Biology subjects

White, C.

Publications and source records attributed to White, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Interactions between thermal and nutritional stress reveal cryptic adaptive potential

Predicting whether populations can adapt fast enough to persist under global change requires understanding how adaptive potential changes with the environment. Theory predicts that cryptic genetic variation hidden under benign conditions may be released under stress, but empirical tests are rare and typically manipulate single stressors in isolation, which is not realistic under global change. Using a quantitative genetic breeding design with Drosophila melanogaster, we quantified additive genetic variance in fitness (female productivity) across combinations of temperature and nutritional stress. We found that nutritional stress increased genetic variance at cold and hot margins. Temperature and diet also interacted to shape which genotypes performed best: nutritional stress weakened genetic correlations across temperatures at the hot margin, whereas genetic correlations across diets strengthened at the cold margin. Adaptive potential is therefore environment-dependent and multidimensional, meaning single stressor experiments are likely to systematically misrepresent adaptive capacity under realistic global change scenarios.

evolutionary biology↗

bioRxiv2026

Role of small non-coding RNAs in DSB repair in Arabidopsis thaliana

DNA double-strand breaks (DSB) are highly toxic lesions that must be repaired to avoid major losses of genetic materials or genome rearrangements. A number of highly conserved molecular pathways are involved in DSB repair, each resulting in different repair outcomes for a given DSB. Over the past decade, accumulating evidence has revealed the emergence of an unexpected new actor in DSB repair: RNA. Notably, small RNAs have been observed at DSB-flanking sequences and hypothesized to be involved in their repair. However, these DSB-induced small RNAs (diRNAs) were so far observed in studies using reporter systems, and their natural occurrence as well as their role in DNA repair remains debated. To address this question, we investigated diRNA biogenesis in Arabidopsis thaliana using CRISPR/Cas12a to induce targeted DSBs at three actively transcribed loci and one untranscribed locus. We found that 21-nt diRNAs are generated at transcribed loci, in a Dicer-like 4 (DCL4) dependent manner, but not at the untranscribed locus, indicating that active transcription is required for diRNA production. Remarkably, long-read DNA sequencing analysis shows that these diRNAs do not detectably influence DSB repair via either end-joining or microhomology-mediated end-joining. Furthermore, endogenous diRNAs have a modest effect on homologous recombination-associated repair, as impairment of the diRNA pathway in ago2 mutants resulted in only a slight reduction in RAD51 focus formation following Cas12a-induced DSBs. Together, these findings indicate that diRNAs are not essential for DSB repair itself but may function in the post-transcriptional silencing of damaged genes, likely to prevent aberrant transcription until proper repair is completed.

genetics↗

bioRxiv2026

Passive thrust production in animal propulsion: exploitation of velocity gradients for energy conservation

Animals move through fluid environments that are rich in velocity gradients, yet how they exploit these flows to reduce locomotor costs remains elusive. We hypothesize that vertebrates utilize shear layers to passively produce thrust and establish a force equilibrium, thereby reducing locomotor cost. We discovered a shear-layer gait where fish preferentially position themselves within velocity gradients to maintain a steady posture and position at ~50% of their sustained maximum speed. Compared to the matching speed of uniform flow, fish moved into an adjacent velocity gradient reduced active propulsion effort by 98% and metabolic costs by 74%, reaching a resting state. The mechanism is a force equilibrium between viscous drag on the high-velocity side of the body and anteriorly directed suction forces on the low-velocity side, fundamentally a passive thrust production driven by the pressure gradients. Such discovery has direct applications in bioinspired propulsion design and broad implications for movement ecology.

physiology↗

bioRxiv2026

Regional connectivity and viability selection in a range-expanding marine species

