Polarization Induced Electro-Functionalization of Pore Walls: A Contactless Technology.

This review summarizes recent advances in micro- and nanopore technologies with a focus on the functionalization of pores using a promising method named contactless electro-functionalization (CLEF). CLEF enables the localized grafting of electroactive entities onto the inner wall of a micro- or nano-sized pore in a solid-state silicon/silicon oxide membrane. A voltage or electrical current applied across the pore induces the surface functionalization by electroactive entities exclusively on the inside pore wall, which is a significant improvement over existing methods. CLEF's mechanism is based on the polarization of a sandwich-like silicon/silicon oxide membrane, creating electronic pathways between the core silicon and the electrolyte. Correlation between numerical simulations and experiments have validated this hypothesis. CLEF-induced micro- and nanopores functionalized with antibodies or oligonucleotides were successfully used for the detection and identification of cells and are promising sensitive biosensors. This technology could soon be successfully applied to planar configurations of pores, such as restrictions in microfluidic channels.

Numerical modelling of the V-J combinations of the T cell receptor TRA/TRD locus.

T-Cell antigen Receptor (TR) repertoire is generated through rearrangements of V and J genes encoding alpha and beta chains. The quantification and frequency for every V-J combination during ontogeny and development of the immune system remain to be precisely established. We have addressed this issue by building a model able to account for Valpha-Jalpha gene rearrangements during thymus development of mice. So we developed a numerical model on the whole TRA/TRD locus, based on experimental data, to estimate how Valpha and Jalpha genes become accessible to rearrangements. The progressive opening of the locus to V-J gene recombinations is modeled through windows of accessibility of different sizes and with different speeds of progression. Furthermore, the possibility of successive secondary V-J rearrangements was included in the modelling. The model points out some unbalanced V-J associations resulting from a preferential access to gene rearrangements and from a non-uniform partition of the accessibility of the J genes, depending on their location in the locus. The model shows that 3 to 4 successive rearrangements are sufficient to explain the use of all the V and J genes of the locus. Finally, the model provides information on both the kinetics of rearrangements and frequencies of each V-J associations. The model accounts for the essential features of the observed rearrangements on the TRA/TRD locus and may provide a reference for the repertoire of the V-J combinatorial diversity.

Dynamic aspects of TCRalpha gene recombination: qualitative and quantitative assessments of the TCRalpha chain repertoire in man and mouse.

Most T-lymphocytes express a highly specific antigen receptor (TCR) on their cell surface, consisting of a clonotypic alphabeta-heterodimer. Both alpha- and beta chains are products of somatic rearrangements of V, (D) and J gene segments encoded on the respective loci. The qualitative, quantitative and dynamic aspects of the TCRalpha chain repertoire of humans and mice have been difficult to estimate, mainly due to locus complexity. Analyses of the T-cell repertoire were first performed at the transcriptional level using classical cloning and sequencing strategies and then later at the genomic level using sensitive multiplex PCR assays that allow surveying the global rearrangement of the TCRAD locus. These all converge and support the conclusion that the V-J recombination pattern in both human and mouse thymus is not random but depends on the reciprocal V and J positions within the locus, thereby limiting the combinatorial diversity of the TCRalpha chain repertoire. The recombination profile is compatible with a sequential opening of the V region with progressive tracking along the two regions in opposite directions starting from the nearest and then moving towards the most distant V and J gene segments. In this chapter, we report new insights into the degree of human and mouse TCRalpha chain diversity in thymic and peripheral T-lymphocytes. Since the comparison of human and mouse V-J recombination shows a similar pattern of rearrangement, we suggest that spatial and temporal synchronization on the accessibility of V and J gene segments are general features of V-J rearrangements that are conserved throughout evolution.

Analysis of the TCR alpha-chain rearrangement profile in human T lymphocytes.

The size of the available human alphabeta T cell repertoire is difficult to determine and is open to debate. Empirical analysis of TCR beta-chain diversity reveals approximately 10(6) different beta chains in peripheral blood. Due in part to locus complexity, comparable information for TCR alpha is lacking. Rather, current estimates for human TCR alpha diversity, and hence, total repertoire diversity, are based on theoretical analyses that assume equal probabilities of rearrangement between any V alpha gene and J alpha gene. Here, we report on a systematic locus-wide rearrangement analysis of the TCR alpha-chain in human T cells. We first demonstrate that the V-J alpha recombination in the thymus is not random but depends on the reciprocal V alpha and J alpha position within the locus. Characterization of the frequency of gene usage combined with identification of five previously unrecognized pseudogenes enables us to empirically estimate the human TCR alpha combinatorial repertoire. The number of V-J alpha combinations achieved is approximately 44-56% of the total combinatorial possibilities, significantly lower than theoretical estimates. We also demonstrate that TCR alpha-chain diversity in peripheral T lymphocytes mimics the same general patterns of rearrangement as observed in the thymus, and these patterns appear conserved among different individuals. This unexpected observation indicates that, unlike the TCR beta locus, the human TCR alpha-chain repertoire is primarily predetermined by genetic recombination and its size is restricted by limits on the combinatorial repertoire rather than post-thymic selection.

IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations.

BACKGROUND: Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cell receptor (TR) loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS). Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files) and are difficult to extract. DESCRIPTION: IMGT/GeneInfo is an online information system that provides, through a user-friendly interface, exhaustive information resulting from the complex mechanisms of T cell receptor V-J and V-D-J recombinations. T cells comprise two populations which express the alphabeta and gammadelta TR, respectively. The first version of the system dealt with the Homo sapiens and Mus musculus TRA and TRB loci whose gene rearrangements allow the synthesis of the alphabeta TR chains. In this paper, we present the second version of IMGT/GeneInfo where we complete the database for the Homo sapiens and Mus musculus TRG and TRD loci along with the introduction of a quality control procedure for existing and new data. We also include new functionalities to the four loci analysis, giving, to date, a very informative tool which allows to work on V(D)J genes of all TR loci in both human and mouse species. IMGT/GeneInfo provides more than 59,000 rearrangement combinations with a full gene description which is freely available at http://imgt.cines.fr/GeneInfo. CONCLUSION: IMGT/GeneInfo allows all TR information sequences to be in the same spot, and are now available within two computer-mouse clicks. This is useful for biologists and bioinformaticians for the study of T lymphocyte V(D)J gene rearrangements and their applications in immune response analysis.

A polypyrrole protein microarray for antibody-antigen interaction studies using a label-free detection process.

Protein microarray is a promising technology that should combine rapidity and easy use with high throughput and versatility. This article describes a method in which an electrocopolymerization process is employed to graft biological molecules on to a chip so that surface plasmon resonance imaging may be used to detect molecular interactions. Copolymerization of pyrrole-modified protein and pyrrole is an efficient grafting process which immobilizes molecules at defined positions on a gold surface. Surface plasmon resonance imaging is an optical technique that allows real-time simultaneous detection of molecular interactions on a large number of spots without labeling. This method was successfully used to analyze antibody-antigen interactions. This illustrates its high specificity and good sensitivity and demonstrates its suitability for biological studies.

p53-dependent and p53-independent pathways for radiation-induced immature thymocyte differentiation.

The pre-T-cell receptor (TCR) delivers essential survival/differentiation signals to the developing thymocytes. Severe combined immunodeficient (SCID) and recombination-activating gene (RAG)-deficient mice are unable to assemble antigen receptor genes, and therefore cannot express a pre-TCR. Consequently, T lymphocyte differentiation is arrested at an early stage in the thymus of these animals, and immature thymocytes are eliminated through apoptotic processes. This maturation arrest can be relieved and thymocyte differentiation rescued after the exposure of these mice to whole-body gamma-irradiation. Whereas the promotion of immature thymocyte survival/differentiation was shown to require p53 activity in irradiated SCID mice, it was suggested, on the other hand, that p53 activation prevents immature thymocytes survival/differentiation in irradiated RAG-deficient mice. However, SCID mice have impaired responses to ionizing radiation. In this paper, we analysed p53 requirement in radiation-induced thymocyte differentiation in CD3epsilon(Delta5/Delta5) mice, where pre-TCR deficiency also results in an early block of lymphocyte development. Our results show at the cellular and molecular levels that, in this DNA repair-proficient model, irradiation-induced thymocyte differentiation proceeds either by a p53-dependent or by a p53-independent pathway, which differ in their sensitivity to the radiation dose delivered.

IMGT/GeneInfo: enhancing V(D)J recombination database accessibility.

IMGT/GeneInfo is a user-friendly online information system that provides information on data resulting from the complex mechanisms of immunoglobulin (IG) and T cell receptor (TR) V(D)J recombinations. For the first time, it is possible to visualize all the rearrangement parameters on a single page. IMGT/GeneInfo is part of the international ImMunoGeneTics information system (IMGT), a high-quality integrated knowledge resource specializing in IG, TR, major histocompatibility complex (MHC), and related proteins of the immune system of human and other vertebrate species. The IMGT/GeneInfo system was developed by the TIMC and ICH laboratories (with the collaboration of LIGM), and is the first example of an external system being incorporated into IMGT. In this paper, we report the first part of this work. IMGT/GeneInfo_TR deals with the human and mouse TRA/TRD and TRB loci of the TR. Data handling and visualization are complementary to the current data and tools in IMGT, and will subsequently allow the modelling of V(D)J gene use, and thus, to predict non-standard recombination profiles which may eventually be found in conditions such as leukaemias or lymphomas. Access to IMGT/GeneInfo is free and can be found at http://imgt.cines.fr/GeneInfo.

