Phosphatidic acid is required for the constitutive ruffling and macropinocytosis of phagocytes

Macrophages and dendritic cells continuously survey their environment in search of foreign particles and soluble antigens. Such surveillance involves the ongoing extension of actin-rich protrusions and the consequent formation of phagosomes and macropinosomes. The signals inducing this constitutive cytoskeletal remodeling have not been defined. We report that, unlike nonphagocytic cells, macrophages and immature dendritic cells have elevated levels of phosphatidic acid (PA) in their plasma membrane. The plasmalemmal PA is synthesized by phosphorylation of diacylglycerol, which is in turn generated by a G protein–stimulated phospholipase C. Inhibition of diacylglycerol kinase activity results in the detachment of T-cell lymphoma invasion and metastasis–inducing protein 1 (TIAM1)—a Rac guanine exchange factor—from the plasma membrane, thereby depressing Rac activity and abolishing the constitutive ruffling and macropinocytosis that characterize macrophages and immature dendritic cells. Accumulation of PA and binding of TIAM1 to the membrane require the activity of phosphatidylinositol-4,5-bisphosphate 3-kinase. Thus a distinctive, constitutive pathway of PA biosynthesis promotes the actin remodeling required for immune surveillance.     

A method of quantification of stress shielding in the proximal femur using hierarchical computational modeling

Stress shielding is a biomechanical phenomenon causing adaptive changes in bone strength and stiffness around metallic implants, which potentially lead to implant loosening. Accordingly, there is a need for standard, objective engineering measures of the “stress shielding” performances of an implant that can be employed in the process of computer-aided implant design. To provide and test such measures, we developed hierarchical computational models of adaptation of the trabecular microarchitecture at different sites in the proximal femur, in response to insertion of orthopaedic screws and in response to hypothetical reductions in hip joint and gluteal muscle forces. By identifying similar bone adaptation outcomes from the two scenarios, we were able to quantify the stress shielding caused by screws in terms of analogous hypothetical reductions in hip joint and gluteal muscle forces. Specifically, we developed planar lattice models of trabecular microstructures at five regions of interest (ROI) in the proximal femur. The homeostatic and abnormal loading conditions for the lattices were determined from a finite element model of the femur at the continuum scale and fed to an iterative algorithm simulating the adaptation of each lattice to these loads. When screws were inserted to the femur model, maximal simulated bone loss (17% decrease in apparent density, 10% decrease in thickness of trabeculae) was at the greater trochanter and this effect was equivalent to the effect of 50% reduction in gluteal force and normal hip joint force. We conclude that stress shielding performances can be quantified for different screw designs using model-predicted hypothetical musculoskeletal load fractions that would cause a similar pattern and extent of bone loss to that caused by the implants.     

Trends in pollen season characteristics of Alnus,Poaceae and Artemisia allergenic taxa in Bratislava,central Europe

Over the period 2002–2019, air temperature and precipitation significantly increased regionally for Bratislava, which could lead to phenological changes in some plant species. This study aimed to analyse the changes in the intensity, timing, and duration of pollen seasons of three allergological important plant taxa (Alnus, Poaceae, Artemisia) in the study area over 18 years. The pollen sampling was performed using a Hirst-type sampler. Mann–Kendall tau test was used to determine trends in pollen season characteristics, while Spearman’s correlation analysis was used to identify the relationships between the characteristics of pollen seasons and both air temperature and precipitation trends. The notable changes in the pollen-season-related features were observed for all analysed taxa. The Alnus pollen season now reaches the peak earlier and its intensity is rising in line with the summer-autumn temperature increasing trend, while unexpectedly intensity and duration of the Artemisia pollen season are declining in line with the increased precipitation and/or temperature trends. On the other hand, the intensity of the Poaceae pollen season is also declining, however, without statistically significant correlations with recorded increases in meteorological parameters considered. This phenomenon is probably related to both the reduction of the area of grasslands due to urbanization and the implementation of effective maintenance of urban green areas (e.g., timely mowing preventing the repeatedly flowering of grasses).

     

Beyond cells: The extracellular circulating 20S proteasomes

Accumulating evidence arising from numerous clinical studies indicate that assembled and functional 20S proteasome complexes circulate freely in plasma. Elevated levels of this core proteolytic complex have been found in the plasma of patients suffering from blood, skin and solid cancers, autoimmune disorders, trauma and sepsis. Moreover, in various diseases, there is a positive correlation between circulating 20S proteasome (c20S) levels and treatment efficacy and survival rates, suggesting the involvement of this under-studied c20S complex in pathophysiology. However, many aspects of this system remain enigmatic, as we still do not know the origin, biological role or mechanisms of extracellular transport and regulation of c20S proteasomes. In this review, we provide an overview of the current understanding of the c20S proteasome system and discuss the remaining gaps in knowledge.     

