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Regulatory Properties (regulatory + property)
Selected AbstractsAnalysis of regulatory elements of E-cadherin with reporter gene constructs in transgenic mouse embryosDEVELOPMENTAL DYNAMICS, Issue 2 2003Marc P. Stemmler Abstract Proper regulation of E-cadherin,mediated cell adhesion is important during early embryonic development and in organogenesis. In mice, E-cadherin is expressed from the fertilized egg onward and becomes down-regulated during gastrulation in mesoderm and its derivatives, but its expression is maintained in all epithelia. E-cadherin promoter analyses led to the identification of binding sites for two transcriptional repressors, Snail and SIP1, which are able to mediate down-regulation in vitro, but little is known about the regulatory elements that govern E-cadherin transcriptional activity in vivo. Here, we compared the developmentally regulated expression of a series of lacZ -reporter transgenes fused to different sequences of the murine E-cadherin gene between ,6 kb, including the promoter, and +16 kb, covering one third of intron 2. Four different segments with distinct regulatory properties were identified. The promoter fragment from +0.1 to ,1.5 kb remains inactive in most cases but occasionally induces ectopic expression in mesodermal tissues, although it contains binding sites for the repressors Snail and SIP1. This promoter fragment also lacks positive elements needed for the activation of transcription in ectoderm and endoderm. Sequences from ,1.5 to ,6 kb harbor regulatory elements for brain-specific expression and, in addition, insulator or silencer elements, because they are consistently inactive in the mesoderm. Only if sequences from +0.1 to +11 kb are combined with the promoter fragments is E-cadherin,specific transgene expression observed in endoderm and certain epithelia. Sequences between +11 and +16 kb contain cis -active elements that generally enhance transcription. Our analyses show that E-cadherin expression is governed by a complex interplay of multiple regulatory regions dispersed throughout large parts of the locus. Developmental Dynamics 227:238,245, 2003. © 2003 Wiley-Liss, Inc. [source] Structural and biophysical simulation of angiogenesis and vascular remodeling ,DEVELOPMENTAL DYNAMICS, Issue 4 2001Ralf Gödde Abstract The purpose of this report is to introduce a new computer model for the simulation of microvascular growth and remodeling into arteries and veins that imitates angiogenesis and blood flow in real vascular plexuses. A C++ computer program was developed based on geometric and biophysical initial and boundary conditions. Geometry was defined on a two-dimensional isometric grid by using defined sources and drains and elementary bifurcations that were able to proliferate or to regress under the influence of random and deterministic processes. Biophysics was defined by pressure, flow, and velocity distributions in the network by using the nodal-admittance-matrix-method, and accounting for hemodynamic peculiarities like Fahraeus-Lindqvist effect and exchange with extravascular tissue. The proposed model is the first to simulate interdigitation between the terminal branches of arterial and venous trees. This was achieved by inclusion of vessel regression and anastomosis in the capillary plexus and by remodeling in dependence from hemodynamics. The choice of regulatory properties influences the resulting vascular patterns. The model predicts interdigitating arteriovenous patterning if shear stress-dependent but not pressure-dependent remodeling was applied. By approximating the variability of natural vascular patterns, we hope to better understand homogeneity of transport, spatial distribution of hemodynamic properties and biomass allocation to the vascular wall or blood during development, or during evolution of circulatory systems. © 2001 Wiley-Liss, Inc. [source] Suppressive properties of human CD4+CD25+ regulatory T,cells are dependent on CTLA-4 expressionEUROPEAN JOURNAL OF IMMUNOLOGY, Issue 12 2004Brigitte Birebent Abstract It has been demonstrated that T,cells with regulatory properties are present within the peripheral blood CD4+CD25+ T,cell compartment. Here, we describe an original method to purify human CD4+CD25+CD152+ T,lymphocytes as living cells by forcing the exportation of CTLA-4 molecules stored in intracellular vesicules at the cell surface. By doing so, we demonstrate that CD4+CD25+ T,cells contain a smaller and more homogeneous population enriched in cells with in vitro regulatory activity. Moreover, we show that this enrichment in regulatory T,cells is associated with