Use of complex DNA and antibody microarrays as tools in functional analyses.

While the deciphering of basic sequence information on a genomic scale is yielding complete genomic sequences in ever-shorter intervals, experimental procedures for elucidating the cellular effects and consequences of the DNA-encoded information become critical for further analyses. In recent years, DNA microarray technology has emerged as a prime candidate for the performance of many such functional assays. Technically, array technology has come a long way since its conception some 15 years ago, initially designed as a means for large-scale mapping and sequencing.

Whole genome analysis of a wine yeast strain.

Saccharomyces cerevisiae strains frequently exhibit rather specific phenotypic features needed for adaptation to a special environment. Wine yeast strains are able to ferment musts, for example, while other industrial or laboratory strains fail to do so. The genetic differences that characterize wine yeast strains are poorly understood, however.

Microarray study of gene expression in uterine leiomyoma.

Unlabelled: Uterine leiomyoma is a most common benign neoplasm in women of reproductive age. It arises from the myometrial compartment of the uterus and may transform in some cases to a malignant phenotype.

Aim: To identify the genes involved in pathogenesis of uterine leiomyoma.

Electromagnetic field-based navigation for percutaneous punctures on C-arm CT: experimental evaluation and clinical application.

The aim of this study was to prospectively evaluate the needle visualization and placement error and use of an electromagnetic field-based tracking navigation device for puncture procedures based on C-arm CT (CACT) images. A commercially available navigation device was mounted on an angiographic X-ray system setup for CACT. After the target was defined, needle placement was performed under real-time visualization of the virtual needle in CACT images.

DNA microarray preparation by light-controlled in situ synthesis.

This unit describes the in situ synthesis of DNA microarrays using a light-controlled process. In a highly parallel fashion, multiple oligonucleotide probes are created from scratch on a glass support using phosphoramidite building blocks carrying a photolabile protecting group. Spatial resolution is achieved by carefully controlling the illumination of defined spots on the glass substrate, on which the oligonucleotide probes are synthesized using straightforward phosphoramidite chemistry.

Derivatization of glass and polypropylene surfaces.

This unit describes the derivatization of solid support media, particularly glass and polypropylene, with a linker system by an iterative process that forms a dendrimeric structure, thereby increasing stepwise the loading capacity of the surface. The procedure permits the production of various types of linkers whose characteristics can be tailored to the requirements of the eventual applications. The specific modifications described here are used either for attaching prefabricated DNA oligonucleotides, PCR products, and peptide nucleic acid (PNA) oligomers, or for in situ synthesis of DNA microarrays.

Synthesis of 5'-O-phosphoramidites with a photolabile 3'-O-protecting group.

This unit describes the chemical synthesis of phosphoramidite building blocks that carry a protecting group at the 3' position. These inversely oriented synthons expose a 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) group as the photolabile protecting group of choice. Among other applications, the building blocks can be employed for light-controlled in situ synthesis of DNA microarrays, producing arrayed oligonucleotides that are attached to the support via their 5' ends, leaving their 3' termini available to act as substrates for polymerases.

[Friend or foe: combination therapy with inhaled corticosteroids and long-acting beta2-agonists in chronic obstructive pulmonary disease (COPD)].

Inhaled corticosteroids (ICS) used in COPD (chronic obstructive pulmonary disease) are recommended only in combination with a long-acting beta2-agonist (LABA) in stage 3 and higher in COPD treatment guidelines. In comparison to placebo and the single components, a superior control by means of the ICS/LABA fixed combination therapy has been demonstrated for clinical improvement in the following parameters: reduction of exacerbation rate and hospitalisations, reduction of dyspnoea and improvement of forced expiratory volume in one second (FEV1). In contrast to data from database studies, the large prospective TORCH (Towards a Revolution in COPD Health) trial found in the ICS/LABA group a beneficial effect on the reduction of mortality only as a trend in the ICS/LABA group, which did not reach statistical significance.

[Clinical features and diagnosis of bronchopulmonary infections in the elderly].

Diseases of the lung are one of the main causes of morbidity and mortality in the elderly. The risk of respiratory infections is increased due to structural changes, malnutrition, co-morbidity, and a variety of other factors. Bacterial and viral pathogens cause acute bronchitis and exacerbations of chronic bronchitis (AECB).

Influence of postprandial triglyceride-rich lipoproteins on lipid-mediated gene expression in smooth muscle cells of the human coronary artery.

Aims: Postprandial triglyceride-rich lipoproteins (TRL) have a direct effect on vascular smooth muscle cells (SMC) and they increase the risk of atherogenesis. Here, we have tested the hypothesis that the different fatty acid composition of TRL is capable of differentially modifying gene expression in human coronary artery SMC (CASMC). In addition, the effect of TRL on cell proliferation and transcription factor activation was also evaluated.

[DNA methylation profiling in cancer: from single nucleotides towards methylome].

Genomic DNA methylation pattern (methylome) represents epigenetic program of a cell. It controls expression of genetic information. In tumor cells, significant alterations in DNA methylation take place, which can be identified as one of the earliest and most consistent features of tumorigenesis.

Genotypic resistance testing in HIV by arrayed primer extension.

The analysis of mutations that are associated with the occurrence of drug resistance is important for monitoring the antiretroviral therapy of patients infected with human immunodeficiency virus (HIV). Here, we describe the establishment and successful application of Arrayed Primer Extension (APEX) for genotypic resistance testing in HIV as a rapid and economical alternative to standard sequencing. The assay is based on an array of oligonucleotide primers that are immobilised via their 5'-ends.

Dorsal horn neurons having input from low back structures in rats.

