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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 -
Journal of Neuroengineering and... Mar 2024Effective stroke rehabilitation requires high-dose, repetitive-task training, especially during the early recovery phase. However, the usability of upper-limb...
BACKGROUND
Effective stroke rehabilitation requires high-dose, repetitive-task training, especially during the early recovery phase. However, the usability of upper-limb rehabilitation technology in acute and subacute stroke survivors remains relatively unexplored. In this study, we introduce subacute stroke survivors to MyoGuide, a mobile training platform that employs surface electromyography (sEMG)-guided neurofeedback training that specifically targets wrist extension. Notably, the study emphasizes evaluating the platform's usability within clinical contexts.
METHODS
Seven subacute post-stroke patients (1 female, mean age 53.7 years, mean time post-stroke 58.9 days, mean duration per training session 48.9 min) and three therapists (one for eligibility screening, two for conducting training) participated in the study. Participants underwent ten days of supervised one-on-one wrist extension training with MyoGuide, which encompassed calibration, stability assessment, and dynamic tasks. All training records including the Level of Difficulty (LoD) and Stability Assessment Scores were recorded within the application. Usability was assessed through the System Usability Scale (SUS) and participants' willingness to continue home-based training was gauged through a self-developed survey post-training. Therapists also documented the daily performance of participants and the extent of support required.
RESULTS
The usability analysis yielded positive results, with a median SUS score of 82.5. Compared to the first session, participants significantly improved their performance at the final session as indicated by both the Stability Assessment Scores (p = 0.010, mean = 229.43, CI = [25.74-433.11]) and the LoD (p < 0.001; mean: 45.43, CI: [25.56-65.29]). The rate of progression differed based on the initial impairment levels of the patient. After training, participants expressed a keen interest in continuing home-based training. However, they also acknowledged challenges related to independently using the Myo armband and software.
CONCLUSIONS
This study introduces the MyoGuide training platform and demonstrates its usability in a clinical setting for stroke rehabilitation, with the assistance of a therapist. The findings support the potential of MyoGuide for wrist extension training in patients across a wide range of impairment levels. However, certain usability challenges, such as donning/doffing the armband and navigating the application, need to be addressed to enable independent MyoGuide training requiring only minimal supervision by a therapist.
Topics: Humans; Female; Middle Aged; Wrist; Stroke; Stroke Rehabilitation; Upper Extremity; Wrist Joint
PubMed: 38515192
DOI: 10.1186/s12984-024-01334-9 -
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 2023Guava ( L.) is an important fruit crop of the Indian sub-continent, with potential for improvements in quality and yield. The goal of the present study was to construct...
Guava ( L.) is an important fruit crop of the Indian sub-continent, with potential for improvements in quality and yield. The goal of the present study was to construct a genetic linkage map in an intraspecific cross between the elite cultivar 'Allahabad Safeda' and the Purple Guava landrace to identify the genomic regions responsible for important fruit quality traits, viz., total soluble solids, titratable acidity, vitamin C, and sugars. This population was phenotyped in field trials (as a winter crop) for three consecutive years, and showed moderate-to-high values of heterogeneity coefficients along with higher heritability (60.0%-97.0%) and genetic-advance-over-mean values (13.23%-31.17%), suggesting minimal environmental influence on the expression of fruit-quality traits and indicating that these traits can be improved by phenotypic selection methods. Significant correlations and strong associations were also detected among fruit physico-chemical traits in segregating progeny. The constructed linkage map consisted of 195 markers distributed across 11 chromosomes, spanning a length of 1,604.47 cM (average inter-loci distance of 8.80 markers) and with 88.00% coverage of the guava genome. Fifty-eight quantitative trait loci (QTLs) were detected in three environments with best linear unbiased prediction (BLUP) values using the composite interval mapping algorithm of the BIP (biparental populations) module. The QTLs were distributed on seven different chromosomes, explaining 10.95%-17.77% of phenotypic variance, with the highest LOD score being 5.96 for qTSS.AS.pau-6.2. Thirteen QTLs detected across multiple environments with BLUPs indicate stability and utility in a future breeding program for guava. Furthermore, seven QTL clusters with stable or common individual QTLs affecting two or more different traits were located on six linkage groups (LGs), explaining the correlation among fruit-quality traits. Thus, the multiple environmental evaluations conducted here have increased our understanding of the molecular basis of phenotypic variation, providing the basis for future high-resolution fine-mapping and paving the way for marker-assisted breeding of fruit-quality traits.
PubMed: 37426984
DOI: 10.3389/fpls.2023.1123274 -
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 -
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 -
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 -
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 -
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