Biology subjects

Thompson, A. R.

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

14 recordsLinked to original sources

bioRxiv2026

Comparative connectomics of parasite esophagus suggests evolutionary simplification of a nervous system

Several prominent examples suggest that the evolution of parasitism is accompanied by nervous system simplification. However, it is unclear if this is a generalizable rule and whether parasite- associated simplification occurs at the level of synaptic connectivity. The nematode esophagus is a specialized neuromuscular feeding organ that varies with diet and lifestyle. Plant-parasitic nematodes are major agricultural pests that feed through a protrusible stylet and release of extensive glandular effectors; however, the neuronal mechanisms controlling parasite feeding are unclear. Here, we used serial-section electron microscopy to reconstruct the esophageal connectome of the infective second-stage juvenile of the soybean cyst nematode, Heterodera glycines, and compared it with those of the free-living species Caenorhabditis elegans and Pristionchus pacificus. Similar to these species, H. glycines has 20 esophageal neurons with relatively conserved cell body positions. Despite this conservation, the H. glycines chemical synaptic network is highly reduced in output to musculature. A unique ensheathment of neurons by a gland cell facilitates novel synaptic connectivity in H. glycines. The H. glycines esophageal network is strongly biased toward monadic synapses and shows a greater proportion of neuron- neuron and neuron-gland connections. Consistent with a reduction in motor output, network analysis indicates that the H. glycines esophageal network is smaller and less clustered than free-living species. Using centrality analysis and synthetic ablation, we predict that control of multiple feeding modules in H. glycines depends on distinct neurons compared to free-living species. These findings show how parasitism reshapes a feeding circuit and identify candidate species-specific circuits for parasite control. Significance statementAnimal nervous systems are tuned to the behaviors they support. Nematodes occupy diverse ecological niches, and their feeding organ, the esophagus, is specialized to their diet. Understanding the esophageal nervous system provides evolutionary insights into parasitism as well as pathways for future control targets. We present the esophageal connectome of the soybean cyst nematode Heterodera glycines, which causes devastating damage to soybean production worldwide. By comparing H. glycines and free-living species, which diverged over 350 million years ago, we identify evolutionarily conserved features of the feeding circuit and highlight parasite-specific circuits as candidate targets for control.

neuroscience↗

bioRxiv2025

Evidence for trace gas metabolism and widespread antibiotic synthesis in an abiotically-1 driven, Antarctic soil ecosystem

The McMurdo Dry Valleys (MDVs) of Antarctica offer microbial ecologists a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition, and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analyzed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality MAGs ([≥] 50% completeness and contamination < 10%) and 201 high-quality MAGs ([≥] 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: 1) community composition shifts along environmental gradients correlated with soil moisture, elevation, and distance to the coast; 2) many MDV bacteria are capable of performing trace gas metabolism; 3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and 4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.

microbiology↗

bioRxiv2024

Diet and Size-at-Birth Affect Larval Rockfish Condition and Survival

Feeding success and maternal effects on larval size have long been hypothesized as important contributors to interannual recruitment variability in marine fishes. This study examined the feeding ecology and influences of diet and size-at-birth on length and growth of larval rockfishes (Sebastes spp.). Prey carbon biomass and selection were calculated from gut contents, size-at-birth was estimated using otolith core size, and recent growth was derived from outer otolith increment widths. Biomass contributions of preferred prey and otolith data were integrated into Bayesian hierarchical models predicting length and growth. Larvae primarily fed on and selected for copepod nauplii and Calanoid copepodites, modulating feeding with ontogeny and in response to prey availability. Based on carbon weight, the relative contribution of Calanoid copepodites to the diet was more strongly and positively correlated with length and growth than that of nauplii. Younger larvae experienced faster growth in association with Calanoid copepodite consumption than older larvae. Positive effects of core radius suggest that initial larval size, believed to be mediated by maternal provisioning, increases the likelihood of survival, larger size and faster growth. These findings ultimately provide evidence that selective feeding and size-at-birth mediate rockfish survival in early life stages.

