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  • 1
    Language: English
    In: Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 05 November 2016, Vol.371(1707)
    Description: Infection is a complicated balance, with both pathogen and host struggling to tilt the result in their favour. Bacterial infection biology has relied on forward genetics for many of its advances, defining phenotype in terms of replication in model systems. However, many known virulence factors fail to produce robust phenotypes, particularly in the systems most amenable to genetic manipulation, such as cell-culture models. This has particularly been limiting for the study of the bacterial regulatory small RNAs (sRNAs) in infection. We argue that new sequencing-based technologies can work around this problem by providing a 'molecular phenotype', defined in terms of the specific transcriptional dysregulation in the infection system induced by gene deletion. We illustrate this using the example of our recent study of the PinT sRNA using dual RNA-seq, that is, simultaneous RNA sequencing of host and pathogen during infection. We additionally discuss how other high-throughput technologies, in particular genetic interaction mapping using transposon insertion sequencing, may be used to further dissect molecular phenotypes. We propose a strategy for how high-throughput technologies can be integrated in the study of non-coding regulators as well as bacterial virulence factors, enhancing our ability to rapidly generate hypotheses with regards to their function.This article is part of the themed issue 'The new bacteriology'.
    Keywords: Pint ; Tn-Seq ; Dual RNA-Seq ; Host–Pathogen Interaction ; Infection ; Small Non-Coding RNA ; Chromosome Mapping -- Methods ; High-Throughput Nucleotide Sequencing -- Methods ; RNA, Bacterial -- Genetics ; RNA, Small Untranslated -- Genetics ; Sequence Analysis, RNA -- Methods
    ISSN: 09628436
    E-ISSN: 1471-2970
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  • 2
    Language: English
    In: PLoS ONE, 2011, Vol.6(3), p.e17296
    Description: P-bodies are dynamic aggregates of RNA and proteins involved in several post-transcriptional regulation processes. P-bodies have been shown to play important roles in regulating viral infection, whereas their interplay with bacterial pathogens, specifically intracellular bacteria that extensively manipulate host cell pathways, remains unknown. Here, we report that Salmonella infection induces P-body disassembly in a cell type-specific manner, and independently of previously characterized pathways such as inhibition of host cell RNA synthesis or microRNA-mediated gene silencing. We show that the Salmonella -induced P-body disassembly depends on the activation of the SPI-2 encoded type 3 secretion system, and that the secreted effector protein SpvB plays a major role in this process. P-body disruption is also induced by the related pathogen, Shigella flexneri , arguing that this might be a new mechanism by which intracellular bacterial pathogens subvert host cell function.
    Keywords: Research Article ; Biology ; Medicine ; Infectious Diseases ; Microbiology ; Molecular Biology ; Cell Biology
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: Cold Spring Harbor perspectives in medicine, 01 September 2013, Vol.3(9), pp.a010298
    Description: Pathogenic bacteria possess intricate regulatory networks that temporally control the production of virulence factors, and enable the bacteria to survive and proliferate after host infection. Regulatory RNAs are now recognized as important components of these networks, and their study may not only identify new approaches to combat infectious diseases but also reveal new general control mechanisms involved in bacterial gene expression. In this review, we illustrate the diversity of regulatory RNAs in bacterial pathogens, their mechanism of action, and how they can be integrated into the regulatory circuits that govern virulence-factor production.
    Keywords: Bacteria -- Pathogenicity ; RNA, Bacterial -- Physiology ; RNA, Small Untranslated -- Physiology ; Virulence Factors -- Biosynthesis
    E-ISSN: 2157-1422
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  • 4
    Language: English
    In: Journal of neurology, March 2006, Vol.253(3), pp.349-56
    Description: Motor dysfunction is an important clinical finding in patients with liver cirrhosis and mild forms of hepatic encephalopathy. The mechanisms and clinical appearance of motor impairment in patients with liver cirrhosis are not completely understood. We studied fine motor control in forty four patients with advanced liver cirrhosis (excluding those with hepatic encephalopathy grade II) and 48 healthy controls using a kinematic analysis of standardized handwriting tests. We analysed parameters of velocity, the ability to coordinate and the level of automatisation of handwriting movements. Furthermore, we studied the association between impairment of handwriting and clinical neuro-psychiatric symptoms. As compared with control subjects, patients showed a statistically significant reduction of movement peak velocity in all handwriting tasks as well as a substantial increase of number of velocity inversions per stroke. Using a z-score based assessment we found impairment of handwriting in fourteen out of forty four patients (31.8 %). The deterioration of handwriting was associated with clinical symptoms of motor dysfunction, such as bradykinesia, adiadochokinesia, dysmetria of upper extremities and gait ataxia. This is the first study that quantitatively investigates impairment of handwriting in patients with liver cirrhosis. Our findings suggest the application of kinematic analysis of handwriting for diagnostics of motor dysfunction in patients with mild forms of hepatic encephalopathy.
    Keywords: Handwriting ; Liver Cirrhosis -- Complications ; Movement Disorders -- Etiology ; Psychomotor Performance -- Physiology
    ISSN: 0340-5354
    E-ISSN: 14321459
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  • 5
    Language: English
    In: IEEE transactions on medical imaging, June 2009, Vol.28(6), pp.951-67
    Description: Electromagnetic tracking is currently one of the most promising means of localizing flexible endoscopic instruments such as flexible laparoscopic ultrasound transducers. However, electromagnetic tracking is also susceptible to interference from ferromagnetic material, which distorts the magnetic field and leads to tracking errors. This paper presents new methods for real-time online detection and reduction of dynamic electromagnetic tracking errors when localizing a flexible laparoscopic ultrasound transducer. We use a hybrid tracking setup to combine optical tracking of the transducer shaft and electromagnetic tracking of the flexible transducer tip. A novel approach of modeling the poses of the transducer tip in relation to the transducer shaft allows us to reliably detect and significantly reduce electromagnetic tracking errors. For detecting errors of more than 5 mm, we achieved a sensitivity and specificity of 91% and 93%, respectively. Initial 3-D rms error of 6.91 mm were reduced to 3.15 mm.
