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PloS One 2024This study investigated the close kinship structure of southern right whales on feeding grounds during austral summer seasons. The study was based on biopsy samples of...
This study investigated the close kinship structure of southern right whales on feeding grounds during austral summer seasons. The study was based on biopsy samples of 171 individual whales, which were genotyped with 14 microsatellite DNA loci. Kinship was investigated by using the LOD (Log Odds) score, a relatedness index for a pair of genotypes. Based on a cut-off point of LODPO > 6, which was chosen to balance false positives and negatives, a total of 28 dyads were inferred. Among these, 25 were classified as parent-offspring pairs. Additional genetic (mitochondrial DNA haplotypes) and biological (estimated body length, sex) data were used to provide additional information on the inferred close kin pairs. The elapsed time between sampling varied from 0 (close kin detected in the same austral summer season) to 17 years. All the kin pairs occurred within the Antarctic Indo sector (85°-135°E) and no pair occurred between whales within and outside of this sector. Six pairs were between individuals in high (Antarctic) and lower latitudes. Results of the present analysis on kinship are consistent with the views that whales in the Indo sector of the Antarctic are related with the breeding ground in Southwest Australia, and that whales from this population can occupy different feeding grounds. The present study has the potential to contribute to the conservation of the southern right whales through the monitoring of important population parameters such as population sizes and growth rate, in addition to assist the interpretation of stock structure derived from standard population genetic analyses.
Topics: Animals; Whales; Microsatellite Repeats; Female; DNA, Mitochondrial; Feeding Behavior; Haplotypes; Male; Antarctic Regions; Genotype; Seasons; Geography
PubMed: 38662742
DOI: 10.1371/journal.pone.0301588 -
Plants (Basel, Switzerland) Nov 2023Premature senescence is a common occurrence in rice production, and seriously affects rice plants' nutrient utilization and growth. A total of 120 recombinant inbred...
Premature senescence is a common occurrence in rice production, and seriously affects rice plants' nutrient utilization and growth. A total of 120 recombinant inbred lines (RILs) were obtained from successive self-crossing of F generations derived from Huazhan and Nekken2. The superoxide dismutase (SOD) activity, malondialdehyde (MDA), content and catalase (CAT) activity related to the anti-senescence traits and enzyme activity index of rice were measured for QTL mapping using 4858 SNPs. Thirteen QTLs related to anti-senescence were found, among which the highest LOD score was 5.70. Eighteen anti-senescence-related genes were found in these regions, and ten of them differed significantly between the parents. It was inferred that , , and became involved in the regulation of the anti-senescence molecular network upon upregulation of their expression levels. The identified anti-senescence-related QTLs and candidate genes provide a genetic basis for further research on the mechanism of the molecular network that regulates premature senescence.
PubMed: 38005709
DOI: 10.3390/plants12223812 -
International Journal of Cardiology Apr 2024The clinical chemistry score (CCS) comprising high-sensitivity cardiac troponins (hs-cTn), glucose and estimated glomerular filtration rate has been previously validated... (Comparative Study)
Comparative Study
Comparison of the clinical chemistry score to other biomarker algorithms for rapid rule-out of acute myocardial infarction and risk stratification in patients with suspected acute coronary syndrome.
BACKGROUND
The clinical chemistry score (CCS) comprising high-sensitivity cardiac troponins (hs-cTn), glucose and estimated glomerular filtration rate has been previously validated with superior accuracy for detection and risk stratification of acute myocardial infarction (AMI) compared to hs-cTn alone.
METHODS
The CCS was compared to other biomarker-based algorithms for rapid rule-out and prognostication of AMI including the hs-cTnT limit-of-blank (LOB, <3 ng/L) or limit-of-detection (LOD, <5 ng/L) and a dual marker strategy (DMS) (copeptin <10 pmol/L and hs-cTnT ≤14 ng/L) in 1506 emergency department (ED) patients with symptoms suggestive of acute coronary syndrome. Negative predictive values (NPV) and sensitivities for AMI rule-out, and 12-month combined endpoint rates encompassing mortality, myocardial re-infarction, as well as stroke were assessed.
RESULTS
NPVs of 100% (95% CI: 98.3-100%) were observed for CCS = 0, hs-cTnT LoB and hs-cTnT LoD with rule-out efficacies of 11.1%, 7.6% and 18.3% as well as specificities of 13.0% (95% CI: 9.9-16.6%), 8.8% (95% CI: 7.3-10.5%) and 21.4% (95% CI: 19.2-23.8%), respectively. A CCS ≤ 1 achieved a rule-out in 32.2% of all patients with a NPV of 99.6% (95% CI: 98.4-99.9%) and specificity of 37.4% (95% CI: 34.2-40.5%) compared to a rule-out efficacy of 51.2%, NPV of 99.0 (95% CI: 98.0-99.5) and specificity of 59.7% (95% CI: 57.0-62.4%) for the DMS. Rates of the combined end-point of death/AMI within 30 days ranged between 0.0% and 0.7% for all fast-rule-out protocols.