Generative probabilistic models for protein-protein interaction networks--the biclique perspective

MOTIVATION: Much of the large-scale molecular data from living cells can be represented in terms of networks. Such networks occupy a central position in cellular systems biology. In the protein-protein interaction (PPI) network, nodes represent proteins and edges represent connections between them, based on experimental evidence. As PPI networks are rich and complex, a mathematical model is sought to capture their properties and shed light on PPI evolution. The mathematical literature contains various generative models of random graphs. It is a major, still largely open question, which of these models (if any) can properly reproduce various biologically interesting networks. Here, we consider this problem where the graph at hand is the PPI network of Saccharomyces cerevisiae. We are trying to distinguishing between a model family which performs a process of copying neighbors, represented by the duplication-divergence (DD) model, and models which do not copy neighbors, with the Barabási-Albert (BA) preferential attachment model as a leading example. RESULTS: The observed property of the network is the distribution of maximal bicliques in the graph. This is a novel criterion to distinguish between models in this area. It is particularly appropriate for this purpose, since it reflects the graph's growth pattern under either model. This test clearly favors the DD model. In particular, for the BA model, the vast majority (92.9%) of the bicliques with both sides ≥4 must be already embedded in the model's seed graph, whereas the corresponding figure for the DD model is only 5.1%. Our results, based on the biclique perspective, conclusively show that a na?ve unmodified DD model can capture a key aspect of PPI networks.     

Ccr5 deficiency regulates the proliferation and trafficking of natural killer cells under physiological conditions

Chemokines were shown to govern the trafficking of immune cells and may also play important roles in the survival and activation of these cells. We report here that under physiological conditions, the bone marrow (BM), spleen, blood and liver of Ccr5, but not of Ccr1-deficient mice, contain reduced numbers of NK cells. NK cells in the BM of Ccr5-deficient mice proliferate to a lesser extent compared to WT mice. Furthermore, spleen NK cells derived from Ccr5-deficient mice that were transplanted into irradiated recipients failed to proliferate in the host. Ccr5, but not Ccr1-deficient NK cells, failed to migrate in vitro in response to RANTES and MIP-1β but not MIP-1β or SDF-1 and had reduced activation, lower expression levels of NK cell markers and a slightly reduced capacity to adhere to target cells and stimulate their killing. Using the polyI:C mouse model for NK trafficking, we found that in the absence of Ccr5, but not Ccr1, NK cells failed to accumulate in the liver. In contrast, using the influenza viral infection as a model to evaluate NK cell proliferation, we found that Ccr5-deficient NK cells in the BM had a higher proliferation rate than WT NK cells. These results suggest a role for Ccr5 in NK cell proliferation and circulation under physiological conditions and a complex role for Ccr5 in determining the fate of NK cells under pathological conditions.     

Proteopedia: a status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules

Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other biomolecule structures. Created as a means for communicating biomolecule structures to a diverse scientific audience, Proteopedia (http://www.proteopedia.org) presents structural annotation in an intuitive, interactive format and allows members of the scientific community to easily contribute their own annotations. Here, we provide a status report on Proteopedia by describing advances in the web resource since its inception three and a half years ago, focusing on features of potential direct use to the scientific community. We discuss its progress as a collaborative 3D-encyclopedia of structures as well as its use as a complement to scientific publications and PowerPoint presentations. We also describe Proteopedia's use for 3D visualization in structure-related pedagogy.     

Generic sorting of raft lipids into secretory vesicles in yeast

Previous work has showed that ergosterol and sphingolipids become sorted to secretory vesicles immunoisolated using a chimeric, artificial raft membrane protein as bait. In this study, we have extended this analysis to three populations of secretory vesicles isolated using natural yeast plasma membrane (PM) proteins: Pma1p, Mid2p and Gap1*p as baits. We compared the lipidomes of the immunoisolated vesicles with each other and with the lipidomes of the donor compartment, the trans-Golgi network, and the acceptor compartment, the PM, using a quantitative mass spectrometry approach that provided a complete lipid overview of the yeast late secretory pathway. We could show that vesicles captured with different baits carry the same cargo and have almost identical lipid compositions; being highly enriched in ergosterol and sphingolipids. This finding indicates that lipid raft sorting is a generic feature of vesicles carrying PM cargo and suggests a common lipid-based mechanism for their formation.