Biology subjects

Thompson, J. R.

Publications and source records attributed to Thompson, J. R..

29 records · Page 2Linked to original sources

bioRxiv2021

The development and neuronal complexity of bipinnaria larvae of the sea star Asterias rubens

Free-swimming planktonic larvae are a key stage in the development of many marine phyla, and studies of these organisms have contributed to our understanding of major genetic and evolutionary processes. Although transitory, these larvae often attain a remarkable degree of tissue complexity, with well-defined musculature and nervous systems. Amongst the best studied are larvae belonging to the phylum Echinodermata, but with work largely focused on the pleuteus larvae of sea urchins (class Echinoidea). The greatest diversity of larval strategies amongst echinoderms is found in the class Asteroidea (sea-stars), organisms that are rapidly emerging as experimental systems for genetic and developmental studies. However, the bipinnaria larvae of sea stars have only been studied in detail in a small number of species and the full complexity of the nervous system is, in particular, poorly understood. Here we have analysed embryonic development and bipinnaria larval anatomy in the common North Atlantic sea-star Asterias rubens, employing use of a variety of staining methods in combination with confocal microscopy. Importantly, the complexity of the nervous system of bipinnaria larvae was revealed in greater detail than ever before, with identification of at least three centres of neuronal complexity: the anterior apical organ, oral region and ciliary bands. Furthermore, the anatomy of the musculature and sites of cell division in bipinnaria larvae were analysed. Comparisons of developmental progression and molecular anatomy across the Echinodermata provided a basis for hypotheses on the shared evolutionary and developmental processes that have shaped this group of animals. We conclude that bipinnaria larvae appear to be remarkably conserved across ~200 million years of evolutionary time and may represent a strong evolutionary and/or developmental constraint for species utilizing this larval strategy.

developmental biology↗

bioRxiv2020

Post-metamorphic skeletal growth in the sea urchin Paracentrotus lividus and implications for body plan evolution

Understanding the molecular and cellular processes that underpin animal development are crucial for understanding the diversity of body plans found on the planet today. Because of their abundance in the fossil record, and tractability as a model system in the lab, skeletons provide an ideal experimental model to understand the origins of animal diversity. We herein use molecular and cellular markers to understand the growth and development of the juvenile sea urchin (echinoid) skeleton. We developed a detailed staging scheme based off of the first [~]four weeks of post-metamorphic life of the regular echinoid Paracentrotus lividus. We paired this scheme with immunohistochemical staining for neuronal, muscular, and skeletal tissues, and fluorescent assays of skeletal growth and cell proliferation to understand the molecular and cellular mechanisms underlying skeletal growth and development of the sea urchin body plan. Our experiments highlight the role of skeletogenic proteins in accretionary skeletal growth and cell proliferation in the addition of new metameric tissues. Furthermore, our work provides a framework for understanding the developmental evolution of sea urchin body plans on macroevolutionary timescales.

developmental biology↗

bioRxiv2020

A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape

Several unique properties of echinoids (sea urchins) make them useful for exploring macroevolutionary dynamics, including their remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. However, this potential cannot be exploited without a robust resolution of the echinoid tree of life. We revisit the phylogeny of crown group Echinoidea using both the largest phylogenomic dataset compiled for the clade, as well as a large-scale morphological matrix with a dense fossil sampling. We also gather a new compendium of both tip and node age constraints, allowing us to combine phylogenomic, morphological and stratigraphic data using a total-evidence dating approach. For this, we develop a novel method for subsampling phylogenomic datasets that selects loci with high phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our approach restructure much of the higher-level phylogeny of echinoids, and demonstrates that combining different data sources increases topological accuracy. We are able to resolve multiple alleged conflicts between molecular and morphological datasets, such as the position of Echinothurioida and Echinoneoida, as well as unravelling the relationships between sand dollars and their closest relatives. We then use this topology to trace the evolutionary history of echinoid body size through more than 270 million years, revealing a complex pattern of convergent evolution to stable peaks in macroevolutionary adaptive landscape. Our efforts show how combining phylogenomic and paleontological evidence offers new ways of exploring evolutionary forces operating across deep timescales.

evolutionary biology↗

bioRxiv2019

Use of polygenic risk scores and other molecular markers to enhance cardiovascular risk prediction: Prospective cohort study and modelling analysis

