Biology subjects

Ardell, D. H.

Publications and source records attributed to Ardell, D. H..

5 recordsLinked to original sources

bioRxiv2021

Restoration of DNA Integrity and Cell Cycle by Electric Stimulation in Planarian Tissues Damaged by Ionizing Radiation

Exposure to high levels of ionizing {gamma}-radiation leads to irreversible DNA damage and cell death. Here, we establish that exogenous application of electric stimulation enables cellular plasticity to reestablish stem cell activity in tissues damaged by ionizing radiation. We show that sub-threshold direct current stimulation (DCS) rapidly restores pluripotent stem cell populations previously eliminated by lethally {gamma}-irradiated tissues of the planarian flatworm Schmidtea mediterranea. Our findings reveal that DCS enhances DNA repair, transcriptional activity, and cell cycle entry in post-mitotic cells. These responses involve rapid increases in cytosolic [Ca2+] through the activation of L-type Cav channels and intracellular Ca2+ stores leading to the activation of immediate early genes and ectopic expression of stem cell markers in postmitotic cells. Overall, we show the potential of electric current stimulation to reverse damaging effects of high dose {gamma}-radiation in adult tissues. Furthermore, our results provide mechanistic insights describing how electric stimulation effectively translates into molecular responses capable of regulating fundamental cellular functions without the need for genetic or pharmacological intervention.

developmental biology↗

bioRxiv2020

Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure-Function Map

The evolution of tRNA multigene families remains poorly understood, exhibiting unusual phenomena such as functional conversions of tRNA genes through anticodon shift substitutions. We improved FlyBase tRNA gene annotations from twelve Drosophila species, incorporating previously identified ortholog sets to compare substitution rates across tRNA bodies at single-site and base-pair resolution. All rapidly evolving sites fell within the same metal ion-binding pocket, that lies at the interface of the two major stacked helical domains. We applied our tRNA Structure-Function Mapper (tSFM) method independently to each Drosophila species and one outgroup species Musca domestica and found that, although predicted tRNA structure-function maps are generally highly conserved in flies, one tRNA Class-Informative Feature (CIF) within the rapidly-evolving ion-binding pocket -- Cytosine 17 (C17), ancestrally informative for lysylation identity -- independently gained asparaginylation identity and substituted in parallel across tRNAAsn paralogs at least once, possibly multiple times, during evolution of the genus. In D. melanogaster, most tRNALys and tRNAAsn genes are co-arrayed in one large heterologous gene cluster, suggesting that heterologous gene conversion as well as structural similarities of tRNA-binding interfaces in the closely related asparaginyl-tRNA synthetase (AsnRS) and lysyl-tRNA synthetase (LysRS) proteins may have played a role in these changes. A previously identified Asn-to-Lys anticodon shift substitution in D. ananassae may have arisen to compensate for the convergent and parallel gains of C17 in tRNAAsn paralogs in that lineage. Our results underscore the functional and evolutionary relevance of our tRNA structure-function map predictions and illuminate multiple genomic and structural factors contributing to rapid, parallel and compensatory evolution of tRNA multigene families.

molecular biology↗

bioRxiv2019

Targeting tRNA-Synthetase Interactions towards Novel Therapeutic Discovery Against Eukaryotic Pathogens

