Deducing corticotropin-releasing hormone receptor type 1 signaling networks from gene expression data by usage of genetic algorithms and graphical Gaussian models

<p>Abstract</p> <p>Background</p> <p>Dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis is a hallmark of complex and multifactorial psychiatric diseases such as anxiety and mood disorders. About 50-60% of patients with major depression show HPA axis dysfunction, i.e. hyperactivity and impaired negative feedback regulation. The neuropeptide corticotropin-releasing hormone (CRH) and its receptor type 1 (CRHR1) are key regulators of this neuroendocrine stress axis. Therefore, we analyzed CRH/CRHR1-dependent gene expression data obtained from the pituitary corticotrope cell line AtT-20, a well-established <it>in vitro </it>model for CRHR1-mediated signal transduction. To extract significantly regulated genes from a genome-wide microarray data set and to deduce underlying CRHR1-dependent signaling networks, we combined supervised and unsupervised algorithms.</p> <p>Results</p> <p>We present an efficient variable selection strategy by consecutively applying univariate as well as multivariate methods followed by graphical models. First, feature preselection was used to exclude genes not differentially regulated over time from the dataset. For multivariate variable selection a maximum likelihood (MLHD) discriminant function within GALGO, an R package based on a genetic algorithm (GA), was chosen. The topmost genes representing major nodes in the expression network were ranked to find highly separating candidate genes. By using groups of five genes (chromosome size) in the discriminant function and repeating the genetic algorithm separately four times we found eleven genes occurring at least in three of the top ranked result lists of the four repetitions. In addition, we compared the results of GA/MLHD with the alternative optimization algorithms greedy selection and simulated annealing as well as with the state-of-the-art method random forest. In every case we obtained a clear overlap of the selected genes independently confirming the results of MLHD in combination with a genetic algorithm.</p> <p>With two unsupervised algorithms, principal component analysis and graphical Gaussian models, putative interactions of the candidate genes were determined and reconstructed by literature mining. Differential regulation of six candidate genes was validated by qRT-PCR.</p> <p>Conclusions</p> <p>The combination of supervised and unsupervised algorithms in this study allowed extracting a small subset of meaningful candidate genes from the genome-wide expression data set. Thereby, variable selection using different optimization algorithms based on linear classifiers as well as the nonlinear random forest method resulted in congruent candidate genes. The calculated interacting network connecting these new target genes was bioinformatically mapped to known CRHR1-dependent signaling pathways. Additionally, the differential expression of the identified target genes was confirmed experimentally.</p

Alpine Freiräume in der räumlichen Planung - Ein Plädoyer für mehr grenzüberschreitende Zusammenarbeit

