SBMDb: First whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications

© 2015 The Author(s) 2015. DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world's first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of 'mono' repeat (76.82%) over 'di' repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of bioethanol and biogas production along with reaping advantage of crop efficiency in terms of low water and carbon footprint especially in era of climate change

PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome Data

Microsatellites are ubiquitously distributed, polymorphic repeat sequence valuable for association, selection, population structure and identification. They can be mined by genomic library, probe hybridization and sequencing of selected clones. Such approach has many limitations like biased hybridization and selection of larger repeats. In silico mining of polymorphic markers using data of various genotypes can be rapid and economical. Available tools lack in some or other aspects like: targeted user defined primer generation, polymorphism discovery using multiple sequence, size and number limits of input sequence, no option for primer generation and e-PCR evaluation, transferability, lack of complete automation and user-friendliness. They also lack the provision to evaluate published primers in e-PCR mode to generate additional allelic data using re-sequenced data of various genotypes for judicious utilization of previously generated data. We developed the tool (PolyMorphPredict) using Perl, R, Java and launched at Apache which is available at http://webtom.cabgrid.res.in/polypred/. It mines microsatellite loci and computes primers from genome/transcriptome data of any species. It can perform e-PCR using published primers for polymorphism discovery and across species transferability of microsatellite loci. Present tool has been evaluated using five species of different genome size having 21 genotypes. Though server is equipped with genomic data of three species for test run with gel simulation, but can be used for any species. Further, polymorphism predictability has been validated using in silico and in vitro PCR of four rice genotypes. This tool can accelerate the in silico microsatellite polymorphism discovery in re-sequencing projects of any species of plant and animal for their diversity estimation along with variety/breed identification, population structure, MAS, QTL and gene discovery, traceability, parentage testing, fungal diagnostics and genome finishing

Thermal Properties of Graphene, Carbon Nanotubes and Nanostructured Carbon Materials

Recent years witnessed a rapid growth of interest of scientific and engineering communities to thermal properties of materials. Carbon allotropes and derivatives occupy a unique place in terms of their ability to conduct heat. The room-temperature thermal conductivity of carbon materials span an extraordinary large range - of over five orders of magnitude - from the lowest in amorphous carbons to the highest in graphene and carbon nanotubes. I review thermal and thermoelectric properties of carbon materials focusing on recent results for graphene, carbon nanotubes and nanostructured carbon materials with different degrees of disorder. A special attention is given to the unusual size dependence of heat conduction in two-dimensional crystals and, specifically, in graphene. I also describe prospects of applications of graphene and carbon materials for thermal management of electronics.Comment: Review Paper; 37 manuscript pages; 4 figures and 2 boxe

BASELINE CARDIORESPIRATORY AS A PREDICTOR OF BP STATUS IN INSUFFICIENTLY ACTIVE ADULTS

Zachary S. Leicht1, Nathan R. Weeldreyer1, Marc A. Adams2, Siddhartha S. Angadi, FACSM1. 1University of Virginia, Charlottesville, VA. 2Arizona State University, Phoenix, AZ. Background: Blood pressure and peak oxygen uptake (VO2peak) are strong independent predictors of all-cause and cardiovascular mortality. Individuals with a VO2peak of 8 METs or greater have decreased risk of cardiovascular disease compared to those with a VO2peak less than 8 METs. Increasing physical activity in insufficiently active adults is associated with improvements in both cardiorespiratory fitness (CRF) and blood pressure (BP), however approximately 90% of adults in the United States do not meet current physical activity guidelines. Additionally, the relationship between CRF and the odds of having an elevated blood pressure (SBP ≥ 120 and/or DBP ≥ 80) or hypertension (SBP ≥ 140 and/or DBP ≥ 90) are unknown. Therefore, we determined the odds of having elevated blood pressure or hypertension in individuals stratified based on VO2peak (\u3c 8METS or ≥ 8 METS). Methods: Insufficiently active (as determined by accelerometry) individuals (N=518) underwent blood pressure and anthropometric testing followed by a treadmill-based graded exercise test (modified Balke protocol) with ventilatory gas exchange assessment to determine VO2peak. Only valid VO2peak tests (defined as achieving ≥90% age-predicted heart rate max and RER \u3e 1.05) were used for analyses. Adjusted Logistic Regression examined the role of CRF in whether subjects would have normal (SBP \u3c 120 and DBP \u3c 80) , elevated BP or hypertension. Data are presented as means ± SD or odds ratios with α was set at 0.05. Results: Three hundred and seventy five individuals had BP measured and met the criteria for a valid VO2peak test (age = 44.8 ± 9.1 years; BMI = 32.9 ± 6.6; VO2peak = 24.5 ± 4.8 mL/kg/min; SBP = 121 ± 13; DBP = 81 ± 10 mmHg; Males/Females = 124/251). One-hundred and twenty-seven individuals had normal BP, 164 had elevated BP, and 84 individuals were hypertensive. After adjusting for age and sex, those with a VO2peak less than 8 METs did not have significantly different odds of having elevated BP (OR = 1.3, 95% CI: 0.7 - 2.4, p = 0.33). However, those with a VO2peak less than 8 METs were more likely to be hypertensive compared to individuals with a VO2peak greater than 8 METs (OR = 2.5, 95% CI: 1.2 - 5.2, p = 0.01). Conclusions: Approximately 33.9% of our cohort had a BP that was in the normotensive range, 43.7% had elevated BP, and 22.4% were hypertensive. Importantly, the present study found that low CRF in inactive adults was associated with an increased odds of being hypertensive. This underscores the high CVD burden in this population and the need for targeted interventions to optimize outcomes. Supported by R01CA19891

