Showing papers by "University of Freiburg published in 2008"

Quantum dots versus organic dyes as fluorescent labels

Abstract: Suitable labels are at the core of Luminescence and fluorescence imaging and sensing. One of the most exciting, yet also controversial, advances in label technology is the emerging development of quantum dots (QDs)--inorganic nanocrystals with unique optical and chemical properties but complicated surface chemistry--as in vitro and in vivo fluorophores. Here we compare and evaluate the differences in physicochemical properties of common fluorescent labels, focusing on traditional organic dyes and QDs. Our aim is to provide a better understanding of the advantages and limitations of both classes of chromophores, to facilitate label choice and to address future challenges in the rational design and manipulation of QD labels.

The LHCb detector at the LHC

Abstract: The LHCb experiment is dedicated to precision measurements of CP violation and rare decays of B hadrons at the Large Hadron Collider (LHC) at CERN (Geneva). The initial configuration and expected performance of the detector and associated systems, as established by test beam measurements and simulation studies, is described.

The NALP3 inflammasome is involved in the innate immune response to amyloid-beta.

Abstract: The events leading to the inflammation and tissue damage associated with Alzheimer's disease are unclear. Golenbock and colleagues now show that amyloid-β activates the NALP3 inflammasome, which triggers the release of proinflammatory and neurotoxic factors. The fibrillar peptide amyloid-β (Aβ) has a chief function in the pathogenesis of Alzheimer's disease. Interleukin 1β (IL-1β) is a key cytokine in the inflammatory response to Aβ. Insoluble materials such as crystals activate the inflammasome formed by the cytoplasmic receptor NALP3, which results in the release of IL-1β. Here we identify the NALP3 inflammasome as a sensor of Aβ in a process involving the phagocytosis of Aβ and subsequent lysosomal damage and release of cathepsin B. Furthermore, the IL-1β pathway was essential for the microglial synthesis of proinflammatory and neurotoxic factors, and the inflammasome, caspase-1 and IL-1β were critical for the recruitment of microglia to exogenous Aβ in the brain. Our findings suggest that activation of the NALP3 inflammasome is important for inflammation and tissue damage in Alzheimer's disease.

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

Abstract: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

A reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells

Abstract: The embryonic programme 'epithelial-mesenchymal transition' (EMT) is thought to promote malignant tumour progression. The transcriptional repressor zinc-finger E-box binding homeobox 1 (ZEB1) is a crucial inducer of EMT in various human tumours, and was recently shown to promote invasion and metastasis of tumour cells. Here, we report that ZEB1 directly suppresses transcription of microRNA-200 family members miR-141 and miR-200c, which strongly activate epithelial differentiation in pancreatic, colorectal and breast cancer cells. Notably, the EMT activators transforming growth factor beta2 and ZEB1 are the predominant targets downregulated by these microRNAs. These results indicate that ZEB1 triggers an microRNA-mediated feedforward loop that stabilizes EMT and promotes invasion of cancer cells. Alternatively, depending on the environmental trigger, this loop might switch and induce epithelial differentiation, and thus explain the strong intratumorous heterogeneity observed in many human cancers.

Coordinated regulation of Arabidopsis thaliana development by light and gibberellins

Abstract: Light and gibberellins (GAs) mediate many essential and partially overlapping plant developmental processes. DELLA proteins are GA-signalling repressors that block GA-induced development. GA induces degradation of DELLA proteins via the ubiquitin/proteasome pathway, but light promotes accumulation of DELLA proteins by reducing GA levels. It was proposed that DELLA proteins restrain plant growth largely through their effect on gene expression. However, the precise mechanism of their function in coordinating GA signalling and gene expression remains unknown. Here we characterize a nuclear protein interaction cascade mediating transduction of GA signals to the activity regulation of a light-responsive transcription factor. In the absence of GA, nuclear-localized DELLA proteins accumulate to higher levels, interact with phytochrome-interacting factor 3 (PIF3, a bHLH-type transcription factor) and prevent PIF3 from binding to its target gene promoters and regulating gene expression, and therefore abrogate PIF3-mediated light control of hypocotyl elongation. In the presence of GA, GID1 proteins (GA receptors) elevate their direct interaction with DELLA proteins in the nucleus, trigger DELLA protein's ubiquitination and proteasome-mediated degradation, and thus release PIF3 from the negative effect of DELLA proteins.

