Differential transcriptomic and metabolic profiles of M. africanum- and M. tuberculosis-infected patients after, but not before, drug treatment.

The epidemiology of Mycobacterium tuberculosis (Mtb) and M. africanum (Maf) suggests differences in their virulence, but the host immune profile to better understand the pathogenesis of tuberculosis (TB) have not been studied. We compared the transcriptomic and metabolic profiles between Mtb- and Maf-infected TB cases to identify host biomarkers associated with lineages-specific pathogenesis and response to anti-TB chemotherapy. Venous blood samples from Mtb- and Maf-infected patients obtained before and after anti-TB treatment were analyzed for cell composition, gene expression and metabolic profiles. Prior to treatment, similar transcriptomic profiles were seen in Maf- and Mtb-infected patients. In contrast, post treatment, over 1600 genes related to immune responses and metabolic diseases were differentially expressed between the groups. Notably, the upstream regulator hepatocyte nuclear factor 4-alpha (HNF4α), which regulated 15% of these genes, was markedly enriched. Serum metabolic profiles were similar in both group pre-treatment, but the decline in pro-inflammatory metabolites post treatment were most pronounced in Mtb-infected patients. Together, the differences in both peripheral blood transcriptomic and serum metabolic profiles between Maf- and Mtb-infected patients observed over the treatment period, might be indicative of intrinsic host factors related to susceptibility to TB and/or differential efficacy of the standard anti-TB treatment on the two lineages.

M. tuberculosis Gene Expression during Transition to the "Non-Culturable" State.

We analyzed the gene expression profile under specific conditions during reversible transition of M. tuberculosis cells to the "non-culturable" (NC) state in a prolonged stationary phase. More than 500 genes were differentially regulated, while 238 genes were upregulated over all time points during NC cell formation. Approximately a quarter of these upregulated genes belong to insertion and phage sequences indicating a possible high intensity of genome modification processes taking place under transition to the NC state. Besides the high proportion of hypothetical/conserved hypothetical genes in the cohort of upregulated genes, there was a significant number of genes belonging to intermediary metabolism, respiration, information pathways, cell wall and cell processes, and genes encoding regulatory proteins. We conclude that NC cell formation is an active process involved in the regulation of many genes of different pathways. A more detailed analysis of the experimental data will help to understand the precise molecular mechanisms of dormancy/latency/persistence of M. tuberculosis in the future. The list of upregulated genes obtained in this study includes many genes found to be upregulated in other models of M. tuberculosis persistence. Thirteen upregulated genes, which are common for different models, can be considered as potential targets for the development of new anti-tuberculosis drugs directed mainly against latent tuberculosis.

Deconfounding microarray analysis - independent measurements of cell type proportions used in a regression model to resolve tissue heterogeneity bias.

OBJECTIVES: Microarray analysis requires standardized specimens and evaluation procedures to achieve acceptable results. A major limitation of this method is caused by heterogeneity in the cellular composition of tissue specimens, which frequently confounds data analysis. We introduce a linear model to deconfound gene expression data from tissue heterogeneity for genes exclusively expressed by a single cell type. METHODS: Gene expression data are deconfounded from tissue heterogeneity effects by analyzing them using an appropriate linear regression model. In our illustrating data set tissue heterogeneity is being measured using flow cytometry. Gene expression data are determined in parallel by real time quantitative polymerase chain reaction (qPCR) and microarray analyses. Verification of deconfounding is enabled using protein quantification for the respective marker genes. RESULTS: For our illustrating dataset, quantification of cell type proportions for peripheral blood mononuclear cells (PBMC) from tuberculosis patients and controls revealed differences in B cell and monocyte proportions between both study groups, and thus heterogeneity for the tissue under investigation. Gene expression analyses reflected these differences in celltype distribution. Fitting an appropriate linear model allowed us to deconfound measured transcriptome levels from tissue heterogeneity effects. In the case of monocytes, additional differential expression on the single cell level could be proposed. Protein quantification verified these deconfounded results. CONCLUSIONS: Deconfounding of transcriptome analyses for cellular heterogeneity greatly improves interpretability, and hence the validity of transcriptome profiling results.

A method for extracting RNA from dormant and germinating Bacillus subtilis strain 168 endospores.

