Biology subjects

Phillips, J. D.

Publications and source records attributed to Phillips, J. D..

5 recordsLinked to original sources

bioRxiv2026

Mining association rules for targeted spatiotemporal aquatic environmental DNA (eDNA) sampling

Environmental DNA (eDNA) offers a non-invasive alternative to traditional, more destructive sampling methods for determining species occupancy at ecological sites of interest. Aquatic eDNA sampling entails filtering a known volume of water to capture and detect genetic material shed by organisms. While the influence of individual environmental properties on the presence of target eDNA has been widely studied, it remains unclear how variables like temperature, pH, flow rate and conductivity correlate collectively with site electrofishing counts and eDNA concentrations. Resolving this question is important for two reasons: (1) typically, only eDNA, not physical specimens, is collected and measured, and (2) when methods like electrofishing and eDNA sampling are used in tandem, results often differ. Here unsupervised association rule-based machine learning is employed to discover interesting relationships among sampled covariates within a previously published case study of native brook trout (Salvelinus fontinalis) collected from Hanlon Creek (Guelph, Ontario, Canada) in September 2019. From a dataset of only 126 observations, the mining process revealed over 12000 plausible association rules linking covariates to eDNA concentrations (low/high) and electrofishing outcomes (absence/presence of brook trout). A strict pruning strategy reduced this ruleset to a manageable size of 153 associations, some of which were corroborated by existing literature, and some of which were novel (such as those potentially relating electrical conductivity to microbial and enzymatic activity). The entire workflow is included as a new R package called RulesTools. These results highlight the promise of association rule mining as a tool for guiding eDNA metadata collection, complementing statistical modelling, and informing conservation and management decision-making.

ecology↗

bioRxiv2024

Statistical modelling of seafood fraud in the Canadian supply chain

AbstractSeafood misrepresentation, encompassing product adulteration, mislabelling, and substitution, among other fraudulent practices, has been rising globally over the past decade, greatly impacting both the loss of important fish species and the behaviour of human consumers alike. While much effort has been spent attempting to localise the extent of seafood mislabelling within the supply chain, strong associations likely existing among key players have prevented timely management and swift action within Canada and the USA in comparison to European nations. To better address these shortcomings, herein frequentist and Bayesian logistic Generalised Linear Models (GLMs) are developed in R and Stan for estimation, prediction and classification of product mislabelling in Metro Vancouver, British Columbia, Canada. Obtained results based on odds ratios and probabilities paint a grim picture and are consistent with general trends found in past studies. This work paves the way to rapidly assess the current state of knowledge surrounding seafood fraud nationally and on a global scale using established statistical methodology.

genetics↗

bioRxiv2023

A highly-contiguous genome assembly of the inbred Babraham pig (Sus scrofa) quantifies breed homozygosity and illuminates porcine immunogenetic variation

The inbred Babraham pig serves as a valuable biomedical model for research due to its high level of homozygosity, including in the major histocompatibility complex (MHC) loci and likely other important immune-related gene complexes, which are generally highly diverse in outbred populations. As the ability to control for this diversity using inbred organisms is of great utility, we sought to improve this resource by generating a long-read whole genome assembly of a Babraham pig. The Babraham genome was de novo assembled using PacBio long-reads and error-corrected using Illumina short-reads. The assembled contigs were then mapped to the current porcine reference assembly, Sscrofa11.1, to generate chromosome-level scaffolds. The resulting Babraham pig assembly is nearly as contiguous as Sscrofa11.1 with a contig N50 of 34.95 Mb and contig L50 of 23. The remaining sequence gaps are generally the result of poor assembly across large and highly repetitive regions such as the centromeres and tandemly duplicated gene families, including immune-related gene complexes, that often vary in gene content between haplotypes. We also further confirm homozygosity across the Babraham pig MHC and characterize the allele content across several immune-related gene complexes, including the contiguous assemblies of the antibody heavy chain locus and leukocyte receptor complex. The Babraham pig genome assembly provides an alternate highly contiguous porcine genome assembly as a resource for the livestock genomics community. The assembly will also aid biomedical and veterinary research that utilizes this animal model such as when controlling for genetic variation is critical.

genomics↗

bioRxiv2022

A low-power communication scheme for wireless, 1000 channel brain-machine interfaces

ObjectiveBrain-machine interfaces (BMIs) have the potential to restore motor function but are currently limited by electrode count and long-term recording stability. These challenges may be solved through the use of free-floating "motes" which wirelessly transmit recorded neural signals, if power consumption can be kept within safe levels when scaling to thousands of motes. Here, we evaluated a pulse-interval modulation (PIM) communication scheme for infrared (IR)-based motes that aims to reduce the wireless data rate and system power consumption. ApproachTo test PIMs ability to efficiently communicate neural information, we simulated the communication scheme in a real-time closed-loop BMI with non-human primates. Additionally, we performed circuit simulations of an IR-based 1000-mote system to calculate communication accuracy and total power consumption. Main ResultsWe found that PIM at 1kb/s per channel maintained strong correlations with true firing rate and matched online BMI performance of a traditional wired system. Closed-loop BMI tests suggest that lags as small as 30 ms can have significant performance effects. Finally, unlike other IR communication schemes, PIM is feasible in terms of power, and neural data can accurately be recovered on a receiver using 3mW for 1000 channels. SignificanceThese results suggest that PIM-based communication could significantly reduce power usage of wireless motes to enable higher channel-counts for high-performance BMIs.

bioengineering↗

bioRxiv2020

CLPX regulates erythroid heme synthesis by control of mitochondrial heme synthesis enzymes and iron utilization

Heme is a prosthetic group that plays a critical role in catalyzing life-essential redox reactions in all cells, including critical metabolic processes. Heme synthesis must be tightly co-regulated with cellular requirements in order to maximize utilization and minimize toxicity. Terminally differentiating erythroid cells have an extremely high demand for heme for hemoglobin synthesis. While the enzymatic reactions of heme synthesis are extremely well studied, the mechanisms by which the mitochondrial homeostatic machinery interacts with and regulates heme synthesis are poorly understood. Knowledge of these regulatory mechanisms are key to understanding how red cells couple heme production with heme demand. Heme synthesis is tightly regulated by the mitochondrial AAA+ unfoldase CLPX, which has been reported to promote heme synthesis by activation of yeast {delta}-aminolevulinate synthase (ALAS/Hem1). CLPX was also reported to mediate heme-induced turnover of ALAS1 in human cells. However, a mutation in the ATP binding domain of CLPX that abrogated ATP binding caused an increase in ALAS activity, contrary to previous predictions that CLPX activated ALAS. Using loss-of-function assays in murine cells and zebrafish, we interrogated the mechanisms by which CLPX regulates erythroid heme synthesis. We found that consistent with previous studies, CLPX is required for erythroid heme synthesis. We show that ALAS2 stability and activity were both increased in the absence of CLPX, suggesting that CLPX primarily regulates ALAS2 by control of its turnover. However, we also showed that CLPX is required for PPOX activity and maintenance of FECH levels, likely accounting for the heme deficiency in the absence of CLPX. Lastly, CLPX is required for iron metabolism during erythroid terminal differentiation. Our results show that the role of CLPX in heme synthesis is not conserved across eukaryotes. Our studies reveal a potential mechanism for the role of CLPX in anemia and porphyria, and reveal multiple nodes at which heme synthesis is regulated by the mitochondrial housekeeping machinery.

biochemistry↗