CONCLUSIONS
The CCS ensures reliable AMI rule-out with low short and long-term outcome rates for a specific ED patient subset. However, compared to a single or dual biomarker strategy, the CCS displays reduced efficacy and specificity, limiting its clinical utility.
Topics: Humans; Acute Coronary Syndrome; Algorithms; Biomarkers; Chemistry, Clinical; Emergency Service, Hospital; Myocardial Infarction; Prospective Studies; Risk Assessment; Troponin T
PubMed: 38278492
DOI: 10.1016/j.ijcard.2024.131815 -
Scientific Reports Sep 2023Type 1 diabetes (T1D) is characterized by the progressive destruction of pancreatic β-cells, leading to insulin deficiency and lifelong dependency on exogenous insulin....
Type 1 diabetes (T1D) is characterized by the progressive destruction of pancreatic β-cells, leading to insulin deficiency and lifelong dependency on exogenous insulin. Higher estimates of heritability rates in monozygotic twins, followed by dizygotic twins and sib-pairs, indicate the role of genetics in the pathogenesis of T1D. The incidence and prevalence of T1D are alarmingly high in Kuwait. Consanguineous marriages account for 50-70% of all marriages in Kuwait, leading to an excessive burden of recessive allele enrichment and clustering of familial disorders. Thus, genetic studies from this Arab region are expected to lead to the identification of novel gene loci for T1D. In this study, we performed linkage analyses to identify the recurrent genetic variants segregating in high-risk Kuwaiti families with T1D. We studied 18 unrelated Kuwaiti native T1D families using whole exome sequencing data from 86 individuals, of whom 37 were diagnosed with T1D. The study identified three potential loci with a LOD score of ≥ 3, spanning across four candidate genes, namely SLC17A1 (rs1165196:pT269I), SLC17A3 (rs942379: p.S370S), TATDN2 (rs394558:p.V256I), and TMEM131L (rs6848033:p.R190R). Upon examination of missense variants from these genes in the familial T1D dataset, we observed a significantly increased enrichment of the genotype homozygous for the minor allele at SLC17A3 rs56027330_p.G279R accounting for 16.2% in affected children from 6 unrelated Kuwaiti T1D families compared to 1000 genomes Phase 3 data (0.9%). Data from the NephQTL database revealed that the rs1165196, rs942379, rs394558, and rs56027330 SNPs exhibited genotype-based differential expression in either glomerular or tubular tissues. Data from the GTEx database revealed rs942379 and rs394558 as QTL variants altering the expression of TRIM38 and IRAK2 respectively. Global genome-wide association studies indicated that SLC17A1 rs1165196 and other variants from SLC17A3 are associated with uric acid concentrations and gout. Further evidence from the T1D Knowledge portal supported the role of shortlisted variants in T1D pathogenesis and urate metabolism. Our study suggests the involvement of SLC17A1, SLC17A3, TATDN2, and TMEM131L genes in familial T1D in Kuwait. An enrichment selection of genotype homozygous for the minor allele is observed at SLC17A3 rs56027330_p.G279R variant in affected members of Kuwaiti T1D families. Future studies may focus on replicating the findings in a larger T1D cohort and delineate the mechanistic details of the impact of these novel candidate genes on the pathophysiology of T1D.
Topics: Child; Humans; Diabetes Mellitus, Type 1; Kuwait; Exome Sequencing; Genome-Wide Association Study; Insulin; Sodium-Phosphate Cotransporter Proteins, Type I
PubMed: 37696853
DOI: 10.1038/s41598-023-42255-2 -
Talanta May 2024Due to their susceptibility to degradation, vitamin levels in food formulations may differ from those found in the finished product. Vitamin levels can be impacted by...
Due to their susceptibility to degradation, vitamin levels in food formulations may differ from those found in the finished product. Vitamin levels can be impacted by processing and storage. In this work, the ingredients of Strong B50 ® film-coated tablets were estimated simultaneously using simple efficient stability indicating HPLC method. Strong B50 ® film-coated tablets contain thiamine (VB1), riboflavin (VB2), calcium pantothenate (VB5), pyridoxine (VB6), vitamin C (VC), folic acid (FA), biotin (BT), inositol (IS), niacin (NC), para-aminobenzoic acid (PB), cyanocobalamine (B12), choline bitartarate, and iron gluconate. Hypersil BDS C18 column was used for achieving reasonable separation. Mobile phases (A) and (B) were utilized, the mobile phase (A) consisted of 0.015 M Hexane sulfonic acid sodium salt + 0.1 % Triethylamine and orthophosphoric acid was used to adjust the pH to (2.9) while (B) system consisted of acetonitrile. Validation of the method was assessed using International Conference of Harmonization (ICH) parameters, where linearity, accuracy, selectivity, and robustness of the method were investigated. Correlations were above 0.99, accuracy results ranged from 97.6 to 102.8 % and limits for detection and quantitation (LOD and LOQ) values were determined for each vitamin in μg/mL except for FA and BT in ng/mL. LOD values were between 0.006 and 15.08 μg/mL while LOQ values ranged from 0.031 to 49.77 μg/mL. Stability studies were conducted under stressed conditions and degradation percentages were computed. Where, VB5, VB6, FA and PB, VC, and NC were the most degradable vitamins. Whiteness evaluation using the modern RGB 12 algorithm compared our method and the old reported one by Sasaki et al., 2020. The comparison favored our newly developed method in terms of analytical performance, practical applicability and greenness. Besides, AGREE and GAPI soft wares were used to assess the greenness of the method. It was clear that the results of colored pictograms confirm low hazardous impact and that the new method is greener with AGREE score of 0.66. Furthermore, the functionality and applicability of the novel HPLC approach were concluded via the Blue Applicability Grade Index (BAGI) tool with a final score of 82.5.
