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Molecular Processes (molecular + process)
Selected AbstractsCan molecular mechanisms of biological processes be extracted from expression profiles?BIOESSAYS, Issue 12 2001Case study: endothelial contribution to tumor-induced angiogenesis Whereas the genome contains all potential developmental programs, expression profiles permit the determination of genes that are actively transcribed under defined physiological conditions. In this article, the idea of extracting biological mechanisms from expression data is tested. Molecular processes of the endothelial contribution to angiogenesis are derived from recently published expression profiles. The analysis reveals the sensitivity limits of experimental detection of transcriptional changes and how sequence-analytic techniques can help to identify the function of genes in question. We conclude that the transcripts (http://mendel.imp.univie.ac.at/SEQUENCES/TEMS/) found to be up-regulated in angiogenesis are involved in extracellular matrix remodeling, cellular migration, adhesion, cell-cell communication rather than in angiogenesis initiation or integrative control. Comparison with tissue-specific patterns of EST occurrence shows that, indeed, the presumptive tumor-specific endothelial markers are more generally expressed by cell types involved in migration and matrix remodeling processes. This exemplary study demonstrates how bioinformatics approaches can be helpful in deriving mechanistic information from diverse sources of experimental data. BioEssays 23:1159,1175, 2001. © 2001 John Wiley & Sons, Inc. [source] An Analysis of Two Liquid-State Adaptive Feedback ExperimentsISRAEL JOURNAL OF CHEMISTRY, Issue 1 2007Paul Brumer Adaptive feedback experiments, which provide an engineering oriented approach to optimizing a desired target in a molecular process, have been extensively developed over the past decade. Efforts to extract the control mechanisms that underlie the observed control have, however, only recently begun in earnest. We describe the results of the analyses of two liquid state adaptive feedback experiments, showing that the resultant control takes little advantage of coherent quantum effects. [source] The molecular basis of factor V and VIII procofactor activationJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 12 2009R. M. CAMIRE Summary., Activation of precursor proteins by specific and limited proteolysis is a hallmark of the hemostatic process. The homologous coagulation factors (F)V and FVIII circulate in an inactive, quiescent state in blood. In this so-called procofactor state, these proteins have little, if any procoagulant activity and do not participate to any significant degree in their respective macromolecular enzymatic complexes. Thrombin is considered a key physiological activator, cleaving select peptide bonds in FV and FVIII which ultimately leads to appropriate structural changes that impart cofactor function. As the active cofactors (FVa and FVIIIa) have an enormous impact on thrombin and FXa generation, maintaining FV and FVIII as inactive procofactors undoubtedly plays an important regulatory role that has likely evolved to maintain normal hemostasis. Over the past three decades there has been widespread interest in studying the proteolytic events that lead to the activation of these proteins. While a great deal has been learned, mechanistic explanations as to how bond cleavage facilitates conversion to the active cofactor species remain incompletely understood. However, recent advances have been made detailing how thrombin recognizes FV and FVIII and also how the FV B-domain plays a dominant role in maintaining the procofactor state. Here we review our current understanding of the molecular process of procofactor activation with a particular emphasis on FV. [source] Collagen types I, III, and V constitute the thick collagen fibrils of the mouse deciduaMICROSCOPY RESEARCH AND TECHNIQUE, Issue 1 2007Karin Spiess Abstract A mammal's endometrium is deeply remodeled while receiving and implanting an embryo. In addition to cell proliferation and growth, endometrial remodeling also comprises synthesis and degradation of several molecular components of the extracellular matrix. All of these events are orchestrated by a precise sequence of ovarian hormones and influenced by several types of cytokines. As we have previously reported, an intriguing and rapid increase in collagen fibril diameter occurs in the decidualized areas of the endometrium, surrounding the implantation crypt, whereas collagen fibrils situated far from the embryo remain unchanged. Collagen fibrilogenesis is a complex molecular process coordinated by a number of factors, such as the types and amounts of glycosaminoglycans and proteoglycans associated with collagen molecules. Collagen genetic type, mechanical stress, aging, and other factors not yet identified also contribute to this development. A recent study suggests that thick fibrils from mouse decidua are formed, at least in part, by aggregation of