Mural Cell Associated VEGF Is Required for Organotypic Vessel Formation

Background: Blood vessels comprise endothelial cells, mural cells (pericytes/vascular smooth muscle cells) and basement membrane. During angiogenesis, mural cells are recruited to sprouting endothelial cells and define a stabilizing context, comprising cell-cell contacts, secreted growth factors and extracellular matrix components, that drives vessel maturation and resistance to anti-angiogenic therapeutics. Methods and Findings: To better understand the basis for mural cell regulation of angiogenesis, we conducted high content imaging analysis on a microtiter plate format in vitro organotypic blood vessel system comprising primary human endothelial cells co-cultured with primary human mural cells. We show that endothelial cells co-cultured with mural cells undergo an extensive series of phenotypic changes reflective of several facets of blood vessel formation and maturation: Loss of cell proliferation, pathfinding-like cell migration, branching morphogenesis, basement membrane extracellular matrix protein deposition, lumen formation, anastamosis and development of a stabilized capillary-like network. This phenotypic sequence required endothelial-mural cell-cell contact, mural cell-derived VEGF and endothelial VEGFR2 signaling. Inhibiting formation of adherens junctions or basement membrane structures abrogated network formation. Notably, inhibition of mural cell VEGF expression could not be rescued by exogenous VEGF. Conclusions: These results suggest a unique role for mural cell-associated VEGF in driving vessel formation and maturation

PDBe-KB: collaboratively defining the biological context of structural data

The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive

Conservation Planning for Ecosystem Services

Despite increasing attention to the human dimension of conservation projects, a rigorous, systematic methodology for planning for ecosystem services has not been developed. This is in part because flows of ecosystem services remain poorly characterized at local-to-regional scales, and their protection has not generally been made a priority. We used a spatially explicit conservation planning framework to explore the trade-offs and opportunities for aligning conservation goals for biodiversity with six ecosystem services (carbon storage, flood control, forage production, outdoor recreation, crop pollination, and water provision) in the Central Coast ecoregion of California, United States. We found weak positive and some weak negative associations between the priority areas for biodiversity conservation and the flows of the six ecosystem services across the ecoregion. Excluding the two agriculture-focused services—crop pollination and forage production—eliminates all negative correlations. We compared the degree to which four contrasting conservation network designs protect biodiversity and the flow of the six services. We found that biodiversity conservation protects substantial collateral flows of services. Targeting ecosystem services directly can meet the multiple ecosystem services and biodiversity goals more efficiently but cannot substitute for targeted biodiversity protection (biodiversity losses of 44% relative to targeting biodiversity alone). Strategically targeting only biodiversity plus the four positively associated services offers much promise (relative biodiversity losses of 7%). Here we present an initial analytical framework for integrating biodiversity and ecosystem services in conservation planning and illustrate its application. We found that although there are important potential trade-offs between conservation for biodiversity and for ecosystem services, a systematic planning framework offers scope for identifying valuable synergies

A Role for the Unfolded Protein Response (UPR) in Virulence and Antifungal Susceptibility in Aspergillus fumigatus

Filamentous fungi rely heavily on the secretory pathway, both for the delivery of cell wall components to the hyphal tip and the production and secretion of extracellular hydrolytic enzymes needed to support growth on polymeric substrates. Increased demand on the secretory system exerts stress on the endoplasmic reticulum (ER), which is countered by the activation of a coordinated stress response pathway termed the unfolded protein response (UPR). To determine the contribution of the UPR to the growth and virulence of the filamentous fungal pathogen Aspergillus fumigatus, we disrupted the hacA gene, encoding the major transcriptional regulator of the UPR. The ΔhacA mutant was unable to activate the UPR in response to ER stress and was hypersensitive to agents that disrupt ER homeostasis or the cell wall. Failure to induce the UPR did not affect radial growth on rich medium at 37°C, but cell wall integrity was disrupted at 45°C, resulting in a dramatic loss in viability. The ΔhacA mutant displayed a reduced capacity for protease secretion and was growth-impaired when challenged to assimilate nutrients from complex substrates. In addition, the ΔhacA mutant exhibited increased susceptibility to current antifungal agents that disrupt the membrane or cell wall and had attenuated virulence in multiple mouse models of invasive aspergillosis. These results demonstrate the importance of ER homeostasis to the growth and virulence of A. fumigatus and suggest that targeting the UPR, either alone or in combination with other antifungal drugs, would be an effective antifungal strategy

