A finite difference Poisson solver for irregular geometries

The motivation for this work comes from the development of a 3D quasi-geostrophic Contour Advective Semi-Lagrangian model for vortex interaction in the ocean. The existing code is limited to circular cylindrical geometry and uses polar coordinates. We wish to extend the method to more general cross-sections. The crucial aspect is the solution of the Poisson equation that allows the determination of the stream function from the potential vorticity at each time-step, as this is the part of the algorithm that must be performed on a grid: the advection of potential vorticity contours is fully Lagrangian and hence is easily modified for irregular domains. We develop a 2D algorithm for inverting the Poisson equation for the stream function on an arbitrarily shaped domain, in the special case when the boundary is a streamline, as is the case for our problem. However, the method is also valid for non-zero Dirichlet boundary conditions. The approach uses finite differences with the domain embedded in a rectangular Cartesian grid. We show that the algorithm is second-order accurate and provide several numerical examples

Overexpression of HTRA1 Leads to Ultrastructural Changes in the Elastic Layer of Bruch's Membrane via Cleavage of Extracellular Matrix Components

Variants in the chromosomal region 10q26 are strongly associated with an increased risk for age-related macular degeneration (AMD). Two potential AMD genes are located in this region: ARMS2 and HTRA1 (high-temperature requirement A1). Previous studies have suggested that polymorphisms in the promotor region of HTRA1 result in overexpression of HTRA1 protein. This study investigated the role of HTRA1 overexpression in the pathogenesis of AMD. Transgenic Htra1 mice overexpressing the murine protein in the retinal pigment epithelium (RPE) layer of the retina were generated and characterized by transmission electron microscopy, immunofluorescence staining and Western Blot analysis. The elastic layer of Bruch's membrane (BM) in the Htra1 transgenic mice was fragmented and less continuous than in wild type (WT) controls. Recombinant HTRA1 lacking the N-terminal domain cleaved various extracellular matrix (ECM) proteins. Subsequent Western Blot analysis revealed an overexpression of fibronectin fragments and a reduction of fibulin 5 and tropoelastin in the RPE/choroid layer in transgenic mice compared to WT. Fibulin 5 is essential for elastogenesis by promoting elastic fiber assembly and maturation. Taken together, our data implicate that HTRA1 overexpression leads to an altered elastogenesis in BM through fibulin 5 cleavage. It highlights the importance of ECM related proteins in the development of AMD and links HTRA1 to other AMD risk genes such as fibulin 5, fibulin 6, ARMS2 and TIMP3

Advancing river monitoring using image-based techniques: Challenges and opportunities

Enhanced and effective hydrological monitoring plays a crucial role in understanding water-related processes in a rapidly changing world. Within this context, image-based river monitoring has shown to significantly enhance data collection, improve analysis and accuracy, and support effective and timely decision-making. The integration of remote and proximal sensing technologies, with citizen science, and artificial intelligence may revolutionize monitoring practices. Therefore, it is crucial to quantify the quality of current research and ongoing initiatives to envision the potential trajectories for research activities within this specific field. The evolution of monitoring strategies is progressing in multiple directions that should converge to build critical mass around relevant challenges to meet the need for innovative solutions to overcome limitations of traditional approaches. The present study reviews showcases and good practices of enhanced hydrological monitoring in different applications, reflecting the strengths and limitations of new approaches

Compact Polyelectrolyte Complexes: “Saloplastic” Candidates for Biomaterials

Precipitates of polyelectrolyte complexes were transformed into rugged shapes suitable for bioimplants by ultracentrifugation in the presence of high salt concentration. Salt ions dope the complex, creating a softer material with viscous fluid-like properties. Complexes that were compacted under the centrifugal field (CoPECs) were made from poly(diallyldimethyl ammonium), PDADMA, as polycation, and poly(styrene sulfonate), PSS, or poly(methacrylic acid), PMAA, as polyanion. Dynamic mechanical testing revealed a rubbery plateau at lower frequencies for PSS/PDADMA with moduli that decreased with increasing salt concentration, as internal ion pair cross-links were broken. CoPECs had significantly lower modulii compared to similar polyelectrolyte complexes prepared by the “multilayering ” method. The difference in mechanical properties was ascribed to higher water content (located in micropores) for the former and, more importantly, to their nonstoichiometric polymer composition. The modulus of PMAA/PDADMA CoPECs, under physiological conditions, demonstrated dynamic mechanical properties that were close to those of the nucleus pulposus in an intervertebral disk

