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opencc-zeroJan 2024View details →

Naked mole rats have distinctive cardiometabolic and genetic adaptations to their underground low-oxygen lifestyles (non-genetic data)

The naked mole-rat Heterocephalus glaber is a eusocial mammal exhibiting extreme longevity (37-year lifespan), extraordinary resistance to hypoxia and absence of cardiovascular disease. To identify the mechanisms behind these exceptional traits, metabolomics and RNAseq of cardiac tissue from naked mole-rats were compared to other African mole-rat genera. We identified metabolic and genetic adaptations unique to naked mole-rats including elevated glycogen, thus enabling glycolytic ATP generation during cardiac ischemia. Elevated normoxic expression of HIF-1α was observed while downstream hypoxia-responsive genes were down-regulated, suggesting adaptation to low-oxygen environments. Naked mole-rat hearts showed reduced succinate build-up during ischemia and negligible tissue damage following ischemia-reperfusion injury. These adaptive evolutionary traits reflect a unique hypoxic and eusocial lifestyle that collectively may contribute to their longevity and health span.

opencc-by-4.0Apr 2018View details →

Fig. 1 in Cryptosporidium viatorum from the native Australian swamp rat Rattus lutreolus - An emerging zoonotic pathogen?

Fig. 1. Phylogenetic relationships of small subunit of nuclear ribosomal RNA (SSU) gene nucleotide sequence data (aligned over 563 bp) of selected Cryptosporidium taxa in relation to the novel C. viatorum genotype using the neighbor joining distance method. Individual GenBank accession numbers precede species name, followed by host common name and locality descriptors. Bootstrap support values (based on 2000 iterations) are indicated next to supported branches. Cryptosporidium baileyi was chosen as the outgroup. The novel genotype from this study is in bold-type. Scale bar indicates the number of nucleotide substitutions per site.

opencc-zeroMar 2024View details →

Disentangling developmental effects of play aspects in rat rough-and-tumble play

Animal play encompasses a variety of aspects, with kinematic and social aspects being particularly prevalent in mammalian play behaviour. While the developmental effects of play have been increasingly documented in recent decades, understanding the specific contributions of different play aspects remains crucial to understand the function and evolutionary benefit of animal play. In our study, developing male rats were exposed to rough-and-tumble (RT) play selectively reduced in either the kinematic or the social aspect. We then assessed the developmental effects of reduced play on their appraisal of standardised human-rat play ('tickling') by examining their emission of 50-kHz ultrasonic vocalisations (USVs). Using a deep learning framework, we efficiently classified five subtypes of these USV across six behaviour states. Our results revealed that rats lacking the kinematic aspect in play emitted fewer USVs during tactile contacts by human and generally produced fewer USVs of positive valence compared to control rats. Rats lacking the social aspect did not differ from the control and the kinematically reduced group. These results indicate aspects of play have different developmental effects, underscoring the need for researchers to further disentangle how each aspect affects animals.

opencc-by-4.0Mar 2024View details →

DNA methylation in sperm of rats at two ages exposed or not to 2,2',4,4'-tetrabromodiphenyl ether