an increased expression of Foxp3 and that CD4+CD25+CD152+ T,lymphocytes display a much stronger suppressive activity in controlling in vitro proliferation of alloantigen-specific T,cells than CD4+CD25+CD152, T,lymphocytes purified in parallel. Lastly, by purifying such cells expressing CTLA-4, we demonstrate that indeed CTLA-4 is involved in CD4+CD25+CD152+ T,cell regulatory activity, while suppressive cytokines are not. [source] Deamidation of labile asparagine residues in the autoregulatory sequence of human phenylalanine hydroxylaseFEBS JOURNAL, Issue 5 2003Structural, functional implications Two dimensional electrophoresis has revealed a microheterogeneity in the recombinant human phenylalanine hydroxylase (hPAH) protomer, that is the result of spontaneous nonenzymatic deamidations of labile asparagine (Asn) residues [Solstad, T. and Flatmark, T. (2000) Eur. J. Biochem.267, 6302,6310]. Using of a computer algorithm, the relative deamidation rates of all Asn residues in hPAH have been predicted, and we here verify that Asn32, followed by a glycine residue, as well as Asn28 and Asn30 in a loop region of the N-terminal autoregulatory sequence (residues 19,33) of wt-hPAH, are among the susceptible residues. First, on MALDI-TOF mass spectrometry of the 24 h expressed enzyme, the E. coli 28-residue peptide, L15,K42 (containing three Asn residues), was recovered with four monoisotopic mass numbers (i.e., m/z of 3106.455, 3107.470, 3108.474 and 3109.476, of decreasing intensity) that differed by 1 Da. Secondly, by reverse-phase chromatography, isoaspartyl (isoAsp) was demonstrated in this 28-residue peptide by its methylation by protein- l -isoaspartic acid O -methyltransferase (PIMT; EC 2.1.1.77). Thirdly, on incubation at pH 7.0 and 37 °C of the phosphorylated form (at Ser16) of this 28-residue peptide, a time-dependent mobility shift from tR,,34 min to ,,31 min (i.e., to a more hydrophilic position) was observed on reverse-phase chromatography, and the recovery of the tR,,34 min species decreased with a biphasic time-course with t0.5 -values of 1.9 and 6.2 days. The fastest rate is compatible with the rate determined for the sequence-controlled deamidation of Asn32 (in a pentapeptide without 3D structural interference), i.e., a deamidation half-time of ,,1.5 days in 150 mm Tris/HCl, pH 7.0 at 37 °C. Asn32 is located in a cluster of three Asn residues (Asn28, Asn30 and Asn32) of a loop structure stabilized by a hydrogen-bond network. Deamidation of Asn32 introduces a negative charge and a partial ,-isomerization (isoAsp), which is predicted to result in a change in the backbone conformation of the loop structure and a repositioning of the autoregulatory sequence and thus affect its regulatory properties. The functional implications of this deamidation was further studied by site-directed mutagenesis, and the mutant form (Asn32,Asp) revealed a 1.7-fold increase in the catalytic efficiency, an increased affinity and positive cooperativity of L-Phe binding as well as substrate inhibition. [source] The CD8+ dendritic cell subsetIMMUNOLOGICAL REVIEWS, Issue 1 2010Ken Shortman Summary:, Mouse lymphoid tissues contain a subset of dendritic cells (DCs) expressing CD8, together with a pattern of other surface molecules that distinguishes them from other DCs. These molecules include particular Toll-like receptor and C-type lectin pattern recognition receptors. A similar DC subset, although lacking CD8 expression, exists in humans. The mouse CD8+ DCs are non-migrating resident DCs derived from a precursor, distinct from monocytes, that continuously seeds the lymphoid organs from bone marrow. They differ in several key functions from their CD8, DC neighbors. They efficiently cross-present exogenous cell-bound and soluble antigens on major histocompatibility complex class I. On activation, they are major producers of interleukin-12 and stimulate inflammatory responses. In steady state, they have immune regulatory properties and help maintain tolerance to self-tissues. During infection with intracellular pathogens, they become major presenters of pathogen antigens, promoting CD8+ T-cell responses to the invading pathogens. Targeting vaccine antigens to the CD8+ DCs has proved an effective way to induce cytotoxic T lymphocytes and antibody responses. [source] Suppressor of cytokine signalling-3 at pathological levels does not regulate lipopolysaccharide or interleukin-10 control of tumour necrosis factor-, production by human monocytesIMMUNOLOGY, Issue 1 2006Cecilia M. Prêle Summary Interleukin-10 (IL-10) is a potent anti-inflammatory cytokine that suppresses the production of tumour necrosis factor-, (TNF-,) by