Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs

BACKGROUND: Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition motifs located upstream of the coding region of the regulated gene. The computational identification of such motifs is made easier by the fact that they often appear several times in the upstream region of the regulated genes, so that the number of occurrences of relevant motifs is often significantly larger than expected by pure chance. RESULTS: To exploit this fact, we construct sets of genes characterized by the statistical overrepresentation of a certain motif in their upstream regions. Then we study the functional characterization of these sets by analyzing their annotation to Gene Ontology terms. For the sets showing a statistically significant specific functional characterization, we conjecture that the upstream motif characterizing the set is a binding site for a transcription factor involved in the regulation of the genes in the set. CONCLUSIONS: The method we propose is able to identify many known binding sites in S. cerevisiae and new candidate targets of regulation by known transcription factors. Its application to less well studied organisms is likely to be valuable in the exploration of their regulatory interaction network.Comment: 19 pages, 1 figure. Published version with several improvements. Supplementary material available from the author

Therapeutic Efficacy and Immunological Response of CCL5 Antagonists in Models of Contact Skin Reaction

Skin-infiltrating T-cells play a predominant role in allergic and inflammatory skin diseases such as atopic dermatitis, psoriasis and allergic contact dermatitis. These T-cells are attracted by several chemotactic factors including the chemokine CCL5/RANTES, a CC chemokine inducing both the migration and activation of specific leukocyte subsets. CCL5 has been found to be associated with various cell-mediated hypersensitive disorders such as psoriasis, atopic dermatitis and irritant contact dermatitis. We have used two antagonists, the first, Met-CCL5, a dual CCR1/CCR5 antagonist and the second, a variant in which GAG binding is abrogated, 44AANA47-CCL5, which acts as a dominant negative inhibitor of CCL5. The antagonists were tested in two models of contact skin reaction. The first, irritant contact dermatitis (ICD) is a pathological non-specific inflammatory skin condition arising from the release of pro-inflammatory cytokines by keratinocytes in response to haptens, usually chemicals. The second, contact hypersensitivity (CHS) is a T-cell dependent model, mimicking in part the T-cell-mediated skin diseases such as psoriasis. In both models, the CCL5 antagonists showed therapeutic efficacy by reducing swelling by 50% as well as the reduction of soluble mediators in homogenates derived from challenged ears. These results demonstrate that blocking the receptor or the ligand are both effective strategies to inhibit skin inflammation

CLOE: Identification of putative functional relationships among genes by comparison of expression profiles between two species

BACKGROUND: Public repositories of microarray data contain an incredible amount of information that is potentially relevant to explore functional relationships among genes by meta-analysis of expression profiles. However, the widespread use of this resource by the scientific community is at the moment limited by the limited availability of effective tools of analysis. We here describe CLOE, a simple cDNA microarray data mining strategy based on meta-analysis of datasets from pairs of species. The method consists in ranking EST probes in the datasets of the two species according to the similarity of their expression profiles with that of two EST probes from orthologous genes, and extracting orthologous EST pairs from a given top interval of the ranked lists. The Gene Ontology annotation of the obtained candidate partners is then analyzed for keywords overrepresentation. RESULTS: We demonstrate the capabilities of the approach by testing its predictive power on three proteomically-defined mammalian protein complexes, in comparison with single and multiple species meta-analysis approaches. Our results show that CLOE can find candidate partners for a greater number of genes, if compared to multiple species co-expression analysis, but retains a comparable specificity even when applied to species as close as mouse and human. On the other hand, it is much more specific than single organisms co-expression analysis, strongly reducing the number of potential candidate partners for a given gene of interest. CONCLUSIONS: CLOE represents a simple and effective data mining approach that can be easily used for meta-analysis of cDNA microarray experiments characterized by very heterogeneous coverage. Importantly, it produces for genes of interest an average number of high confidence putative partners that is in the range of standard experimental validation techniques

Studio di Microzonazione Sismica di I Livello per un comune montano con applicazione del Metodo di Indagine HVSR