Introduction This study was designed to determine the potential of environmentally relevant levels of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) to induce age-dependent changes in a rat’s sperm epigenome. The methods used to generate the files are described below.   Experimental design Twelve seven-week-old pregnant Wistar rats were divided into two groups (6 per group) – control and BDE-47 exposed group. Between pregnancy day 8 and postnatal day 21 (PND21), dams in each group were fed from the tip of pipette 0.2 µL/g body weight of the vehicle (tocopherol-stripped corn oil) or the same volume of a 1 mg/mL solution of BDE-47 daily. The BDE-47 group resulted in an exposure level of 0.2 mg/kg body weight of BDE-47 per day. On PND65 and PND120, one male pup randomly selected from each litter was euthanized, and epididymal motile spermatozoa were collected via the swim-up procedure as described in detail elsewhere (Suvorov et al., 2018). Sperm DNA was extracted using the rapid method (Wu et al., 2015). Extracted sperm DNA was subjected to reduced representation bisulfite sequencing (RRBS).   Reduced representation bisulfite sequencing For RRBS, bisulfite-converted libraries were prepared from 100 ng of the sperm DNA using Ovation RRBS Methyl-Seq System and EpiTect Fast DNA Bisulfite Kit (Cat. #59824, Qiagen) following manufacturers’ protocols. Sequencing of libraries was done using the HiSeq 2500 sequencing system (Illumina) in Deep Sequencing Core Facility of the University of Massachusetts Medical School (Schrewsbury, MA) with an average of 18.0 million unique reads per sample.   Bioinformatic analysis Raw reads from the sequence were processed following the recommended protocol for libraries prepared with Ovation RRBS Methyl-Seq System (NuGEN) and then mapped to the rn6 Rattus norvegicus reference genome using Bismark (version 0.16.1) and bowtie-2 (version 2.2.9). PCR duplicates were removed using nudup.py (version 2.2). The resulting SAM files for the control and BDE-47 group for the two ages, PND65 and 120 are uploaded.

opencc-by-4.0Apr 2024View details →

Impacts of black rat invasion on the primary rodent host of Lassa virus, Mastomys natalensis

Shared here is code and data supporting the manuscript, "Reservoir displacement by an invasive rodent reduces Lassa virus zoonotic spillover risk." The project directory, which contains numerous large raster data files, was stored as a split zip archive to facilitate upload to Zenodo and consists of the files "rat_invasion.z01", "rat_invasion.z02", "rat_invasion.z03", and "rat_invasion.zip". Following download, these files may need to be decompressed using dedicated archiver software (such as The Unarchiver [https://theunarchiver.com/] on macOS). Note that the entire project repository is ~7 GB when uncompressed. The files shared here mirror the GitHub project repository (https://github.com/eveskew/rat_invasion) with the addition of the large environmental raster data in the "data/environmental" subdirectory.

opencc-by-4.0Nov 2024View details →

HISTOLOGICAL EVALUATION OF THE EFFECTS OF ACTION BITTERS ON THE TESTES OF ADULT MALE WISTAR RATS

Action Bitters, a popular herbal concoction, has been traditionally used to treat various health conditions, including those related to the male reproductive system. Despite its widespread use, there is a dearth of scientific evidence on its effects on the testes. This study aimed to investigate the histological changes in the testes of adult male Wistar rats following administration of Action Bitters. Methods: Fifteen adult male Wistar rats were randomly divided into three groups (n = 5). Group A served as the normal control, while groups B and C received 10% (0.66ml/kg) and 5% (0.33ml/kg) lethal dose 50 (Ld50) of Action Bitters, respectively. The Ld50 values were calculated based on the median lethal dose of the herbal remedy. The rats were administered the herbal remedy for a period of one month, after which they were sacrificed, and their testes collected for histological examination. Results: Microscopic examination of the testicular tissue samples revealed no evidence of abnormal cellular changes or tissue damage. The tissue samples appeared normal, with no signs of inflammation, necrosis, or apoptosis. Discussion: The findings of this study suggest that Action Bitters does not induce histological changes in the testes of adult male Wistar rats. These results provide new insights into the potential mechanism of action of the herbal medication on testicular function. The study highlights the importance of considering both histological and biochemical assessments when evaluating the effects of herbal remedies on reproductive health. Conclusion: This study contributes to the growing body of knowledge on the effects of herbal remedies on the male reproductive system. The findings suggest that Action Bitters may be a safe and effective herbal remedy for treating reproductive health issues, and further research is warranted to explore its potential benefits and mechanisms of action.