PubMed: 38820824
DOI: 10.1016/j.talanta.2024.126324 -
Analytica Chimica Acta Mar 2024Vitamins are micronutrients that are required for normal growth and development of living organisms. However, due to their various chemical properties (e.g., acid-base...
Fast, sustainable, and simultaneous analysis of water- and fat-soluble vitamins by the two-dimensional microcarbon fiber fractionation system hyphenated with MS detection.
BACKGROUND
Vitamins are micronutrients that are required for normal growth and development of living organisms. However, due to their various chemical properties (e.g., acid-base behavior, the presence of numerous forms) and fluctuating concentration levels within complex matrices, simultaneous analysis of multi-class vitamins, including their active forms, is a challenging task. The growing nutrient shortage in foods is concerning for food consumers, manufacturers, and quality control organizations. Hence, a simple, fast, and greener approach that can simultaneously analyze multi-class vitamins is required to aid food testing and clinical laboratories in evaluating vitamin content more rapidly and accurately.
RESULTS
A green and rapid analytical method based on online two-dimensional microscale carbon fiber/activated carbon fiber fractionation-mass spectrometry (2DμCFs-MS) was developed and validated for simultaneous determination of vitamins (water- and fat-soluble vitamins and some analogs) in food supplements and fortified energy drinks. Vitamins have been successfully separated into three different fractions using the minimum toxic solvent (only 0.7 mL of organic solvent) in a single run within 6 min. The limit of detection (LOD) ranges from 0.1 to 10.4 ng/mL, and the limit of quantification (LOQ) ranges from 0.39 to 34.5 ng/mL. The method also showed adequate repeatability and intermediate precision, with RSD<10 % and R > 0.99 for most vitamins. The analytical method was evaluated in terms of greenness, with an analytical greenness (AGREE) score of 0.68.
SIGNIFICANCE
The 2DμCFs-MS system was developed to separate and detect multi-class vitamins simultaneously, which can be used as a beneficial tool to investigate vitamin content for food labeling and determining the vitamins in biological fluids and other complex samples. The developed method can tackle the challenge of simultaneous and fast routine analysis of multi-class vitamins.
Topics: Water; Vitamins; Dietary Supplements; Nutrients; Solvents
PubMed: 38355222
DOI: 10.1016/j.aca.2024.342288 -
PloS One 2023Next-generation sequencing has led to an explosion of genetic findings for many rare diseases. However, most of the variants identified are very rare and were also...
Next-generation sequencing has led to an explosion of genetic findings for many rare diseases. However, most of the variants identified are very rare and were also identified in small pedigrees, which creates challenges in terms of penetrance estimation and translation into genetic counselling in the setting of cascade testing. We use simulations to show that for a rare (dominant) disorder where a variant is identified in a small number of small pedigrees, the penetrance estimate can both have large uncertainty and be drastically inflated, due to underlying ascertainment bias. We have developed PenEst, an app that allows users to investigate the phenomenon across ranges of parameter settings. We also illustrate robust ascertainment corrections via the LOD (logarithm of the odds) score, and recommend a LOD-based approach to assessing pathogenicity of rare variants in the presence of reduced penetrance.
Topics: Genetic Counseling; Penetrance; Virulence; High-Throughput Nucleotide Sequencing; Lod Score
PubMed: 37733810
DOI: 10.1371/journal.pone.0290336 -
The Analyst Jun 2024Surface enhanced Raman scattering (SERS) provides a label free method of analyzing molecules from diverse and complex signals, potentially with single molecule...
Surface enhanced Raman scattering (SERS) provides a label free method of analyzing molecules from diverse and complex signals, potentially with single molecule sensitivity. The chemical specificity inherent in the SERS spectrum can identify molecules; however signal variability arising from the diversity of plasmonic environments can limit quantification, particularly at low concentrations. Here we show that digitizing, or counting SERS events, can decrease the limit of detection in flowing solutions enabling quantification of single molecules. By using multivariate curve resolution and establishing a score threshold, each individual spectrum can be classified as containing an event or not. This binary "yes/no" can then be quantified, and a linear region can be established. This method was shown to lower the limit of detection to the lowest physical limit, and lowered the limit of detection by an order of magnitude from the traditional, intensity based LOD calculations.
PubMed: 38895849
DOI: 10.1039/d4an00801d -
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 -
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