8 results on '"Bosch T"'
Search Results
2. Creating a kidney organoid-vasculature interaction model using a novel organ-on-chip system
- Author
-
Bas-Cristóbal Menéndez, Amanda, primary, Du, Z., additional, van den Bosch, T. P. P., additional, Othman, A., additional, Gaio, N., additional, Silvestri, C., additional, Quirós, W., additional, Lin, H., additional, Korevaar, S., additional, Merino, A., additional, Mulder, J., additional, and Hoogduijn, M. J., additional
- Published
- 2022
- Full Text
- View/download PDF
3. Behavioral performance and visual strategies during skill acquisition using a novel tool use motor learning task
- Author
-
Bosch, T. J., Hanna, T., Fercho, K. A., and Baugh, L. A.
- Published
- 2018
- Full Text
- View/download PDF
4. Higher off-target amplicon detection rate in MiSeq v3 compared to v2 reagent kits in the context of 16S-rRNA-sequencing.
- Author
-
Odendaal ML, Groot JA, Hasrat R, Chu MLJN, Franz E, Bogaert D, Bosch T, and de Steenhuijsen Piters WAA
- Subjects
- DNA, Bacterial genetics, Indicators and Reagents, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA methods, DNA genetics, High-Throughput Nucleotide Sequencing methods
- Abstract
One of the most widely used techniques in microbiota research is 16S-rRNA-sequencing. Several laboratory processes have been shown to impact sequencing results, especially in low biomass samples. Low biomass samples are prone to off-target amplification, where instead of bacterial DNA, host DNA is erroneously amplified. Knowledge on the laboratory processes influencing off-target amplification and detection is however scarce. We here expand on previous findings by demonstrating that off-target amplification is not limited to invasive biopsy samples, but is also an issue in low bacterial biomass respiratory (mucosal) samples, especially when below 0.3 pg/μL. We show that off-target amplification can partly be mitigated by using gel-based library purification methods. Importantly, we report a higher off-target amplicon detection rate when using MiSeq reagent kit v3 compared to v2 (mean 13.3% vs 0.1% off-target reads/sample, respectively), possibly as a result of differences in reagents or sequencing recipes. However, since after bioinformatic removal of off-target reads, MiSeq reagent kit v3 still results in a twofold higher number of reads when compared to v2, v3 is still preferred over v2. Together, these results add to the growing knowledge base on off-target amplification and detection, allowing researchers to anticipate this problem in 16S-rRNA-based microbiome studies involving low biomass samples., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
5. Associations and recovery dynamics of the nasopharyngeal microbiota during influenza-like illness in the aging population.
- Author
-
Shetty SA, van Beek J, Bijvank E, Groot J, Kuiling S, Bosch T, van Baarle D, and Fuentes S
- Subjects
- Age Factors, Aged, Bacterial Load, Dysbiosis, Female, Humans, Influenza, Human diagnosis, Male, Middle Aged, Phylogeny, Population Dynamics, Time Factors, Viral Load, Aging, Influenza, Human microbiology, Influenza, Human virology, Microbiota, Nasopharynx microbiology, Nasopharynx virology
- Abstract
Influenza-like illness (ILI), a disease caused by respiratory pathogens including influenza virus, is a major health concern in older adults. There is little information on changes and recovery dynamics of the nasopharyngeal (NP) microbiota of older adults associated with an ILI. Here, we compared the NP microbiota in older adults reporting (n = 240) or not (n = 157) ILI during the 2014-2015 influenza season at different times of the ILI event. A small but significant effect of the ILI was observed on the microbiota community composition and structure when compared to controls and samples collected at recovery. Corynebacterium was negatively associated with ILI and its abundance increased after recovery. Potential pathobionts such as Haemophilus, Porphyromonas and Gemella had higher abundances during acute-ILI. Stability and changes in the NP microbial community showed individual dynamics. Key core genera, Corynebacterium, Moraxella and Dolosigranulum exhibited higher inter-individual variability in acute-ILI, but showed comparable variability to controls after recovery. Participants in the ILI group with higher core microbiota abundances at the acute phase showed higher microbiota stability after recovery. Our findings demonstrate that acute-ILI is associated with alterations in the phylogenetic structure of the NP microbiota in older adults. The variation in the core microbiota suggests imbalances in the ecosystem, which could potentially play a role in the susceptibility and recovery of the NP microbiota after an ILI event., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
