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Journal of the American College of... Jul 2020Low values of high-sensitivity cardiac troponin (hs-cTn) and coronary artery calcium (CAC) scores of zero are associated with a low risk for atherosclerotic...
BACKGROUND
Low values of high-sensitivity cardiac troponin (hs-cTn) and coronary artery calcium (CAC) scores of zero are associated with a low risk for atherosclerotic cardiovascular disease (ASCVD).
OBJECTIVES
The purpose of this study was to evaluate baseline hs-cTnT and CAC in relation to ASCVD.
METHODS
Baseline hs-cTnT (limit of detection [LoD] 3 ng/l) and CAC measurements were analyzed across participants age 45 to 84 years without clinical cardiovascular disease from the prospective MESA (Multi-Ethnic Study of Atherosclerosis) in relationship to incident ASCVD.
RESULTS
Among 6,749 participants, 1,002 ASCVD events occurred during a median follow-up of 15 years. Participants with detectable CAC (20.1 vs. 5.0 events per 1,000 person-years; adjusted hazard ratio [HR]: 2.35; 95% confidence interval [CI]: 2.0 to 2.76; p < 0.001) and detectable hs-cTnT (15.4 vs. 5.2 per 1,000 person-years; adjusted HR: 1.47; 95% CI: 1.21 to 1.77; p < 0.001) had higher rates of ASCVD than those with undetectable results. Individuals with undetectable hs-cTnT (32%) had similar risk for ASCVD as did those with a CAC of zero (50%) (5.2 vs. 5.0 per 1,000 person-years). Together, hs-cTnT and CAC (discordance 38%) resulted in the following ASCVD event rates: hs-cTnT < LoD/CAC = 0: 2.8 per 1,000 person-years (reference), hs-cTnT ≥ LoD/CAC = 0: 6.8 per 1,000 person-years (HR: 1.59; 95% CI: 1.17 to 2.16; p = 0.003), hs-cTnT < LoD/CAC > 0: 11.1 per 1,000 person-years (HR: 2.74; 95% CI: 1.96 to 3.83; p < 0.00001), and hs-cTnT ≥ LoD/CAC > 0: 22.6 per 1,000 person-years (HR: 3.50; 95% CI: 2.60 to 4.70; p < 0.00001).
CONCLUSIONS
An undetectable hs-cTnT identifies patients with a similar, low risk for ASCVD as those with a CAC score of zero. The increased risk among those with discordant results supports their conjoined use for risk prediction.
Topics: Aged; Calcium; Coronary Artery Disease; Female; Heart Disease Risk Factors; Humans; Incidence; Male; Middle Aged; Primary Prevention; Reproducibility of Results; Risk Assessment; Risk Factors; Troponin; United States; Vascular Calcification
PubMed: 32703505
DOI: 10.1016/j.jacc.2020.05.057 -
Schizophrenia Research Feb 2020Schizophrenia is a clinically and genetically heterogeneous neuropsychiatric disorder, with a polygenic basis but identification of the specific determinants is a...
Schizophrenia is a clinically and genetically heterogeneous neuropsychiatric disorder, with a polygenic basis but identification of the specific determinants is a continuing challenge. In this study, we analyzed a multigenerational family, with all healthy individuals in the first two generations, and four progeny affected with schizophrenia in the subsequent two generations, using whole exome sequencing. We identified five rare protein sequence altering heterozygous variants, in five different genes namely SMARCA5, PDE1B, TNIK, SMARCA2 and FLRT shared among all affected members and predicted to be damaging. Variants in SMARCA5 and PDE1B were inherited from the unaffected father whereas variants in TNIK, SMARCA2 and FLRT1 were inherited from the unaffected mother in all the three affected individuals in the third generation; and notably all these five variants were transmitted by an affected mother to her affected son. Microsatellite based analysis lent a modest linkage support (LOD score of 1.2; θ=0.0 at each variant). Of note, analysis of exome data of an ancestry matched unrelated schizophrenia cohort (n = 350), revealed a total of 16 rare variants (MAF < 0.01) in these five genes. Interestingly, these five genes involved in neurodevelopmental and/or neurotransmitter signaling processes are implicated in the etiology of schizophrenia previously. This study provides good evidence for a likely cumulative contribution of multiple rare variants from disease relevant genes with a threshold effect in disease development and seems to explain the unusual disease transmission pattern generally witnessed in such conditions, but warrants extensive replication efforts in families with similar complex disease inheritance profiles.