Venous thromboembolism and mortality associated with recombinant erythropoietin and darbepoetin administration for the treatment of cancer-associated anemia.

Abstract: Context The erythropoiesis-stimulating agents (ESAs) erythropoietin and darbepoetin are licensed to treat chemotherapy-associated anemia in patients with nonmyeloid malignancies. Although systematic overviews of trials have identified venous thromboembolism (VTE) risks, none have identified mortality risks with ESAs. Objective To evaluate VTE and mortality rates associated with ESA administration for the treatment of anemia among patients with cancer. Data Sources A published overview from the Cochrane Collaboration (search dates: January 1, 1985-April 1, 2005) and MEDLINE and EMBASE databases (key words: clinical trial, erythropoietin, darbepoetin, and oncology), the public Web site of the US Food and Drug Administration and ESA manufacturers, and safety advisories (search dates: April 1, 2005-January 17, 2008). Study Selection Phase 3 trials comparing ESAs with placebo or standard of care for the treatment of anemia among patients with cancer. Data Extraction Mortality rates, VTE rates, and 95% confidence intervals (CIs) were extracted by 3 reviewers from 51 clinical trials with 13 611 patients that included survival information and 38 clinical trials with 8172 patients that included information on VTE. Data Synthesis Patients with cancer who received ESAs had increased VTE risks (334 VTE events among 4610 patients treated with ESA vs 173 VTE events among 3562 control patients; 7.5% vs 4.9%; relative risk, 1.57; 95% CI, 1.31-1.87) and increased mortality risks (hazard ratio, 1.10; 95% CI, 1.01-1.20). Conclusions Erythropoiesis-stimulating agent administration to patients with cancer is associated with increased risks of VTE and mortality. Our findings, in conjunction with basic science studies on erythropoietin and erythropoietin receptors in solid cancers, raise concern about the safety of ESA administration to patients with cancer.

The metzincins--topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a superfamily of zinc-peptidases.

Abstract: The three-dimensional structures of the zinc endopeptidases human neutrophil collagenase, adamalysin II from rattle snake venom, alkaline proteinase from Pseudomonas aeruginosa, and astacin from crayfish are topologically similar, with respect to a five-stranded beta-sheet and three alpha-helices arranged in typical sequential order. The four proteins exhibit the characteristic consensus motif HEXXHXXGXXH, whose three histidine residues are involved in binding of the catalytically essential zinc ion. Moreover, they all share a conserved methionine residue beneath the active site metal as part of a superimposable "Met-turn." This structural relationship is supported by a sequence alignment performed on the basis of topological equivalence showing faint but distinct sequential similarity. The alkaline proteinase is about equally distant (26% sequence identity) to both human neutrophil collagenase and astacin and a little further away from adamalysin II (17% identity). The pairs astacin/adamalysin II, astacin/human neutrophil collagenase, and adamalysin II/human neutrophil collagenase exhibit sequence identities of 16%, 14%, and 13%, respectively. Therefore, the corresponding four distinct families of zinc peptidases, the astacins, the matrix metalloproteinases (matrixins, collagenases), the adamalysins/reprolysins (snake venom proteinases/reproductive tract proteins), and the serralysins (large bacterial proteases from Serratia, Erwinia, and Pseudomonas) appear to have originated by divergent evolution from a common ancestor and form a superfamily of proteolytic enzymes for which the designation "metzincins" has been proposed. There is also a faint but significant structural relationship of the metzincins to the thermolysin-like enzymes, which share the truncated zinc-binding motif HEXXH and, moreover, similar topologies in their N-terminal domains.

IFN-lambda (IFN-lambda) is expressed in a tissue-dependent fashion and primarily acts on epithelial cells in vivo.

