Thyroid in a jar: towards an integrated in vitro testing strategy for thyroid-active compounds

Jomaa, B. (2015). Thyroid in a Jar: Towards an Integrated In Vitro Testing Strategy for Thyroid-Active Compounds. PhD thesis, Wageningen University, the Netherlands Abstract The aim of this thesis was to find in vitro and toxicogenomics-based alternatives to in vivo thyroid hormone disruption tests. In vitro alternatives can help reduce the amount of animal testing required under the European Union regulation for the registration, evaluation, authorization and restriction of chemicals (REACH). Moreover, with the use of human cell lines and human-identical synthetic proteins, interspecies differences can be reduced and in some cases eliminated. This thesis has shed light on the relevance of current in vitro assays for thyroid and pituitary cell proliferation, has led to the development of the TSH screen, a luminol-based thyroid peroxidase inhibition assay and the zebrafish-based general development score (GDS) for the detection of developmental toxicants, including those that act through the thyroid hormone system. Moreover, the microarray assay for real-time coregulator-nuclear receptor interaction (MARCoNI) assay was used to reveal the modulating effects of thyroid-active compounds on TRα and TRβ interactions with a peptide array representing 66 different coregulators. These developments along with an in-depth analysis of the thyroid hormone system and the presentation of the state of the art in thyroid disruption testing have highlighted the progress made and at the same time have underlined the challenges that lay ahead.</p

Parameter Changes from Upscaling of a Local Scale, Process-Based Erosion Model

Soil erosion affects agricultural productivity, the natural environment and infrastructure security. Soil loss and its associated impacts are important environmental problems. Consequently, model-based predictions of erosion are beneficial for a variety of applications. Process-based erosion models are used to forecast sediment transport concentration as it varies temporally and spatially. Of these, the one-dimensional Hairsine-Rose model describes multiple particle size classes, rainfall detachment, flow-driven entrainment and deposition. This model has been evaluated for different experiments, and has been shown to reliably explain experimental data in a consistent manner. It is common on both the hillslope and laboratory scales to apply one-dimensional erosion models even though the overland flow and sediment transport is two-dimensional. One-dimensional parameter determinations, which are based typically on outflow data, implicitly average the two-dimensional flow. Here we compare experimentally and numerically this averaging process for the Hairsine-Rose model. For this purpose, laboratory experiments were performed using different configurations of the 2 m × 6 m EPFL erosion flume. The flume was divided into 4 smaller flumes, with widths of 1 m, 0.5 m, and 2 × 0.25 m, but otherwise identical. A series of experiments was to provide data sets for analysis by the Hairsine-Rose model. After running the experiments, the amount of the eroded sediment in each subplot was assessed by comparing the temporal variation of eroded mass to evaluate the effect of, and sensitivity to, transverse width on erosion dynamics. The surface elevation changes due to erosion were examined to provide further understanding of the erosion data. A high resolution laser scanner provided details of the soil surface in the form of digital terrain maps before and after the experiment. This method presents a promising way for identification of spatial distribution pattern of eroded soil. In addition, we ran simulations using a fully two dimensional implementation of the Hairsine-Rose model for erosive flows with varying topography with spatially dependent flow and erosion input parameters to produce both outflow hydrographs and suspended sediment graphs. The data were integrated transversely and, as for the experimental data, the one-dimensional Hairsine-Rose model was used to fit the integrated data and so provide parameter estimates to compare with the two-dimensional input values

Factors Defining the Functional Oligomeric State of Escherichia coli DegP Protease

Escherichia coli DegP protein is a periplasmic protein that functions both as a protease and as a chaperone. In the absence of substrate, DegP oligomerizes as a hexameric cage but in its presence DegP reorganizes into 12 and 24-mer cages with large chambers that house the substrate for degradation or refolding. Here, we studied the factors that determine the oligomeric state adopted by DegP in the presence of substrate. Using size exclusion chromatography and electron microscopy, we found that the size of the substrate molecule is the main factor conditioning the oligomeric state adopted by the enzyme. Other factors such as temperature, a major regulatory factor of the activity of this enzyme, did not influence the oligomeric state adopted by DegP. In addition, we observed that substrate concentration exerted an effect only when large substrates (full-length proteins) were used. However, small substrate molecules (peptides) always triggered the same oligomeric state regardless of their concentration. These results clarify important aspects of the regulation of the oligomeric state of DegP

Using the raindrop size distribution to quantify the soil detachment rate at the laboratory scale

