Imaging regulatory T cell dynamics and CTLA4-mediated suppression of T cell priming

Foxp3(+) regulatory T cells (Tregs) maintain immune homoeostasis through mechanisms that remain incompletely defined. Here by two-photon (2P) imaging, we examine the cellular dynamics of endogenous Tregs. Tregs are identified as two non-overlapping populations in the T-zone and follicular regions of the lymph node (LN). In the T-zone, Tregs migrate more rapidly than conventional T cells (Tconv), extend longer processes and interact with resident dendritic cells (DC) and Tconv. Tregs intercept immigrant DCs and interact with antigen-induced DC: Tconv clusters, while continuing to form contacts with activated Tconv. During antigen-specific responses, blocking CTLA4-B7 interactions reduces Treg-Tconv interaction times, increases the volume of DC: Tconv clusters and enhances subsequent Tconv proliferation in vivo. Our results demonstrate a role for altered cellular choreography of Tregs through CTLA4-based interactions to limit T-cell priming

Calcium release through P2X4 activates calmodulin to promote endolysosomal membrane fusion

Intra-endolysosomal Ca(2+) release is required for endolysosomal membrane fusion with intracellular organelles. However, the molecular mechanisms for intra-endolysosomal Ca(2+) release and the downstream Ca(2+) targets involved in the fusion remain elusive. Previously, we demonstrated that endolysosomal P2X4 forms channels activated by luminal adenosine triphosphate in a pH-dependent manner. In this paper, we show that overexpression of P2X4, as well as increasing endolysosomal P2X4 activity by alkalinization of endolysosome lumen, promoted vacuole enlargement in cells and endolysosome fusion in a cell-free assay. These effects were prevented by inhibiting P2X4, expressing a dominant-negative P2X4 mutant, and disrupting the P2X4 gene. We further show that P2X4 and calmodulin (CaM) form a complex at endolysosomal membrane where P2X4 activation recruits CaM to promote fusion and vacuolation in a Ca(2+)-dependent fashion. Moreover, P2X4 activation-triggered fusion and vacuolation were suppressed by inhibiting CaM. Our data thus suggest a new molecular mechanism for endolysosomal membrane fusion involving P2X4-mediated endolysosomal Ca(2+) release and subsequent CaM activation

WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications

<p>Abstract</p> <p>Background</p> <p>In recent years, there has been a huge increase in the amount of publicly-available and proprietary information pertinent to drug discovery. However, there is a distinct lack of data mining tools available to harness this information, and in particular for knowledge discovery across multiple information sources. At Indiana University we have an ongoing project with Eli Lilly to develop web-service based tools for integrative mining of chemical and biological information. In this paper, we report on the first of these tools, called WENDI (Web Engine for Non-obvious Drug Information) that attempts to find non-obvious relationships between a query compound and scholarly publications, biological properties, genes and diseases using multiple information sources.</p> <p>Results</p> <p>We have created an aggregate web service that takes a query compound as input, calls multiple web services for computation and database search, and returns an XML file that aggregates this information. We have also developed a client application that provides an easy-to-use interface to this web service. Both the service and client are publicly available.</p> <p>Conclusions</p> <p>Initial testing indicates this tool is useful in identifying potential biological applications of compounds that are not obvious, and in identifying corroborating and conflicting information from multiple sources. We encourage feedback on the tool to help us refine it further. We are now developing further tools based on this model.</p

Charm and Strange Quark Masses and \u3cem\u3ef\u3csub\u3eD\u3csub\u3es\u3c/sub\u3e\u3c/sub\u3e\u3c/em\u3e from Overlap Fermions

We use overlap fermions as valence quarks to calculate meson masses in a wide quark mass range on the 2 + 1-flavor domain-wall fermion gauge configurations generated by the RBC and UKQCD Collaborations. . . . For the remainder of the abstract, please download this article or visit https://doi.org/10.1103/PhysRevD.92.03451

The clock genes Period 2 and Cryptochrome 2 differentially balance bone formation