Oxidative stress impairs intracellular events involved in antigen processing and presentation to T cells.

For T cells to recognize foreign antigens, the latter must be processed into peptides and associated to major histocompatibility complex (MHC) class II molecules by antigen-presenting cells (APC). APCs frequently operate under stress conditions induced by tissue damage, antigens, or inflammatory reactions. We analyze the effects of oxidative stress on intracellular processing using APC B cell lines. Before being tested for APC function, B cells (IIA1.6) were exposed for 2 hours to hydrogen peroxide (H2O2), a treatment that impairs their capacity to stimulate specific T cell clones. Because paraformaldehyde-fixed H2O2-treated B cells can still present extracellular peptides to T cell clones, the intracellular events of processing were investigated. Purified lysosomes from H2O2-treated B cells show increased proteolytic activity and increased generation of antigenic peptides. In addition, H2O2 treatment targets antigens to compartments that express low levels of MHC II and proteins (H-2M, H-2O) required for peptide loading onto this molecule. Finally, we suggest that impairment of antigen processing by oxidative stress reduces the induction of a T cell's response because H2O2 decreases the activation of naive T lymphocytes by dendritic cells. Together, these data indicate that oxidative stress inhibits the capacity of APCs to process antigens and to initiate a primary T cell response. The role of such modifications on the outcome of the specific immune response is discussed.

Fibroblasts inhibit the production of interleukin-12p70 by murine dendritic cells.

Interleukin-12 p70 (IL-12p70) is a key cytokine produced by dendritic cells (DC) able to drive the development of T helper type 1 (Th1) lymphocytes. We showed that thymic and other fibroblasts strongly inhibit IL-12p70 production by splenic DC stimulated by lipopolysaccharide plus either anti-CD40 or interferon-gamma (IFN-gamma) and by purified splenic DC stimulated by Pansorbin plus IFN-gamma. This IL-12p70 inhibitory activity is secreted in the conditioned medium of primary fibroblasts and fibroblast cell lines but not by haematopoietic cell lines. As IL-10 was the unique factor able to inhibit IL-12p70 produced by cultured splenic DC, we showed that a neutralizing antibody to IL-10 did not suppress the IL-12p70 inhibitory activity of thymic fibroblast-conditioned medium (FCM). This FCM potently inhibits the maturation and expression of major histocompatibility complex class II and co-stimulatory molecules induced by stimulation of spleen-derived DC. While thymic FCM suppressed the IL-12p70 expression by stimulated spleen-derived DC, tumour necrosis factor-alpha production is not affected. This inhibitory activity is able to down-regulate the IL-12p35 subunit transcription and expression, resulting in the impaired assembly of IL-12p70 heterodimer. As fibroblasts are present in the tissue microenvironment and are active players in the establishment of an immune response, the nature and role of the fibroblastic inhibitory activity remain to be established.

Quantitative and qualitative changes in V-J alpha rearrangements during mouse thymocytes differentiation: implication for a limited T cell receptor alpha chain repertoire.

Knowledge of the complete nucleotide sequence of the mouse TCRAD locus allows an accurate determination V-J rearrangement status. Using multiplex genomic PCR assays and real time PCR analysis, we report a comprehensive and systematic analysis of the V-J recombination of TCR alpha chain in normal mouse thymocytes during development. These respective qualitative and quantitative approaches give rise to four major points describing the control of gene rearrangements. (a) The V-J recombination pattern is not random during ontogeny and generates a limited TCR alpha repertoire; (b) V-J rearrangement control is intrinsic to the thymus; (c) each V gene rearranges to a set of contiguous J segments with a gaussian-like frequency; (d) there are more rearrangements involving V genes at the 3' side than 5' end of V region. Taken together, this reflects a preferential association of V and J gene segments according to their respective positions in the locus, indicating that accessibility of both V and J regions is coordinately regulated, but in different ways. These results provide a new insight into TCR alpha repertoire size and suggest a scenario for V usage during differentiation.

Monocyte chemotactic protein-1 secretion and expression after Toxoplasma gondii infection in vitro depend on the stage of the parasite.

Infection of human fibroblasts with tachyzoites of RH and Prugniaud strains, two different strains of Toxoplasma gondii, significantly increased monocyte chemotactic protein (MCP)-1 secretion contrary to what happened with bradyzoites of the cystogenetic strain. Quantification of MCP-1 mRNA by RT-PCR showed that this phenomenon is regulated at the transcriptional level. Thus, the stage of parasite can be deciding in MCP-1 induction since only tachyzoites induced MCP-1 expression and secretion. MCP-1 induced by tachyzoites could be involved in cell recruitment, as shown by the quantification of MCP1 ARNm by real-time PCR (LightCycler, Roche Diagnostics), in the pathogenesis of T. gondii infection.