Abstract: Interferons (IFN) exert antiviral, immunomodulatory and cytostatic activities. IFN-alpha/beta (type I IFN) and IFN-lambda (type III IFN) bind distinct receptors, but regulate similar sets of genes and exhibit strikingly similar biological activities. We analyzed to what extent the IFN-alpha/beta and IFN-lambda systems overlap in vivo in terms of expression and response. We observed a certain degree of tissue specificity in the production of IFN-lambda. In the brain, IFN-alpha/beta was readily produced after infection with various RNA viruses, whereas expression of IFN-lambda was low in this organ. In the liver, virus infection induced the expression of both IFN-alpha/beta and IFN-lambda genes. Plasmid electrotransfer-mediated in vivo expression of individual IFN genes allowed the tissue and cell specificities of the responses to systemic IFN-alpha/beta and IFN-lambda to be compared. The response to IFN-lambda correlated with expression of the alpha subunit of the IFN-lambda receptor (IL-28R alpha). The IFN-lambda response was prominent in the stomach, intestine and lungs, but very low in the central nervous system and spleen. At the cellular level, the response to IFN-lambda in kidney and brain was restricted to epithelial cells. In contrast, the response to IFN-alpha/beta was observed in various cell types in these organs, and was most prominent in endothelial cells. Thus, the IFN-lambda system probably evolved to specifically protect epithelia. IFN-lambda might contribute to the prevention of viral invasion through skin and mucosal surfaces.

Size-driven structural and thermodynamic complexity in iron oxides.

Abstract: Iron oxides occur ubiquitously in environmental, geological, planetary, and technological settings. They exist in a rich variety of structures and hydration states. They are commonly fine-grained (nanophase) and poorly crystalline. This review summarizes recently measured thermodynamic data on their formation and surface energies. These data are essential for calculating the thermodynamic stability fields of the various iron oxide and oxyhydroxide phases and understanding their occurrence in natural and anthropogenic environments. The competition between surface enthalpy and the energetics of phase transformation leads to the general conclusion that polymorphs metastable as micrometer-sized or larger crystals can often be thermodynamically stabilized at the nanoscale. Such size-driven crossovers in stability help to explain patterns of occurrence of different iron oxides in nature.

Facilitated PCI in patients with ST-elevation myocardial infarction.

Abstract: In this international, double-blind, placebo-controlled study, we randomly assigned patients with ST-segment elevation myocardial infarction who presented 6 hours or less after the onset of symptoms to receive combination-facilitated PCI, abciximabfacilitated PCI, or primary PCI. All patients received unfractionated heparin or enoxaparin before PCI and a 12-hour infusion of abciximab after PCI. The primary end point was the composite of death from all causes, ventricular fibrillation occurring more than 48 hours after randomization, cardiogenic shock, and congestive heart failure during the first 90 days after randomization. Results A total of 2452 patients were randomly assigned to a treatment group. Significantly more patients had early ST-segment resolution with combination-facilitated PCI (43.9%) than with abciximab-facilitated PCI (33.1%) or primary PCI (31.0%; P = 0.01 and P = 0.003, respectively). The primary end point occurred in 9.8%, 10.5%, and 10.7% of the patients in the combination-facilitated PCI group, abciximab-facilitated PCI group, and primary-PCI group, respectively (P = 0.55); 90-day mortality rates were 5.2%, 5.5%, and 4.5%, respectively (P = 0.49). Conclusions Neither facilitation of PCI with reteplase plus abciximab nor facilitation with abciximab alone significantly improved the clinical outcomes, as compared with abciximab given at the time of PCI, in patients with ST-segment elevation myocardial infarction. (ClinicalTrials.gov number, NCT00046228.)

Toll-like receptor–induced arginase 1 in macrophages thwarts effective immunity against intracellular pathogens

Abstract: Toll-like receptor (TLR) signaling in macrophages is required for antipathogen responses, including the biosynthesis of nitric oxide from arginine, and is essential for immunity to Mycobacterium tuberculosis, Toxoplasma gondii and other intracellular pathogens. Here we report a 'loophole' in the TLR pathway that is advantageous to these pathogens. Intracellular pathogens induced expression of the arginine hydrolytic enzyme arginase 1 (Arg1) in mouse macrophages through the TLR pathway. In contrast to diseases dominated by T helper type 2 responses in which Arg1 expression is greatly increased by interleukin 4 and 13 signaling through the transcription factor STAT6, TLR-mediated Arg1 induction was independent of the STAT6 pathway. Specific elimination of Arg1 in macrophages favored host survival during T. gondii infection and decreased lung bacterial load during tuberculosis infection.