Rainfall simulators are beneficial tools for studying soil erosion processes and sediment transport for different circumstances and scales. They are useful to better understand soil erosion mechanisms and, therefore, to develop and validate process-based erosion models. Simulators permit experimental replicates for both simple and complex configurations. The 2 m × 6 m EPFL erosion flume is equipped with a hydraulic slope control and a sprinkling system located on oscillating bars 3 m above the surface. It provides a near-uniform spatial rainfall distribution. The intensity of the precipitation can be adjusted by changing the oscillation interval. The flume is filled to a depth of 0.32 m with an agricultural loamy soil. Raindrop detachment is an important process in interrill erosion, the latter varying with the soil properties as well as the raindrop size distribution and drop velocity. Since the soil detachment varies with the kinetic energy of raindrops, an accurate characterization of drop size distribution (DSD, measured, e.g., using a laser disdrometer) can potentially support erosion calculations. Here, a laser disdrometer was used at different rainfall intensities in the EPFL flume to quantify the rainfall event in terms of number of drops, diameter and velocity. At the same time, soil particle motion was measured locally using splash cups. These cups measured the detached material rates into upslope and downslope compartments. In contrast to previously reported splash cup experiments, the cups used in this study were equipped at the top with upside-down funnels, the upper part having the same diameter as the soil sampled at the bottom. This ensured that the soil detached and captured by the device was not re-exposed to rainfall. The experimental data were used to quantify the relationship between the raindrop distribution and the splash-driven sediment transport

Effect of antecedent conditions and fixed rock fragment coverage on soil erosion dynamics through multiple rainfall events

The effect of antecedent conditions and specific rock fragment coverage on precipitation-driven soil erosion dynamics through multiple rainfall events was investigated using a pair of 6-m × 1-m flumes with 2.2% slope. Four sequential experiments – denoted E1, E2, E3 and E4, involved 2-h precipitation (rates of 28, 74, 74 and 28 mm h-1, respectively) and 22 h without rainfall – were conducted. In each experiment, one flume was bare while the other had 40% rock fragment coverage. The soil was hand-cultivated and smoothed before the first event (E1) only, and left untouched subsequently. Sediment yields at the flume exit reached steady-state conditions over time scales that increased with sediment size. Experiments were designed such that both steady and non-steady effluent sediment yields were reached at the conclusion of E1. Results from subsequent experiments showed that short-time soil erosion was dependent on whether steady-state erosion was achieved during the preceding event, although consistent steady-state effluent sediment yields were reached for each sediment size class. Steady-state erosion rates were, however, dependent on the rainfall intensity and its duration. If steady-state sediment yields were reached for a particular size class, that class’s effluent sediment yield peaked rapidly in the next rainfall event. The early peak was followed by a gradual decline to the steady-state condition. On the other hand, for size classes in which steady state was not reached at the end of the rainfall event (i.e., E1), in the following event (E2), the sediment yields for those classes increased gradually to steady state, i.e., the sharp peak was not observed. The effect of rock fragment cover (40%) on the soil surface was also found to be significant in terms of the time to reach steady state, i.e., their presence reduced the time for steady conditions to be attained. Effluent sediment yields for the bare and rock fragment-covered flumes (E1) showed steady conditions were reached for the latter, in contrast to the former. We used the Hairsine-Rose (H-R) model to simulate the experimental data as it explicitly models soil particle size classes. Experiments E1 and E2 involved soil compaction by raindrops, and in this case the model predictions were found to be unsatisfactory. However, compaction was effectively completed by the end of experiment E2, and the model provided reasonable predictions for experiments E3 and E4

Human neutrophil clearance of bacterial pathogens triggers anti-microbial gamma delta T cell responses in early infection

