Exposure to apoptotic activated CD4+ T cells induces maturation and APOBEC3G-mediated inhibition of HIV-1 infection in dendritic cells

Dendritic cells (DCs) are activated by signaling via pathogen-specific receptors or exposure to inflammatory mediators. Here we show that co-culturing DCs with apoptotic HIV-infected activated CD4(+) T cells (ApoInf) or apoptotic uninfected activated CD4(+) T cells (ApoAct) induced expression of co-stimulatory molecules and cytokine release. In addition, we measured a reduced HIV infection rate in DCs after co-culture with ApoAct. A prerequisite for reduced HIV infection in DCs was activation of CD4(+) T cells before apoptosis induction. DCs exposed to ApoAct or ApoInf secreted MIP-1α, MIP-1β, MCP-1, and TNF-α; this effect was retained in the presence of exogenous HIV. The ApoAct-mediated induction of co-stimulatory CD86 molecules and reduction of HIV infection in DCs were partially abrogated after blocking TNF-α using monoclonal antibodies. APOBEC3G expression in DCs was increased in co-cultures of DCs and ApoAct but not by apoptotic resting CD4(+) T cells (ApoRest). Silencing of APOBEC3G in DC abrogated the HIV inhibitory effect mediated by ApoAct. Sequence analyses of an env region revealed significant induction of G-to-A hypermutations in the context of GG or GA dinucleotides in DNA isolated from DCs exposed to HIV and ApoAct. Thus, ApoAct-mediated DC maturation resulted in induction of APOBEC3G that was important for inhibition of HIV-infection in DCs. These findings underscore the complexity of differential DC responses evoked upon interaction with resting as compared with activated dying cells during HIV infection.     

Simplified and Cost Effective Syntheses of Fully Protected Phosphoramidite Monomers Suitable for the Assembly of Oligo(2′-O-allylribonucleotides)

Abstract

Simplified, high yielding syntheses of suitably protected 2′-O-allylribonucleoside-3′-O-phosphoramidites starting from standard ribonucleosides have been elucidated. Specific 2′-O-allylation is readily achieved using amidine protection of the exocyclic amino groups of adenosine and cytidine and in the case of guanosine the allylation is carried out on an easily prepared intermediate bearing transient protection of the lactam function.     

Identification of copy number variants from exome sequence data

Background

With advances in next generation sequencing technologies and genomic capture techniques, exome sequencing has become a cost-effective approach for mutation detection in genetic diseases. However, computational prediction of copy number variants (CNVs) from exome sequence data is a challenging task. Whilst numerous programs are available, they have different sensitivities, and have low sensitivity to detect smaller CNVs (1–4 exons). Additionally, exonic CNV discovery using standard aCGH has limitations due to the low probe density over exonic regions. The goal of our study was to develop a protocol to detect exonic CNVs (including shorter CNVs that cover 1–4 exons), combining computational prediction algorithms and a high-resolution custom CGH array.

Results

We used six published CNV prediction programs (ExomeCNV, CONTRA, ExomeCopy, ExomeDepth, CoNIFER, XHMM) and an in-house modification to ExomeCopy and ExomeDepth (ExCopyDepth) for computational CNV prediction on 30 exomes from the 1000 genomes project and 9 exomes from primary immunodeficiency patients. CNV predictions were tested using a custom CGH array designed to capture all exons (exaCGH). After this validation, we next evaluated the computational prediction of shorter CNVs. ExomeCopy and the in-house modified algorithm, ExCopyDepth, showed the highest capability in detecting shorter CNVs. Finally, the performance of each computational program was assessed by calculating the sensitivity and false positive rate.

Conclusions

In this paper, we assessed the ability of 6 computational programs to predict CNVs, focussing on short (1–4 exon) CNVs. We also tested these predictions using a custom array targeting exons. Based on these results, we propose a protocol to identify and confirm shorter exonic CNVs combining computational prediction algorithms and custom aCGH experiments.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-661) contains supplementary material, which is available to authorized users.     

Structure and activities of ectomycorrhizal and microbial communities in the rhizosphere of Fagus sylvatica under ozone and pathogen stress in a lysimeter study

The aim was to study the influence of abiotic (elevated ozone) or biotic stress (Phytophthora citricola) or their combination on soil biological components and processes in the rhizosphere of young beech trees. Ectomycorrhizal and overall microbial community composition was studied at two soil depths in a lysimeter experiment with 7 year old trees of Fagus sylvatica. As a functional parameter, potential enzyme activities were measured in mycorrhizosphere soil and on excised mycorrhizal tips. The degree of mycorrhization, structure and potential enzymatic activities of mycorrhizal communities were only slightly influenced by treatments. Soil enzyme activities were depressed under elevated ozone and stimulated by P. citricola under ambient but not under elevated ozone. Overall microbial community composition (PLFA) and ectomycorrhizal diversity changed with depth. PLFA analyses not only suggested a reaction of the microbial community to elevated ozone but also indicated an increase in plant stress related components. No influence of the biotic stress on ectomycorrhizal or overall microbial community structure was detected. Changes in the mycorrhizosphere community structure and function due to ozone may be explained by the quality of plant derived carbon.     