PDBe-KB: collaboratively defining the biological context of structural data

The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive

A Market-Based Recommender System

We have designed, implemented, deployed and evaluated a large-scale agent-oriented information system that recommends relevant documents to users. Our recommender system is now being used across several European institutions. Its two key features are a modular design capable of accomodating multiple recommendation methods, and the use of a marketplace to select and rank the best recommendations for the user. As part of our evaluation, we have extensively simulated this marketplace in order to understand its dynamics and validate its suitability for a recommender system

FT011M reduced Iba1-immunolabeled microglia in the retina of Ren-2 rats diabetic for 8 weeks.

<p>Non-diab, non-diabetic. Diab, diabetic. V, vehicle. Three-μm paraffin sections. ILM, inner limiting membrane. GCL, ganglion cell layer. IPL, inner plexiform layer. INL, inner nuclear layer. Counterstain, haematoxylin. Original magnification, 400X. Bar, 40 μm. (A to C) In diab + V, Iba1 immunolabeling (arrowheads) was increased compared to non-diab + V. In diabetic rats, FT011M reduced Iba1 immunolabeling to the level of non-diab + V. (D) **P < 0.01 to non-diab + V. ##P < 0.01 to diab + V. N = 4 to 6 rats per group. Values are Mean ± SEM.</p

FT011M reduced Müller cell gliosis in the retina of Ren-2 rats diabetic for 8 weeks.

<p>Non-diab, non-diabetic. Diab, diabetic. V, vehicle. Three-μm paraffin sections. IPL, inner plexiform layer. INL, inner nuclear layer. OPL, outer plexiform layer. ONL, outer nuclear layer. Original magnification, 400X. Bar, 40 μm. (A to C) Central retina. (D to F) Mid retina. (G to I) Peripheral retina. In non-diab + V, GFAP immunolabeling is present on the retinal surface (asterisk) and in Müller cell processes (arrows) extending throughout the retinal layers and in the central, mid and peripheral retina (A, D, G). GFAP immunolabeling is increased in diab + V (B, E, H). In diabetic rats, FT011M reduced GFAP immunolabeling in the central (G), mid (F) and peripheral (I) retina to the level of non-diab + V. (J to M) *P < 0.01 and ***P < 0.001 to non-diab + V. ##P < 0.01 and ###P < 0.001 to diab + V. N = 4 to 6 rats per group. Values are Mean ± SEM.</p

FT011M reduced acellular capillaries and extracellular matrix proteins in retina from Ren-2 rats diabetic for 32 weeks.

<p>Non-diab, non-diabetic. Diab, diabetic. V, vehicle. Stain, Periodic acid-Schiff’s reagent. Bar, 40 μm. (A to C) In diab + V, acellular capillaries (asterisk) were increased in all regions of retina compared to non-diabetic + V. In diabetic rats, FT011M reduced acellular capillaries in all regions of the retina. Arrow, pericyte ghost. (D to G) *P < 0.05 to non-diab + V. #P < 0.05 to diab + V. N = 8 to 11 rats per group. (H) Collagen IV mRNA levels in retina. (I) Fibronectin mRNA levels in retina. *P < 0.05, **P < 0.01 to non-diab + V. ###P < 0.001 to diab + V. N = 5 to 9 rats per group. Values are Mean±SEM.</p

Animal characteristics.

<p>*P < 0.05 versus control. N = 8 rats per group. Values are mean ± SEM.</p><p>Animal characteristics.</p