Topics: Cohort Studies; Exome; Female; Genetic Linkage; Humans; Pedigree; Schizophrenia; Exome Sequencing
PubMed: 31813803
DOI: 10.1016/j.schres.2019.11.041 -
BMC Plant Biology May 2020Muscadine (Muscadinia rotundifolia) is known as a resistance source to many pests and diseases in grapevine. The genetics of its resistance to two major grapevine pests,...
BACKGROUND
Muscadine (Muscadinia rotundifolia) is known as a resistance source to many pests and diseases in grapevine. The genetics of its resistance to two major grapevine pests, the phylloxera D. vitifoliae and the dagger nematode X. index, vector of the Grapevine fanleaf virus (GFLV), was investigated in a backcross progeny between the F1 resistant hybrid material VRH8771 (Vitis-Muscadinia) derived from the muscadine R source 'NC184-4' and V. vinifera cv. 'Cabernet-Sauvignon' (CS).
RESULTS
In this pseudo-testcross, parental maps were constructed using simple-sequence repeats markers and single nucleotide polymorphism markers from a GBS approach. For the VRH8771 map, 2271 SNP and 135 SSR markers were assembled, resulting in 19 linkage groups (LG) and an average distance between markers of 0.98 cM. Phylloxera resistance was assessed by monitoring root nodosity number in an in planta experiment and larval development in a root in vitro assay. Nematode resistance was studied using 10-12 month long tests for the selection of durable resistance and rating criteria based on nematode reproduction factor and gall index. A major QTL for phylloxera larval development, explaining more than 70% of the total variance and co-localizing with a QTL for nodosity number, was identified on LG 7 and designated RDV6. Additional QTLs were detected on LG 3 (RDV7) and LG 10 (RDV8), depending on the in planta or in vitro experiments, suggesting that various loci may influence or modulate nodosity formation and larval development. Using a Bulked Segregant Analysis approach and a proportion test, markers clustered in three regions on LG 9, LG 10 and LG 18 were shown to be associated to the nematode resistant phenotype. QTL analysis confirmed the results and QTLs were thus designated respectively XiR2, XiR3 and XiR4, although a LOD-score below the significant threshold value was obtained for the QTL on LG 18.
CONCLUSIONS
Based on a high-resolution linkage map and a segregating grapevine backcross progeny, the first QTLs for resistance to D. vitifoliae and to X. index were identified from a muscadine source. All together these results open the way to the development of marker-assisted selection in grapevine rootstock breeding programs based on muscadine derived resistance to phylloxera and to X. index in order to delay GFLV transmission.
Topics: Animals; Breeding; Chromosome Mapping; Disease Resistance; Genetic Linkage; Genotype; Hemiptera; Lod Score; Microsatellite Repeats; Nematoda; Nepovirus; Phenotype; Plant Diseases; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Vitis
PubMed: 32398088
DOI: 10.1186/s12870-020-2310-0 -
Frontiers in Plant Science 2023Bacterial blight disease of rice caused by pv. () is one of the most serious constraints in rice production. The most sustainable strategy to combat the disease is the...
