Biology subjects

Roberts, N.

Publications and source records attributed to Roberts, N..

10 recordsLinked to original sources

bioRxiv2026

Evolution of novel host-microbiota coupling underlies adaptation to nutrient-scarce environments.

Animals colonizing food-limited environments need to overcome growth constraints by adapting to low, inconsistent nutritional inputs. Comparative studies of surface and cave populations of the Mexican tetra fish species Astyanax mexicanus provide a powerful system to explore evolution to food scarcity. In nutrient-scarce caves, evolved traits such as eye loss and increased fat storage have been shown to conserve energy in cavefish1-3 . However, the role of microbiota-mediated metabolism in sustaining growth and survival under food limitation remains poorly understood. Here, we demonstrate that surface and cave populations distinctly modulate their gut microbiota, with cavefish recruiting microbes whose predicted metabolites specifically promote growth under nutrient-limited conditions. Using microbiota data from three distinct dietary regimes and a fasting treatment, integrated topological data analysis4 and sparse modeling identify sugar and fatty acid degradation pathways coupled with growth in cavefish. Notably, the metabolites of these pathways are beneficial only for cavefish growth, and not for surface fish. Fasting in cavefish led to the recruitment of gut microbes capable of metabolizing aromatic compounds inaccessible to the host, whereas it recruited few microbial associates in surface fish. Our findings indicate that cavefish evolved novel host-microbiota coupling to sustain growth and resilience in their nutrient-scarce niche. We anticipate that our findings will broadly inform studies of evolution under extreme nutritional conditions and provide insights into the role of host-microbiota interactions in resilience to food scarcity at varied time scales.

evolutionary biology↗

bioRxiv2026

Diet-dependent microbiota and diet-independent immunometabolic responses to probiotic supplementation in broiler chickens

Probiotics are widely used in food animal production to support gut health and immune function, but the indicators of probiotic efficacy and the conditions under which they translate to host benefit remain unclear. Microbiota composition is the most accessible data supporting probiotic effects, yet whether compositional change reliably predicts host outcomes is not well understood. We investigated this question in broiler chickens fed two nutritionally similar basal diets, with or without a commercial probiotic. Microbiota composition was profiled across 6 gastrointestinal regions using 16S rRNA sequencing. To assess systemic functional effects, an in vitro assay building on prior observations of elevated circulating immune cell ATP in probiotic-fed animals was developed. In this assay, serum from each treatment group was applied to a chicken T-lymphocyte cell line before ATP quantitation. Basal diet was the primary driver of microbial community structure, with probiotic-induced compositional shifts observed predominantly in one diet context but minimally in the other. Despite this difference, serum from probiotic-supplemented animals increased T-lymphocyte ATP production across both diets, supporting prior findings and revealing a systemic immunometabolic response independent of broad microbiota restructuring. Functional predictions revealed enrichment of pathways related to mevalonate and carbohydrate metabolism in probiotic-supplemented birds within the more responsive diet context, driven largely by Lactobacillaceae family taxa. These findings demonstrate that basal diet modulates the detectability and nature of probiotic effects on the microbiota, but not the physiological host response. This disconnect has implications for how probiotic efficacy is evaluated and for microbiome targeted interventions across species. ImportanceProbiotics are used widely in food animal production to support gut health and immune function, yet predicting which probiotic preparations will produce meaningful effects remains a challenge. Microbiota composition, profiled by 16S rRNA sequencing, is the most accessible measure of probiotic activity, but it captures only one aspect of the host-microbe dynamic. These data demonstrate that probiotic-induced compositional changes vary substantially between basal diets, while the host immunometabolic response is consistent across diets, demonstrating that compositional readouts alone cannot reliably predict host outcomes. The findings have practical implications for how probiotic efficacy is evaluated and inform the broader effort to design microbiome targeted interventions across both veterinary and human contexts.

microbiology↗

bioRxiv2025

Mini-agrin prevents calcium leakage and restores the dystrophin complex.

