M. Hecker

Gene regulatory network inference : Data integration in dynamic models-A review

Systems biology aims to develop mathematical models of biological systems by integrating experimental and theoretical techniques. During the last decade, many systems biological approaches that base on genome-wide data have been developed to unravel the complexity of gene regulation. This review deals with the reconstruction of gene regulatory networks (GRNs) from experimental data through computational methods. Standard GRN inference methods primarily use gene expression data derived from microarrays. However, the incorporation of additional information from heterogeneous data sources, e.g. genome sequence and protein-DNA interaction data, clearly supports the network inference process. This review focuses on promising modelling approaches that use such diverse types of molecular biological information. In particular, approaches are discussed that enable the modelling of the dynamics of gene regulatory systems. The review provides an overview of common modelling schemes and learning algorithms and outlines current challenges in GRN modelling.

Molecular discrimination of responders and nonresponders to anti-TNFalpha therapy in rheumatoid arthritis by etanercept

IntroductionAbout 30% of rheumatoid arthritis patients fail to respond adequately to TNFα-blocking therapy. There is a medical and socioeconomic need to identify molecular markers for an early prediction of responders and nonresponders.MethodsRNA was extracted from peripheral blood mononuclear cells of 19 rheumatoid arthritis patients before the first application of the TNFα blocker etanercept as well as after 72 hours. Clinical response was assessed over 3 months using the 28-joint-count Disease Activity Score and X-ray scans. Supervised learning methods were applied to Affymetrix Human Genome U133 microarray data analysis to determine highly selective discriminatory gene pairs or triplets with prognostic relevance for the clinical outcome evinced by a decline of the 28-joint-count Disease Activity Score by 1.2.ResultsEarly downregulation of expression levels secondary to TNFα neutralization was associated with good clinical responses, as shown by a decline in overall disease activity 3 months after the start of treatment. Informative gene sets include genes (for example, NFKBIA, CCL4, IL8, IL1B, TNFAIP3, PDE4B, PPP1R15A and ADM) involved in different pathways and cellular processes such as TNFα signalling via NFκB, NFκB-independent signalling via cAMP, and the regulation of cellular and oxidative stress response. Pairs and triplets within these genes were found to have a high prognostic value, reflected by prediction accuracies of over 89% for seven selected gene pairs and of 95% for 10 specific gene triplets.ConclusionOur data underline that early gene expression profiling is instrumental in identifying candidate biomarkers to predict therapeutic outcomes of anti-TNFα treatment regimes.

Structure and thermal stability of graded Ta–TaN diffusion barriers between Cu and SiO2

Abstract Sputter deposited Ta and TaN single layers of 10 nm thickness as well as graded TaN/Ta and Ta/TaN/Ta layer stacks that act as diffusion barriers for Cu metallization were investigated after annealing at temperatures between T an =300 and 700 °C. By means of glancing angle X-ray diffraction, glow discharge optical emission spectroscopy and transmission electron microscopy, results of microstructure and phase characterization were correlated with diffusion phenomena. For the pure Ta barrier, Ta diffusion through the Cu cap layer to the sample surface is observed at T an =500 °C, and the transformation of initially grown metastable β-Ta into the equilibrium α-Ta phase occurs at T an =600 °C. In contrast, a fcc TaN layer remains stable at least up to T an =700 °C. In the case of the graded layer stacks, first signs of N diffusion out of the TaN film into the adjacent Ta layers are observed after annealing at T an =300 °C, and formation of hexagonal Ta 2 N starts at T an =500 °C. Whereas in the course of thermal treatments for the threefold graded Ta/TaN/Ta barrier all TaN reacts with Ta to form Ta 2 N, some fcc TaN remains in the twofold graded TaN/Ta barrier.

Long-term genome-wide blood RNA expression profiles yield novel molecular response candidates for IFN-β-1b treatment in relapsing remitting MS

AIMS In multiple sclerosis patients, treatment with recombinant IFN-beta (rIFN-beta) is partially efficient in reducing clinical exacerbations. However, its molecular mechanism of action is still under scrutiny. MATERIALS & METHODS We used DNA microarrays (Affymetrix, CA, USA) and peripheral mononuclear blood cells from 25 relapsing remitting multiple sclerosis patients to analyze the longitudinal transcriptional profile within 2 years of rIFN-beta administration. Sets of differentially expressed genes were attained by applying a combination of independent criteria, thereby providing efficient data curation and gene filtering that accounted for technical and biological noise. Gene ontology term-association analysis and scientific literature text mining were used to explore evidence of gene interaction. RESULTS Post-therapy initiation, we identified 42 (day 2), 175 (month 1), 103 (month 12) and 108 (month 24) differentially expressed genes. Increased expression of established IFN-beta marker genes, as well as differential expression of circulating IFN-beta-responsive candidate genes, were observed. MS4A1 (CD20), a known target of B-cell depletion therapy, was significantly downregulated after one month. CMPK2, FCER1A, and FFAR2 appeared as hitherto unrecognized multiple sclerosis treatment-related differentially expressed genes that were consistently modulated over time. Overall, 84 interactions between 54 genes were attained, of which two major gene networks were identified at an earlier stage of therapy: the first (n = 15 genes) consisted of mostly known IFN-beta-activated genes, whereas the second (n = 12) mainly contained downregulated genes that to date have not been associated with IFN-beta effects in multiple sclerosis array research. CONCLUSION We achieved both a broadening of the knowledge of IFN-beta mechanism-of-action-related constituents and the identification of time-dependent interactions between IFN-beta regulated genes.