Human blood Vc9/Vd2 T cells, monocytes and neutrophils share a responsiveness toward inflammatory chemokines and are rapidly recruited to sites of infection. Studying their interaction in vitro and relating these findings to in vivo observations in patients may therefore provide crucial insight into inflammatory events. Our present data demonstrate that Vc9/Vd2 T cells provide potent survival signals resulting in neutrophil activation and the release of the neutrophil chemoattractant CXCL8 (IL-8). In turn, Vc9/Vd2 T cells readily respond to neutrophils harboring phagocytosed bacteria, as evidenced by expression of CD69, interferon (IFN)-c and tumor necrosis factor (TNF)-a. This response is dependent on the ability of these bacteria to produce the microbial metabolite (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), requires cell-cell contact of Vc9/Vd2 T cells with accessory monocytes through lymphocyte function-associated antigen-1 (LFA-1), and results in a TNF-a dependent proliferation of Vc9/Vd2 T cells. The antibiotic fosmidomycin, which targets the HMB-PP biosynthesis pathway, not only has a direct antibacterial effect on most HMB-PP producing bacteria but also possesses rapid anti-inflammatory properties by inhibiting cd T cell responses in vitro. Patients with acute peritoneal-dialysis (PD)-associated bacterial peritonitis – characterized by an excessive influx of neutrophils and monocytes into the peritoneal cavity – show a selective activation of local Vc9/Vd2 T cells by HMB-PP producing but not by HMB-PP deficient bacterial pathogens. The cd T celldriven perpetuation of inflammatory responses during acute peritonitis is associated with elevated peritoneal levels of cd T cells and TNF-a and detrimental clinical outcomes in infections caused by HMB-PP positive microorganisms. Taken together, our findings indicate a direct link between invading pathogens, neutrophils, monocytes and microbe-responsive cd T cells in early infection and suggest novel diagnostic and therapeutic approaches.Martin S. Davey, Chan-Yu Lin, Gareth W. Roberts, Sinéad Heuston, Amanda C. Brown, James A. Chess, Mark A. Toleman, Cormac G.M. Gahan, Colin Hill, Tanya Parish, John D. Williams, Simon J. Davies, David W. Johnson, Nicholas Topley, Bernhard Moser and Matthias Eber

One-dimensional Hairsine-Rose Erosion Model: Parameter Consistency in the Presence of Rainfall Splash.

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Sensors in the stream: the high-frequency wave of the present

New scientific understanding is catalysed by novel technologies that enhance measurement precision, resolution or type, and that provide new tools to test and develop theory. Over the last 50 years, technology has transformed the hydrologic sciences by enabling direct measurements of watershed fluxes (evapotranspiration, streamflow) at time scales and spatial extents aligned with variation in physical drivers. High frequency water quality measurements, increasingly obtained by in-situ water quality sensors, are extending that transformation. Widely available sensors for some physical (temperature) and chemical (conductivity, dissolved oxygen) attributes have become integral to aquatic science, and emerging sensors for nutrients, dissolved CO2, turbidity, algal pigments, and dissolved organic matter are now enabling observations of watersheds and streams at timescales commensurate with their fundamental hydrological, energetic, elemental, and biological drivers. Here we synthesize insights from emerging technologies across a suite of applications, and envision future advances, enabled by sensors, in our ability to understand, predict, and restore watershed and stream systems

One-Dimensional Hairsine-Rose Erosion Model: Parameter Consistency for Soil Erosion in the Presence of Rainfall Splash

Process-based erosion modelling has proven to be an efficient tool for description and prediction of soil erosion and sediment transport. The one-dimensional Hairsine-Rose (HR) erosion model, which describes the time variation of suspended sediment concentration of multiple particle sizes, accounts for key soil erosion mechanisms: rainfall detachment, overland-flow entrainment and gravity deposition. In interrill erosion, it is known that raindrop splash is an important mechanism of sediment detachment and therefore of sediment delivery. In addition, studies have shown that the mass transported from a point source by raindrop splash decreases exponentially with radial distance and is controlled by drop characteristics and soil properties. Here we test experimentally and numerically the HR parameter consistency at different transversal widths for soil erosion in the presence of splash. To achieve this, soil erosion experiments were conducted using different configurations of the 2 m × 6 m EPFL erosion flume. The flume was divided into four identical smaller flumes, with different widths of 1 m, 0.5 m, and 2 × 0.25 m. Total sediment concentration and the concentrations for the individual size classes were measured. The experimental results indicate that raindrop splash dominated in the flumes having the larger widths (1 m and 0.5 m). This process generated a short time peak for all individual size classes. However, the effect of raindrop splash was less present in observed sediment concentrations of the collected data from the smaller width flumes (0.25 m). For these flumes, the detached sediment was controlled by the transversal width of the flume. An amount of detached sediment adhered to the barriers instead of being removed in the overland flow. Moreover, the experimental results showed that the boundary conditions affect the concentration of the mid-size and the larger particles. The one-dimensional Hairsine-Rose model was used to fit the integrated data and to provide parameter estimates for each flume. The analytical results agreed with the total sediment concentrations but not the measured sediment concentrations of all individual size classes. The observed sediment concentrations for the individual size classes could be predicted only when the initial sediment concentration was adjusted and a new calculation of the settling velocities was used. This new settling velocity calculation was conducted by taking the effect of raindrop splash on the deposition force of the particles into account