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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 -
G3 (Bethesda, Md.) Dec 2023Hop production utilizes exclusively female plants, whereas male plants only serve to generate novel variation within breeding programs through crossing. Currently, hop...
Hop production utilizes exclusively female plants, whereas male plants only serve to generate novel variation within breeding programs through crossing. Currently, hop lacks a rapid and accurate diagnostic marker to determine whether plants are male or female. Without a diagnostic marker, breeding programs may take 1-2 years to determine the sex of new seedlings. Previous research on sex-linked markers was restricted to specific populations or breeding programs and therefore had limited transferability or suffered from low scalability. A large collection of 765 hop genotypes with known sex phenotypes, genotyping-by-sequencing, and genome-wide association mapping revealed a highly significant marker on the sex chromosome (LOD score = 208.7) that predicted sex within our population with 96.2% accuracy. In this study, we developed a PCR allele competitive extension (PACE) assay for the diagnostic SNP and tested three quick DNA extraction methodologies for rapid, high-throughput genotyping. Additionally, the marker was validated in a separate population of 94 individuals from 15 families from the USDA-ARS hop breeding program in Prosser, WA with 96% accuracy. This diagnostic marker is located in a gene predicted to encode the basic helix-loop-helix transcription factor protein, a family of proteins that have been previously implicated in male sterility in a variety of plant species, which may indicate a role in determining hop sex. The marker is diagnostic, accurate, affordable, and highly scalable and has the potential to improve efficiency in hop breeding.
Topics: Humans; Genome-Wide Association Study; Plant Breeding; Chromosome Mapping; Phenotype; Genotype
PubMed: 37963231
DOI: 10.1093/g3journal/jkad216 -
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 -
Tropical Biomedicine Sep 2023Chikungunya virus (CHIKV) is a mosquito-borne alphavirus with widespread distribution across the globe. Since 2016, CHIKV re-emerged in several countries including...
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus with widespread distribution across the globe. Since 2016, CHIKV re-emerged in several countries including Indian subcontinent and Southeast Asia. A proper diagnostic tool for early diagnosis of CHIKV infection is crucial to facilitate patient management and control virus transmission at the earliest stage of outbreak. Therefore, a TaqMan minor groove binder (MGB) probe-based quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay was developed to detect and quantify the CHIKV. The primers and probe were designed based on a conserved genomic region of 730 global CHIKV sequences that is located between nsP1 and nsP2 genes. The nucleotide mismatches of primers and probe with 730 global CHIKV sequences and 13 alphaviruses were then analysed in silico. In this study, the last 5 nucleotides at 3' end of primers and 5' end of probe were considered to be the critical regions for priming. In silico analysis revealed that the critical regions of primers and probe were at least 99.6% matched with the 730 global CHIKV sequences. Besides, the primers and probe showed at least 5/20 (25.0%) and 4/17 (23.5%) nucleotide mismatches with 13 alphaviruses respectively. The amplification efficiency of qRT-PCR assay was 100.59% (95% CI= 93.06, 109.33) with a R score of 0.957. Its limit of detection (LOD) at 95% probability level was 16.6 CHIKV RNA copies (95% CI= 12.9, 28.9). The qRT-PCR assay was specific to CHIKV without cross-reacting with all dengue virus serotypes, Getah virus, Tembusu virus and Zika virus. The diagnostic results of qRT-PCR assay were perfectly agreed (k=1.000, p=0.003) with a commercial trioplex assay, with sensitivity of 100% (95% CI= 61, 100) and specificity of 100% (95% CI= 44, 100). Overall, the developed qRT-PCR assay is ideal for rapid, sensitive and specific detection as well as quantification of CHIKV.
Topics: Animals; Humans; Chikungunya virus; Reverse Transcription; Sensitivity and Specificity; Reverse Transcriptase Polymerase Chain Reaction; Zika Virus; DNA Primers; Nucleotides; Zika Virus Infection; Real-Time Polymerase Chain Reaction; RNA, Viral
PubMed: 37897164
DOI: 10.47665/tb.40.3.007 -
Diagnostics (Basel, Switzerland) Oct 2023The study aims to develop a decision pathway based on HEAR score and 0 h high-sensitivity cardiac troponin T (hs-cTnT) to safely avoid a second troponin test for...
