Settling of cohesive sediment: particle-resolved simulations

We develop a physical and computational model for performing fully coupled, particle-resolved Direct Numerical Simulations of cohesive sediment, based on the Immersed Boundary Method. The model distributes the cohesive forces over a thin shell surrounding each particle, thereby allowing for the spatial and temporal resolution of the cohesive forces during particle-particle interactions. The influence of the cohesive forces is captured by a single dimensionless parameter in the form of a cohesion number, which represents the ratio of cohesive and gravitational forces acting on a particle. We test and validate the cohesive force model for binary particle interactions in the Drafting-Kissing-Tumbling (DKT) configuration. The DKT simulations demonstrate that cohesive particle pairs settle in a preferred orientation, with particles of very different sizes preferentially aligning themselves in the vertical direction, so that the smaller particle is drafted in the wake of the larger one. To test this mechanism in a system of higher complexity, we perform large simulations of 1,261 polydisperse settling particles starting from rest. These simulations reproduce several earlier experimental observations by other authors, such as the accelerated settling of sand and silt particles due to particle bonding. The simulations demonstrate that cohesive forces accelerate the overall settling process primarily because smaller grains attach to larger ones and settle in their wakes. For the present cohesion number values, we observe that settling can be accelerated by up to 29%. We propose physically based parametrization of classical hindered settling functions proposed by earlier authors, in order to account for cohesive forces. An investigation of the energy budget shows that the work of the collision forces can substantially modify the relevant energy conversion processes.Comment: 39 page

Histaminylation of glutamine residues is a novel posttranslational modification implicated in G-protein signaling

Posttranslational modifications (PTM) have been shown to be essential for protein function and signaling. Here we report the identification of a novel modification, protein transfer of histamine, and provide evidence for its function in G protein signaling. Histamine, known as neurotransmitter and mediator of the inflammatory response, was found incorporated into mastocytoma proteins. Histaminylation was dependent on transglutaminase II. Mass spectrometry confirmed histamine modification of the small and heterotrimeric G proteins Cdc42, Galphao1 and Galphaq. The modification was specific for glutamine residues in the catalytic core, and triggered their constitutive activation. TGM2-mediated histaminylation is thus a novel PTM that functions in G protein signaling. Protein alphamonoaminylations, thus including histaminylation, serotonylation, dopaminylation and norepinephrinylation, hence emerge as a novel class of regulatory PTMs

Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches.

During embryogenesis, organisms undergo considerable cellular remodelling requiring the combined action of thousands of proteins. In case of the well-studied model Drosophila melanogaster, transcriptomic studies, most notably from the modENCODE project, have described in detail changes in gene expression at the mRNA level across development. Although such data are clearly very useful to understand how the genome is regulated during embryogenesis, it is important to understand how changes in gene expression are reflected at the level of the proteome. In this study, we describe a combination of two quantitative label-free approaches, SWATH and data-dependent acquisition, to monitor changes in protein expression across a timecourse of D. melanogaster embryonic development. We demonstrate that both approaches provide robust and reproducible methods for the analysis of proteome changes. In a preliminary analysis of Drosophila embryogenesis, we identified several pathways, including the heat-shock response, nuclear protein import and energy production that are regulated during embryo development. In some cases changes in protein expression mirrored transcript levels across development, whereas other proteins showed signatures of post-transcriptional regulation. Taken together, our pilot study provides a solid platform for a more detailed exploration of the embryonic proteome.Funding: B.F, D.K and L.G are funded by BBSRC (Ref: BB/L002817/1). MR and JV acknowledge funding by the Wellcome Trust (RG 093735/Z/10/Z) the ERC (Starting grant 260809), M.R. is a Wellcome Trust Research Career Development and Wellcome-Beit Prize fellow.  This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/pmic.20150048

Physics of Cohesive Sediment Flocculation and Transport: State-of-the-Art Experimental and Numerical Techniques