Riassunto In questo lavoro di tesi vengono presentati i risultati di uno studio di valutazione della risposta sismica locale finalizzato alla Microzonazione Sismica (MS) di I Livello di un comune montano; il lavoro è stato svolto nell'ambito di uno specifico progetto affidato alla Fondazione Prato Ricerche. La valutazione della risposta sismica locale mira all'individuazione dei possibili fenomeni di amplificazione del moto del suolo che si verificano quando la geologia superficiale è caratterizzata da forti contrasti di impedenza sismica. Questi fenomeni occorrono tipicamente nei bacini intermontani, all'interfaccia fra il basamento roccioso (bedrock) e la coltre sedimentaria. Una delle metodologie maggiormente impiegate per tali valutazioni è la tecnica HVSR (Horizontal to Vertical Spectral Ratio; Nakamura, 1989), basata sulla misura dei rapporti medi fra le ampiezze spettrali delle componenti orizzontali e verticale del rumore sismico ambientale (funzione H/V). I valori di picco della funzione H/V individuano le frequenze di risonanza dei terreni; l'ampiezza dei picchi è proporzionale, anche se non linearmente, all'entità del contrasto di impedenza sismica esistente all'interfaccia fra il basamento roccioso e la copertura sedimentaria. Dopo una prima fase di ricerca bibliografica sulle metodologie di indagine pertinenti la MS e la normativa di riferimento, questo lavoro si è articolato secondo i seguenti passi: 1. Raccolta e analisi dei dati preesistenti, con particolare riferimento alle informazioni di carattere geologico e geomorfologico, la pericolosità di base e degli eventi di riferimento, la sismicità storica e le indagini geologico-geofisiche precedenti; 2. Creazione di una banca dati georeferenziata su base cartografica, utilizzando un sistema informativo geografico (GIS); 3. Esecuzione della campagna di misura per la raccolta delle registrazioni di rumore sismico ambientale da utilizzare per il successivo calcolo delle funzioni H/V; 4. Sulla base dei risultati ottenuti al punto precedente, ricostruzione di un modello del sottosuolo per l'abitato comunale e altri abitati minori. Questi risultati sono poi stati raccolti con la stesura di elaborati cartografici che comprendono la mappatura delle indagini svolte, la distribuzione spaziale delle frequenze fondamentali dei depositi, la definizione delle microzone omogenee in prospettiva sismica (MOPS). L’elaborazione dei dati ha riguardato il calcolo del Rapporto Spettrale H/V, e la sua modellizzazione in termini di ricostruzione di profili di velocità sismica. Per tale inversione, vengono presentati e confrontati i risultati ottenuti utilizzando due diversi codici di calcolo: il software Grilla® (Micromed s.p.a.), e le funzioni Matlab Model HVSR (Herak, 2008). In particolare, la modellazione diretta dei rapporti H/V implementata in questi due codici si differenzia per le assunzioni teoriche di partenza riguardo alla composizione predominante del campo d’onda del noise (rispettivamente, onde di superficie contro onde di volume). Vengono anche presentate due funzioni di calcolo sviluppate nell'ambito di questo studio, una per il calcolo e la regolarizzazione dei rapporti H/V ottenuti da registrazioni weak motion ed una per il calcolo dei rapporti H/V tramite la modellazione diretta della risposta sismica sulla base di una determinata distribuzione dei parametri elastici con la profondità. Infine, vengono presentati i risultati ottenuti dall’analisi del noise con quelli derivati da osservazioni weak motion associate a terremoti di bassa energia (M < 4) registrati durante lo svolgimento dello studio

An integrated framework for environmental management and protection in Zambia

This study identifies the major environmental issues andproblems affecting Zambia and examines the current state andpractice of environmental protection and management. Areview of the existing legislation relating to environmentalprotection in Zambia is made.The relationship between the development process and theenvironment is explored, in particular giving an overview ofthe evolution of paradigms in environmental management anddevelopment. An outline of the environmental trends in sub-Saharan Africa and the environmental policy in the UnitedKingdom and how it relates to the framework of ECenvironmental policy is made. With such a background keyissues have been identified to be addressed when consideringenvironmental policy in Zambia.The mining, agricultural and tourism industries form thesectoral case studies of this study. These sectors have beenselected on the basis of their dominance in Zambia'sdevelopment strategy and their impact on the environment.The immense scale of the mining industry warrants itsconsideration; agriculture has now been given priority asthe sector with the highest potential in the overall economyand; in diversifying the economy, tourism development isemerging as one of the most important sectors.The study recognises that the absence of definite crosssectoralguidelines for environmental resources managementand a general paucity of information on the environment havebeen major constraints for the development of environmentalprotection strategies in Zambia. This has been due toinsufficient institutional support for sustained research andmonitoring of the environment. Therefore, the study mak?sgeneral sectoral recommendations for addressing theenvironmental problems identified in the study