ecology↗

bioRxiv2023

Trophic Efficiency Facilitates Larval Shortbelly Rockfish (Sebastes jordani) Development

Identifying the factors influencing fish recruitment is critical for fishery management, and failure to do so can have major ecological and economic consequences. Many hypotheses over the past century have been proposed, and the recently postulated Trophic Efficiency in Early Life (TEEL) hypothesis argues that a shorter food chain length can result in more efficient energy transfer from primary producers to young fishes, thereby increasing growth rate and larval condition, reducing early-life mortality and ultimately leading to a stronger recruitment cohort. To test this hypothesis, we analyzed the trophic position (TP) through compound-specific isotopic analysis of amino acids, as well as otolith microstructure and stomach content of larval shortbelly rockfish (Sebastes jordani). Results show larval rockfish that ate lower TP prey were both heavier and faster growing. This suggests the trophic characteristics of early life diet are critical to larval survival, and provide evidence in support of the TEEL hypothesis.

ecology↗

bioRxiv2023

Environment-driven trends in fish larval abundance predict fishery recruitment in two temperature reef congeners: mechanisms and implications for management

Environmental and biological processes acting on fish larvae can drive fishery cohort strength, but predictive ability oftentimes falls short, and larval abundance is generally considered more useful as a proxy for spawning biomass. Under a changing ocean, studies that relate environmental covariates, larval abundance, and fishery recruitment are worthy of continued research, especially in data-limited contexts. We focus on a popular, recreational-only, multispecies saltwater bass fishery (genus Paralabrax) whose population status and recovery potential are uncertain. We used 54 years of ichthyoplankton data (1963-2016) and a species distribution model to 1) deconstruct species-specific standardized indices of larval abundance, 2) test these indices as indicators of adult stock status or predictors of future fishery recruitment, and 3) evaluate spatiotemporal trends in their population dynamics relative to environmental variables. Contrary to expectation, species-specific larval abundance predicted future catch, with recent elevated larval abundance suggesting imminent fishery recovery. Additionally, we identified strong relationships with environmental variables, thereby providing additional tools for predicting fishery recruitment and anticipating population change. Our findings paint a path forward for improving estimates of current and future fishery status under changing natural and anthropogenic influences and the incorporation of ecosystem considerations into fishery management.

ecology↗

bioRxiv2023

Allosteric coupling asymmetry mediates paradoxical activation of BRAF

The type II class of RAF inhibitors currently in clinical trials paradoxically activate BRAF at subsaturating concentrations. Activation is mediated by induction of BRAF dimers, but why activation rather than inhibition occurs remains unclear. Using biophysical methods tracking BRAF dimerization and conformation we built an allosteric model of inhibitor-induced dimerization that resolves the allosteric contributions of inhibitor binding to the two active sites of the dimer, revealing key differences between type I and type II RAF inhibitors. For type II inhibitors the allosteric coupling between inhibitor binding and BRAF dimerization is distributed asymmetrically across the two dimer binding sites, with binding to the first site dominating the allostery. This asymmetry results in efficient and selective induction of dimers with one inhibited and one catalytically active subunit. Our allosteric models quantitatively account for paradoxical activation data measured for 11 RAF inhibitors. Unlike type II inhibitors, type I inhibitors lack allosteric asymmetry and do not activate BRAF homodimers. Finally, NMR data reveal that BRAF homodimers are dynamically asymmetric with only one of the subunits locked in the active C-in state. This provides a structural mechanism for how binding of only a single C-in inhibitor molecule can induce potent BRAF dimerization and activation.

biophysics↗

bioRxiv2023

FRET assay for live-cell high-throughput screening of the cardiac SERCA pump yields multiple classes of small-molecule allosteric modulators