Identifying spatial and temporal patterns of connectivity among populations is fundamental to marine ecology, evolutionary biology, and fisheries management. Yet, due to large population sizes and low genetic differentiation among populations, empirical quantification of population connectivity across a species entire range has not been achieved for an open-coast marine organism. Here, we leverage experimental transcriptomics to develop a genotyping-in-thousands by sequencing (GT-seq) panel to support assignment of recruits of the kelp forest gastropod, Kellets whelk (Kelletia kelletii), collected across the species biogeographic range. Over a three-year period, we identified high self-recruitment in the historical range (100%) and low self-recruitment in the expanded range (10.53 - 13.73%). Additionally, self-recruitment within the expanded range generally increased with recruit age, from 27.14% at 0.93 years to 43.40% at 1.93 years, indicating that the locally spawned individuals were more likely to survive to older ages than migrants from the historical range. Together, these results reveal limited self-recruitment in the expanded range and suggest that a post-settlement selective filter contributes to differential survival in a high gene flow marine system.

evolutionary biology↗

bioRxiv2026

Generation and characterization of human iPSC-derived NPC1I1061T/I10161T i3Neurons as a model for NPC1 disease

Niemann-Pick disease, type C is an autosomal recessive, fatal, neurodegenerative disorder caused by pathological variants in NPC1 or NPC2. Dysfunction of either NPC1 or NPC2 results in impaired intracellular cholesterol transport and subsequent storage of unesterified cholesterol in endolysosomal compartments. Earlier cell-based studies utilized patient fibroblasts to study this disease; however, neuronal cells allow for investigation of the neurodegenerative aspect of NPC1. Expression of neurogenin in induced pluripotent stem cells leads to the generation of i3Neurons (integrated, isogenic, and inducible), allowing for rapid, synchronized growth of homogenous neurons. In this study, we report the development and characterization of a human iPSC-derived NPC1I1061T/I1061Ti3Neuronal model system. NPC1I1061Tis a missense variant resulting in a misfolded protein targeted for proteasomal degradation in the ER. NPC1I1061T/I1061T i3Neurons phenocopied the cellular pathological features of NPC1 disease including endolysosomal cholesterol accumulation, lysosomal morphological changes, and response to the proteostasis modulator, mo56HC. The NPC1 phenotype was alleviated by 2-hydroxypropyl-{beta}-cyclodextrin treatment, a drug demonstrating efficacy both in vitro and in vivo. This NPC1I1061T/I1061T i3Neuronal cell line can facilitate future high-throughput drug and genomic screens, particularly those aimed at identifying proteostasis regulators that improve the expression/stability of the mutant NPC1 protein.

neuroscience↗

bioRxiv2025

GABA-GABA_A Receptor Signaling Orchestrates Invasion and Metastasis in Triple Negative Breast Cancer

Cancer is a leading cause of death globally, with the majority of cancer-related deaths resulting from cancer metastasis -the process by which cancer cells disseminate to distant sites. To metastasize, cancer cells acquire traits in support of diverse cellular processes that enable dissemination, survival, and colonization. Tumor cell dissemination requires invasion at local and distant sites and this process can be influenced by intrinsic and extrinsic factors. Here, we investigate the role of the neurotransmitter gamma-aminobutyric acid (GABA) in triple-negative breast cancer (TNBC) invasion and metastasis. TNBC cells increased invasion in response to GABA and this was found to be mediated through the GABAA receptor family. TNBC cell lines were found to be responsive to exogenous GABA and also produced endogenous GABA. Pharmacological inhibition of GABAA receptors reduced TNBC invasion and cancer cell dissemination and resulted in inhibition of GSK3 activity. TNBC cell lines were found to express the GABRE subunit and loss of GABRE impaired GABA-mediated invasion and tumor cell dissemination. These findings support a role for GABA signaling through GABAA receptors in mediating TNBC progression.

cancer biology↗

bioRxiv2025

IS-capades of Klebsiella pneumoniae: Insertion sequences drive metabolic loss in obscure sub-lineages

