Spiking neural P systems are a class of distributed and parallel computing models inspired by the neurophysiological behavior of neurons sending electrical impulses (spikes) along axons to other... Show moreSpiking neural P systems are a class of distributed and parallel computing models inspired by the neurophysiological behavior of neurons sending electrical impulses (spikes) along axons to other neurons. In this thesis, we consider that the spiking neural P systems are universal even if the systems work in limited asynchronous mode. And we also investigated different variants of spiking neural P systems with other additional features, such as the axon functioning, the growth of dendritic trees in neurons, the positive or negative weights on synapses, and the astrocytes having excitatory and inhibitory influence on synapses. Show less
Stevens, K.N.; Garcia-Closas, M.; Fredericksen, Z.; Kosel, M.; Pankratz, V.S.; Hopper, J.L.; ... ; Australian Ovarian Cancer Study Gr 2011
Autosomal-recessive immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is mainly characterized by recurrent, often fatal, respiratory and gastrointestinal infections.... Show moreAutosomal-recessive immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is mainly characterized by recurrent, often fatal, respiratory and gastrointestinal infections. About 50% of patients carry mutations in the DNA methyltransferase 3B gene (DNMT3B) (ICF1). The remaining patients carry unknown genetic defects (ICF2) but share with ICF1 patients the same immunological and epigenetic features, including hypomethylation of juxtacentromeric repeat sequences. We performed homozygosity mapping in five unrelated ICF2 patients with consanguineous parents and then performed whole-exome sequencing in one of these patients and Sanger sequencing in all to identify mutations in the zinc-finger- and BTB (bric-a-bric, tramtrack, broad complex)-domain-containing 24 (ZBTB24) gene in four consanguineously descended ICF2 patients. Additionally, we found ZBTB24 mutations in an affected sibling pair and in one patient for whom it was not known whether his parents were consanguineous. ZBTB24 belongs to a large family of transcriptional repressors that include members, such as BCL6 and PATZ1, with prominent regulatory roles in hematopoietic development and malignancy. These data thus indicate that ZBTB24 is involved in DNA methylation of juxtacentromeric DNA and in B cell development and/or B and T cell interactions. Because ZBTB24 is a putative DNA-binding protein highly expressed in the lymphoid lineage, we predict that by studying the molecular function of ZBTB24, we will improve our understanding of the molecular pathophysiology of ICF syndrome and of lymphocyte biology in general. Show less
Autosomal-recessive immunodeficiency, centromeric instability, and facial anomalies (ICE) syndrome is mainly characterized by recurrent, often fatal, respiratory and gastrointestinal infections.... Show moreAutosomal-recessive immunodeficiency, centromeric instability, and facial anomalies (ICE) syndrome is mainly characterized by recurrent, often fatal, respiratory and gastrointestinal infections. About 50% of patients carry mutations in the DNA methyltransferase 3B gene (DNMT3B) (ICF1). The remaining patients carry unknown genetic defects (1072) but share with ICF1 patients the same immunological and epigenetic features, including hypomethylation of juxtacentromeric repeat sequences. We performed homozygosity mapping in five unrelated ICF2 patients with consanguineous parents and then performed whole-exome sequencing in one of these patients and Sanger sequencing in all to identify mutations in the zinc-finger- and BTB (bric-a-bric, tramtrack, broad complex)-domain-containing 24 (ZBTB24) gene in four consanguineously descended ICF2 patients. Additionally, we found ZBTB24 mutations in an affected sibling pair and in one patient for whom it was not known whether his parents were consanguineous. ZBTB24 belongs to a large family of transcriptional repressors that include members, such as BCL6 and PATZ1, with prominent regulatory roles in hematopoietic development and malignancy. These data thus indicate that ZBTB24 is involved in DNA methylation of juxtacentromeric DNA and in B cell development and/or B and cell interactions. Because ZBTB24 is a putative DNA-binding protein highly expressed in the lymphoid lineage, we predict that by studying the molecular function of ZBTB24, we will improve our understanding of the molecular pathophysiology of ICF syndrome and of lymphocyte biology in general. Show less