thin fibrils existing in the stroma before the onset of decidualization. In the present ultrastructural study using single and double immunogold localization, we showed that both thin and thick collagen fibrils present in the mouse pregnant endometrium endometrium are heterotypic structures formed at least by type I, type III, and type V collagens. However, type V collagen predominates in the thick collagen fibrils, whereas it is almost absent of the thin collagen fibrils. The putative role of type V homotrimer in the rapid increase of the diameter of collagen fibrils of the mouse decidua is discussed. Microsc. Res. Tech., 2006. © 2006 Wiley-Liss, Inc. [source] Prevalidation of potential protein biomarkers in toxicology using iTRAQÔ reagent technologyPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 10 2007Matthias Glückmann Abstract Today, toxicoproteomics still relies mainly on 2-DE followed by MS for detection and identification of proteins, which might characterize a certain state of disease, indicate toxicity or even predict carcinogenicity. We utilized the classical 2-DE/MS approach for the evaluation of early protein biomarkers which are predictive for chemically induced hepatocarcinogenesis in rats. We were able to identify statistically significantly deregulated proteins in N -nitrosomorpholine exposed rat liver tissue. Based on literature data, biological relevance in the early molecular process of hepatocarcinogenicity could be suggested for most of these potential biomarkers. However, in order to ensure reliable results and to create the prerequisites necessary for integration in routine toxicology studies in the future, these protein expression patterns need to be prevalidated using independent technology platforms. In the current study, we evaluated the usefulness of iTRAQÔ reagent technology (Applied Biosystems, Framingham, USA), a recently introduced MS-based protein quantitation method, for verification of the 2-DE/MS biomarkers. In summary, the regulation of 26 2-DE/MS derived protein biomarkers could be verified. Proteins like HSP 90-beta, annexin A5, ketohexokinase, N -hydroxyarylamine sulfotransferase, ornithine aminotransferase, and adenosine kinase showed highly comparable fold changes using both proteomic quantitation strategies. In addition, iTRAQ analysis delivered further potential biomarkers with biological relevance to the processes of hepatocarcinogenicity: e.g. placental form of glutathione S-transferase (GST-P), carbonic anhydrase, and aflatoxin B1 aldehyde reductase. Our results show both the usefulness of iTRAQ reagent technology for biomarker prevalidation as well as for identification of further potential marker proteins, which are indicative for liver hepatocarcinogenicity. [source] Climatic variability and the evolution of insect freeze toleranceBIOLOGICAL REVIEWS, Issue 2 2003BRENT J. SINCLAIR ABSTRACT Insects may survive subzero temperatures by two general strategies: Freeze-tolerant insects withstand the formation of internal ice, while freeze-avoiding insects die upon freezing. While it is widely recognized that these represent alternative strategies to survive low temperatures, and mechanistic understanding of the physical and molecular process of cold tolerance are becoming well elucidated, the reasons why one strategy or the other is adopted remain unclear. Freeze avoidance is clearly basal within the arthropod lineages, and it seems that freeze tolerance has evolved convergently at least six times among the insects (in the Blattaria, Orthoptera, Coleoptera, Hymenoptera, Diptera and Lepidoptera). Of the pterygote insect species whose cold-tolerance strategy has been reported in the literature, 29% (69 of 241 species studied) of those in the Northern Hemisphere, whereas 85%(11 of 13 species) in the Southern Hemisphere exhibit freeze tolerance. A randomization test indicates that this predominance of freeze tolerance in the Southern Hemisphere is too great to be due to chance, and there is no evidence of a recent publication bias in favour of new reports of freeze-tolerant species. We conclude from this that the specific nature of cold insect habitats in the Southern Hemisphere, which are characterized by oceanic influence and climate variability must lead to strong selection in favour of freeze tolerance in this hemisphere. We envisage two main scenarios where it would prove advantageous for insects to be freeze tolerant. In the first, characteristic of cold continental habitats of the Northern Hemisphere, freeze tolerance allows insects to survive very low temperatures for long periods of time, and to avoid desiccation. These responses tend to be strongly seasonal, and insects in these habitats are only freeze tolerant for the overwintering period. By contrast, in mild and unpredictable environments, characteristic of habitats influenced by the Southern Ocean, freeze tolerance allows insects which habitually have ice nucleators in their guts to survive summer cold snaps, and to take advantage of mild winter periods without the need for extensive