opencc-by-4.0Nov 2023View details →

Serial multiparametric MRI dataset of hypertensive and normotensive rats

Paper: http://dx.doi.org/10.1177/0271678X241310732 Part of: https://doi.org/10.5281/zenodo.13889416

Polyadenylation landscape of in vivo long-term potentiation in the rat brain

<h3>This repository contains data published along our corresponding manuscript and additional data resources generated/used throughout this work.  ______________________________________________________________________________</h3> <h2>Source data accompanying the manuscript: </h2> Supplementary Table 1. Key resource table. (A) Characteristics of analyzed material (e.g. sample identifiers, number of animals used, reads produced, accession numbers). (B) Key resources (antibodies, reagents, software). Supplementary Table 2. Summary of dentate gyri DRS data per gene. (A) Differential expression and differential adenylation data for 10 min timepoint. (B) Differential expression and differential adenylation data for 60 min timepoint. (C) GO-terms for genes with significantly elongated poly(A) tails in 10 min timepoint. (D) GO-terms for genes with significantly elongated poly(A) tails in 60 min timepoint. (E) GO-terms for upregulated genes in 10 min timepoint. (F) GO-terms for upregulated genes in 60 min timepoint. (G) GO-terms for upregulated genes with CPEB-binding motifs in 10 min timepoint. (H) GO-terms for upregulated genes with CPEB-binding motifs in 60 min timepoint. Supplementary Table 3. Summary of dentate gyri cDNA data per gene. (A) Differential expression and differential adenylation data for 10 min timepoint. (B) Differential expression and differential adenylation data for 60 min timepoint. (C) GO-terms for genes with significantly elongated poly(A) tails in 10 min timepoint. (D) GO-terms for genes with significantly elongated poly(A) tails in 60 min timepoint. (E) GO-terms for upregulated genes in 10 min timepoint. (F) GO-terms for upregulated genes in 60 min timepoint. (G) GO-terms for upregulated genes with CPEB-binding motifs in 10 min timepoint. (H) GO-terms for upregulated genes with CPEB-binding motifs in 60 min timepoint. Supplementary Table 4. High-confidence PASs. (A) PASs predicted for datasets obtained 10 min after LTP induction by TAPAS. (B) High confidence poly(A) clusters predicted by LAPA for datasets obtained 10 min after LTP induction. (C) PASs predicted for datasets obtained 60 min after LTP induction. (D) High confidence poly(A) clusters predicted by LAPA for datasets obtained 60 min after LTP induction. Supplementary Table 5. Nonadenosine profiling upon LTP induction. (A) Summary of Ninetails pipeline for dentate gyrus. (B) List of genes containing semi-templated poly(A) tails with their adjacent nucleotide contexts. Supplementary Table 6. Summary of synaptoneurosomal DRS/cDNA data per gene. (A) Differential expression and differential adenylation data for unfractionated synaptoneurosomes DRS sequencing. (B)  Summary of Ninetails pipeline for unfractionated synaptoneurosomes DRS sequencing. (C) Differential expression and differential adenylation data for monoribosome-bound mRNA synaptoneurosomes cDNA sequencing. (D) Differential expression and differential adenylation data for polyribosome-bound mRNA synaptoneurosomes cDNA sequencing. (E) Differential expression and differential adenylation data for unfractionated synaptoneurosomes cDNA sequencing. Supplementary Information - supplementary figures and captions. ______________________________________________________________________________ <h2>Additional data resources:</h2> CPEB1_motif.meme - CPE1 motif sequence represented as position-dependent letter-probability matrice required by FIMO to make predictions. CPEB2_4_motif.meme - CPE2,4 motif sequence represented as position-dependent letter-probability matrice required by FIMO to make predictions. mRatBN7.2_TAPAS_ref_flat.txt - mRatBN7.2 reference annotation in format required by TAPAS mRatBN7.2_LAPA.gtf - mRatBN7.2 reference annotation in format required by LAPA FIMO_output.zip - compressed folder with motif predictions provided by FIMO software. LAPA_output_dentate_gyrus.zip - compressed folder with poly(A) clusters predicted by LAPA software. Each timepoint is represented by separate output.  TAPAS_output_dentate_gyrus.zip - compressed folder with raw outputs produced by TAPAS software. Each timepoint is represented by separate output.  Ninetails_output_dentate_gyrus.zip - compressed folder with raw outputs produced by Ninetails software for samples from dentate gyrus. Subfolders are named according to the sample identifiers provided in Supplementary Table 1. For each sequencing run, 2 tsv files are produced: read classification and nonadenosine residue classification. Ninetails_output_synaptoneurosomes.zip - compressed folder with raw outputs produced by Ninetails software for samples from synaptoneurosomes. Subfolders are named according to the sample identifiers provided in Supplementary Table 1. For each sequencing run, 2 tsv files are produced: read classification and nonadenosine residue classification. PolyA_clusters_high_confident.bed - High-confidence poly(A) clusters annotation in bed format.

