Biology subjects

Bell, T.

Publications and source records attributed to Bell, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Multidecadal Remote Sensing of Macrocystis Pyrifera in Argentina

The Southern Hemisphere is home to extensive forests of giant kelp (Macrocystis pyrifera), including in Argentina and the southern islands of Tierra del Fuego, which has been proposed as a potential climate refugium. This study presents the first regional time series of M. pyrifera canopy dynamics in Argentina using Landsat satellite imagery from 1985 to 2023. The forests analyzed support 247.61 km{superscript 2} of emergent canopy and are situated in the coastal waters of Argentina and a small portion of Chilean islands, with 4%, 28%, and 68% in the Chubut, Santa Cruz, and Tierra del Fuego A.e.I.A.S, respectively. The small portion of Chilean Islands are included as part of the Tierra del Fuego province analyses. Range limits were scrutinized, in part, using expert knowledge and multisatellite comparisons. Linear regression shows that between 1998 and 2023, 7.4% of kelp sites exhibited a significant trend in annual canopy area, with all observed significant trends in the positive direction. Partitioning by province boundaries, linear regression produces significant positive increases in kelp canopy area across all three provinces, although reassessment when longer temporal continuity is also warranted, where available. Observed seawater nitrate concentrations were high throughout the region (7-23 {micro}mol L-{superscript 1}), suggesting that nitrate availability was not a primary driver of canopy variability. However, positive relationships between kelp canopy and the Antarctic Oscillation suggest that regional climate variability--which alters sea surface temperature and other oceanographic conditions--may be exerting a strong influence on kelp dynamics in this region. These findings document relative stability of kelp forest area in Argentina over the most recent two and a half decades and provide preliminary evidence supporting possible increases in kelp area for the region.

ecology↗

bioRxiv2026

Prevalence of electricity production among culturable bacteria

Microbial fuel cells (MFCs) technology offers sustainable electricity production. Current research largely focuses on few select model organisms, therefore the true prevalence of exoelectrogenesis amongst bacteria remaining largely unknown. We present a broad-scale survey of monomicrobial electricity production among environmental bacterial isolates inoculated in MFCs, using model organism Shewanella oneidensis MR-1 as a benchmark. Of the assessed taxa, 11-22% displayed exoelectrogenic activity, exceeding current predictions and identifying a further three novel exoelectrogenic species. Phylogenetic analysis based on the 16S sequences enabled the evolutionary relationship between isolates to be visualised, revealing that exoelectrogenesis is non-randomly distributed and phylogenetically conserved. Polarisation studies were implemented, revealing that numerous electron transfer mechanism were being utilised to perform exoelectrogenesis. The results of this study imply that bacterial electricity production is more widespread amongst culturable bacteria than previously estimated, with implications for bioprospecting novel exoelectrogens and predicting electrogenic activity in diverse microbial communities.

microbiology↗

bioRxiv2026

Structural Complementarity Maximizes Feasibility and Stability in Microbial Community Coalescence

Microbial communities frequently coalesce through dispersal, disturbance, or deliberate transplantation, yet the dynamical consequences of such coalescence remain poorly understood. Here, we show that coalescence can function as a structural design mechanism to enhance microbial community robustness. Using a mechanistic consumer-resource model in which the balance between competition and metabolic cooperation is explicitly tunable, we quantify how interaction structure shapes both feasibility, namely the environmental domain supporting coexistence, and dynamical stability. Cooperation-dominated communities exhibit greater but more variable feasibility and intrinsic stability than competition-dominated communities. Strikingly, coalescing communities with maximally distinct interaction structures consistently maximizes both feasibility and stability by reducing alignment among interaction vectors and strengthening effective self-regulation in the resulting assemblage. Heterogeneous coalescence balances reduced facilitation, moderated interspecific effects, and stronger self-regulation. These results identify structural complementarity as a general principle for assembling robust microbial ecosystems and provide a theoretical foundation for microbiome engineering strategies that enhance persistence and functional stability.

ecology↗

bioRxiv2025

On-target mutations confer resistance to WRN helicase inhibitors in Microsatellite Unstable Cancer Cells.