seasonal cold hardening. Thus, we conclude that the climates of the two hemispheres have led to the parallel evolution of freeze tolerance for very different reasons, and that this hemispheric difference is symptomatic of many wide-scale disparities in Northern and Southern ecological processes. [source] Analysis of Particle Pumping Using SOLDOR/NEUT2D Code in the JT-60U TokamakCONTRIBUTIONS TO PLASMA PHYSICS, Issue 1-3 2008H. Kawashima Abstract In order to understand the particle pumping on JT-60U, we analyze the roles of atomic and molecular processes using SOLDOR/NEUT2D code. A case of short strike point distance shows that most of neutrals produced on the targets go toward the exhaust slot directly. Whereas, neutrals are scattered in the spherically at random for the long distance case by collision processes and a few of them go toward the slot. It is clarified that the incident neutrals to the slot at low ne/high Te divertor plasma condition are dominated by atoms. Those at high ne/low Te condition are dominated by molecules due to elastic collision. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Hypertrophic Scars and Keloids,A Review of Their Pathophysiology, Risk Factors, and Therapeutic ManagementDERMATOLOGIC SURGERY, Issue 2 2009DOLORES WOLFRAM MD BACKGROUND Hypertrophic scars and keloids result from an abnormal fibrous wound healing process in which tissue repair and regeneration-regulating mechanism control is lost. These abnormal fibrous growths present a major therapeutic dilemma and challenge to the plastic surgeon because they are disfiguring and frequently recur. OBJECTIVE To provide updated clinical and experimental information on hypertrophic scars and keloids so that physicians can better understand and properly treat such lesions. METHODS A Medline literature search was performed for relevant publications and for diverse strategies for management of hypertrophic scars and keloids. CONCLUSION The growing understanding of the molecular processes of normal and abnormal wound healing is promising for discovery of novel approaches for the management of hypertrophic scars and keloids. Although optimal treatment of these lesions remains undefined, successful healing can be achieved only with combined multidisciplinary therapeutic regimens. [source] Probing events with single molecule sensitivity in zebrafish and Drosophila embryos by fluorescence correlation spectroscopyDEVELOPMENTAL DYNAMICS, Issue 12 2009Xianke Shi Abstract Zebrafish and Drosophila are animal models widely used in developmental biology. High-resolution microscopy and live imaging techniques have allowed the investigation of biological processes down to the cellular level in these models. Here, using fluorescence correlation spectroscopy (FCS), we show that even processes on a molecular level can be studied in these embryos. The two animal models provide different advantages and challenges. We first characterize their autofluorescence pattern and determine usable penetration depth for FCS especially in the case of zebrafish, where tissue thickness is an issue. Next, the applicability of FCS to study molecular processes is shown by the determination of blood flow velocities with high spatial resolution and the determination of diffusion coefficients of cytosolic and membrane-bound enhanced green fluorescent protein,labeled proteins in different cell types. This work provides an approach to study molecular processes in vivo and opens up the possibility to relate these molecular processes to developmental biology questions. Developmental Dynamics 238:3156,3167, 2009. © 2009 Wiley-Liss, Inc. [source] Liposome-mediated transfection of mature taste cellsDEVELOPMENTAL NEUROBIOLOGY, Issue 1 2005Ana Marie Landin Abstract The introduction and expression of exogenous DNA in neurons is valuable for analyzing a range of cellular and molecular processes in the periphery, e.g., the roles of transduction-related proteins, the impact of growth factors on development and differentiation, and the function of promoters specific to cell type. However, sensory receptor cells, particularly chemosensory cells, have been difficult to transfect. We have successfully introduced plasmids expressing green and Discosoma Red fluorescent proteins (GFP and DsRed) into rat taste buds in primary culture. Transfection efficiency increased when delaminated taste epithelium was redigested with fresh protease, suggesting that a protective barrier of extracellular matrix surrounding taste cells may normally be present. Because taste buds are heterogeneous aggregates of cells, we used ,-gustducin, neuronal cell adhesion molecule (NCAM), and neuronal ubiquitin carboxyl terminal hydrolase (PGP9.5), markers for defined subsets of mature taste cells, to demonstrate that liposome-mediated transfection targets multiple taste cell types. After testing eight commercially available lipids, we identified one, Transfast, that is most effective on taste cells. We also demonstrate the effectiveness of two common "promiscuous" promoters and one promoter that taste cells