Muscle cell death in muscular dystrophies depends upon calcium ion (Ca++) leakage through sarcolemma and sarcoplasmic reticulum, triggered by muscle stretch during eccentric contraction. We show here that Ca++ spikes are detected in dystrophic myogenic cells in culture since early differentiation, before sarcomere assembly and contraction. Healthy and genetically corrected dystrophic myotubes do not display Ca++ spikes which are blocked by co-culturing DMD myogenic cells with embryonic mouse motoneurons or treating them with agrin proteoglycan. Same effect is elicited by a muscle spliced, COOH peptide of agrin (termed here mini-agrin) that interacts with dystroglycan, favouring its binding to the basal lamina. Lack of dystrophin in DMD myotubes results in decreased expression of CaV1.1 (CACNA1S), a Ca++ sensor component of the Dihydropyridine Receptor (DHPR) complex, known to regulate Ryanodine Receptor 1 (RyR1). These events explain the emergence of Ca++ spikes. Mini-agrin addition to medium, or lentivector-mediated mini-agrin expression in transplanted cells in vivo, stabilize the expression of CaV1.1 on the membrane. This leads to disappearance of Ca++ spikes and to reappearance of -dystroglycan, -sarcoglycan and n-NOS, indicating the reconstitution of the dystrophin complex in the absence of dystrophin. These findings unveil a novel regulatory mechanism and offer a new therapeutic opportunity for targeting calcium ion influx as a co-treatment strategy.

cell biology↗

bioRxiv2025

Increased surface area of Heschl's gyrus following music-cued motor training.

Previous work found that adding musical cues to a four-week, left-handed, visuomotor sequence training task increased white matter connectivity between contralateral auditory and motor regions. In this study, grey matter measures are investigated by examining changes in cortical auditory and motor regions, specifically the superior and transverse temporal gyri, precentral gyrus, and paracentral lobule. Thirty healthy young adults trained on left-handed finger sequences over four weeks, either with visual cues only (Control group) or with added musical cues (Music group). Participants underwent MRI and behavioral assessments pre- and post-training. Results revealed evidence of a time-group-hemisphere interaction, showing increased surface area of the contralateral, right Heschls gyrus in the Music group only, after training. Additional exploratory analyses revealed that behavioral performance was associated with surface area decreases in cortical motor areas in the Music group only, but these results did not survive multiple comparison correction. The results demonstrate auditory-specific neuroplastic changes related to adding musical cues to short-term visuomotor training in a controlled setting, furthering our understanding of patterns of neuroplasticity related to music-based movement, with implications for cued movement paradigms in health settings.

neuroscience↗

bioRxiv2023

Active regulatory elements recruit cohesin to establish cell-specific chromatin domains.

As the structure of the genome is analysed at ever increasing resolution it is becoming clear that there is considerable variation in the 3D chromatin architecture across different cell types. It has been proposed that this may, in part, be due to increased recruitment of cohesin to activated cis-elements (enhancers and promoters) leading to cell-type specific loop extrusion underlying the formation of new subTADs. Here we show that cohesin correlates well with the presence of active enhancers and this varies in an allele-specific manner with the presence or absence of polymorphic enhancers which vary from one individual to another. Using the alpha globin cluster as a model, we show that when all enhancers are removed, peaks of cohesin disappear from these regions and the erythroid specific subTAD is no longer formed. Re-insertion of the major alpha globin enhancer (R2) is associated with the appearance of a new peak of cohesin at the site of insertion. In complementary experiments insertion of R2 into a "neutral" region of the genome recruits cohesin, induces transcription and creates a new large (75kb) erythroid specific domain. Together these findings support the proposal that active enhancers recruit cohesin, stimulate loop extrusion and promote the formation of cell specific subTADs.

genomics↗

bioRxiv2022

β-catenin obstructs γδ T cell immunosurveillance in colon cancer through loss of BTNL expression

WNT/{beta}-catenin signaling endows cancer cells with proliferative capacity and immune-evasive functions that impair anti-cancer immunosurveillance by conventional, cytoxtoic T cells. However, the impact of dysregulated WNT signalling on unconventional, tissue-resident T cells, specifically in colon cancer is unknown. Here, we show that cancer cells in Apc-mutant mouse models escape immunosurveillance from gut-resident intraepithelial lymphocytes (IELs) expressing {gamma}{delta} T cell receptors ({gamma}{delta}TCRs). Analysis of late-stage tumors from mice and humans revealed that {gamma}{delta}IELs are largely absent from the tumor microenvironment, and that butyrophilin-like (BTNL) molecules, which can critically regulate {gamma}{delta}IEL through direct {gamma}{delta}TCR-interactions, are also downregulated. We could attribute this to {beta}-catenin stabilization, which rapidly decreased expression of the transcription factors, HNF4A and HNF4G, that we found to bind promoter regions of Btnl genes, thereby driving their expression in normal gut epithelial cells. Indeed, inhibition of {beta}-catenin signaling restored Btnl1 gene expression and {gamma}{delta} T cell infiltration into tumors. These observations highlight an immune-evasion mechanism specific to WNT-driven colon cancer cells that disrupts {gamma}{delta}IEL immunosurveillance and furthers cancer progression.

