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European Journal of Human Genetics :... Dec 2023We have mapped a locus on chromosome 7p22.3-7p15.3 spanning a 22.4 Mb region for ulcerative colitis (UC) by whole genome linkage analyses of a large Danish family. The...
We have mapped a locus on chromosome 7p22.3-7p15.3 spanning a 22.4 Mb region for ulcerative colitis (UC) by whole genome linkage analyses of a large Danish family. The family represent three generations with UC segregating as an autosomal dominant trait with variable expressivity. The whole-genome scan resulted in a logarithm of odds score (LOD score) of Z = 3.31, and a whole genome sequencing (WGS) of two affected excluded disease-causing mutations in the protein coding genes. Two rare heterozygote variants, rs182281985:G>A and rs541426369:G>A, both with low allele frequencies (MAF A:0.0001, gnomAD ver3.1.2), were found in clusters of ChiP-seq transcription factors binding sites close to the AHR (aryl hydrocarbon receptor) gene and the UC associated SNP rs1077773:G>A. Testing the two SNPs in a promoter reporter assay for regulatory activity revealed that rs182281985:G>A influenced the AHR promoter. These results suggest a regulatory region that include rs182281985:G>A close to the UC GWAS SNP rs1077773:G>A and further demonstrate evidence that the AHR gene on the 7p-tel region is a candidate susceptible gene for UC.
Topics: Humans; Colitis, Ulcerative; Genetic Linkage; Phenotype; Polymorphism, Single Nucleotide; Receptors, Aryl Hydrocarbon
PubMed: 36732664
DOI: 10.1038/s41431-023-01298-9 -
BMC Chemistry Mar 2024Montelukast sodium (MLK) and Levocetirizine dihydrochloride (LCZ) are widely prescribed medications with promising therapeutic potential against COVID-19. However,...
Four chemometric models enhanced by Latin hypercube sampling design for quantification of anti-COVID drugs: sustainability profiling through multiple greenness, carbon footprint, blueness, and whiteness metrics.
Montelukast sodium (MLK) and Levocetirizine dihydrochloride (LCZ) are widely prescribed medications with promising therapeutic potential against COVID-19. However, existing analytical methods for their quantification are unsustainable, relying on toxic solvents and expensive instrumentation. Herein, we pioneer a green, cost-effective chemometrics approach for MLK and LCZ analysis using UV spectroscopy and intelligent multivariate calibration. Following a multilevel multifactor experimental design, UV spectral data was acquired for 25 synthetic mixtures and modeled via classical least squares (CLS), principal component regression (PCR), partial least squares (PLS), and genetic algorithm-PLS (GA-PLS) techniques. Latin hypercube sampling (LHS) strategically constructed an optimal validation set of 13 mixtures for unbiased predictive performance assessment. Following optimization of the models regarding latent variables (LVs) and wavelength region, the optimum root mean square error of cross-validation (RMSECV) was attained at 2 LVs for the 210-400 nm spectral range (191 data points). The GA-PLS model demonstrated superb accuracy, with recovery percentages (R%) from 98 to 102% for both analytes, and root mean square error of calibration (RMSEC) and prediction (RMSEP) of (0.0943, 0.1872) and (0.1926, 0.1779) for MLK and LCZ, respectively, as well bias-corrected mean square error of prediction (BCMSEP) of -0.0029 and 0.0176, relative root mean square error of prediction (RRMSEP) reaching 0.7516 and 0.6585, and limits of detection (LOD) reaching 0.0813 and 0.2273 for MLK and LCZ respectively. Practical pharmaceutical sample analysis was successfully confirmed via standard additions. We further conducted pioneering multidimensional sustainability evaluations using state-of-the-art greenness, blueness, and whiteness tools. The method demonstrated favorable environmental metrics across all assessment tools. The obtained Green National Environmental Method Index (NEMI), and Complementary Green Analytical Procedure Index (ComplexGAPI) quadrants affirmed green analytical principles. Additionally, the method had a high Analytical Greenness Metric (AGREE) score (0.90) and a low carbon footprint (0.021), indicating environmental friendliness. We also applied blueness and whiteness assessments using the high Blue Applicability Grade Index (BAGI) and Red-Green-Blue 12 (RGB 12) algorithms. The high BAGI (90) and RGB 12 (90.8) scores confirmed the method's strong applicability, cost-effectiveness, and sustainability. This work puts forward an optimal, economically viable green chemistry paradigm for pharmaceutical quality control aligned with sustainable development goals.