We have used FRET-based biosensors in live cells, in a robust high-throughput screening (HTS) platform, to identify small-molecules that alter the structure and activity of the cardiac sarco/endoplasmic reticulum calcium ATPase (SERCA2a). Our primary aim is to discover drug-like small-molecule activators that improve SERCAs function for the treatment of heart failure. We have previously demonstrated the use of an intramolecular FRET biosensor, based on human SERCA2a, by screening a small validation library using novel microplate readers that can detect the fluorescence lifetime or emission spectrum with high speed, precision, and resolution. Here we report results from a 50,000-compound screen using the same biosensor, with hit compounds functionally evaluated using Ca2+-ATPase and Ca2+-transport assays. We focused on 18 hit compounds, from which we identified eight structurally unique compounds and four compound classes as SERCA modulators, approximately half of which are activators and half are inhibitors. While both activators and inhibitors have therapeutic potential, the activators establish the basis for future testing in heart disease models and lead development, toward pharmaceutical therapy for heart failure.

biophysics↗

bioRxiv2022

Message in a Bottle: Archived DNA Reveals Marine Heatwave-Associated Shifts in Fish Assemblages

Marine heatwaves can drive large-scale shifts in marine ecosystems but studying their impacts on whole species assemblages can be difficult. Here, we leverage the taxonomic breadth and resolution of DNA sequences derived from environmental DNA (eDNA) in the ethanol of a set of 23-year longitudinal ichthyoplankton samples, combining these with microscopy-derived ichthyoplankton identification to yield higher-resolution, species-specific quantitative abundance estimates of fish assemblages in the California Current Large Marine Ecosystem during and after the 2014-16 Pacific marine heatwave. This integrated dataset reveals patterns of tropicalization with increases in southern, mesopelagic species and associated declines in important temperate fisheries targets (e.g., North Pacific Hake (Merluccius productus) and Pacific Sardine (Sardinops sagax)). We observed novel assemblages of southern, mesopelagic fishes and temperate species (e.g., Northern Anchovy, Engraulis mordax) even after the return to average water temperatures. Our innovative preservative derived eDNA metabarcoding and quantitative modeling approaches open the door to reconstructing the historical dynamics of assemblages from modern and archived samples worldwide. SummaryNovel quantitative abundance estimates from archived DNA reveals marine heatwave-associated shifts in fish assemblages.

ecology↗

bioRxiv2022

Optimizing immunostaining of archival fish samples to enhance museum collection potential

Immunohistochemistry (IHC) is a powerful biochemical technique that uses antibodies to specifically label and visualize proteins of interests within biological samples. However, fluid-preserved specimens within natural history collection often use fixatives and protocols that induce high background signal (autofluorescence), which hampers IHC as it produces low signal-to-noise ratio. Here, we explored techniques to reduce autofluorescence using sodium borohydride (SBH), citrate buffer, and their combination on fish tissue preserved with paraformaldehyde, formalin, ethanol, and glutaraldehyde. We found SBH was the most effective quenching technique, and applied this pretreatment to the gill or skin of 10 different archival fishes - including specimens that had been preserved in formalin or ethanol for up to 65 and 37 years, respectively. The enzyme Na+/K+-ATPase (NKA) was successfully immunostained and imaged using confocal fluorescence microscopy, allowing for the identification and characterization of NKA-rich ionocytes essential for fish ionic and acid-base homeostasis. Altogether, our SBH-based method facilitates the use of IHC on archival samples, and unlocks the historical record on fish biological responses to environmental factors (such as climate change) using specimens from natural history collections that were preserved decades to centuries ago. HighlightsO_LISodium borohydride pretreatment reduced aldehyde-induced autofluorescence C_LIO_LISuccessfully immunostained archival samples of various fixative and fixation time C_LIO_LILarval fish that was formalin-fixed for 63-65 years was successfully immunostained C_LI

biochemistry↗

bioRxiv2021

High-throughput screen using fluorescence lifetime detects compounds that modulate myosin-binding protein C interactions with actin

