP1-P63A[(4R)-FP] showed enhanced biophysical properties of protein. -- Abstract: Here we enhanced the stability and biophysical properties of mRFP1 through a combination of canonical and non-canonical amino acid mutagenesis. The global replacement of proline residue with (2S, 4R)-4-fluoroproline [(4R)-FP] into mRFP1 led to solublemore » protein but lost its fluorescence, whereas (2S, 4S)-4-fluoroproline [(4S)-FP] incorporation resulted in insoluble protein. The bioinformatics analysis revealed that (4R)-FP incorporation at Pro63 caused fluorescence loss due to the steric hindrance of fluorine atom of (4R)-FP with the chromophore. Therefore, Pro63 residue was mutated with the smallest amino acid Ala to maintain non coplanar conformation of the chromophore and helps to retain its fluorescence with (4R)-FP incorporation. The incorporation of (4R)-FP into mRFP1-P63A showed about 2–3-fold enhancement in thermal and chemical stability. The rate of maturation is also greatly accelerated over the presence of (4R)-FP into mRFP1-P63A. Our study showed that a successful enhancement in the biophysical property of mRFP1-P63A[(4R)-FP] using non-canonical amino acid mutagenesis after mutating non-permissive site Pro63 into Ala.« less

Relationships between range access as monitored by radio frequency identification technology, fearfulness, and plumage damage in free-range laying hens.

PubMed

Hartcher, K M; Hickey, K A; Hemsworth, P H; Cronin, G M; Wilkinson, S J; Singh, M

2016-05-01

Severe feather-pecking (SFP), a particularly injurious behaviour in laying hens (Gallus gallus domesticus), is thought to be negatively correlated with range use in free-range systems. In turn, range use is thought to be inversely associated with fearfulness, where fearful birds may be less likely to venture outside. However, very few experiments have investigated the proposed association between range use and fearfulness. This experiment investigated associations between range use (time spent outside), fearfulness, plumage damage, and BW. Two pens of 50 ISA Brown laying hens (n=100) were fitted with radio frequency identification (RFID) transponders (contained within silicone leg rings) at 26 weeks of age. Data were then collected over 13 days. A total of 95% of birds accessed the outdoor run more than once per day. Birds spent an average duration of 6.1 h outside each day over 11 visits per bird per day (51.5 min per visit). The top 15 and bottom 15 range users (n=30), as determined by the total time spent on the range over 13 days, were selected for study. These birds were tonic immobility (TI) tested at the end of the trial and were feather-scored and weighed after TI testing. Birds with longer TI durations spent less time outside (P=0.01). Plumage damage was not associated with range use (P=0.68). The small group sizes used in this experiment may have been conducive to the high numbers of birds utilising the outdoor range area. The RFID technology collected a large amount of data on range access in the tagged birds, and provides a potential means for quantitatively assessing range access in laying hens. The present findings indicate a negative association between fearfulness and range use. However, the proposed negative association between plumage damage and range use was not supported. The relationships between range use, fearfulness, and SFP warrant further research.

Temporal Feeding Pattern May Influence Reproduction Efficiency, the Example of Breeding Mares

PubMed Central

Benhajali, Haifa; Ezzaouia, Mohammed; Lunel, Christophe; Charfi, Faouzia; Hausberger, Martine

2013-01-01

Discomfort in farm animals may be induced by inappropriate types or timing of food supplies. Thus, time restriction of meals and lack of roughage have been shown to be one source of emergence of oral stereotypies and abnormal behaviour in horses which have evolved to eat high-fibre diets in small amounts over long periods of time. This feeding pattern is often altered in domestic environment where horses are often fed low fibre meals that can be rapidly consumed. This study aimed at determining the effect of the temporal pattern of feeding on reproductive efficiency of breeding mares, One hundred Arab breeding mares were divided into two groups that differed only in the temporal pattern of roughage availability: only at night for the standard feeding pattern group (SFP mares), night and day for the “continuous feeding” group (CF mares). The total amount of roughage provided was the same as the CF mares received half of the hay during the day while in paddock (haynets). Mares were tested for oestrus detection by teasing with one stallion and were then examined clinically by rectal palpations and ultrasound before being mated naturally or inseminated by fresh or frozen semen. Multivariate logistic regression was used to analyse data. The treatment affected significantly the reproductive efficiency of the mares with fewer oestrus abnormalities (p = 0.0002) and more fertility (p = 0.024) in CF mares (conception rate = 81% versus 55% in SFP mares). Ensuring semi-continous feeding by providing roughage may be a way of fulfilling the basic physiological needs of the horses' digestive system, reducing stress and associated inhibitors of reproduction. To our knowledge, this study provides the first evidence of an impact of temporal feeding patterns on reproductive success in a Mammal. Temporal patterns of feeding may be a major and underestimated factor in breeding. PMID:24098636

Association of CRTC1 polymorphisms with obesity markers in subjects from the general population with lifetime depression.

PubMed

Quteineh, Lina; Preisig, Martin; Rivera, Margarita; Milaneschi, Yuri; Castelao, Enrique; Gholam-Rezaee, Mehdi; Vandenberghe, Frederik; Saigi-Morgui, Nuria; Delacrétaz, Aurélie; Cardinaux, Jean-René; Willemsen, Gonneke; Boomsma, Dorret I; Penninx, Brenda W J H; Ching-López, Ana; Conus, Philippe; Eap, Chin B

2016-07-01

Psychiatric disorders have been hypothesized to share common etiological pathways with obesity, suggesting related neurobiological bases. We aimed to examine whether CRTC1 polymorphisms were associated with major depressive disorder (MDD) and to test the association of these polymorphisms with obesity markers in several large case-control samples with MDD. The association between CRTC1 polymorphisms and MDD was investigated in three case-control samples with MDD (PsyCoLaus n1=3,362, Radiant n2=3,148 and NESDA/NTR n3=4,663). The effect of CRTC1 polymorphisms on obesity markers was then explored. CRTC1 polymorphisms were not associated with MDD in the three samples. CRTC1 rs6510997C>T was significantly associated with fat mass in the PsyCoLaus study. In fact, a protective effect of this polymorphism was found in MDD cases (n=1,434, β=-1.32%, 95% CI -2.07 to -0.57, p<0.001), but not in controls. In the Radiant study, CRTC1 polymorphisms were associated with BMI, exclusively in individuals with MDD (n=2,138, β=-0.75kg/m(2), 95% CI -1.30 to -0.21, p=0.007), while no association with BMI was found in the NESDA/NTR study. Estimated fat mass using bioimpedance that capture more accurately adiposity was only present in the PsyCoLaus sample. CRTC1 polymorphisms seem to play a role with obesity markers in individuals with MDD rather than non-depressive individuals. Therefore, the weak association previously reported in the population-based samples was driven by cases diagnosed with lifetime MDD. However, CRTC1 seems not to be implicated directly in the development of psychiatric diseases. Copyright © 2016 Elsevier B.V. All rights reserved.

XPG genetic polymorphisms and clinical outcome of patients with advanced non-small cell lung cancer under platinum-based treatment: a meta-analysis of 12 studies.

PubMed

Xiang, Tianxin; Kang, Xiuhua; Gong, Zhenghua; Bai, Wei; Chen, Chuanhui; Zhang, Wei

2017-04-01

A number of studies on the relationship between xeroderma pigmentosum group G (XPG) polymorphisms and clinical outcomes in non-small cell cancer (NSCLC) have led to inconclusive results. This meta-analysis evaluates the predictive value of XPG polymorphisms on the treatment response rate and overall survival of patients with NSCLC. To measure the correlative strength of the relationship between XPG polymorphisms and outcomes of patients with NSCLC, we searched electronic databases, including PubMed and China National Knowledge Infrastructure, to retrieve studies up to August 2016. We also employed pooled odds ratios (ORs) and hazard ratios (HRs) corresponding to 95% confidence intervals (95% CIs). Twelve studies involving 2877 patients with NSCLC were included: 8 studies involving 1473 patients examined the correlation between XPG polymorphisms and tumor response rate and 7 studies involving 2329 patients reported on the correlation of XPG polymorphisms with overall survival. None of the XPG His1104Asp(C>G)/His46His(C>T) polymorphisms exhibited a correlation with treatment response rate or overall survival. However, in a further stratified analysis by ethnicity, carriers of the 1104G allele were associated with good response among Asians in the homozygote model (GG vs. CC: OR = 1.57, 95% CI: 1.05-2.34, P = 0.027). Meanwhile, further stratified by ethnicity, His46His polymorphism was not associated with RR and OS in any genetic models. No strong evidence was found to support the use of XPG polymorphisms as tumor response and prognostic factors of patients with NSCLC receiving a platinum-based treatment regimen, which is attributed to marginal association. Studies with large-scale and multiple ethnicities need to be conducted to verify the conclusion.

[The morphology, typical combinations of polymorphic genes of hemostasis, and specific features of the pathogenesis of retrochorial hematoma in missed abortion].

PubMed

Milovanov, A P; Kuznetsova, N B; Bushtyreva, I O

to identify mutations and hemostatic gene polymorphisms typical for retrochorial hematoma (RCH) and to study its pathogenesis in missed abortion. A PCR assay was used to detect the genetic forms of thrombophilia in 270 patients with ultrasonographically verified RCH. Logistic regression analysis revealed that with the F7 (proconvertin, coagulation factor (CF) VII G10976A polymorphism or with the F13 (fibrinase, CF XIII) G>T, or FGB (fibrinogen β-chain) G455A polymorphism, the risk of RCH was 2.72, 2.16, and 1.92 times higher, respectively. First trimester missed abortion was found in 42 (15.5%) cases; among them there were 24 (8.8%) women with different polymorphism combinations: F7 (G10976A), F13 (fibrinase, G>T), FGB (G455A). A total of 18 cases of missed abortion due to morphologically verified endometritis, endocrinopathies, and antiphospholipid syndrome were excluded from the sample. Compared to the morphology of medical abortions of the same period (16 women), patients with polymorphic genes of hemostasis were found to have statistically significant incomplete endometrial decidualization, thinning or absence of a Rohr's fibrinoid layer, a smaller number and shortening of syncytiotrophoblast microvilli, and the maximum amount of dissecting hemorrhage and RCH in the utero-chorionic region. The stages of RCH pathogenesis were determined; these included penetration of maternal erythrocytes deep into the decidua ~ dissociation of a layer of decidual cells with impairment of a «hemostatic envelope» ~ formation of RCH with a dense network of fibrin threads ~ final necrosis of surrounding cells and tissues. The investigators identified for the first time the typical combinations of polymorphic genes of predisposition to a high risk for RCH; its complete formation requires additional changes in maternal and placental components that provide local hemostasis.

The role of brain-derived neurotrophic factor (BDNF) Val66Met genetic polymorphism in bipolar disorder: a case-control study, comorbidities, and meta-analysis of 16,786 subjects.

PubMed

González-Castro, Thelma Beatriz; Nicolini, Humberto; Lanzagorta, Nuria; López-Narváez, Lilia; Genis, Alma; Pool García, Sherezada; Tovilla-Zárate, Carlos Alfonso

2015-02-01

The aim of this study was to evaluate the association of Val66Met brain-derived neurotrophic factor (BDNF) polymorphism with bipolar disorder in (i) a meta-analysis and (ii) a case-control study in a Mexican population. We also investigated the possible association of this polymorphism with clinical features. We performed a keyword search of the PubMed and Web of Science databases. A total of 22 studies that have investigated the association of Val66Met (rs6265) with bipolar disorder were selected for inclusion and combined with random effects meta-analysis, using allelic, additive, dominant, and recessive models. Finally, the single nucleotide polymorphism (rs6265) Val66Met in the BDNF gene was genotyped and compared between 139 patients with bipolar disorder and 141 healthy volunteers in a Mexican population. The pooled results from the meta-analysis (9,349 cases and 7,437 controls) did not show a significant association in any of the models. The same results were obtained in our case-control study when analyzing the distribution of the genotypic frequencies of the Val66Met polymorphism in patients with bipolar disorder. However, when we analyzed the association between rs6265 and lifetime history of suicidal behavior, we found an association between genotype Val-Val and suicide attempt (p = 0.02). Although the present study has some limitations, the results indicate a lack of association between the Val66Met polymorphism and bipolar disorder. However, in our case-control study in a Mexican population, the Val66Met polymorphism was associated with suicidal behavior in patients with bipolar disorder. Nevertheless, it is important to consider potential interactions of the BDNF gene, the environment, and different inheritance patterns, when carrying out future genetic studies with larger samples. © 2014 The Authors. Bipolar Disorders Published by John Wiley & Sons Ltd.

Solid-state NMR and IR for the analysis of pharmaceutical solids: polymorphs of fosinopril sodium.

PubMed

Brittain, H G; Morris, K R; Bugay, D E; Thakur, A B; Serajuddin, A T

1993-01-01

The two polymorphic modifications of fosinopril sodium have been characterized as to their differences in melting behaviour, powder X-ray diffraction patterns, Fourier transform infrared spectra (FTIR), and solid-state 31P- and 13C-NMR spectra. The polymorphs were found to be enantiotropically related based upon melting point, heat of fusion, and solution mediated transformation data. Analysis of the solid-state FTIR and 13C-NMR data indicated that the environment of the acetal side chain of fosinopril sodium differed in two polymorphs, and that there might be cis-trans isomerization about the C6-N peptide bond. These conformational differences are postulated as the origin of the observed polymorphism.

[Interleukin-10-1082 promoter polymorphism and the risk of gastric cancer].

PubMed

Yin, Yi-qiong; Liu, Chun-juan; Zhang, Ming-ming; Zhou, Yong

2012-05-01

To investigate the association between Interleukin-10 (IL-10) promoter polymorphism and the gastric cancer risk in Chinese Han patients. DNA was extracted from blood samples of gastric cancer patients (n = 75) and controls (n = 75). IL-10 -1082 promoter polymorphism in both patient and control group (three genotypes distribution: AA, AG and GG) was identified by PCR-RFLP and its relationship with gastric cancer risk, clinic and pathologic features was also analyzed. Patients with gastric cancer had a significantly lower frequency of AA (OR = 0.43, 95% CI = 0.20, 0.92; P = 0.03) than controls. Patients with proximal gastric cancer had a significantly higher frequency of GG (OR = 3.06, 95% CI = 1.12, 8.36; P = 0.03) than those with distant gastric cancer. Patients with advanced (stage II/IV) gastric cancer had a significantly higher frequency of AA (OR = 5.09, 95% CI = 1.05, 24.70; P = 0.04) than those with early (stage I /IV) gastric cancer. When stratified by the Lauren's classification, histological differentiation of gastric cancer, no statistically significant results was observed. This study suggests that the IL-1 1082 promoter polymorphism may be associated with gastric cancer in Chinese Han patients, and the difference in genotype distribution may be associated with the location and stage of gastric cancer.

Collapsed state of polyglutamic acid results in amyloid spherulite formation

PubMed Central

Stehli, Daniel; Mulaj, Mentor; Miti, Tatiana; Traina, Joshua; Foley, Joseph; Muschol, Martin

2015-01-01

Self-assembly of proteins and peptides into amyloid fibrils involves multiple distinct intermediates and late-stage fibrillar polymorphs. Understanding the conditions and mechanisms that promote the formation of one type of intermediate and polymorph over the other represents a fundamental challenge. Answers to this question are also of immediate biomedical relevance since different amyloid aggregate species have been shown to have distinct pathogenic potencies. One amyloid polymorph that has received comparatively little attention are amyloid spherulites. Here we report that self-assembly of the intrinsically disordered polymer poly(L-glutamic) acid (PLE) can generate amyloid spherulites. We characterize spherulite growth kinetics, as well as the morphological, optical and tinctorial features of this amyloid polymorph previously unreported for PLE. We find that PLE spherulites share both tinctorial and structural characteristics with their amyloid fibril counterparts. Differences in PLE's molecular weight, polydispersity or chemistry could not explain the selective propensity toward either fibril or spherulite formation. Instead, we provide evidence that PLE polymers can exist in either a collapsed globule or an extended random coil conformation. The collapsed globule consistently produces spherulites while the extended coil assembles into disordered fibril bundles. This results suggests that these 2 PLE conformers directly affect the morphology of the resulting macroscopic amyloid assembly. PMID:28232889

Collapsed state of polyglutamic acid results in amyloid spherulite formation.

PubMed

Stehli, Daniel; Mulaj, Mentor; Miti, Tatiana; Traina, Joshua; Foley, Joseph; Muschol, Martin

2015-01-01

Self-assembly of proteins and peptides into amyloid fibrils involves multiple distinct intermediates and late-stage fibrillar polymorphs. Understanding the conditions and mechanisms that promote the formation of one type of intermediate and polymorph over the other represents a fundamental challenge. Answers to this question are also of immediate biomedical relevance since different amyloid aggregate species have been shown to have distinct pathogenic potencies. One amyloid polymorph that has received comparatively little attention are amyloid spherulites. Here we report that self-assembly of the intrinsically disordered polymer poly(L-glutamic) acid (PLE) can generate amyloid spherulites. We characterize spherulite growth kinetics, as well as the morphological, optical and tinctorial features of this amyloid polymorph previously unreported for PLE. We find that PLE spherulites share both tinctorial and structural characteristics with their amyloid fibril counterparts. Differences in PLE's molecular weight, polydispersity or chemistry could not explain the selective propensity toward either fibril or spherulite formation. Instead, we provide evidence that PLE polymers can exist in either a collapsed globule or an extended random coil conformation. The collapsed globule consistently produces spherulites while the extended coil assembles into disordered fibril bundles. This results suggests that these 2 PLE conformers directly affect the morphology of the resulting macroscopic amyloid assembly.

Two single-nucleotide polymorphisms of the RELN gene and symptom-based and developmental deficits among children and adolescents with autistic spectrum disorders in the Tianjin, China.

PubMed

Wang, Geng-Fu; Ye, Sheng; Gao, Lei; Han, Yu; Guo, Xuan; Dong, Xiao-Peng; Su, Yuan-Yuan; Zhang, Xin

2018-05-10

Increasing evidence has revealed that genetic variants in Reelin (RELN) gene, especially single-nucleotide polymorphisms (SNPs), correlate with autistic spectrum disorders (ASD) risk; however, no consensus have been reached. This study aimed to provide additional evidence for the association between two SNPs of RELN (i.e., rs736707, rs2229864) and ASD risk, as well as the relationship between RELN gene and symptom-based and developmental deficits of ASD patients in Chinese Han children and adolescents. 157 ASD subjects and 256 typical development (TD) controls were genotyped by TaqMan® genotyping assay. ASD patients were assessed by Childhood Autism Rating Scale (CARS), Autism Behavior Checklist (ABC), and Early Childhood Development Questionnaire (ECDQ). We found that SNP rs2229864 was associated with the genetic predisposition of ASD, whereas a negative association between SNP rs2229864 and symptom-based and developmental features was detected. In contrast, RELN rs736707 correlated with the sensory subscale of the ABC, the relating subscale of the ABC and the total score of ABC, although we did not detect a significant association between SNP rs736707 and ASD risk. Furthermore, a significant rs736707-rs2229864 haplotype was detected. Individuals with a CC haplotype were more likely to have ASD, but individuals with a CT haplotype had more chance be TD controls. Further studies using more samples and including more gene variants in RELN are warranted to confirm our results. Copyright © 2018 Elsevier B.V. All rights reserved.

Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species

PubMed Central

Buyyarapu, Ramesh; Kantety, Ramesh V.; Yu, John Z.; Saha, Sukumar; Sharma, Govind C.

2011-01-01

New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum   EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations

PubMed Central

2012-01-01

Background Through the wealth of information contained within them, genome-wide association studies (GWAS) have the potential to provide researchers with a systematic means of associating genetic variants with a wide variety of disease phenotypes. Due to the limitations of approaches that have analyzed single variants one at a time, it has been proposed that the genetic basis of these disorders could be determined through detailed analysis of the genetic variants themselves and in conjunction with one another. The construction of models that account for these subsets of variants requires methodologies that generate predictions based on the total risk of a particular group of polymorphisms. However, due to the excessive number of variants, constructing these types of models has so far been computationally infeasible. Results We have implemented an algorithm, known as greedy RLS, that we use to perform the first known wrapper-based feature selection on the genome-wide level. The running time of greedy RLS grows linearly in the number of training examples, the number of features in the original data set, and the number of selected features. This speed is achieved through computational short-cuts based on matrix calculus. Since the memory consumption in present-day computers can form an even tighter bottleneck than running time, we also developed a space efficient variation of greedy RLS which trades running time for memory. These approaches are then compared to traditional wrapper-based feature selection implementations based on support vector machines (SVM) to reveal the relative speed-up and to assess the feasibility of the new algorithm. As a proof of concept, we apply greedy RLS to the Hypertension – UK National Blood Service WTCCC dataset and select the most predictive variants using 3-fold external cross-validation in less than 26 minutes on a high-end desktop. On this dataset, we also show that greedy RLS has a better classification performance on independent test data than a classifier trained using features selected by a statistical p-value-based filter, which is currently the most popular approach for constructing predictive models in GWAS. Conclusions Greedy RLS is the first known implementation of a machine learning based method with the capability to conduct a wrapper-based feature selection on an entire GWAS containing several thousand examples and over 400,000 variants. In our experiments, greedy RLS selected a highly predictive subset of genetic variants in a fraction of the time spent by wrapper-based selection methods used together with SVM classifiers. The proposed algorithms are freely available as part of the RLScore software library at http://users.utu.fi/aatapa/RLScore/. PMID:22551170

Anagostic interactions in chiral separation. Polymorphism in a [Co(II)(L)] complex: Crystallographic and theoretical studies

NASA Astrophysics Data System (ADS)

Awwadi, Firas F.; Hodali, Hamdallah A.

2018-02-01

Syntheses and crystal structures of two polymorphs of the complex [Co(II)(L)], where H2L = 2,2'-[cis-1,2-diaminocyclohexanediylbis (nitrilo-methylidyne)]bis (5-dimethyl-amino]phenol, have been studied. The two polymorphs concomitantly crystallized by vapour diffusion of solvent. The first polymorph (I) crystallized as a racemate in the centrosymmetric tetragonal I41/a space group. The second polymorph (II) crystallized in the chiral orthorhombic space group P212121. The chiral conformers of symmetrical cis-1,2-disubstituted cyclohexane molecules cannot be resolved in the liquid or gas phases, due to the rapid ring inversion. In the present study, the two chiral conformers are present in crystals of polymorph I, whereas, only one chiral conformer is present in crystals of polymorph II. Crystal structure analysis indicated that the formation of two different polymorphs of [Co(II)(L)] complex can be rationalized based on Csbnd H⋯Co anagostic interactions. Density Functional Theory (DFT) calculations indicated that Csbnd H⋯Co interactions are due to HOMO-LUMO interactions.

An Induced Pluripotent Stem Cell Patient Specific Model of Complement Factor H (Y402H) Polymorphism Displays Characteristic Features of Age-Related Macular Degeneration and Indicates a Beneficial Role for UV Light Exposure.

PubMed

Hallam, Dean; Collin, Joseph; Bojic, Sanja; Chichagova, Valeria; Buskin, Adriana; Xu, Yaobo; Lafage, Lucia; Otten, Elsje G; Anyfantis, George; Mellough, Carla; Przyborski, Stefan; Alharthi, Sameer; Korolchuk, Viktor; Lotery, Andrew; Saretzki, Gabriele; McKibbin, Martin; Armstrong, Lyle; Steel, David; Kavanagh, David; Lako, Majlinda

2017-11-01

Age-related macular degeneration (AMD) is the most common cause of blindness, accounting for 8.7% of all blindness globally. Vision loss is caused ultimately by apoptosis of the retinal pigment epithelium (RPE) and overlying photoreceptors. Treatments are evolving for the wet form of the disease; however, these do not exist for the dry form. Complement factor H polymorphism in exon 9 (Y402H) has shown a strong association with susceptibility to AMD resulting in complement activation, recruitment of phagocytes, RPE damage, and visual decline. We have derived and characterized induced pluripotent stem cell (iPSC) lines from two subjects without AMD and low-risk genotype and two patients with advanced AMD and high-risk genotype and generated RPE cells that show local secretion of several proteins involved in the complement pathway including factor H, factor I, and factor H-like protein 1. The iPSC RPE cells derived from high-risk patients mimic several key features of AMD including increased inflammation and cellular stress, accumulation of lipid droplets, impaired autophagy, and deposition of "drüsen"-like deposits. The low- and high-risk RPE cells respond differently to intermittent exposure to UV light, which leads to an improvement in cellular and functional phenotype only in the high-risk AMD-RPE cells. Taken together, our data indicate that the patient specific iPSC model provides a robust platform for understanding the role of complement activation in AMD, evaluating new therapies based on complement modulation and drug testing. Stem Cells 2017;35:2305-2320. © 2017 The Authors Stem Cells published by Wiley Periodicals, Inc. on behalf of AlphaMed Press.