PubMed: 38500132
DOI: 10.1186/s13065-024-01158-7 -
Frontiers in Genetics 2023Hereditary necrotizing myelopathy (HNM) in young Kooiker dogs is characterized by progressive ataxia and paralysis with autosomal recessive inheritance. The basic...
Hereditary necrotizing myelopathy (HNM) in young Kooiker dogs is characterized by progressive ataxia and paralysis with autosomal recessive inheritance. The basic genetic defect is unknown. We investigated the possible cause by a genome-wide analysis using six affected and 17 unrelated unaffected Kooiker dogs and by functional follow-up studies. The HNM locus was mapped by a case-control study using a dense SNP array and confirmed by linkage analysis of two pedigrees. The gene exons in the critical region were analyzed by next-generation sequencing. The functional effect of the candidate canine pathogenic variant was biochemically examined in an established HeLa cell culture model in which the endogenous gene product was depleted by RNAi. The basic defect was localized in the centromeric 5 Mb region of canine chromosome 14. The most associated SNP co-segregated fully with HNM and reached an LOD score of 6.1. A candidate pathogenic mutation was found in the iron-sulfur cluster assembly gene and led to the amino acid substitution R147W. The expression of human IBA57 harboring the canine R147W exchange could only partially restore the biochemical defects of several mitochondrial [4Fe-4S] proteins upon IBA57 depletion, showing that the mutant protein is functionally impaired. Pathogenic variants in human cause multiple mitochondrial dysfunction syndrome 3 (MMDS3), a neurodegenerative disorder with distant similarities to HNM. The incomplete functional complementation of IBA57-depleted human cells by IBA57-R147W identifies the DNA mutation in affected Kooiker dogs as the genetic cause of HNM. Our findings further expand the phenotypic spectrum of pathogenic variants.
PubMed: 37588046
DOI: 10.3389/fgene.2023.1190222 -
RSC Advances Jul 2023The integration of molecular modelling simulation and electrochemical sensors is of high interest. Herein, for the first time, a portable solid-contact potentiometric...
The integration of molecular modelling simulation and electrochemical sensors is of high interest. Herein, for the first time, a portable solid-contact potentiometric electrode was designed for the sensitive determination of mirabegron (MIR) in human plasma and pharmaceutical formulation. A two-step optimization protocol was investigated for the fabrication of an ion on sensing polymeric membrane. First, molecular docking was used for optimum ionophore selection. Calix[6]arene showed the highest affinity towards MIR with a better docking score (-4.35) and potential energy (-65.23) compared to other calixarene derivatives. Second, carbon nanotubes and gold nanoparticles were investigated as ion-electron transducers using a drop-casting procedure. Gold nanoparticle-based sensors showed better slope, potential stability, and rapid response compared to carbon nanotubes. The proposed solid contact sensors (V-VII) showed comparable sensitivity and ease of handling compared to liquid contact sensors (I-IV). The optimized gold nanoparticles sensor VII produced a Nernstian response over the range of 9.77 × 10 to 1 × 10 M with LOD of 2.4 × 10 M. It has also been used to determine MIR in its pharmaceutical formulation in the presence of a co-formulated antioxidant butylated hydroxytoluene and spiked human plasma. This would offer a feasible and economic platform for monitoring MIR in pharmaceutical preparation and biological fluids.
PubMed: 37533779
DOI: 10.1039/d3ra02343e -
The Journals of Gerontology. Series A,... May 2024Grip strength is a robust indicator of overall health, is moderately heritable, and predicts longevity in older adults.
Whole Genome Linkage and Association Analyses Identify DLG Associated Protein-1 as a Novel Positional and Biological Candidate Gene for Muscle Strength: The Long Life Family Study.
BACKGROUND
Grip strength is a robust indicator of overall health, is moderately heritable, and predicts longevity in older adults.
METHODS
Using genome-wide linkage analysis, we identified a novel locus on chromosome 18p (mega-basepair region: 3.4 - 4.0) linked to grip strength in 3755 individuals from 582 families aged 64 ± 12 years (range 30-110 years; 55% women). There were 26 families that contributed to the linkage peak (cumulative logarithm of the odds [LOD] score = 10.94), with six families (119 individuals) accounting for most of the linkage signal (LOD = 6.4). In these 6 families, using whole genome sequencing data, we performed association analyses between the 7312 single nucleotide (SNVs) and insertion deletion (INDELs) variants in the linkage region and grip strength. Models were adjusted for age, age2, sex, height, field center, and population substructure.