Cardiac myosin-binding protein C (cMyBP-C) interacts with actin and myosin to modulate cardiac contractility. These interactions are regulated by cMyBP-C phosphorylation. Heart failure patients often have decreased cMyBP-C phosphorylation and phosphorylation in model systems appears to be cardioprotective for heart failure. Therefore, cMyBP-C is a potential target for heart failure drugs that mimic phosphorylation and/or perturb its interactions with actin/myosin. We have used a novel fluorescence lifetime-based assay to identify small-molecule inhibitors of actin-cMyBP-C binding. Actin was labeled with a fluorescent dye (Alexa Fluor 568, AF568) near its cMyBP-C binding sites. When combined with cMyBP-C N-terminal fragment, C0-C2, the fluorescence lifetime of AF568-actin decreases. Using this reduction in lifetime as a readout of actin binding, a high-throughput screen of a 1280-compound library identified 3 reproducible Hit compounds that reduced C0-C2 binding to actin in the micromolar range. Binding of phosphorylated C0-C2 was also blocked by these compounds. That they specifically block binding was confirmed by a novel actin-C0-C2 time-resolved FRET (TR-FRET) binding assay. Isothermal titration calorimetry (ITC) and transient phosphorescence anisotropy (TPA) confirmed that the Hit compounds bind to cMyBP-C but not to actin. TPA results were also consistent with these compounds inhibiting C0-C2 binding to actin. We conclude that the actin-cMyBP-C lifetime assay permits detection of pharmacologically active compounds that affect cMyBP-Cs actin binding function. TPA, TR-FRET, and ITC can then be used to understand the mechanism by which the compounds alter cMyBP-C interactions with actin.

biophysics↗

bioRxiv2020

Development of a genome-scale metabolic model of Clostridium thermocellum and its applications for integration of multi-omics datasets and strain design

Solving environmental and social challenges such as climate change requires a shift from our current non-renewable manufacturing model to a sustainable bioeconomy. To lower carbon emissions in the production of fuels and chemicals, plant biomass feedstocks can replace petroleum using microorganisms as catalysts. The anaerobic thermophile Clostridium thermocellum is a promising bacterium for bioconversion due to its capability to efficiently degrade untreated lignocellulosic biomass. However, the complex metabolism of C. thermocellum is not fully understood, hindering metabolic engineering to achieve high titers, rates, and yields of targeted molecules. In this study, we developed an updated genome-scale metabolic model of C. thermocellum that accounts for recent metabolic findings, has improved prediction accuracy, and is standard-conformant to ensure easy reproducibility. We illustrated two applications of the developed model. We first formulated a multi-omics integration protocol and used it to understand redox metabolism and potential bottlenecks in biofuel (e.g., ethanol) production in C. thermocellum. Second, we used the metabolic model to design modular cells for efficient production of alcohols and esters with broad applications as flavors, fragrances, solvents, and fuels. The proposed designs not only feature intuitive push-and-pull metabolic engineering strategies, but also novel manipulations around important central metabolic branch-points. We anticipate the developed genome-scale metabolic model will provide a useful tool for system analysis of C. thermocellum metabolism to fundamentally understand its physiology and guide metabolic engineering strategies to rapidly generate modular production strains for effective biosynthesis of biofuels and biochemicals from lignocellulosic biomass.

systems biology↗

bioRxiv2019

Errors associated with compound specific δ15N analysis of amino acids in preserved fish samples purified by high pressure liquid chromatography

Compound specific isotopic analysis of amino acids (CSIA-AA) is increasingly used in ecological and biogeochemical studies tracking the origin and fate of nitrogen (N). Its advantages include the potential for resolving finer-scale trophic dynamics than possible with standard bulk SIA and for reconstructing historical changes in the food webs of consumers from analyses of specimens in preserved sample archives. For the latter, assessing the effects of chemical preservatives on {delta}15NAA has been inconclusive because the conventional CSIA approach for derivatized AAs by gas chromatography - combustion - isotope ratio mass spectrometry (GC-C-IRMS) has analytical errors (0.4 - 1.0 {per thousand}) in the range expected from chemical preservation. Here, we show improved analytical precision (0.15 {+/-} 0.08 {per thousand}) for 11 underivatized AA standards analyzed by high pressure liquid chromatography followed by offline elemental analysis - IRMS (HPLC/EA-IRMS), an approach originally developed by Broek and McCarthy (2014). Using this method, we report the first high-precision tests of preservation effects on {delta}15NAA in Northern Anchovy (Engraulis mordax) kept 1[1/2]-year in ethanol and up to 27-years in formaldehyde. We found minimal methodological induced fractionation for 8 AAs, and preservation effects on {delta}15N were similar regardless of duration and preservative used. Although some of the AAs differed significantly from frozen control samples (average +1.0 {+/-} 0.8 {per thousand}), changes in {delta}15N in the source AA Phenylalanine and trophic position estimates were statistically insignificant. Our results are encouraging for resolving fine-scale natural variability using HPLC/EA-IRMS on chemically preserved specimens and for ultimately reconstructing biogeochemical records and trophic dynamics over long time scales.