Bacterial blight disease of rice caused by pv. () is one of the most serious constraints in rice production. The most sustainable strategy to combat the disease is the deployment of host plant resistance. Earlier, we identified an introgression line, IR 75084-15-3-B-B, derived from possessing broad-spectrum resistance against . In order to understand the inheritance of resistance in the accession and identify genomic region(s) associated with resistance, a recombinant inbred line (RIL) mapping population was developed from the cross Samba Mahsuri (susceptible to bacterial blight) × IR 75084-15-3-B-B (resistant to bacterial blight). The F population derived from the cross segregated in a phenotypic ratio of 3: 1 (resistant susceptible) implying that resistance in IR 75084-15-3-B-B is controlled by a single dominant gene/quantitative trait locus (QTL). In the F generation, a set of 47 homozygous resistant lines and 47 homozygous susceptible lines was used to study the association between phenotypic data obtained through screening with and genotypic data obtained through analysis of 7K rice single-nucleotide polymorphism (SNP) chip. Through composite interval mapping, a major locus was detected in the midst of two flanking SNP markers, viz., Chr11.27817978 and Chr11.27994133, on chromosome 11L with a logarithm of the odds (LOD) score of 10.21 and 35.93% of phenotypic variation, and the locus has been named . search in the genomic region between the two markers flanking identified 10 putatively expressed genes located in the region of interest. The quantitative expression and DNA sequence analysis of these genes from contrasting parents identified the encoding an NB-ARC domain-containing protein as the most promising gene associated with resistance. Interestingly, a 16-bp insertion was noticed in the untranslated region (UTR) of the gene in the resistant parent, IR 75084-15-3-B-B, which was absent in Samba Mahsuri. The association of with resistance phenotype was further established by sequence-based DNA marker analysis in the RIL population. A co-segregating PCR-based INDEL marker, Marker_Xa48, has been developed for use in the marker-assisted breeding of .
PubMed: 37692438
DOI: 10.3389/fpls.2023.1173063 -
Genetic analysis and QTL mapping of yield and fruit traits in bitter gourd (Momordica charantia L.).Scientific Reports Feb 2021Bitter gourd (Momordica charantia L.) is an economically important vegetable crop grown in tropical parts of the world. In this study, a high-density linkage map of M....
Bitter gourd (Momordica charantia L.) is an economically important vegetable crop grown in tropical parts of the world. In this study, a high-density linkage map of M. charantia was constructed through genotyping-by-sequencing (GBS) technology using F mapping population generated from the cross DBGy-201 × Pusa Do Mausami. About 2013 high-quality SNPs were assigned on a total of 20 linkage groups (LGs) spanning over 2329.2 CM with an average genetic distance of 1.16 CM. QTL analysis was performed for six major yield-contributing traits such as fruit length, fruit diameter, fruit weight, fruit flesh thickness, number of fruits per plant and yield per plant. These six quantitative traits were mapped with 19 QTLs (9 QTLs with LOD > 3) using composite interval mapping (CIM). Among 19 QTLs, 12 QTLs derived from 'Pusa Do Mausami' revealed a negative additive effect when its allele increased trait score whereas 7 QTLs derived from 'DBGy-201' revealed a positive additive effect when its allele trait score increased. The phenotypic variation (R%) elucidated by these QTLs ranged from 0.09% (fruit flesh thickness) on LG 14 to 32.65% (fruit diameter) on LG 16 and a total of six major QTLs detected. Most QTLs detected in the present study were located relatively very close, maybe due to the high correlation among the traits. This information will serve as a significant basis for marker-assisted selection and molecular breeding in bitter gourd crop improvement.
Topics: Alleles; Chromosome Mapping; Fruit; Genetic Linkage; Genetic Testing; Momordica charantia; Phenotype; Polymorphism, Single Nucleotide; Quantitative Trait Loci
PubMed: 33603131
DOI: 10.1038/s41598-021-83548-8 -
Talanta Jul 2024A new simple, fast and environmentally friendly deep eutectic solvent based dispersive liquid-liquid microextraction (DES-based DLLME) methodology assisted by vortex is...
Determination of Fe, Cu, and Pb in edible oils using choline chloride:ethylene glycol deep eutectic solvent-based dispersive liquid-liquid microextraction associated with microwave-induced plasma optical emission spectrometry.
A new simple, fast and environmentally friendly deep eutectic solvent based dispersive liquid-liquid microextraction (DES-based DLLME) methodology assisted by vortex is presented for the separation and preconcentration of three elements (i.e., Fe, Cu and Pb) from edible oil samples (i.e., soybean, sunflower, rapeseed, sesame, and olive oil) prior to the determination by microwave-induced plasma optical emission spectrometry (MIP-OES). The deep eutectic solvent selected as extractant (i.e., choline chloride and ethylene glycol, 1:2) is synthesized and characterized by Fourier transform infrared spectroscopy (FT-IR), proton nuclear magnetic resonance spectroscopy (H NMR) and differential scanning calorimetry (DSC), and the extraction conditions are optimized by a two steps experimental design. Under the optimum extraction conditions (i.e., diluted sample weight: 8.6 g; DES volume: 100 μL; extraction time: 1 min; centrifugation time and speed: 3 min and 3000 rpm; and dispersion system: vortex) the analytical method presents excellent linearity (i.e., R values higher than 0.99) in the range 10-500 μg kg, repeatability (i.e., CV values lower than 9.2%), and limits of detection (LOD) values of 3, 2 and 0.7 μg kg for Pb, Fe and Cu, respectively. None of the analytes displayed amounts over the upper limit permitted by law, and recovery values of all analytes evaluated in the different samples using external standard calibration were close to 100%, which excludes significant matrix effects. Finally, AGREEprep metric has been used to evaluate the method greenness (final score of 0.47) and it has been compared successfully with previous publications for the same type of analytes and matrices.
