Tiny Microbes, Big Data:Gut Microbiota Profiling for Clinical Diagnostics

Savelkoul, P.H.M. [Promotor]Bodegraven, A.A. van [Copromotor]Budding, A.E. [Copromotor

High-Q Gold and Silicon Nitride Bilayer Nanostrings

Low-mass, high-Q, silicon nitride nanostrings are at the cutting edge of nanomechanical devices for sensing applications. Here we show that the addition of a chemically functionalizable gold overlayer does not adversely affect the Q of the fundamental out-of-plane mode. Instead the device retains its mechanical responsiveness while gaining sensitivity to molecular bonding. Furthermore, differences in thermal expansion within the bilayer give rise to internal stresses that can be electrically controlled. In particular, an alternating current excites resonant motion of the nanostring. This AC thermoelastic actuation is simple, robust, and provides an integrated approach to sensor actuation.Comment: 5 pages, 4 figures + supplementary materia

Nanosecond surface interferometry measurements on designed and commercial polymers

The effect of the ablation mechanism on surface morphology changes during an ablation process was studied by comparing three different polymers: a triazene polymer, a polyimide and poly(methylmethacrylate) (PMMA) with nanosecond surface interferometry. The triazene polymer, for which only indications for a photochemical ablation mechanism had been detected in previous studies, revealed no surface swelling, which could be attributed to a thermal ablation mechanism. For polyimide, a photothermal ablation mechanism is usually used to describe the ablation process at irradiation wavelengths ≥248nm. However, the interferometric measurements do not show any surface swelling, which would be a clear indication for a thermal ablation mechanism. A surface swelling was only detected for PMMA with irradiation at 248nm and fluences below the threshold of permanent surface modification. The detected phase shift, which is proportional to the change of the film thickness and the refractive index, can be explained by the opposite signs of the thermal expansion coefficient and the thermal refractive-index coefficien

Enhanced Anandamide Plasma Levels in Patients with Complex Regional Pain Syndrome following Traumatic Injury: A Preliminary Report

The complex regional pain syndrome (CRPS) is a disabling neuropathic pain condition that may develop following injuries of the extremities. The pathogenesis of this syndrome is not clear; however, it includes complex interactions between the nervous and the immune system resulting in chronic inflammation, pain and trophic changes. This interaction may be mediated by chronic stress which is thought to activate the endogenous cannabinoid (endocannabinoid) system (ECS). We conducted an open, prospective, comparative clinical study to determine plasma level of the endocannabinoid anandamide by high-performance liquid chromatography and a tandem mass spectrometry system in 10 patients with CRPS type I versus 10 age- and sex-matched healthy controls. As compared to healthy controls, CRPS patients showed significantly higher plasma concentrations of anandamide. These results indicate that the peripheral ECS is activated in CRPS. Further studies are warranted to evaluate the role of the ECS in the limitation of inflammation and pain. Copyright (C) 2009 S. Karger AG, Base

A study of the interaction of x-rays and acoustic, stress and shock waves in solids

The primary emphasis of this thesis involves an investigation of techniques for the control and modulation of x-ray radiation through acoustic perturbation of solids. The use of x-ray diffraction and x-ray optical techniques for the study of acoustic fields and atomic motion was also investigated. Analysis of the basic properties of x-ray propagation in solids reveals that practical methods for x-ray control or modulation must involve changes in the spatial configuration of x-ray scatterers. Numerical methods for the study of x-ray propagation in acoustically perturbated crystals are formulated. In developing these methods special emphasis has been placed on Borrmann transmission in thick crystals. Modulation and shuttering (on a micro-second timescale) of x-rays are experimentally demonstrated. A quantitative investigation of the basic interactions used to produce modulation and shuttering is presented. Agreement between the experimental observations and the theoretical predictions is within experimental error. An analytical investigation of the basic potential and limitations of x-ray modulation shuttering and control devices is presented. Basic design criteria for x-ray modulation devices is formulated and applied to practical configurations

Phonon quantum nondemolition measurements in nonlinearly coupled optomechanical cavities

In the field of cavity optomechanics, proposals for quantum nondemolition (QND) measurements of phonon number provide a promising avenue by which one can study the quantum nature of nanoscale mechanical resonators. Here we investigate these QND measurements for an optomechanical system whereby quadratic coupling arises due to shared symmetries between a single optical resonance and a mechanical mode. We establish a relaxed limit on the amount of linear coupling that can exist in this type of system while still allowing for QND measurements of mechanical Fock states. The ability to perform optomechanical QND measurements of this nature would allow one to probe the decoherence of these mesoscopic states, providing an experimental test bed for quantum collapse theories

Genome assembly of the chemosynthetic endosymbiont of the hydrothermal vent snail Alviniconcha adamantis from the Mariana Arc

Chemosynthetic animal-microbe symbioses sustain hydrothermal vent communities in the global deep sea. In the Indo-Pacific Ocean, hydrothermal ecosystems are often dominated by gastropod species of the genus Alviniconcha, which live in association with chemosynthetic Gammaproteobacteria or Campylobacteria. While the symbiont genomes of most extant Alviniconcha species have been sequenced, no genome information is currently available for the gammaproteobacterial endosymbiont of Alviniconcha adamantis—a comparatively shallow living species that is thought to be the ancestor to all other present Alviniconcha lineages. Here, we report the first genome sequence for the symbiont of A. adamantis from the Chamorro Seamount at the Mariana Arc. Our phylogenomic analyses show that the A. adamantis symbiont is most closely related to Chromatiaceae endosymbionts of the hydrothermal vent snails Alviniconcha strummeri and Chrysomallon squamiferum, but represents a distinct bacterial species or possibly genus. Overall, the functional capacity of the A. adamantis symbiont appeared to be similar to other chemosynthetic Gammaproteobacteria, though several flagella and chemotaxis genes were detected, which are absent in other gammaproteobacterial Alviniconcha symbionts. These differences might suggest potential contrasts in symbiont transmission dynamics, host recognition, or nutrient transfer. Furthermore, an abundance of genes for ammonia transport and urea usage could indicate adaptations to the oligotrophic waters of the Mariana region, possibly via recycling of host- and environment-derived nitrogenous waste products. This genome assembly adds to the growing genomic resources for chemosynthetic bacteria from hydrothermal vents and will be valuable for future comparative genomic analyses assessing gene content evolution in relation to environment and symbiotic lifestyles