Initial differentiation of vertical soil organic matter distribution and composition under juvenile beech (Fagus sylvatica L.) trees

In a lysimeter experiment with juvenile beech trees (Fagus sylvatica L.) we studied the development of depth gradients of soil organic matter (SOM) composition and distribution after soil disturbance. The sampling scheme applied to the given soil layers (0–2 cm, 2–5 cm, 5–10 cm and 10–20 cm) was crucial to study the subtle reformation of SOM properties with depth in the artificially filled lysimeters. Due to the combination of physical SOM fractionation with the application of ¹⁵N-labelled beech litter and ¹³C-CPMAS NMR spectroscopy we were able to obtain a detailed view on vertical differentiation of SOM properties. Four years after soil disturbance a significant decrease of the mass of particulate OM (POM) with depth could be found. A clear depth distribution was also shown for carbon (C) and nitrogen (N) within the SOM fractions related to bulk soil. The mineral fractions <63 µm clearly dominated C storage (between 47 to 60% of bulk soil C) and N storage (between 68 to 86% of bulk soil N). A drastic increase in aliphatic C structures concomitant to decreasing O/N-alkyl C was detected with depth, increasing from free POM to occluded POM. Only a slight depth gradient was observed for ¹³C but a clear vertical incorporation of ¹⁵N from the applied labelled beech litter was demonstrated probably resulting from faunal and fungal incorporation. We clearly demonstrated a significant reformation of a SOM depth profile within a very short time of soil evolution. One important finding of this study is that especially in soils with reforming SOM depth gradients after land-use changes selective sampling of whole soil horizons can bias predictions of C and N dynamics as it overlooks a potential development of gradients of SOM properties on smaller scales.     

Surface electromyography and peak torque of repetitive maximum isokinetic plantar flexions in relation to aspects of muscle morphology.

This study investigates the relationships between surface electromyography (EMG [Mean frequency of the power spectrum (MNF)]) and peak torque variables obtained during 100 maximum concentric plantar flexions with the right limb at 60 degrees s(-1) and different muscle morphological variables. Surface EMG was recorded from the right gastrocnemius lateralis and muscle biopsies were taken from the same site as the EMG electrodes were positioned. Muscle fibre area and fibre type composition were determined on serial muscle cross sections using both histochemistry (myofibrillar adenosine triphosphatase) and immunohistochemistry (monoclonal antibodies against specific myosin heavy chain isoforms). Forty-three female and nine male students participated in the study. Gastrocnemius lateralis contained predominantly type I fibres (50%) and type IIA fibres (40%) in both sexes and large individual differences were found. Principal component analysis (PCA) was used for the intercorrelation analyses, and projection to latent structures (PLS) was used for the multivariate regression analysis. MNF correlated positively with different fibre areas and with the proportion of type I fibres. Fibre areas and sex were the most important factors in the regression of maximum peak torque. High proportion of type I fibres and sex were the most important regressors of peak torque endurance normalised for lean body mass. More studies are needed to understand the complex interrelationships between intrinsic muscle properties and the frequency content of the surface EMG before theoretical models can be formulated that incorporate both fibre areas and fibre type proportions.     

RANKL induces components of the extrinsic coagulation pathway in osteoclasts

Prothrombin is converted to thrombin by factor Xa in the cell-associated prothrombinase complex. Prothrombin is present in calcified bone matrix and thrombin exerts effects on osteoblasts as well as on bone resorption by osteoclasts.We investigated whether (1) osteoclasts display factor Xa-dependent prothrombinase activity and (2) osteoclasts express critical regulatory components upstream of the prothrombinase complex.The osteoclast differentiation factor RANKL induced formation of multinucleated TRAP positive cells concomitant with induction of prothrombinase activity in cultures of RAW 264.7 cells and bone marrow osteoclast progenitors.Expression analysis of extrinsic coagulation factors revealed that RANKL enhanced protein levels of factor Xa as well as of coagulation factor III (tissue factor). Inhibition assays indicated that factor Xa and tissue factor were involved in the control of prothrombinase activity in RANKL-differentiated osteoclasts, presumably at two stages (1) conversion of prothrombin to thrombin and (2) conversion of factor X to factor Xa, respectively.Activation of the extrinsic coagulation pathway during osteoclast differentiation through induction of tissue factor and factor Xa by a RANKL-dependent pathway indicates a novel role for osteoclasts in converting prothrombin to thrombin.     

R-Ras Regulates Migration through an Interaction with Filamin A in Melanoma Cells

Background

Changes in cell adhesion and migration in the tumor microenvironment are key in the initiation and progression of metastasis. R-Ras is one of several small GTPases that regulate cell adhesion and migration on the extracellular matrix, however the mechanism has not been completely elucidated. Using a yeast two-hybrid approach we sought to identify novel R-Ras binding proteins that might mediate its effects on integrins.

Methods and Findings

We identified Filamin A (FLNa) as a candidate interacting protein. FLNa is an actin-binding scaffold protein that also binds to integrin β1, β2 and β7 tails and is associated with diverse cell processes including cell migration. Indeed, M2 melanoma cells require FLNa for motility. We further show that R-Ras and FLNa interact in co-immunoprecipitations and pull-down assays. Deletion of FLNa repeat 3 (FLNaΔ3) abrogated this interaction. In M2 melanoma cells active R-Ras co-localized with FLNa but did not co-localize with FLNa lacking repeat 3. Thus, activated R-Ras binds repeat 3 of FLNa. The functional consequence of this interaction was that active R-Ras and FLNa coordinately increased cell migration. In contrast, co-expression of R-Ras and FLNaΔ3 had a significantly reduced effect on migration. While there was enhancement of integrin activation and fibronectin matrix assembly, cell adhesion was not altered. Finally, siRNA knockdown of endogenous R-Ras impaired FLNa-dependent fibronectin matrix assembly.

Conclusions

These data support a model in which R-Ras functionally associates with FLNa and thereby regulates integrin-dependent migration. Thus in melanoma cells R-Ras and FLNa may cooperatively promote metastasis by enhancing cell migration.