Biomedical subjects

Andreas Beyer

Publications and source records attributed to Andreas Beyer.

15 recordsLinked to original sources

PubMed2025

Lymphoid gene expression supports neuroprotective microglia function.

Microglia, the innate immune cells of the brain, play a defining role in the progression of Alzheimer's disease (AD)1. The microglial response to amyloid plaques in AD can range from neuroprotective to neurotoxic2. Here we show that the protective function of microglia is governed by the transcription factor PU.1, which becomes downregulated following microglial contact with plaques. Lowering PU.1 expression in microglia reduces the severity of amyloid disease pathology in mice and is linked to the expression of immunoregulatory lymphoid receptor proteins, particularly CD28, a surface receptor that is critical for T cell activation3,4. Microglia-specific deficiency in CD28, which is expressed by a small subset of plaque-associated PU.1low microglia, promotes a broad inflammatory microglial state that is associated with increased amyloid plaque load. Our findings indicate that PU.1low CD28-expressing microglia may operate as suppressive microglia that mitigate the progression of AD by reducing the severity of neuroinflammation. This role of CD28 and potentially other lymphoid co-stimulatory and co-inhibitory receptor proteins in governing microglial responses in AD points to possible immunotherapy approaches for treating the disease by promoting protective microglial functions.

Microglia↗

PubMed2006

DASS: efficient discovery and p-value calculation of substructures in unordered data.

MOTIVATION: Pattern identification in biological sequence data is one of the main objectives of bioinformatics research. However, few methods are available for detecting patterns (substructures) in unordered datasets. Data mining algorithms mainly developed outside the realm of bioinformatics have been adapted for that purpose, but typically do not determine the statistical significance of the identified patterns. Moreover, these algorithms do not exploit the often modular structure of biological data. RESULTS: We present the algorithm DASS (Discovery of All Significant Substructures) that first identifies all substructures in unordered data (DASS(Sub)) in a manner that is especially efficient for modular data. In addition, DASS calculates the statistical significance of the identified substructures, for sets with at most one element of each type (DASS(P(set))), or for sets with multiple occurrence of elements (DASS(P(mset))). The power and versatility of DASS is demonstrated by four examples: combinations of protein domains in multi-domain proteins, combinations of proteins in protein complexes (protein subcomplexes), combinations of transcription factor target sites in promoter regions and evolutionarily conserved protein interaction subnetworks. AVAILABILITY: The program code and additional data are available at http://www.fli-leibniz.de/tsb/DASS

Algorithms↗

PubMed2006

Integrated assessment and prediction of transcription factor binding.

Systematic chromatin immunoprecipitation (chIP-chip) experiments have become a central technique for mapping transcriptional interactions in model organisms and humans. However, measurement of chromatin binding does not necessarily imply regulation, and binding may be difficult to detect if it is condition or cofactor dependent. To address these challenges, we present an approach for reliably assigning transcription factors (TFs) to target genes that integrates many lines of direct and indirect evidence into a single probabilistic model. Using this approach, we analyze publicly available chIP-chip binding profiles measured for yeast TFs in standard conditions, showing that our model interprets these data with significantly higher accuracy than previous methods. Pooling the high-confidence interactions reveals a large network containing 363 significant sets of factors (TF modules) that cooperate to regulate common target genes. In addition, the method predicts 980 novel binding interactions with high confidence that are likely to occur in so-far untested conditions. Indeed, using new chIP-chip experiments we show that predicted interactions for the factors Rpn4p and Pdr1p are observed only after treatment of cells with methyl-methanesulfonate, a DNA-damaging agent. We outline the first approach for consistently integrating all available evidences for TF-target interactions and we comprehensively identify the resulting TF module hierarchy. Prioritizing experimental conditions for each factor will be especially important as increasing numbers of chIP-chip assays are performed in complex organisms such as humans, for which "standard conditions" are ill defined.

Algorithms↗

PubMed2006

The new classification scheme of the genetic code, its early evolution, and tRNA usage.

We present a new classification scheme of the genetic code. In contrast to the standard form it clearly shows five codon symmetries: codon-anticodon, codon-reverse codon, and sense-antisense symmetry, as well as symmetries with respect to purine-pyrimidine (A versus G, U versus C) and keto-aminobase (G versus U, A versus C) exchanges. We study the number of tRNA genes of 16 archaea, 81 bacteria and 7 eucaryotes to analyze whether these symmetries are reflected in the corresponding tRNA usage patterns. Two features are especially striking: reverse stop codons do not have their own tRNAs (just one exception in human), and A** anticodons are significantly suppressed. Our classification scheme of the genetic code and the identified tRNA usage patterns support recent speculations about the early evolution of the genetic code. In particular, pre-tRNAs might have had the ability to bind their codons in two directions to the corresponding codons.