monocytes and macrophages. Suppressor of cytokine signalling-3 (SOCS3), a negative regulator of the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway, is induced following IL-10 exposure but recent studies in mice suggest that SOCS3 only targets gp-130-dependent signal transduction pathways. Understanding the signalling pathways responsible for IL-10-mediated effects in primary human monocytes is relevant to human inflammatory disease and necessary for the identification of potential therapeutic targets. An adenoviral transfection system was used to express different levels of SOCS3 (quantified experimentally with its tag green fluorescent protein (GFP)) with the aim of investigating the role of SOCS3 in LPS-induced and IL-10-mediated suppression of TNF-, production by non-transformed human monocytes. SOCS3 over-expression had no effect on TNF-, mRNA levels induced by LPS or LPS plus IL-10, or on IL-10 phosphorylation of STAT3, STAT1 and ERK1/2. When data from all donors were combined, adenoviral overexpression of SOCS3 significantly reversed the suppressive effects of IL-10 on LPS-induced TNF-, production after 2 hr. However, there was a direct correlation between mean GFP intensity (extent of viral infection) and extent of reversal of IL-10's inhibitory effects. Physiological levels of SOCS3 detected in IL-10-exposed human monocytes had no effect on LPS-induced TNF-, production. Although overexpression of SOCS3 to supraphysiological levels transiently antagonized the regulatory properties of IL-10 by a post-transcriptional mechanism, these findings suggest that under pathological conditions SOCS3 does not control LPS-activation or the anti-inflammatory properties of IL-10 in primary human monocytes. [source] Orthogonal Chemical Genetic Approaches for Unraveling Signaling PathwaysIUBMB LIFE, Issue 6 2005Kavita Shah Abstract While chemical genetic approach uses small molecules to probe protein functions in cells or organisms, orthogonal chemical genetics refers to strategies that utilize reengineered protein-small molecule interfaces, to alter specificities, in order to probe their functions. The advantage of orthogonal chemical genetics is that the changes at the interfaces are generally so minute that it goes undetected by natural processes, and thus depicts a true physiological picture of biological phenomenon. This review highlights the recent advances in the area of orthogonal chemical genetics, especially those designed to probe signaling processes. Dynamic protein-protein and enzyme-substrate interactions following stimuli form the foundation of signal transduction. These processes not only break spatial and temporal boundaries between interacting proteins, but also impart distinct regulatory properties by creating functional diversity at the interfaces. Functional and temporal modulation of these dynamic interactions by specific chemical probes provides extremely powerful tools to initiate, ablate, decouple and deconvolute different components of a signaling pathway at multiple stages. Not surprisingly, multiple receptor-ligand reengineering approaches have been developed in the last decade to selectively manipulate these transient interactions with the aim of unraveling signaling events. However, given the diversity of protein-protein interactions and novel chemical genetic probes developed to perturb these processes, a short review cannot do adequate justice to all aspects of signaling. For this reason, this review focuses on some orthogonal chemical-genetic strategies that are developed to study signaling processes involving enzyme-substrate interactions. IUBMB Life, 57: 397-405, 2005 [source] Gluconic acid production by Aspergillus terreusLETTERS IN APPLIED MICROBIOLOGY, Issue 3 2010C. Dowdells Abstract Aim:,Aspergillus terreus produces itaconic acid at low pH but lovastatin and other secondary metabolites at higher pH in the fermentation. The utilization of glucose as a carbon substrate was investigated for secondary metabolite production by A. terreus. Methods and Results:, With a starting pH of 6·5, glucose was rapidly metabolized to gluconic acid by the wild-type strain and by transformants harbouring Aspergillus niger genes encoding 6-phosphofructo-1-kinases with superior kinetic and regulatory properties for bioproduction of metabolites from glucose. On exhaustion of the glucose in batch fermentations, the accumulated gluconic acid was utilized as a carbon source. Conclusions:, A novel pathway of glucose catabolism was demonstrated in A. terreus, a species whose wild type is, without any strain development, capable of producing gluconic acid at high molar conversion