opencc-by-4.0Mar 2022View details →

Monte-Carlo-simulated MR spectra of the rat brain and their quantification results obtained with QUEST and QUEST-MM jMRUI algorithms

MC-simulated spectra of the rat brain along with the corresponding basis set (metabolite signals simulated using NMRScopeB from jMRUI) and the QUEST-MM, QUEST, QUEST(Met+Back) and QUEST(Met+MM) quantification results are stored in the MC_results folder. Results of an in-vivo rat brain MRS signal (SPECIAL, dead time t0 = 0.134 ms, TE = 2.8 ms, at 9.4 T) quantification performed with the QUEST-MM jMRUI algorithm (origin for MC-simulation) are stored in the folder rat_results. All files can be loaded to jMRUI software version 5 and later.

opencc-by-4.0May 2022View details →

Data set of Reversing anterior insular cortex neuronal hypoexcitability attenuates compulsive behavior in juvenile rats

Development of self-regulatory competencies during adolescence is partially dependent on normative brain maturation. Here we report that adolescent rats as compared to adults exhibit impulsive and compulsive-like behavioral traits, the latter being associated with lower expression of mRNA levels of the immediate early gene zif268 in the anterior insula cortex (AIC). This suggests that underdeveloped AIC function in adolescent rats could contribute to an immature pattern of interoceptive cue integration in decision-making and a compulsive phenotype.  In support of this, we report that layer 5 pyramidal neurons in the adolescent rat AIC are hypoexcitable and receive fewer glutamatergic synaptic inputs compared to adults. Chemogenetic activation of the AIC attenuated compulsive traits in adolescent rats supporting the idea that in early stages of AIC maturity there exists a suboptimal integration of sensory and cognitive information that contributes to inflexible behaviors in specific conditions of reward availability.

opencc-by-4.0Jun 2022View details →

Data and code of "Post-trauma behavioral phenotype predicts the degree of vulnerability to fear relapse after extinction in male rats"

This dataset contains behavioral and transcriptomic data, and the original code related to the following article: Post-trauma behavioral phenotype predicts the degree of vulnerability to fear relapse after extinction in male rats. Fanny Demars, Ralitsa Todorova, Gabriel Makdah, Antonin Forestier, Marie-Odile Krebs, Bill P Godsil, Thérèse M Jay, Sidney I Wiener, & Marco N Pompili (2022) Current Biology 32. https://doi.org/10.1016/j.cub.2022.05.050

