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NPJ Genomic Medicine Aug 2023Genomic sequences residing within introns of few genes have been shown to act as enhancers affecting expression of neighboring genes. We studied an autosomal recessive...
Genomic sequences residing within introns of few genes have been shown to act as enhancers affecting expression of neighboring genes. We studied an autosomal recessive phenotypic continuum of microphthalmia, anophthalmia and ocular coloboma, with no apparent coding-region disease-causing mutation. Homozygosity mapping of several affected Jewish Iranian families, combined with whole genome sequence analysis, identified a 0.5 Mb disease-associated chromosome 2q35 locus (maximal LOD score 6.8) harboring an intronic founder variant in NHEJ1, not predicted to affect NHEJ1. The human NHEJ1 intronic variant lies within a known specifically limb-development enhancer of a neighboring gene, Indian hedgehog (Ihh), known to be involved in eye development in mice and chickens. Through mouse and chicken molecular development studies, we demonstrated that this variant is within an Ihh enhancer that drives gene expression in the developing eye and that the identified variant affects this eye-specific enhancer activity. We thus delineate an Ihh enhancer active in mammalian eye development whose variant causes human microphthalmia, anophthalmia and ocular coloboma. The findings highlight disease causation by an intronic variant affecting the expression of a neighboring gene, delineating molecular pathways of eye development.
PubMed: 37580330
DOI: 10.1038/s41525-023-00364-x -
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 Plant Genome Dec 2023Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine...
Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine deployment of genomic-assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping population (ICGV 00440 × ICGV 06040;). Genetic mapping and quantitative trait locus (QTL) analysis (474 mapped single-nucleotide polymorphism loci; 1536.33 cM) using 2 seasons of phenotypic data together with genotypic data identified 5 major main-effect QTLs for Fe content. These QTLs exhibited log-of-odds (LOD) scores ranging from 6.5 to 7.4, explaining phenotypic variation (PVE) ranging from 22% (qFe-Ah01) to 30.0% (qFe-Ah14). Likewise, four major main effect QTLs were identified for Zn content, with LOD score ranging from 4.4 to 6.8 and PVE ranging from 21.8% (qZn-Ah01) to 32.8% (qZn-Ah08). Interestingly, three co-localized major and main effect QTLs (qFe-Ah01, qZn-Ah03, and qFe-Ah11) were identified for both Fe and Zn contents. These genomic regions harbored key candidate genes, including zinc/iron permease transporter, bZIP transcription factor, and vacuolar iron transporter which likely play pivotal roles in the accumulation of Fe and Zn contents in seeds. The findings of this study hold potential for fine mapping and diagnostic marker development for high Fe and Zn contents in groundnut.
Topics: Quantitative Trait Loci; Zinc; Plant Breeding; Fabaceae; Iron
PubMed: 37408143
DOI: 10.1002/tpg2.20361 -
Clinica Chimica Acta; International... Aug 2023The Enhanced Liver Fibrosis (ELF) Test comprises 3 direct serum markers of fibrosis-hyaluronic acid (HA), amino-terminal pro-peptide of type III procollagen (PIIINP),...
BACKGROUND
The Enhanced Liver Fibrosis (ELF) Test comprises 3 direct serum markers of fibrosis-hyaluronic acid (HA), amino-terminal pro-peptide of type III procollagen (PIIINP), and tissue inhibitor of matrix metalloproteinase 1 (TIMP-1)-whose results are combined in an algorithm to generate the ELF score. Outside the U.S., the ELF Test and score are CE marked for assessment of liver fibrosis severity in patients with signs, symptoms, or risk factors of chronic liver disease to support diagnosis of fibrosis staging or prognosis for likelihood of progression to cirrhosis and liver-related clinical events. In the U.S., the FDA granted de novo marketing authorization to aid prognostic evaluation of disease progression (to cirrhosis and liver-related clinical events) in nonalcoholic steatohepatitis patients with advanced liver fibrosis. We describe the analytical performance of the ELF analytes and score on the Atellica® IM Analyzer.
METHODS
Clinical and Laboratory Standards Institute protocols were followed for detection capability (limits of blank [LoB], detection [LoD], and quantitation [LoQ]), precision, interference, linearity, hook effect, and ELF reference interval.
RESULTS
All parameters met predetermined requirements: HA (LoB 1.00 ng/mL, LoD 2.00 ng/mL, LoQ 3.00 ng/mL); PIIINP (LoB 0.50 ng/mL, LoD 0.75 ng/mL, LoQ 1.00 ng/mL); TIMP-1 (LoB 3.0 ng/mL, LoD 4.0 ng/mL, LoQ 5.0 ng/mL). Across the 3 assays, repeatability was ≤5.4% CV; within-lab precision was ≤8.5% CV. ELF score repeatability was ≤0.6% CV, within-lab precision ≤1.3% CV, and reproducibility ≤1.1% CV. Good correlation was obtained between the Atellica IM ELF and ADVIA Centaur ELF Tests (y = 1.01x - 0.22, r = 0.997). Assays were linear across analytical measuring ranges.
CONCLUSIONS
Analytical performance validation results for the ELF Test and ELF score were excellent making the test acceptable for routine clinical use.