Due to climate change, sea level rise and anthropogenic development, coastal communities have been facing increasing threats from flooding, land loss, and deterioration of water quality, to name just a few. Most of these pressing problems are directly or indirectly associated with the transport of cohesive fine-grained sediments that form porous aggregates of particles, called flocs. Through their complex structures, flocs are vehicles for the transport of organic carbon, nutrients, and contaminants. Most coastal/estuarine models neglect the flocculation process, which poses a considerable limitation of their predictive capability. We describe a set of experimental and numerical tools that represent the state-of-the-art and can, if combined properly, yield answers to many of the aforementioned issues. In particular, we cover floc measurement techniques and strategies for grain-resolving simulations that can be used as an accurate and efficient means to generate highly-resolved data under idealized conditions. These data feed into continuum models in terms of population balance equations to describe the temporal evolution of flocs. The combined approach allows for a comprehensive investigation across the scales of individual particles, turbulence and the bottom boundary layer to gain a better understanding of the fundamental dynamics of flocculation and their impact on fine-grained sediment transport

The atrial and ventricular myocardial proteome of endstage lamin heart disease

Lamins A/C (encoded by LMNA gene) can lead to dilated cardiomyopathy (DCM). This pilot study sought to explore the postgenomic phenotype of end-stage lamin heart disease. Consecutive patients with end-stage lamin heart disease (LMNA-group, n = 7) and ischaemic DCM (ICM-group, n = 7) undergoing heart transplantation were prospectively enrolled. Samples were obtained from left atrium (LA), left ventricle (LV), right atrium (RA), right ventricle (RV) and interventricular septum (IVS), avoiding the infarcted myocardial segments in the ICM-group. Samples were analysed using a discovery 'shotgun' proteomics approach. We found that 990 proteins were differentially abundant between LMNA and ICM samples with the LA being most perturbed (16-fold more than the LV). Abundance of lamin A/C protein was reduced, but lamin B increased in LMNA LA/RA tissue compared to ICM, but not in LV/RV. Carbonic anhydrase 3 (CA3) was over-abundant across all LMNA tissue samples (LA, LV, RA, RV, and IVS) when compared to ICM. Transthyretin was more abundant in the LV/RV of LMNA compared to ICM, while sarcomeric proteins such as titin and cardiac alpha-cardiac myosin heavy chain were generally less abundant in RA/LA of LMNA. Protein expression profiling and enrichment analysis pointed towards sarcopenia, extracellular matrix remodeling, deficient myocardial energetics, redox imbalances, and abnormal calcium handling in LMNA samples. Compared to ICM, end-stage lamin heart disease is a biventricular but especially a biatrial disease appearing to have an abundance of lamin B, CA3 and transthyretin, potentially hinting to compensatory responses

[11C]-DPA-713 and [18F]-DPA-714 as New PET Tracers for TSPO: A Comparison with [11C]-(R)-PK11195 in a Rat Model of Herpes Encephalitis

Background: Activation of microglia cells plays an important role in neurological diseases. Positron emission tomography (PET) with [C-11]-(R)-PK11195 has already been used to visualize activated microglia cells in neurological diseases. However, [C-11]-(R)-PK11195 may not possess the required sensitivity to visualize mild neuroinflammation. In this study, we evaluated the PET tracers [C-11]-DPA-713 and [F-18]-DPA-714 as agents for imaging of activated microglia in a rat model of herpes encephalitis. Materials and Methods: Rats were intranasally inoculated with HSV-1. On day 6 or 7 after inoculation, small animal PET studies were performed to compare [C-11]-(R)-PK11195, [C-11]-DPA-713, and [F-18]-DPA-714. Results: Uptake of [C-11]-DPA-713 in infected brain areas was comparable to that of [C-11]-(R)-PK11195, but [C-11]-DPA-713 showed lower non-specific binding. Non-specific uptake of [F-18]-DPA-714 was lower than that of [C-11]-(R)-PK11195. In the infected brain, total [F-18]-DPA-714 uptake was lower than that of [C-11]-(R)-PK11195, with comparable specific uptake. Conclusions: [C-11]-DPA-713 may be more suitable for visualizing mild inflammation than [C-11]-(R)-PK11195. In addition, the fact that [F-18]-DPA-714 is an agonist PET tracer opens new possibilities to evaluate different aspects of neuroinflammation. Therefore, both tracers warrant further investigation in animal models and in a clinical setting

Intracellular Serotonin Modulates Insulin Secretion from Pancreatic β-Cells by Protein Serotonylation

Non-neuronal, peripheral serotonin deficiency causes diabetes mellitus and identifies an intracellular role for serotonin in the regulation of insulin secretion