We have recently shown that IgG1 directed against antigens thought to be involved in the pathogenesis of rheumatoid arthritis harbor different glycan moieties on their Fc-tail, as compared with... Show moreWe have recently shown that IgG1 directed against antigens thought to be involved in the pathogenesis of rheumatoid arthritis harbor different glycan moieties on their Fc-tail, as compared with total sera IgG1. Given the crucial roles of Fc-linked N-glycans for the structure and biological activity of IgG, Fc-glycosylation of antibodies is receiving considerable interest. However, so far little is known about the signals and factors that could influence the composition of these carbohydrate structures on secreted IgG produced by B lymphocytes. Here we show that both "environmental" factors, such as all-trans retinoic acid (a natural metabolite of vitamin A), as well as factors stimulating the innate immune system (i.e. CpG oligodeoxynucleotide, a ligand for toll-like receptor 9) or coming from the adaptive immune system (i.e. interleukin-21, a T-cell derived cytokine) can modulate IgG1 Fc-glycosylation. These factors affect Fc-glycan profiles in different ways. CpG oligodeoxynucleotide and interleukin-21 increase Fc-linked galactosylation and reduce bisecting N-acetylglucosamine levels, whereas all-trans retinoic acid significantly decreases galactosylation and sialylation levels. Moreover, these effects appeared to be stable and specific for secreted IgG1 as no parallel changes of the corresponding glycans in the cellular glycan pool were observed. Interestingly, several other cytokines and molecules known to affect B-cell biology and antibody production did not have an impact on IgG1 Fc-coupled glycan profiles. Together, these data indicate that different stimuli received by B cells during their activation and differentiation can modulate the Fc-linked glycosylation of secreted IgG1 without affecting the general cellular glycosylation machinery. Our study, therefore, furthers our understanding of the regulation of IgG1 glycosylation at the cellular level. Molecular & Cellular Proteomics 10: 10.1074/mcp.M110.004655, 1-12, 2011. Show less
Wang, J.; Bax, M.; Balog, C.I.A.; Stavenhagen, K.; Koeleman, C.A.M.; Scherer, H.U.; ... ; Wuhrer, M. 2011
This thesis consists of two parts, focusing on CD4+CD25+ regulatory T cells (Tregs) (Part I) and IgG glycosylations (Part II), respectively. Part I (Chapter 2-5) is mainly dedicated to a better... Show moreThis thesis consists of two parts, focusing on CD4+CD25+ regulatory T cells (Tregs) (Part I) and IgG glycosylations (Part II), respectively. Part I (Chapter 2-5) is mainly dedicated to a better identification/characterization and generation of functional human Tregs in vitro. In Chapter 2, we investigated the dynamics of endogenous FOXP3 expression and its relation to the suppressive function in activated human CD4+ T cells. In Chapter 3, we discovered an inverse correlation between membrane-bound TNF-alpha expression and cell suppressive abilities within human CD4+CD25++ T-cell compartment. In Chapter 4 & 5, we developed efficient approaches to consistently convert effector T cells into Tregs both in mice and humans. The underlying mechanisms responsible for the inconsistency in Treg conversion were unraveled as well. Part II (Chapter 6-7) aims to analyze the glycosylation pattern of antigen-specific antibodies and to obtain more insights on how glycosylation is regulated during an active immune response. Chapter 6 describes a method for the microscale purification and Fc-glycosylation analysis of auto-antibodies in patients with rheumatoid arthritis. In Chapter 7, we identified, by using an in vitro culture system, some factors that can influence the gylcan pattern of secreted IgG1 during the activation and differentiation of B cells. Show less
Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide... Show moreGenomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies. Show less
