Tristan Vincent de Jong

Tristan Vincent de Jong
University of Groningen | RUG · European Research Institute for the Biology of Ageing

Phd

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73
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Publications

Publications (73)
Preprint
Substance use disorder (SUD) is associated with a cluster of cognitive disturbances that engender vulnerability to ongoing drug seeking and relapse. Two of these endophenotypes, risky decision-making and impulsivity, are amplified in individuals with substance use disorder and are augmented by repeated exposure to illicit drugs. Thus, identifying t...
Article
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The WMI and WLI inbred rats were generated from the stress-prone, and not yet fully inbred, Wistar Kyoto (WKY) strain. These were selected using bi-directional selection for immobility in the forced swim test and were then sib-mated for over 38 generations. Despite the low level of genetic diversity among WKY progenitors, the WMI substrain is signi...
Article
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Finding novel biomarkers for human pathologies and predicting clinical outcomes for patients is challenging. This stems from the heterogeneous response of individuals to disease and is reflected in the inter-individual variability of gene expression responses that obscures differential gene expression analysis. Here, we developed an alternative app...
Preprint
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Background The WMI and WLI inbred rat substrains were generated from the stress-prone, and not yet fully inbred, Wistar Kyoto (WKY) strain using bi-directional selection for immobility in the forced swim test followed by over 38 generations of inbreeding. Despite the low level of genetic diversity among WKY progenitors, the WMI substrain is more vu...
Article
Transforming growth factor-β (TGF-β)-induced fibroblast-to-myofibroblast differentiation contributes to remodeling in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis, but whether this impacts the ability of fibroblasts to support lung epithelial repair remains little explored. We pre-treated human lung fibroblasts (primary [...
Article
Transcriptome sequencing is a powerful technique to study molecular changes that underlie the differences in physiological conditions and disease progression. A typical question that is posed in such studies is finding genes with significant changes between sample groups. In this respect expression variability is regarded as a nuisance factor that...
Data
Table 4 GO-term analysis of genes upregulated in livers of old C/EBPβΔuORF mice. Functional annotation of genes upregulated in livers of old C/EBPβΔuORF female mice compared to livers of old wt female mice (FDR < 0.01; 103 from 127 genes; 24 unknown IDs) using the DAVID database (Huang et al., 2009).
Data
Table 2 Tumour spectrum in wt and C/EBPβΔuORF mice. *incl. lymphoid leukaemia **incl. malignant round cell neoplasms ***tumour type could not be unequivocally determined due to inadequate quality of the fixed tumour tissue Absolute numbers of mice with the indicated tumour type of tumours found during necropsy for wt and C/EBPβΔuORF males and femal...
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Table 3 Occurrence of ageing-associated pathologies in wt and C/EBPβΔuORF mice. Mice were part of the ageing cohort and the age at analysis was 20 months for females and 22 months for males. 1 Number of animals showing the pathology (out of the total number of animals analyzed). 2 mean grade of the pathology as calculated from the total number of a...
Data
Table 5 GO-term analysis of genes downregulated in livers of old C/EBPβΔuORF mice. Functional annotation of genes downregulated in livers of old C/EBPβΔuORF female mice compared to livers of old wt female mice (FDR < 0.01; 23 from 25 genes, two unknown IDs) using the DAVID database (Huang et al., 2009).
Data
Table 7 GO-term analysis of genes showing high inter-individual variation between livers of old C/EBPβΔuORF female mice. Functional annotation of genes showing a high inter-individual variation between livers from old wt female mice. Coefficient of variation of transcript levels of the corresponding gene in the livers of C/EBPβΔuORF mice is at leas...
Data
Table 1 Lifespan experiment summary of results. 1 Number of animals in the cohort 2 Median survival of the cohort (days) 3 Increase of the median survival (percent) 4 P-value of the increased survival (log-rank test) 5 Mean lifespan of the cohort (days) 6 Standard error of the mean 7 Number of mice in the cohort in the longest-lived decile of the c...
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Table 6 GO-term analysis of genes showing high inter-individual variation between livers of old wt female mice. Functional annotation of genes showing a high inter-individual variation between livers from old wt female mice. Coefficient of variation of transcript levels of the corresponding gene in the livers of wt mice is at least twice as big as...
Article
Full-text available
ELife digest The risks of major diseases including type II diabetes, cancer and Alzheimer’s are linked to the biological process of ageing. By finding ways to slow ageing, we can help more people to live longer healthier lives while avoiding these illnesses. Placing some animals on a diet that contains only two-thirds as many calories as they would...
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Document S1. Supplemental Experimental Procedures, Figures S1–S6, and Tables S3–S7
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Table S2. List of Downregulated Genes upon Stretch Identified by the RNA-Seq Analysis, Related to Figure 5 The table represents fold change of gene expression, significance (p value and FDR), and gene description.
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Table S1. List of Upregulated Genes upon Stretch Identified by the RNA-Seq Analysis, Related to Figure 5 The table represents fold change of gene expression, significance (p value and FDR), and gene description.
Article
Full-text available
Cardiac hypertrophy accompanies many forms of cardiovascular diseases. The mechanisms behind the development and regulation of cardiac hypertrophy in the human setting are poorly understood, which can be partially attributed to the lack of a human cardiomyocyte-based preclinical test system recapitulating features of diseased myocardium. The object...
Preprint
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Ageing is associated with physical decline and the development of age-related diseases such as metabolic disorders and cancer. Few conditions are known that attenuate the adverse effects of ageing, including calorie restriction (CR) and reduced signalling through the mechanistic target of rapamycin complex 1 (mTORC1) pathway. Synthesis of the metab...
Article
