Biology subjects

Ogden, M.

Publications and source records attributed to Ogden, M..

5 recordsLinked to original sources

bioRxiv2026

Mechanism-guided Discovery of Fluoroacetate Dehalogenase (FAcD) Variants for Enzymatic PFAS Defluorination

Per- and polyfluoroalkyl substances (PFAS) are persistent anthropogenic "forever chemicals" whose strong C-F bonds (~460-533 kJ mol-1) resist defluorination, and the recast EU Drinking Water Directive sets parametric values of 0.10 ug L-1 for the sum of 20 specified PFAS and 0.50 ug L-1 for total PFAS. Here, we present DeFluorX, a mechanism-first pipeline that uses Boltz-2 to co-fold 2,150 bacterial fluoroacetate dehalogenase (FAcD) variants with 26 PFAS and fluoroacetate, generating uniformly high model confidence (rho = +0.08) but poorly tracked catalytic competence. Thus, the complexes were ranked and tiered by SN2-defluorination geometry based on the known mechanism of control of FAcDs RPA1163 with fluoroacetate: Odelta...C-alpha distance and Odelta-C-alpha-F angle; relay; carboxylate clamp; F-stabiliser; F-cradle; and penalties for scissile bond strength, backside occlusion, beta-fluorination and bond multiplicity. The tiering identified eight complexes (med angle 173.2 degrees, distance 2.91 A) with a high probability of degradation, including Alphaproteobacterial enzymes, with mono-, di- and trifluoroacetate attacking at 172-178 degrees versus 163 degrees for the control. We performed WaterMap, restrained 1 us Desmond MD, MM-GBSA and scans of the three WaterMap-aware best MD frames per complex using B3LYP/6-31G** QM/MM. All 12 frames exhibited product-end C-F cleavage with barriers ranging from 1.1 to 11.8 kcal mol-1, and the departing fluoride carried -0.43 to -0.63 e. The Laboratory validation is ongoing.

bioinformatics↗

bioRxiv2025

The expanded Bostrychia moritziana genome unveils evolution in the most diverse and complex order of red algae

Red seaweeds form part of an ancient lineage of eukaryotes that were one of the first to evolve multicellularity. Although they share a common evolutionary origin with modern-day plants and display complex multicellular development, we still lack comprehensive genome data from the most highly-evolved groups of red algae. Here, we present a chromosome-level genome assembly of Bostrychia moritziana, a species that is classified into the Rhodomelaceae family of the Ceramiales order, both of which constitute the largest and most diverse family and order of red algae, respectively. Contrary to the commonly held view that red algae generally have small genomes, we report significant genome size expansion in Bostrychia and other Ceramiales species, which we posit as one of at least three independent genome expansion events that occurred during red algal evolution. Our analyses suggest that these expansions do not involve polyploidy or ancient whole genome duplications, but in the case of Bostrychia appear to be largely driven by the dramatic proliferation of a single lineage of giant Plavaka DNA transposons. Consistent with increased genome size, we identify a substantial increase in gene content in Bostrychia that was shaped both by de novo gene emergence and by the amplification of gene families in common with other Ceramiales seaweeds, providing key insight into the genetic adaptations underpinning the evolutionary success of this species-rich order. Finally, our sex-specific assemblies enabled us to resolve the UV sex chromosomes in Bostrychia, which feature expanded gene-rich sex-linked regions. Notably, these sex-linked regions each harbour a distinct TALE-HD transcription factor orthologous to ancient regulators of haploid-diploid transitions in other multicellular lineages. Together, our findings offer a unique perspective of the genomic adaptations driving red algal diversity and demonstrate how this highly successful group of red seaweeds can provide insight into the evolutionary origins and universal principles of complex multicellular plant life.

genomics↗

bioRxiv2024

The fnr-like mutants enhance isoxaben tolerance by initiating mitochondrial retrograde signalling