use endogenously. These studies should permit ex vivo strategies for studying development and cellular function in taste cells. © 2005 Wiley Periodicals, Inc. J. Neurobiol, 2005 [source] Laser capture microdissection and microarray analysis of dividing neural progenitor cells from the adult rat hippocampusEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 5 2007Ulf Gurok Abstract Neural progenitor cells reside in the hippocampus of adult rodents and humans and generate granule neurons throughout life. Knowledge about the molecular processes regulating these neurogenic cells is fragmentary. In order to identify genes with a role in the proliferation of adult neural progenitor cells, a protocol was elaborated to enable the staining and isolation of such cells under RNA-preserving conditions with a combination of immunohistochemistry and laser capture microdissection. We increased proliferation of neural progenitor cells by electroconvulsive treatment, one of the most effective antidepressant treatments, and isolated Ki-67-positive cells using this new protocol. RNA amplification via in vitro transcription and subsequent microarray analysis revealed over 100 genes that were differentially expressed in neural progenitor cells due to electroconvulsive treatment compared to untreated control animals. Some of these genes have already been implicated in the functioning of neural progenitor cells or have been induced by electroconvulsive treatment; these include brain-derived neurotrophic factor (Bdnf), PDZ-binding kinase (Pbk) and abnormal spindle-like microcephaly-associated (Aspm). In addition, genes were identified for which no role in the proliferation of neurogenic progenitors has been described so far, such as enhancer of zeste homolog 2 (Ezh2). [source] FMRFamide gene and peptide expression during central nervous system development of the cephalopod mollusk, Idiosepius notoidesEVOLUTION AND DEVELOPMENT, Issue 2 2010Tim Wollesen SUMMARY Mollusks are a showcase of brain evolution represented by several classes with a varying degree of nervous system centralization. Cellular and molecular processes involved in the evolution of the highly complex cephalopod brain from a simple, monoplacophoran-like ancestor are still obscure and homologies on the cellular level are poorly established. FMRFamide (Phe-Ile-Arg-Phe-NH2)-related peptides (FaRPs) constitute an evolutionarily conserved and diverse group of neuropeptides in the central nervous system (CNS) of many metazoans. Herein, we provide a detailed description of the developing FMRFamide-like immunoreactive (Fa-lir) CNS of the pygmy squid Idiosepius notoides using gene expression analyses and immunocytochemistry. The open reading frame of the I. notoides FMRFamide gene InFMRF predicts one copy each of FIRFamide, FLRFamide (Phe-Leu-Arg-Phe-NH2), ALSGDAFLRFamide (Ala-Leu-Ser-Gly-Asp-Ala-Phe-Leu-Arg-Phe-NH2), and 11 copies of FMRFamide. Applying matrix-assisted laser desorption/ionization time-of-flight (ToF) mass spectrometry-based peptide profiling, we characterized all predicted FaRPs except ALSGDAFLRFamide. Two cell clusters express InFMRF and show FMRFamide-like-immunoreactivity within the palliovisceral ganglia, that is, the future posterior subesophageal mass, during the lobe differentiation phase. They project neurites via ventral axonal tracts, which form the scaffold of the future subesophageal mass. In the supraesophageal mass, InFMRF is first expressed during mid-embryogenesis in the superior and inferior buccal lobes. A neurite of the peduncle commissure represents the first Fa-lir element. Later, the sub- and supraesophageal mass interconnect via Fa-lir neurites and more brain lobes express InFMRF and FMRFamide-like peptides. InFMRF expression was observed in fewer brain lobes than Fa-lir elements. The early expression of InFMRF and FMRFamide-lir peptides in the visceral system and not the remaining CNS of the cephalopod I. notoides resembles the condition found in the majority of investigated gastropods. [source] Memory retrieval after contextual fear conditioning induces c-Fos and JunB expression in CA1 hippocampusGENES, BRAIN AND BEHAVIOR, Issue 1 2003T. Strekalova Using specific polyclonal antisera against c-Fos, JunB, c-Jun and JunD, we tried to identify the candidate transcription factors of the immediate early gene family which may contribute to the molecular processes during contextual memory reconsolidation. For that purpose we analyzed the expression of these proteins in the hippocampus after contextual memory retrieval in a mouse model of fear conditioning. A single exposure to a foot shock of 0.8 mA was sufficient to induce robust contextual fear conditioning in C57Bl/6N mice. In these mice context dependent memory retrieval evoked a marked induction of c-Fos and JunB, but not of c-Jun and JunD, in pyramidal CA1 neurons of the dorsal hippocampus. In contrast, mice exposed and re-exposed only to the context, without foot shock, did not show behavioral signs of contextual fear conditioning and exhibited significantly less expression