Biological Evolution↗

PubMed2005

Common patterns in type II restriction enzyme binding sites.

Restriction enzymes are among the best studied examples of DNA binding proteins. In order to find general patterns in DNA recognition sites, which may reflect important properties of protein-DNA interaction, we analyse the binding sites of all known type II restriction endonucleases. We find a significantly enhanced GC content and discuss three explanations for this phenomenon. Moreover, we study patterns of nucleotide order in recognition sites. Our analysis reveals a striking accumulation of adjacent purines (R) or pyrimidines (Y). We discuss three possible reasons: RR/YY dinucleotides are characterized by (i) stronger H-bond donor and acceptor clusters, (ii) specific geometrical properties and (iii) a low stacking energy. These features make RR/YY steps particularly accessible for specific protein-DNA interactions. Finally, we show that the recognition sites of type II restriction enzymes are underrepresented in host genomes and in phage genomes.

Bacteriophages↗

PubMed2005

Comparing estimates of persistence and long-range transport potential among multimedia models.

Overall persistence (Pov) and long-range transport potential (LRTP) of organic chemicals are environmental hazard metrics calculated with multimedia fate and transport models. Since there are several models of this type, it is important to know whether and how different model designs (model geometry, selection of compartments and processes, process descriptions) affect the results for Pov and LRTP. Using a set of 3175 hypothetical chemicals covering a broad range of partition coefficients and degradation half-lives, we systematically analyze the Pov and LRTP results obtained with nine multimedia models. We have developed several methods that make it possible to visualize the model results efficiently and to relate differences in model results to mechanistic differences between models. Rankings of the hypothetical chemicals according to Pov and LRTP are highly correlated among models and are largely determined by the chemical properties. Domains of chemical properties in which model differences lead to different results are identified, and guidance on model selection is provided for model users.

Environmental Monitoring↗

PubMed2005

Identification and characterization of protein subcomplexes in yeast.

Protein complexes are major components of cellular organization. Based on large-scale protein complex data, we present the first statistical procedure to find insightful substructures in protein complexes: we identify protein subcomplexes (SCs), i.e., multiprotein assemblies residing in different protein complexes. Four protein complex datasets with different origins and variable reliability are separately analyzed. Our method identifies well-characterized protein assemblies with known functions, thereby confirming the utility of the procedure. In addition, we also identify hitherto unknown functional entities consisting of either functionally unknown proteins or proteins with different functional annotation. We show that SCs represent more reliable protein assemblies than the original complexes. Finally, we demonstrate unique properties of subcomplex proteins that underline the distinct roles of SCs: (i) SCs are functionally and spatially more homogeneous than complete protein complexes (this fact is utilized to predict functional roles and subcellular localizations for so far unannotated proteins); (ii) the abundance of subcomplex proteins is less variable than the abundance of other proteins; (iii) SCs are enriched with essential and synthetic lethal proteins; and (iv) mutations in SC-proteins have higher fitness effects than mutations in other proteins.

Gene Deletion↗

PubMed2005

Influence of distributional shape of substance parameters on exposure model output.

Uncertainty of environmental concentrations is calculated with the regional multimedia exposure model of EUSES 1.0 by considering probability input distributions for aqueous solubility, vapor pressure, and octanol-water partition coefficient, K(ow). Only reliable experimentally determined data are selected from available literature for eight reference chemicals representing a wide substance property spectrum. Monte Carlo simulations are performed with uniform, triangular, and log-normal input distributions to assess the influence of the choice of input distribution type on the predicted concentration distributions. The impact of input distribution shapes on output variance exceeds the effect on the output mean by one order of magnitude. Both are affected by influence and uncertainty (i.e., variance) of the input variable as well. Distributional shape has no influence when the sensitivity function of the respective parameter is perfectly linear. For nonlinear relationships, overlap of probability mass of input distribution with influential ranges of the parameter space is important. Differences in computed output distribution are greatest when input distributions differ in the most influential parameter range.

Environmental Exposure↗

PubMed2004

Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale.