cancer biology↗

bioRxiv2021

Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases

Programmable and multiplexed genome integration of large, diverse DNA cargo independent of DNA repair remains an unsolved challenge of genome editing. Current gene integration approaches require double-strand breaks that evoke DNA damage responses and rely on repair pathways that are inactive in terminally differentiated cells. Furthermore, CRISPR-based approaches that bypass double stranded breaks, such as Prime editing, are limited to modification or insertion of short sequences. We present Programmable Addition via Site-specific Targeting Elements, or PASTE, which achieves efficient and versatile gene integration at diverse loci by directing insertion with a CRISPR-Cas9 nickase fused to both a reverse transcriptase and serine integrase. Without generating double stranded breaks, we demonstrate integration of sequences as large as [~]36 kb with rates between 10-50% at multiple genomic loci across three human cell lines, primary T cells, and quiescent non-dividing primary human hepatocytes. To further improve PASTE, we discover thousands of novel serine integrases and cognate attachment sites from metagenomes and engineer active orthologs for high-efficiency integration using PASTE. We apply PASTE to fluorescent tagging of proteins, integration of therapeutically relevant genes, and production and secretion of transgenes. Leveraging the orthogonality of serine integrases, we engineer PASTE for multiplexed gene integration, simultaneously integrating three different genes at three genomic loci. PASTE has editing efficiencies comparable to or better than those of homology directed repair or non-homologous end joining based integration, with activity in non-dividing cells and fewer detectable off-target events. For therapeutic applications, PASTE can be delivered as mRNA with synthetically modified guides to programmably direct insertion of DNA templates carried by AAV or adenoviral vectors. PASTE expands the capabilities of genome editing via drag-and-drop gene integration, offering a platform with wide applicability for research, cell engineering, and gene therapy. One Sentence SummaryA new technology combining CRISPR-mediated genome editing and site-specific integrases enables efficient programmable gene integration at any targeted genomic locus without double-strand DNA breaks, leading to broad applications in basic science research, cell engineering, and gene therapy.

bioengineering↗

bioRxiv2020

Targeted high-resolution chromosome conformation capture at genome-wide scale.

Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at up to several hundred loci. All 3C methods are affected to varying degrees by inefficiency, bias and noise. As such, generation of reproducible high-resolution interaction profiles has not been achieved at scale. To overcome this barrier, we systematically tested and improved upon current methods. We show that isolation of 3C libraries from intact nuclei, as well as shortening and titration of enrichment oligonucleotides used in high-resolution methods reduces noise and increases on-target sequencing. We combined these technical modifications into a new method Nuclear-Titrated (NuTi) Capture-C, which provides a >3-fold increase in informative sequencing content over current Capture-C protocols. Using NuTi Capture-C we target 8,061 promoters in triplicate, demonstrating that this method generates reproducible high-resolution genome-wide 3C interaction profiles at scale.

genomics↗

bioRxiv2017

Selective and mechanistic sources of recurrent rearrangements across the cancer genome

Cancer cells can acquire profound alterations to the structure of their genomes, including rearrangements that fuse distant DNA breakpoints. We analyze the distribution of somatic rearrangements across the cancer genome, using whole-genome sequencing data from 2,693 tumor-normal pairs. We observe substantial variation in the density of rearrangement breakpoints, with enrichment in open chromatin and sites with high densities of repetitive elements. After accounting for these patterns, we identify significantly recurrent breakpoints (SRBs) at 52 loci, including novel SRBs near BRD4 and AKR1C3. Taking into account both loci fused by a rearrangement, we observe different signatures resembling either single breaks followed by strand invasion or two separate breaks that become joined. Accounting for these signatures, we identify 90 pairs of loci that are significantly recurrently juxtaposed (SRJs). SRJs are primarily tumor-type specific and tend to involve genes with tissue-specific expression. SRJs were frequently associated with disruption of topology-associated domains, juxtaposition of enhancer elements, and increased expression of neighboring genes. Lastly, we find that the power to detect SRJs decreases for short rearrangements, and that reliable detection of all driver SRJs will require whole-genome sequencing data from an order of magnitude more cancer samples than currently available.

cancer biology↗

bioRxiv2017

Patterns of structural variation in human cancer

A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments ranging in size from kilobases to whole chromosomes. We developed methods to group, classify and describe structural variants, applied to >2,500 cancer genomes. Nine signatures of structural variation emerged. Deletions have trimodal size distribution; assort unevenly across tumour types and patients; enrich in late-replicating regions; and correlate with inversions. Tandem duplications also have trimodal size distribution, but enrich in early-replicating regions, as do unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy number gains and frequent inverted rearrangements. One prominent structure consists of 1-7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, frequently activating the telomerase gene, TERT, in liver cancer. Cancers access many rearrangement processes, flexibly sculpting the genome to maximise oncogenic potential.

cancer biology↗