The mechanisms of nociception in the low back are poorly understood, partly because systematic recordings from dorsal horn neurons with input from the low back are largely missing. The purpose of this investigation was to (1) identify spinal segments and dorsal horn neurons receiving input from the low back, (2) test the effect of nerve growth factor (NGF) injected into the multifidus muscle (MF) on the neurons' responsiveness, and (3) study the influence of a chronic MF inflammation on the responses. In rats, microelectrode recordings were made in the segments L2, L3, and L5 to find dorsal horn neurons having input from the low back (LB neurons).

Influence of a chronic myositis on rat spinal field potentials evoked by TTX-resistant unmyelinated skin and muscle afferents.

A recent study of our group has shown that in the segments L4 and L5 of the rat, the synaptic field potentials (SFPs) evoked by tetrodotoxin-resistant (TTX-r, presumably nociceptive) muscle afferents differ in size and peak location from those of cutaneous afferents from the same body region [Lambertz D, Hoheisel U, Mense S. Distribution of synaptic field potentials induced by TTX-resistant skin and muscle afferents in rat segment L4 and L5. Neurosci Lett 2006;409:14-8].

Neuroanatomical pathway of nociception originating in a low back muscle (multifidus) in the rat.

The neural mechanisms of low back pain (LBP) are still enigmatic. Presently, low back muscles are being discussed as an important source of LBP. Here, the neuroanatomical pathway of the nociceptive information from the caudal multifidus muscle (MF) was studied.

Small trypanosome RNA-binding proteins TbUBP1 and TbUBP2 influence expression of F-box protein mRNAs in bloodstream trypanosomes.

In the African trypanosome Trypanosoma brucei nearly all control of gene expression is posttranscriptional; sequences in the 3'-untranslated regions of mRNAs determine the steady-state mRNA levels by regulation of RNA turnover. Here we investigate the roles of two related proteins, TbUBP1 and TbUBP2, containing a single RNA recognition motif, in trypanosome gene expression. TbUBP1 and TbUBP2 are in the cytoplasm and nucleus, comprise ca.

Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples.

Background: Genetic variants in immune regulator genes have been associated with numerous diseases, including allergies and cancer. Increasing evidence suggests a substantially elevated disease risk in individuals who carry a combination of disease-relevant single nucleotide polymorphisms (SNPs). For the genotyping of immune regulator genes, such as cytokines, chemokines and transcription factors, an oligonucleotide microarray for the analysis of 99 relevant SNPs was established.

Sensitization of rat dorsal horn neurons by NGF-induced subthreshold potentials and low-frequency activation. A study employing intracellular recordings in vivo.

Intramuscular injection of NGF in human subjects has been reported not to elicit pain, whereas 5% NaCl does. On the other hand, NGF injections induce a long-lasting hyperalgesia. In the present study, the possible neuronal basis of these effects was studied at the spinal level.

Breath condensate nitrite correlates with hyperinflation in chronic obstructive pulmonary disease.

Estimating the degree of pulmonary hyperinflation in chronic obstructive pulmonary disease (COPD) is not always straight forward. Standard pulmonary function tests provide only a crude estimate of this important aspect of COPD. In addition, good patient cooperation cannot always be achieved and therefore adds to the uncertainties with regard to the extent of hyperinflation of the lung.

Treatment of invasive pulmonary aspergillosis in neutropenic patients by additional bronchoscopic amphotericin B instillation.

Background: Invasive pulmonary aspergillosis (IPA) remains a life-threatening condition despite systemic antifungal therapy.

Objectives: This retrospective analysis investigated whether additional bronchoscopic instillation of amphotericin B (amB) would improve efficacy of antifungal treatment in patients with haematological malignancies suffering from IPA.

Methods: Twenty patients (40.

[Diagnostics and therapy of idiopathic pulmonary hemosiderosis].

Idiopathic pulmonary hemosiderosis (IPH) is a rare clinical entity characterized by recurrent episodes of diffuse alveolar hemorrhage. The disease--also called Ceelen's syndrome--was subsequently defined as a clinical entity comprising the triade of hemoptysis, opacities in X-ray, and anemia, in which the etiology is still unknown. Intensive search for a specific etiology ends up negative, and there are no features, which are specifically pathognomonic for IPH.

[New perspectives in GINA Asthma Guideline 2006].

The GINA (Global Initiative for Asthma) 2006 guideline contains far-reaching innovations in asthma management and control. The dose and choice of recommended medication depend on the degree of asthma severity and the quality of asthma control, rather than using the known stepwise severity approach. This flexible scheme gives the treating physician great freedom in the choice of substance used.

Antibody microarray-based profiling of complex specimens: systematic evaluation of labeling strategies.

Antibody microarrays have often had limited success in detection of low abundant proteins in complex specimens. Signal amplification systems improve this situation, but still are quite laborious and expensive. However, the issue of sensitivity is more likely a matter of kinetically appropriate microarray design as demonstrated previously.

Solid type clear cell carcinoma of the pancreas: differential diagnosis of an unusual case and review of the literature.

Pancreatic neoplasms have been reliably classified on the basis of their histopathology and immunophenotype. In this study, we report on a pancreatic tumor whose phenotype and genotype could not be assigned to any known tumor entity. The tumor was observed in the pancreatic head of a 54-year-old woman.

Troglitazone induces differentiation in Trypanosoma brucei.

Trypanosoma brucei, a protozoan parasite causing sleeping sickness, is transmitted by the tsetse fly and undergoes a complex lifecycle including several defined stages within the insect vector and its mammalian host. In the latter, differentiation from the long slender to the short stumpy form is induced by a yet unknown factor of trypanosomal origin. Here we describe that some thiazolidinediones are also able to induce differentiation.