Calculation of Electronic and Optical Properties of AgGaO2 Polymorphs Using Many-Body Approaches

NASA Astrophysics Data System (ADS)

Dadsetani, Mehrdad; Nejatipour, Reihan

2018-02-01

Ab initio calculations based on many-body perturbation theory have been used to study the electronic and optical properties of AgGaO2 in rhombohedral, hexagonal, and orthorhombic phases. GW calculations showed that AgGaO2 is an indirect-bandgap semiconductor in all three phases with energy bandgap of 2.35 eV, 2.23 eV, and 2.07 eV, in good agreement with available experimental values. By solving the Bethe-Salpeter equation (BSE) using the full potential linearized augmented plane wave basis, optical properties of the AgGaO2 polymorphs were calculated and compared with those obtained using the GW-corrected random phase approximation (RPA) and with existing experimental data. Strong anisotropy in the optical absorption spectra was observed, and the excitonic structures which were absent in the RPA calculations were reproduced in GWBSE calculations, in good agreement with the optical absorption spectrum of the rhombohedral phase. While modifying peak positions and intensities of the absorption spectra, the GWBSE gave rise to the redistribution of oscillator strengths. In comparison with the z-polarized response, excitonic effects in the x-polarized response were dominant. In the x- (and y-) polarized responses of r- and h-AgGaO2, spectral features and excitonic effects occur at the lower energies, but in the case of o-AgGaO2, the spectral structures of the z-polarized response occur at lower energies. In addition, the low-energy loss functions of AgGaO2 were calculated and compared using the GWBSE approach. Spectral features in the energy loss function components near the bandgap region were attributed to corresponding excitonic structures in the imaginary part of the dielectric function.

Photovoltaic Performance of Vapor-Assisted Solution-Processed Layer Polymorph of Cs3Sb2I9.

PubMed

Singh, Anupriya; Boopathi, Karunakara Moorthy; Mohapatra, Anisha; Chen, Yang Fang; Li, Gang; Chu, Chih Wei

2018-01-24

The presence of toxic lead (Pb) remains a major obstruction to the commercial application of perovskite solar cells. Although antimony (Sb)-based perovskite-like structures A 3 M 2 X 9 can display potentially useful photovoltaic behavior, solution-processed Sb-based perovskite-like structures usually favor the dimer phase, which has poor photovoltaic properties. In this study, we prepared a layered polymorph of Cs 3 Sb 2 I 9 through solution-processing and studied its photovoltaic properties. The exciton binding energy and exciton lifetime of the layer-form Cs 3 Sb 2 I 9 were approximately 100 meV and 6 ns, respectively. The photovoltaic properties of the layered polymorph were superior to those of the dimer polymorph. A solar cell incorporating the layer-form Cs 3 Sb 2 I 9 exhibited an open-circuit voltage of 0.72 V and a power conversion efficiency of 1.5%-the highest reported for an all-inorganic Sb-based perovskite.

Lack of association between temporal lobe epilepsy and a novel polymorphism in the alpha 2 subunit gene (ATP1A2) of the sodium potassium transporting ATPase.

PubMed

Buono, R J; Ferraro, T N; O'Connor, M J; Sperling, M R; Abbey, M; Finanger, E; Lohoff, F; Mulholland, N; Berrettini, W H

2000-02-07

Genetic linkage studies in rodents and humans have identified specific chromosomal regions harboring seizure susceptibility genes. We have identified a novel polymorphism in the human alpha 2 subunit gene (ATP1A2) of the sodium potassium transporting ATPase (NaK-pump), a candidate gene for human temporal lobe epilepsy (TLE) based on its chromosomal location and function in ion homeostasis. The polymorphism consists of a four base pair insertion 12 base pairs upstream of the start of exon 2. We performed an association study between this polymorphism and TLE. Our study did not find a significant difference in the frequency of this polymorphism between TLE patients and controls, indicating that this variation is not a major susceptibility factor. However, since the number of patients studied so far is small and the functional consequence of the polymorphism is unknown, the variation may yet be found to play a minor role in increased risk for seizure susceptibility. In contrast to the findings in TLE patients and controls, we did find a significant difference in the frequency of the variation between African Americans and persons of European descent. This finding demonstrates the potential effect of population stratification on studies of this type and supports the growing use of parental and familial samples for controls in association studies. Further study of this polymorphism is warranted as it may be involved in other disease processes for which there are known ethnic-specific susceptibilities. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:79-83, 2000. Copyright 2000 Wiley-Liss, Inc.

Polymorphic amplified typing sequences (PATS) and pulsed-field gel electrophoresis (PFGE) yield comparable results in the strain typing of a diverse set of bovine Escherichia coli O157 isolates

USDA-ARS?s Scientific Manuscript database

The PCR-based Escherichia coli O157 (O157) strain typing system, Polymorphic Amplified Typing Sequences (PATS), targets insertions-deletions (Indels) and single nucleotide polymorphisms (SNPs) at the XbaI and AvrII(BlnI) restriction enzyme sites, respectively, besides amplifying four known virulenc...

Prolonged neutropenia after irinotecan-based chemotherapy in a child with polymorphisms of UGT1A1 and SLCO1B1.

PubMed

Sakaguchi, S; Garcia-Bournissen, F; Kim, R; Schwarz, U I; Nathan, P C; Ito, S

2009-12-01

Genetic polymorphisms of uridine diphosphate glucuronosyl transferase 1A1 (UGT1A1), and SLCO1B1 coding organic anion-transporter polypeptide 1B1, are independent risk factors known to increase irinotecan toxicity in adults. Although combined occurrence of polymorphisms in these 2 genes is likely to influence susceptibility to irinotecan toxicity, data are scarce, especially in children. We report an 11-year-old female with severe and prolonged neutropenia after irinotecan-based chemotherapy. The patient's genotyping revealed polymorphisms in both UGT1A1 and SLCO1B1. To our knowledge, this is the first case report of combined genotyping of both UGT1A1 and SLCO1B1 in a child with severe irinotecan toxicity.

Molecular basis of length polymorphism in the human zeta-globin gene complex.

PubMed Central

Goodbourn, S E; Higgs, D R; Clegg, J B; Weatherall, D J

1983-01-01

The length polymorphism between the human zeta-globin gene and its pseudogene is caused by an allele-specific variation in the copy number of a tandemly repeating 36-base-pair sequence. This sequence is related to a tandemly repeated 14-base-pair sequence in the 5' flanking region of the human insulin gene, which is known to cause length polymorphism, and to a repetitive sequence in intervening sequence (IVS) 1 of the pseudo-zeta-globin gene. Evidence is presented that the latter is also of variable length, probably because of differences in the copy number of the tandem repeat. The homology between the three length polymorphisms may be an indication of the presence of a more widespread group of related sequences in the human genome, which might be useful for generalized linkage studies. PMID:6308667

Residue-Specific Side-Chain Polymorphisms via Particle Belief Propagation.

PubMed

Ghoraie, Laleh Soltan; Burkowski, Forbes; Li, Shuai Cheng; Zhu, Mu

2014-01-01

Protein side chains populate diverse conformational ensembles in crystals. Despite much evidence that there is widespread conformational polymorphism in protein side chains, most of the X-ray crystallography data are modeled by single conformations in the Protein Data Bank. The ability to extract or to predict these conformational polymorphisms is of crucial importance, as it facilitates deeper understanding of protein dynamics and functionality. In this paper, we describe a computational strategy capable of predicting side-chain polymorphisms. Our approach extends a particular class of algorithms for side-chain prediction by modeling the side-chain dihedral angles more appropriately as continuous rather than discrete variables. Employing a new inferential technique known as particle belief propagation, we predict residue-specific distributions that encode information about side-chain polymorphisms. Our predicted polymorphisms are in relatively close agreement with results from a state-of-the-art approach based on X-ray crystallography data, which characterizes the conformational polymorphisms of side chains using electron density information, and has successfully discovered previously unmodeled conformations.

Polymorphisms in exons 1B and 1C of the type I interleukin-1 receptor gene in patients with endometriosis.

PubMed

D'Amora, Paulo; Sato, Hélio; Girão, Manoel J B C; Silva, Ismael D C G; Schor, Eduardo

2006-09-01

To study possible correlation between the prevalence of polymorphisms in the type I interleukin-1 receptor gene and pelvic endometriosis. Genotypes of 223 women were analyzed: 109 women with surgically and histologically confirmed endometriosis and 114 healthy women. Distributions of two single-base polymorphisms of the human interleukin-1 receptor type I (IL-1RI) gene were evaluated: PstI, due to a C-->T transition in exon 1B and BsrBI a C-->A transition at position 52 in exon 1C. Polymorphisms were detected by polymerase chain reaction (PCR) followed by restriction fragment length polymorphism analysis (RFLP) resolved on 3% agarose gels stained with ethidium bromide. Genotypes for PstI polymorphisms did not differ significantly among control and endometriosis (P = 0.058). However, in relation to BsrBI polymorphism, protective risk was observed for the development of endometriosis [OR 0.39-IC 95% (0.2-0.9)]. BsrBI heterozygote genotype (C/A) showed protective effect against endometriosis development.

Association between ADAM metallopeptidase domain 33 gene polymorphism and risk of childhood asthma: a meta-analysis.

PubMed

Sun, F J; Zou, L Y; Tong, D M; Lu, X Y; Li, J; Deng, C B

2017-08-31

This study aimed to investigate the association between ADAM metallopeptidase domain 33 (ADAM33) gene polymorphisms and the risk of childhood asthma. The relevant studies about the relationship between ADAM33 gene polymorphisms and childhood asthma were searched from electronic databases and the deadline of retrieval was May 2016. The single nucleotide polymorphisms (SNPs) of ADAM33 (rs511898, rs2280092, rs3918396, rs528557, rs2853209, rs44707, rs2280091 and rs2280089) were analyzed based on several models including the allele, codominant, recessive and dominant models. The results showed that the ADAM33 rs2280091 polymorphism in all four genetic models was associated with an increased risk of childhood asthma. Positive associations were also found between the polymorphisms rs2280090, rs2787094, rs44707 and rs528557 and childhood asthma in some genetic models. This meta-analysis suggested that ADAM33 polymorphisms rs2280091, rs2280090, rs2787094, rs44707 and rs528557 were significantly associated with a high risk of childhood asthma.

Alterations of leaf cell ultrastructures and AFLP DNA profiles in Earth-grown tomato plants propagated from long-term six years Mir-flown seeds

NASA Astrophysics Data System (ADS)

Liu, Min; Xue, Huai; Pan, Yi; Zhang, Chunhua; Lu, Jinying

Leaf cell ultrastructures and DNA variations in the firstand the second-generation of Earthgrown tomato (Lycopersicon esculentun Mill) plants that had been endured a long-term six years spaceflight in the Mir were compared to their ground-based control plants, under observations with a Transmission Electron Microscope and the Amplification Fragment Length Polymorphism (AFLP) analysis. For alterations in the morphological ultrastructures, one plant among the 11 first-generation plants generated from 30 Mir-flown seeds had a three-layered palisade cell structure, while other 10 first-generation plants and all ground-based controls had one-layered palisade cell structure in leaves. Starch grains were larger and in clusters, numbers of starch grains increased in the chloroplasts in the Mir-flown plants. Leaf cells became contracted and deformed, and cell shape patterns were different in the Mir-flown plants. For the leaf genomic DNA alterations, 34 DNA bands were polymorphic with a 1.32% polymorphism among 2582 DNA bands in the first-generation Mir-flown plants. Band types in the spaceflight treated plants were also different from those in the ground-based control. Of 11 survived first-generation plants, 7 spaceflight treated plants (Plant Nos. 1-6 and No. 9) had a same 7 polymorphic bands and a same 0.27%DNA mutation. The DNA mutation rate was greatest in Plants No.10 and No.7 (0.90% and 0.94%), less in Plant No.11 (0.31%) and least in Plant No.8 (0.20%). For the 38 send-generation plants propagated from the No. 5 Mir-flown seed, 6 DNA bands were polymorphic with a 0.23% polymorphism among 2564 amplified DNA bands. Among those 38 second-generation plants amplified by primer pair (E4: ACC, M8: CTT), one DNA band disappeared in 29 second-generation plants and in the original Mir-flown No. 5 plant, compared to the ground-base controls. Among the 38 second-generation plants generated from the Mir-flown No. 5 seed, the DNA band types of 29 second-generation plants were different from that of the ground-base controls and had a same 6 polymorphic bands and a same 0.23% DNA mutation. For the 49 second-generation plants derived from the Mir-flown No. 6 seed, 7 DNA bands were polymorphic with 0.27% polymorphism among 2564 amplified DNA bands. With only one exception among those 49 second-generation plants amplified by primer pair (E3: ACA, M3: CAG), one DNA band disappeared in 48 second-generation plants and in the original Mir-flown No. 6 plant, compared to the ground-based controls. Among the 49 second-generation plants generated from the Mir-flown No. 6 seed, the DNA band types of 48 second-generation plants were different from that of the ground-base controls and had a same 7 polymorphic bands and a same 0.27% DNA mutation. Our results indicated that leaf cell ultrastructures had been altered and heredity variations had been induced by seeds being exposed to a long-term outer-space environment. Further research is needed to elucidate the dynamics and mechanisms resulting in such variations. Plant biology studies in the space environment may open potential approaches to induce mutations and to screen new plant varieties by ground-based selections among spaceflight treated seeds or seedlings.

Polymorphic mountain whitefish (Prosopium williamsoni) in a coastal riverscape: size class assemblages, distribution, and habitat associations

USGS Publications Warehouse

Starr, James C.; Torgersen, Christian E.

2015-01-01

We compared the assemblage structure, spatial distributions, and habitat associations of mountain whitefish (Prosopium williamsoni) morphotypes and size classes. We hypothesised that morphotypes would have different spatial distributions and would be associated with different habitat features based on feeding behaviour and diet. Spatially continuous sampling was conducted over a broad extent (29 km) in the Calawah River, WA (USA). Whitefish were enumerated via snorkelling in three size classes: small (10–29 cm), medium (30–49 cm), and large (≥50 cm). We identified morphotypes based on head and snout morphology: a pinocchio form that had an elongated snout and a normal form with a blunted snout. Large size classes of both morphotypes were distributed downstream of small and medium size classes, and normal whitefish were distributed downstream of pinocchio whitefish. Ordination of whitefish assemblages with nonmetric multidimensional scaling revealed that normal whitefish size classes were associated with higher gradient and depth, whereas pinocchio whitefish size classes were positively associated with pool area, distance upstream, and depth. Reach-scale generalised additive models indicated that normal whitefish relative density was associated with larger substrate size in downstream reaches (R2 = 0.64), and pinocchio whitefish were associated with greater stream depth in the reaches farther upstream (R2 = 0.87). These results suggest broad-scale spatial segregation (1–10 km), particularly between larger and more phenotypically extreme individuals. These results provide the first perspective on spatial distributions and habitat relationships of polymorphic mountain whitefish.

Single Nucleotide Polymorphisms Predict Symptom Severity of Autism Spectrum Disorder

ERIC Educational Resources Information Center

Jiao, Yun; Chen, Rong; Ke, Xiaoyan; Cheng, Lu; Chu, Kangkang; Lu, Zuhong; Herskovits, Edward H.

2012-01-01

Autism is widely believed to be a heterogeneous disorder; diagnosis is currently based solely on clinical criteria, although genetic, as well as environmental, influences are thought to be prominent factors in the etiology of most forms of autism. Our goal is to determine whether a predictive model based on single-nucleotide polymorphisms (SNPs)…

A Web-Based Genetic Polymorphism Learning Approach for High School Students and Science Teachers

ERIC Educational Resources Information Center

Amenkhienan, Ehichoya; Smith, Edward J.

2006-01-01

Variation and polymorphism are concepts that are central to genetics and genomics, primary biological disciplines in which high school students and undergraduates require a solid foundation. From 1998 through 2002, a web-based genetics education program was developed for high school teachers and students. The program included an exercise on using…

Gene and Stress History Interplay in Emergence of PTSD-like Features

DTIC Science & Technology

2015-05-27

35–50. [9] Hetherington MM, Cecil JE. Gene–environment interactions in obesity . Forum Nutr 2010;63:195–203. [10] Lau JY, Eley TC. Gene–environment...Psychiatry 2010;34(3):459–62. [56] Binder EB, et al. Association of FKBP5 polymorphisms and childhood abuse with risk of posttraumatic stress disorder

Correlation of PD-1/PD-L1 polymorphisms and expressions with clinicopathologic features and prognosis of ovarian cancer.

PubMed

Tan, Dan; Sheng, Li; Yi, Qing-Hua

2018-02-06

To explore the correlation of PD-1/PD-L1 polymorphisms and their expressions with clinicopathologic features and prognosis of ovarian cancer. A total of 164 patients with ovarian cancer were enrolled as case group and 170 healthy women as control group. We conducted quantitative reverse transcription-PCR (qRT-PCR) to determine PD-1/PD-L1 expressions in peripheral blood mononuclear cells (PBMCs). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and allele-specific amplification were used to detect PD-1 rs2227982 C>T and PD-L1 rs4143815 C>G. PD-1 rs2227982 C>T and PD-L1 rs4143815 C>G polymorphisms increased the risk for ovarian cancer. PD-1 rs2227982 C>T was associated with FIGO stage and differentiation grade, while PD-L1 rs4143815 C>G was correlated with histological type and differentiation grade. Besides, PD-1/PD-L1 expressions were positively correlated in PBMCs of patients with ovarian cancer to be associated with differentiation grade. Compared with wild homozygous patients, PD-1/PD-L1 expressions were significantly decreased in PBMCs of ovarian cancer patients carried with the mutant genotypes of rs2227982 C>T and rs4143815 C>G. The PFS and OS in ovarian cancer patients with wild homozygous genotype of rs2227982 C>T and rs4143815 C>G were significantly higher than those with mutant genotypes, which were significantly lower in patients with low expressions of PD-1/PD-L1 than those with high expressions. Univariate COX regression analysis identified FIGO staging, differentiation grade, rs2227982 C>T, rs4143815 C>G and expressions of PD-1/PD-L1 as the prognostic factors, and multivariate COX regression analysis demonstrated that high FIGO stage and low expressions of PD-1/PD-L1 were independent risk factors for the prognosis of ovarian cancer. PD-1 rs2227982 C>T and PD-L1 rs4143815 C>G polymorphisms increased the risk of ovarian cancer, leading to a poor prognosis, associated with low expressions of PD-1 and PD-L1. While high PD-1 and PD-L1 expressions are indicators of a favorable prognosis in ovarian cancer.

Fas and Fas ligand gene polymorphisms in Turkish patients with Familial Mediterranean Fever.

PubMed

Ozel, Emine Gulce; Duran, Gulay Gulbol; Celik, Muhammet Murat; Duran, Nizami; Gunesacar, Ramazan

2017-08-05

Familial Mediterranean Fever (FMF) is an autosomal recessive autoinflammatory disorder characterized by recurrent fever, serositis, abdominal pain, arthritis, arthralgia and erysipelas like erythema. Fas and Fas ligand molecules play a central role in the apoptosis signaling of various cell types including neutrophils. Neutrophils are the major cell population involved in acute inflammation in patients with FMF and the role of Fas and Fas ligand molecules in this cells of FMF patients may be crucial. Therefore, in the present study, we aimed to investigate whether the Fas cell surface receptor gene (FAS); NM_000043.5: c.-671A>G (rs1800682, MvaI) and Fas ligand gene (FASLG), NM_000639.2: c.-844C>T (rs763110, BsrD1) functional polymorphisms in patients with FMF and their relation to the main clinical features of the disease. The polymorphisms in the promoter regions of FAS c.-671A>G and FASLG c.-844C>T were investigated in 97 non-related FMF patients and 70 non-related healthy controls by using PCR-RFLP technique. The frequencies of FAS c-671AG genotype and G allele were not significantly different between FMF patients and healthy subjects. The frequency of FASLG -844TC genotype was found significantly different between the patients with FMF and healthy controls whereas T or C allele frequency was not significantly different between the groups. Haplotype frequencies of the studied polymorphisms were also not significantly different between FMF patients and controls. There were no correlations between the studied FAS c.-671A>G and FASLG c.-844C>T polymorphisms and the main clinical features of FMF such as fever, arthritis, abdominal and chest pain, arthralgia and erysipelas-like erythema. Our findings suggest that FAS c.-671AG genotype or G allele and FASLG c.-844 allele are not to be a risk factor, whereas FASLG c.-844TC genotype may be protective in the studied Turkish population. According to our results we may suggest that although not statistically significant, higher frequencies of FASLG c.-844CC genotype in FMF patients may be related to delayed apoptosis of neutrophils and ultimately cause neutrophilic inflammation by increasing FASLG expression. Copyright © 2017 Elsevier B.V. All rights reserved.

One-Carbon Metabolism and Breast Cancer Survival in a Population-Based Study

DTIC Science & Technology

2007-06-01

methylation patterns; gene promoter methylation pattern and overall survival; and one-carbon polymorphisms and treatment regimen in relation to survival... treatment strategy. BODY Task 1. To genotype polymorphisms in one-carbon-metabolizing genes on 1087 BC cases (Months 1- 24) Genotyping...modifying effect of one-carbon gene polymorphisms on chemotherapy response in relation to breast cancer survival. Results were summarized in Table 2. The

DPYD*2A and MTHFR C677T predict toxicity and efficacy, respectively, in patients on chemotherapy with 5-fluorouracil for colorectal cancer.

PubMed

Nahid, Noor Ahmed; Apu, Mohd Nazmul Hasan; Islam, Md Reazul; Shabnaz, Samia; Chowdhury, Surid Mohammad; Ahmed, Maizbha Uddin; Nahar, Zabun; Islam, Md Siddiqul; Islam, Mohammad Safiqul; Hasnat, Abul

2018-01-01

Significant inter-individual variation in the sensitivity to 5-fluorouracil (5-FU) represents a major therapeutic hindrance either by impairing drug response or inducing adverse drug reactions (ADRs). This study aimed at exploring the cause behind this inter-individual alterations in consequences of 5-fluorouracil-based chemotherapy by investigating the effects of DPYD*2A and MTHFR C677T polymorphisms on toxicity and response of 5-FU in Bangladeshi colorectal cancer patients. Colorectal cancer patients (n = 161) receiving 5-FU-based chemotherapy were prospectively enrolled. DPYD and MTHFR polymorphisms were assessed in peripheral leukocytes. Multivariate analyses were applied to evaluate which variables could predict chemotherapy-induced toxicity and efficacy. Multivariate analyses showed that DPYD*2A polymorphism was a predictive factor (P = 0.023) for grade 3 and grade 4 5-fluorouracil-related toxicities. Although MTHFR C677T polymorphism might act as forecasters for grade 3 or grade 4 neutropenia, diarrhea, and mucositis, this polymorphism was found to increase significantly (P = 0.006) the response of 5-FU. DPYD*2A and MTHFR C677T polymorphisms could explain 5-FU toxicity or clinical outcome in Bangladeshi colorectal patients.

Selection and use of microsatellite markers for individual identification and meat traceability of six swine breeds in the Chinese market.

PubMed

Zhao, Jie; Li, Tingting; Zhu, Chao; Jiang, Xiaoling; Zhao, Yan; Xu, Zhenzhen; Yang, Shuming; Chen, Ailiang

2018-06-01

Meat traceability based on molecular markers is exerting a great influence on food safety and will enhance its key role in the future. This study aimed to investigate and verify the polymorphism of 23 microsatellite markers and select the most suitable markers for individual identification and meat traceability of six swine breeds in the Chinese market. The mean polymorphism information content value of these 23 loci was 0.7851, and each locus exhibited high polymorphism in the pooled population. There were 10 loci showing good polymorphism in each breed, namely, Sw632, S0155, Sw2406, Sw830, Sw2525, Sw72, Sw2448, Sw911, Sw122 and CGA. When six highly polymorphic loci were combined, the match probability value for two random individual genotypes among the pig breeds (Beijing Black, Sanyuan and Taihu) was lower than 1.151 E-06. An increasing number of loci indicated a gradually decreasing match probability value and therefore enhanced traceability accuracy. The validation results of tracing 18 blood and corresponding meat samples based on five highly polymorphic loci (Sw2525, S0005, Sw0107, Sw911 and Sw857) were successful, with 100% conformation probability, which provided a foundation for establishing a traceability system for pork in the Chinese market.

Exploring the role of ionic liquids to tune the polymorphic outcome of organic compounds.

