Microcoil MRI of plants and algae at ultra-high field : an exploration of metabolic imaging

This thesis investigates the relations between metabolism and anatomy through the use of Magnetic Resonance Imaging (MRI). Two model systems are studied: Botryococcus braunii, a green oleaginous algae and Medicago truncatula, a small leguminous plant in symbiosis with Sinorhizobium meliloti bacteria. In order to map the variation of metabolic profiles across tissues, MRI is used extensively, including Chemical Shift Imaging, Magnetic Resonance Spectroscopy and Diffusion-Weigthed Imaging. Home-built microcoils for ultra-high magnetic field strength are developed for studying the model organisms. Solid state NMR/Biophysical Organic Chemistr

Toetsontwikkeling op virussen in Zantedeschia

Zantedeschia (=Calla) heeft zich ontwikkeld tot een belangrijk siergewas. Voor de productie van snijbloemen en potplanten is een goede kwaliteit vereist. Virus kan een sterk negatieve invloed hebben op de kwaliteit door o.a. groeimisvorming en kleurbreking op blad en bloem. Een kleine tien jaar geleden is de BKD op verzoek van het vak gestart met een keuring op o.a. zichtbaar virus. Sinds het groeiseizoen van 2003 zijn de virusproblemen ondanks de keuring alleen maar groter geworden. Het beperken van virusverspreiding in Zantedeschia is daarom recent in detail bestudeerd (PT-project 12048). Daarnaast is een goed toetsenpakket belangrijk om virusvrij uitgangsmateriaal te kunnen realiseren. Zonder robuuste toetsen op virussen in Zantedeschia is dit haast onmogelijk te verwezenlijken. Er zijn veel verschillende virussen gevonden in Zanedeschia en dit aantal is de afgelopen jaren verder gestegen. Een aantal virussen in Zanedeschia kan prima via serologische methoden als ELISA worden aangetoond; andere virussen alleen door middel van PCR. Voor sommige virussen in Zantedeschia waren bij de Bloembollenkeuringsdienst (BKD) en Praktijkonderzoek Plant en Omgeving (PPO-BBF) geen goede detectiemethoden aanwezig, of was bekend dat ze slecht met de bestaande toetsmethoden te detecteren zijn. Dit was een onbevredigende situatie, met name voor bedrijven die schoon uitgangsmateriaal willen uitleveren. Daarom heeft dit project als belangrijkste doel de kennis over virussen in Zantedeschia te vergroten en het pakket aan toetsmogelijkheden compleet te maken. De ELISA- en PCR-toetsen zijn binnen dit project gevalideerd met praktijkmateriaal en het protocol voor het toetsen op uitgangsmateriaal is geëvalueerd

The positive prognostic effect of stromal CD8+tumor-infiltrating T cells is restrained by the expression of HLA-E in non-small cell lung carcinoma

Analysis and Stochastic

Acute cigarette smoke exposure leads to higher viral infection in human bronchial epithelial cultures by altering interferon, glycolysis and GDF15-related pathways

Background Acute exacerbations of chronic inflammatory lung diseases, such as chronic obstructive pulmonary disease (COPD), are frequently associated with rhinovirus (RV) infections. Despite these associations, the pathogenesis of virus-induced exacerbations is incompletely understood. We aimed to investigate effects of cigarette smoke (CS), a primary risk factor for COPD, on RV infection in airway epithelium and identify novel mechanisms related to these effects. Methods Primary bronchial epithelial cells (PBEC) from COPD patients and controls were differentiated by culture at the air-liquid interface (ALI) and exposed to CS and RV-A16. Bulk RNA sequencing was performed using samples collected at 6 and 24 h post infection (hpi), and viral load, mediator and l-lactate levels were measured at 6, 24 and 48hpi. To further delineate the effect of CS on RV-A16 infection, we performed growth differentiation factor 15 (GDF15) knockdown, l-lactate and interferon pre-treatment in ALI-PBEC. We performed deconvolution analysis to predict changes in the cell composition of ALI-PBEC after the various exposures. Finally, we compared transcriptional responses of ALI-PBEC to those in nasal epithelium after human RV-A16 challenge. Results CS exposure impaired antiviral responses at 6hpi and increased viral replication at 24 and 48hpi in ALI-PBEC. At 24hpi, CS exposure enhanced expression of RV-A16-induced epithelial interferons, inflammation-related genes and CXCL8. CS exposure increased expression of oxidative stress-related genes, of GDF15, and decreased mitochondrial membrane potential. GDF15 knockdown experiments suggested involvement of this pathway in the CS-induced increase in viral replication. Expression of glycolysis-related genes and l-lactate production were increased by CS exposure, and was demonstrated to contribute to higher viral replication. No major differences were demonstrated between COPD and non-COPD-derived cultures. However, cellular deconvolution analysis predicted higher secretory cells in COPD-derived cultures at baseline. Conclusion Altogether, our findings demonstrate that CS exposure leads to higher viral infection in human bronchial epithelium by altering not only interferon responses, but likely also through a switch to glycolysis, and via GDF15related pathways.Pathogenesis and treatment of chronic pulmonary disease

Cigarette smoke restricts the ability of mesenchymal cells to support lung epithelial organoid formation