PubMed: 38547838
DOI: 10.1016/j.talanta.2024.125939 -
Analytical Chemistry Aug 2020Fast-scan cyclic voltammetry (FSCV) is widely used for in vivo detection of neurotransmitters, but identifying analytes, particularly mixtures, is difficult. Data...
Fast-scan cyclic voltammetry (FSCV) is widely used for in vivo detection of neurotransmitters, but identifying analytes, particularly mixtures, is difficult. Data analysis has focused on identifying dopamine from cyclic voltammograms, but it would be better to analyze all the data in the three-dimensional FSCV color plot. Here, the goal was to use image analysis-based analysis of FSCV color plots for the first time, specifically the structural similarity index (SSIM), to identify rapid neurochemical events. Initially, we focused on identifying spontaneous adenosine events, as adenosine cyclic voltammograms have a primary oxidation at 1.3 V and a secondary oxidation peak that grows in over time. Using SSIM, sample FSCV color plots were compared with reference color plots, and the SSIM cutoff score was optimized to distinguish adenosine. High-pass digital filtering was also applied to remove the background drift and lower the noise, which produced a better LOD. The SSIM algorithm detected more adenosine events than a previous algorithm based on current versus time traces, with 99.5 ± 0.6% precision, 95 ± 3% recall, and 97 ± 2% F score ( = 15 experiments from three researchers). For selectivity, it successfully rejected signals from pH changes, histamine, and HO. To prove it is a broad strategy useful beyond adenosine, SSIM analysis was optimized for dopamine detection and is able to detect simultaneous events with dopamine and adenosine. Thus, SSIM is a general strategy for FSCV data analysis that uses three-dimensional data to detect multiple analytes in an efficient, automated analysis.
Topics: Adenosine; Adenosine Triphosphate; Dopamine; Electrochemical Techniques; Histamine; Image Processing, Computer-Assisted; Microelectrodes; Sensitivity and Specificity
PubMed: 32628450
DOI: 10.1021/acs.analchem.0c01214 -
PloS One 2022All stage resistance to stripe rust races prevalent in India was investigated in the European winter wheat cultivar 'Acienda'. In order to dissect the genetic basis of...
All stage resistance to stripe rust races prevalent in India was investigated in the European winter wheat cultivar 'Acienda'. In order to dissect the genetic basis of the resistance, a backcross population was developed between 'Acienda' and the stripe rust susceptible Indian spring wheat cultivar 'HD 2967'. Inheritance studies revealed segregation for a dominant resistant gene. High density SNP genotyping was used to map stripe rust resistance and marker regression analysis located stripe rust resistance to the distal end of wheat chromosome 1A. Interval mapping located this region between the SNP markers AX-95162217 and AX-94540853, at a LOD score of 15.83 with a phenotypic contribution of 60%. This major stripe rust resistance locus from 'Acienda' has been temporarily designated as Yraci. A candidate gene search in the 2.76 Mb region carrying Yraci on chromosome 1A identified 18 NBS-LRR genes based on wheat RefSeqv1.0 annotations. Our results indicate that as there is no major gene reported in the Yraci chromosome region, it is likely to be a novel stripe rust resistance locus and offers potential for deployment, using the identified markers, to confer all stage stripe rust resistance.
