Purification, characterization, and immunogenicity of a soluble trimeric envelope protein containing a partial deletion of the V2 loop derived from SF162, an R5-tropic human immunodeficiency virus type 1 isolate

The envelope (Env) glycoprotein of human immunodeficiency virus type 1 (HIV-1) is the major target of neutralizing antibody responses and is likely to be a critical component of an effective vaccine against AIDS. Although monomeric HIV envelope subunit vaccines (gp120) have induced high-titer antibody responses and neutralizing antibodies against laboratory-adapted HIV-1 strains, they have failed to induce neutralizing antibodies against diverse heterologous primary HIV isolates. Most probably, the reason for this failure is that the antigenic structure(s) of these previously used immunogens does not mimic that of the functional HIV envelope, which is a trimer, and thus these immunogens do not elicit high titers of relevant functional antibodies. We recently reported that an Env glycoprotein immunogen (o-gp140SF162DeltaV2) containing a partial deletion in the second variable loop (V2) derived from the R5-tropic HIV-1 isolate SF162, when used in a DNA priming-protein boosting vaccine regimen in rhesus macaques, induced neutralizing antibodies against heterologous subtype B primary isolates as well as protection to the vaccinated animals upon challenge with pathogenic SHIV(SF162P4) virus. Here we describe the purification of this protein to homogeneity, its characterization as trimer, and its ability to induce primary isolate-neutralizing responses in rhesus macaques. Optimal mutations in the primary and secondary protease cleavage sites of the env gene were identified that resulted in the stable secretion of a trimeric Env glycoprotein in mammalian cell cultures. We determined the molecular mass and hydrodynamic radius (R(h)) using a triple detector analysis (TDA) system. The molecular mass of the oligomer was found to be 324 kDa, close to the expected M(w) of a HIV envelope trimer protein (330 kDa), and the hydrodynamic radius was 7.27 nm. Negative staining electron microscopy of o-gp140SF162DeltaV2 showed that it is a trimer with considerable structural flexibility and supported the data obtained by TDA. The structural integrity of the purified trimeric protein was also confirmed by determinations of its ability to bind the HIV receptor, CD4, and its ability to bind a panel of well-characterized neutralizing monoclonal antibodies. No deleterious effect of V2 loop deletion was observed on the structure and conformation of the protein, and several critical neutralization epitopes were preserved and well exposed on the purified o-gp140SF162DeltaV2 protein. In an intranasal priming and intramuscular boosting regimen, this protein induced high titers of functional antibodies, which neutralized the vaccine strain, i.e., SF162. These results highlight a potential role for the trimeric o-gp140SF162DeltaV2 Env immunogen in a successful HIV vaccine.     

Network compression as a quality measure for protein interaction networks

With the advent of large-scale protein interaction studies, there is much debate about data quality. Can different noise levels in the measurements be assessed by analyzing network structure? Because proteomic regulation is inherently co-operative, modular and redundant, it is inherently compressible when represented as a network. Here we propose that network compression can be used to compare false positive and false negative noise levels in protein interaction networks. We validate this hypothesis by first confirming the detrimental effect of false positives and false negatives. Second, we show that gold standard networks are more compressible. Third, we show that compressibility correlates with co-expression, co-localization, and shared function. Fourth, we also observe correlation with better protein tagging methods, physiological expression in contrast to over-expression of tagged proteins, and smart pooling approaches for yeast two-hybrid screens. Overall, this new measure is a proxy for both sensitivity and specificity and gives complementary information to standard measures such as average degree and clustering coefficients.     

Identification and Isolation of Slow-Dividing Cells in Human Glioblastoma Using Carboxy Fluorescein Succinimidyl Ester (CFSE)