IntroductionKlebsiella pneumoniae is an opportunistic pathogen which causes a wide spectrum of infections within healthcare settings and the community. Four K. pneumoniae sub-lineages defined with cgMLST/LINcodes are known to cause distinct infections of the nasal and/or upper respiratory passages: SL91 and SL10031 (also referred to as subspecies ozaenae), SL10032 (subspecies rhinoscleromatis) and SL82. These sub-lineages have also demonstrated reduced carbon source utilisation, which in other species has been linked with high loads of insertion sequences (IS). MethodsWe performed comparative genomics, analysed IS and constructed genome-scale metabolic models for available public sequences from these four sub-lineages and compared them to other sub-lineages from the wider K. pneumoniae population. ResultsThe four focal sub-lineages displayed significantly higher IS loads (median range 88 to 120 per genome) compared to other K. pneumoniae sub-lineages (median range 12 to 73). Notably, each K. pneumoniae sub-lineage had unique IS profiles, consistent with distinct evolutionary trajectories of IS acquisition and expansion. Across sub-lineages, higher IS loads were inversely associated with the number of metabolic model genes per genome (R2 = 0.16, p <0.001), as well as predicted aerobic substrate utilisation for phosphorus sources (R2 = 0.39, p<0.001) as per a second-degree polynomial regression model (n = 1,664 genomes). Additionally, the four IS-dense sub-lineages displayed a combination of convergent sub-lineage-specific substrate utilisation losses including parallel loss of 3-Phospho-D-glycerate, D-Glycerate-2-phosphate, Phosphoenolpyruvate utilisation as carbon/phosphorus sources. Finally, inspection of IS insertion sites demonstrated frequent and non-destructive insertion next to transcriptional, carbohydrate and amino acid metabolism genes. ConclusionsIS loads were significantly and inversely associated with metabolic substrate usage within K. pneumoniae, whereby sub-lineages that had higher numbers of IS also had reduced metabolic capacity. We hypothesise that an insertional tolerance model explains these findings, whereby IS can only insert into "metabolically-tolerable" sites for the individual cell and any impacts on metabolism are not detrimental for survival.

genomics↗

bioRxiv2024

De novo assembled databases enable species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition

BackgroundProtein-based stable isotope probing (Protein-SIP) is a powerful approach that can directly link individual taxa to activity and substrate assimilation, elucidating metabolic pathways and trophic relationships within microbial communities. In Protein-SIP, peptides and corresponding taxa are identified by database matching, making database quality crucial for accurate analyses. For samples with unknown community composition, Protein-SIP typically employs either unrestricted reference databases or metagenome-derived databases. While (meta)genome-derived databases represent the gold standard, they may be incomplete and are typically resource-intensive to generate. In contrast, unrestricted reference databases can inflate the search space and require complex post-processing. ResultsHere, we explore the feasibility of using de novo peptide sequencing to construct peptide databases directly from mass spectrometry raw data. We then use the mass spectrometric data from labeled cultures to quantify isotope incorporation into specific peptides. We benchmark our approach against the canonical approach in which a sample-matching (meta)genome-derived protein sequence database is used on three different datasets: 1) a proteome analysis from a defined microbial community containing 13C-labeled E. coli cells, 2) time-course data of an anammox-dominated continuous reactor after feeding with 13C-labeled bicarbonate, and 3) a model of the human distal gut simulating a high-protein and high-fiber diet cultivated in either 2H2O or H218O. Our results show that de novo peptide databases are applicable to different isotopes, detecting similar amounts of labeled peptides compared to sample-matching (meta)genome-derived databases, and also identify labeled peptides missed by this canonical approach. Furthermore, we show that peptide-centric Protein-SIP allows up to species-specific resolution and enables the assessment of activity related to individual biological processes. Finally, we provide access to our modular Python pipeline to assist the construction of de novo peptide databases and subsequent peptide-centric Protein-SIP data analysis (https://git.ufz.de/meb/denovo-sip). ConclusionsDe novo peptide databases enable Protein-SIP of microbial communities without prior knowledge of the composition and can be used complementarily to (meta)genome-derived databases or as a standalone alternative in exploratory or resource-limited settings.

bioinformatics↗

bioRxiv2023

Exogenous mitochondrial transfer increases energy expenditure and attenuates adiposity gains in mice with diet-induced obesity