BackgroundThere is debate about the value of adding information on genetic and other molecular markers to conventional cardiovascular disease (CVD) risk predictors.\n\nMethodsUsing data on 306,654 individuals without a history of CVD from UK Biobank, we calculated measures of risk-discrimination and reclassification upon addition of polygenic risk scores (PRS) and a panel of 27 clinical biochemistry markers to a conventional risk prediction model (i.e., including age, sex, systolic blood pressure, smoking status, history of diabetes, total cholesterol and HDL cholesterol). We then modelled implications of initiating guideline-recommended statin therapy after the assessment of molecular markers for a UK primary-care setting.\n\nFindingsThe C-index was 0.710 (95% CI, 0.703-0.717) for a CVD prediction model containing conventional risk predictors alone. The C-index increased by similar amounts when adding information on PRS or biochemistry markers (0.011 and 0.014, respectively; P<0.001), and it increased still further (0.022; P<0.001) when information on both was combined. Among cases and controls, continuous net reclassification improvements were about 12% and 19%, respectively, when both PRS and biochemistry markers were added. If PRS and biochemistry markers were to be assessed in the entire primary care population aged 40-75, then it could help prevent one additional CVD event for every 893 individuals screened. By contrast, targeted assessment only among people at intermediate (i.e., 5-10%) 10-year CVD risk could help prevent one additional CVD event for every 233 individuals screened. This targeted strategy could help reclassify 16% of the intermediate-risk group to the high-risk (i.e., [≥]10%) category, preventing 11% more CVD events than conventional risk prediction.\n\nInterpretationAdding information on both PRS and selected biochemistry markers moderately enhanced CVD predictive accuracy and could improve primary prevention of CVD. However, our modelling suggested that targeted assessment of molecular markers among individuals at intermediate-risk would be more efficient than blanket approaches.

genomics↗

bioRxiv2019

Potential impacts of insect-induced harvests in the mixed forests of New England

Forest insects and pathogens (FIPs) have significant impacts on U.S. forests, each year affecting an area nearly three times the area of wildfires and timber harvesting combined. We surveyed family forest owners (FFOs) in the northeastern U.S. and 84% of respondents indicated they would harvest in at least one of the presented FIP infestation scenarios. This harvest response represents a potentially significant shift in the timing, extent, and species selection of harvesting in the Northeast. Here we used the landowner survey, regional forest inventory data, and characteristics of the emerald ash borer (EAB, Agrilus planipennis) invasion to examine the potential for a rapidly spreading FIP to alter harvest regimes and affect regional forest conditions. Twenty-five percent of the FFO parcels in the Connecticut River Watershed in New England are likely to be harvested in response to EAB within 10 years. This prediction represents an increase in harvest frequencies, from 2.9%/yr (historically) to 3.7%/yr, on FFO woodlands. At typical harvest intensities, this would result in 13% of the total aboveground biomass removed through these harvests, with 81% of that biomass from species other than ash, creating a forest disturbance that is over twice the magnitude of the disturbance from EAB alone.

ecology↗

bioRxiv2019

Landowner Functional Types to Characterize Response to Forest Insects

Forest insects and pathogens (FIPs) play an important role in the complex interactions between woodland owners and the ecosystems they manage. Understanding the specifics of woodland owner decision-making with regard to trees impacted by FIPs can facilitate projections of future forest conditions and insect spread. Our first objective is to: (i) characterize agent functional types (AFTs) of New England family forest owners (FFOs) using a set of contingent behavior questions contained in a mail survey of FFOs concerning response to FIPs. We establish AFTs as a form of dimension reduction, effectively assigning individual FFOs to particular decision-making classes, each with distinct probabilities of behavior with respect to the harvest of impacted trees. Our second objective is to: (ii) model AFT membership to predict the distribution of AFTs across the landscape. Predictors are chosen from a set of survey, geographic, and demographic features. Accomplishing (i) establishes three functional classes of landowners: cutters (46% of respondents; highly likely to cut timber impacted by FIPs), responsive cutters (42% of respondents; sensitive to pest severity), and non-cutters (12% of respondents; highly unlikely to cut). Fulfilling (ii) provides a high-resolution probability surface of AFTs across the landscape, delivering key input for simulation models of forest and land cover change in New England. Predictors in our best model of AFT membership include parcel size (hectares of forest), region, and town-level forested fraction.

ecology↗

bioRxiv2019

Compounding the disturbance: Family forest owner reactions to invasive forest insects

Invasive forest insect and pathogens (FIP) are having significant, direct, adverse impacts. Interactions between FIPs and forest owners have the potential to create ecosystem impacts that compound direct impacts. We assessed family forest owners responses to numerous contingent behavior, FIP-outbreak scenarios in the northeastern U.S. based on FIP outbreak attributes. Sixty-two percent of scenario responses (n=2,752) reflected a harvest intent as a result of FIPs; 84% of respondents (n=688) would consider harvesting in at least one of the four hypothetical scenarios presented to them. Harvest intention increased with greater FIP-related tree mortality and decreased with delayed total tree mortality. Owners with larger holdings, who had previously harvested forest products, and live on their forestland had greater intentions to harvest in response to FIPs. Results suggest that FIPs could transform the regional harvest regime with socio-ecological impacts that are distinct from those caused by FIPs or harvesting alone.

ecology↗

bioRxiv2018

PLANT-Dx: A Molecular Diagnostic for Point of Use Detection of Plant Pathogens

Synthetic biology based diagnostic technologies have improved upon gold standard diagnostic methodologies by decreasing cost, increasing accuracy, and enhancing portability. However there has been little effort in adapting these technologies towards applications related to point-of-use monitoring of plant and crop health. Here, we take a step towards this vision by developing an approach that couples isothermal amplification of specific plant pathogen genomic sequences with customizable synthetic RNA regulators that are designed to trigger the production of a colorimetric output in cell-free gene expression reactions. We demonstrate our system can sense viral derived sequences with high-sensitivity and specificity, and can be utilized to directly detect viruses from infected plant material. Furthermore, we demonstrate that the entire system can operate using only body heat and naked-eye visual analysis of outputs. We anticipate these strategies to be important components of user-friendly and deployable diagnostic systems that can be configured to detect a range of important plant pathogens.