of c-Fos and JunB in CA1 neurons. Mice which received a foot shock but were not re-exposed to the context revealed no immediate early gene induction. These results demonstrate that contextual memory retrieval is associated with de novo synthesis of specific members of the Fos/Jun transcription factor family. Therefore we suggest that these genes may contribute to plasticity and reconsolidation accompanying the retrieval process. The specific activation of CA1 neurons during the retrieval of contextual fear associations supports the postulated concept of a mnemonic role of this hippocampal subsector during the retrieval of contextual informations. [source] From molecules to ecosystems through dynamic energy budget modelsJOURNAL OF ANIMAL ECOLOGY, Issue 6 2000R. M. Nisbet Summary 1. Dynamic energy budget (DEB) models describe how individuals acquire and utilize energy, and can serve as a link between different levels of biological organization. 2. We describe the formulation and testing of DEB models, and show how the dynamics of individual organisms link to molecular processes, to population dynamics, and (more tenuously) to ecosystem dynamics. 3. DEB models offer mechanistic explanations of body-size scaling relationships. 4. DEB models constitute powerful tools for applications in toxicology and biotechnology. 5. Challenging questions arise when linking DEB models with evolutionary theory. [source] Morphological variations in a tooth family through ontogeny in Pleurodeles waltl (Lissamphibia, Caudata)JOURNAL OF MORPHOLOGY, Issue 9 2006Tiphaine Davit-Béal Abstract Most nonmammalian species replace their teeth continuously (so-called polyphyodonty), which allows morphological and structural modifications to occur during ontogeny. We have chosen Pleurodeles waltl, a salamander easy to rear in the laboratory, as a model species to establish the morphological foundations necessary for future molecular approaches aiming to understand not only molecular processes involved in tooth development and replacement, but also their changes, notably during metamorphosis, that might usefully inform studies of modifications of tooth morphology during evolution. In order to determine when (in which developmental stage) and how (progressively or suddenly) tooth modifications take place during ontogeny, we concentrated our observations on a single tooth family, located at position I, closest to the symphysis on the left lower jaw. We monitored the development and replacement of the six first teeth in a large growth series ranging from 10-day-old embryos (tooth I1) to adult specimens (tooth I6), using light (LM), scanning (SEM), and transmission electron (TEM) microscopy. A timetable of the developmental and functional period is provided for the six teeth, and tooth development is compared in larvae and young adults. In P. waltl the first functional tooth is not replaced when the second generation tooth forms, in contrast to what occurs for the later generation teeth, leading to the presence of two functional teeth in a single position during the first 2 months of life. Larval tooth I1 shows dramatically different features when compared to adult tooth I6: a dividing zone has appeared between the dentin cone and the pedicel; the pulp cavity has enlarged, allowing accommodation of large blood vessels; the odontoblasts are well organized along the dentin surface; tubules have appeared in the dentin; and teeth have become bicuspidate. Most of these modifications take place progressively from one tooth generation to the next, but the change from monocuspid to bicuspid tooth occurs during the tooth I3 to tooth I4 transition at metamorphosis. J. Morphol. © 2006 Wiley-Liss, Inc. [source] Target-dependent modulation of neurotransmitter release in cultured Helix neurons involves adhesion moleculesJOURNAL OF NEUROSCIENCE RESEARCH, Issue 2 2001Mirella Ghirardi Abstract The secretory capabilities of the serotonergic neuron C1 of cerebral ganglion of Helix pomatia were markedly reduced when it was cultured in contact with the wrong target neuron, C3. When the neuron B2, one of its physiological targets, was micromanipulated within the network made of intermingled neurites originating from the axonal stumps of both C1 and C3 neurons, C1 increased the amount of the evoked transmitter release, which, after 30 min, reached the level observed when cocultured with the appropriate target. The removal of the appropriate target brought C1 back to the low release condition. By imaging C1 neurites with a fluorescent dye, morphological changes involving a local increase in the number of varicosities could be observed as early as 30 min after contact with the appropriate target. Monoclonal antibody 4E8 against apCAM, a family of Aplysia adhesion molecules, recognizes apCAM-like molecules of the Helix central nervous system on immunocytochemistry and Western blot analysis. The contact with the appropriate target previously incubated in a 4E8 solution, which did not interfere with its capacity to respond to serotonin, failed to increase the