opencc-zeroDec 2021View details →

Characteristics of the urban sewer system and rat presence in Seattle

Rats are abundant and ubiquitous in urban environments. There has been increasing attention to the need for evidence-based, integrated rat management and surveillance approaches because rats can compromise public health and impose economic costs. Yet there are few studies that characterize rat distributions in sewers and there are no studies that incorporate the complexity of sewer networks that encompass multiple sewer lines, all comprised of their own unique characteristics. To address this knowledge gap, this study identifies sewer characteristics that are associated with rat presence in the city of Seattle's urban sewer system. We obtained sewer baiting data from 1752 geotagged manholes to monitor rat presence and constructed generalized additive models to account for spatial autocorrelation. Sewer rats were unevenly distributed across sampled manholes with clusters of higher rat presence at upper elevations, within sanitary pipes, narrower pipes, pipes at a shallower depth, and older pipes. These findings are important because identifying features of urban sewers that promote rat presence may allow municipalities to target areas for rat control activities and sewer maintenance. These findings suggest the need to evaluate additional characteristics of the surface environment and identify the factors driving rat movement within sewers, across the surface, and between the surface and the sewers.

opencc-by-4.0Sep 2022View details →

Data from: Differential gene expression during recall of behaviorally conditioned immune enhancement in rats: a pilot study

Background: Behaviorally conditioned immune functions are suggested to be regulated by bidirectional interactions between CNS and peripheral immune system via the hypothalamic-pituitary-adrenal (HPA) axis, sympathetic nervous system (SNS), and the parasympathetic nervous system (PNS). Since the current knowledge about biochemical pathways triggering conditioned immune enhancement is limited, the aim of this pilot study was gaining more insights into that. Methods: Rats were conditioned with camphor smell and poly I:C injection, mimicking a viral infection. Following stimulus re-exposure, animals were sacrificed at different time points, and neural tissues along the HPA axis was analyzed with a rat genome array together with plasma protein using Luminex analysis. Results: In the hypothalamus, we observed a strong upregulation of genes related to Wnt/β-catenin signaling (Otx2, Spp1, Fzd6, Zic1), monoaminergic transporter Slc18a2 and opioid-inhibitory G-protein Gpr88 as well as downregulation of dopaminergic receptors, vasoactive intestinal peptide Vip, and pro-melanin-concentrating hormone Pmch. In the pituitary, we recognized mostly upregulation of steroid synthesis in combination with GABAergic, cholinergic and opioid related neurotransmission, in adrenal glands, altered genes showed a pattern of activated metabolism plus upregulation of adrenoceptors Adrb3 and Adra1a. Data obtained from spleen showed a strong upregulation of immunomodulatory genes, chemo-/cytokines and glutamatergic/cholinergic neurotransmission related genes, as also confirmed by increased chemokine and ACTH levels in plasma. Conclusions: Our data indicate that in addition to the classic HPA axis, there could be additional pathways as e.g. the cholinergic anti-inflammatory pathway (CAIP), connecting brain and immune system, modulating and finetuning communication between brain and immune system.

opencc-by-4.0Oct 2022View details →

High-resolution hard X-ray tomography and histology of a rat jaw for stem cell-mediated distraction osteogenesis

Histology and microtomography of a rat jaw after distraction. These datasets appear in "Combining high-resolution hard X-ray tomography and histology for stem cell-mediated distraction osteogenesis" Applied Sciences 12(12) (2022) 6268. Micromography (hdr/img files) has pixel size of 10.0228 µm. Histology (.tif file) has pixel size of 0.243094 µm. Slice to volume registration scripts can be found at https://github.com/grodgers1/SliceToVolume.

opencc-zeroMay 2024View details →

Supplementary data for: Comparison of transcriptomic profiles between HFPO-DA and prototypical PPARa, PPARg, and cytotoxic agents in mouse, rat, and pooled human hepatocytes

