Biology subjects

Lewis, F.

Publications and source records attributed to Lewis, F..

5 recordsLinked to original sources

bioRxiv2025

Extreme somatic mutation variation through time and space in walnut clones

Many plants, unlike most animals, can reproduce as clones1. Cloning plants is critical for agriculture2,3 and biotechnology4, but the extent of somatic mutation arising during different propagation methods remains an important question for both fundamental research and agriculture. Here, we discover a surprisingly complex mutational history in a multi-decade natural experiment of isogenic walnut clones derived and maintained through three alternative methods: budwood propagation of field-grown trees, in vitro shoot culturing, and in vitro somatic embryogenesis. We generated a haplotype-phased reference genome assembly and revealed a >3500% increase in somatic embryo mutation rates compared to field-grown trees, along with a distinct mutation spectrum. The assembly also helped reveal extreme genomic instability in the somatic embryos, including multiple chromosomal duplications, megabase-scale deletions, telomere expansions, somatic recombination events, and ongoing transposable element activation. Our survey of somatic mutation also provides high-resolution insight into clonal stem cell dynamics, confirming the canonical meristem layers of flowering plants in the tree and shoot clones, while uncovering clear evidence of frequent single-cell bottlenecks in the somatic embryos. These discoveries inform practical questions about mutagenesis through plant tissue culture and serve as a benchmark to complement emerging paradigms of somatic mutation research in humans and other organisms.

genomics↗

bioRxiv2024

Randomised Badger Culling Trial lacks evidence for proactive badger culling effect on tuberculosis in cattle: comment on Mills et al. 2024, Parts I & II

Re-evaluation of statistical analysis of the Randomised Badger Culling Trial (RBCT) by Torgerson et al. 2024 was rebutted by Mills et al. 2024 Parts I and II. The rebuttal defended the use of count rather than rate when considering bovine tuberculosis herd incidence. The defence makes biologically implausible use of Information Criterion for appraisal diagnostics; overfits data; and has erroneous Bayesian analyses. It favours goodness of fit over predictive power, for a small data set, when the study was to inform application. Importantly, for total bTB breakdown: ( confirmed (OTF-W) +unconfirmed (OTF-S)), where modern interpretation of the main diagnostic bTB test better indicates the incidence rate of herd breakdown, there is no effect in cull and neighbouring areas, across all statistical models. The RBCT was a small, single experiment with unknown factors. With respect to the paradigm of reproducibility and the FAIR principles, the original RBCT analysis and recent efforts to support it are wholly unconvincing. The 2006 conclusion of the RBCT that "badger culling is unlikely to contribute positively to the control of cattle TB in Britain" is supported, but the route to such a position is revised in the light of modern veterinary understanding and statistical reappraisal.

microbiology↗

bioRxiv2024

A comparative study of circulating tumor cell isolation and enumeration technologies in lung cancer

Circulating tumor cells (CTCs) have potential as diagnostic, prognostic and predictive biomarkers in solid tumors. Despite FDA approval of CTC devices in various cancers, their rarity and limited comparison between analysis methods hinder their clinical integration for lung cancer. This study aimed to evaluate five CTC isolation technologies using a standardized spike-in protocol: the CellMag (EpCAM-based enrichment), EasySep and RosetteSep (blood cell depletion), and the Parsortix(R) PR1 and next generation Parsortix(R) Plus (PX+) (size-based enrichment). The Parsortix(R) systems were also evaluated for any difference in recovery rates between cell harvest versus in- cassette staining. Healthy donor blood (5 mL) was spiked with 100 fluorescently labeled H1975 lung adenocarcinoma cell line, processed through each system and the isolation efficiency was calculated. All tested systems yielded discordant recovery rates with the CellMag having the highest mean recovery (70 {+/-} 14%) followed by the PR1 (in-cassette staining) with a recovery of 49 {+/-} 2% while the EasySep had the lowest recovery (18 {+/-} 8%). The CellMag and Parsortix(R) PR1 may have potential clinical applications for lung cancer patients, albeit needing further optimization and validation.

cancer biology↗

bioRxiv2023

Characterization of the RBM15 protein binding with XCI-escaping long noncoding RNAs

The RNA binding motif 15 protein (RBM15) plays a critical role in post-transcriptional regulation. Its role in facilitating N6-methyladenosine (m6A) modification, specifically through guiding the writer complex (WTAP METTL13 METTL14) to DRACH sequence motifs, has been demonstrated for several classes of RNA, including long noncoding RNAs (lncRNAs). The structural mechanism that underlies how RBM15 interacts with RNA has yet to be elucidated. In this study, we mined and bioinformatically assessed publicly available genome-wide RNA 2D structural probing and RBP cross-linking and immunoprecipitation data to investigate how RBM15 interacts with RNA, with a focus on lncRNA transcripts. RBM15, which possesses three RNA recognition motifs (RRMs), primarily interacts with stem-loop structured RNA motifs. Structural modeling reveals RRMs 2 and 3 are coaxially stacked in solution; these two RRMs are responsible for driving RBM15s interaction with RNA. We further demonstrate this experimentally with two RNA hairpins, revealing low micromolar binding affinities. Altogether, this work provides insight into the structural mechanism by which RBM15 interacts with RNAs to govern biological function.

biochemistry↗

bioRxiv2020

A combined microphysiological-computational omics approach in dietary protein evaluation

The ever-growing world population puts pressure on food security. To tackle this, waste stream proteins and novel protein sources need to be evaluated for nutritional value, which requires information on digesta peptide composition in comparison to established protein sources and coupling to biological parameters. Here, we present a novel combined experimental and computational approach comparing seventeen protein sources with cows whey protein (WPC) as benchmark. In vitro digestion was followed by proteomics analysis and statistical model clustering based on Bayesian Information Criterion. Next, we incorporated functional protein data after evaluating the effects of eighteen protein digests on intestinal barrier integrity, viability, brush border enzyme activity and immune parameters using a bioengineered intestine. Our data show that a holistic approach allows evaluating a dietary proteins potential for delivery of bioactive peptides, where protein source (animal, plant or novel source-derived) does not seem to be the driving force for clustering.

bioengineering↗