efficiency (up to 0·7 mol mol,1 glucose consumed). Significance and Impact of the Study:,Aspergillus terreus is a potential novel producer organism for gluconic acid, a compound with many uses as a bulk chemical. With a new knowledge of glucose catabolism by A. terreus, fermentation strategies for secondary metabolite production can be devised with glucose feeding using feedback regulation by pH. [source] T cell-mediated immunoregulation in the gastrointestinal tractALLERGY, Issue 4 2009L. Saurer In the intestinal tract, only a single layer of epithelial cells separates innate and adaptive immune effector cells from a vast amount of antigens. Here, the immune system faces a considerable challenge in tolerating commensal flora and dietary antigens while preventing the dissemination of potential pathogens. Failure to tightly control immune reactions may result in detrimental inflammation. In this respect, ,conventional' regulatory CD4+ T cells, including naturally occurring and adaptive CD4+ CD25+ Foxp3+ T cells, Th3 and Tr1 cells, have recently been the focus of considerable attention. However, regulatory mechanisms in the intestinal mucosa are highly complex, including adaptations of nonhaematopoietic cells and innate immune cells as well as the presence of unconventional T cells with regulatory properties such as resident TCR,, or TCR,, CD8+ intraepithelial lymphocytes. This review aims to summarize the currently available knowledge on conventional and unconventional regulatory T cell subsets (Tregs), with special emphasis on clinical data and the potential role or malfunctioning of Tregs in four major human gastrointestinal diseases, i.e. inflammatory bowel diseases, coeliac disease, food allergy and colorectal cancer. We conclude that the clinical data confirms some but not all of the findings derived from experimental animal models. [source] Modus operandi of the bacterial RNA polymerase containing the ,54 promoter-specificity factorMOLECULAR MICROBIOLOGY, Issue 3 2008Sivaramesh Wigneshweraraj Summary Bacterial sigma (,) factors confer gene specificity upon the RNA polymerase, the central enzyme that catalyses gene transcription. The binding of the alternative , factor ,54 confers upon the RNA polymerase special functional and regulatory properties, making it suited for control of several major adaptive responses. Here, we summarize our current understanding of the interactions the ,54 factor makes with the bacterial transcription machinery. [source] Riboregulation by DsrA RNA: trans -actions for global economyMOLECULAR MICROBIOLOGY, Issue 4 2000MicroReview DsrA is an 87 nucleotide Escherichia coli RNA with extraordinary regulatory properties. The profound impact of its actions stems from DsrA regulating translation of two global transcription regulators, H-NS and RpoS (,s), by sequence-specific RNA,RNA interactions. H-NS is a major nucleoid-structuring and global repressor protein, and RpoS is the stationary phase and stress response sigma factor of RNA polymerase. DsrA changes its conformation to bind to these two different mRNA targets and thereby inhibits H-NS translation, while stimulating that of RpoS in a mechanistically distinct fashion. DsrA apparently binds both the start and the stop codons of hns mRNA and sharply decreases the mRNA half-life. DsrA also binds sequences in the 5,-untranslated leader region of rpoS mRNA, enhancing rpoS mRNA stability and RpoS translation. A cohort of genes, governed by H-NS repression and RpoS activation, are thus regulated. Low temperatures increase the levels of DsrA, with differential effects on H-NS and RpoS. Additionally, the RNA chaperone protein Hfq is involved with DsrA regulation, as well as with other small RNAs that also act on RpoS to co-ordinate stress responses. We address the possible functions of this genetic regulatory mechanism, as well as the advantages of using small RNAs as global regulators to orchestrate gene expression. [source] CO2 -concentrating mechanisms in Egeria densa, a submersed aquatic plantPHYSIOLOGIA PLANTARUM, Issue 4 2002María V. Lara Egeria densa is an aquatic higher plant which has developed different mechanisms to deal with photosynthesis under conditions of low CO2 availability. On the one hand it shows leaf pH-polarity, which has been proposed to be used for bicarbonate utilization. In this way, at high light intensities and low dissolved carbon concentration, this species generates a low pH at the adaxial leaf surface. This acidification shifts the equilibrium HCO3,/CO2 towards CO2, which enters the cell by passive diffusion. By this means, E. densa increases the concentration of CO2 available for photosynthesis