ecology↗

bioRxiv2019

Myosin Orientation in a Muscle Fiber Determined with High Angular Resolution Using Bifunctional Spin Labels

We have measured the orientation of the myosin light chain domain (lever arm) elements in demembranated muscle fibers by electron paramagnetic resonance (EPR), using a bifunctional spin label (BSL), with angular resolution of 4 degrees. Despite advances in X-ray crystallography and cryo-electron microscopy (cryo-EM), and fluorescence polarization, none of these techniques provide high-resolution structural information about the myosin light chain domain under ambient conditions in a muscle fiber. Two cysteines, 4 residues apart, were engineered on two -helices in the myosin regulatory light chain (RLC), permitting stereoselective site-directed labeling with BSL. One labeled helix (helix E) is adjacent to the myosin lever arm, the other helix (helix B) is located farther apart from the motor domain beyond the "hinge" of the myosin. By exchanging BSL-labeled RLC onto oriented muscle fibers, we obtained EPR spectra that determined angular distributions of BSL with high resolution, which enabled the accurate determination of helix orientation of individual structural elements with respect to the muscle fiber axis. In the absence of ATP (rigor), each of the two labeled helices exhibited both ordered ({sigma} ~ 9-11 degrees) and disordered ({sigma} > 38 degrees) populations. We used these angles to determine the orientation of the myosin lever arm, concluding that the oriented population has lever arms that are perpendicular to the muscle fiber axis. This orientation is ~33 degrees different than predicted from a standard "lever arm down" model based on cryo-EM of actin decorated with isolated myosin heads, but it is compatible with fluorescence polarization and EM data obtained from muscle fibers. The addition of ATP, in the absence of Ca2+, shifted the orientation to a much more disordered distribution. SummaryWe used electron paramagnetic resonance to determine the orientation of elements within the myosin regulatory light chain in skinned skeletal muscle fibers. A bifunctional spin label provided sufficient resolution to detect an ordered population of lever arms perpendicular to actin.

biophysics↗

bioRxiv2018

High-resolution models of actin-bound myosin from EPR of a bifunctional spin label

We have employed two complementary high-resolution electron paramagnetic resonance (EPR) techniques with a bifunctional spin label (BSL) to test and refine protein structural models based on crystal structures and cryo-EM. We demonstrate this approach by investigating the effects of nucleotide binding on the structure of myosins catalytic domain (CD), while myosin is in complex with actin. Unlike conventional spin labels attached to single Cys, BSL reacts with a pair of Cys; in this study, we thoroughly characterize BSLs rigid, highly stereoselective attachment to protein -helices, which permits accurate measurements of orientation and distance. Distance constraints were obtained from double electron-electron resonance (DEER) on myosin constructs labeled with BSL specifically at two sites. Constraints for orientation of individual helices were obtained previously from continuous-wave EPR (CW-EPR) of myosin labeled at specific sites with BSL in oriented muscle fibers. We have shown previously that CW-EPR of BSL quantifies helix orientation within actin-bound myosin; here we show that the addition of high-resolution distance constraints by DEER alleviates remaining spatial ambiguity, allowing for direct testing and refinement of atomic structural models. This approach is applicable to any orientable complex (e.g., membranes or filaments) in which site-specific di- Cys mutation is feasible.

biophysics↗