Biology subjects

Hurt, C.

Publications and source records attributed to Hurt, C..

6 recordsLinked to original sources

bioRxiv2022

Solid-state NMR of paired helical filaments formed by the core tau fragment tau(297-391)

Aggregation of the tau protein into fibrillar cross-{beta} aggregates is a hallmark of Alzheimers diseases (AD) and many other neurodegenerative tauopathies. Recently, several core structures of patient-derived tau paired helical filaments (PHFs) have been solved revealing a structural variability that often correlates with a specific tauopathy. To further characterize the dynamics of these fibril cores, to screen for strain-specific small molecules as potential biomarkers and therapeutics, and to develop strain-specific antibodies, recombinant in-vitro models of tau filaments are needed. We recently showed that a 95-residue fragment of tau (from residue 297 to 391), termed dGAE, forms filaments in vitro in the absence of polyanionic co-factors often used for in vitro aggregation of full length tau. Tau(297-391) was identified as the proteolytic resistant core of tau PHFs and overlaps with the structures characterized by cryo-electron microscopy in ex-vivo PHFs, making it a promising model for the study of AD tau filaments in vitro. In the present study, we used solid-state NMR to characterize tau(297-391) filaments and show that such filaments assembled under non-reducing conditions are more dynamic and less ordered than those made in the presence of the reducing agent, DTT. We further report the resonance assignment of tau(297-392)+DTT filaments and compare it to existing core structures of tau.

biophysics↗

bioRxiv2021

Conservation Genomics of Urban Populations of Streamside Salamander (Ambystoma barbouri)

In Tennessee, populations of the state endangered Streamside Salamander (Ambystoma barbouri) are in decline as their distribution lies mostly within rapidly developing areas in the Nashville Basin. Information regarding the partitioning of genetic variation among populations of A. barbouri, and the taxonomic status of these populations relative to northern populations and their congener, the smallmouth salamander (A. texanum), have important implications for management and conservation of this species. Here we combined mitochondrial sequencing and genome-wide single nucleotide polymorphism (SNP) data generated using Genotyping-by-Sequencing (GBS) to investigate patterns of genetic variation within Tennessee populations of A. barbouri, to assess their relationship to populations in Kentucky, and to examine their phylogenetic relationship to the closely related A. texanum. Results from phylogenetic reconstructions reveal a complex history of Tennessee A. barbouri populations with regards to northern populations, unisexual A. barbouri, and A. texanum. Patterns of mitochondrial sequence variation suggest that A. barbouri may have originated within Tennessee and expanded north multiple times into Kentucky, Ohio, Indiana and West Virginia. Phylogenetic reconstructions based on genome-wide SNP data contradict results based on mitochondrial DNA and correspond to geographic and taxonomic boundaries. Variation in allele frequencies at SNP genotypes, as identified by multivariate analyses and Bayesian assignment tests, identified three evolutionary significant units (ESUs) for A. barbouri within the state of Tennessee. Collectively, these results emphasize the need for prioritizing conservation needs of Tennessee populations of A. barbouri to ensure the long-term persistence of this species.

evolutionary biology↗

bioRxiv2020

Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama

The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. To estimate this genomewide neutral mutation rate (), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated to be 2.64E-9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. This estimate is remarkably similar to experimentally derived mutation rates in model arthropod systems, strengthening the argument for a recent closure of the CAS. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.

evolutionary biology↗

bioRxiv2020

TailTimer: an open-source device for automating the rodent tail immersion assay

The tail immersion assay is a widely used method for measuring acute thermal pain in a way which is quantifiable and reproducible. It is non-invasive and measures response to a stimulus that may be encountered by an animal in its natural environment. However, tail withdrawal latency data are usually collected manually, and precise temperatures of the water at the time of measurement are most often not recorded. These two factors can reduce the reproducibility of tail immersion assay data. We designed a device, TailTimer, which uses the Raspberry Pi single-board computer and a temperature sensor, to automatically record both tail withdrawal latency and water temperature. The device has a radio frequency identification (RFID) system that can record the ID of animals. Our software recognizes several specific RFID keys as user interface commands, which allows TailTimer to be operated via RFID fobs. We also programmed the device to only allow tests to be conducted when the water is within {+/-} 0.25 {degrees}C of the target temperature. Data recorded using the TailTimer device showed a linear relationship between tail withdrawal latency and water temperature when tested between 47 - 50 {degrees}C. We also observed a profound effect of water mixing speed on tail withdrawal latency. Our data further revealed significant strain and sex differences, valorizing TailTimer in its ability to detect genetically-determined variations in thermal pain sensitivity. Significance StatementQuantification of tail withdrawal latency in response to thermal pain has essentially remained the same since the method was first introduced decades ago and relies on manual recording of water temperature and tail withdrawal latency. Such manual methods engender relatively substantial variability and are potential contributors to some of the discrepancies present among relevant research. The open source TailTimer device we report here is simple and inexpensive to manufacture. The RFID-based user interface is ergonomic, especially in animal facilities where space is limited and gloves are mandatory. We anticipate that the increased reproducibility of tail withdrawal latency provided by TailTimer will augment its utility in nociception and addiction research.

animal behavior and cognition↗

bioRxiv2019

The Emerging Gait Dysfunction Phenotype in Idiopathic Parkinson’s Disease

ObjectiveSeverity of motor symptoms in Parkinsons disease (PD), and rate of change of these symptoms, suggests the existence of disease subgroups. One important PD subgroup is defined by postural instability and gait dysfunction (PIGD), which is associated with disability, lower quality of life, and cognitive deterioration. In this study, we evaluate what clinical factors at baseline are associated with early development of postural instability in PD.\n\nMethodsData was downloaded from the Parkinsons Progressive Markers Initiative (PPMI). Several clinical features predict development of postural instability. We provisionally term the associated phenotype the emerging gait disorder (eGD) phenotype. We evaluate validity of the phenotype in two held-out populations.\n\nResultsIndividuals with the proposed eGD phenotype have a significantly higher risk of developing postural instability in both validation sets (p < 0.00001 in both sets). The proposed eGD phenotype occurred before development of postural instability (HY stage [≥] 3) in 289 of 301 paired comparisons (Fischer Exact Test, p < 0.000001), with a median progression time from development of eGD phenotype to postural instability of 972 days. Individuals with the proposed eGD phenotype at baseline had more rapid cognitive decline as measured by the Montreal Cognitive Assessment (p = 0.002) and Hopkins Verbal Learning Test (Total Recall, p = 0.008).\n\nInterpretationWe describe a clinical phenotype, detectable at baseline in a subset of individuals with PD, that is associated with accelerated development of postural instability. Within the sample, development of the eGD phenotype reliably precedes development of disability, and is a harbinger of more rapid cognitive progression.

neuroscience↗

bioRxiv2018

Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping

Decoding the functional connectivity of the nervous system is facilitated by transgenic methods that express a genetically encoded reporter or effector in specific neurons; however, most transgenic lines show broad spatiotemporal and cell-type expression. Increased specificity can be achieved using intersectional genetic methods which restrict reporter expression to cells that co-express multiple drivers, such as Gal4 and Cre. To facilitate intersectional targeting in zebrafish, we have generated more than 50 new Cre lines, and co-registered brain expression images with the Zebrafish Brain Browser, a cellular resolution atlas of 264 transgenic lines. Lines labeling neurons of interest can be identified using a web-browser to perform a 3D spatial search (zbbrowser.com). This resource facilitates the design of intersectional genetic experiments and will advance a wide range of precision circuit-mapping studies.

neuroscience↗