Werner helicase inhibitors (WRNi) are in clinical development for microsatellite-unstable (MSI) tumors with defective DNA mismatch repair. Here, we investigate how cancer cell evolution shapes response to WRN inhibition and informs potential resistance mechanisms. Genome-wide CRISPR screens combined with WRN knockout did not identify bypass mechanisms, underscoring WRNs essential, non-redundant function in MSI cells. Pharmacogenomic screens identified modulators of WRNi sensitivity, including SMARCAL1, which links it to WRN-MSI synthetic lethality. Semi-saturation mutagenesis of WRN and prolonged drug treatment identified on-target WRN mutations driving acquired resistance to multiple WRNi in vitro and in vivo, which was mitigated by combination with standard chemotherapies. Some resistance mutations conferred broad cross-resistance, whereas others preserved sensitivity to alternative clinical-grade WRNi with distinct mechanism of action. Our findings could inform clinical trial design by suggesting the feasibility of real-time tracking of emerging resistance and enabling early therapeutic adaptations. SignificanceWe present the first exploration of how MSI cancer cells evolve under the selective pressure of WRN helicase inhibition, providing a framework for understanding adaptive responses to this newly identified synthetic-lethal dependency. This study identifies on-target WRN mutations as key drivers of resistance in MSI cancers, supporting the use of combination strategies with other standard-of-care treatments to prevent resistance. It highlights how mutation tracking can guide therapeutic switching to clinically available WRN inhibitors with distinct mechanisms of action, thereby refining clinical development and potentially improving biomarker-informed patient outcomes.

cancer biology↗

bioRxiv2025

Exploring influenza A virus receptor distribution in the lactating mammary gland of domesticated livestock and in human breast tissue.

The spread of the highly pathogenic avian influenza (HPAI) H5N1 virus among dairy cattle illustrates the adaptability of influenza A viruses (IAV) to infect non-traditional species. While IAV-specific sialic acid (SA) receptors have been identified in the mammary glands of dairy cattle, their presence in pigs, sheep, goats, and alpacas has not been studied until now. The zoonotic transmission of HPAI H5N1 to dairy and poultry farm workers during outbreaks raises public health concerns. This study employed lectin histochemistry to examine the mammary glands of livestock and humans. We found that these tissues were rich in SA 2,6-Gal receptors, followed by SA 2,3-Gal receptors, essential for IAV binding. Notably, the A(H5N1) clade 2.3.4.4b virus could bind to mammary tissue from both cattle and pigs. These findings highlight the potential for HPAI H5N1 to infect and spread within the mammary glands of production animals and humans.

immunology↗

bioRxiv2025

Phylogenetic clustering of microbial communities as a biomarker for chemical pollution

Microbial communities play a critical role in ecosystem functioning and offer promising potential as bioindicators of chemical pollution in aquatic environments. Here we examine the responses of both bacterial isolates and microbial communities to a range of pollutants, focusing on the phylogenetic predictability of their responses. We found that bacterial isolates exhibited a strong phylogenetic signal in their growth responses, with closely related taxa responding similarly to chemical stress. In microbial communities, pollutants that significantly impacted isolates also reduced community diversity and growth, causing shifts in community structure toward increased phylogenetic clustering, suggesting environmental filtering. The net relatedness index (NRI) effectively captured these shifts, indicating its potential as a simple metric for monitoring pollution. Our findings highlight the predictability of microbial responses to pollution and suggest that microbial-based bioindicators, coupled with rapid sequencing technologies, could transform environmental monitoring.

microbiology↗

bioRxiv2024

The Role of Metabolic Strategies in Determining Microbial Community Diversity along Temperature Gradients