RNAalifold: improved consensus structure prediction for RNA alignments

Abstract: Background: The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a set of aligned sequences, is one of the oldest and most widely used tools for this task. In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach. Results: We show that the accuracy of RNAalifold predictions can be improved substantially by introducing a different, more rational handling of alignment gaps, and by replacing the rather simplistic model of covariance scoring with more sophisticated RIBOSUM-like scoring matrices. These improvements are achieved without compromising the computational efficiency of the algorithm. We show here that the new version of RNAalifold not only outperforms the old one, but also several other tools recently developed, on different datasets. Conclusion: The new version of RNAalifold not only can replace the old one for almost any application but it is also competitive with other approaches including those based on SCFGs, maximum expected accuracy, or hierarchical nearest neighbor classifiers.

The Transcriptional Repressor ZEB1 Promotes Metastasis and Loss of Cell Polarity in Cancer

Abstract: Invasion and metastasis are the hallmarks of malignant tumor progression and the main cause of death in cancer. The embryonic program "epithelial-mesenchymal transition" (EMT) is thought to trigger invasion by allowing tumor cell dissemination. Here, we describe that the EMT-inducing transcriptional repressor ZEB1 promotes colorectal cancer cell metastasis and loss of cell polarity. Thereby, ZEB1 suppresses the expression of cell polarity factors, in particular of Lgl2, which we found reduced in colorectal and breast cancers. We further show that retention of Lgl2 expression is critical for the epithelial phenotype and that its loss might be involved in metastasis. Thus, by linking EMT, loss of polarity, and metastasis, ZEB1 is a crucial promoter of malignant tumor progression.

Formation of ultracold polar molecules in the rovibrational ground state.

Abstract: Ultracold LiCs molecules in the absolute ground state $X^{1}\ensuremath{\Sigma}^{+}$, ${v}^{\ensuremath{'}\ensuremath{'}}=0$, ${J}^{\ensuremath{'}\ensuremath{'}}=0$ are formed via a single photoassociation step starting from laser-cooled atoms. The selective production of ${v}^{\ensuremath{'}\ensuremath{'}}=0$, ${J}^{\ensuremath{'}\ensuremath{'}}=2$ molecules with a 50-fold higher rate is also demonstrated. The rotational and vibrational state of the ground state molecules is determined in a setup combining depletion spectroscopy with resonant-enhanced multiphoton ionization time-of-flight spectroscopy. Using the determined production rate of up to $5\ifmmode\times\else\texttimes\fi{}{10}^{3}\text{ }\text{ }\mathrm{\text{molecules}}/\mathrm{s}$, we describe a simple scheme which can provide large samples of externally and internally cold dipolar molecules.

Classification and control of the origin of photoluminescence from Si nanocrystals

Abstract: Silicon dominates the electronics industry, but its poor optical properties mean that III–V compound semiconductors are preferred for photonics applications. Photoluminescence at visible wavelengths was observed from porous Si at room temperature in 1990, but the origin of these photons (do they arise from highly localized defect states or quantum confinement effects?) has been the subject of intense debate ever since. Attention has subsequently shifted from porous Si to Si nanocrystals, but the same fundamental question about the origin of the photoluminescence has remained. Here we show, based on measurements in high magnetic fields, that defects are the dominant source of light from Si nanocrystals. Moreover, we show that it is possible to control the origin of the photoluminescence in a single sample: passivation with hydrogen removes the defects, resulting in photoluminescence from quantum-confined states, but subsequent ultraviolet illumination reintroduces the defects, making them the origin of the light again.

Tourism climate and thermal comfort in Sun Moon Lake, Taiwan

Abstract: Bioclimate conditions at Sun Moon Lake, one of Taiwan's most popular tourist destinations, are presented Existing tourism-related climate is typically based on mean monthly conditions of air temperature and precipitation and excludes the thermal perception of tourists This study presents a relatively more detailed analysis of tourism climate by using a modified thermal comfort range for both Taiwan and Western/Middle European conditions, presented by frequency analysis of 10-day intervals Furthermore, an integrated approach (climate tourism information scheme) is applied to present the frequencies of each facet under particular criteria for each 10-day interval, generating a time-series of climate data with temporal resolution for tourists and tourism authorities

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

Abstract: Motivation: During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing target prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches. Results: We introduce INTARNA, a new general and fast approach to the prediction of RNA–RNA interactions incorporating accessibility of target sites as well as the existence of a user-definable seed. We successfully applied INTARNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs. Availability: http://www.bioinf.uni-freiburg.de/Software/ Contact: IntaRNA@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online.