RESULTS
We found significant associations between genetic variants (8 SNVs and 4 INDELs, p<5*10-5) in the Disks Large-associated Protein 1 (DLGAP1) gene and grip strength. Haplotypes constructed using these variants explained up to 98.1% of the LOD score. Finally, RNAseq data showed that these variants were significantly associated with the expression of nearby Myosin Light Chain 12A (MYL12A), Structural Maintenance of Chromosomes Flexible Hinge Domain Containing 1 (SMCHD1), Erythrocyte Membrane Protein Band 4.1 Like 3 (EPB41L3) genes (p< .0004).
CONCLUSIONS
The DLGAP1 gene plays an important role in the post-synaptic density of neurons; thus, it is both a novel positional and biological candidate gene for follow-up studies aimed at uncovering genetic determinants of muscle strength.
PubMed: 38808484
DOI: 10.1093/gerona/glae144 -
PloS One 2024Although spinach is predominantly dioecious, monoecious plants with varying proportions of female and male flowers are also present. Recently, monoecious inbred lines...
Although spinach is predominantly dioecious, monoecious plants with varying proportions of female and male flowers are also present. Recently, monoecious inbred lines with highly female and male conditions have been preferentially used as parents for F1-hybrids, rather than dioecious lines. Accordingly, identifying the loci for monoecism is an important issue for spinach breeding. We here used long-read sequencing and Hi-C technology to construct SOL_r2.0_pseudomolecule, a set of six pseudomolecules of spinach chromosomes (total length: 879.2 Mb; BUSCO complete 97.0%) that are longer and more genetically complete than our previous version of pseudomolecules (688.0 Mb; 81.5%). Three QTLs, qFem2.1, qFem3.1, and qFem6.1, responsible for monoecism were mapped to SOL_r2.0_pseudomolecule. qFem3.1 had the highest LOD score and corresponded to the M locus, which was previously identified as a determinant of monoecious expression, by genetic analysis of progeny from female and monoecious plants. The other QTLs were shown to modulate the ratio of female to male flowers in monoecious plants harboring a dominant allele of the M gene. Our findings will enable breeders to efficiently produce highly female- and male-monoecious parental lines for F1-hybrids by pyramiding the three QTLs. Through fine-mapping, we narrowed the candidate region for the M locus to a 19.5 kb interval containing three protein-coding genes and one long non-coding RNA gene. Among them, only RADIALIS-like-2a showed a higher expression in the reproductive organs, suggesting that it might play a role in reproductive organogenesis. However, there is no evidence that it is involved in the regulation of stamen and pistil initiation, which are directly related to the floral sex differentiation system in spinach. Given that auxin is involved in reproductive organ formation in many plant species, genes related to auxin transport/response, in addition to floral organ formation, were identified as candidates for regulators of floral sex-differentiation from qFem2.1 and qFem6.1.
Topics: Spinacia oleracea; Plant Breeding; Quantitative Trait Loci; Chromosomes, Plant; Indoleacetic Acids
PubMed: 38394294
DOI: 10.1371/journal.pone.0296675 -
Neurobiology of Aging Jan 2024There is a paucity of genetic studies of Alzheimer Disease (AD) in individuals of African Ancestry, despite evidence suggesting increased risk of AD in the African...
There is a paucity of genetic studies of Alzheimer Disease (AD) in individuals of African Ancestry, despite evidence suggesting increased risk of AD in the African American (AA) population. We performed whole-genome sequencing (WGS) and multipoint linkage analyses in 51 multi-generational AA AD families ascertained through the Research in African American Alzheimer Disease Initiative (REAAADI) and the National Institute on Aging Late Onset Alzheimer's disease (NIA-LOAD) Family Based Study. Variants were prioritized on minor allele frequency (<0.01), functional potential of coding and noncoding variants, co-segregation with AD and presence in multi-ancestry ADSP release 3 WGS data. We identified a significant linkage signal on chromosome 5q35 (HLOD=3.3) driven by nine families. Haplotype segregation analysis in the family with highest LOD score identified a 3'UTR variant in INSYN2B with the most functional evidence. Four other linked AA families harbor within-family shared variants located in INSYN2B's promoter or enhancer regions. This AA family-based finding shows the importance of diversifying population-level genetic data to better understand the genetic determinants of AD on a global scale.
Topics: Humans; Alzheimer Disease; Lod Score; Genetic Linkage; Haplotypes; Chromosomes; Genetic Predisposition to Disease
PubMed: 37952397
DOI: 10.1016/j.neurobiolaging.2023.10.010 -
Frontiers in Plant Science 2024Wheat is an important cereal crop constrained by several biotic and abiotic stresses including drought stress. Understating the effect of drought stress and the genetic...