PubMed

Zeng, Qingying; Mukherjee, Arijit; Müller, Peter; Rogers, Robin D; Myerson, Allan S

2018-02-14

While molecular solvents are commonly used in the screening of polymorphs, the choices are often restricted. Ionic liquids (ILs) - also referred as designer solvents - have immense possibility in this regard because of their wide flexibility of tunability. More importantly, the interactions among the IL components are completely unique compared to those present in the molecular solvents. In this context, we have chosen tetrolic acid (TA) and isonicotinamide (INA), which showed solution-structure link in molecular solvents in the past, as probes to investigate the role of imidazolium based ionic liquids in the polymorphism of these two systems and whether the different solute-solvent interactions in ILs affect the polymorphic outcome. It is observed that the selected imidazolium-based ILs, with varying anion basicity have influenced the crystallization outcome by the interaction between ILs and model compounds. Later, we have utilized the concept of double salt ionic liquids (DSIL) for INA, a penta-morphic system, to investigate the variation in the polymorphic outcome. This approach helped to obtain the forms that were otherwise inaccessible in ILs.

KRAS polymorphisms are associated with survival of CRC in Chinese population.

PubMed

Dai, Qiong; Wei, Hui Lian; Huang, Juan; Zhou, Tie Jun; Chai, Li; Yang, Zhi-Hui

2016-04-01

rs12245, rs12587, rs9266, rs1137282, rs61764370, and rs712 of KRAS oncogene are characterized in the 3'UTR. The study highlights the important role of these polymorphisms playing in the susceptibility, oxaliplatin-based chemotherapy sensitivity, progression, and prognosis of CRC. Improved multiplex ligation detection reaction (iMLDR) technique is used for genotyping. An unconditional logistic regression model was used to estimate the association of certain polymorphism and CRC risk. The Kaplan-Meier method, log-rank test, and Cox regression model were used to evaluate the effects of polymorphisms on survival analysis. Results demonstrated that TT genotype and T allele of rs712 were associated with the increased risk of CRC; the patients with GG genotype and G allele of rs61764370 had a shorter survival and a higher risk of relapse or metastasis of CRC. Our studies supported the conclusions that rs61764370 and rs712 polymorphisms of the KRAS are functional and it may play an important role in the development of CRC and oxaliplatin-based chemotherapy efficiency and prognosis of CRC.

Polymorphisms in RAI and in genes of nucleotide and base excision repair are not associated with risk of testicular cancer.

PubMed

Laska, Magdalena J; Nexø, Bjørn A; Vistisen, Kirsten; Poulsen, Henrik Enghusen; Loft, Steffen; Vogel, Ulla

2005-07-28

Testicular cancer has been suggested to be primed in utero and there is familiar occurrence, particularly brothers and sons of men with testicular cancer have increased risk. Although no specific causative genotoxic agents have been identified, variations in DNA repair capacity could be associated with the risk of testicular cancer. A case-control study of 184 testicular cancer cases and 194 population-based controls living in the Copenhagen Greater Area in Denmark was performed. We found that neither polymorphisms in several DNA repair genes nor alleles of several polymorphisms in the chromosomal of region 19q13.2-3, encompassing the genes ASE, ERCC1, RAI and XPD, were associated with risk of testicular cancer in Danish patients. This is in contrast to other cancers, where we reported strong associations between polymorphisms in ERCC1, ASE and RAI and occurrence of basal cell carcinoma, breast cancer and lung. To our knowledge this is the first study of DNA repair gene polymorphisms and risk of testicular cancer.

A preliminary report on the genetic variation in pointed gourd (Trichosanthes dioica Roxb.) as assessed by random amplified polymorphic DNA.

PubMed

Adhikari, S; Biswas, A; Bandyopadhyay, T K; Ghosh, P D

2014-06-01

Pointed gourd (Trichosanthes dioica Roxb.) is an economically important cucurbit and is extensively propagated through vegetative means, viz vine and root cuttings. As the accessions are poorly characterized it is important at the beginning of a breeding programme to discriminate among available genotypes to establish the level of genetic diversity. The genetic diversity of 10 pointed gourd races, referred to as accessions was evaluated. DNA profiling was generated using 10 sequence independent RAPD markers. A total of 58 scorable loci were observed out of which 18 (31.03%) loci were considered polymorphic. Genetic diversity parameters [average and effective number of alleles, Shannon's index, percent polymorphism, Nei's gene diversity, polymorphic information content (PIC)] for RAPD along with UPGMA clustering based on Jaccard's coefficient were estimated. The UPGMA dendogram constructed based on RAPD analysis in 10 pointed gourd accessions were found to be grouped in a single cluster and may represent members of one heterotic group. RAPD analysis showed promise as an effective tool in estimating genetic polymorphism in different accessions of pointed gourd.

Polymorphism complexity and handedness inversion in serum albumin amyloid fibrils.

PubMed

Usov, Ivan; Adamcik, Jozef; Mezzenga, Raffaele

2013-12-23

Protein-based amyloid fibrils can show a great variety of polymorphic structures within the same protein precursor, although the origins of these structural homologues remain poorly understood. In this work we investigate the fibrillation of bovine serum albumin--a model globular protein--and we follow the polymorphic evolution by a statistical analysis of high-resolution atomic force microscopy images, complemented, at larger length scales, by concepts based on polymer physics formalism. We identify six distinct classes of coexisting amyloid fibrils, including flexible left-handed twisted ribbons, rigid right-handed helical ribbons and nanotubes. We show that the rigid fibrils originate from flexible fibrils through two diverse polymorphic transitions, first, via a single-fibril transformation when the flexible left-handed twisted ribbons turn into the helical left-handed ribbons, to finally evolve into nanotube-like structures, and second, via a double-fibril transformation when two flexible left-handed twisted ribbons wind together resulting in a right-handed twisted ribbon, followed by a rigid right-handed helical ribbon polymorphic conformation. Hence, the change in handedness occurs with an increase in the level of the fibril's structural organization.

Prevalence of combinatorial CYP2C9 and VKORC1 genotypes in Puerto Ricans: implications for warfarin management in Hispanics.

PubMed

Duconge, Jorge; Cadilla, Carmen L; Windemuth, Andreas; Kocherla, Mohan; Gorowski, Krystyna; Seip, Richard L; Bogaard, Kali; Renta, Jessica Y; Piovanetti, Paola; D'Agostino, Darrin; Santiago-Borrero, Pedro J; Ruaño, Gualberto

2009-01-01

Polymorphisms in the cytochrome P450 2C9 (CYP2C9) and vitamin K epoxide reductase complex subunit 1 (VKORC1) genes significantly alter the effective warfarin dose. We determined the frequencies of alleles, single carriers, and double carriers of single nucleotide polymorphisms (SNPs) in the CYP2C9 and VKORC1 genes in a Puerto Rican cohort and gauged the impact of these polymorphisms on warfarin dosage using a published algorithm. A total of 92 DNA samples were genotyped using Luminex x-MAP technology. The polymorphism frequencies were 6.52%, 5.43% and 28.8% for CYP2C9 *2, *3 and VKORC1-1639 C>A polymorphisms, respectively. The prevalence of combinatorial genotypes was 16% for carriers of both the CYP2C9 and VKORC1 polymorphisms, 9% for carriers of CYP2C9 polymorphisms, 35% for carriers of the VKORC1 polymorphism, and the remaining 40% were non-carriers for either gene. Based on a published warfarin dosing algorithm, single, double and triple carriers of functionally deficient polymorphisms predict reductions of 1.0-1.6, 2.0-2.9, and 2.9-3.7 mg/day, respectively, in warfarin dose. Overall, 60% of the population carried at least a single polymorphism predicting deficient warfarin metabolism or responsiveness and 13% were double carriers with polymorphisms in both genes studied. Combinatorial genotyping of CYP2C9 and VKORC1 can allow for individualized dosing of warfarin among patients with gene polymorphisms, potentially reducing the risk of stroke or bleeding.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, Shea N.; McLoughlin, Kevin; Be, Nicholas A.

Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne alphavirus that has caused large outbreaks of severe illness in both horses and humans. New approaches are needed to rapidly infer the origin of a newly discovered VEEV strain, estimate its equine amplification and resultant epidemic potential, and predict human virulence phenotype. We performed whole genome single nucleotide polymorphism (SNP) analysis of all available VEE antigenic complex genomes, verified that a SNP-based phylogeny accurately captured the features of a phylogenetic tree based on multiple sequence alignment, and developed a high resolution genome-wide SNP microarray. We used the microarray to analyze a broadmore » panel of VEEV isolates, found excellent concordance between array- and sequence-based SNP calls, genotyped unsequenced isolates, and placed them on a phylogeny with sequenced genomes. The microarray successfully genotyped VEEV directly from tissue samples of an infected mouse, bypassing the need for viral isolation, culture and genomic sequencing. Lastly, we identified genomic variants associated with serotypes and host species, revealing a complex relationship between genotype and phenotype.« less

Shock-induced transformations in crystalline RDX: a uniaxial constant-stress Hugoniostat molecular dynamics simulation study.

PubMed

Bedrov, Dmitry; Hooper, Justin B; Smith, Grant D; Sewell, Thomas D

2009-07-21

Molecular dynamics (MD) simulations of uniaxial shock compression along the [100] and [001] directions in the alpha polymorph of hexahydro-1,3,5-trinitro-1,3,5-triazine (alpha-RDX) have been conducted over a wide range of shock pressures using the uniaxial constant stress Hugoniostat method [Ravelo et al., Phys. Rev. B 70, 014103 (2004)]. We demonstrate that the Hugoniostat method is suitable for studying shock compression in atomic-scale models of energetic materials without the necessity to consider the extremely large simulation cells required for an explicit shock wave simulation. Specifically, direct comparison of results obtained using the Hugoniostat approach to those reported by Thompson and co-workers [Phys. Rev. B 78, 014107 (2008)] based on large-scale MD simulations of shocks using the shock front absorbing boundary condition (SFABC) approach indicates that Hugoniostat simulations of systems containing several thousand molecules reproduced the salient features observed in the SFABC simulations involving roughly a quarter-million molecules, namely, nucleation and growth of nanoscale shear bands for shocks propagating along the [100] direction and the polymorphic alpha-gamma phase transition for shocks directed along the [001] direction. The Hugoniostat simulations yielded predictions of the Hugoniot elastic limit for the [100] shock direction consistent with SFABC simulation results.

The modulator driven polymorphism of Zr(IV) based metal–organic frameworks

PubMed Central

Drache, Franziska; Bon, Volodymyr; Getzschmann, Jürgen; Kaskel, Stefan

2017-01-01

The reaction of ZrCl4 and 2,5-thiophenedicarboxylic acid (H2tdc) in the presence of trifluoroacetic acid (Htfa) as modulator results in the formation of the new metal–organic framework (MOF) named DUT-126 (DUT = Dresden University of Technology). The nature and concentration of modulators are found to be decisive synthetic parameters affecting the topology of the formed product. DUT-126 (hbr) extends the series of polymorphs differing in topology, namely DUT-67 (reo), DUT-68 (bon) and DUT-69 (bct) to four, where DUT-67 and DUT-68 show the same eight-connected secondary building units as in DUT-126. In DUT-126, linker molecules have a peculiar orientation, resulting in hbr topology, which is described for the first time in this work for MOFs. DUT-126 contains three pore types, including two micropores surrounding mesoporous channels. DUT-126 is stable against hydrolysis and features permanent porosity with a specific surface area of 1297 m2 g−1 and a total pore volume of 0.48 cm3 g−1, calculated from the nitrogen physisorption isotherm measured at 77 K. This article is part of the themed issue ‘Coordination polymers and metal–organic frameworks: materials by design’. PMID:27895257

Use of inter-simple sequence repeats and amplified fragment length polymorphisms to analyze genetic relationships among small grain-infecting species of ustilago.

PubMed

Menzies, J G; Bakkeren, G; Matheson, F; Procunier, J D; Woods, S

2003-02-01

ABSTRACT In the smut fungi, few features are available for use as taxonomic criteria (spore size, shape, morphology, germination type, and host range). DNA-based molecular techniques are useful in expanding the traits considered in determining relationships among these fungi. We examined the phylogenetic relationships among seven species of Ustilago (U. avenae, U. bullata, U. hordei, U. kolleri, U. nigra, U. nuda, and U. tritici) using inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs) to compare their DNA profiles. Fifty-four isolates of different Ustilago spp. were analyzed using ISSR primers, and 16 isolates of Ustilago were studied using AFLP primers. The variability among isolates within species was low for all species except U. bullata. The isolates of U. bullata, U. nuda, and U. tritici were well separated and our data supports their speciation. U. avenae and U. kolleri isolates did not separate from each other and there was little variability between these species. U. hordei and U. nigra isolates also showed little variability between species, but the isolates from each species grouped together. Our data suggest that U. avenae and U. kolleri are monophyletic and should be considered one species, as should U. hordei and U. nigra.

Thermodynamics of HMX Polymorphs and HMX/RDX Mixtures

DOE PAGES

Myint, Philip C.; Nichols, Albert L.

2016-12-09

In this paper, we present thermodynamic models for the five most commonly studied phases of the energetic material octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX): liquid HMX and four solid polymorphs (α-, β-, γ-, and δ-HMX). We show results for the density, heat capacity, bulk modulus, and sound speed, as well as a phase diagram that illustrates the temperature and pressure regions over which the various HMX phases are most thermodynamically stable. The models are based on the same equation of state presented in our recently published paper [Myint et al., Ind. Eng. Chem. Res., 2016, 55, 2252] on another energetic material, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Wemore » combine our HMX and RDX models together so that the equation of state can also be applied to liquid and solid mixtures of HMX/RDX. This allows us to generate an HMX/RDX phase diagram and calculate the enthalpy change associated with a few different kinds of phase transitions that these mixtures may undergo. Our paper is the first to present a single equation of state that is capable of modeling both pure HMX and HMX/RDX mixtures. A distinct feature of HMX is the strongly metastable nature of its polymorphs. This has caused some ambiguity in the literature regarding the thermodynamic stability of α-HMX. Finally, by examining possible arrangements for the relative order of the six different solid-solid transition (α–β, α–γ, α–δ, β–γ, β–δ, and γ–δ) temperatures, we conclude that α-HMX must be thermodynamically stable so that the HMX phase diagram must have an α phase region.« less

Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms

PubMed Central

Mahoney, J. Matthew; Taroni, Jaclyn; Martyanov, Viktor; Wood, Tammara A.; Greene, Casey S.; Pioli, Patricia A.; Hinchcliff, Monique E.; Whitfield, Michael L.

2015-01-01

Systemic sclerosis (SSc) is a rare systemic autoimmune disease characterized by skin and organ fibrosis. The pathogenesis of SSc and its progression are poorly understood. The SSc intrinsic gene expression subsets (inflammatory, fibroproliferative, normal-like, and limited) are observed in multiple clinical cohorts of patients with SSc. Analysis of longitudinal skin biopsies suggests that a patient's subset assignment is stable over 6–12 months. Genetically, SSc is multi-factorial with many genetic risk loci for SSc generally and for specific clinical manifestations. Here we identify the genes consistently associated with the intrinsic subsets across three independent cohorts, show the relationship between these genes using a gene-gene interaction network, and place the genetic risk loci in the context of the intrinsic subsets. To identify gene expression modules common to three independent datasets from three different clinical centers, we developed a consensus clustering procedure based on mutual information of partitions, an information theory concept, and performed a meta-analysis of these genome-wide gene expression datasets. We created a gene-gene interaction network of the conserved molecular features across the intrinsic subsets and analyzed their connections with SSc-associated genetic polymorphisms. The network is composed of distinct, but interconnected, components related to interferon activation, M2 macrophages, adaptive immunity, extracellular matrix remodeling, and cell proliferation. The network shows extensive connections between the inflammatory- and fibroproliferative-specific genes. The network also shows connections between these subset-specific genes and 30 SSc-associated polymorphic genes including STAT4, BLK, IRF7, NOTCH4, PLAUR, CSK, IRAK1, and several human leukocyte antigen (HLA) genes. Our analyses suggest that the gene expression changes underlying the SSc subsets may be long-lived, but mechanistically interconnected and related to a patients underlying genetic risk. PMID:25569146

Association of PCK1 with Body Mass Index and Other Metabolic Features in Patients With Psychotropic Treatments.

PubMed

Saigi-Morgui, Núria; Vandenberghe, Frederik; Delacrétaz, Aurélie; Quteineh, Lina; Choong, Eva; Gholamrezaee, Mehdi; Magistretti, Pierre; Aubry, Jean-Michel; von Gunten, Armin; Preisig, Martin; Castelao, Enrique; Vollenweider, Peter; Waeber, Gerard; Kutalik, Zoltán; Conus, Philippe; Eap, Chin B

2015-10-01

Weight gain is a major health problem among psychiatric populations. It implicates several receptors and hormones involved in energy balance and metabolism. Phosphoenolpyruvate carboxykinase 1 is a rate-controlling enzyme involved in gluconeogenesis, glyceroneogenesis and cataplerosis and has been related to obesity and diabetes phenotypes in animals and humans. The aim of this study was to investigate the association of phosphoenolpyruvate carboxykinase 1 polymorphisms with metabolic traits in psychiatric patients treated with psychotropic drugs inducing weight gain and in general population samples. One polymorphism (rs11552145G > A) significantly associated with body mass index in the psychiatric discovery sample (n = 478) was replicated in 2 other psychiatric samples (n1 = 168, n2 = 188), with AA-genotype carriers having lower body mass index as compared to G-allele carriers. Stronger associations were found among women younger than 45 years carrying AA-genotype as compared to G-allele carriers (-2.25 kg/m, n = 151, P = 0.009) and in the discovery sample (-2.20 kg/m, n = 423, P = 0.0004). In the discovery sample for which metabolic parameters were available, AA-genotype showed lower waist circumference (-6.86 cm, P = 0.008) and triglycerides levels (-5.58 mg/100 mL, P < 0.002) when compared to G-allele carriers. Finally, waist-to-hip ratio was associated with rs6070157 (proxy of rs11552145, r = 0.99) in a population-based sample (N = 123,865, P = 0.022). Our results suggest an association of rs11552145G > A polymorphism with metabolic-related traits, especially in psychiatric populations and in women younger than 45 years.

Homocysteine and the C677T Gene Polymorphism of Its Key Metabolic Enzyme MTHFR Are Risk Factors of Early Renal Damage in Hypertension in a Chinese Han Population

PubMed Central

Yun, Lin; Xu, Rui; Li, Guohua; Yao, Yucai; Li, Jiamin; Cong, Dehong; Xu, Xingshun; Zhang, Lihua

2015-01-01

Abstract The combined hyperhomocysteinemia condition is a feature of the Chinese hypertensive population. This study used the case-control method to investigate the association between plasma homocysteine and the C677T gene polymorphism of its key metabolic enzyme, 5, 10-methylenetetrahydrofolate reductase (MTHFR), and early renal damage in a hypertensive Chinese Han population. A total of 379 adult essential hypertensive patients were selected as the study subjects. The personal information, clinical indicators, and the C677T gene polymorphism of MTHFR were texted. This study used the urine microalbumin/urine creatinine ratio (UACR) as a grouping basis: the hypertension without renal damage group (NRD group) and the hypertension combined with early renal damage group (ERD group). Early renal damage in the Chinese hypertensive population was associated with body weight, systolic pressure, diastolic pressure, urea nitrogen, serum creatinine, cystatin C, uric acid, aldosterone, and glomerular filtration rate. The homocysteine level and the UACR in the TT genotype group were higher than those in the CC genotype group. The binary logistic regression analysis results showed that after sex and age were adjusted, the MTHFR C677T gene polymorphism was correlated with early renal damage in hypertension in both the recessive model and in the additive model. Plasma homocysteine and the C677T gene polymorphism of its key metabolic enzyme MTHFR might be independent risk factors of early renal damage in the hypertensive Chinese Han population. PMID:26717388

TSHR intronic polymorphisms (rs179247 and rs12885526) and their role in the susceptibility of the Brazilian population to Graves' disease and Graves' ophthalmopathy.

PubMed

Bufalo, N E; Dos Santos, R B; Marcello, M A; Piai, R P; Secolin, R; Romaldini, J H; Ward, L S

2015-05-01

Intronic thyroid-stimulating hormone receptor polymorphisms have been associated with the risk for both Graves' disease and Graves' ophthalmopathy, but results have been inconsistent among different populations. We aimed to investigate the influence of thyroid-stimulating hormone receptor intronic polymorphisms in a large well-characterized population of GD patients. We studied 279 Graves' disease patients (231 females and 48 males, 39.80 ± 11.69 years old), including 144 with Graves' ophthalmopathy, matched to 296 healthy control individuals. Thyroid-stimulating hormone receptor genotypes of rs179247 and rs12885526 were determined by Real Time PCR TaqMan(®) SNP Genotyping. A multivariate analysis showed that the inheritance of the thyroid-stimulating hormone receptor AA genotype for rs179247 increased the risk for Graves' disease (OR = 2.821; 95 % CI 1.595-4.990; p = 0.0004), whereas the thyroid-stimulating hormone receptor GG genotype for rs12885526 increased the risk for Graves' ophthalmopathy (OR = 2.940; 95 % CI 1.320-6.548; p = 0.0083). Individuals with Graves' ophthalmopathy also presented lower mean thyrotropin receptor antibodies levels (96.3 ± 143.9 U/L) than individuals without Graves' ophthalmopathy (98.3 ± 201.9 U/L). We did not find any association between the investigated polymorphisms and patients clinical features or outcome. We demonstrate that thyroid-stimulating hormone receptor intronic polymorphisms are associated with the susceptibility to Graves' disease and Graves' ophthalmopathy in the Brazilian population, but do not appear to influence the disease course.

Development of novel polymorphic microsatellite markers for the silver fox (Vulpes vulpes).

PubMed

Yan, S Q; Bai, C Y; Qi, S M; Li, Y M; Li, W J; Sun, J H

2015-06-01

The silver fox (Vulpes vulpes), a coat color variant of the red fox, is one of the most important fur-bearing animals. To date, development of microsatellite loci for the silver fox has been limited and mainly based on cross-amplification by using canine SSR primers. In this study, 28 polymorphic microsatellite markers were isolated and identified for silver fox through the construction and screening of an (AC)n-enriched library. The number of alleles per locus ranged from 2 to 8 based on 48 individuals tested. The expected and observed hetero- zygosity and polymorphism information content per locus ranged from 0.2544 to 0.859, 0.2083 to 0.7917, and 0.2181 to 0.821, respectively. The polymorphic markers presented in this study may be useful for future analysis of the genetic diversity and population structure of farmed silver fox and wild red fox.

Improved prediction of biochemical recurrence after radical prostatectomy by genetic polymorphisms.

PubMed

Morote, Juan; Del Amo, Jokin; Borque, Angel; Ars, Elisabet; Hernández, Carlos; Herranz, Felipe; Arruza, Antonio; Llarena, Roberto; Planas, Jacques; Viso, María J; Palou, Joan; Raventós, Carles X; Tejedor, Diego; Artieda, Marta; Simón, Laureano; Martínez, Antonio; Rioja, Luis A

2010-08-01

Single nucleotide polymorphisms are inherited genetic variations that can predispose or protect individuals against clinical events. We hypothesized that single nucleotide polymorphism profiling may improve the prediction of biochemical recurrence after radical prostatectomy. We performed a retrospective, multi-institutional study of 703 patients treated with radical prostatectomy for clinically localized prostate cancer who had at least 5 years of followup after surgery. All patients were genotyped for 83 prostate cancer related single nucleotide polymorphisms using a low density oligonucleotide microarray. Baseline clinicopathological variables and single nucleotide polymorphisms were analyzed to predict biochemical recurrence within 5 years using stepwise logistic regression. Discrimination was measured by ROC curve AUC, specificity, sensitivity, predictive values, net reclassification improvement and integrated discrimination index. The overall biochemical recurrence rate was 35%. The model with the best fit combined 8 covariates, including the 5 clinicopathological variables prostate specific antigen, Gleason score, pathological stage, lymph node involvement and margin status, and 3 single nucleotide polymorphisms at the KLK2, SULT1A1 and TLR4 genes. Model predictive power was defined by 80% positive predictive value, 74% negative predictive value and an AUC of 0.78. The model based on clinicopathological variables plus single nucleotide polymorphisms showed significant improvement over the model without single nucleotide polymorphisms, as indicated by 23.3% net reclassification improvement (p = 0.003), integrated discrimination index (p <0.001) and likelihood ratio test (p <0.001). Internal validation proved model robustness (bootstrap corrected AUC 0.78, range 0.74 to 0.82). The calibration plot showed close agreement between biochemical recurrence observed and predicted probabilities. Predicting biochemical recurrence after radical prostatectomy based on clinicopathological data can be significantly improved by including patient genetic information. Copyright (c) 2010 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Human Alu insertion polymorphisms in North African populations.