By conservative estimates, microbes make up about 17% of the worlds biomass and are essential for most ecosystem functions. However, the mechanisms driving the variation in microbial species diversity in response to both natural and anthropogenic temperature gradients remain unclear. In this study, we integrate ecological metabolic theory with a community assembly model to predict that microbial community diversity generally follows a unimodal pattern with temperature. The position and magnitude of peak diversity are determined by interaction-driven species sorting acting on variations in the temperature dependence of carbon use efficiency (CUE) and generalist-specialist tradeoff. Specifically, trait sorting across temperatures favours communities with high mean and low variance in species-level CUEs. We provide empirical evidence supporting our qualitative predictions of the unimodal temperature-diversity pattern along the global geological temperature gradient, which peaks at about 10-15 {degrees}C. Our findings indicate that the response of diversity as well as CUE to temperature of microbial communities can be predicted from relatively feasible life-history trait measurements, paving the way for interlinking microbial community diversity and carbon cycling along spatial and temporal thermal gradients.

ecology↗

bioRxiv2024

Drivers of spatio-temporal variability in a marine foundation species

Marine foundation species are critical for the structure and functioning of ecosystems and constitute the pillar of trophic chains while also providing a variety of ecosystem services. In recent decades many foundation species have declined in abundance, sometimes threatening their current geographical distribution. Kelps (Laminariales) are the primary foundation species in temperate coastal systems worldwide. Kelp ecosystems are notoriously variable and identifying the key factors that control the dynamics of kelp abundance is key to predicting the fate of kelp ecosystems under climatic change and informing management and conservation decisions such as forest restoration. Here, we used in situ data from long-term monitoring programs across 1,350 km of coast spanning multiple biogeographic regions in the state of California (USA) to identify the major regional drivers of density of two dominant canopy-forming kelp species and to elucidate the spatial and temporal scales over which they operate. We used generalized additive models to identify the key drivers of density of two dominant kelp species (Nereocystis luetkeana and Macrocystis pyrifera) across four ecological regions of the state of California (north, central, south-west and south-east) and for the past two decades (2004-2021). Our study identified that the dominant drivers of kelp density varied between regions and species but always included some combination of nitrate availability, wave energy and exposure, density of purple sea urchins, and temperature as the most important predictors explaining 63% of the variability of bull kelp in the north and central regions, and 45% and 51.4% of the variability in giant kelp for the central/south-west and south-east regions, respectively. These large-scale analyses infer that a combination of lower nutrient availability, changes in wave energy and exposure, and increases in temperature and purple sea urchin counts have contributed to the decline of kelp observed in the last decade. Understanding the drivers of kelp dynamics can be used to identify regions and periods of significant change and historical stability, ultimately informing resource management and conservation decisions such as site selection for kelp protection and restoration. Open research statementData (Giraldo-Ospina et al. 2023) are available in DataOne at doi:10.25494/P6/When_where_and_how_kelp_restoration_guidebook_2.

ecology↗

bioRxiv2023

Renal Angptl4 is a key fibrogenic molecule in progressive diabetic kidney disease

Angiopoietin-like 4 (ANGPTL4) is the key protein involved in lipoprotein metabolism and has been shown to have diverse effects on tissue protection. In clinical settings, there is a reported association between higher levels of plasma Angptl4 and features of diabetic kidney disease, however, the association between kidney Angptl4 with features of diabetic kidney disease has not been well investigated. We show that both podocyte-and tubule-specific ANGPTL4 are crucial fibrogenic molecules in diabetes. Results from mRNA-array analysis in control (non-fibrotic) and diabetic (fibrotic) kidneys suggest time-dependent emergence of Angplt4 expression. Diabetes accelerates the fibrogenic phenotype in control mice but not in ANGPTL4 mutant mice. The protective effect observed in ANGPTL4 mutant mice is correlated with a reduction in the levels of pro-inflammatory cytokines, epithelial-to-mesenchymal transition, endothelial-to-mesenchymal transition and augmented fatty acid oxidation. Mechanistically, we demonstrate that podocyte-or tubule-secreted Angptl4 interacts with Integrin-{beta}1 and influences the association between dipeptidyl-4 with Integrin-{beta}1 and promotes heterodimerization of transforming growth factor-{beta} receptor 1 (TGF{beta}R1) and TGF{beta}R2 in cultured cells. This in turn results in Smad3 phosphorylation and subsequent downregulation of the expression of genes involved in fatty acid oxidation; these cumulative effects led to the activation of fibrogenic phenotypes. We demonstrate the utility of a targeted pharmacologic therapy that specifically inhibits Angptl4 gene expression in the kidneys and protects diabetic kidneys from proteinuria and fibrosis. Importantly, use of this kidney-specific targeted strategy is beneficial and does not cause any harmful effect suggesting it can be used as a novel drug molecule for treatment of diabetic kidney disease. Taken together, these data demonstrate that podocyte-and tubule-derived Angptl4 is fibrogenic in diabetic kidneys.

