Biology subjects

Lewis, H.

Publications and source records attributed to Lewis, H..

6 recordsLinked to original sources

bioRxiv2026

Sedimentary ancient DNA reveals Late Pleistocene faunal connectivity between Ireland and Eurasia

Late Pleistocene sea-level fluctuations and glacial corridors intermittently connected the island of Ireland to Britain and continental Eurasia, shaping patterns of megafaunal dispersal and occupation. However, the scarcity of genetic data from ancient Irish fauna has limited our understanding of their demographic histories and relationships to continental populations. To address this, we generated sedimentary ancient DNA sequences from Castlepook Cave in southwest Ireland, detecting twelve ancient taxa, including two without zooarchaeological records at the site. We recovered the first mitochondrial sequences from Irish cave hyenas and woolly mammoths, providing new insights into their maternal population history: cave hyenas carried mtDNA haplogroup A1, previously identified in Late Pleistocene European populations, while woolly mammoths belonged to clade III/B2, which was replaced in Europe at approximately the same time. We also identify two mitochondrial clades (1b and 2), consistent with pre-Last Glacial Maximum mitochondrial lineage turnover in Ireland. Together, these results indicate that Irish megafauna formed a biogeographical continuum with their conspecifics in Europe, extend the known geographical range of several mtDNA lineages, and support faunal connectivity at the northwestern edge of Europe prior to the Last Glacial Maximum.

evolutionary biology↗

bioRxiv2025

Community, Belonging, and Peer-Engagement: Participant Experiences Reflect Consistency of Facilitation Practices in Inclusive STEM Teaching Learning Communities

A primary reason for the persistent underrepresentation of minoritized people in STEM careers are their marginalizing experiences in STEM courses, which has spurred efforts to prepare STEM faculty to implement inclusive teaching practices. The Inclusive STEM Teaching Project (ISTP) addresses this nationwide challenge by providing STEM faculty a free, online course and associated learning communities (LCs) led by project-trained facilitators. ISTP centers identity, power, privilege and positionality and has successfully shifted educators mindsets and abilities. A central question is whether local LCs across contexts maintain equity-minded core practices and achieve inclusive, reflective practitioner outcomes. Our mixed methods analysis of LC participant (n = 165) and facilitator (n = 83) matching survey data spanning five course offerings over two years directly explores the relationship between the learning environments created by facilitators and their participant experiences. Findings demonstrate high fidelity of implementation to training by facilitators that resulted in consistent LC experiences of participants, especially around building a community, sense of belonging and positive peer engagement. Participants overall speak to the importance of facilitated LCs as an inclusive space where they can critically engage with one another as they reflect on, discuss, and ultimately improve their inclusive teaching practices.

scientific communication and education↗

bioRxiv2024

Nationwide Inclusive Facilitator Training: Mindsets, Practices and Growth

Advancing diversity in STEM requires competent and confident faculty and staff who can lead local professional development in inclusive teaching to improve classroom instruction and support all learners. This paper examines how a facilitator training model designed to promote inclusive facilitation impacted inclusive learning community facilitator self-reported confidence and practices. This mixed methods study reports on survey data from project trained facilitators (n=71) collected over four course runs. Facilitators reported significant increases in confidence, with the largest effect sizes in areas related to diversity, equity, and inclusion (DEI) and identity. Qualitative findings indicate the training model effectively aligned facilitators with our approach to inclusive facilitation. Findings demonstrate that professional development in inclusive teaching, and by extension in other equity and diversity topics, can be successfully done at a national scale by centering identity, power, and positionality while upholding do no harm. This paper provides a strategy for how DEI-focused faculty development efforts can select, train, and support facilitators on a national scale while maintaining high fidelity to project values and goals.

scientific communication and education↗

bioRxiv2022

Accelerating the Validation of Endogenous On-Target Engagement and In-cellulo Kinetic Assessment for Covalent Inhibitors of KRASG12C in Early Drug Discovery

