Rattus norvegicus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1111810 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29063091_1.fastq.gz | Fastqsanger.gz | |||
| SRR29063091_2.fastq.gz | Fastqsanger.gz | |||
| SRR29063092_1.fastq.gz | Fastqsanger.gz | |||
| SRR29063092_2.fastq.gz | Fastqsanger.gz | |||
| SRR29063093_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: To further identify the genes and pathways involved in the necrotic phenotype of NtCBL5A-OE lines, the leaf transcriptome profiling of WT and OE-2 lines grown under control conditions and salt stress (100 mM NaCl) at 4 DAT were sequenced and compared. Methods: Two datasets of differentially expressed genes (DEGs) were made in which we identified the genes that were differentially expressed as a result of the overexpression of NtCBL5A: Control-WT vs Control-OE2 (C-WT/C-OE2), Salt-WT vs Salt-OE2 (S-WT/S-OE2). Another two datasets were also used to identify the transcripts that were responsive to the salt treatments: Control-WT vs Salt-WT (C-WT/S-WT) and Control-OE2 vs Salt-OE2 (C-OE2/S-OE2). DEGs from C-WT/C-OE2 and S-WT/S-OE2 were compared to select the transcripts affected by NtCBL5A overexpression only under salt stress. We also compared DEGs from C-WT/S-WT and C-OE2/S-OE2 to identify the specific transcripts affected by salt stress and only in NtCBL5A-OE lines. This procedure was done for two independent experiments, and only DEGs that were identified in both experiments were considered. Results: The OE-affected DEGs and salt-affected DEGs together resulted in 2079 up-regulated DEGs and 1154 down-regulated DEGs, strongly affected by the combination of NtCBL5A overexpression and salt stress.
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Project description:This SuperSeries is composed of the SubSeries listed below.
2015-01-01 | GSE58692 | GEO
Project description:The Norway rat has important impacts on our life. They are amongst the most used research subjects, resulting in ground-breaking advances. At the same time, wild rats live in close association with us, leading to various adverse interactions. In face of this relevance, it is surprising how little is known about their natural behaviour. While recent laboratory studies revealed their complex social skills, little is known about their social behaviour in the wild. An integration of these different scientific approaches is crucial to understand their social life, which will enable us to design more valid research paradigms, develop more effective management strategies, and to provide better welfare standards. Hence, I first summarise the literature on their natural social behaviour. Second, I provide an overview of recent developments concerning their social cognition. Third, I illustrate why an integration of these areas would be beneficial to optimise our interactions with them.
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Project description:BackgroundMurine kobuviruses (MuKV) are newly recognized picornaviruses first detected in murine rodents in the USA in 2011. Little information on MuKV epidemiology in murine rodents is available. Therefore, we conducted a survey of the prevalence and genomic characteristics of rat kobuvirus in Guangdong, China.ResultsFecal samples from 223 rats (Rattus norvegicus) were collected from Guangdong and kobuviruses were detected in 12.6% (28) of samples. Phylogenetic analysis based on partial 3D and complete VP1 sequence regions showed that rat kobuvirus obtained in this study were genetically closely related to those of rat/mouse kobuvirus reported in other geographical areas. Two near full-length rat kobuvirus genomes (MM33, GZ85) were acquired and phylogenetic analysis of these revealed that they shared very high nucleotide/amino acids identity with one another (95.4%/99.4%) and a sewage-derived sequence (86.9%/93.5% and 87.5%/93.7%, respectively). Comparison with original Aichivirus A strains, such human kobuvirus, revealed amino acid identity values of approximately 80%.ConclusionOur findings indicate that rat kobuvirus have distinctive genetic characteristics from other Aichivirus A viruses. Additionally, rat kobuvirus may spread via sewage.
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Project description:Living organisms are intricate systems with dynamic internal processes. Their RNA, protein, and metabolite levels fluctuate in response to variations in health and environmental conditions. Among these, RNA expression is particularly accessible for comprehensive analysis, thanks to the evolution of high throughput sequencing technologies in recent years. This progress has enabled researchers to identify unique RNA patterns associated with various diseases, as well as to develop predictive and prognostic biomarkers for therapy response. Such cross-sectional studies allow for the identification of differentially expressed genes (DEGs) between groups, but they have limitations. Specifically, they often fail to capture the temporal changes in gene expression following individual perturbations and may lead to significant false discoveries due to inherent noise in RNA sequencing sample preparation and data collection. To address these challenges, our study hypothesized that frequent, longitudinal RNA sequencing (RNAseq) analysis of blood samples could offer a more profound understanding of the temporal dynamics of gene expression in response to drug interventions, while also enhancing the accuracy of identifying genes influenced by these drugs. In this research, we conducted RNAseq on 829 blood samples collected from 84 Sprague-Dawley lab rats. Excluding the control group, each rat was administered one of four different compounds known for liver toxicity: tetracycline, isoniazid, valproate, and carbon tetrachloride. We developed specialized bioinformatics tools to pinpoint genes that exhibit temporal variation in response to these treatments.