It is well established that naive cells can be converted by TGF-beta into CD4(+)CD25(+) regulatory T (Treg) cells with therapeutic potentials Likewise it is shown that all-trans retinoic acid (ATRA... Show moreIt is well established that naive cells can be converted by TGF-beta into CD4(+)CD25(+) regulatory T (Treg) cells with therapeutic potentials Likewise it is shown that all-trans retinoic acid (ATRA) can greatly enhance TGF-beta-induced Treg conversion a phenomenon which has mainly been studied in C57BL/6 mice Here we show that although purified naive cells are highly susceptible to Treg generation total CD4(+) T-cell populations from different mouse strains display significantly different sensitivities to TGF-beta/ATRA-induced Treg conversion The resistance of non-responder strains is associated with an enhanced production of IL-4 by memory T cells as well as an Increased sensitivity of naive T cells to the action of IL-4 Importantly neutralization of IL-4 overcomes the differences thereby enabling TGF-beta/ATRA to generate large numbers of functional Treg cells from total CD4(+) T cells in a consistent manner across different mouse strains Likewise blockade of IL-4 significantly enhances TGF-beta/ATRA-induced Treg conversion from human naive T cells in the presence of memory cells These results show that the inherent resistance of "non-responder mouse strains to Treg conversion induced by TGF-beta and ATRA can be reverted by neutralization of IL-4 and that Inhibiting the action of IL-4 is beneficial or even necessary for consistent inducible Treg generation (C) 2010 Elsevier Ltd All rights reserved Show less
It is well established that naive cells can be converted by TGF-β into CD4(+)CD25(+) regulatory T (Treg) cells with therapeutic potentials. Likewise, it is shown that all-trans retinoic acid (ATRA)... Show moreIt is well established that naive cells can be converted by TGF-β into CD4(+)CD25(+) regulatory T (Treg) cells with therapeutic potentials. Likewise, it is shown that all-trans retinoic acid (ATRA) can greatly enhance TGF-β-induced Treg conversion, a phenomenon which has mainly been studied in C57BL/6 mice. Here we show that, although purified naive cells are highly susceptible to Treg generation, total CD4(+) T-cell populations from different mouse strains display significantly different sensitivities to TGF-β/ATRA-induced Treg conversion. The resistance of "non-responder" strains is associated with an enhanced production of IL-4 by memory T cells as well as an increased sensitivity of naive T cells to the action of IL-4. Importantly, neutralization of IL-4 overcomes the differences, thereby enabling TGF-β/ATRA to generate large numbers of functional Treg cells from total CD4(+) T cells in a consistent manner across different mouse strains. Likewise, blockade of IL-4 significantly enhances TGF-β/ATRA-induced Treg conversion from human naive T cells in the presence of memory cells. These results show that the inherent resistance of "non-responder" mouse strains to Treg conversion induced by TGF-β and ATRA can be reverted by neutralization of IL-4 and that inhibiting the action of IL-4 is beneficial or even necessary for consistent inducible Treg generation. Show less
The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we... Show moreThe 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10(-8) per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research. Show less
The phagocyte NAPDH-oxidase complex consists of several phagocyte oxidase (phox) proteins, generating reactive oxygen species (ROS) upon activation. ROS are involved in the defense against... Show moreThe phagocyte NAPDH-oxidase complex consists of several phagocyte oxidase (phox) proteins, generating reactive oxygen species (ROS) upon activation. ROS are involved in the defense against microorganisms and also in immune regulation. Defective ROS formation leads to chronic granulomatous disease (CGD) with increased incidence of autoimmunity and disturbed resolution of inflammation. Because regulatory T cells (Tregs) suppress autoimmune T-cell responses and are crucial in down-regulating immune responses, we hypothesized that ROS deficiency may lead to decreased Treg induction. Previously, we showed that in p47(phox)-mutated mice, reconstitution of macrophages (Mph) with ROS-producing capacity was sufficient to protect the mice from arthritis. Now, we present evidence that Mph-derived ROS induce Tregs. In vitro, we showed that Mph ROS-dependently induce Treg, using an NADPH-oxidase inhibitor. This finding was confirmed genetically: rat or human CGD Mph with mutated p47(phox) or gp91(phox) displayed hampered Treg induction and T-cell suppression. However, basal Treg numbers in these subjects were comparable to those in controls, indicating a role for ROS in induction of peripheral Tregs. Induction of allogeneic delayed-type hypersensitivity with p47(phox)-mutated Mph confirmed the importance of Mph-derived ROS in Treg induction in vivo. We conclude that NAPDH oxidase activity in Mph is important for the induction of Tregs to regulate T cell-mediated inflammation. Show less