cell biology↗

bioRxiv2023

Replaying the tape of ecology to domesticate wild microbiomes

Humanity has benefited from the domestication of nature and there is an increasing need to predict and control ecosystems. Domesticating bacterial communities would be particularly useful. Bacterial communities play key roles in global biogeochemical cycles, in industry (e.g. sewage treatment, fermented food and drink manufacturing), in agriculture (e.g. by fixing nitrogen and suppressing pathogens), and in human health and animal husbandry. There is therefore great interest in understanding bacterial community dynamics so that they can be controlled and engineered to optimise ecosystem services. We assessed the reproducibility and predictability of bacterial community dynamics by creating a frozen archive of hundreds of naturally-occuring bacterial communities that were repeatedly revived and tracked in a standardised, complex environment. Replicate communities followed reproducible trajectories and the community dynamics could be closely mapped to ecosystem functioning. However, even under standardised conditions, the communities exhibited tipping-points, where a small difference in initial community composition created divergent outcomes. We accurately predicted ecosystem outcomes based on initial bacterial community composition, and identified the conditions under which divergent ecosystem outcomes may be expected. In conclusion, we have shown the feasibility of our approach to reproducibly achieve predictable compositions and functions from wild communities. Nonetheless, the predictability of community trajectories, and therefore their utility in domestication, requires detailed knowledge of rugged compositional landscapes where ecosystem properties are not the inevitable result of prevailing environmental conditions but can be tilted toward different outcomes depending on the initial community composition.

microbiology↗

bioRxiv2023

Bacterial responses to complex mixtures of chemical pollutants

Our understanding of how microbes respond to pollutants is almost wholly based on single-species responses to individual chemicals. However, in natural environments, microbes experience the effects of multiple pollutants simultaneously, and their responses to these mixtures of chemicals may not be readily predictable based on their responses to each pollutant in isolation. Here we extended the scope and complexity of previous multi-stressor experiments by assaying the growth of model and non-model strains of bacteria in all 255 combinations of 8 chemical stressors. This approach allowed us to identify fitness effects arising from potential high-order interactions among stressor responses. We found that the bacterial strains responded in different ways to stressor mixtures, which could not be predicted simply from their phylogenetic relatedness. Responses to increasingly complex chemical mixtures were more likely to show a significant deviation from a null model based on the responses to each chemical alone. However, these net responses were mainly driven by lower-order interactions among a small number of chemicals, suggesting a limited role for complex high-order interactions. These results simplify the predictability of microbial populations and communities responding to multiple stressors, paving the way for the development of efficient next-generation eco-toxicological assays.

microbiology↗

bioRxiv2023

Surveillance of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We recovered nine (two novel) complete genomes across six bat species: four alphacoronaviruses, a MERS-related betacoronavirus, and four closely related sarbecoviruses. We demonstrate that at least one of these sarbecoviruses can bind and use the human ACE2 receptor for infecting human cells, albeit suboptimally. Additionally, the spike proteins of these sarbecoviruses possess an R-A-K-Q motif, which lies only one nucleotide mutation away from a furin cleavage site (FCS) that enhances infectivity in other coronaviruses, including SARS-CoV-2. However, mutating this motif to an FCS does not enable spike cleavage. Overall, while UK sarbecoviruses would require further molecular adaptations to infect humans, their zoonotic risk is unknown and warrants closer surveillance.