PubMed

Cherni, Loth; Frigi, Sabeh; Ennafaa, Hajer; Mtiraoui, Nabil; Mahjoub, Touhami; Benammar-Elgaaied, Amel

2011-10-01

Several features make Alu insertions a powerful tool used in population genetic studies: the polymorphic nature of many Alu insertions, the stability of an Alu insertion event and, furthermore, the ancestral state of an Alu insertion is known to be the absence of the Alu element at a particular locus and the presence of an Alu insertion at the site that forward mutational change. This study analyses seven Alu insertion polymorphisms in a sample of 297 individuals from the autochthonous population of Tunisia (Thala, Smar, Zarzis, and Bou Salem) and Libya with the aim of studying their genetic structure with respect to the populations of North Africa, Western, Eastern and Central Europe. The comparative analyses carried out using the MDS and AMOVA methods reveal the existence of spatial heterogeneity, and identify four population groups. Study populations (Libya, Smar, Zarzis, and Bou Salem) are closest to North African populations whereas Thala is isolated and is closest to Western European populations. In conclusion, Results of the present study support the important role that migratory movements have played in the North African gene pool, at least since the Neolithic period.

Analysis of the association between CD40 and CD40 ligand polymorphisms and systemic sclerosis.

PubMed

Teruel, María; Simeon, Carmen P; Broen, Jasper; Vonk, Madelon C; Carreira, Patricia; Camps, Maria Teresa; García-Portales, Rosa; Delgado-Frías, Esmeralda; Gallego, Maria; Espinosa, Gerard; Beretta, Lorenzo; Airó, Paolo; Lunardi, Claudio; Riemekasten, Gabriela; Witte, Torsten; Krieg, Thomas; Kreuter, Alexander; Distler, Jörg H W; Hunzelmann, Nicolas; Koeleman, Bobby P; Voskuyl, Alexandre E; Schuerwegh, Annemie J; González-Gay, Miguel Angel; Radstake, Timothy R D J; Martin, Javier

2012-06-25

The aim of the present study was to investigate the possible role of CD40 and CD40 ligand (CD40LG) genes in the susceptibility and phenotype expression of systemic sclerosis (SSc). In total, 2,670 SSc patients and 3,245 healthy individuals from four European populations (Spain, Germany, The Netherlands, and Italy) were included in the study. Five single-nucleotide polymorphisms (SNPs) of CD40 (rs1883832, rs4810485, rs1535045) and CD40LG (rs3092952, rs3092920) were genotyped by using a predesigned TaqMan allele-discrimination assay technology. Meta-analysis was assessed to determine whether an association exists between the genetic variants and SSc or its main clinical subtypes. No evidence of association between CD40 and CD40LG genes variants and susceptibility to SSc was observed. Similarly, no significant statistical differences were observed when SSc patients were stratified by the clinical subtypes, the serologic features, and pulmonary fibrosis. Our results do not suggest an important role of CD40 and CD40LG gene polymorphisms in the susceptibility to or clinical expression of SSc.

Selecting the spin crossover profile with controlled crystallization of mononuclear Fe(iii) polymorphs.

PubMed

Vicente, Ana I; Ferreira, Liliana P; Carvalho, Maria de Deus; Rodrigues, Vítor H N; Dîrtu, Marinela M; Garcia, Yann; Calhorda, Maria José; Martinho, Paulo N

2018-05-08

Two polymorphic species of the [Fe(5-Br-salEen)2]ClO4 compound were obtained, each of them being selectively recovered after evaporation of the solvent at a controlled rate. While polymorph 1a is formed during slow evaporation, fast evaporation favors polymorph 1b. The importance of the evaporation rate was recognized after detailed studies of the reaction temperature, solvent evaporation rate and crystallization temperature effects. The complex in the new polymorphic form 1a showed an abrupt spin crossover at 172 K with a small 1 K hysteresis window and over a narrow 10 K range. 57Fe Mössbauer spectroscopy and differential scanning calorimetry, complemented by X-ray studies for both the high-spin and low-spin forms, were used to further characterize the new polymorphic phase 1a. Both polymorphs are based on the same Fe(iii) complex cation hydrogen bonded to the perchlorate anion. These units are loosely bound in the crystals via weak interactions. In the new polymorph 1a, the hydrogen bonds are stronger, while the weak hydrogen and halogen bonds, as well as π-π stacking, create a cooperative network, not present in 1b, responsible for the spin transition profile.

Association of ACE Gene I/D polymorphism with migraine in Kashmiri population.

PubMed

Wani, Irfan Yousuf; Sheikh, Saleem; Shah, Zafar Amin; Pandith, Arshid A; Wani, Mushtaq; Asimi, Ravouf; Wani, Maqbool; Sheikh, Shahnawaz; Mehraj, Iqra

2016-01-01

Migraine is a complex, recurrent headache disorder that is one of the most common complaints in neurology practice. The role of various genes in its pathogenesis is being studied. We did this study to see whether an association exists between ACE gene I/D polymorphism and migraine in our region. The study included 100 patients diagnosed with migraine and 121 healthy controls. The study subject were age and gender matched. The analysis was based on Polymerase Chain Reaction (PCR) and included following steps: DNA extraction from blood, PCR and Restriction Fragment Length Polymorphism (RFLP). Out of 100 cases, 69 were females and 31 were males. Fifty-seven were having migraine without aura and 43 had migraine with aura. 45 of the cases had II polymorphism, 40 had ID polymorphism and 15 had DD polymorphism in ACE gene. We were not able to find a statistically significant association between ACE gene I/D polymorphism with migraine. The reason for difference in results between our study and other studies could be because of different ethnicity in study populations. So a continuous research is needed in this regard in order to find the genes and different polymorphism that increase the susceptibility of Kashmiri population to migraine.

Evaluation of Genetic Variations in Maize Seedlings Exposed to Electric Field Based on Protein and DNA Markers

PubMed Central

AL-Huqail, Asma A.; Abdelhaliem, Ekram

2015-01-01

The current study analyzed proteins and nuclear DNA of electric fields (ELF) exposed and nonexposed maize seedlings for different exposure periods using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), isozymes, random amplified polymorphic DNA (RAPD), and comet assay, respectively. SDS-PAGE analysis revealed total of 46 polypeptides bands with different molecular weights ranging from 186.20 to 36.00 KDa. It generated distinctive polymorphism value of 84.62%. Leucine-aminopeptidase, peroxidase, and catalase isozymes showed the highest values of polymorphism (100%) based on zymograms number, relative front (R f), and optical intensity while esterase isozyme generated polymorphism value of 83.33%. Amino acids were analyzed using high-performance liquid chromatography, which revealed the presence of 17 amino acids of variable contents ranging from 22.65% to 28.09%. RAPD revealed that 78 amplified DNA products had highly polymorphism value (95.08%) based on band numbers, with variable sizes ranging from 120 to 992 base pairs and band intensity. Comet assay recorded the highest extent of nuclear DNA damage as percentage of tailed DNA (2.38%) and tail moment unit (5.36) at ELF exposure of maize nuclei for 5 days. The current study concluded that the longer ELF exposing periods had genotoxic stress on macromolecules of maize cells and biomarkers used should be augmented for reliable estimates of genotoxicity after exposure of economic plants to ELF stressors. PMID:26180815

RAPD and SSR Polymorphisms in Mutant Lines of Transgenic Wheat Mediated by Low Energy Ion Beam

NASA Astrophysics Data System (ADS)

Wang, Tiegu; Huang, Qunce; Feng, Weisen

2007-10-01

Two types of markers-random amplified polymorphic DNA (RAPD) and simple sequence repeat DNA (SSR)-have been used to characterize the genetic diversity among nine mutant lines of transgenic wheat intermediated by low energy ion beam and their four receptor cultivars. The objectives of this study were to analyze RAPD-based and SSR-based genetic variance among transgenic wheat lines and with their receptors, and to find specific genetic markers of special traits of transgenic wheat lines. 170 RAPD primers were amplified to 733 fragments in all the experimental materials. There were 121 polymorphic fragments out of the 733 fragments with a ratio of polymorphic fragments of 16.5%. 29 SSR primer pairs were amplified to 83 fragments in all the experiment materials. There were 57 polymorphic fragments out of the 83 fragments with a ratio of polymorphic fragments of 68.7%. The dendrograms were prepared based on a genetic distance matrix using the UPGMA (Unweighted Pair-group Method with Arithmetic averaging) algorithm, which corresponded well to the results of the wheat pedigree analysis and separated the 13 genotypes into four groups. Association analysis between RAPD and SSR markers with the special traits of transgenic wheat mutant lines discovered that three RAPD markers, s1, opt-16, and f14, were significantly associated with the muticate trait, while three SSR markers, Rht8 (Xgwm261), Rht-B1b, and Rht-D1b, highly associated with the dwarf trait. These markers will be useful for marker-assistant breeding and can be used as candidate markers for further gene mapping and cloning.

The role of the RTEL1 rs2297440 polymorphism in the risk of glioma development: a meta-analysis.

PubMed

Zhang, Cuiping; Lu, Yu; Zhang, Xiaolian; Yang, Dongmei; Shang, Shuxin; Liu, Denghe; Jiang, Kongmei; Huang, Weiqiang

2016-07-01

The regulator of the telomere elongation helicase1 (RTEL1) gene plays a crucial role in the DNA double-stand break-repair pathway by maintaining genomic stability. Recent epidemiological studies showed that the rs2297440 polymorphism in the RTEL1 gene was a potential risk locus for glioma development, but the results were inconclusive. To clarify the association between this polymorphism and the risk of glioma, we performed a comprehensive meta-analysis. The PubMed, EMBASE, Web of Science, and China National Knowledge Infrastructure databases were systematically searched to identify all relevant published studies up to 30 August 2015. Four eligible studies were finally included. The pooled results indicated that the RTEL1 rs2297440 polymorphism moderately increased the risk of glioma in all genetic models. A comparison of the dominant model CT + CC versus TT (OR 1.40; 95 % CI 1.24-1.60; p < 0.001) indicated that having the C allele conferred a 40 % increased risk of developing glioma. In a subgroup analysis based on geographic location (Europe, Asia, and America), there was an association between the rs2297440 polymorphism and the risk of glioma in all three areas. The results of the subgroup analysis based on source of control indicated an elevated risk of glioma in population-based control studies. This meta-analysis demonstrates that the RTEL1 rs2297440 polymorphism plays a moderate, but significant role in the risk of glioma. Further studies with larger sample sizes are necessary to confirm this finding.

Association of P53 gene polymorphism with gastric cancer in Northern Iran as a high-risk region.

PubMed

Hedayatizadeh-Omran, Akbar; Alizadeh-Navaei, Reza; Janbabaei, Ghasem; Omrani-Nava, Versa; Hasheminasab, Yahya; Amjadi, Omolbanin; Tehrani, Mohsen

2018-05-01

Gastric cancer has the fourth highest morbidity rate of all cancers worldwide. Genetic factors including alterations in oncogenes and tumor suppressor genes serve an important role in gastric cancer development and progression. The P53 gene acts as a tumor suppressor gene by regulating the cell cycle, DNA transcription and repair, apoptosis, senescence and genome stability. In addition to somatic P53 mutations in cancer development, germline polymorphisms are also involved in different malignancies. The polymorphism of P53 at codon 72 (Arg72Pro) is established as a common variant that increases susceptibility to various cancers. The present case-control study was conducted to evaluate the possible association between this P53 polymorphism and gastric cancer in the Iranian population. A total of 59 patients with gastric cancer and 59 healthy controls were enrolled in the present study. Genomic DNA was extracted from peripheral blood mononuclear cells and genotype analysis was performed using a polymerase chain reaction-based restriction fragment length polymorphism assay. Genotype frequencies did not differ significantly between the patients and controls (P=0.4); the frequencies of the three genotypes Arg/Arg, Arg/Pro and Pro/Pro in gastric cancer patients were 28.8, 49.2 and 22.0%, and in controls were 37.3, 49.2 and 13.6%. Additionally, there were no differences in genotype frequencies based on tumor location, histological differentiation or tumor stage. Based on these findings, it may be concluded that the P53 codon 72 polymorphism does not contribute to gastric cancer susceptibility in Northern Iran.

First principles study of pressure induced polymorphic phase transition in KNO3

NASA Astrophysics Data System (ADS)

Yedukondalu, N.; Vaitheeswaran, G.

2015-06-01

We report the structural, elastic, electronic, and vibrational properties of polymorphic phases II and III of KNO3 based on density functional theory (DFT). Using semi-empirical dispersion correction (DFT-D2) method, we predicted the correct thermodynamic ground state of KNO3 and the obtained ground state properties of the polymorphs are in good agreement with the experiments. We further used this method to calculate the elastic constants, IR and Raman spectra, vibrational frequencies and their assignment of these polymorphs. The calculated Tran Blaha-modified Becke Johnson (TB-mBJ) electronic structure shows that both the polymorphic phases are direct band gap insulators with mixed ionic and covalent bonding. Also the TB-mBJ band gaps are improved over standard DFT functionals which are comparable with the available experiments.

LRP-1 polymorphism is associated with global and regional amyloid load in Alzheimer's disease in humans in-vivo

PubMed Central

Grimmer, Timo; Goldhardt, Oliver; Guo, Liang-Hao; Yousefi, Behrooz H.; Förster, Stefan; Drzezga, Alexander; Sorg, Christian; Alexopoulos, Panagiotis; Förstl, Hans; Kurz, Alexander; Perneczky, Robert

2014-01-01

Objective Impaired amyloid clearance has been proposed to contribute to β-amyloid deposition in sporadic late-onset Alzheimer's disease (AD). Low density lipoprotein receptor-related protein 1 (LRP-1) is involved in the active outward transport of β-amyloid across the blood–brain barrier (BBB). The C667T polymorphism (rs1799986) of the LRP-1 gene has been inconsistently associated with AD in genetic studies. We aimed to elucidate the association of this polymorphism with in-vivo brain amyloid load of AD patients using amyloid PET with [11C]PiB. Materials and methods 72 patients with very mild to moderate AD were examined with amyloid PET and C667T polymorphism was obtained using TaqMan PCR assays. The association of C667T polymorphism with global and regional amyloid load was calculated using linear regression and voxel based analysis, respectively. The effect of the previously identified modulator of amyloid uptake, the apolipoprotein E genotype, on this association was also determined. Results The regression analysis between amyloid load and C667T polymorphism was statistically significant (p = 0.046, β = 0.236). In an additional analysis ApoE genotype and gender were identified to explain further variability of amyloid load. Voxel based analysis revealed a significant (p < 0.05) association between C667T polymorphism and amyloid uptake in the temporo-parietal cortex bilaterally. ApoE did not interact significantly with the LRP-1 polymorphism. Discussion In conclusion, C667T polymorphism of LRP-1 is moderately but significantly associated with global and regional amyloid deposition in AD. The relationship appears to be independent of the ApoE genotype. This finding is compatible with the hypothesis that impaired amyloid clearance contributes to amyloid deposition in late-onset sporadic AD. PMID:24596678

Interaction between cholesteryl ester transfer protein and hepatic lipase encoding genes and the risk of type 2 diabetes: results from the Telde study.

PubMed

López-Ríos, Laura; Nóvoa, Francisco J; Chirino, Ricardo; Varillas, Francisco; Boronat-Cortés, Mauro; Wägner, Ana M

2011-01-01

Diabetic dyslipidaemia is common in type 2 diabetes (T2D) and insulin resistance and often precedes the onset of T2D. The Taq1B polymorphism in CETP (B1 and B2 alleles) (rs708272) and the G-250A polymorphism in LIPC (rs2070895) are associated with changes in enzyme activity and lipid concentrations. Our aim was to assess the effects of both polymorphisms on the risk of T2D. In a case-control study from the population-based Telde cohort, both polymorphisms were analysed by PCR-based methods. Subjects were classified, according to an oral glucose tolerance test, into diabetic (N = 115) and pre-diabetic (N = 116); 226 subjects with normal glucose tolerance, matched for age and gender, were included as controls. Chi-square (comparison between groups) and logistic regression (identification of independent effects) were used for analysis. The B1B1 Taq1B CETP genotype frequency increased with worsening glucose metabolism (42.5%, 46.1% and 54.3% in control, IGR and diabetic group; p = 0.042). This polymorphism was independently associated with an increased risk of diabetes (OR: 1.828; IC 95%: 1.12-2.99; p = 0.016), even after adjusting by confounding variables, whereas the LIPC polymorphism was not. Regarding the interaction between both polymorphisms, in the B1B1 genotype carriers, the absence of the minor (A) allele of the LIPC polymorphism increased the risk of having diabetes. The presence of the B1B1 Taq1B CETP genotype contributes to the presence of diabetes, independently of age, sex, BMI and waist. However, among carriers of B1B1, the presence of GG genotype of the -250 LIPC polymorphism increases this risk further.

Three reversible polymorphic copper(I) complexes triggered by ligand conformation: insights into polymorphic crystal habit and luminescent properties.

PubMed

Chai, Wenxiang; Hong, Mingwei; Song, Li; Jia, Guohua; Shi, Hongsheng; Guo, Jiayu; Shu, Kangying; Guo, Bing; Zhang, Yicheng; You, Wenwu; Chen, Xueyuan

2015-05-04

Three luminescent polymorphs based on a new copper(I) complex Cu(2-QBO)(PPh3)PF6 (1, PPh3 = triphenylphosphine, 2-QBO = 2-(2'-quinolyl)benzoxazole) have been synthesized and characterized by FT-IR, UV-vis, elemental analyses, and single-crystal X-ray diffraction analyses. Each polymorph can reversibly convert from one to another through appropriate procedures. Interestingly, such interconversion can be distinguished by their intrinsic crystal morphologies and colors (namely α, dark yellow plate, β, orange block, γ, light yellow needle) as well as photoluminescent (PL) properties. X-ray crystal structure analyses of these three polymorphs show three different supramolecular structures from 1D to 3D, which are expected to be responsible for the formation of three different crystal morphologies such as needle, plate, and block. Combination of the experimental data with DFT calculations on these three polymorphs reveals that the polymorphic interconversion is triggered by the conformation isomerization of the 2-QBO ligand and can be successfully controlled by the polarity of the process solvents (affecting the molecular dipole moment) and thermodynamics (affecting the molecular total energy). It is also found that the different crystal colors of polymorphs and their PL properties are derived from different θ values (dihedral angle between benzoxazolyl and quinolyl group of the 2-QBO ligand) and P-Cu-P angles based on TD-DFT calculations. Moreover, an interesting phase interconversion between γ and β has also been found under different temperature, and this result is consistent with the DFT calculations in which the total energy of β is larger than that of γ. This polymorphism provides a good model to study the relationship between the structure and the physical properties in luminescent copper(I) complexes as well as some profound insights into their PL properties.

A novel, non-functional, COL1A1 polymorphism is not associated with lumbar disk disease in young male Greek subjects unlike that of the Sp1 site

PubMed Central

Bei, Thalia; Tilkeridis, Constantinos; Garantziotis, Stavros; Boikos, Sosipatros A.; Kazakos, Konstantinos; Simopoulos, Constantinos; Stratakis, Constantine A.

2011-01-01

OBJECTIVE We recently reported the association of the Sp1 site polymorphism of the COL1A1 gene with lumbar disk disease (LDD). In the present study we searched for a different polymorphism of the COL1A1 gene (which is usually not in linkage disequilibrium with the Sp1 site) in subjects with LDD. DESIGN Blood was collected from 24 Greek army recruits, aged 29±7.6 years, with LDD, and 66 healthy men, aged 26±4.38 years, matched for body mass index (BMI) and age, with normal BMD and with no history of trauma or fractures, who served as controls. DNA was extracted and the COL1A1 gene was sequenced. Of the control subjects, 12 were army recruits and 54 were selected from the general population. RESULTS The four base-pair insertion polymorphism in the COL1A1 gene analyzed by polymerase chain reaction amplification of DNA produces two different fragments (alleles A1 and A2): 14 patients (58.3%) were homozygous for A2A2, versus 35 controls (53%), while 3 patients (12.5%) were A1A1, and 8 of the control subjects (12%) had this genotype. There were no statistically significant differences in the presence of the two alleles of this polymorphism between patients with LDD and control subjects. CONCLUSIONS A four base-pair insertion polymorphism of the COL1A1 gene is not associated with the presence of LDD in young males, unlike the Sp1 site polymorphism of the same gene. These data reinforce the association between LDD and the functional polymorphisms of the Sp1 site by showing that other polymorphic sites of the of the COL1A1 gene in the same population of patients are not linked to the disease. PMID:18694864

Genetic and epigenetic status of triple exotic consanguinity cotton introgression lines.

PubMed

He, S P; Sun, J L; Du, X M

2011-10-03

Introgression lines are some of the most important germplasm for breeding applications and other research conducted on cotton crops. The DNA methylation level among 10 introgression lines of cotton (Gossypium hirsutum) and three exotic parental species (G. arboreum, G. thurberi and G. barbadense) were assessed by methylation-sensitive amplified polymorphism (MSAP) technology. The methylation level in the introgression lines ranged from 33.3 to 51.5%. However, the lines PD0111 and PD0113 had the lowest methylation level (34.6 and 33.3%, respectively) due to demethylation of most non-coding sequences. Amplified fragment length polymorphism (AFLP) was used to evaluate the genetic polymorphism in the cotton introgression lines. A high degree of polymorphism was observed in all introgression lines (mean 47.2%) based on AFLP and MSAP analyses. This confirmed the effects of genetic improvement on cotton introgression lines. The low methylation varieties, PD0111 and PD0113 (introgression lines), clustered outside of the introgression lines based on MSAP data, which was incongruent with an AFLP-based dendrogram. This phenomenon could be caused by environmental changes or introgression of exotic DNA fragments.

Detection of Variation in Long-Term Micropropagated Mature Pistachio via DNA-Based Molecular Markers.

PubMed

Akdemir, Hülya; Suzerer, Veysel; Tilkat, Engin; Onay, Ahmet; Çiftçi, Yelda Ozden

2016-12-01

Determination of genetic stability of in vitro-grown plantlets is needed for safe and large-scale production of mature trees. In this study, genetic variation of long-term micropropagated mature pistachio developed through direct shoot bud regeneration using apical buds (protocol A) and in vitro-derived leaves (protocol B) was assessed via DNA-based molecular markers. Randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and amplified fragment length polymorphism (AFLP) were employed, and the obtained PIC values from RAPD (0.226), ISSR (0.220), and AFLP (0.241) showed that micropropagation of pistachio for different periods of time resulted in "reasonable polymorphism" among donor plant and its 18 clones. Mantel's test showed a consistence polymorphism level between marker systems based on similarity matrices. In conclusion, this is the first study on occurrence of genetic variability in long-term micropropagated mature pistachio plantlets. The obtained results clearly indicated that different marker approaches used in this study are reliable for assessing tissue culture-induced variations in long-term cultured pistachio plantlets.

Distributed and dynamic intracellular organization of extracellular information.

PubMed

Granados, Alejandro A; Pietsch, Julian M J; Cepeda-Humerez, Sarah A; Farquhar, Iseabail L; Tkačik, Gašper; Swain, Peter S

2018-06-05

Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.

[Morphological pathology of vessels in granulomatosis with polyangiitis (Wegener's disease)].

PubMed

Zerbino, D D; Zimba, E A

2015-01-01

to investigate the incidence of injuries in different vascular beds and the morphopathological changes in vessels in granulomatosis with polyangiitis. The morphopathological features of vascular injuries were investigated in 11 dead patients aged 16--74 years with granulomatosis with polyangiitis. Proliferative and destructive angiitis with predominant involvement of microcirculatory vessels and with development of necrosis-prone granulomas in their walls and perivascularly was established to underlie the clinical manifestations of granulomatosis with polyangiitis. The most typical localization of the pathologic process is the vessels of the upper respiratory tract, lungs, and kidneys. Cardiopulmonary and renal failures are causes of death in the majority of cases. It should be noted that the vessels of the heart, liver, and gastrointestinal tract are frequently involved in the pathological process. Vascular changes in these organs determine the clinical features of granulomatosis with polyangiitis and lead to a number of fatal complications. Granulomatosis with polyangiitis is a systemic disease with polymorphism of clinical manifestations, which requires in-depth analysis based on current precision patient examination methods, including a histopathological study.

Single crystal growth in spin-coated films of polymorphic phthalocyanine derivative under solvent vapor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Higashi, T.; Ohmori, M.; Ramananarivo, M. F.

2015-12-01

The effects of solvent vapor on spin-coated films of a polymorphic phthalocyanine derivative were investigated. Growth of single crystal films via redissolving organic films under solvent vapor was revealed by in situ microscopic observations of the films. X-ray diffraction measurement of the films after exposing to solvent vapor revealed the phase transition of polymorphs under solvent vapor. The direction of crystal growth was clarified by measuring the crystal orientation in a grown monodomain film. The mechanism of crystal growth based on redissolving organic films under solvent vapor was discussed in terms of the different solubilities of the polymorphs.

No association between catechol-O-methyltransferase polymorphisms and neurotic disorders among mainland Chinese university students.