Like many per- or polyfluorinated alkyl substances (PFAS), toxicity studies with HFPO-DA (ammonium,2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate), a short-chain PFAS used in the manufacture of some types of fluorinated polymers, indicate that the liver is the primary target of toxicity in rodents following oral exposure. Although the current weight of evidence supports the PPARa mode of action (MOA) for liver effects in HFPO-DA-exposed mice, alternate MOAs have also been hypothesized including PPARg or cytotoxicity. To further evaluate the MOA for HFPO-DA in rodent liver, transcriptomic analyses were conducted on samples from primary mouse, rat and pooled human hepatocytes treated for 12, 24 or 72 hours with various concentrations of HFPO-DA, or agonists of PPARa (GW7647), PPARg (rosiglitazone), or cytotoxic agents (i.e., acetaminophen or d-galactosamine). Concordance analyses of enriched pathways across chemicals within each species demonstrated greatest concordance between HFPO-DA and PPARa agonist GW7647-treated hepatocytes compared to the other chemicals evaluated. These findings were supported by benchmark concentration modeling and predicted upstream regulator results. In addition, transcriptomic analyses across species demonstrated a greater transcriptomic response in rodent hepatocytes treated with HFPO-DA or agonists of PPARa or PPARg, indicating rodent hepatocytes are more sensitive to HFPO-DA or PPARa/g agonist treatment. These results are consistent with previously published transcriptomic analyses and further support that liver effects in HFPO-DA-exposed rodents are mediated through rodent-specific PPARa signaling mechanisms as part of the MOA for PPARa activator-induced rodent hepatocarcinogenesis. Thus, effects observed in mouse liver are not appropriate endpoints for toxicity value development for HFPO-DA in human health risk assessment.

opencc-by-4.0Apr 2024View details →

Correlative microscopy of rat cultured hippocampal pyramidal cell from 40x confocal imaging to super-resolution 93x 3D STED of dendritic spines

This dataset contain multi-scale image of rat hippocampal pyramidal cell related to our paper "From tissues to segmentation: a modular framework for multi-scale neuron isolation" by Cauzzo et al. Nature Comm (2024).

Figure 6 in Oral glutamine dipeptide or oral glutamine free amino acid reduces burned injury progression in rats

Figure 6. Graphical representation of Glutathione (ΜM) in the seven days after injury in G1-Control, G2-Dip, and G3-Free AA. G2-Dip presented a larger amount concerning the G1-Control *(P<0.05).

Figure 4 in Oral glutamine dipeptide or oral glutamine free amino acid reduces burned injury progression in rats

Figure 4. Graphical representation of interspace (stasis) regions length (mm) in the seven days after injury in G1-Control,G2-Dip, and G3-FreeAA.G1-Control presented smaller interspaces in 666 relation to the treated groups G2-Dip (P<0.01) and G3-FreeAA *(P<0.01).

Figure 5 in Oral glutamine dipeptide or oral glutamine free amino acid reduces burned injury progression in rats

Figure 5. Graphical representation of fibroblast counts in three fields of the interspace dermis among in the seven days after injury in G1-Control, G2-Dip, and G3-FreeAA. G1-Control presented less amount of fibroblast concerning the treated groups G2-Dip (P<0.01) and G3-Free AA *(P<0.01).

Figure 3 in Oral glutamine dipeptide or oral glutamine free amino acid reduces burned injury progression in rats

Figure 3. Histopathology study of the necrotic areas: (A) Photomicrograph of G2-Dip animal, with necrosis presence in the dermis (superior arrows) just below the epidermis (E) and in the hypodermis (arrows below in the right). Hair follicle (HF). Masson's trichrome; 100x; (B) Photomicrograph of G1-Control animal, hemorrhagic foci are observed in both dermis and hypodermis (arrows). Central blood vessel (BV). Masson's trichrome; 400x; (C) Photomicrograph of G3-FreeAA animal, with a large area of edema in both dermis and hypodermis (arrows). Hair follicle (HF). Masson's trichrome; 100x; (D) Photomicrograph of G1-Control animal: hemorrhagic focus can be observed in the hypodermis and many neutrophils (minor arrows) in a blood vessel (BV) lumen, some in diapedesis through its wall (larger arrow). The thinner arrows show a small intercellular inflammatory infiltrate. Giemsa; 400x.