genomics↗

bioRxiv2022

Changes in brain metabolite levels across childhood

Metabolites play important roles in brain development and their levels change rapidly in the prenatal period and during infancy. Metabolite levels are thought to stabilize during childhood, but the development of neurochemistry across early-middle childhood remains understudied. We examined the developmental changes of key metabolites (total N-acetylaspartate, tNAA; total choline, tCho; total creatine, tCr; glutamate+glutamine, Glx; and myo-inositol, mI) using short echo-time magnetic resonance spectroscopy (MRS) in the anterior cingulate cortex (ACC) and the left temporo-parietal cortex (LTP) using a mixed cross-sectional/longitudinal design in children aged 2-11 years (ACC: N=101 children, 112 observations; LTP: N=95 children, 318 observations). We found age-related effects for all metabolites. tNAA increased with age in both regions, while tCho decreased with age in both regions. tCr increased with age in the LTP only, and mI decreased with age in the ACC only. Glx did not show linear age effects in either region, but a follow-up analysis in only participants with [≥]3 datapoints in the LTP revealed a quadratic effect of age following an inverted U-shape. These substantial changes in neurochemistry throughout childhood likely underlie various processes of structural and functional brain development.

neuroscience↗

bioRxiv2022

Shared and unique responses in the microbiome of allopatric lizards reared in a standardized environment

The gut microbiome can influence host fitness and, consequently, the ecology and evolution of natural populations. Microbiome composition can be driven by environmental exposure but also by the hosts genetic background and phenotype. To contrast environmental and genetic effects on the microbiome we leverage preserved specimens of eastern fence lizards from allopatric lineages east and west of the Mississippi River but reared in standardized conditions. Bacterial composition was indistinguishable between lineages but responded significantly to host age - a proxy for environmental exposure. This was accompanied by a continuous decrease in bacterial diversity in both lineages, partially driven by decreasing evenness seen only in western lizards. These findings indicate that longer exposure to a homogeneous habitat may have a depreciating effect on microbiome diversity in eastern fence lizards, a response shared by both lineages. We highlight the importance of such effects when extrapolating patterns from laboratory experiments to the natural world.

microbiology↗

bioRxiv2022

Kelpwatch: A new visualization and analysis tool to explore kelp canopy dynamics reveals variable resistance and resilience to marine heat waves

Giant kelp and bull kelp forests are increasingly at risk from marine heatwave events, herbivore outbreaks, and the loss or alterations in the behavior of key herbivore predators. The dynamic floating canopy of these kelps is well-suited to study via satellite imagery, which provides high temporal and spatial resolution data of floating kelp canopy across the western United States and Mexico. However, the size and complexity of the satellite image dataset has made ecological analysis difficult for scientists and managers. To increase accessibility of this rich dataset, we created Kelpwatch, a web-based visualization and analysis tool. This tool allows researchers and managers to quantify kelp forest change in response to disturbances, assess historical trends, and allow for effective and actionable kelp forest management. Here, we demonstrate how Kelpwatch can be used to analyze long-term trends in kelp canopy across regions, quantify spatial variability in the response to and recovery from the 2014 to 2016 marine heatwave events, and provide a local analysis of kelp canopy status around the Monterey Peninsula, California. We found that 18.6% of regional sites displayed a significant trend in kelp canopy area over the past 38 years and that there was a latitudinal response to heatwave events for each kelp species. The recovery from heatwave events was more variable across space, with some local areas like Bahia Tortugas in Baja California Sur showing high recovery while kelp canopies around the Monterey Peninsula continued a slow decline and patchy recovery compared to the rest of the Central California region. Kelpwatch provides near real time spatial data and analysis support and makes complex earth observation data actionable for scientists and managers, which can help identify areas for research, monitoring, and management efforts.