CHANGES IN BLOOD PRESSURE ACROSS THE LIFESPAN AMONG INSUFFICIENTLY ACTIVE ADULTS IN THE AMERICAN SOUTHWEST

Nathan R. Weeldreyer1, Zachary S. Leicht1, Marc A. Adams2, Siddhartha S. Angadi, FACSM1. 1University of Virginia, Charlottesville, VA. 2Arizona State University, Phoenix, AZ. Purpose: Hypertension is one of the leading risk factors for cardiovascular disease (CVD) and is strongly associated with increased mortality risk. Increasing physical activity (PA) has been shown to reduce the risk of hypertension and CVD, however roughly 90% of US adults don’t meet PA guidelines. Therefore, the purpose of this study was to cross-sectionally assess blood pressure across the lifespan in adults a priori selected for being insufficiently active. Methods: Data from this cross sectional, secondary analysis came from a larger clinical trial that included insufficiently active, mostly overweight/obese (93%) adults from the Phoenix region. Subjects had anthropometric and blood pressure testing performed on them at baseline. Multiple regression was used to describe the relationships between age and systolic (SBP) and diastolic blood pressure (DBP). Additionally, sex differences across adult age-groups and differences between obesity classifications were examined. Data are presented as mean ± SD and α was set at 0.05. Results: Five hundred and sixteen subjects were analyzed (Age: 44.8±9.2 (range 19-60), BMI: 33.8±7.2, SBP: 121±13, DBP: 81±10, M/F: 184/332). Regression models revealed a linear increase in SBP across the lifespan. SBP increased by 0.4 mmHg per year with mean SBP in males being 5 mmHg greater than females. DBP had a curvilinear increase with the greatest increase seen between 19-40 years old and a plateau between 40-60. When dividing the cohort by decades of life, individuals 51-60 years old had SBP ~10 mmHg greater than 19-29 years old and 6 mmHg greater than 30-40 years old (124±13 vs 115±12, p = 0.001; and 124±13 vs 118±13, p \u3c 0.001, respectively). In addition, obese inactive individuals had an SBP 6 mmHg greater than normal weight (122±13 vs. 116±11, p = 0.02) and ~4 mmHg greater than those who were overweight (122±13 vs 119±14, p = 0.03) respectively. Conclusion: Our cross-sectional analyses of insufficiently active adults suggests that there is a linear increase in SBP with age. Males on average have SBP 5 mmHg greater than females. Additionally, obese subjects had greater SBP than those in either the normal or overweight BMI groups. Implications for CVD risk reduction in inactive obese populations will be discussed. Supported by R01CA19891

PolyMorphPredict: Web server for rapid polymorphic SSR locus discovery from whole genome and transcriptome data

Not AvailableMicrosatellites are ubiquitously distributed, polymorphic repeat sequence valuable for association, selection, population structure and identification. They can be mined by genomic library, probe hybridization and sequencing of selected clones. Such approach has many limitations like biased hybridization and selection of larger repeats. In silico mining of polymorphic markers using data of various genotypes can be rapid and economical. Available tools lack in some or other aspects like: targeted user defined primer generation, polymorphism discovery using multiple sequence, size and number limits of input sequence, no option for primer generation and e-PCR evaluation, transferability, lack of complete automation and user-friendliness. They also lack the provision to evaluate published primers in e-PCR mode to generate additional allelic data using re-sequenced data of various genotypes for judicious utilization of previously generated data. We developed the tool (PolyMorphPredict) using Perl, R, Java and launched at Apache which is available at http://webtom.cabgrid.res.in/polypred/. It mines microsatellite loci and computes primers from genome/transcriptome data of any species. It can perform e-PCR using published primers for polymorphism discovery and across species transferability of microsatellite loci. Present tool has been evaluated using five species of different genome size having 21 genotypes. Though server is equipped with genomic data of three species for test run with gel simulation, but can be used for any species. Further, polymorphism predictability has been validated using in silico and in vitro PCR of four rice genotypes. This tool can accelerate the in silico microsatellite polymorphism discovery in re-sequencing projects of any species of plant and animal for their diversity estimation along with variety/breed identification, population structure, MAS, QTL and gene discovery, traceability, parentage testing, fungal diagnostics and genome finishing.Not Availabl