Database resources of the National Center for Biotechnology Information in 2023

Sayers, Eric W; Bolton, Evan; Brister, J. Rodney; Canese, Kathi; Chan, Jessica; Comeau, Donald C.; Farrell, Catherine; Feldgarden, Michael; Fine, Anna M.; Funk, Kathryn; Hatcher, Eneida L.; Kannan, Sivakumar; Kelly, Christopher E.; Kim, Sunghwan; Klimke, William; Landrum, Melissa; Lathrop, Stacy; Lu, Zhiyong; Madden, Thomas; Malheiro, Adriana; Marchler‐Bauer, Aron; Murphy, Terence; Phan, Lon; Pujar, Shashikant; Rangwala, Sanjida H; Schneider, Valérie; Tse, Tony; Wang, Jiyao; Ye, Jian; Trawick, Barton W.; Pruitt, Kim D.; Sherry, Stephen T.

doi:10.1093/nar/gkac1032

Cited by 205 publications

(139 citation statements)

References 41 publications

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“…In zebrafish, the pls1 protein is involved in actin filament bundle assembly and actin filament network formation and is expressed in the sensory system. 32 Microinjection of a mutant pls1 mRNA into zebrafish embryos caused decreases in the mean otolith distance, anterior otolith diameter, posterior otolith diameter, and cochlear diameter, suggesting that ear structures were disrupted by the variant. Moreover, the mutant zebrafish showed a shorter swimming distance and a slower swimming speed, indicating the maladjustment of body balance and impaired position perception function.…”

Section: Discussionmentioning

confidence: 99%

“…The zebrafish pls1 protein has a relatively high similarity (73%) to the human PLS1 protein 31 (Supplementary Figure 8). In zebrafish, the pls1 protein is involved in actin filament bundle assembly and actin filament network formation and is expressed in the sensory system 32 . Microinjection of a mutant pls1 mRNA into zebrafish embryos caused decreases in the mean otolith distance, anterior otolith diameter, posterior otolith diameter, and cochlear diameter, suggesting that ear structures were disrupted by the variant.…”

Section: Discussionmentioning

confidence: 99%

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A novel PLS1 c.981+1G>A variant causes autosomal‐dominant hereditary hearing loss in a family

Wang

et al. 2023

Clinical Genetics

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The fimbrin protein family contains a variety of proteins, among which Plastin1 (PLS1) is an important member. According to recent studies, variations in the coding region of the PLS1 gene are associated with the development of deafness. However, the molecular mechanism of deafness caused by PLS1 gene variants remains unknown. Whole-exome sequencing was performed on hearing-impaired family members and hearing family members to identify pathogenic variants, followed by Sanger sequencing. A minigene assay was conducted to investigate the effect of the variant on PLS1 mRNA splicing. The pathogenicity of the variant was further investigated in zebrafish. RNA-sequencing (RNA-seq) was performed to analyze the dysregulation of downstream signaling pathways caused by knockdown of PLS1 expression. We identified a novel variant, PLS1 c.981+1G>A, in a large Chinese family with hearing loss and showed that the variant is responsible for the occurrence of hearing loss by inducing exon 8 skipping. The variant caused abnormal inner ear phenotypes, characterized by decreases in the mean otolith distance, anterior otolith diameter, posterior otolith diameter, cochlear diameter, and swimming speed and distance in zebrafish. Furthermore, silencing PLS1 expression significantly upregulated the expression of genes in the PI3K-Akt signaling pathway, including Col6a3, Spp1,

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A novel PLS1 c.981+1G>A variant causes autosomal‐dominant hereditary hearing loss in a family

Wang

et al. 2023

Clinical Genetics

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“…This approach allowed us to remove 190 non-independent variants from the 820 Pathways and enrichment analyses. We used NBCI's dbSNP 67,68 to ascribe the significant variants associated (suggestive cutoff p-value of 1 × 10 −6 ) 22 with pulmonary function identified using GWAS to specific genes. This yielded a list of genes associated with pulmonary function in Europeans or Africans.…”

Section: Methodsmentioning

confidence: 99%

A genome-wide association study identifies distinct variants associated with pulmonary function among European and African ancestries from the UK Biobank

et al. 2023

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Pulmonary function is an indicator of well-being, and pulmonary pathologies are the third major cause of death worldwide. We analysed the UK Biobank genome-wide association summary statistics of pulmonary function for Europeans and individuals of recent African descent to identify variants associated with the trait in the two ancestries. Here, we show 627 variants in Europeans and 3 in Africans associated with three pulmonary function parameters. In addition to the 110 variants in Europeans previously reported to be associated with phenotypes related to pulmonary function, we identify 279 novel loci, including an ISX intergenic variant rs369476290 on chromosome 22 in Africans. Remarkably, we find no shared variants among Africans and Europeans. Furthermore, enrichment analyses of variants separately for each ancestry background reveal significant enrichment for terms related to pulmonary phenotypes in Europeans but not Africans. Further analysis of studies of pulmonary phenotypes reveals that individuals of European background are disproportionally overrepresented in datasets compared to Africans, with the gap widening over the past five years. Our findings extend our understanding of the different variants that modify the pulmonary function in Africans and Europeans, a promising finding for future GWASs and medical studies.

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“…New ToBRFV genomes became available on public databases within the last six months. An additional 113 (total 183) from NCBI (28) and 250 assembled ToBRFV genomes from a study of wastewater from Southern California (29) were downloaded (Table 1).…”

Section: Assembly and Analysis Of Tobrfv Genomes And Design Of Hydrol...mentioning

confidence: 99%

Tomato brown rugose fruit virus Mo gene is a novel microbial source tracking marker

Fremin

Schmidtke

Wolfe

et al. 2023

Preprint

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Microbial source tracking (MST) identifies sources of fecal contamination in the environment using fecal host-associated markers. While there are numerous bacterial MST markers, there are few viral markers. Here we design and test novel viral MST markers based on tomato brown rugose fruit virus (ToBRFV) genomes. We assembled eight nearly complete genomes of ToBRFV from wastewater and stool samples from the San Francisco Bay Area in the United States of America. Next, we developed two novel probe-based RT-PCR assays based on conserved regions of the ToBRFV genome, and tested the markers’ sensitivities and specificities using human and non-human animal stool as well as wastewater. TheToBRFV markers are sensitive and specific; in human stool and wastewater, they are more prevalent and abundant than a currently used marker, the pepper mild mottle virus (PMMoV) coat protein (CP) gene. We applied the assays to detect fecal contamination in urban stormwater samples and found that the ToBRFV markers matched cross-assembly phage (crAssphage), an established viral MST marker, in prevalence across samples. Taken together, ToBRFV is a promising viral human-associated MST marker.

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Database resources of the National Center for Biotechnology Information in 2023

Cited by 205 publications

References 41 publications

A novel PLS1 c.981+1G>A variant causes autosomal‐dominant hereditary hearing loss in a family

A novel PLS1 c.981+1G>A variant causes autosomal‐dominant hereditary hearing loss in a family

A genome-wide association study identifies distinct variants associated with pulmonary function among European and African ancestries from the UK Biobank

Tomato brown rugose fruit virus Mo gene is a novel microbial source tracking marker

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