    Keywords: Electromagnetic Fields ; Laparoscopy -- Methods ; Surgery, Computer-Assisted -- Instrumentation ; Ultrasonography -- Instrumentation
    ISSN: 02780062
    E-ISSN: 1558-254X
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  • 6
    Language: English
    In: Chest, October 2012, Vol.142(4), pp.1020-1026
    Description: BackgroundWe previously identified amplification of the fibroblast growth factor receptor 1 gene (FGFR1) as a potential therapeutic target for small-molecule inhibitor therapy in squamous cell lung cancer (L-SCC). Currently, clinical phase I trials are underway to examine whether patients with FGFR1-amplified L-SCC benefit from a targeted therapy approach using small-molecule inhibitors. Because most patients with lung cancer present with metastatic disease, we investigated whether lymph node metastases in L-SCC share the FGFR1 amplification status of their corresponding primary tumor. MethodsThe study cohort consisted of 72 patients with L-SCC, 39 with regional lymph node metastases. Tissue microarrays were constructed from formalin-fixed, paraffin-embedded tissue of the primary tumors and, where present, of the corresponding lymph node metastasis. A biotin-labeled target probe spanning the FGFR1 locus (8p11.22-23) was used to determine the FGFR1 amplification status by fluorescence in situ hybridization. ResultsFGFR1 amplification was detected in 16% (12 of 72) of all primary L-SCCs. In metastatic tumors, 18% (seven of 39) of the lymph node metastases displayed FGFR1 amplification with an exact correlation of FGFR1 amplification status between tumor and metastatic tissue. ConclusionsFGFR1 amplification is a common genetic event occurring at a frequency of 16% in L-SCCs. Moreover, lymph node metastases derived from FGFR1-amplified L-SCCs also exhibit FGFR1 amplification. Therefore, we suggest that the FGFR1 amplification is a clonal event in tumor progression. Beyond this biologically relevant observation, the findings carry potential therapeutic implications in that small-molecule inhibitors may be applicable to the treatment of a subset of patients with metastatic L-SCC.
    Keywords: Medicine;
    ISSN: 0012-3692
    E-ISSN: 19313543
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  • 7
    Language: English
    In: PLoS ONE, 2012, Vol.7(3), p.e32568
    Description: The blood-brain barrier (BBB) represents an insurmountable obstacle for most drugs thus obstructing an effective treatment of many brain diseases. One solution for overcoming this barrier is a transport by binding of these drugs to surface-modified nanoparticles. Especially apolipoprotein E (ApoE) appears to play a major role in the nanoparticle-mediated drug transport across the BBB. However, at present the underlying mechanism is incompletely understood. ; In this study, the uptake of the ApoE-modified nanoparticles into the brain capillary endothelial cells was investigated to differentiate between active and passive uptake mechanism by flow cytometry and confocal laser scanning microscopy. Furthermore, different co-incubation experiments were performed with competing ligands of the respective receptor. ; This study confirms an active endocytotic uptake mechanism and shows the involvement of low density lipoprotein receptor family members, notably the low density lipoprotein receptor related protein, on the uptake of the ApoE-modified nanoparticles into the brain capillary endothelial cells. This knowledge of the uptake mechanism of ApoE-modified nanoparticles enables future developments to rationally create very specific and effective carriers to overcome the blood-brain barrier.
    Keywords: Research Article ; Biology ; Materials Science ; Medicine ; Biotechnology ; Pharmacology ; Biochemistry
    E-ISSN: 1932-6203
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  • 8
    In: Rheumatology, 2017, Vol. 56(3), pp.451-456
    Description: Objectives. To evaluate the effect of autologous stem cell transplantation (aSCTrans) on antibody (Ab) reactivity towards topo I in patients with SSc, and to see whether it may correlate with clinical outcome after aSCTrans. Methods. Eighteen anti-topo/Scl70–positive patients with SSc in whom non-myeloablative aSCTrans had been performed were analysed. Seven patients showed good response without relapse for several years (group 1), eight primarily responded but later relapsed and three did not respond (group 2). A total of 74 sera were analysed at different time points and tested by ELISA against full length ( fl ) topo I, truncated ( tr ) topo I and a previously identified immunodominant epitope covering amino acid 489–573. Results. Eighty-three percent had IgG Abs to topo fl and topo tr . Ab reactivity significantly decreased after aSCTrans, but remained positive in 10 of the 11 patients followed for up to 24 months. The decrease did not correlate with the clinical outcome after aSCTrans. Fifty-six percent of the patients reacted with topo489–573, and reactivity was nearly confined to group 2. There was no correlation between Ab reactivity towards topo fl or topo489–573 and the modified Rodnan Skin Score before aSCTrans or its decrease after aSCTrans. Conclusions. Although aSCTrans is a good treatment option in patients with progressive SSc, it does not abrogate Ab reactivity towards topo I. The presence of anti-topo489–573 Abs before aSCTrans may indicate a less favourable course after aSCTrans.
    Keywords: Systemic Sclerosis ; Autologous Stem Cell Transplantation ; Anti - Topoisomerase I Antibodies ; Immunodominant Epitope
    ISSN: 1462-0324
    E-ISSN: 1462-0332
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  • 9
    Language: English
    In: The Journal of Urology, April 2012, Vol.187(4), pp.e535-e535
    Keywords: Medicine;
    ISSN: 0022-5347
    E-ISSN: 15273792
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  • 10
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