Obesity is associated with chronic multi-system bioenergetic stress that may be improved by increasing the number of healthy mitochondria available across organ systems. However, treatments capable of increasing mitochondrial content are generally limited to endurance exercise training paradigms, which are not always sustainable long-term, let alone feasible for many patients with obesity. Recent studies have shown that local transfer of exogenous mitochondria from healthy donor tissues can improve bioenergetic outcomes and alleviate the effects of tissue injury in recipients with organ specific disease. Thus, the aim of this project was to determine the feasibility of systemic mitochondrial transfer for improving energy balance regulation in the setting of diet-induced obesity. We found that transplantation of mitochondria from lean mice into mice with diet-induced obesity attenuated adiposity gains by increasing energy expenditure and promoting the mobilization and oxidation of lipids. Additionally, mice that received exogenous mitochondria demonstrated improved glucose uptake, greater insulin responsiveness, and complete reversal of hepatic steatosis. These changes were, in part, driven by adaptations occurring in white adipose tissue. Together, these findings are proof-of-principle that mitochondrial transplantation is an effective therapeutic strategy for limiting the deleterious metabolic effects of diet-induced obesity in mice.

physiology↗

bioRxiv2023

Reinforcement motor learning after cerebellar damage is related to state estimation

Recent work showed that individuals with cerebellar degeneration could leverage intact reinforcement learning (RL) to alter their movement. However, there was marked inter-individual variability in learning, and the factors underlying it were unclear. Cerebellum-dependent sensory prediction may contribute to RL in motor contexts by enhancing body state estimates, which are necessary to solve the credit-assignment problem. The objective of this study was to test the relationship between the predictive component of state estimation and RL in individuals with cerebellar degeneration. Individuals with cerebellar degeneration and neurotypical control participants completed two tasks: an RL task that required them to alter the angle of reaching movements and a state estimation task that tested the somatosensory perception of active and passive movement. The state estimation task permitted calculation of the active benefit shown by each participant, which is thought to reflect the cerebellum-dependent predictive component of state estimation. We found that the cerebellar and control groups showed similar magnitudes of learning with reinforcement and active benefit on average, but there was substantial variability across individuals. Using multiple regression, we assessed potential predictors of RL. Our analysis included active benefit, somatosensory acuity, clinical ataxia severity, movement variability, movement speed, and age. We found a significant relationship in which greater active benefit predicted better learning with reinforcement in the cerebellar, but not the control group. No other variables showed significant relationships with learning. Overall, our results support the hypothesis that the integrity of sensory prediction is a strong predictor of RL after cerebellar damage.

neuroscience↗

bioRxiv2023

Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet's whelk

Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in extracting and purifying their genomic DNA due to high polysaccharide content and other secondary metabolites. In this study, we help resolve this issue by developing and testing DNA extraction protocols for Kellets whelk (Kelletia kelletii), a subtidal gastropod with ecological and commercial importance, by comparing four DNA extraction methods commonly used in marine invertebrate studies. We identified an optimized protocol that balances efficiency, cost, and DNA extraction quality; the Salting out protocol. We validated the protocol using an independent set of tissue samples, then applied it to extract high-molecular-weight (HMW) DNA from over three thousand Kellets whelk tissue samples. The protocol demonstrated scalability and, with added clean-up, suitability for RAD-seq, GT-seq, as well as whole genome sequencing using both long read (ONT MinION) and short read (Illumina Novaseq) sequencing platforms. Our findings offer a robust and versatile DNA extraction and clean-up protocol for supporting genomic research efforts on non-model marine organisms, to help mediate the under-representation of invertebrates in genomic studies.

genomics↗

bioRxiv2022

Effects of finfish farms on pelagic protist communities in a semi-closed stratified embayment

Coastal aquaculture operations for feed additive species results in the release of waste into the surrounding environment, with the potential for adverse environmental change. Ubiquitous pelagic protists are sensitive to environmental changes making them potential sentinels for detecting and monitoring impacts. This study used 18S rRNA high-throughput amplicon sequencing as a molecular tool to study the pelagic protist community, with the aim of evaluating their potential as bioindicators of aquaculture activity in a low-oxygen, highly stratified marine embayment. Sampling occurred at three different depths along a distance gradient from two leases and at three control sites. Our results showed that the diversity and composition of both phytoplankton and other protist communities were more strongly influenced by depth stratification than the aquaculture activity. Nonetheless, differential abundance and machine learning analyses revealed a suite of potential bioindicators for aquaculture activity; this included the phytoplankton taxa Chrysophyceae, Gymnodiniphycidae (Gyrodinium), Cryptomonadales and Ciliophora (Philasterides armatalis, Plagiopylida, and Strombidium). Among the other protists, ciliates were also more abundant in closer proximity to the leases in both surface and bottom samples. Overall, our findings indicated that the use of 18S rRNA sequencing of protist communities is a promising tool for identifying environmental changes from aquaculture in the water column.

microbiology↗

bioRxiv2022

A cross-disease human microglial framework identifies disease-enriched subsets and tool compounds for microglial polarization.