Covalent inhibition is a valuable modality in drug-discovery due to its potential ability in decoupling pharmacokinetics from pharmacodynamics by prolonging the residence time of the drug on the target of interest. This increase in target occupancy is limited only by the rate of target turnover. However, a limitation in such studies is to translate the in-vitro inhibition assessment to the appropriate in-cellulo target engagement parameter by covalent probes. Estimation of such parameters is often impeded by the low-throughput nature of current label-free approaches. In this study, an ultra-performance liquid chromatography-multiple reaction monitoring (UPLC-MRM) mass spectrometry platform was utilised to develop a targeted proteomics workflow that can evaluate cellular on-target engagement of covalent molecules in an increased throughput manner. This workflow enabled a throughput increase of 5-10 fold when compared to traditional nanoLC-based proteomics studies. To demonstrate the applicability of the method, KRASG12C was used as a model system to interrogate the interaction of an irreversible covalent small-molecule, compound 25, both in-vitro and in-cellulo. Initial biochemical studies confirmed that the small-molecule forms an adduct with the targeted cysteine on the protein, as assessed at the level of both intact protein and on the target peptide. In-cellulo studies were carried out to quantify target engagement and selectivity assessment in heterozygous NCI-H358 cell line with both WT type and KRASG12C alleles. The workflow enabled evaluation of in-cellulo target engagement kinetics providing mechanistic insights into the irreversible mode of inhibition. In summary, the method has the potential for target agnostic application in the assessment of on-target engagement of covalent probes compatible with the high-throughput requirements of early drug discovery.

biochemistry↗

bioRxiv2021

Insights into single hiPSC-derived cardiomyocyte phenotypes and maturation using ConTraX, an efficient pipeline for tracking contractile dynamics

Cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) are powerful in-vitro models to study the mechanisms underlying cardiomyopathies and cardiotoxicity. To understand how cellular mechanisms affect the heart, it is crucial to quantify the contractile function in single hiPSC-CMs over time, however, such measurements remain demanding and low-throughput, and are too seldom considered. We developed an open-access, versatile, streamlined, and highly automated pipeline to address these challenges and enable quantitative tracking of the contractile dynamics of single hiPSC- CMs over time: ConTraX. Three interlocking software modules enable: (i) parameter-based localization and selection of single hiPSC-CMs; (ii) automated video acquisition of >200 cells/hour; and (iii) streamlined measurements of the contractile parameters via traction force microscopy. Using ConTraX, we analyzed >2,753 hiPSC-CMs over time under orthogonal experimental conditions in terms of culture media and substrate stiffnesses. Using undirected high-dimensional clustering, we dissected the complex diversity of contractile phenotypes in hiPSC-CM populations and revealed converging maturation patterns. Our modular ConTraX pipeline empowers biologists with a potent quantitative analytic tool applicable to the development of cardiac therapies.

bioengineering↗

bioRxiv2018

Miltefosine increased cholesterol efflux, induced autophagy and inhibited NLRP3-inflammasome assembly and IL-1β release.

Miltefosine is an FDA approved oral drug for treating cutaneous and visceral leishmaniasis. Leishmania is a flagellated protozoa, which infects and differentiates in macrophages. Here, we studied the effects of Miltefosine on macrophages lipid homeostasis, autophagy, and NLRP3 inflammasome assembly/activity. Miltefosine treatment conferred multiple effects on macrophage lipid homeostasis leading to increased cholesterol release from cells, increased lipid-raft disruption, decreased phosphatidylserine (PS) flip from the cell-surface, and redistribution of phosphatidylinositol 4,5-bisphosphate (PIP2) from the plasma membrane to actin rich regions in the cells. Enhanced basal autophagy, lipophagy and mitophagy was observed in cells treated with Miltefosine vs. control. Miltefosine treated cells showed marked increased in phosphorylation of kinases involved in autophagy induction such as; Adenosine monophosphate-activated protein kinase (AMPK) and Unc-51 like autophagy activating kinase (ULK1). The Toll like receptor (TLR) signaling pathway was blunted by Miltefosine treatment, resulting in decreased TLR4 recruitment to cell-surface and ~75% reduction in LPS induced pro-IL-1{beta} mRNA levels. Miltefosine reduced endotoxin-mediated mitochondrial reactive oxygen species and protected the mitochondrial membrane potential. Miltefosine treatment induced mitophagy and dampened NLRP3 inflammasome assembly. Collectively, our data shows that Miltefosine induced ABCA1 mediated cholesterol release, induced AMPK phosphorylation and mitophagy, while dampening NLRP3 inflammasome assembly and IL-1{beta} release.\n\nSignificance StatementAtherosclerosis is driven by cholesterol accumulation and inflammation, and the arterial macrophage is a key cell type in both of these processes. The macrophage characteristics that protect against atherosclerosis include increased cholesterol efflux/reverse cholesterol transport, increased autophagy, and deceased inflammatory cytokine production and signaling. Here, we show that one single orally available compound, Miltefosine, can target multiple macrophage pathways involved in lipid homeostasis and inflammation. Miltefosine activated cholesterol release and autophagy while inhibiting pro IL-1{beta} gene expression and NLRP3 inflammasome assembly. Miltefosine activated AMPK signaling pathway and mitophagy, leading to reduced NLRP3 inflammasome assembly and IL-1{beta} release.

cell biology↗