transmitter release of C1 cocultured in the presence of the wrong target, C3. These results suggest that the apCAM-like antigens bound to the target membrane participate in the molecular processes responsible for the assembly of the "release machinery" present in the functional presynaptic structure. J. Neurosci. Res. 65:111,120, 2001. © 2001 Wiley-Liss, Inc. [source] Exploring prokaryotic diversity: there are other molecular worldsMOLECULAR MICROBIOLOGY, Issue 1 2005Luis Angel Fernández Summary Prokaryotes are the major source of biological diversity on earth. This is not simply because of the large number of species present, or because of their diverse growth conditions and environmental niches populated by them, but because of the wealth of genes, metabolic pathways and molecular processes that are only found in prokaryotic cells. Therefore, Bacteria and Archaea (and their phages) cannot be considered any longer as miniaturized models of Eukaryotes, but as a genuine source of unique biological processes that are mediated by unique sets of genes and molecular devices. A true understanding of complex biological phenomena will require a deeper knowledge of this vast prokaryotic world. The second European Molecular Biology Organization (EMBO) conference on Molecular Microbiology entitled ,Exploring Prokaryotic Diversity' explored many aspects of this newly emerging interest in the prokaryotic world. [source] Recombination, repair and replication in the pathogenic Neisseriae: the 3 R,s of molecular genetics of two human-specific bacterial pathogensMOLECULAR MICROBIOLOGY, Issue 1 2003Kimberly A. Kline Summary Most of the detailed mechanisms that have been established for the molecular biological processes that mediate recombination, repair and replication of DNA have come from studies of the Escherichia coli paradigm. The human specific pathogens, Neisseria gonorrhoeae and N. meningitidis, are Gram-negative bacteria that have some molecular processes that are similar to E. coli and others that appear to be divergent. We propose that the pathogenic Neisseriae have evolved a specialized collection of molecular mechanisms to adapt to life limited to human hosts. In this MicroReview, we explore what is known about the basic processes of DNA repair, DNA recombination (genetic exchange and pilin variation) and DNA replication in these human specific pathogens. [source] Cutaneous effects of infrared radiation: from clinical observations to molecular response mechanismsPHOTODERMATOLOGY, PHOTOIMMUNOLOGY & PHOTOMEDICINE, Issue 5 2003Stefan M. Schieke Human skin is exposed to infrared (IR) radiation (760 nm,1 mm) from natural as well as artificial sources that are increasingly used for cosmetic or medical purposes. Epidemiological data and clinical observations, however, indicate that IR radiation cannot be considered as totally innocuous to human skin. In particular, IR radiation, similar to ultraviolet radiation, seems to be involved in photoaging and potentially also in photocarcinogenesis. The molecular consequences resulting from IR exposure are virtually unknown. Recent studies, however, have begun to shed light on the basic molecular processes such as cellular signal transduction and gene expression triggered by exposure to IR radiation. In response to IR irradiation, mitogen-activated protein kinase signaling pathways were activated mediating the upregulation of matrix metalloproteinase-1 expression. This previously unrecognized molecular ,IR response' shows that IR radiation is capable of specifically interfering with cellular functions and provides a molecular basis for biological effects of IR on human skin. [source] Understanding dendritic cell biology and its role in immunological disorders through proteomic profilingPROTEOMICS - CLINICAL APPLICATIONS, Issue 2 2010Gabriela Bomfim Ferreira Abstract Dendritic cells (DC) have always been present on the bright spot of immune research. They have been extensively studied for the last 35 years, and much is known about their different phenotypes, stimulatory capacity, and role in the immune system. During the last 15 years, great attention has been given to studies on global gene and protein expression profiles during the differentiation and maturation processes of these cells. It is well understood that studying the proteome, together with information on the role of protein post-translational modifications (PTM), will reveal the real dynamics of a living cell. The rapid increase of proteomic studies during the last decade describing the differentiation and maturation process in DCs, as well as modifications brought by the use of different compounds that either increase or decrease their immunogenicity, reflects the importance of understanding the molecular processes behind the functional properties of these cells. In the present review, we will give an overview of proteomic studies focusing on DCs. Thereby we will concentrate on the importance of these studies in understanding DC behavior from a molecular point of view and how these findings have aided in