Alpine Freiräume werden zusehends knapper. Diese Aussage gilt in den Alpen für den naturgemäß raren Dauersiedlungsraum, der z.B. in Tirol nur 11,8 % des Landesgebietes umfasst. Die Bevölkerung und damit auch die erforderliche Infrastruktur wachsen in vielen Talschaften. Aber auch die Freiräume, die in den darüber gelegenen Höhenstufen der Alpen liegen, werden sukzessiv zerschnitten und mit technischen Anlagen (z.B. Seilbahnen, hydroelektrische Anlagen) erschlossen bzw. sind mit immer intensiveren Nutzungen (z.B. E-Mountainbikes) konfrontiert. Im Freistaat Bayern begann die Erhaltung von Freiräumen mit der Implementierung des Alpenplans als raumordnerische Zielsetzung bereits im Jahr 1972. Die dadurch betriebene Zonierung des gesamten bayerischen Alpenraums nach drei Intensitätsstufen der verkehrlichen Nutzung war eine echte Innovation des Normgebers. Sie zielte mit ihrer sogenannten Zone C auf den damals noch jungen Naturschutz und die Verringerung alpiner Naturgefahren ab. In der Hauptsache jedoch galt diese planerische Initiative der nicht anlagengebundenen, landschaftsbezogenen Erholung, d.h. Freizeit- und Tourismusaktivitäten in der Natur. Heute bestehen mehr oder weniger erfolgreiche, verwandte Initiativen in Südtirol (Italien), Österreich und der Schweiz. Sie zu analysieren, ihre Festlegung, Funktionsweise und planerische Umsetzung vergleichend zu beschreiben sowie kritisch zu hinterfragen, ist die Zielsetzung dieses Beitrags. Im Fokus steht die Gegenüberstellung von Analysen zum Erhalt von Freiräumen für den Menschen (Einheimische und ihre traditionellen Wirtschaftsweisen, aber auch Besucher) und das Naturerbe. Neben dem Vorschlag einer forschungsleitenden, ganzheitlichen Definition von Freiräumen werden die heute gängigen Praktiken im Umgang mit alpinen Freiräumen in Raumordnung und räumlicher Planung im deutschsprachigen und Schweizer Alpenraum und deren kritische Bewertung sowie künftige Möglichkeiten grenzüberschreitend harmonisierter Verfahrensweisen dazu debattiert.Alpine open spaces are becoming noticeably scarcer. This statement applies to the inherently restricted area of permanent settlement in the Alps, which, e.g., covers only 11.8 % of the territory of Tyrol. The population is growing in many of the valleys and with it the infrastructure required. However, the open spaces, situated at altitudes above the settlements, are also being successively broken up and exploited using technical equipment (e.g. cable cars, hydro-electric facilities) or increasingly intensive types of use (e.g. e-mountain bikes). In Bavaria the conservation of open space began as early as 1972 with the implementation of the Alpine plan (Alpenplan), which set spatial planning objectives for the entire Alpine area. This led to the division of the Bavarian Alpine area into three zones of varying intensity of traffic use, a true legislative innovation. The so-called Zone C was intended for nature protection, still in its infancy at that time, and also aimed to reduce natural Alpine hazards. Primarily, however, this planning initiative was related to the role of the landscape for recreation, i.e. to leisure and touristic activities in natural surroundings. Today, there are similar initiatives of varying success in South Tyrol (Italy), Austria and Switzerland. This paper aims to analyse these initiatives, comparing and critically assessing their specifications, functioning and planning implementation. The focus of attention is on bringing together approaches for conserving open space for people (local inhabitants and their traditional economic activities, but also visitors) and natural heritage. Presentday regional and spatial planning practices related to Alpine open spaces in the German-speaking Alps are presented and critically evaluated and future options for harmonising approaches across the borders are discussed

TERENO: German network of terrestrial environmental observatories

Central elements of the TERENO network are “terrestrial observatories” at the catchment scale which were selected in climate sensitive regions of Germany for the regional analyses of climate change impacts. Within these observatories small scale research facilities and test areas are placed in order to accomplish energy, water, carbon and nutrient process studies across the different compartments of the terrestrial environment. Following a hierarchical scaling approach (point-plot-field) these detailed information and the gained knowledge will be transferred to the regional scale using integrated modelling approaches. Furthermore, existing research stations are enhanced and embedded within the observatories. In addition, mobile measurement platforms enable monitoring of dynamic processes at the local scale up to the determination of spatial pattern at the regional scale are applied within TERENO

Biophysical Characterization of Pro-apoptotic BimBH3 Peptides Reveals an Unexpected Capacity for Self-Association

Bcl-2 proteins orchestrate the mitochondrial pathway of apoptosis, pivotal for cell death. Yet, the structural details of the conformational changes of pro- and antiapoptotic proteins and their interactions remain unclear. Pulse dipolar spectroscopy (double electron-electron resonance [DEER], also known as PELDOR) in combination with spin-labeled apoptotic Bcl-2 proteins unveils conformational changes and interactions of each protein player via detection of intra- and inter-protein distances. Here, we present the synthesis and characterization of pro-apoptotic BimBH3 peptides of different lengths carrying cysteines for labeling with nitroxide or gadolinium spin probes. We show by DEER that the length of the peptides modulates their homo-interactions in the absence of other Bcl-2 proteins and solve by X-ray crystallography the structure of a BimBH3 tetramer, revealing the molecular details of the inter-peptide interactions. Finally, we prove that using orthogonal labels and three-channel DEER we can disentangle the Bim-Bim, Bcl-xL-Bcl-xL, and Bim-Bcl-xL interactions in a simplified interactome.This work was funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2033—Projektnummer 390677874, the DFG Priority Program SPP1601 “New Frontiers in Sensitivity in EPR Spectroscopy” (to E.B.), DFG BO 3000/5-1 (to E.B.), SFB958 – Z04 (to E.B.), DFG grant INST 130/972-1 FUGG (to E.B.). P.E.C. is supported by an Australian NHMRC fellowship (1079700