Biology subjects

Jordan, D. C.

Publications and source records attributed to Jordan, D. C..

3 recordsLinked to original sources

bioRxiv2025

Gene editing without a genome: generation and validation of F0 CRISPR mutants in gastropod mollusc Crepidula fornicata

BackgroundCRISPR-Cas9 gene editing is a powerful tool to study gene function but to date is mostly applied in traditional model organisms. Due to specific challenges in spiralian genomics such as genome size, complexity, proportion of repetitive regions and high inter individual genome variation, applications of CRISPR-Cas9 in spiralian models have been limited. Within the Spiralia, molluscs are a strikingly diverse phylum with many unique gene family expansions and novelties, yet there are relatively few applications of CRISPR-Cas9 to unravel gene function. ResultsWe generated pax6 knockout F0 CRISPR-Cas9 mutants in the gastropod mollusc Crepidula fornicata using a de novo transcriptome to design single guide RNAs and genotyping primers. In lieu of an assembled genome, alignments with closely related species were used to determine putative intron-exon boundaries and successfully target gene editing to a specific exon of pax6 containing a homeodomain. F0 pax6 knockout mutants had an eye-loss phenotype. Successful CRISPR-Cas9 gene editing was confirmed genotypically using Sanger sequencing and Interference of CRISPR Edits (ICE) analysis. ConclusionsThe generation of F0 CRISPR-Cas9 knockout mutants with a clear phenotype in a mollusc without an assembled genome enhances the applicability of CRISPR for functional genomics in non-traditional emerging model systems. pax6 is highly conserved and is required for eye development across metazoans, including the snail C. fornicata. The pax6 mutants developed in this study suggests the pax6 homeodomain is specifically required for eye formation in gastropods and sheds light on the evolution of eye development in animals.

developmental biology↗

bioRxiv2019

Regulation of FXR1 by alternative splicing is required for muscle development and controls liquid-like condensates in muscle cells

Fragile-X mental retardation autosomal homolog-1 (FXR1) is a muscle-enriched RNA-binding protein. FXR1 depletion is perinatally lethal in mice, Xenopus, and zebrafish; however, the mechanisms driving these phenotypes remain unclear. The FXR1 gene undergoes alternative splicing, producing multiple protein isoforms and mis-splicing has been implicated in disease. Furthermore, mutations that cause frameshifts in muscle-specific isoforms result in congenital multi-minicore myopathy. We observed that FXR1 alternative splicing is pronounced in the serine and arginine-rich intrinsically-disordered domain; these domains are known to promote biomolecular condensation. Here, we show that tissue-specific splicing of fxr1 is required for Xenopus development and alters the disordered domain of FXR1. FXR1 isoforms vary in the formation of RNA-dependent biomolecular condensates in cells and in vitro. This work shows that regulation of tissue-specific splicing can influence FXR1 condensates in muscle development and how mis-splicing promotes disease.\n\nHIGHLIGHTSO_LIThe muscle-specific exon 15 impacts FXR1 functions\nC_LIO_LIAlternative splicing of FXR1 is tissue- and developmental stage specific\nC_LIO_LIFXR1 forms RNA-dependent condensates\nC_LIO_LISplicing regulation changes FXR1 condensate properties\nC_LI

cell biology↗

bioRxiv2017

Concern noted: A descriptive study of editorial expressions of concern in PubMed and PubMed Central.

BackgroundAn editorial expression of concern (EEoC) is issued by editors or publishers to draw attention to potential problems in a publication, without itself constituting a retraction or correction.\n\nMethodsWe searched PubMed, PubMed Central (PMC), and Google Scholar to identify EEoCs issued for publications in PubMed and PMC up to 22 August 2016. We also searched the archives of the Retraction Watch blog, some journal and publisher websites, and studies of EEoCs. In addition, we searched for retractions of EEoCs and affected articles in PubMed up to 8 December 2016. We analyzed overall historical trends, as well as reported reasons and subsequent editorial actions related to EEoCs issued between August 2014 and August 2016.\n\nResultsAfter screening 5,076 records, we identified 230 EEoCs that affect 300 publications indexed in PubMed, the earliest issued in 1985. Half of the primary EEoCs were issued between 2014 and 2016 (52%). We found evidence of some EEoCs that had been removed by the publisher without leaving a record and some were not submitted for PubMed or PMC indexing. A minority of publications affected by EEoCs had been retracted by early December 2016 (25%). For the subset of 92 EEoCs issued between August 2014 and August 2016, affecting 99 publications, the rate of retraction was similar (29%). The majority of EEoCs were issued because of concerns with validity of data, methods, or interpretation of the publication (68%), and 31% of cases remained open. Issues with images were raised in 40% of affected publications. Ongoing monitoring after the study identified another 17 EEoCs to years end in 2016, increasing the number of EEoCs to 247 and publications in PubMed known to be affected by EEoCs to 320 at the end of 2016.\n\nConclusionsEEoCs have been rare publishing events in the biomedical literature, but their use has been increasing. Most have not led to retractions, and many remain unresolved. Lack of prominence and inconsistencies in management of EEoCs reduce the ability of these notices to alert the scientific community to potentially serious problems in publications. EEoCs will be made identifiable in PubMed in 2017.

scientific communication and education↗