Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy

Background: Determining the anatomic compartments that contribute to plasma HIV-1 is critical to understanding the sources of residual viremia during combination antiretroviral therapy (ART). We analyzed viral DNA and RNA populations in the plasma and tissues from macaques infected with SIV containing HIV-1 RT (RT-SHIV) to identify possible sources of persistent viremia and to investigate the effect of ART on viral replication in tissues. Tissues were collected at necropsy from four pigtailed macaques infected for 30 weeks with a diverse population of RT-SHIV. Two animals (6760 and 8232) were untreated and two animals (8030 and 8272) were treated with efavirenz, tenofovir, and emtricitabine for 20 weeks. Results: A total of 1800 single-genome RT-SHIV pol and env DNA and RNA sequences were analyzed from the plasma, PBMCs, axillary and mesenteric lymph nodes, spleen, thymus, small intestine, bone marrow, lung, and brain. Analyses of intracellular DNA and RNA populations revealed that the majority of proviruses in tissues from untreated animal 8232 were not expressed, whereas a greater proportion of proviruses in tissues were expressed from 6760. Few intracellular RNA sequences were detected in treated animals and most contained inactivating mutations, such as frame shifts or large deletions. Phylogenetics showed that RT-SHIV DNA populations in tissues were not different from virus in contemporary plasma samples in the treated or untreated animals, demonstrating a lack of anatomic compartmentalization and suggesting that plasma viremia is derived from multiple tissue sources. No sequence divergence was detected in the plasma or between tissues in the treated animals after 20 weeks of ART indicating a lack of ongoing replication in tissues during treatment. Conclusions: Virus populations in plasma and tissues did not differ significantly in either treated or untreated macaques, suggesting frequent exchange of virus or infected cells between tissues and plasma, consistent with non-compartmentalized and widely disseminated infection. There was no genetic evidence of ongoing replication in tissues during suppressive ART

Technical Aspects for the Evaluation of Circulating Nucleic Acids (CNAs): Circulating Tumor DNA (ctDNA) and Circulating MicroRNAs

Circulating nucleic acids (CNAs), for example, circulating tumor DNA (ctDNA) and circulating microRNA (miRNA), represent promising biomarkers in several diseases including cancer. They can be isolated from many body fluids, such as blood, saliva, and urine. Also ascites, cerebrospinal fluids, and pleural effusion may be considered as a source of CNAs, but with several and intrinsic limitations. Therefore, blood withdrawal represents one of the best sources for CNAs due to the very simple and minimally invasive way of sampling. Moreover, it can be repeated at different time points, giving the opportunity for a real-time monitoring of the disease

Nitroxide-nitroxide and nitroxide-metal distance measurements in transition metal complexes with two or three paramagnetic centres give access to thermodynamic and kinetic stabilities

AG was supported by the EPSRC funded Centre for Doctoral Training in ‘integrated magnetic resonance’ (EP/J500045/1). BEB is grateful for funding from the European Union (REA 334496). This work was supported by the EPSRC (EP/M024660/1), the DFG (Schwerpunktprogramm 1601) and a Wellcome Trust multiuser equipment grant [099149/Z/12/Z].Fundamentally, the stability of coordination complexes and of templated (bio)macromolecular assemblies depends on the thermodynamic and kinetic properties of the intermediates and final complexes formed. Here, we used pulse EPR (electron paramagnetic resonance) spectroscopy to determine the stabilities of nanoscopic assemblies formed between one or two nitroxide spin-labelled tridentate 2,2′:6′,2′′-terpyridine (tpy) ligands and divalent metal ions (FeII, ZnII, CoII and CuII). In three distinct approaches we exploited (a) the modulation depth of pulsed electron–electron double resonance (PELDOR) experiments in samples with increasing metal-to-ligand ratios, (b) the frequencies of PELDOR under broadband excitation using shaped pulses and (c) the distances recovered from well-resolved PELDOR data in fully deuterated solvents measured at 34 GHz. The results demonstrate that PELDOR is highly sensitive to resolving the stability of templated dimers and allows to readily distinguish anti-cooperative binding (for CuII ions) from cooperative binding (for CoII or FeII ions). In the case of paramagnetic ions (CoII and CuII) the use of broadband PELDOR allowed to identify the cooperativity of binding from the time domain and distance data. By using a second labelled tpy ligand and by mixing two homoleptic complexes of the same metal centre we could probe the kinetic stability on a timescale of tens of seconds. Here, tpy complexes of CuII and ZnII were found to be substitutionally labile, CoII showed very slow exchange and FeII was inert under our conditions. Not only do our chemical models allow studying metal–ligand interactions via PELDOR spectroscopy, the design of our study is directly transferable to (bio)macromolecular systems for determining the kinetic and thermodynamic stabilities underpinning (templated) multimerisation. Considering the limited methods available to obtain direct information on the composition and stability of complex assemblies we believe our approach to be a valuable addition to the armoury of methods currently used to study these systems.PostprintPeer reviewe