A generic grid interface for parallel and adaptive scientific computing. Part II: implementation and tests in DUNE

Abstract: In a companion paper (Bastian et al. 2007, this issue) we introduced an abstract definition of a parallel and adaptive hierarchical grid for scientific computing. Based on this definition we derive an efficient interface specification as a set of C++ classes. This interface separates the applications from the grid data structures. Thus, user implementations become independent of the underlying grid implementation. Modern C++ template techniques are used to provide an interface implementation without big performance losses. The implementation is realized as part of the software environment DUNE (http://dune-project.org/). Numerical tests demonstrate the flexibility and the efficiency of our approach.

BRAF gene duplication constitutes a mechanism of MAPK pathway activation in low-grade astrocytomas

Abstract: The molecular pathogenesis of pediatric astrocytomas is still poorly understood. To further understand the genetic abnormalities associated with these tumors, we performed a genome-wide analysis of DNA copy number aberrations in pediatric low-grade astrocytomas by using array-based comparative genomic hybridization. Duplication of the BRAF protooncogene was the most frequent genomic aberration, and tumors with BRAF duplication showed significantly increased mRNA levels of BRAF and a downstream target, CCND1, as compared with tumors without duplication. Furthermore, denaturing HPLC showed that activating BRAF mutations were detected in some of the tumors without BRAF duplication. Similarly, a marked proportion of low-grade astrocytomas from adult patients also had BRAF duplication. Both the stable silencing of BRAF through shRNA lentiviral transduction and pharmacological inhibition of MEK1/2, the immediate downstream phosphorylation target of BRAF, blocked the proliferation and arrested the growth of cultured tumor cells derived from low-grade gliomas. Our findings implicate aberrant activation of the MAPK pathway due to gene duplication or mutation of BRAF as a molecular mechanism of pathogenesis in low-grade astrocytomas and suggest inhibition of the MAPK pathway as a potential treatment.

Hand movement direction decoded from MEG and EEG.

Abstract: Brain activity can be used as a control signal for brain–machine interfaces (BMIs). A powerful and widely acknowledged BMI approach, so far only applied in invasive recording techniques, uses neuronal signals related to limb movements for equivalent, multidimensional control of an external effector. Here, we investigated whether this approach is also applicable for noninvasive recording techniques. To this end, we recorded whole-head MEG during center-out movements with the hand and found significant power modulation of MEG activity between rest and movement in three frequency bands: an increase for ≤7 Hz (low-frequency band) and 62–87 Hz (high-γ band) and a decrease for 10–30 Hz (β band) during movement. Movement directions could be inferred on a single-trial basis from the low-pass filtered MEG activity as well as from power modulations in the low-frequency band, but not from the β and high-γ bands. Using sensors above the motor area, we obtained a surprisingly high decoding accuracy of 67% on average across subjects. Decoding accuracy started to rise significantly above chance level before movement onset. Based on simultaneous MEG and EEG recordings, we show that the inference of movement direction works equally well for both recording techniques. In summary, our results show that neuronal activity associated with different movements of the same effector can be distinguished by means of noninvasive recordings and might, thus, be used to drive a noninvasive BMI.

Mechanical properties of silicones for MEMS

Abstract: This paper focuses on the mechanical properties of polydimethylsiloxane (PDMS) relevant for microelectromechanical system (MEMS) applications. In view of the limited amount of published data, we analyzed the two products most commonly used in MEMS, namely RTV 615 from Bayer Silicones and Sylgard 184 from Dow Corning. With regard to mechanical properties, we focused on the dependence of the elastic modulus on the thinner concentration, temperature and strain rate. In addition, creep and thermal aging were analyzed. We conclude that the isotropic and constant elastic modulus has strong dependence on the hardening conditions. At high hardening temperatures and long hardening time, RTV 615 displays an elastic modulus of 1.91 MPa and Sylgard 184 of 2.60 MPa in a range up to 40% strain.

An important role for type III interferon (IFN-lambda/IL-28) in TLR-induced antiviral activity.