The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between host and parasite, and the evolution of strain-dependent drug resistance. There is a strong need for new nontoxic drugs with broad-spectrum activity against trypanosome parasites such as Leishmania and Trypanosoma. A relatively untested approach is to target macromolecular interactions in parasites rather than small molecular interactions, under the hypothesis that the features specifying macromolecular interactions diverge more rapidly through coevolution. We computed tRNA Class-Informative Features in humans and eight clades of trypanosomes, identifying parasite-specific informative features (including base-pairs and base mis-pairs) that are broadly conserved over approximately 250 million years of trypanosome evolution. Validating these observations, we demonstrated biochemically that tRNA:aminoacyl-tRNA synthetase interactions are a promising target for anti-trypanosomal drug discovery. From a marine natural products extract library, we identified several fractions with inhibitory activity toward Leishmania major alanyl-tRNA synthetase (AlaRS) but no activity against the human homolog. These marine natural products extracts showed cross-reactivity towards Trypanosoma cruzi AlaRS indicating the broad-spectrum potential of our network predictions. These findings support a systems biology model in which combination chemotherapies that target multiple tRNA-synthetase interactions should be comparatively less prone to the emergence of resistance than conventional single drug therapies.\n\nAuthor SummaryTrypanosome parasites pose a significant health risk worldwide. Conventional drug development strategies have proven challenging given the high conservation between humans and pathogens, with off-target toxicity being a common problem. Protein synthesis inhibitors have historically been an attractive target for antimicrobial discovery against bacteria, and more recently for eukaryotic pathogens. Here we propose that exploiting pathogen-specific tRNA-synthetase interactions offers the potential for highly targeted drug discovery. To this end, we improved tRNA gene annotations in trypanosome genomes, identified functionally informative trypanosome-specific tRNA features, and showed that these features are highly conserved over approximately 250 million years of trypanosome evolution. Highlighting the species-specific and broad-spectrum potential of our approach, we identified natural product inhibitors against the parasite translational machinery that have no effect on the homologous human enzyme.

microbiology↗

bioRxiv2018

Robust Estimation of the Phylogenetic Origin of Plastids Using a tRNA-Based Phyloclassifier

The trait of oxygenic photosynthesis was acquired by the last common ancestor of Archaeplastida through endosymbiosis of the cyanobacterial progenitor of modern-day plastids. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies report contradictory evidence that plastids branch either early or late within the cyanobacterial Tree of Life. Here we describe CYANO-MLP, a general-purpose phyloclassifier of cyanobacterial genomes implemented using a Multi-Layer Perceptron. CYANO-MLP exploits consistent phylogenetic signals in bioinformatically estimated structure-function maps of tRNAs. CYANO-MLP accurately classifies cyanobacterial genomes into one of eight well-supported cyanobacterial clades in a manner that is robust to missing data, unbalanced data and variation in model specification. CYANO-MLP supports a late-branching origin of plastids: we classify 99.32% of 440 plastid genomes into one of two late-branching cyanobacterial clades with strong statistical support, and confidently assign 98.41% of plastid genomes to one late-branching clade containing unicellular starch-producing marine/freshwater diazotrophic Cyanobacteria. CYANO-MLP correctly classifies the chromatophore of Paulinella chromatophora and rejects a sister relationship between plastids and the early-branching cyanobacterium Gloeomargarita lithophora. We show that recently applied phylogenetic models and character recoding strategies fit cyanobacterial/plastid phylogenomic datasets poorly, because of heterogeneity both in substitution processes over sites and compositions over lineages.

evolutionary biology↗

bioRxiv2018

Adaptive Partitioning of the tRNA Interaction Interface by Aminoacyl-tRNA-Synthetases

We introduce rugged fitness landscapes called match landscapes for the coevolution of feature-based assortative interactions between P [≥] 2 cognate pairs of tRNAs and aminoacyl-tRNA synthetases (aaRSs) in aaRS-tRNA interaction networks. Our genotype-phenotype-fitness maps assume additive feature-matching energies, a macroscopic theory of aminoacylation kinetics including proofreading, and selection for translational accuracy in multiple, perfectly encoded site-types. We compute the stationary genotype distributions of finite panmictic, asexual populations of haploid aaRs-tRNA interaction networks evolving under mutation, genetic drift, and selection for cognate matching and non-cognate mismatching of aaRS-tRNA pairs. We compared expected genotype frequencies under different matching rules and fitness functions, both with and without linked site-specific modifiers of interaction. Under selection for translational accuracy alone, our model predicts no selection on modifiers to eliminate non-cognate interactions, so long as they are compensated by tighter cognate interactions. Only under combined selection for both translational accuracy and rate do modifiers adaptively eliminate cross-matching in non-cognate aaRS/tRNA pairs. We theorize that the encoding of macromolecular interaction networks is a genetic language that symbolically maps identifying structural and dynamic features of genes and gene-products to functions within cells. Our theory helps explain 1) the remarkable divergence in how aaRSs bind tRNAs, 2) why interaction-informative features are phylogenetically informative, 3) why the Statistical Tree of Life became more tree-like after the Darwinian Transition, and 4) an approach towards computing the probability of the random origin of an interaction network.

evolutionary biology↗