RNA was extracted from dormant and germinating Bacillus subtilis 168 spores (intact spores and chemically decoated spores) by using rapid rupture followed by acid-phenol extraction. Spore germination progress was monitored by assaying colony forming ability before and after heat shock and by reading the optical density at 600 nm. The purity, yield, and composition of the extracted RNA were determined spectrophotometrically from the ratio of absorption at 260 nm to that at 280 nm; in a 2100 BioAnalyzer, giving the RNA yield/10(8) spores or cells and the distribution pattern of rRNA components. The method reported here for the extraction of RNA from dormant spores, as well as during different phases of germination and outgrowth, has proven to be fast, efficient and simple to handle. RNA of a high purity was obtained from dormant spores and during all phases of germination and growth. There was a significant increase in RNA yield during the transition from dormant spores to germination and subsequent outgrowth. Chemically decoated spores were retarded in germination and outgrowth compared with intact spores, and less RNA was extracted; however, the differences were not significant. This method for RNA isolation of dormant, germinating, and outgrowing bacterial endospores is a valuable prerequisite for gene expression studies, especially in studies on the responses of spores to hostile environmental conditions.

[The compatibility of housing needs and housing conditions and and its impact on experiencing attachment to a district]. / Die Ubereinstimmung von Wohnbedürfnissen und Wohnbedingungen und ihr Einfluss auf die erlebte Stadtteilverbundenheit.

Based on the "complementary-congruence model" of person-environment (p-e) fit, this study focuses on housing in old age as an interaction between housing needs and housing conditions in urban settings. The research aims are: (1) To establish a set of housing-related p-e fit indices based on the relationship between environmental needs and existing conditions in different physical and social domains, and to describe housing among elders aged 51-80 years and in different urban districts with these indices. The study distinguishes between basic, higher-order and social needs relating to housing; (2) To explain outdoor place attachment as an indicator for quality of life in different urban districts with a set of predictors including these person-environment fit indices. Data were drawn from telephone-based interviews with 365 older adults (51-80 years) who were questioned about individual housing needs and housing conditions. Results revealed higher p-e fit scores in the domains of higher-order and social housing needs and conditions in the districts which were considered to be more pleasant but had poor access to the city and to public transportation. In contrast, age was more important in explaining differences in the domain of basic housing needs and conditions with higher p-e fit scores among older participants in all settings. In explaining outdoor place attachment, the fit between basic and social housing needs and conditions was important, but the higher-order fit did not play a role.

Identification of proteins from Mycobacterium tuberculosis missing in attenuated Mycobacterium bovis BCG strains.

A proteome approach, combining high-resolution two-dimensional electrophoresis (2-DE) with mass spectrometry, was used to compare the cellular protein composition of two virulent strains of Mycobacterium tuberculosis with two attenuated strains of Mycobacterium bovis Bacillus Calmette-Guerin (BCG), in order to identify unique proteins of these strains. Emphasis was given to the identification of M. tuberculosis specific proteins, because we consider these proteins to represent putative virulence factors and interesting candidates for vaccination and diagnosis of tuberculosis. The genome of M. tuberculosis strain H37Rv comprises nearly 4000 predicted open reading frames. In contrast, the separation of proteins from whole mycobacterial cells by 2-DE resulted in silver-stained patterns comprising about 1800 distinct protein spots. Amongst these, 96 spots were exclusively detected either in the virulent (56 spots) or in the attenuated (40 spots) mycobacterial strains. Fifty-three of these spots were analyzed by mass spectrometry, of which 41 were identified, including 32 M. tuberculosis specific spots. Twelve M. tuberculosis specific spots were identified as proteins, encoded by genes previously reported to be deleted in M. bovis BCG. The remaining 20 spots unique for M. tuberculosis were identified as proteins encoded by genes that are not known to be missing in M. bovis BCG.

Protective efficacy against tuberculosis of ESAT-6 secreted by a live Salmonella typhimurium vaccine carrier strain and expressed by naked DNA.

We have constructed a recombinant (r) attenuated Salmonella typhimurium strain which secretes ESAT-6 of Mycobacterium tuberculosis via the hemolysin secretion system of E. coli. Additionally, we have ligated ESAT-6 to different commercially available mammalian expression systems for use as naked DNA vaccines. We studied protection against M. tuberculosis induced by vaccination with each of these constructs alone or in combination in mice. Vaccination with a single dose of r S. typhimurium secreting ESAT-6 reduced numbers of tubercle bacilli in the lungs throughout the course of infection. The combined prime-boost vaccination did not considerably enhance protection.

Intracellular bacteria as targets and carriers for vaccination.

In this review we discuss intracellular bacteria as targets and carriers for vaccines. For clarity and ease of comprehension, we focus on three microbes, Mycobacterium tuberculosis, Listeria monocytogenes and Salmonella, with an emphasis on tuberculosis, one of the leading causes of death from infectious disease. Novel vaccination strategies against these pathogens are currently being considered. One approach favors the use of live attenuated vaccines and vaccine carrier strains thereof, either for heterologous antigen presentation or DNA vaccine delivery. This strategy includes both the improvement of attenuated vaccine strains as well as the 'de novo' generation of attenuated variants of virulent pathogens. An alternative strategy relies on the application of subunit immunizations, either as nucleic acid vaccines or protein antigens of the pathogen. Finally, we present a short summary of the vaccination strategies against tuberculosis.