Tumor heterogeneity represents a fundamental feature supporting tumor robustness and presents a central obstacle to the development of therapeutic strategies¹. To overcome the issue of tumor heterogeneity, it is essential to develop assays and tools enabling phenotypic, (epi)genetic and functional identification and characterization of tumor subpopulations that drive specific disease pathologies and represent clinically relevant targets. It is now well established that tumors exhibit distinct sub-fractions of cells with different frequencies of cell division, and that the functional criteria of being slow cycling is positively associated with tumor formation ability in several cancers including those of the brain, breast, skin and pancreas as well as leukemia^2-8. The fluorescent dye carboxyfluorescein succinimidyl ester (CFSE) has been used for tracking the division frequency of cells in vitro and in vivo in blood-borne tumors and solid tumors such as glioblastoma^2,7,8. The cell-permeant non-fluorescent pro-drug of CFSE is converted by intracellular esterases into a fluorescent compound, which is retained within cells by covalently binding to proteins through reaction of its succinimidyl moiety with intracellular amine groups to form stable amide bonds⁹. The fluorescent dye is equally distributed between daughter cells upon divisions, leading to the halving of the fluorescence intensity with every cell division. This enables tracking of cell cycle frequency up to eight to ten rounds of division¹⁰. CFSE retention capacity was used with brain tumor cells to identify and isolate a slow cycling subpopulation (top 5% dye-retaining cells) demonstrated to be enriched in cancer stem cell activity². This protocol describes the technique of staining cells with CFSE and the isolation of individual populations within a culture of human glioblastoma (GBM)-derived cells possessing differing division rates using flow cytometry². The technique has served to identify and isolate a brain tumor slow-cycling population of cells by virtue of their ability to retain the CFSE labeling.     

Soil penetration resistance, a suitable soil property to account for variations in root elongation and branching

Background and Aims

Root system development is affected by soil conditions. The effects of bulk density, water content and penetration resistance on root development processes were investigated in peach trees.

Methods

Peach tree rootstocks were grown in various soil conditions, combining two bulk densities (1.2 and 1.5?g soil.cm^-3) and three water contents (0.14, 0.17 and 0.20?g.g^-1soil). Root parameters (tip diameter, length of apical unbranched zone, branching density and diameters of main and lateral roots) and plant growth (leaves, branches, trunk, root dry mass) were measured. Root growth processes (elongation, branching) were studied using relationships between root parameters.

Results

The proportion of biomass allocated to each plant compartment was similar whatever the soil conditions. Variations in root development were best explained by the variation in penetration resistance, rather than other soil properties. Increased soil penetration resistance reduced the root elongation rate, especially for thick roots. In addition, the branching pattern was affected. In soil with a high penetration resistance, the root system shape differs from a typical herringbone pattern.

Conclusions

These results allow quantification of the root system plasticity, and improve our understanding of the interactions between root development and soil properties.     

Regulation of activity of transient receptor potential melastatin 8 (TRPM8) channel by its short isoforms

One important mechanism of the regulation of membrane ion channels involves their nonfunctional isoforms generated by alternative splicing. However, knowledge of such isoforms for the members of the transient receptor potential (TRP) superfamily of ion channels remains quite limited. This study focuses on the TRPM8, which functions as a cold receptor in sensory neurons but is also expressed in tissues not exposed to ambient temperatures, as well as in cancer tissues. We report the cloning from prostate cancer cells of new short splice variants of TRPM8, termed short TRPM8α and short TRPM8β. Our results show that both variants are in a closed configuration with the C-terminal tail of the full-length TRPM8 channel, resulting in stabilization of its closed state and thus reducing both its cold sensitivity and activity. Our findings therefore uncover a new mode of regulation of the TRPM8 channel by its splice variants.     

Orai1 and STIM1 mediate SOCE and contribute to apoptotic resistance of pancreatic adenocarcinoma

The store-operated calcium channels (SOCs) represent one of the major calcium-entry pathways in non-excitable cells. SOCs and in particular their major components ORAI1 and STIM1 have been shown to be implicated in a number of physiological and pathological processes such as apoptosis, proliferation and invasion. Here we demonstrate that ORAI1 and STIM1 mediate store-operated calcium entry (SOCE) in pancreatic adenocarcinoma cell lines. We show that both ORAI1 and STIM1 play pro-survival anti-apoptotic role in pancreatic adenocarcinoma cell lines, as siRNA-mediated knockdown of ORAI1 and/or STIM1 increases apoptosis induced by chemotherapy drugs 5-fluorouracil (5-FU) or gemcitabine. We also demonstrate that both 5-FU and gemcitabine treatments increase SOCE in Panc1 pancreatic adenocarcinoma cell line via upregulation of ORAI1 and STIM1. Altogether our results reveal the novel calcium-dependent mechanism of action of the chemotherapy drugs 5-FU and gemcitabine and emphasize the anti-apoptotic role of ORAI1 and STIM1 in pancreatic adenocarcinoma cells. This article is part of a Special Issue entitled: Calcium signaling in health and disease. Guest Editors: Geert Bultynck, Jacques Haiech, Claus W. Heizmann, Joachim Krebs, and Marc Moreau.     