Influence of N content on microstructure and thermal stability of Ta–N thin films for Cu interconnection

Abstract Structural properties of thin Ta and Ta–N films acting as diffusion barriers were investigated. Blanket Ta-based films of 10 nm thickness were deposited by conventional sputtering techniques onto (100)-Si and covered with a Cu cap layer. X-ray diffraction, depth profile analysis and electron microscopy were used to correlate results of microstructure and phase characterization with diffusion phenomena. Different barrier failure mechanisms were observed after annealing at temperatures between 450 and 800 °C. Ta and Cu silicides were formed suddenly in layer stacks with pure Ta and Ta–20 at.% N barrier films at 550 °C. The application of the stoichiometric TaN as a diffusion barrier prevents the formation of Ta silicides and does not lead to significant Cu silicide formation up to 800 °C. However, trace Cu diffusion into the substrate was also detected at lower temperatures. The barrier stability against Cu diffusion is improving with increasing N content.

Annealing of Ni80Fe20/Cu and Co/Cu multilayers

Ni80Fe20/Cu and Co/Cu multilayers with Cu layer thicknesses corresponding to the first and second antiferromagnetic (afm) coupling maximum were prepared by dc-magnetron sputtering and investigated with respect to their annealing behavior. The as-deposited films showed giant magnetoresistance (GMR) up to 50% at room temperature. The annealing behavior of the multilayers belonging to the same Cu layer thickness is found to be very similar up to 200 °C. For both kind of multilayers with a Cu layer thickness of about 1 nm (first afm maximum) the GMR degrades upon annealing in excess of 140 °C. However, with a Cu layer thickness of about 2 nm (second afm maximum) the multilayers are stable with respect to their GMR properties even after prolonged exposure up to 200 °C. Moreover, in some cases even an improvement of GMR upon the annealing procedure may be found.

Monitoring of multiple sclerosis immunotherapy : From single candidates to biomarker networks ()

Applying microarray technology to identify new diagnostic and prognostic markers in peripheral blood cells (PBC) after therapeutic intervention opens great perspectives regarding patient subclassification. Three recombinant products of the pleiotropic agent interferon beta (rIFN-β) are available for disease modifying therapy of relapsing remitting multiple sclerosis (RRMS), a complex inflammatory autoimmune disease that targets the central nervous system. They differ according to formulation, route of administration and dosage regimens. The currently, only partially understood mechanism of action of injected rIFN-β into human organisms needs provision with accessory key molecules; in addition, the significance of established clinical IFN-β response criteria that distinguish responding from non-responding patients remain unclear.With respect to these major questions, we discuss promising candidates on the gene transcription level, attained from scientific MS literature that included a longitudinal aspect. Reviewed studies were in part carried out with distinct gene interrogating platforms (GeneArrays; RT-PCR), settings (in vitro; ex vivo), and study designs (drug formulations and regimen; inclusion criteria and clinical endpoints), hampering meaningful meta-analysis. Nevertheless, PBC from therapy-naïve MS patients, rIFN-β treated MS patients, and healthy controls served to characterize facets of both the disease and its treatment. Hence, the field of MS transcriptomics in immunomodulatory therapy is (by far) not adequately understood and should be embedded into systems biology disciplines, yielding multi-layer analyses that deliver timely identification of MS subjects who will profit from applied rIFN-β therapy.

Interdiffusion in NiFe/Cu/NiFe trilayers: Possible failure mechanism for magnetoelectronic devices

The evolution of electrical resistance, stress, and microstructure during annealing has been studied on 100 nm NiFe(20 wt %)/200 nm Cu/100 nm NiFe trilayers. Irreversible resistance changes and the concentration-depth profiles show that, at and above 200 °C, diffusion of Ni into Cu as well as of Cu into NiFe occurs. The interdiffusion is held for an important failure mechanism of Cu/NiFe-based magnetoelectronic system at elevated temperatures.

Stress development in sputtered NiO thin films during heat treatment

Nickel oxide thin films with a thickness of 100 nm were deposited on oxidized silicon wafers by rf magnetron sputtering from a NiO target in an Ar (nonreactive case) and an Ar+O2 atmosphere with various oxygen contents (reactive cases). The as-deposited films possess high compressive stresses (up to 3700 MPa) which decrease irreversibly during annealing between 150 and 500 °C. Compositional and microstructural analyses were performed on as-deposited and annealed films by means of electron probe microanalysis, transmission electron microscopy, x-ray diffraction, x-ray photoelectron spectroscopy, thermal-desorption spectrometry, and magnetization measurements. All as-deposited thin films consist of NiOx with x ranging between about 1.15 and 1.27. These oxygen-excess films are thermally unstable. They decompose during heat treatment into thermally more stable, oxygen-poorer NiO and/or metallic Ni. This decomposition is the reason for the observed irreversible stress changes.

Crystallization behavior of CoSb3 and (Co,Fe)Sb3 thin films

The crystallization behavior of CoSb3 and Fe-doped (Co,Fe)Sb3 thin films prepared by d.c.-magnetron sputtering was studied via ex situ and in situ X-ray diffraction (XRD) measurements. The as-deposited layers are amorphous. Crystallization takes place at temperatures of approximately 160±16 °C. Decomposition occurs in the temperature ranges of 575–610 °C for CoSb3 and of 640–670 °C for (Co,Fe)Sb3. The decomposition products are CoSb and (Co,Fe)Sb, respectively. Both ex situ XRD measurements on annealed layers and in situ measurements on as-deposited samples show a rare dependence of the cubic lattice parameter of the skutterudite type structure on the temperature. Electron probe microanalysis investigations indicate that the composition varies from Co–Sb 1:4 at low temperatures to Co–Sb 1:3 after heating cycles.