Cellular metabolism is a tightly controlled process in which the cell adapts fluxes through metabolic pathways in response to changes in nutrient supply. Among the transcription factors that regulate gene expression and thereby cause changes in cellular metabolism is the basic leucine-zipper (bZIP) transcription factor CCAAT/enhancer-binding protei...
Article
Introduction COPD is a chronic, progressive, inflammatory disease of the lungs and the third leading cause of death worldwide. The current knowledge of the pathophysiology of COPD is limited and novel insights in underlying disease mechanisms are urgently needed. Since there are clear parallels between ageing and COPD, we investigated genes underly...
Article
Cellular senescence is a state of irreversibly arrested proliferation, often induced by genotoxic stress. Senescent cells participate in a variety of physiological and pathological conditions, including tumor suppression, embryonic development, tissue repair, and organismal aging. The senescence program is variably characterized by several non-excl...
Article
Full-text available
Protein aggregation is associated with age-related neurodegenerative disorders, such as Alzheimer’s and polyglutamine diseases. As a causal relationship between protein aggregation and neurodegeneration remains elusive, understanding the cellular mechanisms regulating protein aggregation will help develop future treatments. To identify such mechani...
Data
Table S3. Analysis of Differential Expression between Q40 and Q40;moag-2/lir-3 Mutants Related to Figures 4 and S4. This table includes raw data showing the changes in transcription between Q40 and Q40;moag-2/lir-3 mutants in Figures 4 and S4.
Data
Related to Figures 1, 4, S4, and S5. This table includes raw data showing the average number of aggregates and p values for the panel(s) in Figures 1, 4, S4, and S5.
Article
Full-text available
Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus Pseudocercospora fijiensis (previously: Mycosphaerella fijiensis), is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase the...
Data
Additional potential pathogenicity-related genes present in the P. fijiensis genome. (DOCX)
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Scaffold sizes, and identification of potential dispensable chromosomes in the genome of Pseudocercospora fijiensis by comparison with the characteristics of those known from Zymoseptoria tritici. (DOCX)
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Comparison of annotated genes in the version 1 and 2 assemblies of the Pseudocercospora fijiensis genome. (DOCX)
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Genotyping strobilurin resistance and mating type in four Costa Rican populations of Pseudocercospora fijiensis. (DOCX)
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Primers used for population genetic diversity and fungicide sensitivity assays in four Pseudocercospora fijiensis populations in Costa Rica. (DOCX)
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The strong positive association between RIP index (where a high index value indicates low RIP) and GC content shows that RIP in P. fijiensis is mostly restricted to repetitive elements rather than genes. (TIF)
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Separation of small size chromosomal bands by electrophoretic karyotyping of five field isolates and the CIRAD139A strain of Pseudocercospora fijiensis. Lane 1, chromosomes from Saccharomyces cerevisiae as high-molecular-weight (HMW) marker; lanes 2 to 6, different field isolates from the Cartagena farm; lane 7, the CIRAD139A strain. Marker sizes a...
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Small secreted proteins in the genome of Pseudocercospora fijiensis compared to those in the genomes of three other Dothideomycetes. (TIF)
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Analysis of polymorphism type [Single-Nucleotide Polymorphisms (SNPs) and insertion/deletion (indels)] and frequency among the 21 largest scaffolds of the sequenced Pseudocercospora fijiensis isolate CIRAD86 and the re-sequenced isolate CIRAD139A. (DOCX)
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Additional information on genome sequencing, assembly and EST support. (DOCX)
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Dot plot showing mesosynteny between the scaffolds of Pseudocercospora fijiensis and Septoria musiva. (TIF)
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Dot plot showing mesosynteny between the scaffolds of Pseudocercospora fijiensis and Zymoseptoria tritici. (TIF)
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Locations of farms in Costa Rica that were sampled to obtain isolates of Pseudocercospora fijiensis for analyses of mating type, fungicide resistance and population genetics. Farms Cartagena, San Pablo and Zent are in a major banana-production area and are sprayed heavily with fungicides; the San Carlos farm is in an area of plantain production (mo...
Data
Summary of G+C contents derived from the melting-curve analyses of DNA extracted from isolates of Pseudocercospora fijiensis, P. eumusae, P. musae and Zymoseptoria tritici. (DOCX)
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Next-generation resequencing information for Pseudocercospora fijiensis isolate CIRAD139A and numbers of Single-Nucleotide Polymorphisms (SNPs) compared with the reference genome of isolate CIRAD86 V2.0. (DOCX)
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Estimates of genetic differentiationa (Jost’s D above the diagonal and the corrected, standardized genetic differentiation G″ST below the diagonal) between pairs of populations of Pseudocercospora fijiensis sampled from four banana plantations in Costa Ricab. (DOCX)
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The RIP index in genes and repeats in AT-rich and–poor regions of the P. fijiensis genome. RIP is mostly absent from the genes but highly prevalent among the repeated elements of the genome. (TIF)
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Dot plot showing mesosynteny between the scaffolds of Septoria musiva and Dothistroma septosporum. (TIF)
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Percent of gene models supported by different kinds of evidence in the initial automated annotation of the genome of Paracercospora fijiensis. (DOCX)
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Automated assignment of the 13,107 genes in the genome of Pseudocercospora fijiensis to broad functional categories. (DOCX)
Article
Full-text available
Background Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accelerated lymphomagenesis, we previously observed whole chromosome copy number changes affecting all lymphoma cells. This suggests th...
Article
Full-text available
p>Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus Pseudocercospora fijiensis (previously: Mycosphaerella fijiensis), is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase th...

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