PubMed

Kou, Changgui; Meng, Xiangfei; Xie, Bing; Shi, Jieping; Yu, Qiong; Yu, Yaqin; D'Arcy, Carl

2012-07-30

This study investigates the genetic association between catechol-O-methyltransferase (COMT) gene polymorphisms and neurotic disorders. Data were derived from a case-control association study of 255 undergraduates affected by neurotic disorders and 269 matched healthy undergraduate controls. The polymorphisms of eight tag single nucleotide polymorphisms (SNPs) on the COMT gene were tested using polymerase chain reaction (PCR)-based Ligase Detection Reaction (PCR-LDR). The eight tag SNPs on the COMT gene assessed were not associated with neurotic disorders. Our finding suggests that the COMT gene may not be a susceptibility gene for neurotic disorders. Copyright © 2012 Elsevier Ltd. All rights reserved.

PREVALENCE OF COMBINATORIAL CYP2C9 AND VKORC1 GENOTYPES IN PUERTO RICANS: IMPLICATIONS FOR WARFARIN MANAGEMENT IN HISPANICS

PubMed Central

Duconge, Jorge; Cadilla, Carmen L.; Windemuth, Andreas; Kocherla, Mohan; Gorowski, Krystyna; Seip, Richard L.; Bogaard, Kali; Renta, Jessica Y.; Piovanetti, Paola; D’Agostino, Darrin; Santiago-Borrero, Pedro J.; Ruaño, Gualberto

2010-01-01

Polymorphisms in the cytochrome P450 2C9 (CYP2C9) and vitamin K epoxide reductase complex subunit 1 (VKORC1) genes significantly alter the effective warfarin dose. We determined the frequencies of alleles, single carriers, and double carriers of single nucleotide polymorphisms (SNPs) in the CYP2C9 and VKORC1 genes in a Puerto Rican cohort and gauged the impact of these polymorphisms on warfarin dosage using a published algorithm. A total of 92 DNA samples were genotyped using Luminex® x-MAP technology. The polymorphism frequencies were 6.52%, 5.43% and 28.8% for CYP2C9 *2, *3 and VKORC1-1639 G>A polymorphisms, respectively. The prevalence of combinatorial genotypes was 16% for carriers of both the CYP2C9 and VKORC1 polymorphisms, 9% for carriers of CYP2C9 polymorphisms, 35% for carriers of the VKORC1 polymorphism, and the remaining 40% were non-carriers for either gene. Based on a published warfarin dosing algorithm, single, double and triple carriers of functionally deficient polymorphisms predict reductions of 1.0–1.6, 2.0–2.9, and 2.9–3.7 mg/day, respectively, in warfarin dose. Overall, 60% of the population carried at least a single polymorphism predicting deficient warfarin metabolism or responsiveness and 13% were double carriers with polymorphisms in both genes studied. Combinatorial genotyping of CYP2C9 and VKORC1 can allow for individualized dosing of warfarin among patients with gene polymorphisms, potentially reducing the risk of stroke or bleeding. PMID:20073138

The role of androgen receptor activity mediated by the CAG repeat polymorphism in the pathogenesis of PCOS.

PubMed

Baculescu, N

2013-03-15

Polycystic ovary syndrome (PCOS), one of the most common and complex endocrine disorders affecting up to 15 % of reproductive age women, is considered a predominantly hyperandrogenic syndrome according to the Androgen Excess Society. It is generally accepted that androgens determine the characteristic features of PCOS; in this context, a hyperactive androgen receptor (AR) at the levels of the GnRH pulse generator in the hypothalamus and at the granulosa cells in the ovary, skeletal muscle or adipocytes senses initially normal testosterone and dihydrotestosterone as biochemical hyperandrogenism and might be a crucial connection between the vicious circles of the PCOS pathogenesis. Polymorphism of the AR gene has been associated with different androgen pattern diseases. Several studies have demonstrated an association between AR with increased activity encoded by shorter CAG repeat polymorphism in the exon 1 of the AR gene and PCOS, although there are conflicting results in this field. The phenomenon is more complex because the AR activity is determined by the epigenetic effect of X chromosome inactivation (XCI). Moreover, we must evaluate the AR as a dynamic heterocomplex, with a large number of coactivators and corepressors that are essential to its function, thus mediating tissue-specific effects. In theory, any of these factors could modify the activity of AR, which likely explains the inconsistent results obtained when this activity was quantified by only the CAG polymorphism in PCOS.

Rapid genetic and epigenetic alterations under intergeneric genomic shock in newly synthesized Chrysanthemum morifolium x Leucanthemum paludosum hybrids (Asteraceae).

PubMed

Wang, Haibin; Jiang, Jiafu; Chen, Sumei; Qi, Xiangyu; Fang, Weimin; Guan, Zhiyong; Teng, Nianjun; Liao, Yuan; Chen, Fadi

2014-01-01

The Asteraceae family is at the forefront of the evolution due to frequent hybridization. Hybridization is associated with the induction of widespread genetic and epigenetic changes and has played an important role in the evolution of many plant taxa. We attempted the intergeneric cross Chrysanthemum morifolium × Leucanthemum paludosum. To obtain the success in cross, we have to turn to ovule rescue. DNA profiling of the amphihaploid and amphidiploid was investigated using amplified fragment length polymorphism, sequence-related amplified polymorphism, start codon targeted polymorphism, and methylation-sensitive amplification polymorphism (MSAP). Hybridization induced rapid changes at the genetic and the epigenetic levels. The genetic changes mainly involved loss of parental fragments and gaining of novel fragments, and some eliminated sequences possibly from the noncoding region of L. paludosum. The MSAP analysis indicated that the level of DNA methylation was lower in the amphiploid (∼45%) than in the parental lines (51.5-50.6%), whereas it increased after amphidiploid formation. Events associated with intergeneric genomic shock were a feature of C. morifolium × L. paludosum hybrid, given that the genetic relationship between the parental species is relatively distant. Our results provide genetic and epigenetic evidence for understanding genomic shock in wide crosses between species in Asteraceae and suggest a need to expand our current evolutionary framework to encompass a genetic/epigenetic dimension when seeking to understand wide crosses.

Chromosome-wide linkage disequilibrium caused by an inversion polymorphism in the white-throated sparrow (Zonotrichia albicollis).

PubMed

Huynh, L Y; Maney, D L; Thomas, J W

2011-04-01

Chromosomal inversions have been of long-standing interest to geneticists because they are capable of suppressing recombination and facilitating the formation of adaptive gene complexes. An exceptional inversion polymorphism (ZAL2(m)) in the white-throated sparrow (Zonotrichia albicollis) is linked to variation in plumage, social behavior and mate choice, and is maintained in the population by negative assortative mating. The ZAL2(m) polymorphism is a complex inversion spanning > 100 Mb and has been proposed to be a strong suppressor of recombination, as well as a potential model for studying neo-sex chromosome evolution. To quantify and evaluate these features of the ZAL2(m) polymorphism, we generated sequence from 8 ZAL2(m) and 16 ZAL2 chromosomes at 58 loci inside and 4 loci outside the inversion. Inside the inversion we found that recombination was completely suppressed between ZAL2 and ZAL2(m), resulting in uniformly high levels of genetic differentiation (F(ST)=0.94), the formation of two distinct haplotype groups representing the alternate chromosome arrangements and extensive linkage disequilibrium spanning ~104 Mb within the inversion, whereas gene flow was not suppressed outside the inversion. Finally, although ZAL2(m) homozygotes are exceedingly rare in the population, occurring at a frequency of < 1%, we detected evidence of historical recombination between ZAL2(m) chromosomes inside the inversion, refuting its potential status as a non-recombining autosome.

The Role of Lattice Matching Techniques in the Characterization of Polymorphic Forms.

PubMed

Mighell, Alan D

2011-01-01

An inspection of the recent literature reveals that polymorphism is a frequently encountered phenomenon. The recognition of polymorphic forms plays a vital role in the materials sciences because such structures are characterized by different crystal packing and accordingly have different physical properties. In the pharmaceutical industry, recognition of polymorphic forms can be critical for, in certain cases, a polymorphic form of a drug may be an ineffective therapeutic agent due to its unfavorable physical properties. A check of the recent literature has revealed that in some cases new polymorphic forms are not recognized. In other instances, a supposedly new polymeric form is actually the result of an incorrect structure determination. Fortunately, lattice-matching techniques, which have proved invaluable in the identification and characterization of crystal structures, represent a powerful tool for analyzing polymorphic forms. These lattice-matching methods are based on either of two strategies: (a) the reduced cell strategy-the matching of reduced cells of the respective lattices or (b) the matrix strategy-the determination of a matrix or matrices relating the two lattices coupled with an analysis of the matrix elements. Herein, these techniques are applied to three typical cases-(a) the identification of a new polymorphic form, (b) the demonstration that a substance may not be a new polymorphic form due to missed symmetry, and (c) the evaluation of pseudo polymorphism because of a missed lattice. To identify new polymorphic forms and to prevent errors, it is recommended that these lattice matching techniques become an integral part of the editorial review process of crystallography journals.

Genetic Variants Associated with Hyperandrogenemia in PCOS Pathophysiology

PubMed Central

2018-01-01

Polycystic ovary syndrome is a multifactorial endocrine disorder whose pathophysiology baffles many researchers till today. This syndrome is typically characterized by anovulatory cycles and infertility, altered gonadotropin levels, obesity, and bulky multifollicular ovaries on ultrasound. Hyperandrogenism and insulin resistance are hallmark features of its complex pathophysiology. Hyperandrogenemia is a salient feature of PCOS and a major contributor to cosmetic anomalies including hirsutism, acne, and male pattern alopecia in affected women. Increased androgen levels may be intrinsic or aggravated by preexisting insulin resistance in women with PCOS. Studies have reported augmented ovarian steroidogenesis patterns attributed mainly to theca cell hypertrophy and altered expression of key enzymes in the steroidogenic pathway. Candidate gene studies have been performed in order to delineate the association of polymorphisms in genes, which encode enzymes in the intricate cascade of steroidogenesis or modulate the levels and action of circulating androgens, with risk of PCOS development and its related traits. However, inconsistent findings have impacted the emergence of a unanimously accepted genetic marker for PCOS susceptibility. In the current review, we have summarized the influence of polymorphisms in important androgen related genes in governing genetic predisposition to PCOS and its related metabolic and reproductive traits. PMID:29670770

Self-assembly of hard helices: a rich and unconventional polymorphism.

PubMed

Kolli, Hima Bindu; Frezza, Elisa; Cinacchi, Giorgio; Ferrarini, Alberta; Giacometti, Achille; Hudson, Toby S; De Michele, Cristiano; Sciortino, Francesco

2014-11-07

Hard helices can be regarded as a paradigmatic elementary model for a number of natural and synthetic soft matter systems, all featuring the helix as their basic structural unit, from natural polynucleotides and polypeptides to synthetic helical polymers, and from bacterial flagella to colloidal helices. Here we present an extensive investigation of the phase diagram of hard helices using a variety of methods. Isobaric Monte Carlo numerical simulations are used to trace the phase diagram; on going from the low-density isotropic to the high-density compact phases a rich polymorphism is observed, exhibiting a special chiral screw-like nematic phase and a number of chiral and/or polar smectic phases. We present full characterization of the latter, showing that they have unconventional features, ascribable to the helical shape of the constituent particles. Equal area construction is used to locate the isotropic-to-nematic phase transition, and the results are compared with those stemming from an Onsager-like theory. Density functional theory is also used to study the nematic-to-screw-nematic phase transition; within the simplifying assumption of perfectly parallel helices, we compare different levels of approximation, that is second- and third-virial expansions and a Parsons-Lee correction.

Non-Canonical G-quadruplexes cause the hCEB1 minisatellite instability in Saccharomyces cerevisiae

PubMed Central

Piazza, Aurèle; Cui, Xiaojie; Adrian, Michael; Samazan, Frédéric; Heddi, Brahim; Phan, Anh-Tuan; Nicolas, Alain G

2017-01-01

G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids in vitro, but the sequence and structural features dictating their formation and function in vivo remains uncertain. Here we report a structure-function analysis of the complex hCEB1 G4-forming sequence. We isolated four G4 conformations in vitro, all of which bear unusual structural features: Form 1 bears a V-shaped loop and a snapback guanine; Form 2 contains a terminal G-triad; Form 3 bears a zero-nucleotide loop; and Form 4 is a zero-nucleotide loop monomer or an interlocked dimer. In vivo, Form 1 and Form 2 differently account for 2/3rd of the genomic instability of hCEB1 in two G4-stabilizing conditions. Form 3 and an unidentified form contribute to the remaining instability, while Form 4 has no detectable effect. This work underscores the structural polymorphisms originated from a single highly G-rich sequence and demonstrates the existence of non-canonical G4s in cells, thus broadening the definition of G4-forming sequences. DOI: http://dx.doi.org/10.7554/eLife.26884.001 PMID:28661396

[Polymorphism of alcohol dehydrogenase gene ADH1B in eastern Slavic and Iranian-speaking populations].

PubMed

2005-11-01

Frequencies of alleles and genotypes for alcohol dehydrogenase gene ADH1B (arg47his polymorphism), associated with alcohol tolerance/sensitivity, were determined. It was demonstrated that the frequency of allele ADH1B*47his, corresponding to atypical alcohol dehydrogenase variant in Russians, Ukrainians, Iranians, and mountain-dwellers of the Pamirs constituted 3, 7, 24, and 22%, respectively. The frequencies established were consistent with the allele frequency distribution pattern among the populations of Eurasia. Russians and Ukrainians were indistinguishable from other European populations relative to the frequency of allele ADH1B*47his, and consequently, relative to specific features of ethanol metabolic pathways. The data obtained provide refinement of the geographic pattern of ADH1B*47his frequency distribution in Eurasia.

Juvenile Spring Eruption: A Variant of Perniosis?

PubMed

Nabatian, Adam S; Rosman, Ilana S; Sturza, Jeffrey; Jacobson, Mark

2015-09-01

Juvenile spring eruption (JSE) is a unique condition that typically affects the helices of the ears of boys and young men. The classical clinical picture of JSE includes the abrupt onset of lesions after spending time outdoors in the early spring. Because of the papulovesicular nature of the rash and the history of sun exposure, JSE is considered a variant of polymorphous light eruption. In addition to the term "juvenile spring eruption," this entity has also been described under other less common terms such as "perniosis juvenilis vernalis aurium" or "spring perniosis," which emphasizes the onset in the spring and the possible pathogenic role of cold weather. We present a case of likely JSE with histopathologic features more consistent with perniosis than polymorphous light eruption and present a review the literature.

Binding of Thioflavin T and Related Probes to Polymorphic Models of Amyloid-β Fibrils.

PubMed

Peccati, Francesca; Pantaleone, Stefano; Riffet, Vanessa; Solans-Monfort, Xavier; Contreras-García, Julia; Guallar, Victor; Sodupe, Mariona

2017-09-28

Alzheimer's disease is a challenge of the utmost importance for contemporary society. An early diagnosis is essential for the development of treatments and for establishing a network of support for the patient. In this light, the deposition in the brain of amyloid-β fibrillar aggregates, which is a distinctive feature of Alzheimer, is key for an early detection of this disease. In this work we propose an atomistic study of the interaction of amyloid tracers with recently published polymorphic models of amyloid-β 1-40 and 1-42 fibrils, highlighting the relationship between marker architectures and binding affinity. This work uncovers the importance of quaternary structure, and in particular of junctions between amyloid-β protofilaments, as the key areas for marker binding.

Characterization of Capsicum species using anatomical and molecular data.

PubMed

Dias, G B; Gomes, V M; Moraes, T M S; Zottich, U P; Rabelo, G R; Carvalho, A O; Moulin, M; Gonçalves, L S A; Rodrigues, R; Da Cunha, M

2013-02-28

Capsicum species are frequently described in terms of genetic divergence, considering morphological, agronomic, and molecular databases. However, descriptions of genetic differences based on anatomical characters are rare. We examined the anatomy and the micromorphology of vegetative and reproductive organs of several Capsicum species. Four Capsicum accessions representing the species C. annuum var. annuum, C. baccatum var. pendulum, C. chinense, and C. frutescens were cultivated in a greenhouse; leaves, fruits and seeds were sampled and their organ structure analyzed by light and scanning electronic microscopy. Molecular accession characterization was made using ISSR markers. Polymorphism was observed among tector trichomes and also in fruit color and shape. High variability among accessions was detected by ISSR markers. Despite the species studied present a wide morphological and molecular variability that was not reflected by anatomical features.

A Hierarchical Feature and Sample Selection Framework and Its Application for Alzheimer’s Disease Diagnosis

NASA Astrophysics Data System (ADS)

An, Le; Adeli, Ehsan; Liu, Mingxia; Zhang, Jun; Lee, Seong-Whan; Shen, Dinggang

2017-03-01

Classification is one of the most important tasks in machine learning. Due to feature redundancy or outliers in samples, using all available data for training a classifier may be suboptimal. For example, the Alzheimer’s disease (AD) is correlated with certain brain regions or single nucleotide polymorphisms (SNPs), and identification of relevant features is critical for computer-aided diagnosis. Many existing methods first select features from structural magnetic resonance imaging (MRI) or SNPs and then use those features to build the classifier. However, with the presence of many redundant features, the most discriminative features are difficult to be identified in a single step. Thus, we formulate a hierarchical feature and sample selection framework to gradually select informative features and discard ambiguous samples in multiple steps for improved classifier learning. To positively guide the data manifold preservation process, we utilize both labeled and unlabeled data during training, making our method semi-supervised. For validation, we conduct experiments on AD diagnosis by selecting mutually informative features from both MRI and SNP, and using the most discriminative samples for training. The superior classification results demonstrate the effectiveness of our approach, as compared with the rivals.

Characterization of six human disease-associated inversion polymorphisms.

PubMed

Antonacci, Francesca; Kidd, Jeffrey M; Marques-Bonet, Tomas; Ventura, Mario; Siswara, Priscillia; Jiang, Zhaoshi; Eichler, Evan E

2009-07-15

The human genome is a highly dynamic structure that shows a wide range of genetic polymorphic variation. Unlike other types of structural variation, little is known about inversion variants within normal individuals because such events are typically balanced and are difficult to detect and analyze by standard molecular approaches. Using sequence-based, cytogenetic and genotyping approaches, we characterized six large inversion polymorphisms that map to regions associated with genomic disorders with complex segmental duplications mapping at the breakpoints. We developed a metaphase FISH-based assay to genotype inversions and analyzed the chromosomes of 27 individuals from three HapMap populations. In this subset, we find that these inversions are less frequent or absent in Asians when compared with European and Yoruban populations. Analyzing multiple individuals from outgroup species of great apes, we show that most of these large inversion polymorphisms are specific to the human lineage with two exceptions, 17q21.31 and 8p23 inversions, which are found to be similarly polymorphic in other great ape species and where the inverted allele represents the ancestral state. Investigating linkage disequilibrium relationships with genotyped SNPs, we provide evidence that most of these inversions appear to have arisen on at least two different haplotype backgrounds. In these cases, discovery and genotyping methods based on SNPs may be confounded and molecular cytogenetics remains the only method to genotype these inversions.

Evaluation of genetic diversity in jackfruit (Artocarpus heterophyllus Lam.) based on amplified fragment length polymorphism markers.

PubMed

Shyamalamma, S; Chandra, S B C; Hegde, M; Naryanswamy, P

2008-07-22

Artocarpus heterophyllus Lam., commonly called jackfruit, is a medium-sized evergreen tree that bears high yields of the largest known edible fruit. Yet, it has been little explored commercially due to wide variation in fruit quality. The genetic diversity and genetic relatedness of 50 jackfruit accessions were studied using amplified fragment length polymorphism markers. Of 16 primer pairs evaluated, eight were selected for screening of genotypes based on the number and quality of polymorphic fragments produced. These primer combinations produced 5976 bands, 1267 (22%) of which were polymorphic. Among the jackfruit accessions, the similarity coefficient ranged from 0.137 to 0.978; the accessions also shared a large number of monomorphic fragments (78%). Cluster analysis and principal component analysis grouped all jackfruit genotypes into three major clusters. Cluster I included the genotypes grown in a jackfruit region of Karnataka, called Tamaka, with very dry conditions; cluster II contained the genotypes collected from locations having medium to heavy rainfall in Karnataka; cluster III grouped the genotypes in distant locations with different environmental conditions. Strong coincidence of these amplified fragment length polymorphism-based groupings with geographical localities as well as morphological characters was observed. We found moderate genetic diversity in these jackfruit accessions. This information should be useful for tree breeding programs, as part of our effort to popularize jackfruit as a commercial crop.

Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data

PubMed Central

Liu, Shi; Gao, Peng; Zhu, Qianglong; Luan, Feishi; Davis, Angela R.; Wang, Xiaolu

2016-01-01

Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). This study detected and converted SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon, for linkage map construction and quantitative trait locus (QTL) analysis. Two inbred lines, Cream of Saskatchewan (COS) and LSW-177 had been re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. 88.7% and 78.5% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. Comparative assembled genome data analysis provided 225,693 and 19,268 SNPs and indels between the two materials. 532 pairs of CAPS markers were designed with 16 restriction enzymes, among which 271 pairs of primers gave distinct bands of the expected length and polymorphic bands, via PCR and enzyme digestion, with a polymorphic rate of 50.94%. Using the new CAPS markers, an initial CAPS-based genetic linkage map was constructed with the F2 population, spanning 1836.51 cM with 11 linkage groups and 301 markers. 12 QTLs were detected related to fruit flesh color, length, width, shape index, and brix content. These newly CAPS markers will be a valuable resource for breeding programs and genetic studies of watermelon. PMID:27162496

Impact of Genetic Polymorphisms on the Smoking-related Risk of Periodontal Disease: the Population-based Study SHIP

PubMed Central

Meisel, P; Heins, G; Carlsson, LE; Giebel, J; John, U; Schwahn, C; Kocher, T

2003-01-01

Periodontitis is a bacterial inflammatory disease leading to attachment loss with the consequence of tooth loss. There exists a multifactorial risk pattern including bacterial challenge, smoking, age, sex, diabetes, socio-economic and genetic factors. Smoking has the highest impact on the course of the disease modulated by all the other factors. Here, we report the relationship between smoking and the polymorphisms of genetic polymorphisms inflicted in the pathogenesis. In a randomly selected population-based study, 1083 subjects were typed for the polymorphisms of the IL-1 genotype, Fcγ RIIIb receptor gene, myeloperoxidase and N-acetyltransferase (NAT2) and related to their periodontal state. Smoking behavior was assessed including present and past quality and quantity of smoking. There is a significant dose-effect relationship between the exposure to tobacco smoke and the extent of periodontal disease assessed as attachment loss and tooth loss. Moreover, there are gene-environmental interactions as subjects bearing variant genotypes show an enhanced smoking-associated risk of the disease modulated by these genotypes. In non-smokers, the impact of these genetic polymorphisms is mostly negligible. This study provides support for the hypothesis that subjects bearing genetic variants of polymorphically expressed phenotypes are at an increased risk of periodontitis when smoking. Mostly, this may be accomplished via the influence of smoking-related impairment on defense mechanisms rather than on the pathogenic pathways. PMID:19570260

Impact of Genetic Polymorphisms on the Smoking-related Risk of Periodontal Disease: the Population-based Study SHIP

PubMed Central

Meisel, P; Heins, G; Carlsson, LE; Giebel, J; John, U; Schwahn, C; Kocher, T

2003-01-01

Periodontitis is a bacterial inflammatory disease leading to attachment loss with the consequence of tooth loss. There exists a multifactorial risk pattern including bacterial challenge, smoking, age, sex, diabetes, socio-economic and genetic factors. Smoking has the highest impact on the course of the disease modulated by all the other factors. Here, we report the relationship between smoking and the polymorphisms of genetic polymorphisms inflicted in the pathogenesis. In a randomly selected population-based study, 1083 subjects were typed for the polymorphisms of the IL-1 genotype, Fcγ RIIIb receptor gene, myeloperoxidase and N-acetyltransferase (NAT2) and related to their periodontal state. Smoking behavior was assessed including present and past quality and quantity of smoking. There is a significant dose-effect relationship between the exposure to tobacco smoke and the extent of periodontal disease assessed as attachment loss and tooth loss. Moreover, there are gene-environmental interactions as subjects bearing variant genotypes show an enhanced smoking-associated risk of the disease modulated by these genotypes. In non-smokers, the impact of these genetic polymorphisms is mostly negligible. This study provides support for the hypothesis that subjects bearing genetic variants of polymorphically expressed phenotypes are at an increased risk of periodontitis when smoking. Mostly, this may be accomplished via the influence of smoking-related impairment on defense mechanisms rather than on the pathogenic pathways.

Solid state characterization and crystal structure from X-ray powder diffraction of two polymorphic forms of ranitidine base.