understanding the differences in functional properties of these cells. [source] Dendritic cells from spondylarthritis-prone HLA,B27,transgenic rats display altered cytoskeletal dynamics, class II major histocompatibility complex expression, and viabilityARTHRITIS & RHEUMATISM, Issue 9 2009Maarten Dhaenens Objective Spondylarthritis (SpA) is characterized by spinal and peripheral joint inflammation, frequently combined with extraarticular manifestations. Despite the well-established association of SpA with the class I major histocompatibility complex (MHC) allele HLA,B27, there are still different, parallel hypotheses on the relationship between HLA,B27 and disease mechanisms. The present study was undertaken to investigate several characteristics of mature dendritic cells (DCs), which are believed to be essential for triggering disease in a model of SpA in HLA,B27,transgenic rats. Methods We combined different whole-proteome approaches (2-dimensional polyacrylamide gel electrophoresis and iTRAQ) to define the most aberrant molecular processes occurring in spleen DCs. Videomicroscopy and flow cytometry were used to confirm both cytoskeletal and class II MHC expression deficiencies. Results Our proteome studies provided evidence of up-regulation of proteins involved in class I MHC loading, and unfolded protein response, along with a striking down-regulation of several cytoskeleton-reorganizing proteins. The latter result was corroborated by findings of deficient motility, altered morphology, and decreased immunologic synapse formation. Furthermore, class II MHC surface expression was reduced in DCs from B27-transgenic rats, and this could be linked to differences in class II MHC,induced apoptotic sensitivity. Finally, we found reduced viability of the CD103+CD4, DC subpopulation, which likely exerts tolerogenic function. Conclusion Taken together, our findings have different important implications regarding the physiology of B27-transgenic rat DCs, which have a putative role in spontaneous disease in these rats. In particular, the reduced motility and viability of putatively tolerogenic CD4+ DCs could play an important role in initiating the inflammatory process, resulting in SpA. [source] Analysis and validation of carbohydrate three-dimensional structuresACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2009Thomas Lütteke Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein,carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein,carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures. [source] Molecular footprints of human lung cancer progressionCANCER SCIENCE, Issue 3 2004Jun Yokota Lung cancer is the leading cause of cancer-related death in the world. To understand the molecular processes and pathways of, and contributing factors to lung cancer progression, genetic alterations in various progression stages of lung cancer cells have been studied, since these alterations can be regarded as molecular footprints representing the individual processes of multistage lung carcinogenesis. The results indicate that defects in both the p53 and RB/p16 pathways are essential for the malignant transformation of lung epithelial cells. Several other genes, such as K- ras, PTEN and MYO18B, are genetically altered less frequently than p53 and RB/p16 in lung cancer cells, suggesting that alterations in these genes are associated with further malignant progression or unique phenotypes in a subset of lung cancer cells. However, it is still unclear what genes control the metastatic potential of lung cancer cells. Further analyses of molecular footprints in lung cancer cells, in particular in the cells of metastatic sites, will give us valuable information to fully understand the process of lung cancer progression, and to find novel ways of controlling it. Molecular footprints at the sites of p53 mutations and p16 deletions further indicate that DNA repair activities for G:C to T:A transversion and non-homologous end-joining of DNA double-strand breaks play important roles in the accumulation of genetic alterations in lung cancer cells. Thus, identification of environmental as well as genetic factors inducing or suppressing the occurrence of such alterations would be a clue to find novel ways of lung cancer prevention. [source] Host responses to a versatile commensal: PAMPs and PRRs interplay leading to tolerance or infection by Candida albicansCELLULAR MICROBIOLOGY, Issue 7 2009Thierry Jouault Summary The molecular interactions between commensal microorganisms and their host are basically different from those triggered by pathogens since they involve tolerance. When the commensal is genetically equipped to become an opportunistic pathogen, as is the case with Candida albicans, the picture becomes more complex. In this case, the balance between protection and invasion depends on host reactivity to altered microbial expression of ligands interacting with innate immune sensors. Based on experimental evidence obtained with C. albicans, we discuss the different molecular processes involved in the sensing