An Analytical Representation of the 2d Generalized Balanced Power Diagram

Tessellations are an important tool to model the microstructure of cellular and polycrystalline materials. Classical tessellation models include the Voronoi diagram and Laguerre tessellation whose cells are polyhedra. Due to the convexity of their cells, those models may be too restrictive to describe data that includes possibly anisotropic grains with curved boundaries. Several generalizations exist. The cells of the generalized balanced power diagram are induced by elliptic distances leading to more diverse structures. So far, methods for computing the generalized balanced power diagram are restricted to discretized versions in the form of label images. In this work, we derive an analytic representation of the vertices and edges of the generalized balanced power diagram in 2d. Based on that, we propose a novel algorithm to compute the whole diagram

Single cell analysis of Vibrio harveyi uncovers functional heterogeneity in response to quorum sensing signals

Background: Vibrio harveyi and closely related species are important pathogens in aquaculture. A complex quorum sensing cascade involving three autoinducers controls bioluminescence and several genes encoding virulence factors. Single cell analysis of a V. harveyi population has already indicated intercellular heterogeneity in the production of bioluminescence. This study was undertaken to analyze the expression of various autoinducer-dependent genes in individual cells. Results: Here we used reporter strains bearing promoter::gfp fusions to monitor the induction/repression of three autoinducer-regulated genes in wild type conjugates at the single cell level. Two genes involved in pathogenesis - vhp and vscP, which code for an exoprotease and a component of the type III secretion system, respectively, and luxC (the first gene in the lux operon) were chosen for analysis. The lux operon and the exoprotease gene are induced, while vscP is repressed at high cell density. As controls luxS and recA, whose expression is not dependent on autoinducers, were examined. The responses of the promoter:: gfp fusions in individual cells from the same culture ranged from no to high induction. Importantly, simultaneous analysis of two autoinducer induced phenotypes, bioluminescence (light detection) and exoproteolytic activity (fluorescence of a promoter:: gfp fusion), in single cells provided evidence for functional heterogeneity within a V. harveyi population. Conclusions: Autoinducers are not only an indicator for cell density, but play a pivotal role in the coordination of physiological activities within the population

Pluripotent Stem Cell-Based Models: A Peephole into Virus Infections during Early Pregnancy

The rubella virus (RV) was the first virus shown to be teratogenic in humans. The wealth of data on the clinical symptoms associated with congenital rubella syndrome is in stark contrast to an incomplete understanding of the forces leading to the teratogenic alterations in humans. This applies not only to RV, but also to congenital viral infections in general and includes (1) the mode of vertical transmission, even at early gestation, (2) the possible involvement of inflammation as a consequence of an activated innate immune response, and (3) the underlying molecular and cellular alterations. With the progress made in the development of pluripotent stem cell-based models including organoids and embryoids, it is now possible to assess congenital virus infections on a mechanistic level. Moreover, antiviral treatment options can be validated, and newly emerging viruses with a potential impact on human embryonal development, such as that recently reflected by the Zika virus (ZIKV), can be characterized. Here, we discuss human cytomegalovirus (HCMV) and ZIKV in comparison to RV as viruses with well-known congenital pathologies and highlight their analysis on current models for the early phase of human development. This includes the implications of their genetic variability and, as such, virus strain-specific properties for their use as archetype models for congenital virus infections. In this review, we will discuss the use of induced pluripotent stem cells (iPSC) and derived organoid systems for the study of congenital virus infections with a focus on their prominent aetiologies, HCMV, ZIKV, and RV. Their assessment on these models will provide valuable information on how human development is impaired by virus infections; it will also add new insights into the normal progression of human development through the analysis of developmental pathways in the context of virus-induced alterations. These are exciting perspectives for both developmental biology and congenital virology

F‐Tag Induced Acyl Shift in the Photochemical Cyclization of o ‐Alkynylated N ‐Alkyl‐ N ‐acylamides to Indoles

A photochemical cyclization of F-tagged, o-alkynylated N-alkylamides to indoles catalyzed by [Ir(dF(CF$_3$)ppy)$_2$(dtbpy)]PF$_6$ is presented. This straightforward and efficient reaction involves an intramolecular rearrangement due to the presence of an electron withdrawing group in the acyl moiety and is the first example of photochemically induced 1,3-acyl shift in the cyclization towards 3-acylindoles. A four-step reaction sequence including the photoreaction as a key step to the desired indoles has been developed and optimized. The compatibility of differently substituted F-tagged precursors with the photocyclization step was investigated and the robustness of this step towards modifications could be shown. In total, 16 so far unknown derivatives with diverse modifications in positions N1 and C2, bearing a pentadecafluorooctanoyl moiety as F-tag, were synthesized in very good yields and fully characterized