PubMed

de Armas, Héctor Novoa; Peeters, Oswald M; Blaton, Norbert; Van Gyseghem, Elke; Martens, Johan; Van Haele, Gerrit; Van Den Mooter, Guy

2009-01-01

Ranitidine hydrochloride (RAN-HCl), a known anti-ulcer drug, is the product of reaction between HCl and ranitidine base (RAN-B). RAN-HCl has been extensively studied; however this is not the case of the RAN-B. The solid state characterization of RAN-B polymorphs has been carried out using different analytical techniques (microscopy, thermal analysis, Fourier transform infrared spectrometry in the attenuated total reflection mode, (13)C-CPMAS-NMR spectroscopy and X-ray powder diffraction). The crystal structures of RAN-B form I and form II have been determined using conventional X-ray powder diffraction in combination with simulated annealing and whole profile pattern matching, and refined using rigid-body Rietveld refinement. RAN-B form I is a monoclinic polymorph with cell parameters: a = 7.317(2), b = 9.021(2), c = 25.098(6) A, beta = 95.690(1) degrees and space group P2(1)/c. The form II is orthorhombic: a = 31.252(4), b = 13.052(2), c = 8.0892(11) A with space group Pbca. In RAN-B polymorphs, the nitro group is involved in a strong intramolecular hydrogen bond responsible for the existence of a Z configuration in the enamine portion of the molecules. A tail to tail packing motif can be denoted via intermolecular hydrogen bonds. The crystal structures of RAN-B forms are compared to those of RAN-HCl polymorphs. RAN-B polymorphs are monotropic polymorphic pairs. (c) 2008 Wiley-Liss, Inc. and the American Pharmacists Association

Genetic diversity analysis of Jatropha curcas L. (Euphorbiaceae) based on methylation-sensitive amplification polymorphism.

PubMed

Kanchanaketu, T; Sangduen, N; Toojinda, T; Hongtrakul, V

2012-04-13

Genetic analysis of 56 samples of Jatropha curcas L. collected from Thailand and other countries was performed using the methylation-sensitive amplification polymorphism (MSAP) technique. Nine primer combinations were used to generate MSAP fingerprints. When the data were interpreted as amplified fragment length polymorphism (AFLP) markers, 471 markers were scored. All 56 samples were classified into three major groups: γ-irradiated, non-toxic and toxic accessions. Genetic similarity among the samples was extremely high, ranging from 0.95 to 1.00, which indicated very low genetic diversity in this species. The MSAP fingerprint was further analyzed for DNA methylation polymorphisms. The results revealed differences in the DNA methylation level among the samples. However, the samples collected from saline areas and some species hybrids showed specific DNA methylation patterns. AFLP data were used, together with methylation-sensitive AFLP (MS-AFLP) data, to construct a phylogenetic tree, resulting in higher efficiency to distinguish the samples. This combined analysis separated samples previously grouped in the AFLP analysis. This analysis also distinguished some hybrids. Principal component analysis was also performed; the results confirmed the separation in the phylogenetic tree. Some polymorphic bands, involving both nucleotide and DNA methylation polymorphism, that differed between toxic and non-toxic samples were identified, cloned and sequenced. BLAST analysis of these fragments revealed differences in DNA methylation in some known genes and nucleotide polymorphism in chloroplast DNA. We conclude that MSAP is a powerful technique for the study of genetic diversity for organisms that have a narrow genetic base.

Effect of GSTP1 and ABCC2 Polymorphisms on Treatment Response in Patients with Advanced Non-Small Cell Lung Cancer Undergoing Platinum-Based Chemotherapy: A Study in a Chinese Uygur Population.

PubMed

Han, Zhi-Gang; Tao, Jie; Yu, Ting-Ting; Shan, Li

2017-04-26

BACKGROUND Gene polymorphisms are associated with sensitivity to platinum drugs. This study aimed to investigate the polymorphisms of GSTP1 rs1695 locus and ABCC2 rs717620 locus, and the sensitivity of patients with advanced non-small cell lung cancer (NSCLC) to platinum drugs in a Xinjiang Uygur population. MATERIAL AND METHODS The gene polymorphisms of GSTP1 rs1695 and ABCC2 rs717620 of Uygur NSCLC patients were assessed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The relationship between the prognosis of advanced NSCLC Uygur patients and the gene polymorphisms of GSTP1 rs1695 and ABCC2 rs717620 was analyzed using progression-free survival (PFS) and overall survival (OS) as the major outcome indicators. RESULTS The median PFS of patients with advanced NSCLC was 6.9 months and the OS of Uygur patients with advanced NSCLC was 10.8 months. Kaplan-Meier survival analysis indicated that survival time of patients with GSTP1 AG + GG was significantly longer than in patients with AA gene (P<0.05), and survival time of patients with ABCC2 CT + TT was significantly longer than in patients with the CC gene (P<0.05). CONCLUSIONS Polymorphisms of GSTP1 rs1695 and ABCC2 rs717620 can be used to predict the outcomes of Uygur patients with advanced NSCLC who have received platinum-based chemotherapy. Additionally, this information could be used to guide the individualized treatment of Uygur patients with advanced NSCLC.

Roles of beta2-adrenergic receptor gene polymorphisms in a Turkish population with obstructive sleep apnea syndrome or obesity.

PubMed

Gök, I; Celebi, I; Hüseyinoğlu, N; Ozic, C

2014-10-20

We determined the distribution of the Arg16Gly and Gln27Glu polymorphisms of the beta-2 adrenergic receptor gene (ADRB2) in patients with obstructive sleep apnea syndrome as well as a control group in Northeastern Turkey. A total of 52 patients diagnosed with obstructive sleep apnea in a sleep laboratory and 78 control subjects were examined. Peripheral blood samples were taken from patients diagnosed with obstructive sleep apnea by polysomnography. DNA was extracted from blood samples and amplified using polymerase chain reaction. Amplification products were digested with restriction enzymes to investigate gene polymorphisms. Restriction products were extracted from agarose gel electrophoresis and polymorphisms were analyzed using gel images. The Arg16Gly polymorphism was observed in 18 of 52 patients and in 23 of 78 controls. The Gln27Glu polymorphism was observed in 21 of 52 patients and in 28 of 78 controls. In conclusion, there was no correlation among polymorphic frequencies between patient and control groups. Based on the results, these polymorphisms do not contribute to the clinical diagnosis of this syndrome. However, the distribution of Arg16Gly vs Gln27Glu polymorphisms may contribute to obesity in patients with a body mass index greater than 30 (P < 0.05). Different results may be obtained if the parameters of obstructive sleep apnea disease are changed.

Genetic variation of clock genes and cancer risk: a field synopsis and meta-analysis

PubMed Central

Benna, Clara; Helfrich-Förster, Charlotte; Rajendran, Senthilkumar; Monticelli, Halenya; Pilati, Pierluigi; Nitti, Donato; Mocellin, Simone

2017-01-01

BACKGROUND The number of studies on the association between clock genes’ polymorphisms and cancer susceptibility has increased over the last years but the results are often conflicting and no comprehensive overview and quantitative summary of the evidence in this field is available. RESULTS Literature search identified 27 eligible studies comprising 96756 subjects (cases: 38231) and investigating 687 polymorphisms involving 14 clock genes. Overall, 1025 primary and subgroup meta-analyses on 366 gene variants were performed. Study distribution by tumor was as follows: breast cancer (n=15), prostate cancer (n=3), pancreatic cancer (n=2), non-Hodgkin's lymphoma (n=2), glioma (n=1), chronic lymphocytic leukemia (n=1), colorectal cancer (n=1), non-small cell lung cancer (n=1) and ovarian cancer (n=1). We identified 10 single nucleotide polymorphisms (SNPs) significantly associated with cancer risk: NPAS2 rs10165970 (mixed and breast cancer shiftworkers), rs895520 (mixed), rs17024869 (breast) and rs7581886 (breast); CLOCK rs3749474 (breast) and rs11943456 (breast); RORA rs7164773 (breast and breast cancer postmenopausal), rs10519097 (breast); RORB rs7867494 (breast cancer postmenopausal), PER3 rs1012477 (breast cancer subgroups) and assessed the level of quality evidence to be intermediate. We also identified polymorphisms with lower quality statistically significant associations (n=30). CONCLUSIONS Our work supports the hypothesis that genetic variation of clock genes might affect cancer risk. These findings also highlight the need for more efforts in this research field in order to fully establish the contribution of clock gene variants to the risk of developing cancer. METHODS We conducted a systematic review and meta-analysis of the evidence on the association between clock genes’ germline variants and the risk of developing cancer. To assess result credibility, summary evidence was graded according to the Venice criteria and false positive report probability (FPRP) was calculated to further validate result noteworthiness. Subgroup meta-analysis was also performed based on participant features and tumor type. The breast cancer subgroup was further stratified by work conditions, estrogen receptor/progesterone receptor status and menopausal status, conditions associated with the risk of breast cancer in different studies. PMID:28177907

Genetic variation of clock genes and cancer risk: a field synopsis and meta-analysis.

PubMed

Benna, Clara; Helfrich-Förster, Charlotte; Rajendran, Senthilkumar; Monticelli, Halenya; Pilati, Pierluigi; Nitti, Donato; Mocellin, Simone

2017-04-04

The number of studies on the association between clock genes' polymorphisms and cancer susceptibility has increased over the last years but the results are often conflicting and no comprehensive overview and quantitative summary of the evidence in this field is available. Literature search identified 27 eligible studies comprising 96756 subjects (cases: 38231) and investigating 687 polymorphisms involving 14 clock genes. Overall, 1025 primary and subgroup meta-analyses on 366 gene variants were performed. Study distribution by tumor was as follows: breast cancer (n=15), prostate cancer (n=3), pancreatic cancer (n=2), non-Hodgkin's lymphoma (n=2), glioma (n=1), chronic lymphocytic leukemia (n=1), colorectal cancer (n=1), non-small cell lung cancer (n=1) and ovarian cancer (n=1).We identified 10 single nucleotide polymorphisms (SNPs) significantly associated with cancer risk: NPAS2 rs10165970 (mixed and breast cancer shiftworkers), rs895520 (mixed), rs17024869 (breast) and rs7581886 (breast); CLOCK rs3749474 (breast) and rs11943456 (breast); RORA rs7164773 (breast and breast cancer postmenopausal), rs10519097 (breast); RORB rs7867494 (breast cancer postmenopausal), PER3 rs1012477 (breast cancer subgroups) and assessed the level of quality evidence to be intermediate. We also identified polymorphisms with lower quality statistically significant associations (n=30). Our work supports the hypothesis that genetic variation of clock genes might affect cancer risk. These findings also highlight the need for more efforts in this research field in order to fully establish the contribution of clock gene variants to the risk of developing cancer. We conducted a systematic review and meta-analysis of the evidence on the association between clock genes' germline variants and the risk of developing cancer. To assess result credibility, summary evidence was graded according to the Venice criteria and false positive report probability (FPRP) was calculated to further validate result noteworthiness. Subgroup meta-analysis was also performed based on participant features and tumor type. The breast cancer subgroup was further stratified by work conditions, estrogen receptor/progesterone receptor status and menopausal status, conditions associated with the risk of breast cancer in different studies.

Beauveria keratitis and biopesticides: case histories and a random amplification of polymorphic DNA comparison.

PubMed

Pariseau, Brett; Nehls, Sarah; Ogawa, Gregory S H; Sutton, Deanna A; Wickes, Brian L; Romanelli, Anna M

2010-02-01

The purposes of this study were to describe 2 contact lens-associated Beauveria keratitis cases and to compare the isolates of 3 contact lens-associated Beauveria keratitis cases with Beauveria-based biopesticides using random amplification of polymorphic DNA (RAPD). A 55-year-old diabetic woman from New Mexico and a 31-year-old healthy woman from southern Wisconsin developed soft contact lens-related corneal ulcers unresponsive to topical moxifloxacin and prednisolone acetate drops. Their corneal cultures grew B. bassiana. These isolates, an isolate from a third soft contact lens-related Beauveria keratitis case, and Beauveria-based biopesticides sold in the United States were analyzed using morphological features, DNA sequencing, and RAPD. A PubMed, Cochrane Library, OVID, UpToDate, and Google search using the term "Beauveria" found only 9 reported Beauveria keratitis infections. Patient 1 responded to topical natamycin, ketoconazole, and 200 mg oral ketoconazole twice daily before developing a secondary bacterial infection requiring penetrating keratoplasty. After subsequent cataract surgery, the best-corrected visual acuity was 20/20. Patient 2 was treated with topical natamycin, topical amphotericin, and 200 mg oral voriconazole twice daily for 1 month with residual scarring and a best-corrected visual acuity of 20/25. RAPD showed that all isolates were unrelated. Although earlier reported Beauveria keratitis cases occurred after corneal injury in patients who did not wear contact lenses, 3 recent patients wore soft contact lenses and denied trauma, mirroring a changing trend in microbial keratitis. RAPD analysis showed that the Beauveria isolates were unrelated to one another and to Beauveria-based biopesticides. In Patient 2, oral voriconazole worked well.

Association between methylenetetrahydrofolate reductase polymorphisms and the relapse of acute lymphoblastic leukemia: a meta-analysis.

PubMed

He, H-R; Chen, S-Y; You, H-S; Hu, S-S; Sun, J-Y; Dong, Y-L; Lu, J

2014-10-01

Relapse is a threat in patients treated for acute lymphoblastic leukemia (ALL). Methylenetetrahydrofolate reductase (MTHFR) activity may affect the sensitivity of patients to folate-based chemotherapeutic drugs, thus influencing the relapse risk. Two polymorphisms of the gene encoding MTHFR, C677T and A1298C, alter MTHFR enzyme activity and may be associated with ALL relapse. The aim of this meta-analysis was to clarify the correlation between the C677T and A1298C polymorphisms and ALL relapse. To this end, data were collected from studies of the association between these two polymorphisms and ALL relapse. Analysis of the data revealed a serious contradiction among the results. A recessive model demonstrated that the ALL relapse risk was significantly increased in carriers of the 677 TT genotype, especially for pediatric ALL, but was unaffected by the A1298C polymorphism. These findings confirm that the MTHFR C677T polymorphism could be considered as a good marker of the pediatric ALL relapse risk.

Apolipoprotein C3 Gene Polymorphisms Are Not a Risk Factor for Developing Non-Alcoholic Fatty Liver Disease: A Meta-Analysis

PubMed Central

Zhang, Haiying; Chen, Lizhen; Xin, Yongning; Lou, Yuangui; Liu, Yang; Xuan, Shiying

2014-01-01

Context: Our objective was to evaluate the effect of gene polymorphisms of apolipoprotein C3 (APOC3) on the development of non-alcoholic fatty liver disease (NAFLD) in different populations. Evidence Acquisition: We performed a meta-analysis of all relevant studies published in the literature. A total of 115 clinical trials or reports were identified, but only seven trials met our inclusion criteria. A meta-analysis was performed according to the Cochrane Reviewers’ Handbook recommendations. Results: Five hospital-based and two population-based case-control studies were included in the final analysis. The overall frequency of APOC3 gene polymorphisms was 67.5% (1177/1745) in NAFLD and 68.8% (988/1437) in controls. The summary odds ratio for the association of gene polymorphisms of APOC3 and the risk of NAFLD was 1.03 (95% CI: 0.89-1.22),which was not statistically significant (P > 0.05). Conclusions: Our meta-analysis, while not ruling out possible publication bias, showed no association between gene polymorphisms of APOC3 and the risk of NAFLD development in different populations in the world. PMID:25477977

4G/5G plasminogen activator inhibitor-1 and -308 A/G tumor necrosis factor-α promoter gene polymorphisms in Argentinean lupus patients: focus on lupus nephritis.

PubMed

Muñoz, Sebastián Andrés; Aranda, Federico; Allievi, Alberto; Orden, Alberto Omar; Perés Wingeyer, Silvia; Trobo, Rosana; Alvarez, Analía; Eimon, Alicia; Barreira, Juan Carlos; Schneeberger, Emilce; Dal Pra, Fernando; Sarano, Judith; Hofman, Julio; Chamorro, Julián; de Larrañaga, Gabriela

2014-02-01

We investigated the relationship between the 4G/5G plasminogen activator inhibitor (PAI-1) and -308 A/G tumor necrosis factor-α (TNF-α) polymorphisms and the clinical and biochemical features of systemic lupus erythematosus (SLE) in an Argentinean patient cohort. A total of 402 patients were studied, including 179 SLE patients and 223 healthy individuals. PCR-RLFP was used to determine the genotypes of the 4G/5G PAI-1 and -308 A/G TNF-α polymorphisms. SLE patients with lupus nephritis (LN) (n = 86) were compared with patients without LN (n = 93). Additionally, LN patients were divided into proliferative LN and non-proliferative LN groups according to the results of the renal biopsies. No significant differences were noted in the genotype distributions or allele frequencies of these TNF-α and PAI-1 polymorphisms between SLE patients and controls. There were higher numbers of criteria for SLE, more lupus flares and higher damage scores in LN patients, but there were similar frequencies of anti-phospholipid antibody (APA) positivity and anti-phospholipid syndrome. No significant difference was noted for any studied variable between the proliferative LN and non-proliferative LN groups except for the presence of APA. We found no significant differences in the TNF-α and PAI-1 genotype distributions or allele frequencies between groups. We found that the -308 A/G TNF-α and 4G/5G PAI-1 polymorphisms are not associated with susceptibility to SLE in an Argentinean population. We also did not find any association between the presence of any specific allele or genotype and the development of LN in SLE patients. Finally, no association was noted between either of the two polymorphisms and the severity of renal disease.

X-ray structural studies and physicochemical characterization of (E)-6-(3,4-dimethoxyphenyl)-1-ethyl-4-mesitylimino-3-methyl- 3,4-dihydro-2(1H)-pyrimidinone polymorphs.

PubMed

Miyamae, A; Kitamura, S; Tada, T; Koda, S; Yasuda, T

1991-10-01

The polymorphism of (E)-6-(3,4-dimethoxyphenyl)-1-ethyl-4-mesitylimino-3-methyl-3,4-di hydro- 2(1 H)-pyrimidinone (FK664; 1) was characterized by using X-ray powder diffractometry, differential scanning calorimetry (DSC), and IR spectroscopy. Structures of two polymorphs (Forms A and B) were determined by X-ray crystallographic analysis. Form A crystallized in the monoclinic space group P2(1)/c, with a = 13.504(2), b = 6.733(1), c = 24.910(8) A, beta = 96.55(4) degrees, z = 4, and dcal = 1.203 g/cm3, while Form B crystallized in the same space group, with a = 8.067(2), b = 15.128(4), c = 18.657(4) A, beta = 102.34(3) degrees, z = 4, and dcal = 1.216 g/cm3. The conformational features of 1 were very similar between the two polymorphs. Compound 1, in both crystal forms, took an energetically reasonable conformation in three rigid planes, such as 2-pyrimidone, trimethylphenyl, and dimethoxyphenyl rings, but the molecules were packed in different ways between the two polymorphs. In the Form B crystal, a short contact was possible, to form pi-pi interactions between two dimethoxyphenyl groups related with the inversion center in the crystal lattice; this interaction seems to contribute to stabilizing the crystal structure of Form B. Both Forms A and B showed only one endothermic peak due to fusion at 115 and 140 degrees C, respectively, on the DSC thermograms; therefore, it is suggested that there are no transition points between the two polymorphs. The heats of fusion obtained from the DSC thermograms were 33.2(2) kJ/mol for Form A and 36.8(1) kJ/mol for Form B.(ABSTRACT TRUNCATED AT 250 WORDS)

Polymorph selection: the role of nucleation, crystal growth and molecular modeling.

PubMed

Erdemir, Deniz; Lee, Alfred Y; Myerson, Allan S

2007-11-01

Solution crystallization is an important separation and purification process used in the chemical, pharmaceutical and food industries. The quality of a crystalline product is generally judged by four main criteria: purity, crystal habit, particle size and solid form. Consistent production of the desired polymorph is crucial as the unanticipated emergence of a different crystal form may have severe consequences. Thus, the selection of a solid-state form for a crystalline product is vital and is ultimately based on knowledge of the properties of the other polymorphs. This review discusses the role of nucleation, crystal growth and molecular modeling on polymorphism in molecular crystals. Examples are presented demonstrating how the first two factors can govern the appearance of a particular crystalline form, and how the latter factor can be used as a tool for understanding polymorphism.

Genotypic and phenotypic predictors of inflammation in patients with chronic kidney disease.

PubMed

Luttropp, Karin; Debowska, Malgorzata; Lukaszuk, Tomasz; Bobrowski, Leon; Carrero, Juan Jesus; Qureshi, Abdul Rashid; Stenvinkel, Peter; Lindholm, Bengt; Waniewski, Jacek; Nordfors, Louise

2016-12-01

In complex diseases such as chronic kidney disease (CKD), the risk of clinical complications is determined by interactions between phenotypic and genotypic factors. However, clinical epidemiological studies rarely attempt to analyse the combined effect of large numbers of phenotype and genotype features. We have recently shown that the relaxed linear separability (RLS) model of feature selection can address such complex issues. Here, it is applied to identify risk factors for inflammation in CKD. The RLS model was applied in 225 CKD stage 5 patients sampled in conjunction with dialysis initiation. Fifty-seven anthropometric or biochemical measurements and 79 genetic polymorphisms were entered into the model. The model was asked to identify phenotypes and genotypes that, when combined, could separate inflamed from non-inflamed patients. Inflammation was defined as a high-sensitivity C-reactive protein concentration above the median (5 mg/L). Among the 60 genotypic and phenotypic features predicting inflammation, 31 were genetic. Among the 10 strongest predictors of inflammation, 8 were single nucleotide polymorphisms located in the NAMPT, CIITA, BMP2 and PIK3CB genes, whereas fibrinogen and bone mineral density were the only phenotypic biomarkers. These results indicate a larger involvement of hereditary factors in inflammation than might have been expected and suggest that inclusion of genotype features in risk assessment studies is critical. The RLS model demonstrates that inflammation in CKD is determined by an extensive panel of factors and may prove to be a suitable tool that could enable a much-needed multifactorial approach as opposed to the commonly utilized single-factor analysis. © The Author 2016. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

Developing a clinical utility framework to evaluate prediction models in radiogenomics

NASA Astrophysics Data System (ADS)

Wu, Yirong; Liu, Jie; Munoz del Rio, Alejandro; Page, David C.; Alagoz, Oguzhan; Peissig, Peggy; Onitilo, Adedayo A.; Burnside, Elizabeth S.

2015-03-01

Combining imaging and genetic information to predict disease presence and behavior is being codified into an emerging discipline called "radiogenomics." Optimal evaluation methodologies for radiogenomics techniques have not been established. We aim to develop a clinical decision framework based on utility analysis to assess prediction models for breast cancer. Our data comes from a retrospective case-control study, collecting Gail model risk factors, genetic variants (single nucleotide polymorphisms-SNPs), and mammographic features in Breast Imaging Reporting and Data System (BI-RADS) lexicon. We first constructed three logistic regression models built on different sets of predictive features: (1) Gail, (2) Gail+SNP, and (3) Gail+SNP+BI-RADS. Then, we generated ROC curves for three models. After we assigned utility values for each category of findings (true negative, false positive, false negative and true positive), we pursued optimal operating points on ROC curves to achieve maximum expected utility (MEU) of breast cancer diagnosis. We used McNemar's test to compare the predictive performance of the three models. We found that SNPs and BI-RADS features augmented the baseline Gail model in terms of the area under ROC curve (AUC) and MEU. SNPs improved sensitivity of the Gail model (0.276 vs. 0.147) and reduced specificity (0.855 vs. 0.912). When additional mammographic features were added, sensitivity increased to 0.457 and specificity to 0.872. SNPs and mammographic features played a significant role in breast cancer risk estimation (p-value < 0.001). Our decision framework comprising utility analysis and McNemar's test provides a novel framework to evaluate prediction models in the realm of radiogenomics.

Substance use outcomes 5½ years past baseline for partnership-based, family-school preventive interventions

PubMed Central

Spoth, Richard L.; Randall, G. Kevin; Trudeau, Linda; Shin, Chungyeol; Redmond, Cleve

2008-01-01

This article reports adolescent substance use outcomes of universal family and school preventive interventions 5½ years past baseline. Participants were 1677 7th grade students from schools (N = 36) randomly assigned to the school-based Life Skills Training plus the Strengthening Families Program: For Parents and Youth 10–14 (LST + SFP 10–14), LST-alone, or a control condition. Self-reports were collected at baseline, 6 months later following the interventions, then yearly through the 12th grade. Measures included initiation—alcohol, cigarette, marijuana, and drunkenness, along with a Substance Initiation Index (SII)—and measures of more serious use—frequency of alcohol, cigarette, and marijuana use, drunkenness frequency, monthly poly-substance use, and advanced poly-substance use. Analyses ruled out differential attrition. For all substance initiation outcomes, one or both intervention groups showed significant, positive point-in-time differences at 12th grade and/or significant growth trajectory outcomes when compared with the control group. Although no main effects for the more serious substance use outcomes were observed, a higher-risk subsample demonstrated significant, positive 12th grade point-in-time and/or growth trajectory outcomes for one or both intervention groups on all measures. The observed pattern of results likely reflects a combination of predispositions of the higher-risk subsample, the timing of the interventions, and baseline differences between experimental conditions favoring the control group. PMID:18434045

Demonstration of protein-based human identification using the hair shaft proteome [Protein-based human identification: A proof of concept using the hair shaft proteome

DOE PAGES

Parker, Glendon J.; Leppert, Tami; Anex, Deon S.; ...