A Systematic Screen to Discover and Analyze Apicoplast Proteins Identifies a Conserved and Essential Protein Import Factor

Parasites of the phylum Apicomplexa cause diseases that impact global health and economy. These unicellular eukaryotes possess a relict plastid, the apicoplast, which is an essential organelle and a validated drug target. However, much of its biology remains poorly understood, in particular its elaborate compartmentalization: four membranes defining four different spaces. Only a small number of organellar proteins have been identified in particular few proteins are known for non-luminal apicoplast compartments. We hypothesized that enlarging the catalogue of apicoplast proteins will contribute toward identifying new organellar functions and expand the realm of targets beyond a limited set of characterized pathways. We developed a bioinformatic screen based on mRNA abundance over the cell cycle and on phyletic distribution. We experimentally assessed 57 genes, and of 30 successful epitope tagged candidates eleven novel apicoplast proteins were identified. Of those, seven appear to target to the lumen of the organelle, and four localize to peripheral compartments. To address their function we then developed a robust system for the construction of conditional mutants via a promoter replacement strategy. We confirm the feasibility of this system by establishing conditional mutants for two selected genes – a luminal and a peripheral apicoplast protein. The latter is particularly intriguing as it encodes a hypothetical protein that is conserved in and unique to Apicomplexan parasites and other related organisms that maintain a red algal endosymbiont. Our studies suggest that this peripheral plastid protein, PPP1, is likely localized to the periplastid compartment. Conditional disruption of PPP1 demonstrated that it is essential for parasite survival. Phenotypic analysis of this mutant is consistent with a role of the PPP1 protein in apicoplast biogenesis, specifically in import of nuclear-encoded proteins into the organelle

The apicomplexan plastid and its evolution

Protistan species belonging to the phylum Apicomplexa have a non-photosynthetic secondary plastid—the apicoplast. Although its tiny genome and even the entire nuclear genome has been sequenced for several organisms bearing the organelle, the reason for its existence remains largely obscure. Some of the functions of the apicoplast, including housekeeping ones, are significantly different from those of other plastids, possibly due to the organelle’s unique symbiotic origin

Thousands of Rab GTPases for the Cell Biologist

Rab proteins are small GTPases that act as essential regulators of vesicular trafficking. 44 subfamilies are known in humans, performing specific sets of functions at distinct subcellular localisations and tissues. Rab function is conserved even amongst distant orthologs. Hence, the annotation of Rabs yields functional predictions about the cell biology of trafficking. So far, annotating Rabs has been a laborious manual task not feasible for current and future genomic output of deep sequencing technologies. We developed, validated and benchmarked the Rabifier, an automated bioinformatic pipeline for the identification and classification of Rabs, which achieves up to 90% classification accuracy. We cataloged roughly 8.000 Rabs from 247 genomes covering the entire eukaryotic tree. The full Rab database and a web tool implementing the pipeline are publicly available at www.RabDB.org. For the first time, we describe and analyse the evolution of Rabs in a dataset covering the whole eukaryotic phylogeny. We found a highly dynamic family undergoing frequent taxon-specific expansions and losses. We dated the origin of human subfamilies using phylogenetic profiling, which enlarged the Rab repertoire of the Last Eukaryotic Common Ancestor with Rab14, 32 and RabL4. Furthermore, a detailed analysis of the Choanoflagellate Monosiga brevicollis Rab family pinpointed the changes that accompanied the emergence of Metazoan multicellularity, mainly an important expansion and specialisation of the secretory pathway. Lastly, we experimentally establish tissue specificity in expression of mouse Rabs and show that neo-functionalisation best explains the emergence of new human Rab subfamilies. With the Rabifier and RabDB, we provide tools that easily allows non-bioinformaticians to integrate thousands of Rabs in their analyses. RabDB is designed to enable the cell biology community to keep pace with the increasing number of fully-sequenced genomes and change the scale at which we perform comparative analysis in cell biology