Biology subjects

Hayden, M.

Publications and source records attributed to Hayden, M..

8 recordsLinked to original sources

bioRxiv2026

Carbon concentrating mechanism and growth response of the diatom P. tricornutum to changes in Zn and carbonate chemistry

The efficiency of marine diatom carbon concentrating mechanisms (CCMs) play a critical role in photosynthesis and enable cells to maintain rapid growth rates under a variety of environmental conditions. To assess the plasticity of the model diatom P. tricornutums CCMs, specifically carbonic anhydrase (CA) enzymes and bicarbonate transporters, we measured growth response, bulk CA activity, and corresponding shifts in the proteome under a range of Zn and pCO2 conditions in culture. CA activity increased with Zn availability and decreased with pCO2. A positive growth effect was observed due to Zn addition and increasing pCO2 from 200 to 400 ppm, however growth rate decreased as pCO2 further increased to 750 ppm. Across the six treatments, the protein abundance of ISIP2A, which functions to bring Fe into the cell via a FeCO3 complex and is used as a biomarker for Fe stress, demonstrated an inverse relationship with [CO32-], consistent with its role as a phytotransferrin. Under conditions of Zn limitation ([Zn2+] = 0.3 pM), the cell appeared to allocate this metal away from CA, instead relying on a Mn-CA with a 100-fold lower intrinsic activity than that of the primary Zn-CA, as calculated using paired abundance-activity measurements. We further observed a continued increase in bicarbonate transport protein abundance after CA activity plateaued at 1.2x10-6 (reactions sec- 1cell-1), suggesting any deficit in DIC required to maintain high growth rates is accomplished through HCO3- uptake. We hypothesize that bicarbonate uptake and CO2 diffusion operate in tandem via CA enzymatic activity to supply adequate CO2 for photosynthesis.

biochemistry↗

bioRxiv2023

Combined Right Ventricular Preload and Afterload Challenge Induces Contractile Dysfunction and Ventricular Arrhythmia in an Age-dependent Manner in Isolated Hearts of Dystrophin-deficient Mice

Duchenne muscular dystrophy (DMD) is an X-linked recessive myopathy due to mutations in the dystrophin gene. Diaphragmatic weakness in DMD causes restrictive lung disease and excessive afterload on the right ventricle (RV). Thus, RV dysfunction in DMD develops early in disease progression. Herein, we deliver a 30-minute sustained RV preload and afterload challenge to isolated hearts of wildtype (Wt) and dystrophic (mdx4CV) mice at both young (2-6 month) and middle-age (8-12 month). Young dystrophic hearts exhibited greater pressure development than wildtype under unloaded conditions but following RV preload/afterload challenge exhibited similar contractile function as wildtype. Following RV preload/afterload challenge, young dystrophic hearts had an increased incidence of ventricular arrhythmias compared to wildtype. Hearts of middle-aged wildtype and dystrophic mice had similar contractile function during unloaded conditions, yet, after RV preload/afterload challenge, hearts of middle-aged dystrophic mice had severe RV contractile dysfunction and ventricular arrhythmogenesis, including ventricular tachycardia. Following load challenge, young and middle-aged dystrophic hearts had greater damage, measured via tissue LDH release, than wildtype mice of similar age. Our data indicate complex age-dependent changes in RV function and arrhythmogenesis with load in dystrophin deficiency, highlighting the need to avoid sustained RV load to forestall RV dysfunction and arrhythmia.

physiology↗

bioRxiv2019

The experimentally obtained functional impact assessments of GT>GC 5' splice site variants differ markedly from those predicted

GT>GC 5 splice site (or +2T>C) variants have been frequently reported to cause human genetic disease. However, although we have demonstrated that GT>GC variants in human disease genes may not invariably be pathogenic, none of the currently available splicing prediction tools appear to be capable of reliably distinguishing those GT>GC variants that generate wild-type transcripts from those that do not. Recently, SpliceAI, a novel deep residual neural network tool, has been developed for splicing prediction. Methodologically distinct from previous approaches that either rely on human-engineered features and/or which focus on short nucleotide windows adjoining exon-intron boundaries, SpliceAI assesses splicing determinants by evaluating 10,000 nucleotides of flanking contextual sequence to predict the functional role in splicing of each position in the pre-mRNA transcript. Herein, we evaluated the performance of SpliceAI in the context of three datasets of GT>GC variants, all of which had been characterized functionally in terms of their impact on mRNA splicing. The first two datasets refer to our recently described "in vivo" dataset of 45 disease-causing GT>GC variants and the "in vitro" dataset of 103 GT>GC substitutions. The third dataset comprised 12 BRCA1 GT>GC variants that were recently analyzed by saturation genome editing. We processed all GT>GC variants using the default settings of SpliceAI. Comparison of the SpliceAI-predicted and experimentally obtained functional impact assessments of the analyzed GT>GC variants revealed that although SpliceAI performed rather better than other prediction tools, it was still far from perfect. A key issue is that the impact of GT>GC (as well as GT>GA or +2T>A) variants that generated wild-type transcripts represents a quantitative change that can vary from barely detectable to almost full expression of wild-type transcripts, with wild-type transcripts often co-existing with aberrantly spliced transcripts. Our findings highlight the challenges that we still face in attempting to accurately identify splice-altering variants.

genetics↗

bioRxiv2019

5’ splice site GC>GT variants differ from GT>GC variants in terms of their functionality and pathogenicity