of this important opportunistic human pathogen by a panel of pattern recognition receptors (PRRs) according to the numerous pathogen-associated molecular patterns (PAMPs) that can be exposed at its surface. Beneficial or deleterious immune responses that either maintain a commensal state or favour damage by the yeast result from this dynamic interplay. [source] Regions of Tau Implicated in the Paired Helical Fragment Core as Defined by NMRCHEMBIOCHEM, Issue 10 2005Alain Sillen Dr. Abstract We have studied the mature Alzheimer-like fibers of tau by fluorescence and NMR spectroscopy. Assembly of the protein into paired helical filaments after incubation with heparin at 37,°C was verified by electron microscopy and size-exclusion chromatography. NMR spectroscopy on these mature fibers revealed different regions of residual mobility for tau: the N-terminal domain was found to maintain solution-like dynamics and was followed by a large domain of decreasing mobility; finally the core region was distinguished by a solid-like character. Heteronuclear-NOE data indicate that the decreasing mobility is due to both a slowing down of the rapid nanosecond movements and the introduction of slower movements that lead to exchange broadening. Fluorescence spectroscopy confirmed the presence of this rigid core, and some degree of protection from hydrogen exchange for those residues was observed. Hence, our data give a more precise picture of the dynamics of tau when it is integrated into mature filaments and should provide further understanding of the molecular processes that govern aggregation. [source] Insights into the molecular basis of rhegmatogenous retinal detachmentACTA OPHTHALMOLOGICA, Issue 2009PN BISHOP Purpose Factors that determine the likelihood of developing posterior vitreous detachment and subsequent rhegmatogenous retinal detachment (RRD) include (i) the degree of vitreous liquefaction (ii) the strength of post-basal vitreoretinal adhesion and (iii) the topology of the posterior border of the vitreous base. The purpose of these studies was to investigate each of these using a combination of ultrastructural and molecular techniques. Methods Ultrastructural studies of the human vitreous and vitreoretinal interface were performed in combination with various antibodies and cationic dyes. Biochemical studies were performed on extracted vitreous components. Results The resultant data suggest that: (i) vitreous liquefaction is caused by the aggregation of vitreous collagen fibrils and this is due to a loss of type IX collagen proteoglycan from the fibril surfaces; (ii) interactions between heparan sulphate proteoglycans in the inner limiting lamina and components on the surface of cortical vitreous collagen fibrils contribute to postbasal vitreoretinal adhesion; (iii) the posterior border of the vitreous base migrates posteriorly with aging due to the synthesis of new vitreous collagen by the peripheral retina. Conclusion The molecular basis of RRD is starting to be unravelled. Furthering our understanding of the underlying molecular processes may lead to the development of novel therapeutic strategies to treat RRD and other vitreoretinal disorders. [source] Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycinaPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 7 2010Giuseppe Gallo Abstract A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially and constitutively expressed protein isoforms, which were associated with 203 ORFs in the A. balhimycina genome. These data, providing insights on the major metabolic pathways/molecular processes operating in this organism, were used to compile 2-DE reference maps covering 3,10, 4,7 and 4.5,5.5 pH gradients available over the World Wide Web as interactive web pages (http://www.unipa.it/ampuglia/Abal-proteome-maps). Functional clustering analysis revealed that differentially expressed proteins belong to functional groups involved in central carbon metabolism, amino acid metabolism and protein biosynthesis, energetic and redox balance, sugar/amino sugar metabolism, balhimycin biosynthesis and transcriptional regulation or with hypothetical and/or unknown function. Interestingly, proteins involved in the biosynthesis of balhimycin precursors, such as amino acids, amino sugars and central carbon metabolism intermediates, were upregulated during antibiotic production. qRT-PCR analysis revealed that 8 out of 14 upregulated genes showed a positive correlation between changes at translational and transcriptional expression level. Furthermore, proteomic analysis of two nonproducing mutants, restricted to a sub-set of differentially expressed proteins, showed that most proteins required for the biosynthesis of balhimycin precursors are downregulated in both mutants. These findings suggest that primary metabolic pathways support anabolic routes leading to balhimycin biosynthesis and the differentially expressed genes are interesting targets for the construction of high-yielding producer strains by rational genetic engineering. [source] | ||||||||||||||||||||||||||||