Based on large-scale data for the yeast Saccharomyces cerevisiae (protein and mRNA abundance, translational status, transcript length), we investigate the relation of transcription, translation, and protein turnover on a genome-wide scale. We elucidate variations between different spatial cell compartments and functional modules by comparing protein-to-mRNA ratios, translational activity, and a novel descriptor for protein-specific degradation (protein half-life descriptor). This analysis helps to understand the cell's strategy to use transcriptional and post-transcriptional regulation mechanisms for managing protein levels. For instance, it is possible to identify modules that are subject to suppressed translation under normal conditions ("translation on demand"). In order to reduce inconsistencies between the datasets, we compiled a new reference mRNA abundance dataset and we present a novel approach to correct large microarray signals for a saturation bias. Accounting for ribosome density based on transcript length rather than ORF length improves the correlation of observed protein levels to translational activity. We discuss potential causes for the deviations of these correlations. Finally, we introduce a quantitative descriptor for protein degradation (protein half-life descriptor) and compare it to measured half-lives. The study demonstrates significant post-transcriptional control of protein levels for a number of different compartments and functional modules, which is missed when exclusively focusing on transcript levels.

Cell Compartmentation↗

PubMed2004

Gene expression profiling of potential PPARgamma target genes in mouse aorta.

Diminished activity of peroxisome proliferator-activated receptor-gamma (PPARgamma) may play a role in the pathogenesis of hypertension and vascular dysfunction. To better understand what genes are regulated by PPARgamma, an experimental data set was generated by microarray analysis, in duplicate, of pooled aortic mRNA isolated from mice treated for 21 days with a PPARgamma agonist (rosiglitazone) or vehicle. Of the 12,488 probe sets present on the array (Affymetrix MG-U74Av2), 181 were differentially expressed between groups according to a statistical metric generated using Affymetrix software. A significant correlation was observed between the microarray results and real-time RT-PCR analysis of 39 of these genes. Cluster analysis revealed 3 expression patterns, 29 transcripts of moderate abundance that were decreased (-93%) to very low levels, 106 transcripts that were downregulated (-42%), and 46 transcripts that were upregulated (+70%). Functional groups that were decreased included inflammatory response (-93%, n = 6), immune response (-86%, n = 7), and cytokines (-82%, n = 7). There was an overall upregulation in the oxidoreductase activity group (+47%, n = 9). Individually, six transcripts in this group were increased (+72%), and three were decreased (-34%). Fourteen of the genes map to regions in the rat genome that have been linked to increased blood pressure, and of 142 upstream regions analyzed, sequences resembling the DNA binding site for PPARgamma were identified in 101 of the differentially expressed genes.

Animals↗

PubMed2004

Probabilistic uncertainty analysis of the European Union system for the evaluation of substances multimedia regional distribution model.

The European Union System for the Evaluation of Substances (EUSES) is a computerized model system to facilitate and harmonize health and environmental risk assessment of previously notified and new substances. For calculation of regional background exposure, a multimedia distribution model is used. In the present study, the uncertainty of this regional model is analyzed. Environmental parameters were collected for North Rhine Westphalia (Germany), which resembles the standard region of EUSES. Probability distribution functions of various types (uniform, triangular, normal, log normal) depending on data availability were derived for environmental input parameters, including geometric parameters. Generic log-normal distribution functions with fixed standard deviations were chosen for solubility in air, water, and n-octanol as well as for degradation half-lives. Monte Carlo simulations were carried out for 10 reference substances having different properties. Contribution of environmental parameter uncertainty to total output uncertainties is higher than that of substance parameters. Range of output uncertainty, defined as the ratio of the logarithms of the 90th and 10th percentiles of the cumulative probability distribution function, shows an increase from air and water to soil. The highest-occurring range is 1.4 orders of magnitude, which means that total uncertainty of the regional model is relatively low and, usually, is lower than the range of measured values. The median of output probability distributions lies above the point estimate. Influence of input parameters was estimated as their rank correlation coefficients to output uncertainty. Substance and environmental parameters contribute differently to output variance depending on individual substance properties and environmental compartment. Hence, the present study underlines the need to perform uncertainty analyses instead of either using a set of simple rules or just looking at certain parameters.

Environment↗

PubMed2003

Toxin-gene profile heterogeneity among endemic invasive European group A streptococcal isolates.

We determined the toxin-gene profiles of 239 endemic, invasive group A streptococcal (GAS) isolates that circulated, within a 5-year period, in European university hospitals. Profiling was performed by use of multiplex polymerase chain reaction that screened for 9 streptococcal pyrogenic exotoxins (speA, speB, speC, speF, speG, speH, speJ, ssa, and smeZ). Analysis revealed that invasive GAS isolates do not share a common toxin-gene profile. Although all emm types were characterized by several different toxin-gene profiles, a predominance of 1 or 2 toxin-gene profiles could be observed, reflecting that a few invasive clones have spread successfully throughout the world. Remarkably, statistical pair-wise analysis of individual toxin genes revealed that strains that did not share the predominant profile still showed a nonrandom distribution of key toxin genes characteristic of the specific emm type. This could indicate that M proteins function, directly or indirectly, as barriers for horizontal gene exchange.