synthetic biology↗

bioRxiv2018

Isolation, Development, and Genomic Analysis of Bacillus megaterium SR7 for Growth and Metabolite Production Under Supercritical Carbon Dioxide

Supercritical carbon dioxide (scCO2) is an attractive substitute for conventional organic solvents due to its unique transport and thermodynamic properties, its renewability and labile nature, and its high solubility for compounds such as alcohols, ketones and aldehydes. However, biological systems that use scCO2 are mainly limited to in vitro processes due to its strong inhibition of cell viability and growth. To solve this problem, we used a bioprospecting approach to isolate a microbial strain with the natural ability to grow while exposed to scCO2. Enrichment culture and serial passaging of deep subsurface fluids from the McElmo Dome scCO2 reservoir in aqueous media under scCO2 headspace enabled the isolation of spore-forming strain Bacillus megaterium SR7. Sequencing and analysis of the complete 5.51 Mbp genome and physiological characterization revealed the capacity for facultative anaerobic metabolism, including fermentative growth on a diverse range of organic substrates. Supplementation of growth medium with O_SCPCAPLC_SCPCAP-alanine for chemical induction of spore germination significantly improved growth frequencies and biomass accumulation under scCO2 headspace. Detection of endogenous fermentative compounds in cultures grown under scCO2 represents the first observation of bioproduct generation and accumulation under this condition. Culturing development and metabolic characterization of B. megaterium SR7 represent initial advancements in the effort towards enabling exploitation of scCO2 as a sustainable solvent for in vivo bioprocessing.

microbiology↗

bioRxiv2018

Changes in lipid and proteome composition accompany growth of Bacillus subterraneus MITOT1 under supercritical CO2 and may promote acclimation to associated stresses.

Recent demonstration that multiple Bacillus strains grow in batch bioreactors containing supercritical (sc) CO2 (i.e. >73 atm, >31{degrees}C) is surprising given the recognized roles of scCO2 as a sterilant and solvent. Growth under scCO2 is of interest for biotechnological applications and for microbially-enhanced geologic carbon sequestration. We hypothesize that Bacillus spp. may alter cell wall and membrane composition in response to scCO2-associated stresses. In this study, protein expression and membrane lipids of B. subterraneus MITOT1 were profiled in cultures grown under headspaces of 1 and 100 atm of CO2 or N2. Growth under 100 atm CO2 revealed significantly decreased fatty acid branching and increased fatty acyl chain lengths relative to 1 atm cultures. Proteomes of MITOT1 grown under 1 and 100 atm pressures of CO2 and N2 were similar (Spearman R>0.65), and principal component analysis revealed variation by treatment with the first two principal components corresponding to headspace gas (CO2 or N2) and pressure (1 atm and 100 atm), respectively. Amino acid metabolic proteins were enriched under CO2, including the glycine cleavage system, previously shown to be upregulated in acid stress response. These results provide insights into the stationary phase physiology of strains grown under scCO2, suggesting modifications of cell membranes and amino acid metabolism may be involved in response to acidic, high CO2 conditions under scCO2.

microbiology↗

bioRxiv2017

Disequilibrium of fire-prone forests sets the stage for a rapid decline in conifer dominance during the 21st century

As trees are long-lived organisms, the impacts of climate change on forest communities may not be apparent on the time scale of years to decades. While lagged responses to environmental change are common in forested systems, potential for abrupt transitions under climate change may occur in environments where alternative vegetation states are influenced by disturbances, such as fire. The Klamath mountains (northern California and southwest Oregon, USA) are currently dominated by carbon rich and hyper-diverse temperate conifer forests, but climate change could disrupt the mechanisms promoting forest stability- regeneration and fire tolerance-- via shifts in the fire regime in conjunction with lower fitness of conifers under a hotter climate. Understanding how this landscape will respond to near-term climate change (before 2100) is critical for predicting potential climate change feedbacks and to developing sound forest conservation and management plans. Using a landscape simulation model, we estimate that 1/3 of the Klamath could transition from conifer forest to shrub/hardwood chaparral, triggered by an enhanced fire activity coupled with lower post-fire conifer establishment. Such shifts were more prevalent under higher climate change forcing (RCP 8.5) but were also simulated under the climate of 1950-2000, reflecting the joint influences of early warming trends and historical forest legacies. Our results demonstrate that there is a large potential for loss of conifer forest dominance--and associated carbon stocks and biodiversity- in the Klamath before the end of the century, and that some losses would likely occur even without the influence of climate change. Thus, in the Klamath and other forested landscapes subject to similar feedback dynamics, major ecosystem shifts should be expected when climate change disrupts key stabilizing feedbacks that maintain the dominance of long-lived, slowly regenerating trees.

ecology↗