2016-09-07

Human identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 singlemore » nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects’ DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European–American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). Furthermore, this study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts.« less

Demonstration of protein-based human identification using the hair shaft proteome [Protein-based human identification: A proof of concept using the hair shaft proteome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parker, Glendon J.; Leppert, Tami; Anex, Deon S.

Human identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 singlemore » nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects’ DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European–American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). Furthermore, this study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts.« less

Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.

PubMed Central

2014-01-01

Background Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species. Result A total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1’ by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei’s genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective. Conclusions A large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species. PMID:24472631

Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv].

PubMed

Zhang, Shuo; Tang, Chanjuan; Zhao, Qiang; Li, Jing; Yang, Lifang; Qie, Lufeng; Fan, Xingke; Li, Lin; Zhang, Ning; Zhao, Meicheng; Liu, Xiaotong; Chai, Yang; Zhang, Xue; Wang, Hailong; Li, Yingtao; Li, Wen; Zhi, Hui; Jia, Guanqing; Diao, Xianmin

2014-01-28

Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species. A total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1' by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei's genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective. A large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species.

Insights into the phase diagram of bismuth ferrite from quasiharmonic free-energy calculations

NASA Astrophysics Data System (ADS)

Cazorla, Claudio; Iñiguez, Jorge

2013-12-01

We have used first-principles methods to investigate the phase diagram of multiferroic bismuth ferrite (BiFeO3 or BFO), revealing the energetic and vibrational features that control the occurrence of various relevant structures. More precisely, we have studied the relative stability of four low-energy BFO polymorphs by computing their free energies within the quasiharmonic approximation, introducing a practical scheme that allows us to account for the main effects of spin disorder. As expected, we find that the ferroelectric ground state of the material (with R3c space group) transforms into an orthorhombic paraelectric phase (Pnma) upon heating. We show that this transition is not significantly affected by magnetic disorder, and that the occurrence of the Pnma structure relies on its being vibrationally (although not elastically) softer than the R3c phase. We also investigate a representative member of the family of nanotwinned polymorphs recently predicted for BFO [S. Prosandeev et al., Adv. Funct. Mater. 23, 234 (2013), 10.1002/adfm.201201467] and discuss their possible stabilization at the boundaries separating the R3c and Pnma regions in the corresponding pressure-temperature phase diagram. Finally, we elucidate the intriguing case of the so-called supertetragonal phases of BFO: Our results explain why such structures have never been observed in the bulk material, despite their being stable polymorphs of very low energy. Quantitative comparison with experiment is provided whenever possible, and the relative importance of various physical effects (zero-point motion, spin fluctuations, thermal expansion) and technical features (employed exchange-correlation energy density functional) is discussed. Our work attests the validity and usefulness of the quasiharmonic scheme to investigate the phase diagram of this complex oxide, and prospective applications are discussed.

MicroRNA-196a2 Biomarker and Targetome Network Analysis in Solid Tumors.

PubMed

Toraih, Eman A; Fawzy, Manal S; Mohammed, Eman A; Hussein, Mohammad H; El-Labban, Mohamad M

2016-12-01

MicroRNAs (miRNAs) have been linked to cancer development and progression. The molecular mechanisms underlying the genetic associations of the miRNA single nucleotide polymorphism with cancer vary by cancer site. As there are no previous studies on the miR-196a2 variant or expression in any type of cancer among our population, we aimed to determine the expression profile of mature miR-196a2 in various types of solid tumors and to analyze the impact of its polymorphism (rs11614913; C/T) on the expression levels. The study included 230 cancer patients (including 17 types of cancer), 26 patients with pre-cancer lesions, and 100 unrelated controls. Archived formalin-fixed, paraffin-embedded specimens (n = 197) were available for both miRNA expression analysis and single nucleotide polymorphism identification. Venous blood was collected from 59 histologically confirmed sporadic cancer patients and the study controls for single nucleotide polymorphism identification. Real-time polymerase chain reaction analysis was performed for allelic discrimination and relative quantification of miR-196a2 in the study samples. In silico target gene prediction and network analysis was performed. We found that individuals with the T variant were associated with cancer risk under all genetic association models, especially in colorectal, esophageal, skin, lung, thyroid, and renal cancer. Overall and stratified analysis showed miR-196a2 over-expression in most of the current malignant tumor samples relative to their corresponding cancer-free tissues. Carriers of the C allele had significantly higher expression levels of miR-196a2. Correlation with the clinicopathological features of cancer showed organ-specific effects. Gene enrichment analysis of predicted and validated targets speculated the putative role of miR-196a2 in cancer-associated biology. We highlighted cancer-type specific expression profiles of miR-196a2, which was correlated with the clinicopathological features in various types of cancer. Taken together, our results suggest that the miRNA signature could have promising diagnostic and prognostic significance.

Molecular analysis of MLH1 variants in Chinese sporadic colorectal cancer patients.

PubMed

Peng, H X; Xu, X; Yang, R; Chu, Y M; Yang, D M; Xu, Y; Zhou, F L; Ma, W Z; Zhang, X J; Guan, M; Yang, Z H; Jin, Z D

2016-04-26

Single nucleotide polymorphisms (SNPs) in mismatch repair genes, especially in the MLH1 gene, are closely associated with susceptibility to hereditary nonpolyposis colorectal cancer. However, few relevant findings are available regarding the association between sporadic colorectal cancer (SCRC) and SNPs of MLH1 in Chinese patients. Therefore, the present study aimed to describe the pathogenic association between three important MLH1 polymorphisms and SCRC in the Chinese population. Peripheral blood samples from 156 SCRC patients and 311 healthy controls were collected. DNA was purified from peripheral blood, and the V384D, R217C, and I219V polymorphisms were evaluated using high-resolution melting analysis and direct sequencing. The association between the three important MLH1 polymorphisms and clinical pathological features of the SCRC patients was analyzed. In addition, PMS2-MLH1 protein interactions were determined by co-immunoprecipitation (Co-IP) to determine the protein functional alteration induced by these SNPs. Among the three polymorphisms, V384D was significantly associated with the risk of SCRC (OR = 31.36, P < 0.0001). The allele frequencies were 4.81 and 0.16% in the SCRC group. No association was found between SCRC and R217C, or between SCRC and I219V. Moreover, the allele frequency of R217C was significantly higher in the SCRC patients younger than 60 years than in those older than 60 years. Co-IP showed that the MLH1 R217C, V384D, and I219V variants had relative binding abilities with PMS2 of 0.59, 0.70, and 0.80, respectively, compared with the wild-type. These findings suggest that MLH1 V384D could be a promising genetic marker for susceptibility to SCRC.

Interferon regulatory factor 5 (IRF5) gene variants are associated with multiple sclerosis in three distinct populations

PubMed Central

Kristjansdottir, G; Sandling, J K; Bonetti, A; Roos, I M; Milani, L; Wang, C; Gustafsdottir, S M; Sigurdsson, S; Lundmark, A; Tienari, P J; Koivisto, K; Elovaara, I; Pirttilä, T; Reunanen, M; Peltonen, L; Saarela, J; Hillert, J; Olsson, T; Landegren, U; Alcina, A; Fernández, O; Leyva, L; Guerrero, M; Lucas, M; Izquierdo, G; Matesanz, F; Syvänen, A-C

2008-01-01

Background: IRF5 is a transcription factor involved both in the type I interferon and the toll-like receptor signalling pathways. Previously, IRF5 has been found to be associated with systemic lupus erythematosus, rheumatoid arthritis and inflammatory bowel diseases. Here we investigated whether polymorphisms in the IRF5 gene would be associated with yet another disease with features of autoimmunity, multiple sclerosis (MS). Methods: We genotyped nine single nucleotide polymorphisms and one insertion-deletion polymorphism in the IRF5 gene in a collection of 2337 patients with MS and 2813 controls from three populations: two case–control cohorts from Spain and Sweden, and a set of MS trio families from Finland. Results: Two single nucleotide polymorphism (SNPs) (rs4728142, rs3807306), and a 5 bp insertion-deletion polymorphism located in the promoter and first intron of the IRF5 gene, showed association signals with values of p<0.001 when the data from all cohorts were combined. The predisposing alleles were present on the same common haplotype in all populations. Using electrophoretic mobility shift assays we observed allele specific differences in protein binding for the SNP rs4728142 and the 5 bp indel, and by a proximity ligation assay we demonstrated increased binding of the transcription factor SP1 to the risk allele of the 5 bp indel. Conclusion: These findings add IRF5 to the short list of genes shown to be associated with MS in more than one population. Our study adds to the evidence that there might be genes or pathways that are common in multiple autoimmune diseases, and that the type I interferon system is likely to be involved in the development of these diseases. PMID:18285424

Methylation-sensitive amplification polymorphism in date palms (Phoenix dactylifera L.) and their off-shoots.

PubMed

Fang, J-G; Chao, C T

2007-07-01

DNA methylation plays an important role in the regulation of gene expression in eukaryotes. In this study, the extent and patterns of DNA methylation were assessed in date palm mother-plants and their off-shoots using the methylation-sensitive amplified polymorphism (MSAP) technique. Three types of bands were generated using 12 pairs of primers. Type I were present in both ECOR I + HPA II and ECOR I + MSP I lanes; type II were present in ECOR I + HPA II lanes, but not in ECOR I + MSP I lanes; and type III bands were present in ECOR I + MSP I lanes, but not in ECOR I + HPA II lanes. The total numbers of these three types of bands were 782, 55, and 34, respectively. Among these three types of bands, the polymorphic bands were, respectively, 37, 10, and 0. The distribution of polymorphic bands among mother-plants and off-shoots suggests the methylation variation was present in both the mother-plants and off-shoots. Forty- four out of these 47 polymorphic bands show clear difference between mother-plant and off-shoots: 38 were present only in off-shoots and 6 in both mother-plants and off-shoots. Compared to methylation status in mother-plants, the methylation variation during off-shoot growth of date palm can be characterized as a process involving primarily de-methylation. Hypomethylation of DNA in off-shoots, compared with mother-plants, reflects the marked expression of this molecular feature, which may be related to gene expression during off-shoot development. The methylation or de-methylation status of specific loci in the mother-plants and their off-shoots were probably random events.

Increased risk of incident stroke associated with the cyclooxygenase 2 (COX-2) G-765C polymorphism in African-Americans: the Atherosclerosis Risk in Communities Study.

PubMed

Kohsaka, Shun; Volcik, Kelly A; Folsom, Aaron R; Wu, Kenneth K; Ballantyne, Christie M; Willerson, James T; Boerwinkle, Eric

2008-02-01

A hallmark feature of atherosclerosis is inflammation mediated by prostaglandins (PGs) catalyzed by the enzyme cyclooxygenase (COX). The present study explored whether the COX-2 G-765C polymorphism contributes to increased incidence of coronary heart disease (CHD) or stroke in the large prospective Atherosclerosis Risk in Communities (ARIC) Study. Incidences of CHD and stroke were identified through annual follow-up and hospital and death certificate surveillance. The study included 1488 incident CHD and 527 stroke events after an average of 14 years of follow-up. The frequency of the -765C variant allele was markedly different between African-Americans and whites, therefore all analyses were performed separately by race. Due to the small number of persons with the -765CC genotype, heterozygous and homozygous variant genotypes were combined for this analysis. The COX-2 G-765C polymorphism was not a significant predictor of CHD in either racial group, but it was a significant predictor of incident stroke in African-Americans. After adjustment for age and gender, the hazard rate ratio for developing stroke for the CG+CC genotypes relative to the GG genotype was 1.34 (95% confidence interval [CI] 1.03-1.74, P=0.03) in African-Americans. This result was essentially unchanged when established predictors such as smoking, diabetes and hypertension were added to the model (HRR 1.34, 95%CI 1.03-1.76, P=0.03). We have found the COX-2 G-765C polymorphism to be a risk factor for incident stroke in African-Americans. This study provides additional evidence for utilizing inflammation-related genetic polymorphisms for identifying individuals at increased risk for stroke.

THE GSTP1 c.313A>G POLYMORPHISM MODULATES THE CARDIORESPIRATORY RESPONSE TO AEROBIC TRAINING.

PubMed

Zarebska, A; Jastrzebski, Z; Kaczmarczyk, M; Ficek, K; Maciejewska-Karlowska, A; Sawczuk, M; Leońska-Duniec, A; Krol, P; Cieszczyk, P; Zmijewski, P; Eynon, N

2014-12-01

The GSTP1 c.313A>G polymorphism is a candidate to explain some of the individual differences in cardiorespiratory fitness phenotypes' responses to aerobic exercise training. We aim to explore the association between the GSTP1 c.313A>G polymorphism and the response to low-high impact aerobic exercise training. Sixty-six Polish Caucasian women were genotyped for the GSTP1 c.313A>G polymorphism; 62 of them completed 12-week aerobic (50-75% HRmax) exercise training and were measured for selected somatic features (body mass and BMI) and cardiorespiratory fitness indices - maximal oxygen uptake (VO2max, maximum heart rate (HRmax), maximum ventilation (VEmax) and anaerobic threshold (AT) - before and after the training period. Two-factor analysis of variance revealed a main training effect for body mass reduction (p=0.007) and BMI reduction (p=0.013), improvements of absolute and relative VO2max (both p<0.001), and increased VEmax (p=0.005), but not for changes in fat-free mass (FFM) (p=0.162). However, a significant training x GSTP1 c.313A>G interaction was found only for FFM (p=0.042), absolute and relative VO2max (p=0.029 and p=0.026), and VEmax (p=0.005). As the result of training, significantly greater improvements in VO2max, VEmax and FFM were gained by the GG+GA group compared to the AA genotype group. The results support the hypothesis that heterogeneity in individual response to training stimuli is at least in part determined by genetics, and GSTP1 c.313A>G may be considered as one (of what appear to be many) target polymorphisms to influence these changes.

THE GSTP1 c.313A>G POLYMORPHISM MODULATES THE CARDIORESPIRATORY RESPONSE TO AEROBIC TRAINING

PubMed Central

Zarebska, A; Jastrzebski, Z; Kaczmarczyk, M; Ficek, K; Maciejewska-Karlowska, A; Sawczuk, M; Leońska-Duniec, A; Krol, P; Cieszczyk, P; Zmijewski, P

2014-01-01

The GSTP1 c.313A>G polymorphism is a candidate to explain some of the individual differences in cardiorespiratory fitness phenotypes’ responses to aerobic exercise training. We aim to explore the association between the GSTP1 c.313A>G polymorphism and the response to low-high impact aerobic exercise training. Sixty-six Polish Caucasian women were genotyped for the GSTP1 c.313A>G polymorphism; 62 of them completed 12-week aerobic (50-75% HRmax) exercise training and were measured for selected somatic features (body mass and BMI) and cardiorespiratory fitness indices – maximal oxygen uptake (VO2max, maximum heart rate (HRmax), maximum ventilation (VEmax) and anaerobic threshold (AT) – before and after the training period. Two-factor analysis of variance revealed a main training effect for body mass reduction (p=0.007) and BMI reduction (p=0.013), improvements of absolute and relative VO2max (both p<0.001), and increased VEmax (p=0.005), but not for changes in fat-free mass (FFM) (p=0.162). However, a significant training x GSTP1 c.313A>G interaction was found only for FFM (p=0.042), absolute and relative VO2max (p=0.029 and p=0.026), and VEmax (p=0.005). As the result of training, significantly greater improvements in VO2max, VEmax and FFM were gained by the GG+GA group compared to the AA genotype group. The results support the hypothesis that heterogeneity in individual response to training stimuli is at least in part determined by genetics, and GSTP1 c.313A>G may be considered as one (of what appear to be many) target polymorphisms to influence these changes. PMID:25435667

Association of the brain-derived neurotrophic factor Val66Met polymorphism with negative symptoms severity, but not cognitive function, in first-episode schizophrenia spectrum disorders.

PubMed

Mezquida, G; Penadés, R; Cabrera, B; Savulich, G; Lobo, A; González-Pinto, A; Penzol, M J; Corripio, I; Fernandez-Egea, E; Gassó, P; Cuesta, M J; Bernardo, M

2016-10-01

A functional polymorphism of the brain-derived neurotrophic factor gene (BDNF) Val66Met has been associated with cognitive function and symptom severity in patients with schizophrenia. It has been suggested that the Val66Met polymorphism has a role as a modulator in a range of clinical features of the illness, including symptoms severity, therapeutic responsiveness, age of onset, brain morphology and cognitive function. However, little work has been done in first-episode schizophrenia (FES) spectrum disorders. The objective of this study is to investigate the association of the BDNF Val66Met polymorphism on cognitive function and clinical symptomatology in FES patients. Using a cross-sectional design in a cohort of 204 patients with FES or a schizophrenia spectrum disorder and 204 healthy matched controls, we performed BDNF Val66Met genotyping and tested its relationship with cognitive testing (attention, working memory, learning/verbal memory and reasoning/problem-solving) and assessment of clinical symptom severity. There was no significant influence of the BDNF allele frequency on cognitive factor scores in either patients or controls. An augmented severity of negative symptoms was found in FES patients that carried the Met allele. The results of this study suggest that in patients with a first-episode of schizophrenia or a schizophrenia spectrum disorder, the BDNF Val66Met polymorphism does not exert an influence on cognitive functioning, but is associated with negative symptoms severity. BDNF may serve as suitable marker of negative symptomatology severity in FES patients within the schizophrenia spectrum. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Analysis of Sequence Diversity at the Highly Polymorphic Cpgp40/15 Locus among Cryptosporidium Isolates from Human Immunodeficiency Virus-Infected Children in South Africa

PubMed Central

Leav, Brett A.; Mackay, Malanie R.; Anyanwu, Akudo; O' Connor, Roberta M.; Cevallos, Ana Maria; Kindra, Gurpreet; Rollins, Nigel C.; Bennish, Michael L.; Nelson, Richard G.; Ward, Honorine D.

2002-01-01

Cryptosporidium sp. is a significant cause of diarrheal disease, particularly in human immunodeficiency virus (HIV)-infected patients in developing countries. We recently cloned and sequenced several alleles of the highly polymorphic single-copy Cryptosporidium parvum gene Cpgp40/15. This gene encodes a precursor protein that is proteolytically cleaved to yield mature cell surface glycoproteins gp40 and gp15, which are implicated in zoite attachment to and invasion of enterocytes. The most-striking feature of the Cpgp40/15 alleles and proteins is their unprecedented degree of sequence polymorphism, which is far greater than that observed for any other gene or protein studied in C. parvum to date. In this study we analyzed nucleic acid and amino acid sequence polymorphism at the Cpgp40/15 locus of 20 C. parvum isolates from HIV-infected South African children. Fifteen isolates exhibited one of four previously identified genotype I alleles at the Cpgp40/15 locus (Ia, Ib, Ic, and Id), while five displayed a novel set of polymorphisms that defined a new Cpgp40/15 genotype I allele, designated genotype Ie. Surprisingly, only 15 of these isolates exhibited concordant type I alleles at the thrombospondin-related adhesive protein of Cryptosporidium and Cryptosporidium oocyst wall protein loci, while five isolates (all of which displayed Cpgp40/15 genotype Ic alleles) displayed genotype II alleles at these loci. Furthermore, the last five isolates also manifested chimeric genotype Ic/Ib or Ic/II alleles at the Cpgp40/15 locus, raising the possibility of sexual recombination within and between prototypal parasite genotypes. Lastly, children infected with isolates having genotype Ic alleles were significantly older than those infected with isolates displaying other genotype I alleles. PMID:12065532

Interferon regulatory factor 5 gene polymorphism in Egyptian children with systemic lupus erythematosus.

PubMed

Hammad, A; Mossad, Y M; Nasef, N; Eid, R

2017-07-01

Background Increased expression of interferon-inducible genes is implicated in the pathogenesis of systemic lupus erythematosus (SLE). Interferon regulatory factor 5 (IRF5) is one of the transcription factors regulating interferon and was proved to be implicated in the pathogenesis of SLE in different populations. Objectives The objective of this study was to investigate the correlation between polymorphisms of the IRF5 gene and SLE susceptibility in a cohort of Egyptian children and to investigate their association with clinico-pathological features, especially lupus nephritis. Subjects and methods Typing of interferon regulatory factor 5 rs10954213, rs2004640 and rs2280714 polymorphisms were done using polymerase chain reaction-restriction fragment length polymorphism for 100 children with SLE and 100 matched healthy controls. Results Children with SLE had more frequent T allele and TT genotype of rs2004640 ( P c  = 0.003 and 0.024, respectively) compared to controls. Patients with nephritis had more frequent T allele of rs2004640 compared to controls ( P c  = 0.003). However the allele and genotype frequencies of the three studied polymorphisms did not show any difference in patients with nephritis in comparison to those without nephritis. Haplotype GTA of rs10954213, rs2004640 and rs2280714, respectively, was more frequent in lupus patients in comparison to controls ( p = 0.01) while the haplotype GGG was more frequent in controls than lupus patients ( p = 0.011). Conclusion The rs2004640 T allele and TT genotype and GTA haplotype of rs rs10954213, rs2004640, and rs2280714, respectively, can be considered as risk factors for the development of SLE. The presence of the rs2004640 T allele increases the risk of nephritis development in Egyptian children with SLE.

Application of virtual phase-shifting speckle-interferometry for detection of polymorphism in the Chlamydia trachomatis omp1 gene

NASA Astrophysics Data System (ADS)

Feodorova, Valentina A.; Saltykov, Yury V.; Zaytsev, Sergey S.; Ulyanov, Sergey S.; Ulianova, Onega V.

2018-04-01

Method of phase-shifting speckle-interferometry has been used as a new tool with high potency for modern bioinformatics. Virtual phase-shifting speckle-interferometry has been applied for detection of polymorphism in the of Chlamydia trachomatis omp1 gene. It has been shown, that suggested method is very sensitive to natural genetic mutations as single nucleotide polymorphism (SNP). Effectiveness of proposed method has been compared with effectiveness of the newest bioinformatic tools, based on nucleotide sequence alignment.

Typing of Human Mycobacterium avium Isolates in Italy by IS1245-Based Restriction Fragment Length Polymorphism Analysis

PubMed Central

Lari, Nicoletta; Cavallini, Michela; Rindi, Laura; Iona, Elisabetta; Fattorini, Lanfranco; Garzelli, Carlo

1998-01-01

All but 2 of 63 Mycobacterium avium isolates from distinct geographic areas of Italy exhibited markedly polymorphic, multibanded IS1245 restriction fragment length polymorphism (RFLP) patterns; 2 isolates showed the low-number banding pattern typical of bird isolates. By computer analysis, 41 distinct IS1245 patterns and 10 clusters of essentially identical strains were detected; 40% of the 63 isolates showed genetic relatedness, suggesting the existence of a predominant AIDS-associated IS1245 RFLP pattern. PMID:9817900

Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project.

PubMed

Cross, Deanna S; Ivacic, Lynn C; Stefanski, Elisha L; McCarty, Catherine A

2010-06-17

There is a lack of knowledge regarding the frequency of disease associated polymorphisms in populations and population attributable risk for many populations remains unknown. Factors that could affect the association of the allele with disease, either positively or negatively, such as race, ethnicity, and gender, may not be possible to determine without population based allele frequencies.Here we used a panel of 51 polymorphisms previously associated with at least one disease and determined the allele frequencies within the entire Personalized Medicine Research Project population based cohort. We compared these allele frequencies to those in dbSNP and other data sources stratified by race. Differences in allele frequencies between self reported race, region of origin, and sex were determined. There were 19544 individuals who self reported a single racial category, 19027 or (97.4%) self reported white Caucasian, and 11205 (57.3%) individuals were female. Of the 11,208 (57%) individuals with an identifiable region of origin 8337 or (74.4%) were German.41 polymorphisms were significantly different between self reported race at the 0.05 level. Stratification of our Caucasian population by self reported region of origin revealed 19 polymorphisms that were significantly different (p = 0.05) between individuals of different origins. Further stratification of the population by gender revealed few significant differences in allele frequencies between the genders. This represents one of the largest population based allele frequency studies to date. Stratification by self reported race and region of origin revealed wide differences in allele frequencies not only by race but also by region of origin within a single racial group. We report allele frequencies for our Asian/Hmong and American Indian populations; these two minority groups are not typically selected for population allele frequency detection. Population wide allele frequencies are important for the design and implementation of studies and for determining the relevance of a disease associated polymorphism for a given population.

