Biology subjects

Patterson, E. C.

Publications and source records attributed to Patterson, E. C..

3 recordsLinked to original sources

bioRxiv2025

Rapid on-site universal vertebrate species identification via multi-barcode nanopore sequencing

The growing illegal wildlife trade (IWT) threatens biodiversity and is a conduit for zoonotic disease, yet its risk of detection is low. Once processed, trafficked species are difficult to identify morphologically, and currently require DNA-based approaches that are time-consuming, costly, and lab-based. There is thus a need for a rapid, cheap, on-site method for species identification. We describe VeRIF-ID (Vertebrate Rapid In-Field Identification via DNA), a method that employs simultaneous on-site nanopore sequencing of four different mitochondrial DNA barcodes. Primers were designed to produce short amplicons to aid analysis of damaged DNA, and to be effective over a broad taxonomic range of vertebrates from lamprey to chimpanzee. Validation demonstrated species-level identification in 91% of 83 tested species, and genus/tribe-level identification of the remaining species (which are also problematic with existing approaches). DNA extraction, PCR and library preparation steps were simplified and optimised so that sampling to species identification takes <3 h for a single sample. Species components are identifiable non-quantitatively in prepared mixtures of muscle tissue from up to five species, and laboratory tests of Traditional East Asian Medicine samples reveal DNA from species including critically endangered saiga antelope and black rhinoceros. In conjunction with a portable BentoLab device the necessary equipment and reagents are easily portable, and we apply the method to analyse seized bushmeat and fish samples within an airport customs zone, identifying mammal and fish species in 15 samples within 6 h. The initial equipment costs for VeRIF-ID are [~]$8K, and the cost per sample of [~]$10-48 (depending on set-up), considerably cheaper than current conventional lab-based approaches. The method requires only basic hands-on skills. Ongoing trials with potential end-users will focus on establishing forensic reporting criteria prior to casework implementation. Future development of user-friendly bioinformatic interfaces will aim to fully democratise species identification.

genetics↗

bioRxiv2023

Mitogenome sequences of domestic cats demonstrate lineage expansions and dynamic mutation processes in a mitochondrial minisatellite

As a population genetic tool, mitochondrial DNA is commonly divided into the [~]1-kb control region (CR), in which single nucleotide variant (SNV) diversity is relatively high, and the coding region, in which selective constraint is greater and diversity lower, but which provides an informative phylogeny. In some species, the CR contains variable tandemly repeated sequences that are understudied due to heteroplasmy. Domestic cats (Felis catus) have a recent origin and therefore traditional CR-based analysis of populations yields only a small number of haplotypes. To increase resolution we used Nanopore sequencing to analyse 119 cat mitogenomes via a long-amplicon approach. This greatly improves discrimination (from 15 to 87 distinct haplotypes) and defines a phylogeny showing similar starlike topologies within all cat haplogroups, likely reflecting post-domestication expansion. We sequenced RS2, a CR tandem array of 80-bp repeat units, placing RS2 array structures within the phylogeny and increasing overall haplotype diversity. Repeat number varies between 3 and 12 (median: 4) with over 30 different repeat unit types differing largely by SNVs. Five SNVs show evidence of independent recurrence within the phylogeny, and seven are involved in at least 11 instances of rapid spread along repeat arrays within haplogroups. In defining mitogenome variation our study provides key information for the forensic genetic analysis of cat hair evidence, and for the first time a phylogenetically informed picture of tandem repeat variation that reveals remarkably dynamic mutation processes at work in the mitochondrion.

genomics↗

bioRxiv2021

Neuropeptidergic regulation of Compulsive Ethanol Seeking in C. elegans

An improved understanding of the molecular basis of alcohol seeking despite the catastrophic consequences of alcohol abuse is likely to enrich our treatments for Alcohol Use Disorders (AUD) and comorbidities. The compulsive seeking is characterized by an imbalance between the superior drive to substance and disruption in control of substance use. To model the development of compulsive engagement of alcohol seeking, we exploit two distinct behavioral programs of C. elegans in conflict, ethanol preference and avoidance of aversive stimulus, simultaneously. We demonstrate that C. elegans exhibited the recapitulation of the pivotal features of compulsive alcohol seeking in mammals, which are repeated attempts, endurance, and finally aversion-resistant ethanol seeking. We find that the neuropeptide signaling via SEB-3, CRF receptor-like GPCR, facilitates the development of ethanol preference and compels animals to seek ethanol compulsively. Furthermore, our functional genomic approach and behavioral elucidation suggest the interaction between neuropeptidergic signaling, SEB-3 and TKR-1, Neurokinin receptor orthologue, to progress compulsive ethanol seeking behavior.

neuroscience↗