The study aims to develop a decision pathway based on HEAR score and 0 h high-sensitivity cardiac troponin T (hs-cTnT) to safely avoid a second troponin test for suspected non-ST elevation myocardial infarction (NSTEMI) in emergency departments. A HEAR score consists of history, electrocardiogram, age, and risk factors. A HEAR pathway is established using a Bayesian approach based on a predefined safety threshold of NSTEMI prevalence in the rule-out group. In total, 7131 patients were retrospectively enrolled, 582 (8.2%) with index visit NSTEMI and 940 (13.2%) with 180-day major adverse cardiovascular events (MACE). For patients with a low-risk HEAR score (0 to 2) and low 0 h hs-cTnT (<14 ng/L), the HEAR pathway recommends early discharge without further testing. After the HEAR pathway had been applied to rule out NSTEMI, the negative predictive value of index visit NSTEMI was 100.0% (95% CI, 99.8% to 100.0%) and false-negative rate of 180-day MACE was 0.40% (95% CI, 0.18% to 0.87%). Compared with the 0 h hs-cTnT < limit of detection (LoD) strategy (<5 ng/L), the HEAR pathway could correctly reclassify 1298 patients without MACE as low risk and lead to a 18.2% decrease (95% CI, 17.4-19.1%) in the need for a second troponin test. The HEAR pathway may lead to a substantial and safe reduction in repeated troponin test for emergency department patients with suspected NSTEMI.
PubMed: 37892038
DOI: 10.3390/diagnostics13203217 -
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 -
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 -
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 -
The Analyst Oct 2023Polycyclic aromatic hydrocarbons (PAHs) have attracted a lot of environmental concern because of their carcinogenic and mutagenic properties, and the fact they can...
Polycyclic aromatic hydrocarbons (PAHs) have attracted a lot of environmental concern because of their carcinogenic and mutagenic properties, and the fact they can easily contaminate natural resources such as drinking water and river water. This study presents a simple and sensitive point-of-care SERS detection of PAHs combined with machine learning algorithms to predict the PAH content more precisely and accurately in real-life samples such as drinking water and river water. We first synthesized multibranched sharp-spiked surfactant-free gold nanostars (GNSs) that can generate strong surface-enhanced Raman scattering (SERS) signals, which were further coated with cetyltrimethylammonium bromide (CTAB) for long-term stability of the GNSs as well as to trap PAHs. We utilized CTAB-capped GNSs for solution-based 'mix and detect' SERS sensing of various PAHs including pyrene (PY), nitro-pyrene (NP), anthracene (ANT), benzo[a]pyrene (BAP), and triphenylene (TP) spiked in drinking water and river water using a portable Raman module. Very low limits of detection (LOD) were achieved in the nanomolar range for the PAHs investigated. More importantly, the detected SERS signal was reproducible for over 90 days after synthesis. Furthermore, we analyzed the SERS data using artificial intelligence (AI) with machine learning algorithms based on the convolutional neural network (CNN) model in order to discriminate the PAHs in samples more precisely and accurately. Using a CNN classification model, we achieved a high prediction accuracy of 90% in the nanomolar detection range and an f1 score (harmonic mean of precision and recall) of 94%, and using a CNN regression model, achieved an RMSE = 1.07 × 10 μM. Overall, our SERS platform can be effectively and efficiently used for the accurate detection of PAHs in real-life samples, thus opening up a new, sensitive, selective, and practical approach for point-of-need SERS diagnosis of small molecules in complex practical environments.
PubMed: 37671999
DOI: 10.1039/d3an00636k -
BMC Chemistry Aug 2023This study aims to develop an effective and sensitive HPLC (High Performance Liquid Chromatography) method to determine the nitrate concentration in fruits and...
This study aims to develop an effective and sensitive HPLC (High Performance Liquid Chromatography) method to determine the nitrate concentration in fruits and vegetables (F & V) using a C column (ZORBAX Eclipse XDB-C, 80Å, 250 × 4.6 mm, 5 μm (Agilent Technologies)) maintained at 40 C, a mobile phase made up of methanol and buffer (pentane sulfonic acid sodium salt solution), and a Photo Diode Array Detector (PDA) at 225 nm. The developed method is validated in terms of selectivity, linearity, accuracy, precision, suitability, the limit of detection (LOD), and the limit of quantification (LOQ) according to the European Union Decision 2002/657/EC. The result revealed that a ratio of 30: 70 of the organic modifier methanol and buffer with pH 2.8 shows the highest efficiency. The calibration curve shows linearity with a correlation coefficient (r) of 0.9985. The LOD and LOQ were found to be 2.26 mg/kg and 7.46 mg/kg. The recovery was in the range of 98.96-100.21%. Moreover, the greenness assessment scores of different approaches (eco-scale score of 76, AGREE score of 0.71, and few red shades in GAPI portray) were at a very excellent level. Thus, our developed method is fully validated and can determine the nitrate content in F & V.
PubMed: 37620944
DOI: 10.1186/s13065-023-01008-y