Wheat is an important cereal crop constrained by several biotic and abiotic stresses including drought stress. Understating the effect of drought stress and the genetic basis of stress tolerance is important to develop drought resilient, high-yielding wheat cultivars. In this study, we investigated the effects of drought stress on seedling characteristics in an association panel consisting of 198 germplasm lines. Our findings revealed that drought stress had a detrimental effect on all the seedling characteristics under investigation with a maximum effect on shoot length (50.94% reduction) and the minimum effect on germination percentage (7.9% reduction). To gain a deeper understanding, we conducted a genome-wide association analysis using 12,511 single nucleotide polymorphisms (SNPs), which led to the identification of 39 marker-trait associations (MTAs). Of these 39 MTAs, 13 were particularly noteworthy as they accounted for >10% of the phenotypic variance with a LOD score >5. These high-confidence MTAs were further utilized to extract 216 candidate gene (CGs) models within 1 Mb regions. Gene annotation and functional characterization identified 83 CGs with functional relevance to drought stress. These genes encoded the WD40 repeat domain, Myb/SANT-like domain, WSD1-like domain, BTB/POZ domain, Protein kinase domain, Cytochrome P450, Leucine-rich repeat domain superfamily, BURP domain, Calmodulin-binding protein60, Ubiquitin-like domain, etc. Findings from this study hold significant promise for wheat breeders as they provide direct assistance in selecting lines harboring favorable alleles for improved drought stress tolerance. Additionally, the identified SNPs and CGs will enable marker-assisted selection of potential genomic regions associated with enhanced drought stress tolerance in wheat.
PubMed: 38510445
DOI: 10.3389/fpls.2024.1351075 -
ACS Omega Nov 2023The detection of trace amounts of sulfosulfuron, a pesticide of increasing importance, has become a pressing issue, prompting the development of effective chemosensors....
The detection of trace amounts of sulfosulfuron, a pesticide of increasing importance, has become a pressing issue, prompting the development of effective chemosensors. In this study, we functionalized cyclotricatechylene (CTC) with propyl-phthalimide due to the presence of electronegative oxygen and nitrogen binding sites. Our optimized ligand displayed the highest docking score with sulfosulfuron, and experimental studies confirmed a significant fluorescence enhancement upon its interaction with sulfosulfuron. To gain a deeper understanding of the binding mechanism, we introduced density functional theory (DFT) studies. We carried out binding constant, Job's plot, and limit of detection (LOD) calculations to establish the effectiveness of our chemosensor as a selective detector for sulfosulfuron. These findings demonstrate the potential of our chemosensor for future applications in the field of pesticide detection.
PubMed: 37969992
DOI: 10.1021/acsomega.3c05510 -
RSC Advances Jan 2024This study presents the development of an eco-friendly and highly selective mitrogen-doped carbon quantum dot based sensor (N-CQDs) for the detection of gabapentin - a...
This study presents the development of an eco-friendly and highly selective mitrogen-doped carbon quantum dot based sensor (N-CQDs) for the detection of gabapentin - a commonly misused drug. A detailed characterization of N-CQDs spectral features and their interaction with gabapentin is provided. The optimal conditions for sensing, including pH value, buffer volume, N-CQDs concentration, and incubation time, were established. The results showed excellent fluorescence quenching at 475 nm ( = 380 nm) due to the dynamic quenching mechanism, and the sensor demonstrated excellent linearity in the 0.5-8.0 μg mL concentration range with correlation coefficients of more than 0.999, a limit of detection (LOD) of 0.160 and limit of quantification (LOQ) of 0.480 μg mL. The accuracy of the proposed sensor was acceptable with a mean accuracy of 99.91 for gabapentin detection. In addition, precision values were within the acceptable range, with RSD% below 2% indicating good repeatability and reproducibility of the sensor. Selectivity was validated using common excipients and pooled plasma samples. The proposed sensor accurately estimated gabapentin concentration in commercial pharmaceutical formulations and spiked plasma samples, exhibiting excellent comparability with previously published methods. The 'greenness' of the sensing system was evaluated using the Analytical GREEnness calculator, revealing low environmental impact and strong alignment with green chemistry principles with a greenness score of 0.76. Thus, the developed N-CQDs-based sensor offers a promising, eco-friendly, and effective tool for gabapentin detection in various situations, ranging from clinical therapeutics to forensic science.
PubMed: 38288149
DOI: 10.1039/d3ra07365c