[Technology in residences for support of a self-determined life style for the elderly. The research project "sentha" and initial results of a social science project]. / Technik im Haushalt zur Unterstützung einer selbstbestimmten Lebensführung im Alter. Das Forschungsprojekt "sentha" und erste Ergebnisse des Sozialwissenschaftlichen Teilprojekts.

Sentha is an interdisciplinary research team involving the Technical University Berlin, the Berlin Institute for Social Research GmbH (BIS), the German Centre for Research on Ageing at the University of Heidelberg (DZFA), the School of Fine Arts Berlin (HdK), and the Brandenburg Technical University Cottbus (BTU). Building on empirical investigations of the role of everyday household products in the everyday life of older people, product-independent design and assessment guidelines and new products are being developed in an intensive interdisciplinary process in order to better meet the needs of older people and to enhance their autonomous living. The following paper describes the contributions from the participating disciplines and presents initial results of the social sciences subproject, describing the problems arising in living independently in old age and detecting the demands on new technological solutions. Data are based on a representative survey conducted in 1999 and including a stratified sample of 1417 men and women aged 55 and older.

Acceptance and use of technological solutions by the elderly in the outdoor environment: findings from a European survey.

This article examines the use and acceptance of ticket machines, automatic teller machines (ATMs) and telephone cards by the elderly in four European regions. The analyses are based on data from an international project entitled "Keeping the Elderly Mobile", collected in Mannheim (former West Germany; N = 404 home-dwelling respondents), Chemnitz (former East Germany; N = 400), Ancona (Italy; N = 600), and Jyväskylä (Finland; N = 618). The random sample was stratified by age and gender in each country. Two generations of men and women (aged 55-74 and 75+ years, respectively) participated in the study. Results show that respondents generally made little use of the three technologies under investigation: in fact, the majority of respondents does not use them at all. The most frequently used devices were ATMs in Chemnitz and ticket machines and telephone cards in Mannheim. On the basis of logistic regression analysis, age was the most important explanatory factor for the three technologies and for all four regions, i.e., the users were mostly the "young-old." Education was a more important variable than gender. In all four regions, the majority of the respondents who used the technologies assessed felt that each of them made life easier; nevertheless, ticket machines make life more difficult to almost every third user in Mannheim. Interesting differences and similarities among the towns were also found. The present study exhibits preliminary results regarding elderly and technology which future research should investigate in greater depth.

Isolation of RNA from mycobacteria grown under in vitro and in vivo conditions.

Isolation of RNA from mycobacteria is very difficult to perform, and the yields are generally very low. We describe an approach to isolate RNA from mycobacterial species which combines the disruption of mycobacterial cells by a silica/ceramic matrix in a reciprocal shaker with the ease and efficiency of subsequent RNA purification on spin columns with silica gel-based membranes. This method is rapid, easy to perform and yields high amounts of pure, intact total RNA. Due to its safety, this method is applicable even to group 3 biological hazard organisms like Mycobacterium tuberculosis. By combining a method for the isolation of phagosomal bacteria from infected primary macrophages with the novel RNA isolation technique, we are able to monitor gene expression during infection even in bacteria which are rather resistant to genetic manipulation, like Mycobacterium bovis.

Identification of immunogenic antigens of Helicobacter pylori via the Escherichia coli hemolysin secretion system(1).

We describe a new procedure allowing the generation and detection of immunogenic antigens from Helicobacter pylori via the hemolysin secretion apparatus of Escherichia coli. The gene (or gene fragment) encoding the H. pylori protein (or protein domain) is inserted in-frame into a residual portion of the hemolysin gene (hlyA), encoding the HlyA secretion signal (HlyA(s)). These fusion proteins are secreted efficiently by E. coli. This new approach allows the identification of immunodominant antigens by using sera derived from H. pylori-infected patients suffering from different gastroduodenal pathologies. Three immunodominant antigens bearing the ureB (urease B-subunit), flaA (flagellin A-subunit), and an unknown ORF (HP0888) encoding an E. coli FecE analogous protein fused to hlyA(s) were identified and characterized.

Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens.