inside the cells, when this gas is limiting. On the other hand, under stress conditions resulting from high temperature and high light intensities, it shows a biochemical adaptation with the induction of a C4 -like mechanism but without Kranz anatomy. Transfer from low to high temperature and light conditions induces increased levels of phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31) and NADP-malic enzyme (NADP-ME, EC 1.1.1.40), both key enzymes participating in the Hatch-Slack cycle in plants with C4 metabolism. Moreover, one PEPC isoform, whose synthesis is induced by high temperature and light, is phosphorylated in the light, and changes in kinetic and regulatory properties are correlated with changes in the phosphorylation state of this enzyme. In the present review, we describe these two processes in this submersed angiosperm that appear to help it perform photosynthesis under conditions of extreme temperatures and high light intensities. [source] Evaluation of the NK2 Homeobox 1 Gene (NKX2-1) as a Hirschsprung's Disease Locus THIS ARTICLE HAS BEEN RETRACTEDANNALS OF HUMAN GENETICS, Issue 2 2008M.-M. Garcia-Barceló Summary Hirschsprung's disease (HSCR, colonic aganglionosis) is an oligogenic entity that usually requires mutations in RET and other interacting loci. Decreased levels of RET expression may lead to the manifestation of HSCR. We previously showed that RET transcription was decreased due to alteration of the NKX2,1 binding site by two HSCR-associated RET promoter single nucleotide polymorphisms (SNPs). This prompted us to investigate whether DNA alterations in NKX2-1 could play a role in HSCR by affecting the RET -regulatory properties of the NKX2,1 protein. Our initial study on 86 Chinese HSCR patients revealed a Gly322Ser amino acid substitution in the NKX2,1 protein. In this study, we have examined 102 additional Chinese and 70 Caucasian patients and 194 Chinese and 60 Caucasian unselected, unrelated, subjects as controls. The relevance of the DNA changes detected in NKX2-1 by direct sequencing were evaluated using bioinformatics, reporter and binding-assays, mouse neurosphere culture, immunohistochemistry and immunofluorescence techniques. Met3Leu and Pro48Pro were identified in 2 Caucasian and 1 Chinese patients respectively. In vitro analysis showed that Met3Leu reduced the activity of the RET promoter by 100% in the presence of the wild-type or HSCR-associated RET promoter SNP alleles. The apparent binding affinity of the NKX2,1 mutated protein was not decreased. The Met3Leu mutation may affect the interaction of NKX2,1 with its protein partners. The absence of NKX2-1 expression in mouse but not in human gut suggests that the role of NKX2,1 in gut development differs between the two species. NKX2-1 mutations could contribute to HSCR by affecting RET expression through defective interactions with other transcription factors. [source] Lumped dynamic model for a bistable genetic regulatory circuit within a variable-volume whole-cell modelling frameworkASIA-PACIFIC JOURNAL OF CHEMICAL ENGINEERING, Issue 6 2009Gheorghe Maria Abstract Genetic regulatory circuits (GRCs) including switches, oscillators, signal amplifiers or filters, and signalling circuits are responsible for the control of cell metabolism. Modelling such complex GRCs is a difficult task due to high complexity of the the process (partly known) and the structural, functional and temporal hierarchical organisation of the cell system. Modular lumped representation, grouping some reactions/components and including different types of variables, is a promising alternative allowing individual module characterisation and elaboration of extended simulation platforms for representing the GRC dynamic properties and designing new cell functions. Such models allow to in-silico design modified micro-organisms with desirable properties for practical applications in bioprocess engineering and biotechnology. In the present work, the analysis of a designed bistable switch formed by two gene expression modules is performed in a variable-volume and whole-cell modelling framework, by mimicking the Escherichia coli cell growth. The advantages but also limitations of such a new approach are investigated, by using a Hill-type kinetics combined with few elementary steps, with the aim of better representing the adjustable levels of key intermediates tuning the GRC regulatory properties in terms of stability strength, species connectivity, responsiveness, and regulatory efficiency under stationary and dynamic perturbations. Copyright © 2009 Curtin University of Technology and John Wiley & Sons, Ltd. [source] | ||||||||||||||||