A 4.5 km resolution Arctic Ocean simulation with the global multi-resolution model FESOM1.4

In the framework of developing a global modeling system which can facilitate modeling studies on Arctic Ocean and high- to midlatitude linkage, we evaluate the Arctic Ocean simulated by the multi-resolution Finite Element Sea ice-Ocean Model (FESOM). To explore the value of using high horizontal resolution for Arctic Ocean modeling, we use two global meshes differing in the horizontal resolution only in the Arctic Ocean (24 km vs. 4.5 km). The high resolution significantly improves the model's representation of the Arctic Ocean. The most pronounced improvement is in the Arctic intermediate layer, in terms of both Atlantic Water (AW) mean state and variability. The deepening and thickening bias of the AW layer, a common issue found in coarse-resolution simulations, is significantly alleviated by using higher resolution. The topographic steering of the AW is stronger and the seasonal and interannual temperature variability along the ocean bottom topography is enhanced in the high-resolution simulation. The high resolution also improves the ocean surface circulation, mainly through a better representation of the narrow straits in the Canadian Arctic Archipelago (CAA). The representation of CAA throughflow not only influences the release of water masses through the other gateways but also the circulation pathways inside the Arctic Ocean. However, the mean state and variability of Arctic freshwater content and the variability of freshwater transport through the Arctic gateways appear not to be very sensitive to the increase in resolution employed here. By highlighting the issues that are independent of model resolution, we address that other efforts including the improvement of parameterizations are still required

Linking information and people in a social system for academic conferences

This paper investigates the feasibility of maintaining a social information system to support attendees at an academic conference. The main challenge of this work was to create an infrastructure where users’ social activities, such as bookmarking, tagging, and social linking could be used to enhance user navigation and maximize the users’ ability to locate two important types of information in conference settings: presentations to attend and attendees to meet. We developed Conference Navigator 3, a social conference support system that integrates a conference schedule planner with a social linking service. We examined its potential and functions in the context of a medium-scale academic conference. In this paper, we present the design of the system’s socially enabled features and report the results of a conference-based study. Our study demonstrates the feasibility of social information systems for supporting academic conferences. Despite the low number of potential users and the short timeframe in which conferences took place, the usage of the system was high enough to provide sufficient data for social mechanisms. The study shows that most critical social features were highly appreciated and used, and provides direction for further research

Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE-PCR

<p>Abstract</p> <p>Background</p> <p>Often high-quality MS/MS spectra of tryptic peptides do not match to any database entry because of only partially sequenced genomes and therefore, protein identification requires <it>de novo </it>peptide sequencing. To achieve protein identification of the economically important but still unsequenced plant pathogenic oomycete <it>Plasmopara halstedii</it>, we first evaluated the performance of three different <it>de novo </it>peptide sequencing algorithms applied to a protein digests of standard proteins using a quadrupole TOF (QStar Pulsar i).</p> <p>Results</p> <p>The performance order of the algorithms was PEAKS online > PepNovo > CompNovo. In summary, PEAKS online correctly predicted 45% of measured peptides for a protein test data set.</p> <p>All three <it>de </it>novo peptide sequencing algorithms were used to identify MS/MS spectra of tryptic peptides of an unknown 57 kDa protein of <it>P. halstedii</it>. We found ten <it>de novo </it>sequenced peptides that showed homology to a <it>Phytophthora infestans </it>protein, a closely related organism of <it>P. halstedii</it>. Employing a second complementary approach, verification of peptide prediction and protein identification was performed by creation of degenerate primers for RACE-PCR and led to an ORF of 1,589 bp for a hypothetical phosphoenolpyruvate carboxykinase.</p> <p>Conclusions</p> <p>Our study demonstrated that identification of proteins within minute amounts of sample material improved significantly by combining sensitive LC-MS methods with different <it>de novo </it>peptide sequencing algorithms. In addition, this is the first study that verified protein prediction from MS data by also employing a second complementary approach, in which RACE-PCR led to identification of a novel elicitor protein in <it>P. halstedii</it>.</p