Antigens, Bacterial↗

PubMed2003

Temperature dependence of the characteristic travel distance.

The effect of temperature variation on the environmental fate of organic chemicals can be evaluated in steady-state multimedia box models by expressing chemical partitioning data and reaction rate coefficients as functions of temperature. Using such a modelthetemperature dependence of the characteristic travel distance in air L(A), which is a measure for the atmospheric long-range transport potential of organic chemicals, is calculated. Simulations are reported for a set of 40 chemicals of environmental interest. Increasing temperature is shown to have two opposing effects on L(A). Rates of chemical transformations in the atmosphere (k(air)) and surface media are increased, which reduces L(A). Rates of atmospheric deposition (k(dep)) are reduced leading to increased mobility and L(A). Accordingly, L(A) can monotonically increase or decrease with increasing temperature, or it can have a maximum in the modeled temperature range, but it cannot have a minimum. For chemicals with a strong temperature dependence of k(air) relative to k(dep), L(A) will increase with increasing temperature. Results for selected polychlorinated biphenyls are compared to monitoring data yielding qualitative agreement when chemical properties are adjusted to mean temperatures for the measurement period. The results demonstrate that the temperature dependence of the characteristic travel distance is highly dependent on chemical characteristics and can be counterintuitive. The use of mass balance models is thus essential. The difference between the L(A) values at 5 degrees C and 30 degrees C can be up to a factor of 6. Accordingly, chemical ranking with respect to L(A) can change significantly if performed at different temperatures. Implications of the different temperature dependencies on long-range transport to polar regions are discussed.

Air Movements↗

PubMed2003

Comparative sequence and expression analyses of four mammalian VPS4 genes.

The VPS4 gene is a member of the AAA-family; it codes for an ATPase which is involved in lysosomal/endosomal membrane trafficking. VPS4 genes are present in virtually all eukaryotes. Exhaustive data mining of all available genomic databases from completely or partially sequenced organisms revealed the existence of up to three paralogues, VPS4a, -b, and -c. Whereas in the genome of lower eukaryotes like yeast only one VPS4 representative is present, we found that mammals harbour two paralogues, VPS4a and VPS4b. Most interestingly, the Fugu fish contains a third VPS4 paralogue (VPS4c). Sequence comparison of the three VPS4 paralogues indicates that the Fugu VPS4c displays sequence features intermediate between VPS4a and VPS4b. Using complete mammalian VPS4a and VPS4b cDNA clones as probes, genomic clones of both VPS4 paralogues in human and mouse were identified and sequenced. The chromosomal loci of all four VPS4 genes were determined by independent methods. A BLAST search of the human genome database with the human VPS4A sequence yielded a double match, most likely due to a faulty assembly of sequence contigs in the human draft sequence. Fluorescent in situ hybridization and radiation hybrid analyses demonstrated that human and mouse VPS4A/a and VPS4B/b are located on syntenic chromosomal regions. Northern blot and semi-quantitative reverse transcription analyses showed that mouse VPS4a and VPS4b are differentially expressed in different organs, suggesting that the two paralogues have developed different functional properties since their divergence. To investigate the subcellular distribution of the murine VPS4 paralogues, we transiently expressed various fluorescent VPS4 fusion proteins in mouse 3T3 cells. All tested VPS4 fusion proteins were found in the cytosol. Expression of dominant-negative mutant VPS4 fusion proteins led to their concentration in the perinuclear region. Co-expression of VPS4a-GFP and VPS4b-dsRed fusion proteins revealed a partial co-localization that was most prominent with mutant VPS4a and VPS4b proteins. A physical interaction between the mouse paralogues was also supported by two-hybrid analyses.

3T3 Cells↗

PubMed2002

Selecting internally consistent physicochemical properties of organic compounds.

Methods are presented for selecting values of chemical properties of vapor pressure, water solubility, Henry's law constant, and octanol-water and octanol-air partition coefficients, which are subject to thermodynamic constraints, while taking advantage of all measurements. The aim of the mathematical procedures is to find the one set of internally consistent partitioning parameters that is minimally divergent from the experimental values. Information about the reliability or uncertainty of reported values can be accounted for by weighing factors. A similar approach is applied to the temperature dependence of these properties. The influence of partial miscibility of the octanol-water system is discussed and a correction is suggested for this effect. The selection method is applied to 50 mostly aromatic chemicals for which multiple measured partitioning data are available. The resulting sets of consistent property data are presented and discussed.

Environmental Pollutants↗