6. Detection of Neisseria meningitidis in saliva and oropharyngeal samples from college students.
- Author
-
Miellet WR, Mariman R, Pluister G, de Jong LJ, Grift I, Wijkstra S, van Logchem EM, van Veldhuizen J, Immink MM, Wijmenga-Monsuur AJ, Rots NY, Sanders EAM, Bosch T, and Trzciński K
- Subjects
- Adolescent, Adult, Carrier State microbiology, Cross-Sectional Studies, Female, Genotype, Humans, Male, Meningococcal Vaccines, Netherlands, Prevalence, Risk Factors, Students, Vaccines, Conjugate, Young Adult, Meningococcal Infections diagnosis, Meningococcal Infections microbiology, Neisseria meningitidis genetics, Neisseria meningitidis, Serogroup B genetics, Oropharynx metabolism, Saliva microbiology
- Abstract
Carriage of Neisseria meningitidis is an accepted endpoint in monitoring meningococcal vaccines effects. We have assessed N. meningitidis and vaccine-type genogroup carriage prevalence in college students at the time of MenACWY vaccine introduction in the Netherlands, and evaluated the feasibility of saliva sampling for the surveillance of carriage. For this, paired saliva and oropharyngeal samples collected from 299 students were cultured for meningococcus. The DNA extracted from all bacterial growth was subjected to qPCRs quantifying meningococcal and genogroup-specific genes presence. Samples negative by culture yet positive for qPCR were cultured again for meningococcus. Altogether 74 (25%) of students were identified as meningococcal carrier by any method. Sixty-one students (20%) were identified as carriers with qPCR. The difference between number of qPCR-positive oropharyngeal (n = 59) and saliva (n = 52) samples was not significant (McNemar's test, p = 0.07). Meningococci were cultured from 72 students (24%), with a significantly higher (p < 0.001) number of oropharyngeal (n = 70) compared with saliva (n = 54) samples. The prevalence of genogroups A, B, C, W, and Y was none, 9%, 1%, 1% and 6%, respectively, and 8% of students carried MenACWY vaccine-type genogroup meningococci. Saliva is easy to collect and when combined with qPCR detection can be considered for meningococcal carriage studies., (© 2021. The Author(s).)
- Published
- 2021
- Full Text
- View/download PDF
7. Benchmarking laboratory processes to characterise low-biomass respiratory microbiota.
- Author
-
Hasrat R, Kool J, de Steenhuijsen Piters WAA, Chu MLJN, Kuiling S, Groot JA, van Logchem EM, Fuentes S, Franz E, Bogaert D, and Bosch T
- Subjects
- Biomass, Humans, Metagenomics methods, Metagenomics standards, Polymerase Chain Reaction methods, Polymerase Chain Reaction standards, RNA, Ribosomal, 16S genetics, Saliva microbiology, Benchmarking methods, Microbiota, Reagent Kits, Diagnostic standards, Respiratory Mucosa microbiology
- Abstract
The low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray-Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies., (© 2021. The Author(s).)
- Published
- 2021
- Full Text
- View/download PDF
8. HDAC1-3 inhibitor MS-275 enhances IL10 expression in RAW264.7 macrophages and reduces cigarette smoke-induced airway inflammation in mice.
- Author
-
Leus NG, van den Bosch T, van der Wouden PE, Krist K, Ourailidou ME, Eleftheriadis N, Kistemaker LE, Bos S, Gjaltema RA, Mekonnen SA, Bischoff R, Gosens R, Haisma HJ, and Dekker FJ
- Subjects
- Animals, Anti-Inflammatory Agents therapeutic use, Benzamides therapeutic use, Cell Line, Histone Deacetylase Inhibitors therapeutic use, Interleukin-10 genetics, Macrophages metabolism, Male, Mice, Mice, Inbred C57BL, NF-kappa B metabolism, Pulmonary Disease, Chronic Obstructive etiology, Pyridines therapeutic use, Anti-Inflammatory Agents pharmacology, Benzamides pharmacology, Histone Deacetylase Inhibitors pharmacology, Interleukin-10 metabolism, Macrophages drug effects, Pulmonary Disease, Chronic Obstructive drug therapy, Pyridines pharmacology, Tobacco Smoke Pollution adverse effects
- Abstract
Chronic obstructive pulmonary disease (COPD) constitutes a major health burden. Studying underlying molecular mechanisms could lead to new therapeutic targets. Macrophages are orchestrators of COPD, by releasing pro-inflammatory cytokines. This process relies on transcription factors such as NF-κB, among others. NF-κB is regulated by lysine acetylation; a post-translational modification installed by histone acetyltransferases and removed by histone deacetylases (HDACs). We hypothesized that small molecule HDAC inhibitors (HDACi) targeting class I HDACs members that can regulate NF-κB could attenuate inflammatory responses in COPD via modulation of the NF-κB signaling output. MS-275 is an isoform-selective inhibitor of HDAC1-3. In precision-cut lung slices and RAW264.7 macrophages, MS-275 upregulated the expression of both pro- and anti-inflammatory genes, implying mixed effects. Interestingly, anti-inflammatory IL10 expression was upregulated in these model systems. In the macrophages, this was associated with increased NF-κB activity, acetylation, nuclear translocation, and binding to the IL10 promoter. Importantly, in an in vivo model of cigarette smoke-exposed C57Bl/6 mice, MS-275 robustly attenuated inflammatory expression of KC and neutrophil influx in the lungs. This study highlights for the first time the potential of isoform-selective HDACi for the treatment of inflammatory lung diseases like COPD.
- Published
- 2017
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.