Background: Clock genes and their protein products regulate circadian rhythms in mammals but have also been implicated in various physiological processes, including bone formation. Osteoblasts build new mineralized bone whereas osteoclasts degrade it thereby balancing bone formation. To evaluate the contribution of clock components in this process, we investigated mice mutant in clock genes for a bone volume phenotype. Methodology/Principal Findings: We found that Per2Brdm1 mutant mice as well as mice lacking Cry2-/- displayed significantly increased bone volume at 12 weeks of age, when bone turnover is high. Per2Brdm1 mutant mice showed alterations in parameters specific for osteoblasts whereas mice lacking Cry2-/- displayed changes in osteoclast specific parameters. Interestingly, inactivation of both Per2 and Cry2 genes leads to normal bone volume as observed in wild type animals. Importantly, osteoclast parameters affected due to the lack of Cry2, remained at the level seen in the Cry2-/- mutants despite the simultaneous inactivation of Per2. Conclusions/Significance: This indicates that Cry2 and Per2 affect distinct pathways in the regulation of bone volume with Cry2 influencing mostly the osteoclastic cellular component of bone and Per2 acting on osteoblast parameters

P2X4 forms functional ATP-activated cation channels on lysosomal membranes regulated by luminal pH.

P2X receptors are commonly known as plasma membrane cation channels involved in a wide variety of cell functions. The properties of these channels have been extensively studied on the plasma membrane. However, studies in amoeba suggest that P2X receptors are also present intracellularly and involved in vesicle fusion with the plasma membrane. Recently, it was shown that in addition to plasma membrane expression, mammalian P2X4 was also localized intracellularly in lysosomes. However, it was not clear whether the lysosomal P2X4 receptors function as channels and how they are activated and regulated. In this paper, we show that both P2X4 and its natural ligand, ATP, are enriched in lysosomes of COS1 and HEK293 cells. By directly recording membrane currents from enlarged lysosomal vacuoles, we demonstrated that lysosomal P2X4 formed channels activated by ATP from the luminal side in a pH-dependent manner. While the acidic pH at the luminal side inhibited P2X4 activity, increasing the luminal pH in the presence of ATP caused P2X4 activation. We further showed that, as for the plasma membrane P2X4, the lysosomal P2X4 was potentiated by ivermectin but insensitive to suramin and PPADS, and it permeated the large cation N-methyl-d-glucamine upon activation. Our data suggest that P2X4 forms functional ATP-activated cation channels on lysosomal membranes regulated by luminal pH. Together with the reported fusion effect of intracellular P2X in lower organisms, we speculate that the lysosome-localized P2X4 may play specific roles in membrane trafficking of acidic organelles in mammalian cells

Effect of anatomic motion on proton therapy dose distributions in prostate cancer treatment

Purpose: To determine the dosimetric impact of interfraction anatomic movements in prostate cancer patients receiving proton therapy. Methods and Materials: For each of the 10 patients studied, 8 computed tomography (CT) scans were selected from sets of daily setup CT images that were acquired from a cohort of prostate cancer patients. The images were acquired in the treatment room using the CT-on-rails system. First, standard proton therapy and intensity-modulated radiation therapy (IMRT) plans were designed for each patient using standard modality-specific methods. The images, the proton plan, and the IMRT plan were then aligned to the eight CT images based on skin marks. The doses were recalculated on these eight CT images using beam from the standard plans. Second, the plans were redesigned and evaluated assuming a smaller clinical target volume to planning target volume margin (3 mm). The images and the corresponding plans were then realigned based on the center of volume of the prostate. Dose distributions were evaluated using isodose displays, dose-volume histograms, and target coverage. Results: For the skin-marker alignment method, 4 of the 10 IMRT plans were deficient, whereas 3 of 10 proton plans were compromised. For the alignment method based on the center of volume of the prostate, only the proton plan for 1 patient was deficient, whereas 3 of the 10 IMRT plans were suboptimal. Conclusion: A comparison of passively scattered proton therapy and highly conformal IMRT plans for prostate cancer revealed that the dosimetric impact of interfractional anatomic motions was similar for both modalities. © 2007 Elsevier Inc. All rights reserved

PPAR? Downregulation by TGF in Fibroblast and Impaired Expression and Function in Systemic Sclerosis: A Novel Mechanism for Progressive Fibrogenesis