Human microglia play a pivotal role in neurological diseases, but few targeted therapies that directly modulate microglial state or function exist due to an incomplete understanding of microglial heterogeneity. We use single-cell RNA sequencing to profile live human microglia from autopsies or surgical resections across diverse neurological diseases and central nervous system regions. We observe a central divide between oxidative and heterocyclic metabolism and identify subsets associated with antigen presentation, motility, and proliferation. Specific subsets are enriched in susceptibility genes for neurodegenerative diseases or the disease-associated microglial signature. We validate subtypes in situ with an RNAscope-immunofluorescence pipeline and leverage our dataset as a classification resource, finding that iPSC model systems recapitulate substantial in vivo heterogeneity. Finally, we identify and validate candidates for chemically inducing subtype-specific states in vitro, showing that Camptothecin downregulates the transcriptional signature of disease-enriched subsets and upregulates a signature previously shown to be depleted in Alzheimers.

neuroscience↗

bioRxiv2022

A resource for generating and manipulating human microglial states in vitro

Microglia have emerged as key players in the pathogenesis of neurodegenerative conditions such as Alzheimers disease (AD). In response to CNS stimuli, these cells adopt distinct transcriptional and functional subtypes known as states. However, an understanding of the function of these states has been elusive, especially in human microglia, due to lack of tools to model and manipulate this cell-type. Here, we provide a platform for modeling human microglia transcriptional states in vitro. Using single-cell RNA sequencing, we found that exposure of human stem-cell differentiated microglia (iMGLs) to brain-related challenges generated extensive transcriptional diversity which mapped to gene signatures identified in human brain microglia. We identified two in vitro transcriptional clusters that were analogous to human and mouse disease-associated microglia (DAMs), a state enriched in neurodegenerative disease contexts. To facilitate scalable functional analyses, we established a lentiviral approach enabling broad and highly efficient genetic transduction of microglia in vitro. Using this new technology, we demonstrated that MITF (Melanocyte Inducing Transcription Factor), an AD-enriched transcription factor in microglia, drives both a disease-associated transcriptional signature and a highly phagocytic state. Finally, we confirmed these results across iMGLs differentiated from multiple iPSC lines demonstrating the broad utility of this platform. Together, these tools provide a comprehensive resource that enables the manipulation and functional interrogation of human microglial states in both homeostatic and disease-relevant contexts.

neuroscience↗

bioRxiv2021

Human and wildlife use of mountain glacier habitat in western North America

ContextThe global recession of glaciers and perennial snowfields is reshaping mountain ecosystems. Beyond physical changes to the landscape and altered downstream hydrology, the implications of glacier decline for biodiversity are poorly known. Before predictions can be made about how climate change will affect wildlife in glacier-associated ecosystems, a more thorough accounting of the role that glaciers play in species life histories is needed. However, typical approaches for documenting wildlife presence and behavior--remote camera traps--are difficult to use in glaciated terrain due to limited options for securing them (e.g., no trees) and dramatic seasonal changes in snowpack. AimsIn this study, we sought to test a novel camera trap designed for glaciated mountain ecosystems. We also aimed to use this approach to gain insight into wildlife and human usage of a mountain glacier in western North America. MethodsWe deployed an elevational transect of uniquely designed camera traps along the western margin of the Paradise Glacier, a rapidly receding mountain glacier on the south side of Mount Rainier, WA, USA. Our simple camera trap design consisted of a wildlife camera attached to a camouflaged cylindrical cooler filled with snow and rocks. Key resultsOur camera design proved ideal for a mountain glacier ecosystem and from June to September 2021, we detected at least 16 vertebrate species (seven birds, nine mammals) over 770 trap nights using glacier-associated habitats. Humans, primarily skiers, were the most common species detected, but we also recorded 99 observations of wildlife (birds and mammals). These included three species of conservation concern in Washington: wolverine (Gulo gulo), Cascade red fox (Vulpes vulpes cascadensis), and white-tailed ptarmigan (Lagopus leucura). ConclusionsCollectively, our results provide proof-of-concept for a novel camera trap design that is ideal for treeless, perennially snow-covered landscapes and revealed a rich diversity of wildlife using mountain glacier habitat in the Pacific Northwest. We highlight the global need for similar studies to better understand the true scale of biodiversity that will be impacted by glacier recession in mountain ecosystems.