Scherer, H.U.; Woude, D. van der; Ioan-Facsinay, A.; Bannoudi, H. el; Trouw, L.A.; Wang, J.; ... ; Toes, R.E.M. 2010
Objective. Anti-citrullinated protein antibodies ( ACPA) exhibit unique specificity for rheumatoid arthritis. However, it is incompletely understood whether and how ACPA contribute to disease... Show moreObjective. Anti-citrullinated protein antibodies ( ACPA) exhibit unique specificity for rheumatoid arthritis. However, it is incompletely understood whether and how ACPA contribute to disease pathogenesis. The Fc part of human IgG carries 2 N-linked glycan moieties that are crucial for the structural stability of the antibody and that modulate both its binding affinity to Fc gamma receptors and its ability to activate complement. We undertook this study to analyze Fc glycosylation of IgG1 ACPA in serum and synovial fluid ( SF) in order to further characterize the immune response to citrullinated antigens. Methods. ACPA were isolated by affinity purification using cyclic citrullinated peptides as antigen. IgG1 Fc glycosylation was analyzed by mass spectrometry. ACPA IgG1 glycan profiles were compared with glycan profiles of total serum IgG1 obtained from 85 well-characterized patients. Glycan profiles of paired SF and serum samples were available from 11 additional patients. Results. Compared with the pool of serum IgG1, ACPA IgG1 lacked terminal sialic acid residues. In SF, ACPA were highly agalactosylated and lacked sialic acid residues, a feature that was not detected for total SF IgG1. Moreover, differential ACPA glycan profiles were detected in rheumatoid factor (RF)-positive and RF-negative patients. Conclusion. ACPA IgG1 exhibit a specific Fc-linked glycan profile that is distinct from that of total serum IgG1. Moreover, Fc glycosylation of ACPA differs markedly between SF and serum. Since Fc glycosylation directly affects the recruitment of Fc-mediated effector mechanisms, these data could further our understanding of the contribution of ACPA to disease pathogenesis. Show less
Gelderman, K.A.; Kraaij, M.D.; Kooij, S.W. van der; Koekkoek, K.; Wang, J.; Holmdahl, R.; Kooten, C. van 2010
OBJECTIVE:: Anti-citrullinated protein antibodies (ACPA) exhibit unique specificity for RA. Whether and how ACPA contribute to disease pathogenesis, however, is incompletely understood. The Fc part... Show moreOBJECTIVE:: Anti-citrullinated protein antibodies (ACPA) exhibit unique specificity for RA. Whether and how ACPA contribute to disease pathogenesis, however, is incompletely understood. The Fc part of human IgG carries two N-linked glycan moieties which are crucial for the structural stability of the antibody and modulate its binding affinity to Fcgamma receptors and its ability to activate complement. We have purified ACPA from serum and synovial fluid and analyzed Fc glycosylation profiles in a specific manner. METHODS:: ACPA were isolated by affinity purification using cyclic citrullinated peptides as antigen. IgG(1) Fc glycosylation was analyzed by mass spectrometry. ACPA glycan profiles were compared to glycan profiles of total serum IgG(1) obtained from 85 well-characterised patients. Glycan profiles of paired synovial fluid and serum samples were available from 11 additional patients. RESULTS:: Compared to the pool of serum IgG(1), ACPA IgG(1) lack terminal sialic acid residues. In synovial fluid, ACPA are highly agalactosylated and lack sialic acid residues, a feature that was not detected for total synovial fluid IgG(1). Moreover, differential ACPA glycan profiles were detected in RF-positive versus -negative patients. CONCLUSION:: ACPA IgG(1) exhibit a specific Fc-linked glycan profile which is distinct from total serum IgG(1). Moreover, Fc glycosylation of ACPA differs markedly between synovial fluid and serum. As Fc glycosylation directly affects the recruitment of Fc-mediated effector mechanisms, these data could further our understanding of the contribution of ACPA to disease pathogenesis. Show less