The nuclear orphan receptor peroxisome proliferator-activated receptor-gamma (PPAR-γ) is expressed in multiple cell types in addition to adipocytes. Upon its activation by natural ligands such as fatty acids and eicosanoids, or by synthetic agonists such as rosiglitazone, PPAR-γ regulates adipogenesis, glucose uptake and inflammatory responses. Recent studies establish a novel role for PPAR-γ signaling as an endogenous mechanism for regulating transforming growth factor-ß (TGF-ß)- dependent fibrogenesis. Here, we sought to characterize PPAR-γ function in the prototypic fibrosing disorder systemic sclerosis (SSc), and delineate the factors governing PPAR-γ expression. We report that PPAR-γ levels were markedly diminished in skin and lung biopsies from patients with SSc, and in fibroblasts explanted from the lesional skin. In normal fibroblasts, treatment with TGF-ß resulted in a time- and dose-dependent down-regulation of PPAR-γ expression. Inhibition occurred at the transcriptional level and was mediated via canonical Smad signal transduction. Genome-wide expression profiling of SSc skin biopsies revealed a marked attenuation of PPAR-γ levels and transcriptional activity in a subset of patients with diffuse cutaneous SSc, which was correlated with the presence of a ''TGF-ß responsive gene signature'' in these biopsies. Together, these results demonstrate that the expression and function of PPAR-γ are impaired in SSc, and reveal the existence of a reciprocal inhibitory cross-talk between TGF-ß activation and PPAR-γ signaling in the context of fibrogenesis. In light of the potent anti-fibrotic effects attributed to PPAR-γ, these observations lead us to propose that excessive TGF-ß activity in SSc accounts for impaired PPAR-γ function, which in turn contributes to unchecked fibroblast activation and progressive fibrosis. © 2010 Wei et al

Local Chirality of Low-Lying Dirac Eigenmodes and the Instanton Liquid Model

The reasons for using low-lying Dirac eigenmodes to probe the local structure of topological charge fluctuations in QCD are discussed, and it is pointed out that the qualitative double-peaked behavior of the local chiral orientation probability distribution in these modes is necessary, but not sufficient for dominance of instanton-like fluctuations. The results with overlap Dirac operator in Wilson gauge backgrounds at lattice spacings ranging from a~0.04 fm to a~0.12 fm are reported, and it is found that the size and density of local structures responsible for double-peaking of the distribution are in disagreement with the assumptions of the Instanton Liquid Model. More generally, our results suggest that vacuum fluctuations of topological charge are not effectively dominated by locally quantized (integer-valued) lumps in QCD.Comment: 29 pages, 13 figures; v2: minor improvements in presentation, results and conclusions unchanged, version to appear in PR

Ab initio many-body calculations on infinite carbon and boron-nitrogen chains

In this paper we report first-principles calculations on the ground-state electronic structure of two infinite one-dimensional systems: (a) a chain of carbon atoms and (b) a chain of alternating boron and nitrogen atoms. Meanfield results were obtained using the restricted Hartree-Fock approach, while the many-body effects were taken into account by second-order M{\o}ller-Plesset perturbation theory and the coupled-cluster approach. The calculations were performed using 6-31$G^{**}$ basis sets, including the d-type polarization functions. Both at the Hartree-Fock (HF) and the correlated levels we find that the infinite carbon chain exhibits bond alternation with alternating single and triple bonds, while the boron-nitrogen chain exhibits equidistant bonds. In addition, we also performed density-functional-theory-based local density approximation (LDA) calculations on the infinite carbon chain using the same basis set. Our LDA results, in contradiction to our HF and correlated results, predict a very small bond alternation. Based upon our LDA results for the carbon chain, which are in agreement with an earlier LDA calculation calculation [ E.J. Bylaska, J.H. Weare, and R. Kawai, Phys. Rev. B 58, R7488 (1998).], we conclude that the LDA significantly underestimates Peierls distortion. This emphasizes that the inclusion of many-particle effects is very important for the correct description of Peierls distortion in one-dimensional systems.Comment: 3 figures (included). To appear in Phys. Rev.