A Theory of Ageements in the Shadow of Conflict: The Genesis of Bargaining Power

We present a novel approach to N-person bargaining, based on the idea that the agreement reached in a negotiation is determined by how the direct conflict resulting from disagreement would be resolved. Our basic building block is the disagreement function, which maps each set of feasible outcomes into a disagreement point. Adding this function to the description of a bargaining problem, a weak axiom based on individual rationality leads to a unique solution: the agreement in the shadow of conflict, ASC. This agreement may be construed as the limit of a sequence of partial agreements, each of which is reached as a function of the parties' relative power in the disagreement scenario. As a result, we identify a link between the circumstances of bargaining and the bargaining powers within it. The rich get the law passed by means of force and arms or get it accepted by fear to their might, aren't things this way? Plato, Republic. © 2007 Springer Science+Business Media LLC.Esteban gratefully acknowledges financial support from Barcelona Economics (CREA), the European Commission contract CIT2-CT-2004506084, the MCYT research grant SEC-2003-1961 and from the Generalitat de Catalunya.Peer Reviewe

The Drosophila neural lineages: a model system to study brain development and circuitry

In Drosophila, neurons of the central nervous system are grouped into units called lineages. Each lineage contains cells derived from a single neuroblast. Due to its clonal nature, the Drosophila brain is a valuable model system to study neuron development and circuit formation. To better understand the mechanisms underlying brain development, genetic manipulation tools can be utilized within lineages to visualize, knock down, or over-express proteins. Here, we will introduce the formation and development of lineages, discuss how one can utilize this model system, offer a comprehensive list of known lineages and their respective markers, and then briefly review studies that have utilized Drosophila neural lineages with a look at how this model system can benefit future endeavors

The human epidermal growth factor receptor (EGFR) gene in European patients with advanced colorectal cancer harbors infrequent mutations in its tyrosine kinase domain

ABSTRACT: BACKGROUND: The epidermal growth factor receptor (EGFR), a member of the ErbB family of receptors, is a transmembrane tyrosine kinase (TK) activated by the binding of extracellular ligands of the EGF-family and involved in triggering the MAPK signaling pathway, which leads to cell proliferation. Mutations in the EGFR tyrosine kinase domain are frequent in non-small-cell lung cancer (NSCLC). However, to date, only very few, mainly non-European, studies have reported rare EGFR mutations in colorectal cancer (CRC). METHODS: We screened 236 clinical tumor samples from European patients with advanced CRC by direct DNA sequencing to detect potential, as yet unknown mutations, in the EGFR gene exons 18 to 21, mainly covering the EGFR TK catalytic domain. RESULTS: EGFR sequences showed somatic missense mutations in exons 18 and 20 at a frequency of 2.1% and 0.4% respectively. Somatic SNPs were also found in exons 20 and 21 at a frequency of about 3.1% and 0.4% respectively. Of these mutations, four have not yet been described elsewhere. CONCLUSIONS: These mutation frequencies are higher than in a similarly sized population characterized by Barber and colleagues, but still too low to account for a major role played by the EGFR gene in CRC.Peer reviewe

