Biology subjects

Meiklejohn, K. A.

Publications and source records attributed to Meiklejohn, K. A..

3 recordsLinked to original sources

bioRxiv2026

Generating, curating, and evaluating trnL reference sequence databases: Benchmarking OBITools3/ecoPCR, RESCRIPt, and MetaCurator

Plant DNA metabarcoding enables the identification of plant taxa in mixed samples, with the trnL (UAA) intron and its P6 loop mini-barcode region performing as well as or better than other commonly used markers. Reliable metabarcoding requires high-quality reference databases, yet a regularly maintained trnL resource is currently lacking. Consequently, most studies use uncurated sequences downloaded directly from public repositories without essential validation. We address these gaps by providing guidance through a systematic comparison of three database curation tools - OBITools3/ecoPCR, RESCRIPt, and MetaCurator - to generate three trnL reference sequence databases and evaluate their classification performance across commonly sequenced trnL regions (CD, CH, and GH). Reference trnL sequences and taxonomy files were retrieved from public sequence repositories and curated using standardized filtering steps to reduce taxonomic errors, sequence ambiguity, and redundancy. Four simulated query datasets--two base sets and their mutated counterparts--were constructed to assess classification performance of the databases using the Naive Bayesian Classifier implemented in DADA2.- The evaluation showed that performance differed by trnL region: MetaCurator and RESCRIPt yielded higher and similar metrics for trnL CD; OBITools3/ecoPCR and RESCRIPt were comparable for trnL CH; and MetaCurator attained the highest performance for trnL GH region. All reference databases, taxonomy, and evaluation files are available at Zenodo (https://doi.org/10.5281/zenodo.17969450). The complete computational workflow and scripts are available on GitHub (https://github.com/oskuddar/trnL_DB). Although evaluation was focused on plant taxa in the United States, the resulting databases are suitable for use as global trnL reference databases.

bioinformatics↗

bioRxiv2025

Mechanism of Ribosome Stalling by the AMD1 C-terminal Tail Arrest Peptide

AMD1 encodes Adenosylmethionine decarboxylase 1 (AMD1), a key enzyme required for polyamine biosynthesis. A subset of ribosomes translating the AMD1 coding sequence (CDS) read through the stop codon and pause at the next in-frame stop codon 384 nucleotides downstream. The resulting C-terminal extension (C-tail) is universally conserved across all vertebrates, implying that its molecular function is critical to their fitness. Despite growing evidence that such cis-acting elements regulate translation of their genes, the molecular mechanism by which the C-tail mediates ribosome stalling remains unclear. Here, we determined the structure of the ribosome nascent chain complex paused by the AMD1 C-tail which traps eukaryotic release factor 1 (eRF1) with the ATP-binding cassette sub-family E member 1 (ABCE1). The nascent chain forms a molecular clamp that positions an arginine finger in the peptidyl-transferase center, occluding the accommodation of the eRF1 GGQ motif thereby hampering translation termination. Analysis of aggregated ribosome profiling data revealed several genes with a pattern of stop codon readthrough followed by ribosome stalling at a specific location, suggesting that regulatory readthrough-stall mechanisms may not be limited to AMD1.

biophysics↗

bioRxiv2025

Evaluation of porcine epidemic diarrhea virus RNA contamination on swine industry transportation vehicles

Porcine epidemic diarrhea virus (PEDV) is one of the most devastating pathogens of global swine health and welfare. It is well known that contaminated fomites and vehicle movements play an important role in farm-to-farm PEDV spread, but the efficacy of cleaning and disinfection (C&D) protocols on the reduction in dissemination risk via vehicles and trailers remains unclear. This study used swine industry data to determine how frequently vehicles and trailers were contaminated with PEDV RNA before and after C&D. Environmental RNA samples were collected at three eastern North Carolina C&D sites from four different vehicle types: crew trucks, feed trucks, pigs-to-farm trucks and trailers, and pigs-to-market trucks and trailers. A total of 2,004 samples were collected from truck cabins, trailers, and tires before and after C&D with two commercial disinfectants at two different concentrations. An in-house RT-qPCR assay was used to detect the presence of PEDV RNA only (not infectivity status). Results suggest that pigs-to-market trucks hauling live pigs were the most likely to be contaminated with PEDV (82.06% of trucks tested positive before C&D and 89.55% tested positive after C&D), while feed trucks were the least likely contaminated (11.73% of trucks testing positive before C&D and 11.25% testing positive after C&D). Based on PEDV RNA detection, we demonstrated that quaternary ammonium and glutaraldehyde is a more effective disinfectant compared to advanced hydrogen peroxide in eliminating detectable PEDV RNA. Results also show that truck cabins are just as contaminated as the exterior of their vehicles. Based on these results, vehicle biosecurity measures should be evaluated and modified to prevent the spread of PEDV.

ecology↗