Functional characterisation and cell walll interactions of peptidoglycan

Bacteriën worden omringd door een stevige celwand die alleen met speciale enzymen kan worden afgebroken: de peptidoglycaanhydrolasen. Anton Steen beschrijft in zijn proefschrift de peptidoglycaanhydrolase AcmA van de kaasbacterie Lactococcus lactis. Dit enzym heeft naast een gedeelte dat betrokken is bij de afbraak van de celwand, een deel dat ervoor zorgt dat het enzym stevig aan de celwand gebonden wordt. Met behulp van de microscoop is vastgesteld dat AcmA niet overal aan de celwand bindt, maar alleen aan de uiteinden van de cel, daar waar na de celdeling de dochtercellen van elkaar gesplitst worden. Uit eerder onderzoek was al bekend dat AcmA betrokken is bij deze celsplitsing: een mutant van Lactococcus die geen AcmA meer maakt, is niet meer in staat de nieuwe dochtercellen helemaal van elkaar los te maken. Deze mutant groeit daarom in lange ketens van cellen. Als de Lactococcus-cellen worden behandeld met zuur, blijkt dat daarna AcmA overal aan de celwand kan binden. Daarnaast kan het bindingsdomein van AcmA, met behulp van moleculair biologische technieken, worden vastgemaakt aan andere eiwitten. In dit proefschrift wordt bijvoorbeeld een eiwit dat aan de buitenkant van de malariaparasiet zit, vastgemaakt aan het bindingsdeel van AcmA. Daarna wordt dit eiwit gebonden aan met zuur behandelde cellen. Dit heeft dan als gevolg dat de buitenkant van deze Lactococcus-cellen lijkt op de buitenkant van de malariaparasiet. Doordat Lactococcus al eeuwen wordt gebruikt in de voedselindustrie weten we dat deze bacterie veilig gebruikt kan worden. Momenteel wordt daarom ook onderzocht of de Lactococcus met bijvoorbeeld malaria-eiwitten gebruikt kunnen worden als vaccin. Het malaria-eiwit wordt daarvoor eerst door genetisch gemanipuleerde bacteriën geproduceerd, waarna het eiwit wordt gebonden aan niet genetisch gemanipuleerde Lactococcus-cellen

Traffic to the inner membrane of the nuclear envelope

Past research has yielded valuable insight into the mechanisms that regulate the nuclear transport of soluble molecules like transcription factors and mRNA. Much less is known about the mechanisms responsible for the transportation of membrane proteins to the inner membrane of the nuclear envelope. The key question is: does the facilitated transport of integral inner membrane proteins exist in the same way as it does for soluble proteins and, if so, what is it used for? Herein, we provide an overview of the current knowledge on traffic to the inner nuclear membrane, and make a case that: (a) known sorting signals and molecular mechanisms in membrane protein biogenesis, membrane protein traffic and nuclear transport are also relevant with respect to INM traffic; and (b) the interplay of the effects of these signals and molecular mechanisms is what determines the rates of traffic to the INM

Measuring and Interpreting Nuclear Transport in Neurodegenerative Disease-The Example of C9orf72 ALS

Transport from and into the nucleus is essential to all eukaryotic life and occurs through the nuclear pore complex (NPC). There are a multitude of data supporting a role for nuclear transport in neurodegenerative diseases, but actual transport assays in disease models have provided diverse outcomes. In this review, we summarize how nuclear transport works, which transport assays are available, and what matters complicate the interpretation of their results. Taking a specific type of ALS caused by mutations in C9orf72 as an example, we illustrate these complications, and discuss how the current data do not firmly answer whether the kinetics of nucleocytoplasmic transport are altered. Answering this open question has far-reaching implications, because a positive answer would imply that widespread mislocalization of proteins occurs, far beyond the reported mislocalization of transport reporters, and specific proteins such as FUS, or TDP43, and thus presents a challenge for future research

Decoupling Strain and Ligand Effects in Ternary Nanoparticles for Improved ORR Electrocatalysis

Ternary Pt–Au–M (M = 3d transition metal) nanoparticles show reduced OH adsorption energies and improved activity for the oxygen reduction reaction (ORR) compared to pure Pt nanoparticles, as obtained by density functional theory.</p

Revealing Cultural Ecosystem Services through Instagram Images: The Potential of Social Media Volunteered Geographic Information for Urban Green Infrastructure Planning and Governance

With the prevalence of smartphones, new ways of engaging citizens and stakeholders in urban planning and governance are emerging. The technologies in smartphones allow citizens to act as sensors of their environment, producing and sharing rich spatial data useful for new types of collaborative governance set-ups. Data derived from Volunteered Geographic Information (VGI) can support accessible, transparent, democratic, inclusive, and locally-based governance situations of interest to planners, citizens, politicians, and scientists. However, there are still uncertainties about how to actually conduct this in practice. This study explores how social media VGI can be used to document spatial tendencies regarding citizens’ uses and perceptions of urban nature with relevance for urban green space governance. Via the hashtag #sharingcph, created by the City of Copenhagen in 2014, VGI data consisting of geo-referenced images were collected from Instagram, categorised according to their content and analysed according to their spatial distribution patterns. The results show specific spatial distributions of the images and main hotspots. Many possibilities and much potential of using VGI for generating, sharing, visualising and communicating knowledge about citizens’ spatial uses and preferences exist, but as a tool to support scientific and democratic interaction, VGI data is challenged by practical, technical and ethical concerns. More research is needed in order to better understand the usefulness and application of this rich data source to governance

Contrast-enhanced micro-CT imaging in murine carotid arteries : a new protocol for computing wall shear stress

Background: Wall shear stress (WSS) is involved in the pathophysiology of atherosclerosis. The correlation between WSS and atherosclerosis can be investigated over time using a WSS-manipulated atherosclerotic mouse model. To determine WSS in vivo, detailed 3D geometry of the vessel network is required. However, a protocol to reconstruct 3D murine vasculature using this animal model is lacking. In this project, we evaluated the adequacy of eXIA 160, a small animal contrast agent, for assessing murine vascular network on micro-CT. Also, a protocol was established for vessel geometry segmentation and WSS analysis. Methods: A tapering cast was placed around the right common carotid artery (RCCA) of ApoE(-/-) mice (n = 8). Contrast-enhanced micro-CT was performed using eXIA 160. An innovative local threshold-based segmentation procedure was implemented to reconstruct 3D geometry of the RCCA. The reconstructed RCCA was compared to the vessel geometry using a global threshold-based segmentation method. Computational fluid dynamics was applied to compute the velocity field and WSS distribution along the RCCA. Results: eXIA 160-enhanced micro-CT allowed clear visualization and assessment of the RCCA in all eight animals. No adverse biological effects were observed from the use of eXIA 160. Segmentation using local threshold values generated more accurate RCCA geometry than the global threshold-based approach. Mouse-specific velocity data and the RCCA geometry generated 3D WSS maps with high resolution, enabling quantitative analysis of WSS. In all animals, we observed low WSS upstream of the cast. Downstream of the cast, asymmetric WSS patterns were revealed with variation in size and location between animals. Conclusions: eXIA 160 provided good contrast to reconstruct 3D vessel geometry and determine WSS patterns in the RCCA of the atherosclerotic mouse model. We established a novel local threshold-based segmentation protocol for RCCA reconstruction and WSS computation. The observed differences between animals indicate the necessity to use mouse-specific data for WSS analysis. For our future work, our protocol makes it possible to study in vivo WSS longitudinally over a growing plaque