Biology subjects

Thompson, J. J.

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

8 recordsLinked to original sources

bioRxiv2026

An Operant-based Touchscreen Morph Discrimination Task Does Not Detect Age-related Mnemonic Similarity Deficits in Rats

The Mnemonic Similarity Task (MST) is highly sensitive to age-related cognitive decline in humans and has been adapted for rodents using 3D objects, where aged animals show deficits in discriminating similar lures. To improve translational alignment with human testing and increase automation, we developed a touchscreen-based rat analog using a morphed Object-Cued Spatial Choice (OCSC) task with 2D image stimuli. Young (4-month) and aged (21-month) male and female Fischer 344 x Brown Norway hybrid rats were trained in Bussey-Saksida touchscreen chambers and tested on discrimination performance using image pairs that varied parametrically in feature overlap. We also assessed perirhinal cortical engagement in a subset of animals using Arc expression as a readout of activity-related principal cell firing following low-and high-overlap task epochs. Across shaping and procedural training, aged rats required more errors to reach criterion on one stimulus set, but both age groups successfully acquired the task. During morph testing, performance declined systematically as stimulus similarity increased, confirming that the task manipulated discrimination difficulty. However, contrary to expectations, young and aged rats performed similarly across overlap conditions, with no significant age-related impairment. In the Arc experiment, discrimination accuracy was again reduced by greater stimulus overlap, but Arc expression in perirhinal cortex did not differ reliably by age or overlap condition, although expression was associated with behavioral accuracy and deep layers showed higher ensemble similarity than superficial layers. These findings indicate that, while the touchscreen morph OCSC task is sensitive to stimulus similarity, it does not detect the robust age-related mnemonic discrimination deficits previously observed with 3D object-based rodent MST paradigms, underscoring the importance of considering ethological relevance when designing translational cognitive assays.

neuroscience↗

bioRxiv2024

Structural perturbation of chromatin domains with multiple developmental regulators can severely impact gene regulation and development

Chromatin domain boundaries delimited by CTCF motifs can restrict the range of enhancer action. However, disruption of domain structure often results in mild gene dysregulation and thus predicting the impact of boundary rearrangements on animal development remains challenging. Here, we tested whether structural perturbation of a chromatin domain with multiple developmental regulators can result in more acute gene dysregulation and severe developmental phenotypes. We targeted clusters of CTCF motifs in a domain of the mouse genome containing three FGF ligand genes--Fgf3, Fgf4, and Fgf15--that regulate several developmental processes. Deletion of the 23.9kb cluster that defines the centromeric boundary of this domain resulted in ectopic interactions of the FGF genes with enhancers located across the deleted boundary that are active in the developing brain. This caused strong induction of FGF expression and perinatal lethality with encephalocele and orofacial cleft phenotypes. Heterozygous boundary deletion was sufficient to cause these fully penetrant phenotypes, and strikingly, loss of a single CTCF motif within the cluster also recapitulated ectopic FGF expression and caused encephalocele. However, such phenotypic sensitivity to perturbation of domain structure did not extend to all CTCF clusters of this domain, nor to all developmental processes controlled by these three FGF genes--for example, the ability to undergo lineage specification in the blastocyst and pre-implantation development were not affected. By tracing the impact of different chromosomal rearrangements throughout mouse development, we start to uncover the determinants of phenotypic robustness and sensitivity to perturbation of chromatin boundaries. Our data show how small sequence variants at certain domain boundaries can have a surprisingly outsized effect and must be considered as potential sources of gene dysregulation during development and disease.

developmental biology↗

bioRxiv2022

Unilateral Perforant Path Transection Does Not Alter Lateral Entorhinal Cortical or Hippocampal CA3 Arc Expression

It is well established that degradation of perforant path fibers is associated with age-related cognitive dysfunction and CA3 hyperactivity. Whether this fiber loss triggers a cascade of other functional changes within the hippocampus circuit has not been causatively established, however. Thus, the current study evaluated the effect of perforant path fiber loss on neuronal activity in CA3 and layer II of the lateral entorhinal cortex (LEC) in relation to mnemonic similarity task performance. Expression of the immediate early gene Arc was quantified in rats that received a unilateral right hemisphere transection of the perforant path or sham surgery that cut the cortex but left the fibers intact. Behavior-related expression of Arc mRNA was measured to test the hypothesis that fiber loss leads to elevated activation of CA3 and LEC neurons, as previously observed in aged rats that were impaired on the mnemonic similarity task. Transection of perforant path fibers, which has previously been shown to lead to a decline in mnemonic similarity task performance, did not alter Arc expression. Arc expression in CA3, however, was correlated with task performance on the more difficult discrimination trials across both surgical groups. These observations further support a link between CA3 activity and mnemonic similarity task performance but suggest the reduced input from the entorhinal cortex to the hippocampus, as observed in old age, does not causatively elevate CA3 activity.

neuroscience↗

bioRxiv2021

Rapid redistribution and extensive binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates

Establishment of divergent cell types from a common progenitor requires transcription factors (TFs) to promote lineage-restricted transcriptional programs while suppressing alternative fates. In the mouse blastocyst, cells of the inner cell mass (ICM) coexpress NANOG and GATA6, two TFs that drive the bifurcation of these progenitors into either the epiblast (Epi) or the primitive endoderm (PrE), respectively. Here, using in vitro differentiation, we describe the molecular mechanisms of how GATA6 quickly induces the PrE fate while repressing the Epi lineage. GATA6 functions as a pioneer TF by inducing nucleosome repositioning at regulatory elements controlling PrE genes, making them accessible for deposition of active histone marks and leading to rewiring of chromatin interactions and ultimately transcriptional activation. GATA6 also binds most regulatory elements of Epi genes followed by eviction of the Epispecific TFs NANOG and SOX2, loss of active histone marks, and reduction in chromatin accessibility that culminates in transcriptional repression. Unexpectedly, evicted NANOG and SOX2 transiently bind PrE regulatory elements occupied by GATA6. Our study shows that GATA6 binds and modulate the same regulatory elements as Epi TFs, a phenomenon we also validated in blastocysts. We propose that the ability of PrE and Epi-specific TFs to extensively bind and regulate the same gene networks contributes to ICM plasticity and allows rapid cell lineage specification by coordinating both activation

developmental biology↗

bioRxiv2021

Single cell chromatin accessibility reveals regulatory elements and developmental trajectories in the embryonic forebrain

A comprehensive characterization of epigemonic organization in the embryonic mouse forebrain will enhance our understanding of neurodevelopment and provide insight into mechanisms of neurological disease. We collected single-cell chromatin accessibility profiles from four distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many restricted to distinct progenitor cell types or brain regions. We integrated snATAC-Seq and single cell transcriptome data to characterize changes of chromatin accessibility at enhancers and promoters with associated transcript abundance. Multi-modal integration of histone modifications (CUT&Tag and CUT&RUN), promoter-enhancer interactions (Capture-C) and high-order chromatin structure (Hi-C) extended these initial observations. This dataset reveals a diverse chromatin landscape with region-specific regulatory mechanisms and genomic interactions in distinct neurogenic regions of the embryonic mouse brain and represents an extensive public resource of a ground truth epigenomic landscape at this critical stage of neurogenesis.

neuroscience↗

bioRxiv2020

Mapping heritability of obesity by brain cell types

The underlying cell types mediating predisposition to obesity remain largely obscure. Here we first integrated recently published single-cell RNA-sequencing (scRNA-seq) data from >380 peripheral and nervous system cell types spanning 19 mouse organs with body mass index (BMI) genome-wide association study (GWAS) data from >450,000 individuals. Leveraging a novel strategy for integrating scRNA-seq data with GWAS data, we identified 22, exclusively neuronal, cell types from the subthalamus, midbrain, hippocampus, thalamus, cortex, pons, medulla, pallidum that were significantly enriched for BMI heritability (P<1.6x10-4). Using genes harboring coding mutations leading to syndromic forms of obesity, we replicate four midbrain cell types from the anterior pretectal nucleus, superior nucleus, periaqueductal gray and pallidum (P<1.7x10-4). Testing an additional set of 347 hypothalamic cell types, ventromedial hypothalamic steroidogenic-factor 1 (SF1) and cholecystokinin b receptor (CCKBR)-expressing neurons (P=4.9x10-5) previously implicated in energy homeostasis and glucose control and three cell types from the preoptic area of the hypothalamus and the lateral hypothalamus enriched for BMI GWAS associations (P<4.9x10-5). Together, our results suggest brain nuclei regulating integration of sensory stimuli, learning and memory are likely to play a key role in obesity and provide testable hypotheses for mechanistic follow-up studies.

genetics↗

bioRxiv2018

Spatial ecology of Paraguay’s last remaining Atlantic forest jaguars (Panthera onca): implications for their long-term survival

Using GPS telemetry we quantified space use and movements of jaguar (Panthera onca) in remnant populations in the Paraguayan Atlantic forest within a comparative context with populations in the Argentine and Brazilian Atlantic forest. Mean estimated home range size was 160 km2; estimated to be nearly equal to jaguars in the Morro do Diabo State Park in Brazil but jaguars in other populations in Argentina and Brazil had a 73% (Iguazu/Iguacu national park complex) and 96% (Ivinhema State Park) probability of having larger home ranges. We found no relationship between home range size or movements and human population or the Human Footprint Index, while 75% of locations from all individuals were in protected areas. Our data and analysis highlight the dependence of Atlantic forest jaguars on protected areas, an avoidance of the landscape matrix and an extreme isolation of the remaining Paraguayan Atlantic forest jaguars.

ecology↗

bioRxiv2017

Space use and movement of jaguar (Panthera onca) in western Paraguay

We estimated home range and core area size for jaguar (Panthera onca) in western Paraguay in the Dry Chaco, Humid Chaco and Pantanal using an autocorrelated kernel density estimator. Mean home range size was 818 km2 (95% CI:425-1981) in the Dry Chaco and 237 km2 (95% CI:90-427) in the Humid Chaco/Pantanal. Core areas, defined as the home range area where use was equal to expected use, was consistent across sexes and systems represented on average by the 59% utility distribution isopleth (range:56-64%). Males had a higher probability of larger home ranges and more directional and greater daily movements than females collectively and within systems. The large home ranges in the Dry Chaco are attributable to the relatively low productivity of that semi-arid ecosystem and high heterogeneity in resource distribution while larger than expected home ranges in the Humid Chaco/Pantanal compared to home range estimates from the Brazilian Pantanal may be due to differences in geomorphology and hydrological cycle. The large home ranges of jaguars in western Paraguay and a low proportional area of protected areas in the region demonstrate the importance of private ranchland for the long-term conservation of the species.

ecology↗