Abstract: Type III IFNs (IFN-lambda/IL-28/29) are cytokines with type I IFN-like antiviral activities, which remain poorly characterized. We herein show that most cell types expressed both types I and III IFNs after TLR stimulation or virus infection, whereas the ability of cells to respond to IFN-lambda was restricted to a narrow subset of cells, including plasmacytoid dendritic cells and epithelial cells. To examine the role of type III IFN in antiviral defense, we generated IL-28Ralpha-deficient mice. These mice were indistinguishable from wild-type mice with respect to clearance of a panel of different viruses, whereas mice lacking the type I IFN receptor (IFNAR(-/-)) were significantly impaired. However, the strong antiviral activity evoked by treatment of mice with TLR3 or TLR9 agonists was significantly reduced in both IL-28RA(-/-) and IFNAR(-/-) mice. The type I IFN receptor system has been shown to mediate positive feedback on IFN-alphabeta expression, and we found that the type I IFN receptor system also mediates positive feedback on IFN-lambda expression, whereas IL-28Ralpha signaling does not provide feedback on either type I or type III IFN expression in vivo. Finally, using bone-marrow chimeric mice we showed that TLR-activated antiviral defense requires expression of IL-28Ralpha only on nonhemopoietic cells. In this compartment, epithelial cells responded to IFN-lambda and directly restricted virus replication. Our data suggest type III IFN to target a specific subset of cells and to contribute to the antiviral response evoked by TLRs.

Reduced basis method for finite volume approximations of parametrized linear evolution equations

Abstract: The model order reduction methodology of reduced basis (RB) techniques offers efficient treatment of parametrized partial differential equations (P2 DEs) by providing both approximate solution procedures and efficient error estimates. RB-methods have so far mainly been applied to finite element schemes for elliptic and parabolic problems. In the current study we extend the methodology to general linear evolution schemes such as finite volume schemes for parabolic and hyperbolic evolution equations. The new theoretic contributions are the formulation of a reduced basis approximation scheme for these general evolution problems and the derivation of rigorous a-posteriori error estimates in various norms. Algorithmically, an offline/online decomposition of the scheme and the error estimators is realized in case of affine parameter-dependence of the problem. This is the basis for a rapid online computation in case of multiple simulation requests. We introduce a new offline basis-generation algorithm based on our a-posteriori error estimator which combines ideas from existing approaches. Numerical experiments for an instationary convection-diffusion problem demonstrate the efficient applicability of the approach.

Altered Th1/Th2 cytokine profiles in the intestinal mucosa of patients with inflammatory bowel disease as assessed by quantitative reversed transcribed polymerase chain reaction (RT‐PCR)

Abstract: Cytokines serve a central function as key factors in the regulation of the intestinal immune response and mediation of tissue damage in inflammatory bowel disease (IBD). Abnormalities in the expression of immunoregulatory cytokines such as IL-2, IL-4, IL-10 and interferon-gamma (IFN-gamma) may indicate a dysregulation of intestinal immunity probably associated with pathogenic events. Therefore, cytokine mRNA concentrations were determined in the mucosa of patients with IBD at sites of active (n = 13) and inactive (n = 12) ulcerative colitis (UC), active (n = 11) and inactive (n = 11) Crohn's disease (CD) and in control patients (n = 14) using quantitative RT-PCR. IL-10 mRNA concentrations were significantly increased in patients with both active UC (P < 0.001) and active CD (P < 0.005) compared with control patients. IFN-gamma mRNA concentrations were also significantly increased both in patients with active UC (P < 0.02) and active CD (P < 0.05) compared with control patients, whereas IL-2 mRNA levels were significantly (P < 0.02) increased only in active CD. IL-4 mRNA expression in the intestinal mucosa was frequently below the detection limit. Our results demonstrate that chronic intestinal inflammation in patients with CD is characterized by an increase of Th1-like cytokines. Furthermore, the increased IL-10 mRNA expression at sites of active IBD suggests that IL-10 is an important regulatory component involved in the control of the inflammatory response in inflammatory bowel disease.

A generic grid interface for parallel and adaptive scientific computing. Part I: abstract framework

Abstract: We give a mathematically rigorous definition of a grid for algorithms solving partial differential equations. Unlike previous approaches (Benger 2005, PhD thesis; Berti 2000, PhD thesis), our grids have a hierarchical structure. This makes them suitable for geometric multigrid algorithms and hierarchical local grid refinement. The description is also general enough to include geometrically non-conforming grids. The definitions in this article serve as the basis for an implementation of an abstract grid interface as C++ classes in the framework (Bastian et al. 2008, this issue).