Topics: Humans; Tissue Inhibitor of Metalloproteinase-1; Reproducibility of Results; Liver Cirrhosis; Fibrosis; Liver; Biomarkers; Hyaluronic Acid
PubMed: 37390944
DOI: 10.1016/j.cca.2023.117461 -
Brain : a Journal of Neurology Sep 2023Moyamoya disease, a cerebrovascular disease leading to strokes in children and young adults, is characterized by progressive occlusion of the distal internal carotid...
Moyamoya disease, a cerebrovascular disease leading to strokes in children and young adults, is characterized by progressive occlusion of the distal internal carotid arteries and the formation of collateral vessels. Altered genes play a prominent role in the aetiology of moyamoya disease, but a causative gene is not identified in the majority of cases. Exome sequencing data from 151 individuals from 84 unsolved families were analysed to identify further genes for moyamoya disease, then candidate genes assessed in additional cases (150 probands). Two families had the same rare variant in ANO1, which encodes a calcium-activated chloride channel, anoctamin-1. Haplotype analyses found the families were related, and ANO1 p.Met658Val segregated with moyamoya disease in the family with an LOD score of 3.3. Six additional ANO1 rare variants were identified in moyamoya disease families. The ANO1 rare variants were assessed using patch-clamp recordings, and the majority of variants, including ANO1 p.Met658Val, displayed increased sensitivity to intracellular Ca2+. Patients harbouring these gain-of-function ANO1 variants had classic features of moyamoya disease, but also had aneurysm, stenosis and/or occlusion in the posterior circulation. Our studies support that ANO1 gain-of-function pathogenic variants predispose to moyamoya disease and are associated with unique involvement of the posterior circulation.
Topics: Child; Humans; Young Adult; Anoctamin-1; Chloride Channels; Moyamoya Disease; Neoplasm Proteins
PubMed: 37253099
DOI: 10.1093/brain/awad172 -
Ear and HearingA multisite clinical trial was conducted to obtain cochlear implant (CI) efficacy data in adults with asymmetric hearing loss (AHL) and establish an evidence-based...
OBJECTIVE
A multisite clinical trial was conducted to obtain cochlear implant (CI) efficacy data in adults with asymmetric hearing loss (AHL) and establish an evidence-based framework for clinical decision-making regarding CI candidacy, counseling, and assessment tools. Study hypotheses were threefold: (1) 6-month postimplant performance in the poor ear (PE) with a CI will be significantly better than preimplant performance with a hearing aid (HA), (2) 6-month postimplant performance with a CI and HA (bimodal) will be significantly better than preimplant performance with bilateral HAs (Bil HAs), and (3) 6-month postimplant bimodal performance will be significantly better than aided, better ear (BE) performance.
DESIGN
Forty adults with AHL from four, metropolitan CI centers participated. Hearing criteria for the ear to be implanted included (1) pure-tone average (PTA, 0.5, 1, 2 kHz) of >70 dB HL, (2) aided, monosyllabic word score of ≤30%, (3) duration of severe-to-profound hearing loss of ≥6 months, and (4) onset of hearing loss ≥6 years of age. Hearing criteria for the BE included (1) PTA (0.5, 1, 2, 4 kHz) of 40 to 70 dB HL, (2) currently using a HA, (3) aided, word score of >40%, and (4) stable hearing for the previous 1-year period. Speech perception and localization measures, in quiet and in noise, were administered preimplant and at 3-, 6-, 9-, and 12-months postimplant. Preimplant testing was performed in three listening conditions, PE HA, BE HA, and Bil HAs. Postimplant testing was performed in three conditions, CI, BE HA, and bimodal. Outcome factors included age at implantation and length of deafness (LOD) in the PE.
RESULTS
A hierarchical nonlinear analysis predicted significant improvement in the PE by 3 months postimplant versus preimplant for audibility and speech perception with a plateau in performance at approximately 6 months. The model predicted significant improvement in postimplant, bimodal outcomes versus preimplant outcomes (Bil HAs) for all speech perception measures by 3 months. Both age and LOD were predicted to moderate some CI and bimodal outcomes. In contrast with speech perception, localization in quiet and noise was not predicted to improve by 6 months when comparing Bil HAs (preimplant) to bimodal (postimplant) outcomes. However, when participants' preimplant everyday listening condition (BE HA or Bil HAs) was compared with bimodal performance, the model predicted significant improvement by 3 months for localization in quiet and noise. Lastly, BE HA results were stable over time; a generalized linear model analysis revealed bimodal performance was significantly better than performance with a BE HA at all postimplant intervals for most speech perception measures and localization.
CONCLUSIONS
Results revealed significant CI and bimodal benefit for AHL participants by 3-months postimplant, with a plateau in CI and bimodal performance at approximately 6-months postimplant. Results can be used to inform AHL CI candidates and to monitor postimplant performance. On the basis of this and other AHL research, clinicians should consider a CI for individuals with AHL if the PE has a PTA (0.5, 1, 2 kHz) >70 dB HL and a Consonant-Vowel Nucleus-Consonant word score ≤40%. LOD >10 years should not be a contraindication.
Topics: Adult; Humans; Cochlear Implants; Prospective Studies; Cochlear Implantation; Hearing Loss; Hearing Aids; Speech Perception; Treatment Outcome
PubMed: 37018114
DOI: 10.1097/AUD.0000000000001354