ecology↗

bioRxiv2021

Small molecule photocatalysis enables drug target identification via energy transfer

The identification of cellular targets that can be exploited for therapeutic benefit, broadly known as target ID, remains a fundamental goal in drug discovery. In recent years, the application of new chemical and biological technologies that accelerate target ID has become commonplace within drug discovery programs, as a complete understanding of how molecules react in a cellular environment can lead to increased binding selectivity, improved safety profiles, and clinical efficacy. Established approaches using photoaffinity labelling (PAL) are often costly and time-consuming due to poor signal-to-noise coupled with extensive probe optimization. Such challenges are exacerbated when dealing with low abundance membrane proteins or multiple protein target engagement, typically rendering target ID unfeasible. Herein, we describe a general platform for photocatalytic small molecule target ID, which hinges upon the generation of high-energy carbene intermediates via visible light-mediated Dexter energy transfer. By decoupling the reactive warhead from the drug, catalytic signal amplification results in multiple labelling events per drug, leading to unprecedented levels of target enrichment. Through the development of cell permeable photo-catalyst conjugates, this method has enabled the quantitative target and off target identification of several drugs including (+)-JQ1, paclitaxel, and dasatinib. Moreover, this methodology has led to the target ID of two GPCRs - ADORA2A and GPR40 - a class of drug target seldom successfully uncovered in small molecule PAL campaigns.

molecular biology↗

bioRxiv2021

A multi-tiered map of EMT defines major transition points and identifies vulnerabilities

Epithelial to mesenchymal transition (EMT) is a complex cellular program proceeding through a hybrid E/M state linked to cancer-associated stemness, migration and chemoresistance. Deeper molecular understanding of this dynamic physiological landscape is needed to define events which regulate the transition and entry into and exit from the E/M state. Here, we quantified >60,000 molecules across ten time points and twelve omic layers in human mammary epithelial cells undergoing TGF{beta}-induced EMT. Deep proteomic profiles of whole cells, nuclei, extracellular vesicles, secretome, membrane and phosphoproteome defined state-specific signatures and major transition points. Parallel metabolomics showed metabolic reprogramming preceded changes in other layers, while single-cell RNA sequencing identified transcription factors controlling entry into E/M. Covariance analysis exposed unexpected discordance between the molecular layers. Integrative causal modeling revealed co-dependencies governing entry into E/M that were verified experimentally using combinatorial inhibition. Overall, this dataset provides an unprecedented resource on TGF{beta} signaling, EMT and cancer.

systems biology↗

bioRxiv2020

Understanding the Human Brain using Brain Organoids and a Structure-Function Theory

A basic neurobiology-clinical trial paradigm motivates our use of constrained mathematical models and analysis of personalized human-derived brain organoids toward predicting clinical outcomes and safely developing new therapeutics. Physical constraints imposed on the brain can guide the analyses an interpretation of experimental data and the construction of mathematical models that attempt to make sense of how the brain works and how cognitive functions emerge. Development of these mathematical models for human-derived brain organoids offer an opportunity for testing new hypotheses about the human brain. When it comes to testing ideas about the brain that require a careful balance between experimental accessibility, manipulation, and complexity, in order to connect neurobiological details with higher level cognitive properties and clinical considerations, we argue that fundamental structure-function constraints applied to models of brain organoids offer a path forward. Moreover, we show these constraints appear in canonical and novel math models of neural activity and learning, and we make the case that constraint-based modeling and use of representations can bridge to machine learning for powerful mutual benefit.

neuroscience↗