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Project description:Inflammation is a key component of pathological angiogenesis. Here we induce cornea neovascularisation using sutures placed into the cornea, and sutures are removed to induce a regression phase. We used whole transcriptome microarray to monitor gene expression profies of several genes
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Project description:Ecological factors, such as predation, have traditionally been used to explain sociability. However, it is increasingly recognised that individuals within a group do not associate randomly, and that these non-random associations can generate fitness advantages. The majority of the empirical evidence on differentiated associations in group-living mammals, however, comes from a limited number of taxa and we still know very little about their occurrence and characteristics in some highly social species, such as rats (Rattus spp.). Here, using network analysis, we quantified association patterns in four groups of male fancy rats. We found that the associations between rats were not randomly distributed and that most individuals had significantly more preferred/avoided associates than expected by random. We also found that these preferences can be stable over time, and that they were not influenced by individuals' rank position in the dominance hierarchy. Our findings are consistent with work in other mammals, but contrast with the limited evidence available for other rat strains. While further studies in groups with different demographic composition are warranted to confirm our findings, the occurrence of differentiated associations in all male groups of rats have important implications for the management and welfare of captive rat populations.
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Project description:Individual differences in behaviors are seen across many species, and investigations have focused on traits linked to aggression, risk taking, emotionality, coping styles, and differences in cognitive systems. The current study investigated whether there were individual differences in proactive interference tasks in rats (Rattus Norvegicus), and tested hypotheses suggesting that these tasks should load onto a single factor and there should be clusters of rats who perform well or poorly on these tasks. The performance of 39 rats was tested across three learning tasks that all involved disengagement from an irrelevant previously learned stimulus to a relevant stimulus: latent inhibition (LI), partial reinforcement extinction effect (PREE), and reversal learning (RL). An exploratory factor analysis revealed the existence of one factor underlying performance. A cluster analysis revealed the existence of sets of rats displaying either weak LI and strong PREE and RL effects, or vice versa. These findings suggest that proactive interference may be based on a single underlying psychological system in rats.
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Project description:Few studies have assessed the patterns of parasite populations of rodents over a longitudinal gradient in Chile. In this work, the gastrointestinal helminthic fauna of invasive rodents in Chile was examined to assess the association between their presence/absence and abundance with latitude, host sex, and host body condition, and to assess the coexistence and correlation of the abundance between parasite species. Rodents were obtained from 20 localities between 33 and 43°S. Helminths were extracted from the gastrointestinal tract and identified morphologically. Overall, 13 helminth taxa were obtained. The most frequently identified parasite species was Heterakis spumosa, and the most abundant was Syphacia muris, while Physaloptera sp. was the most widely distributed. No locality presented with a coexistence that was different from that expected by chance, while the abundance of five helminthic species correlated with the abundance of another in at least one locality, most likely due to co-infection rather than interaction. Host sex was associated with parasite presence or abundance, and female sex-biased parasitism was notably observed in all cases. Body condition and latitude presented either a positive or negative association with the presence or abundance of parasites depending on the species. It is notable that the likely native Physaloptera sp. is widely distributed among invasive rodents. Further, gravid females were found, suggesting spillback of this species to the native fauna. The low frequency and abundance of highly zoonotic hymenolepid species suggest that rodents are of low concern regarding gastrointestinal zoonotic helminths.
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Project description:Gene copy number variation plays a large role in the evolution of genomes. In Rattus norvegicus and other rodent species, the Y-chromosome has accumulated multiple copies of Sry loci. These copy number variations have been previously linked with changes in phenotype of animal models such as the spontaneously hypertensive rat (SHR). This study characterizes the Y-chromosome in the Sry region of Rattus norvegicus, while addressing functional variations seen in the Sry protein products.Eleven Sry loci have been identified in the SHR with one (nonHMG Sry) containing a frame shift mutation. The nonHMGSry is found and conserved in the related WKY and SD rat strains. Three new, previously unidentified, Sry loci were identified in this study (Sry3BII, Sry4 and Sry4A) in both SHR and WKY. Repetitive element analysis revealed numerous LINE-L1 elements at regions where conservation is lost among the Sry copies. In addition we have identified a retrotransposed copy of Med14 originating from spliced mRNA, two autosomal genes (Ccdc110 and HMGB1) and a normal mammalian Y-chromosome gene (Zfy) in the Sry region of the rat Y-chromosome. Translation of the sequences of each Sry gene reveals eight proteins with amino acid differences leading to changes in nuclear localization and promoter activation of a Sry-responsive gene. Sry-? (coded by the Sry2 locus) has an increased cytoplasmic fraction due to alterations at amino acid 21. Sry-? has altered gene regulation of the Sry1 promoter due to changes at amino acid 76.The duplication of Sry on the Rattus norvegicus Y-chromosome has led to proteins with altered functional ability that may have been selected for functions in addition to testis determination. Additionally, several other genes not normally found on the Y-chromosome have duplicated new copies into the region around the Sry genes. These suggest a role of active transposable elements in the evolution of the mammalian Y-chromosome in species such as Rattus norvegicus.
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