Topics: Basidiomycota; Chromosome Mapping; Chromosomes, Plant; Disease Resistance; Gene Expression Regulation, Plant; India; Inheritance Patterns; Plant Diseases; Plant Proteins; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Seasons; Triticum
PubMed: 35171951
DOI: 10.1371/journal.pone.0264027 -
TAG. Theoretical and Applied Genetics.... Apr 2022A major QTL, qBWA12, was fine mapped to a 216.68 kb physical region, and A12.4097252 was identified as a useful KASP marker for breeding peanut varieties resistant to...
A major QTL, qBWA12, was fine mapped to a 216.68 kb physical region, and A12.4097252 was identified as a useful KASP marker for breeding peanut varieties resistant to bacterial wilt. Bacterial wilt, caused by Ralstonia solanacearum, is a major disease detrimental to peanut production in China. Breeding disease-resistant peanut varieties is the most economical and effective way to prevent the disease and yield loss. Fine mapping the QTLs for bacterial wilt resistance is critical for the marker-assisted breeding of disease-resistant varieties. A recombinant inbred population comprising 521 lines was used to construct a high-density genetic linkage map and to identify QTLs for bacterial wilt resistance following restriction-site-associated DNA sequencing. The genetic map, which included 5120 SNP markers, covered a length of 3179 cM with an average marker distance of 0.6 cM. Four QTLs for bacterial wilt resistance were mapped on four chromosomes. One major QTL, qBWA12, with LOD score of 32.8-66.0 and PVE of 31.2-44.8%, was stably detected in all four development stages investigated over the 3 trial years. Additionally, qBWA12 spanned a 2.7 cM region, corresponding to approximately 0.4 Mb and was fine mapped to a 216.7 kb region by applying KASP markers that were polymorphic between the two parents based on whole-genome resequencing data. In a large collection of breeding and germplasm lines, it was proved that KASP marker A12.4097252 can be applied for the marker-assisted breeding to develop peanut varieties resistant to bacterial wilt. Of the 19 candidate genes in the region covered by qBWA12, nine NBS-LRR genes should be further investigated regarding their potential contribution to the resistance of peanut against bacterial wilt.
Topics: Arachis; Chromosome Mapping; Disease Resistance; Phenotype; Plant Breeding; Plant Diseases; Polymorphism, Single Nucleotide
PubMed: 35059781
DOI: 10.1007/s00122-022-04033-y -
TAG. Theoretical and Applied Genetics.... Jan 2020A QTL for aphid resistance on pepper chromosome 2 was identified and validated. This QTL affects aphid survival and reproduction, and was fine mapped to a locus...
A QTL for aphid resistance on pepper chromosome 2 was identified and validated. This QTL affects aphid survival and reproduction, and was fine mapped to a locus containing LRR-RLK analogues. Myzus persicae is one of the most threatening insect pests that adversely affects pepper (Capsicum) cultivation. Resistance to aphids was previously identified in Capsicum baccatum. This study aimed at elucidating the genetics of aphid resistance in C. baccatum. A QTL analysis was carried out for M. persicae resistance in an F population derived from an intraspecific cross between a highly resistant plant and a susceptible plant. Survival and reproduction were used as resistance parameters. Interval mapping detected two QTLs affecting aphid survival (Rmpas-1) and reproduction (Rmprp-1), respectively, both localized in the same area and sharing the same top marker on chromosome 2. Use of this marker as co-factor in multiple-QTL mapping analysis revealed a second, minor QTL (Rmprp-2) only affecting aphid reproduction, on chromosome 4. Fine mapping confirmed the effects of Rmpas-1 and Rmprp-1 and narrowed the major QTL Rmprp-1 down to a genomic region of 96 kb which is predicted to encode four analogues of resistance genes of the receptor-like kinase family containing a leucine-rich repeat domain (LRR-RLKs). This work provides not only initial information for breeding aphid-resistant pepper varieties, but also forms the basis for future molecular analysis of gene(s) involved in aphid resistance.
Topics: Animals; Aphids; Capsicum; Chromosome Mapping; Chromosomes, Plant; Crosses, Genetic; Disease Resistance; Genes, Plant; Genetic Loci; Leucine-Rich Repeat Proteins; Lod Score; Molecular Sequence Annotation; Protein Serine-Threonine Kinases; Proteins; Quantitative Trait Loci; Sequence Homology, Amino Acid
PubMed: 31595336
DOI: 10.1007/s00122-019-03453-7