In 1993, the WHO declared tuberculosis a global emergency on the basis that there are 8 million new cases per year. The complete genome of the strain H37Rv of the causative microorganism, Mycobacterium tuberculosis, comprising 3924 genes has been sequenced. We compared the proteomes of two non-virulent vaccine strains of M. bovis BCG (Chicago and Copenhagen) with two virulent strains of M. tuberculosis (H37Rv and Erdman) to identify protein candidates of value for the development of vaccines, diagnostics and therapeutics. The mycobacterial strains were analysed by two-dimensional electrophoresis (2-DE) combining non-equilibrium pH gradient electrophoresis (NEPHGE) with SDS-PAGE. Distinct and characteristic proteins were identified by mass spectrometry and introduced into a dynamic 2-DE database (http://www.mpiib-berlin.mpg.de/2D-PAGE). Silver-stained 2-DE patterns of mycobacterial cell proteins or culture supernatants contained 1800 or 800 spots, respectively, from which 263 were identified. Of these, 54 belong to the culture supernatant. Sixteen and 25 proteins differing in intensity or position between M. tuberculosis H37Rv and Erdman, and H37Rv and M. bovis BCG Chicago, respectively, were identified and categorized into protein classes. It is to be hoped that the availability of the mycobacterial proteome will facilitate the design of novel measures for prevention and therapy of one of the great health threats, tuberculosis.

A dynamic two-dimensional polyacrylamide gel electrophoresis database: the mycobacterial proteome via Internet.

Proteome analysis by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry, in combination with protein chemical methods, is a powerful approach for the analysis of the protein composition of complex biological samples. Data organization is imperative for efficient handling of the vast amount of information generated. Thus we have constructed a 2-D PAGE database to store and compare protein patterns of cell-associated and culture-supernatant proteins of different mycobacterial strains. In accordance with the guidelines for federated 2-DE databases, we developed a program that generates a dynamic 2-D PAGE database for the World-Wide-Web to organise and publish, via the internet, our results from proteome analysis of different Mycobacterium tuberculosis as well as Mycobacterium bovis BCG strains. The uniform resource locator for the database is http://www.mpiib-berlin.mpg.de/2D-PAGE and can be read with a Java compatible browser. The interactive hypertext markup language documents displayed are generated dynamically in each individual session from a rational data file, a 2-D gel image file and a map file describing the protein spots as polygons. The program consists of common gateway interface scripts written in PERL, minimizing the administrative workload of the database. Furthermore, the database facilitates not only interactive use, but also worldwide active participation of other scientific groups with their own data, requiring only minimal computer hardware and knowledge of information technology.

Differential T cell responses to Mycobacterium tuberculosis ESAT6 in tuberculosis patients and healthy donors.

Vaccination against and diagnosis of tuberculosis are still insufficient. Proteins secreted by Mycobacterium tuberculosis induce strong immune responses in tuberculosis and constitute prime candidates for development of novel vaccines against tuberculosis as well as for immunodiagnostic assays. We investigated the role of the secreted proteins MPT63, MPT64 and ESAT6 from M. tuberculosis in healthy individuals and tuberculosis patients. None of the secreted proteins stimulated peripheral blood mononuclear cells from healthy donors. In contrast, CD4+ T cells from many tuberculosis patients were stimulated in an MHC class II-restricted fashion by ESAT6, but not by MPT63 or MPT64. T cell reactivities of tuberculosis patients were focused on the N-terminal region of ESAT6. The ESAT6 T cell epitopes were presented by different HLA-DR phenotypes. Cell cultures responding to either ESAT6 or synthetic peptides thereof showed mRNA transcripts for macrophage inflammatory protein (MIP)-1alpha, monocyte chemotactic protein (MCP)-1 or IL-8 and production of IFN-gamma and MIP-1alpha. Our results suggest that the secreted M. tuberculosis proteins MPT63, MPT64 or ESAT6 do not stimulate unprimed T cells, and that ESAT6 may be a potential candidate antigen for detection of clinical disease.

Outdoor mobility and social relationships of elderly people.

Social relationships and activities are important elements in the quality of life of older people. With advancing age, they are made more difficult through the possible loss of physical functions, through societal processes of differentiation, and through unfavourable environmental and technological conditions. Therefore, mobility becomes a fundamental prerequisite for the participation in social relations and activities. This article presents some initial findings of a project which investigates the mobility needs of the elderly and the main factors hindering their desired mobility in three European countries. It became apparent that there is a clear connection between the social situation of elderly persons and specific mobility patterns: if they are tied into a closely meshed network of family or friends, then they are away from home more frequently than when this is not the case. In addition, individual factors like the age, the health situation and the driving ability of a person are important influences. External factors which restrict the mobility can be found in the respective spatial or technical conditions, on the one hand, and in affecting social interactions in the public sphere on the other hand.