Beyond interviews and focus groups: a framework for integrating innovative qualitative methods into randomised controlled trials of complex public health interventions

Background Randomised controlled trials (RCTs) are widely used for establishing evidence of the effectiveness of interventions, yet public health interventions are often complex, posing specific challenges for RCTs. Although there is increasing recognition that qualitative methods can and should be integrated into RCTs, few frameworks and practical guidance highlight which qualitative methods should be integrated and for what purposes. As a result, qualitative methods are often poorly or haphazardly integrated into existing trials, and researchers rely heavily on interviews and focus group discussions. To improve current practice, we propose a framework for innovative qualitative research methods that can help address the challenges of RCTs for complex public health interventions. Methods We used a stepped approach to develop a practical framework for researchers. This consisted of (1) a systematic review of the innovative qualitative methods mentioned in the health literature, (2) in-depth interviews with 23 academics from different methodological backgrounds working on RCTs of public health interventions in 11 different countries, and (3) a framework development and group consensus-building process. Results The findings are presented in accordance with the CONSORT (Consolidated Standards of Reporting Trials) Statement categories for ease of use. We identify the main challenges of RCTs for public health interventions alongside each of the CONSORT categories, and potential innovative qualitative methods that overcome each challenge are listed as part of a Framework for the Integration of Innovative Qualitative Methods into RCTs of Complex Health Interventions. Innovative qualitative methods described in the interviews include rapid ethnographic appraisals, document analysis, diary methods, interactive voice responses and short message service, community mapping, spiral walks, pair interviews and visual participatory analysis. Conclusions The findings of this study point to the usefulness of observational and participatory methods for trials of complex public health interventions, offering a novel contribution to the broader literature about the need for mixed methods approaches. Integrating a diverse toolkit of qualitative methods can enable appropriate adjustments to the intervention or process (or both) of data collection during RCTs, which in turn can create more sustainable and effective interventions. However, such integration will require a cultural shift towards the adoption of method-neutral research approaches, transdisciplinary collaborations, and publishing regimes

VEGF and Angiopoietin-1 Exert Opposing Effects on Cell Junctions by Regulating the Rho GEF Syx

Vascular endothelial growth factor (VEGF) and Ang1 (Angiopoietin-1) have opposing effects on vascular permeability, but the molecular basis of these effects is not fully known. We report in this paper that VEGF and Ang1 regulate endothelial cell (EC) junctions by determining the localization of the RhoA-specific guanine nucleotide exchange factor Syx. Syx was recruited to junctions by members of the Crumbs polarity complex and promoted junction integrity by activating Diaphanous. VEGF caused translocation of Syx from cell junctions, promoting junction disassembly, whereas Ang1 maintained Syx at the junctions, inducing junction stabilization. The VEGF-induced translocation of Syx from EC junctions was caused by PKD1 (protein kinase D1)-mediated phosphorylation of Syx at Ser806, which reduced Syx association to its junctional anchors. In support of the pivotal role of Syx in regulating EC junctions, syx−/− mice had defective junctions, resulting in vascular leakiness, edema, and impaired heart function

Optimisation of Biochemical Condition and Substrates In Vitro for Tissue Engineering of Ligament

In this work, we analysed the effect of growth factors on in vitro cell proliferation and collagens synthesis by fibroblasts cultured for 72 h on different substrates (silicon sheet with or without 1% gelatin, and glass as control surface) for ligament tissue engineering. A human fibroblast cell line (CRL-2703) was used. The synthesis of type I and type III collagens were evaluated qualitatively and quantitatively by RT-PCR and confocal microscopy, respectively. Cell proliferation was evaluated by two methods: (1) MTT assay (2) cell cycle analysis. It was found that PDGF-AB stimulate the proliferation of fibroblast cultured on gelatin coated silicon sheet in dose dependant manner with a maximum effect at 10 ng ml(−1). The exogenous TGF-β1 induced the expression of type I and type III collagens in a dose and substrate-dependant manner. We deduce from this work that biochemical conditions and substrates have an important impact for optimisation of the tissue neo synthesis