Influence of Geant4 parameters on dose distribution and computation time for carbon ion therapy simulation

The aim of this work was to study the influence of Geant4 parameters on dose distribution and computational time for simulations of carbon ion therapy. The study was done using Geant4 version 9.0. The dose distribution in water for incident monoenergetic carbon ion beams of 300 MeV/u were compared for different values of secondary particle production threshold and different step limits. Variations of depth dose of about 2 mm were observed in some cases, which induced a 30% variation of dose deposit in the Bragg peak region. Other tests were done using Geant4 version 9.2 to verify the results from this study. The two versions provided converging results and led to the same conclusions.     

Characterization of an extracellular polysaccharide produced by a Pseudomonas strain grown on glycerol

A new extracellular charged polysaccharide composed mainly by galactose, with lower amounts of mannose, glucose and rhamnose, was produced by the cultivation of Pseudomonas oleovorans NRRL B-14682 using glycerol as the sole carbon source. Thermal and solid-state NMR analysis showed that this polymer is essentially amorphous, with a glass transition temperature of 155.7 degrees C. The exopolysaccharide aqueous solutions have viscoelastic properties similar to that of Guar gum, but with affinity to salts as a result of its polyelectrolyte character. In addition, the exopolysaccharide has demonstrated good flocculating and emulsifying properties and film-forming capacity. These properties make this polymer a good alternative to more expensive natural polysaccharides, such as Guar gum, in several applications in the food, pharmaceutical, cosmetic, textile, paper and petroleum industries.     

Use of weighted reference panels based on empirical estimates of ancestry for capturing untyped variation

Many association methods use a subset of genotyped single nucleotide polymorphisms (SNPs) to capture or infer genotypes at other untyped SNPs. We and others previously showed that tag SNPs selected to capture common variation using data from The International HapMap Consortium (Nature 437:1299–1320, 2005), The International HapMap Consortium (Nature 449:851–861, 2007) could also capture variation in populations of similar ancestry to HapMap reference populations (de Bakker et al. in Nat Genet 38:1298–1303, 2006; González-Neira et al. in Genome Res 16:323–330, 2006; Montpetit et al. in PLoS Genet 2:282–290, 2006; Mueller et al. in Am J Hum Genet 76:387–398, 2005). To capture variation in admixed populations or populations less similar to HapMap panels, a “cosmopolitan approach,” in which all samples from HapMap are used as a single reference panel, was proposed. Here we refine this suggestion and show that use of a “weighted reference panel,” constructed based on empirical estimates of ancestry in the target population (relative to available reference panels), is more efficient than the cosmopolitan approach. Weighted reference panels capture, on average, only slightly fewer common variants (minor allele frequency > 5%) than the cosmopolitan approach (mean r ² = 0.977 vs. 0.989, 94.5% variation captured vs. 96.8% at r ² > 0.8), across the five populations of the Multiethnic Cohort, but entail approximately 25% fewer tag SNPs per panel (average 538 vs. 718). These results extend a recent study in two Indian populations (Pemberton et al. in Ann Hum Genet 72:535–546, 2008). Weighted reference panels are potentially useful for both the selection of tag SNPs in diverse populations and perhaps in the design of reference panels for imputation of untyped genotypes in genome-wide association studies in admixed populations. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The impact of seaweed life phase and postharvest storage duration on the chemical and rheological properties of hybrid carrageenans isolated from Portuguese Mastocarpus stellatus

Variations in chemical and gelling characteristics of hybrid carrageenan extracted from Mastocarpus stellatus seaweeds are studied in order to explore potential links between the seaweeds life phase, the seaweeds postharvest storage duration and the phycocolloids properties. Chemical structures of phycocolloids were assessed by Fourier Transform Infrared spectroscopy (FTIR) and ¹H NMR spectroscopy. Rheological properties of hybrid carrageenans, such as intrinsic viscosity ([η]), gel elasticity (G₀), gel setting temperature (T_g) and gel melting temperature (T_m), were measured with a stress rheometer. Seasonal variation in the degree of sulphates of native extracts and in their corresponding gelling properties is found. The minimum in gelling properties coincides with a minimum of fructified gametophytes in populations harvested during the cold season. Alkali treated extracts also show minimum gelling properties during the cold season but no correlation with variations in the chemical characteristics could be identified. The gel setting temperature is the only significant change in the properties of hybrid carrageenans extracted from dried seaweeds stored over 39 months in opaque and sealed plastic bags. These results point to non trivial relationships between the life stages of M. stellatus seaweeds, the chemical structure and gel properties of the alkali-extracted phycocolloids, and suggest a route towards the sustainable exploitation of the natural resource.