In the human genome, most 5 splice sites (~99%) employ the canonical GT dinucleotide whereas a small minority (~1%) use the non-canonical GC dinucleotide. The functionality and pathogenicity of 5 splice site GT>GC (i.e., +2T>C) variants have been extensively studied but we still know very little about 5 splice site GC>GT (+2C>T) variants. Herein, we sought to address this deficiency by performing a meta-analysis of identified +2C>T pathogenic variants together with a functional analysis of +2C>T substitutions using a cell culture-based full-length gene splicing assay. Our results establish a proof of concept that +2C>T variants are qualitatively different from +2T>C variants in terms of their functionality and pathogenicity and suggest that, in sharp contrast with +2T>C variants, most if not all +2C>T variants have no pathological relevance. Our findings have important implications for interpreting the clinical relevance of +2C>T variants but might also improve our understanding of the evolutionary basis of switching between GT and GC 5 splice sites in mammalian genomes.

genetics↗

bioRxiv2019

Integrating past, present and future wheat research with Pretzel

MotivationMajor advances have been made in the assembly of complex genomes such as wheat. Remaining challenges include linking these new resources to legacy research, as well as lowering the bar to entry for members of the research community who may lack specific bioinformatics skills.\n\nResultsPretzel aims to solve these problems by providing an interactive, online environment for data visualisation and analysis which, when loaded with appropriately curated data, can enable researchers with no bioinformatics training to exploit the latest genomic resources. We demonstrate that Pretzel can be used to answer common questions asked by researchers as well as for advanced curation of pseudomolecule structure.\n\nAvailabilityPretzel is implemented in JavaScript and is freely available under a GPLv3 license online at: https://github.com/plantinformatics/pretzel.\n\nContactgabriel.keeble-gagnere@ecodev.vic.gov.au

bioinformatics↗

bioRxiv2018

First estimation of the scale of canonical 5’ splice site GT>GC mutations generating wild-type transcripts and their medical genetic implications

It has long been known that canonical 5 splice site (5SS) GT>GC mutations may be compatible with normal splicing. However, to date, the true scale of canonical 5SS GT>GC mutations generating wild-type transcripts, both in the context of the frequency of such mutations and the level of wild-type transcripts generated from the mutation alleles, remain unknown. Herein, combining data derived from a meta-analysis of 45 informative disease-causing 5SS GT>GC mutations (from 42 genes) and a cell culture-based full-length gene splicing assay of 103 5SS GT>GC mutations (from 30 genes), we estimate that [~]15-18% of the canonical GT 5SSs are capable of generating between 1 and 84% normal transcripts as a consequence of the substitution of GT by GC. We further demonstrate that the canonical 5SSs whose substitutions of GT by GC generated normal transcripts show stronger complementarity to the 5 end of U1 snRNA than those sites whose substitutions of GT by GC did not lead to the generation of normal transcripts. We also observed a correlation between the generation of wild-type transcripts and a milder than expected clinical phenotype but found that none of the available splicing prediction tools were able to accurately predict the functional impact of 5SS GT>GC mutations. Our findings imply that 5SS GT>GC mutations may not invariably cause human disease but should also help to improve our understanding of the evolutionary processes that accompanied GT>GC subtype switching of U2-type introns in mammals.

genetics↗

bioRxiv2018

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

BackgroundNumerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.\n\nResultsUsing chromosome 7A of wheat as a model, sequence-finished megabase scale sections of this chromosome were established by combining a new independent assembly based on a BAC-based physical map, BAC pool paired end sequencing, chromosome arm specific mate-pair sequencing and Bionano optical mapping with the IWGSC RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.\n\nConclusionsSufficient genome sequence information is shown to be now available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and yield attributes are affected by five f-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

genomics↗

bioRxiv2018

Community origins and regional differences in plasmid-mediated fluoroquinolone resistant Enterobacteriaceae infections in children

BackgroundFluoroquinolones (FQs) are uncommonly prescribed in children, yet pediatric multidrug-resistant (MDR)-Enterobacteriaceae (Ent) infections often reveal FQ resistance (FQR). We sought to define the molecular epidemiology of FQR and MDR-Ent in children.\n\nMethodsA case-control analysis of children with MDR-Ent infections at 3 Chicago hospitals was performed. Cases were children with third-generation-cephalosporin-resistant (3GCR) and/or carbapenem-resistant (CR)-Ent infections. PCR and DNA analysis assessed bla and plasmid-mediated FQR (PMFQR) genes. Controls were children with 3GC and carbapenem susceptible-Ent infections matched by age, source and hospital. We assessed clinical-epidemiologic predictors of PMFQR Ent infection.\n\nResultsOf 169 3GCR and/or CR Ent isolates from children (median age 4.8 years), 85 were FQR; 56 (66%) contained PMFQR genes. The predominant organism was E. coli and most common bla gene bla CTX-M-1 group. In FQR isolates, PMFQR gene mutations included aac61b-cr, oqxA/B, qepA, and qnrA/B/D/S in 83%, 15%, 13% and 11% of isolates, respectively. FQR E. coli was often associated with phylogroup B2, ST43/ST131. On multivariable analysis, PMFQR Ent infections occurred mostly in outpatients (OR 33.1) of non-black-white-Hispanic race (OR 6.5). Residents of Southwest Chicago were >5 times more likely to have PMFQR-Ent infections than those in the reference region, while residence in Central Chicago was associated with a 97% decreased risk. Other demographic, comorbidity, invasive-device, antibiotic use, or healthcare differences were not found.\n\nConclusionsThe strong association of infection with MDROs showing FQR with patient residence rather than with traditional risk factors suggests that the community environment is a major contributor to spread of these pathogens in children.

epidemiology↗