Adequate lung epithelial repair relies on supportive interactions within the epithelial niche, including interactions with WNT-responsive fibroblasts. In fibroblasts from patients with chronic obstructive pulmonary disease (COPD) or upon in vitro cigarette smoke exposure, Wnt/β-catenin signalling is distorted, which may affect interactions between epithelial cells and fibroblasts resulting in inadequate lung repair. We hypothesized that cigarette smoke (CS), the main risk factor for COPD, interferes with Wnt/β-catenin signalling in fibroblasts through induction of cellular stress responses, including oxidative- and endoplasmic reticulum (ER) stress, and thereby alters epithelial repair support potential. Therefore, we assessed the effect of CS-exposure and the ER stress inducer Thapsigargin (Tg) on Wnt/β-catenin signalling activation in MRC-5 fibroblasts, and on their ability to support lung epithelial organoid formation. Exposure of MRC-5 cells for 15 min with 5 AU/mL CS extract (CSE), and subsequent 6 h incubation induced oxidative stress (HMOX1). Whereas stimulation with 100 nM Tg increased markers of both the integrated stress response (ISR - GADD34/PPP1R15A, CHOP) and the unfolded protein response (UPR - XBP1spl, GADD34/PPP1R15A, CHOP and HSPA5/BIP), CSE only induced GADD34/PPP1R15A expression. Strikingly, although treatment of MRC-5 cells with the Wnt activator CHIR99021 upregulated the Wnt/β-catenin target gene AXIN2, this response was diminished upon CSE or Tg pre-exposure, which was confirmed using a Wnt-reporter. Furthermore, pre-exposure of MRC-5 cells to CSE or Tg, restricted their ability to support organoid formation upon co-culture with murine pulmonary EpCam+ cells in Matrigel at day 14. This restriction was alleviated by pre-treatment with CHIR99021. We conclude that exposure of MRC-5 cells to CSE increases oxidative stress, GADD34/PPP1R15A expression and impairs their ability to support organoid formation. This inhibitory effect may be restored by activating the Wnt/β-catenin signalling pathway

A glossary for research on human crowd dynamics

This article presents a glossary of terms that are frequently used in research on human crowds. This topic is inherently multidisciplinary as it includes work in and across computer science, engineering, mathematics, physics, psychology and social science, for example. We do not view the glossary presented here as a collection of finalised and formal definitions. Instead, we suggest it is a snapshot of current views and the starting point of an ongoing process that we hope will be useful in providing some guidance on the use of terminology to develop a mutual understanding across disciplines. The glossary was developed collaboratively during a multidisciplinary meeting. We deliberately allow several definitions of terms, to reflect the confluence of disciplines in the field. This also reflects the fact not all contributors necessarily agree with all definitions in this glossary

Toetsontwikkeling op virussen in Zantedeschia

Zantedeschia (=Calla) heeft zich ontwikkeld tot een belangrijk siergewas. Voor de productie van snijbloemen en potplanten is een goede kwaliteit vereist. Virus kan een sterk negatieve invloed hebben op de kwaliteit door o.a. groeimisvorming en kleurbreking op blad en bloem. Een kleine tien jaar geleden is de BKD op verzoek van het vak gestart met een keuring op o.a. zichtbaar virus. Sinds het groeiseizoen van 2003 zijn de virusproblemen ondanks de keuring alleen maar groter geworden. Het beperken van virusverspreiding in Zantedeschia is daarom recent in detail bestudeerd (PT-project 12048). Daarnaast is een goed toetsenpakket belangrijk om virusvrij uitgangsmateriaal te kunnen realiseren. Zonder robuuste toetsen op virussen in Zantedeschia is dit haast onmogelijk te verwezenlijken. Er zijn veel verschillende virussen gevonden in Zanedeschia en dit aantal is de afgelopen jaren verder gestegen. Een aantal virussen in Zanedeschia kan prima via serologische methoden als ELISA worden aangetoond; andere virussen alleen door middel van PCR. Voor sommige virussen in Zantedeschia waren bij de Bloembollenkeuringsdienst (BKD) en Praktijkonderzoek Plant en Omgeving (PPO-BBF) geen goede detectiemethoden aanwezig, of was bekend dat ze slecht met de bestaande toetsmethoden te detecteren zijn. Dit was een onbevredigende situatie, met name voor bedrijven die schoon uitgangsmateriaal willen uitleveren. Daarom heeft dit project als belangrijkste doel de kennis over virussen in Zantedeschia te vergroten en het pakket aan toetsmogelijkheden compleet te maken. De ELISA- en PCR-toetsen zijn binnen dit project gevalideerd met praktijkmateriaal en het protocol voor het toetsen op uitgangsmateriaal is geëvalueerd

Incidence and Relative Prevalence of Distinct Caulimoviruses (Genus Caulimovirus, Family Caulimoviridae) Associated with Dahlia Mosaic in Dahlia variabilis

Dahlia mosaic, caused by Dahlia mosaic virus (DMV), is one of the most important viral diseases of dahlia. Molecular characterization of DMV showed the association of two distinct caulimoviruses (DMV-D10, DMV-Portland) and a D10-like sequence variant (DMV-Holland) with the disease. Using primers specific to these two viruses and the sequence variant, a polymerase chain reaction–based assay was used to determine their relative incidence in several dahlia samples from the United States and the Netherlands. Testing was done on samples collected in 2005 and 2006 in the United States and in 2006 in the Netherlands. Results indicated the predominance of DMV-D10 over DMV-Portland and DMV-Holland in both the United States and the Netherlands. Using conserved regions of the viral genome, primers were designed and used to detect all three sequences. Results suggested that DMV-D10 is predominantly associated with dahlia mosaic, but diagnostics should also include testing for DMV-Portland and DMV-Holland

MRM microcoil performance calibration and usage demonstrated on Medicago truncatula roots at 22 T

Solid state NMR/Biophysical Organic Chemistr