ecology↗

bioRxiv2021

NIfTI-MRS: A standard format for magnetic resonance spectroscopic data

PurposeThe use of multiple data formats in the MRS community currently hinders data sharing and integration. NIfTI-MRS is proposed as a standard MR spectroscopy data format, which is implemented as an extension to the neuroimaging informatics technology initiative (NIfTI) format. Using this standardised format will facilitate data sharing, ease algorithm development, and encourage the integration of MRS analysis with other imaging modalities. MethodsA file format based on the NIfTI header extension framework was designed to incorporate essential spectroscopic metadata and additional encoding dimensions. A detailed description of the specification is provided. An open-source command-line conversion program is implemented to enable conversion of single-voxel and spectroscopic imaging data to NIfTI-MRS. To provide visualisation of data in NIfTI-MRS, a dedicated plugin is implemented for FSLeyes, the FSL image viewer. ResultsAlongside online documentation, ten example datasets are provided in the proposed format. In addition, minimal examples of NIfTI-MRS readers have been implemented. The conversion software, spec2nii, currently converts fourteen formats to NIfTI-MRS, including DICOM and vendor proprietary formats. ConclusionThe proposed format aims to solve the issue of multiple data formats being used in the MRS community. By providing a single conversion point, it aims to simplify the processing and analysis of MRS data, thereby lowering the barrier to use of MRS. Furthermore, it can serve as the basis for open data sharing, collaboration, and interoperability of analysis programs. It also opens possibility of greater standardisation and harmonisation. By aligning with the dominant format in neuroimaging, NIfTI-MRS enables the use of mature tools present in the imaging community, demonstrated in this work by using a dedicated imaging tool, FSLeyes, as a viewer.

neuroscience↗

bioRxiv2021

Host genomic influence on bacterial composition in the switchgrass rhizosphere

Host genetic variation can shape the diversity and composition of associated microbiomes, which may reciprocally influence host traits and performance. While the genetic basis of phenotypic diversity of plant populations in nature has been studied, comparatively little research has investigated the genetics of host effects on their associated microbiomes. Switchgrass (Panicum virgatum) is a highly outcrossing, perennial, grass species with substantial locally adaptive diversity across its native North American range. Here, we compared 383 switchgrass accessions in a common garden to determine the host genotypic influence on rhizosphere bacterial composition. We hypothesized that the composition and diversity of rhizosphere bacterial assemblages would differentiate due to genotypic differences between hosts (potentially due to root phenotypes and associated life history variation). We observed higher alpha diversity of bacteria associated with upland ecotypes and tetraploids, compared to lowland ecotypes and octoploids, respectively. Alpha diversity correlated negatively with flowering time and plant height, indicating that bacterial composition varies along switchgrass life history axes. Narrow-sense heritability (h2) of the relative abundance of twenty-one core bacterial families was observed. Overall compositional differences among tetraploids, due to genetic variation, supports wide-spread genotypic influence on the rhizosphere microbiome. Lastly, a genome-wide association study identified 1,861 single-nucleotide polymorphisms associated with 110 families and genes containing them related to potential regulatory functions. Our findings suggest that switchgrass genomic and life-history variation influences bacterial composition in the rhizosphere, potentially due to host adaptation to local environments.

plant biology↗

bioRxiv2021

Latent functional diversity may accelerate microbial community responses to environmental fluctuations

How complex microbial communities respond to climatic fluctuations remains an open question. Due to their relatively short generation times and high functional diversity, microbial populations harbor great potential to respond as a community through a combination of strain-level phenotypic plasticity, adaptation, and species sorting. However, the relative importance of these mechanisms remains unclear. We conducted a laboratory experiment to investigate the degree to which bacterial communities can respond to changes in environmental temperature through a combination of phenotypic plasticity and species sorting alone. We grew replicate soil communities from a single location at six temperatures between 4{degrees}C and 50{degrees}C. We found that phylogenetically- and functionally-distinct communities emerge at each of these temperatures, with K-strategist taxa favoured under cooler conditions, and r-strategist taxa under warmer conditions. We show that this dynamic emergence of distinct communities across a wide range of temperatures (in essence, community-level adaptation), is driven by the resuscitation of latent functional diversity: the parent community harbors multiple strains pre-adapted to different temperatures that are able to "switch on" at their preferred temperature without immigration or adaptation. Our findings suggest that microbial community function in nature is likely to respond rapidly to climatic temperature fluctuations through shifts in species composition by resuscitation of latent functional diversity.

ecology↗