Association of -604G/A and -501A/C Ghrelin and Obestatin Prepropeptide Gene Polymorphisms with Polycystic Ovary Syndrome.

PubMed

Ghaleh, Talaat Dabbaghi; Skandari, Somayeh Saadat; Najafipour, Reza; Rashvand, Zahra; Darabi, Masoud; Sahmani, Mehdi

2018-04-01

Ghrelin hormone has an important role in a wide range of metabolic and non-metabolic processes. Polymorphisms of ghrelin gene could be associated with a large number of diseases. The aim of this study was to evaluate the association of -604G/A and -501A/C polymorphisms in ghrelin and obestatin prepropeptide gene (GHRL) with polycystic ovary syndrome (PCOS) in a sample of Iranian women. One hundred and fifty-two women with PCOS and 162 age-matched apparently healthy women as control group were enrolled in this study. The study subjects were genotyped for polymorphisms in the ghrelin gene using polymerase chain reaction-restriction fragment length polymorphism-based methods. Biochemical parameters, serum prolactin, luteinizing hormone, follicle stimulating hormone, estradiol, and testosterone were estimated by chemiluminescence assay. Serum lipids and lipoproteins were determined by standard enzymatic methods. The association between the risk of PCOS and ghrelin gene polymorphisms was examined using Multivariate analysis. The frequency of the -604G/A and -501A/C polymorphisms was not statistically different between patients and the control group of women (p = 0.12 and p = 0.21, respectively). A significantly higher level of LDL-C was found in the wild-type AA genotype compared with CC genotype of -501A/C polymorphism (p = 0.02). Our findings indicate that neither -604G/A and nor -501A/C polymorphisms of ghrelin gene are associated with PCOS, but suggest a relation between the presence of polymorphic allele of -501A/C polymorphism and LDL-C level in a sample of Iranian women.

Polymorphic site index curves for red fir in California and southern Oregon

Treesearch

K. Leroy Dolph

1991-01-01

Polymorphic site index curves were developed from stem analysis data of 194 dominant red fir trees in California and southern Oregon. Site index was based on breast-height age and total tree height, with a base age of 50 years at breast height. Site index curves for breast height ages 10 to 160 years are presented for approximate estimates of site index. For more...

Association of "ADAM10" and "CAMK2A" Polymorphisms with Conduct Disorder: Evidence from Family-Based Studies

ERIC Educational Resources Information Center

Jian, Xue-Qiu; Wang, Ke-Sheng; Wu, Tie-Jian; Hillhouse, Joel J.; Mullersman, Jerald E.

2011-01-01

Twin and family studies have shown that genetic factors play a role in the development of conduct disorder (CD). The purpose of this study was to identify genetic variants associated with CD using a family-based association study. We used 4,720 single nucleotide polymorphisms (SNPs) from the Illumina Panel and 11,120 SNPs from the Affymetrix 10K…

A Genomics-Based Model for Prediction of Severe Bioprosthetic Mitral Valve Calcification.

PubMed

Ponasenko, Anastasia V; Khutornaya, Maria V; Kutikhin, Anton G; Rutkovskaya, Natalia V; Tsepokina, Anna V; Kondyukova, Natalia V; Yuzhalin, Arseniy E; Barbarash, Leonid S

2016-08-31

Severe bioprosthetic mitral valve calcification is a significant problem in cardiovascular surgery. Unfortunately, clinical markers did not demonstrate efficacy in prediction of severe bioprosthetic mitral valve calcification. Here, we examined whether a genomics-based approach is efficient in predicting the risk of severe bioprosthetic mitral valve calcification. A total of 124 consecutive Russian patients who underwent mitral valve replacement surgery were recruited. We investigated the associations of the inherited variation in innate immunity, lipid metabolism and calcium metabolism genes with severe bioprosthetic mitral valve calcification. Genotyping was conducted utilizing the TaqMan assay. Eight gene polymorphisms were significantly associated with severe bioprosthetic mitral valve calcification and were therefore included into stepwise logistic regression which identified male gender, the T/T genotype of the rs3775073 polymorphism within the TLR6 gene, the C/T genotype of the rs2229238 polymorphism within the IL6R gene, and the A/A genotype of the rs10455872 polymorphism within the LPA gene as independent predictors of severe bioprosthetic mitral valve calcification. The developed genomics-based model had fair predictive value with area under the receiver operating characteristic (ROC) curve of 0.73. In conclusion, our genomics-based approach is efficient for the prediction of severe bioprosthetic mitral valve calcification.

A Genomics-Based Model for Prediction of Severe Bioprosthetic Mitral Valve Calcification

PubMed Central

Ponasenko, Anastasia V.; Khutornaya, Maria V.; Kutikhin, Anton G.; Rutkovskaya, Natalia V.; Tsepokina, Anna V.; Kondyukova, Natalia V.; Yuzhalin, Arseniy E.; Barbarash, Leonid S.

2016-01-01

Severe bioprosthetic mitral valve calcification is a significant problem in cardiovascular surgery. Unfortunately, clinical markers did not demonstrate efficacy in prediction of severe bioprosthetic mitral valve calcification. Here, we examined whether a genomics-based approach is efficient in predicting the risk of severe bioprosthetic mitral valve calcification. A total of 124 consecutive Russian patients who underwent mitral valve replacement surgery were recruited. We investigated the associations of the inherited variation in innate immunity, lipid metabolism and calcium metabolism genes with severe bioprosthetic mitral valve calcification. Genotyping was conducted utilizing the TaqMan assay. Eight gene polymorphisms were significantly associated with severe bioprosthetic mitral valve calcification and were therefore included into stepwise logistic regression which identified male gender, the T/T genotype of the rs3775073 polymorphism within the TLR6 gene, the C/T genotype of the rs2229238 polymorphism within the IL6R gene, and the A/A genotype of the rs10455872 polymorphism within the LPA gene as independent predictors of severe bioprosthetic mitral valve calcification. The developed genomics-based model had fair predictive value with area under the receiver operating characteristic (ROC) curve of 0.73. In conclusion, our genomics-based approach is efficient for the prediction of severe bioprosthetic mitral valve calcification. PMID:27589735

Polymorphisms of interleukin 6 in Down syndrome individuals: a case-control study.

PubMed

Mattos, M F; Uback, L; Biselli-Chicote, P M; Biselli, J M; Goloni-Bertollo, E M; Pavarino, E C

2017-08-17

Down syndrome (DS) individuals present impaired adaptive immune system. However, the etiology of the immunological deficiency in these individuals is not completely understood. This study investigated the frequency of interleukin 6 polymorphisms (rs1800795, rs1800796, and rs1800797) in individuals with DS and individuals without the syndrome. The study included 282 individuals, 94 with DS attended at the General Genetics Outpatient Service of Hospital de Base, São José do Rio Preto, SP, Brazil, and 188 individuals without DS attended at the Pediatric Service of Hospital de Base de São José do Rio Preto, SP, Brazil. Genotyping was performed by allelic discrimination technique by real-time polymerase chain reaction using TaqMan SNP Genotyping Assays (Applied Biosystems). There was no difference in the genotype frequency between individuals with and without DS for the evaluated polymorphisms (P > 0.05). The frequency of interleukin 6 polymorphisms did not differ significantly between individuals with and without DS in the casuistic analyzed.

A System-Level Pathway-Phenotype Association Analysis Using Synthetic Feature Random Forest

PubMed Central

Pan, Qinxin; Hu, Ting; Malley, James D.; Andrew, Angeline S.; Karagas, Margaret R.; Moore, Jason H.

2015-01-01

As the cost of genome-wide genotyping decreases, the number of genome-wide association studies (GWAS) has increased considerably. However, the transition from GWAS findings to the underlying biology of various phenotypes remains challenging. As a result, due to its system-level interpretability, pathway analysis has become a popular tool for gaining insights on the underlying biology from high-throughput genetic association data. In pathway analyses, gene sets representing particular biological processes are tested for significant associations with a given phenotype. Most existing pathway analysis approaches rely on single-marker statistics and assume that pathways are independent of each other. As biological systems are driven by complex biomolecular interactions, embracing the complex relationships between single-nucleotide polymorphisms (SNPs) and pathways needs to be addressed. To incorporate the complexity of gene-gene interactions and pathway-pathway relationships, we propose a system-level pathway analysis approach, synthetic feature random forest (SF-RF), which is designed to detect pathway-phenotype associations without making assumptions about the relationships among SNPs or pathways. In our approach, the genotypes of SNPs in a particular pathway are aggregated into a synthetic feature representing that pathway via Random Forest (RF). Multiple synthetic features are analyzed using RF simultaneously and the significance of a synthetic feature indicates the significance of the corresponding pathway. We further complement SF-RF with pathway-based Statistical Epistasis Network (SEN) analysis that evaluates interactions among pathways. By investigating the pathway SEN, we hope to gain additional insights into the genetic mechanisms contributing to the pathway-phenotype association. We apply SF-RF to a population-based genetic study of bladder cancer and further investigate the mechanisms that help explain the pathway-phenotype associations using SEN. The bladder cancer associated pathways we found are both consistent with existing biological knowledge and reveal novel and plausible hypotheses for future biological validations. PMID:24535726

Linear data mining the Wichita clinical matrix suggests sleep and allostatic load involvement in chronic fatigue syndrome.

PubMed

Gurbaxani, Brian M; Jones, James F; Goertzel, Benjamin N; Maloney, Elizabeth M

2006-04-01

To provide a mathematical introduction to the Wichita (KS, USA) clinical dataset, which is all of the nongenetic data (no microarray or single nucleotide polymorphism data) from the 2-day clinical evaluation, and show the preliminary findings and limitations, of popular, matrix algebra-based data mining techniques. An initial matrix of 440 variables by 227 human subjects was reduced to 183 variables by 164 subjects. Variables were excluded that strongly correlated with chronic fatigue syndrome (CFS) case classification by design (for example, the multidimensional fatigue inventory [MFI] data), that were otherwise self reporting in nature and also tended to correlate strongly with CFS classification, or were sparse or nonvarying between case and control. Subjects were excluded if they did not clearly fall into well-defined CFS classifications, had comorbid depression with melancholic features, or other medical or psychiatric exclusions. The popular data mining techniques, principle components analysis (PCA) and linear discriminant analysis (LDA), were used to determine how well the data separated into groups. Two different feature selection methods helped identify the most discriminating parameters. Although purely biological features (variables) were found to separate CFS cases from controls, including many allostatic load and sleep-related variables, most parameters were not statistically significant individually. However, biological correlates of CFS, such as heart rate and heart rate variability, require further investigation. Feature selection of a limited number of variables from the purely biological dataset produced better separation between groups than a PCA of the entire dataset. Feature selection highlighted the importance of many of the allostatic load variables studied in more detail by Maloney and colleagues in this issue [1] , as well as some sleep-related variables. Nonetheless, matrix linear algebra-based data mining approaches appeared to be of limited utility when compared with more sophisticated nonlinear analyses on richer data types, such as those found in Maloney and colleagues [1] and Goertzel and colleagues [2] in this issue.

EnsembleGASVR: a novel ensemble method for classifying missense single nucleotide polymorphisms.

PubMed

Rapakoulia, Trisevgeni; Theofilatos, Konstantinos; Kleftogiannis, Dimitrios; Likothanasis, Spiros; Tsakalidis, Athanasios; Mavroudi, Seferina

2014-08-15

Single nucleotide polymorphisms (SNPs) are considered the most frequently occurring DNA sequence variations. Several computational methods have been proposed for the classification of missense SNPs to neutral and disease associated. However, existing computational approaches fail to select relevant features by choosing them arbitrarily without sufficient documentation. Moreover, they are limited to the problem of missing values, imbalance between the learning datasets and most of them do not support their predictions with confidence scores. To overcome these limitations, a novel ensemble computational methodology is proposed. EnsembleGASVR facilitates a two-step algorithm, which in its first step applies a novel evolutionary embedded algorithm to locate close to optimal Support Vector Regression models. In its second step, these models are combined to extract a universal predictor, which is less prone to overfitting issues, systematizes the rebalancing of the learning sets and uses an internal approach for solving the missing values problem without loss of information. Confidence scores support all the predictions and the model becomes tunable by modifying the classification thresholds. An extensive study was performed for collecting the most relevant features for the problem of classifying SNPs, and a superset of 88 features was constructed. Experimental results show that the proposed framework outperforms well-known algorithms in terms of classification performance in the examined datasets. Finally, the proposed algorithmic framework was able to uncover the significant role of certain features such as the solvent accessibility feature, and the top-scored predictions were further validated by linking them with disease phenotypes. Datasets and codes are freely available on the Web at http://prlab.ceid.upatras.gr/EnsembleGASVR/dataset-codes.zip. All the required information about the article is available through http://prlab.ceid.upatras.gr/EnsembleGASVR/site.html. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

[Association between HRE-2 gene polymorphism at codon 655 and genetic susceptibility of colorectal cancer].

PubMed

Liang, Xia; Zhang, Yong-jing; Liu, Bing; Ni, Qin; Jin, Ming-juan; Ma, Xin-yuan; Yao, Kai-yan; Li, Qi-long; Chen, Kun

2009-06-01

To explore the distribution of HER-2 genetic polymorphism at codon 655 and its association with susceptibility of colorectal cancer in Chinese. A population-based case-control study was carried out. 292 patients with colorectal cancer and 842 healthy controls were interviewed. Meanwhile, the genetic polymorphism of HRE-2 was detected using polymerase chain reaction-restriction fragment length polymorphism. The frequencies of Ile/Val+Val/Val genotypes and Val allele were both higher in cases (25.34% and 13.36%) than those in controls (18.41% and 9.74%) (P<0.05). Compared with Ile/Ile genotype, Ile/Val+Val/Val genotypes were significantly associated with colorectal cancer [ORadjusted=1.54, 95% CI: 1.11-2.14]. The adjusted odds ratio of interactions between this polymorphism and smoking, alcohol drinking were 1.43 (95%CI: 0.88-2.30) and 1.29 (95%CI: 0.73-2.29), respectively. The present findings suggest that HER-2 genetic polymorphism at codon 655 may be associated with the risk of colorectal cancer in Chinese. In addition, there are no interactions between this polymorphism and smoking, alcohol drinking, respectively.

Functional analysis of regulatory single-nucleotide polymorphisms.

PubMed

Pampín, Sandra; Rodríguez-Rey, José C

2007-04-01

The identification of regulatory polymorphisms has become a key problem in human genetics. In the past few years there has been a conceptual change in the way in which regulatory single-nucleotide polymorphisms are studied. We revise the new approaches and discuss how gene expression studies can contribute to a better knowledge of the genetics of common diseases. New techniques for the association of single-nucleotide polymorphisms with changes in gene expression have been recently developed. This, together with a more comprehensive use of the old in-vitro methods, has produced a great amount of genetic information. When added to current databases, it will help to design better tools for the detection of regulatory single-nucleotide polymorphisms. The identification of functional regulatory single-nucleotide polymorphisms cannot be done by the simple inspection of DNA sequence. In-vivo techniques, based on primer-extension, and the more recently developed 'haploChIP' allow the association of gene variants to changes in gene expression. Gene expression analysis by conventional in-vitro techniques is the only way to identify the functional consequences of regulatory single-nucleotide polymorphisms. The amount of information produced in the last few years will help to refine the tools for the future analysis of regulatory gene variants.

Sturgeon and paddlefish (Acipenseridae) saggital otoliths are composed of the calcium carbonate polymorphs vaterite and calcite: acipenseridae otoliths are vaterite and calcite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pracheil, Brenda M.; Chakoumakos, Bryan C.; Feygenson, Mikhail

The otoliths of modern fishes are most commonly comprised of the metastable aragonite polymorph of calcium carbonate (CaCO3); however, sturgeons have otoliths reportedly comprised of the least stable of the three most-common polymorphs, vaterite. In this study, we used neutron diffraction to characterize CaCO3 polymorph composition of lake sturgeon and paddlefish otoliths. Based on previous summaries of CaCO3 composition over fish evolutionary history, we hypothesized that sturgeon and paddlefish otoliths would have similar polymorph composition. We found that despite previous reports of sturgeon otoliths being comprised entirely of vaterite, that all otoliths we examined in this study also had amore » calcite fraction that ranged from 17.9+ 6.0 wt. % to 35.9 + 2.9 wt. %. We also conducted a grinding experiment that demonstrated that calcite fractions were due to biological variation and not an artifact of polymorph transformation during preparation. Our study provides the initial characterization of the polymorph composition of the otoliths of lake sturgeon, and paddlefish and also provides the first-ever report of otoliths of Acipenserids as having a calcite fraction.« less

Preproghrelin Leu72Met polymorphism in patients with type 2 diabetes mellitus.

PubMed

Ukkola, O; Kesäniemi, Y A

2003-10-01

The association between the Leu72Met polymorphism of the preproghrelin gene and diabetic complications was examined in patients with type 2 diabetes mellitus. A total of 258 patients with type 2 diabetes mellitus and 522 control subjects were screened. Genotypes were determined by polymerase chain reaction technique. The diagnosis of coronary heart disease was based on clinical and ECG criteria. Laboratory analyses were carried out in the hospital laboratory. No differences in the genotype distributions and allele frequencies of the preproghrelin Leu72Met polymorphism were found between type 2 diabetes mellitus patients and controls. The polymorphism was not associated with macro- or micro-angiopathy or hypertension. However, Leu72Met polymorphism was associated with serum creatinine (P = 0.006) and lipoprotein(a) [Lp(a)] levels (P = 0.006) with Leu72Leu subjects showing the highest values. This association was observed only amongst diabetic group. The Leu72Met polymorphism of the preproghrelin gene was not related to cardiovascular disease in type 2 diabetes mellitus patients. Leu72Met polymorphism was, however, associated with serum creatinine and Lp(a) levels in diabetic patients. The mechanism might be associated with a possible change in ghrelin product and its somatotropic effect.

Sturgeon and paddlefish (Acipenseridae) saggital otoliths are composed of the calcium carbonate polymorphs vaterite and calcite: acipenseridae otoliths are vaterite and calcite

DOE PAGES

Pracheil, Brenda M.; Chakoumakos, Bryan C.; Feygenson, Mikhail; ...

2016-07-27

The otoliths of modern fishes are most commonly comprised of the metastable aragonite polymorph of calcium carbonate (CaCO3); however, sturgeons have otoliths reportedly comprised of the least stable of the three most-common polymorphs, vaterite. In this study, we used neutron diffraction to characterize CaCO3 polymorph composition of lake sturgeon and paddlefish otoliths. Based on previous summaries of CaCO3 composition over fish evolutionary history, we hypothesized that sturgeon and paddlefish otoliths would have similar polymorph composition. We found that despite previous reports of sturgeon otoliths being comprised entirely of vaterite, that all otoliths we examined in this study also had amore » calcite fraction that ranged from 17.9+ 6.0 wt. % to 35.9 + 2.9 wt. %. We also conducted a grinding experiment that demonstrated that calcite fractions were due to biological variation and not an artifact of polymorph transformation during preparation. Our study provides the initial characterization of the polymorph composition of the otoliths of lake sturgeon, and paddlefish and also provides the first-ever report of otoliths of Acipenserids as having a calcite fraction.« less

Breccia dikes from the Beaverhead Impact structure, southwest Montana

NASA Technical Reports Server (NTRS)

Fiske, P. S.; Hougen, S. B.; Hargraves, R. B.

1992-01-01

While shatter cones are generally accepted as indicators of meteorite impact, older petrologic features are not widely recognized in the geologic community. Breccia dikes are one such feature. They are found in many large impact structures occurring over an area at least as extensively as shatter cones. Breccia dikes will survive moderate degrees of metamorphism and tectonism, unlike many other microscopic features (shocked quartz grains, high-pressure polymorphs, etc.) and even large-scale features such as annular or bowl-shaped topographic features. Thus, they are important diagnostic criteria, especially for large, poorly preserved impact structures. The Beaverhead Impact structure is a recently discovered, deeply eroded impact structure in southwestern Montana. The remains of the structure are delineated by the occurrence of shatter cones, found in an area greater than 200 sq km, occurring within the Cabin thrust plate, part of the Cretaceous Sevier fold and thrust system. The distribution of shatter cones is further truncated by Tertiary normal faults. The present remains represent an allochthonous fragment of a larger structure.

Assessing Date Palm Genetic Diversity Using Different Molecular Markers.

PubMed

Atia, Mohamed A M; Sakr, Mahmoud M; Adawy, Sami S

2017-01-01

Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.

[Analysis on genetic polymorphism of 5 STR loci selected from X chromosome].

PubMed

Liu, Qi-ji; Gong, Yao-qin; Zhang, Xi-yu; Gao, Gui-min; Li, Jiang-xia; Guo, Yi-shou

2005-02-01

To select short tandem repeats(STR) from X chromosome. STR is a universal genetic marker that has changeable polymorphism and stable heredity in human genome. It is a specific DNA segment composed of 2-6 base pairs as its core sequence. It is an ideal DNA marker used in linkage analysis and gene mapping. In this study, 8 short tandem repeats were selected from two genomic clones on X chromosome by using BCM Search Launcher. Primers amplifying the STR loci were designed by using Primer 3.0 according to the unique sequence flanking the STRs. Polymorphisms of the short tandem repeats in Chinese population were evaluated by PCR amplification and PAGE. Five of these STRs were polymorphic. Chi-square test indicated that the distribution of genotypes agreed with Hardy-Weinberg equilibrium (P>0.05). Five polymorphic short tandem repeats have been identified on chromosome X and will be useful for linkage analysis and gene mapping.

Association study of interleukin-4 polymorphisms with paranoid schizophrenia in the Polish population: a critical approach.

PubMed

Fila-Danilow, Anna; Kucia, Krzysztof; Kowalczyk, Malgorzata; Owczarek, Aleksander; Paul-Samojedny, Monika; Borkowska, Paulina; Suchanek, Renata; Kowalski, Jan

2012-08-01

Changes in immunological system are one of dysfunctions reported in schizophrenia. Some changes based on an imbalance between Th1 and Th2 cytokines results from cytokine gene polymorphisms. Interleukin-4 gene (IL4) is considered as a potential candidate gene in schizophrenia association studies. The aim of the current case-control study was to examine whether the -590C/T (rs2243250) and -33C/T (rs2070874) IL4 gene polymorphisms are implicated in paranoid schizophrenia development in the Polish population. Genotyping of polymorphisms was performed by using PCR-RFLP technique. The genotypes and alleles distribution of both SNPs were analysed in patients (n = 182) and healthy individuals constituted the control group (n = 215). The connection between some clinical variables and studied polymorphisms has been examined as well. We did not revealed any association between the -590C/T and -33C/T polymorphisms and paranoid schizophrenia. In case of both SNPs the homozygous TT genotype was extremely rare. Both polymorphic sites of the IL4 gene were found to be in a very strong linkage disequilibrium. However we did not identify a haplotype predispose to paranoid schizophrenia. No associations were also observed between the clinical course and psychopathology of the disease and the genotypes of both analysed polymorphisms. Our results suggest that the polymorphisms -590C/T in IL4 gene promoter region and -33C/T in the 5'-UTR are not involved in the pathophysiology of paranoid schizophrenia in Polish residents.

Polymorphisms in BRCA1 and BRCA2 and risk of epithelial ovarian cancer.

PubMed

Wenham, Robert M; Schildkraut, Joellen M; McLean, Kia; Calingaert, Brian; Bentley, Rex C; Marks, Jeffrey; Berchuck, Andrew

2003-10-01

Because inherited BRCA1 or BRCA2 mutations strikingly increase ovarian cancer risk, polymorphisms in these genes could represent low penetrance susceptibility alleles. Previous studies of the BRCA2 N372H polymorphism suggested that HH homozygotes have a modestly increased risk of both breast and ovarian cancer. We have examined whether BRCA2 N372H or common amino acid-changing polymorphisms in BRCA1 predispose to ovarian cancer. A population-based, case control study of ovarian cancer was performed in North Carolina. Cases included 312 women with ovarian cancer (76% invasive and 24% borderline) and 401 age- and race-matched controls. Blood DNA from subjects was genotyped for BRCA2 N372H and BRCA1 Q356R and P871L. There was no association between BRCA2 N372H and risk of borderline or invasive epithelial ovarian cancer. The overall odds ratio (OR) for HH homozygotes was 0.8 [95% confidence interval (CI) = 0.4-1.5] and was similar in all subsets, including invasive serous cases. In addition, neither the BRCA1 Q356R (OR = 0.9, 95% CI 0.5-1.4) nor P871L (OR = 0.9, 95% CI 0.6-1.9) polymorphisms were associated with ovarian cancer risk. There was a significant racial difference in allele frequencies of the P871L polymorphism (P = 0.64 in Caucasians, L = 0.76 in African-Americans, P < 0.0001). In this population-based, case control study, common amino acid changing BRCA1 and 2 polymorphisms were not found to affect the risk of developing ovarian cancer.