Isoxaben is a pre-emergent herbicide used to control broadleaf weeds. While the phytotoxic mechanism is not completely understood, isoxaben interferes with cellulose synthesis. Certain mutations in cellulose synthase complex proteins can confer isoxaben tolerance; however, these mutations cause compromised cellulose synthesis and perturbed plant growth, rendering them unsuitable as herbicide tolerance traits. We conducted a genetic screen to identify new genes associated with isoxaben tolerance by screening a selection of Arabidopsis thaliana T-DNA mutants. We found that mutations in a FERREDOXIN-NADP(+) OXIDOREDUCTASE-LIKE (FNRL) gene enhanced tolerance to isoxaben, exhibited as a reduction in primary root stunting, reactive oxygen species accumulation, and ectopic lignification. The fnrl mutant did not exhibit a reduction in cellulose levels following exposure to isoxaben, indicating that FNRL operates upstream of isoxaben-induced cellulose inhibition. In line with these results, transcriptomic analysis revealed a highly reduced response to isoxaben treatment in fnrl mutant roots. The fnrl mutants displayed constitutively induced mitochondrial retrograde signalling, and the observed isoxaben tolerance is partially dependent on the transcription factor ANAC017, a key regulator of mitochondrial retrograde signalling. Moreover, FNRL is highly conserved across all plant lineages, implying conservation of its function. Notably, fnrl mutants did not show a growth penalty in shoots, making FNRL a promising target for biotechnological applications in breeding isoxaben tolerance in crops.

plant biology↗

bioRxiv2023

Phosphate starvation regulates cellulose synthesis to modify root growth

In the model plant Arabidopsis thaliana, the absence of the essential macro-nutrient phosphate reduces primary root growth through decreased cell division and elongation, requiring alterations to the polysaccharide-rich cell wall surrounding the cells. Despite its significance, the regulation of cell wall synthesis in response to low phosphate levels is not well understood. In this study, we show that plants increase cellulose synthesis in roots under limiting phosphate conditions, which leads to changes in the thickness and structure of the cell wall. These changes contribute to the reduced growth of primary roots in low phosphate conditions. Furthermore, we found that the cellulose synthase complex activity at the plasma membrane increases during phosphate deficiency. Moreover, we show that this increase in the activity of the cellulose synthase complex is likely due to alterations in the phosphorylation status of cellulose synthases in low phosphate conditions. Specifically, phosphorylation of CELLULOSE SYNTHASE 1 at the S688 site decreases in low phosphate conditions. Phosphomimic versions of CELLULOSE SYNTHASE 1 with an S688E mutation showed significantly reduced cellulose induction and primary root length changes in low phosphate conditions. Protein structure modelling suggests that the phosphorylation status of S688 in CELLULOSE SYNTHASE 1 could play a role in stabilizing and activating the cellulose synthase complex. This mechanistic understanding of root growth regulation under limiting phosphate conditions provides potential strategies for changing root responses to soil phosphate content.

plant biology↗

bioRxiv2018

Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets

1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable, and non-invasive. Longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus metabarcode processing, and accurate taxonomic assignment. As bioinformatics tools continue to improve, addressing each of these demands within a single bioinformatics toolkit is becoming a reality.\n\n2. We present the modular metabarcode sequence toolkit Anacapa (https://github.com/limey-bean/Anacapa/), which addresses the above needs, allowing users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data A novel aspect of Anacapa is our database building module, Creating Reference libraries Using eXisting tools (CRUX), which generates comprehensive reference databases for specific user-defined metabarcode loci. The Quality Control and Dereplication module sorts and processes multiple metabarcode loci and processes merged, unmerged and unpaired reads maximizing recovered diversity. Followed by amplicon sequence variants (ASVs) detection using DADA2. The Anacapa Classifier module aligns these ASVs to CRUX-generated reference databases using Bowtie2. Taxonomy is assigned to ASVs with confidence scores using a Bayesian Lowest Common Ancestor (BLCA) method. The Anacapa Toolkit also includes an R package, ranacapa, for automated results exploration through standard biodiversity statistical analysis.\n\n3. We performed a series of benchmarking tests to verify that the Anacapa Toolkit generates comprehensive reference databases that capture wide taxonomic diversity and that it can assign high-quality taxonomy to both MiSeq-length and Hi-Seq length sequence data. We demonstrate the value of the Anacapa Toolkit to assigning taxonomy to eDNA sequences from seawater samples from southern California including capability of this tool kit to process multilocus metabarcoding data.\n\n4. The Anacapa Toolkit broadens the exploration of eDNA and assists in biodiversity assessment and management by generating metabarcode specific databases, processing multilocus data, retaining all read types, and expanding non-traditional eDNA targets. Anacapa software and source code are open and available in a virtual container to ease installation.

bioinformatics↗