Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Development of Organocatalytic stereoselective SN1 type reactions

The proposal in my thesis has been the study of Stereoselective α-alkylation through SN1 type reaction. SN1 type reaction involves a stabilized and reactive carbocation intermediate By taking advantages of stability of particular carbocations, the use of carbocations in selective reactions has been important. In this work has been necessary to know the stability and reactivity of carbocations. And the work of Mayr group has helped to rationalize the behaviour and reactivity between the carbocations and nucleophiles by the use of Mayr’s scale of reactivity. The use of alcohols to performed the stable and reactive carbocations have been the key in my thesis. The direct nucleophilic substitution of alcohols has been a crucial scope in the field of organic synthesis, because offer a wide range of intermediates for the synthesis of natural products and pharmaceutics synthesis. In particular the catalytic nucleophilic direct substitution of alcohols represents a novel methodology for the preparation of a variety of derivatives, and water only as the sub-product in the reaction. The stereochemical control of the transformation C-H bond into stereogenic C-C bond adjacent to carbonyl functionalized has been studied for asymmetric catalysis. And the field of organocatalysis has introduced the use of small organic molecule as catalyst for stereoselective transformations. Merging these two concepts Organocatalysis and Mayr’s scale, my thesis has developed a new approach for the α-alkylation of aldehydes and ketones through SN1 type reaction.

Effects of Global Warming on Berry Composition of cv. Sangiovese: Biochemical and Molecular Aspects and Agronomical Adaptation Approaches

Wine grape must deal with serious problems due to the unfavorable climatic conditions resulted from global warming. High temperatures result in oxidative damages to grape vines. The excessive elevated temperatures are critical for grapevine productivity and survival and contribute to degradation of grape and wine quality and yield. Elevated temperature can negatively affect anthocyanin accumulation in red grape. Particularly, cv. Sangiovese was identified to be very sensitive to such condition. The quantitative real-time PCR analysis showed that flavonoid biosynthetic genes were slightly repressed by high temperature. Also, the heat stress repressed the expression of the transcription factor “VvMYBA1” that activates the expression of UFGT. Moreover, high temperatures had repressing effects on the activity of the flavonoids biosynthetic enzymes “PAL” and “UFGT”.Anthocyanin accumulation in berry skin is due to the balance between its synthesis and oxidation. In grape cv. Sangiovese, the gene transcription and activity of peroxidases enzyme was elevated by heat stress as a defensive mechanism of ROS-scavenging. Among many isoforms of peroxidases genes, one gene (POD 1) was induced in Sangiovese under thermal stress condition. This gene was isolated and evaluated via the technique of genes transformation from grape to Petunia. Reduction in anthocyanins concentration and higher enzymatic activity of peroxidase was observed in POD 1 transformed Petunia after heat shock compared to untrasformed control. Moreover, in wine producing regions, it is inevitable for the grape growers to adopt some adaptive strategies to alleviate grape damages to abiotic stresses. Therefore, in this thesis, the technique of post veraison trimming was done to improve the coupling of phenolic and sugar ripening in Vitis vinifera L. cultivar Sangiovese. Trimming after veraison showed to be executable to slow down the rate of sugar accumulation in grape (to decrease the alcohol potential in wines) without evolution of the main berry flavonoids compounds.

Las variaciones de la “serliana”: aspectos y motivos de la arquitectura del poder desde la Antigüedad al Renacimiento italiano y español

Principales aportaciones: Elenco actualizado y más completo de “serlianas” hasta el momento, incluyendo el más amplio repertorio numismático e iconográfico sobre el tema. Visión de conjunto crítica de la “serliana” y motivos afines en la Antigüedad, la Edad Media y el Renacimiento, atendiendo a una selección de ejemplos en todos los formatos posibles (arquitectura e iconografía). Inclusión y explicación de la “serliana” dentro de los avances de la arquitectura romana, con atención a las fuentes escritas. Identificación de las principales áreas de origen y desarrollo de la “serliana”. Explicación de las causas y resultados de los procesos de innovación arquitectónica. Demostración de la llegada de la “serliana” a Hispania mucho antes que el disco de Teodosio. Indagación en las funciones y posibles implicaciones simbólicas de ejemplos de “serliana”. Hipótesis sobre el papel desempeñado por las arquitecturas efímeras. Hipótesis sobre el papel de la arquitectura militar en época romana para la difusión de la “serliana”. Comentario crítico de la situación de la “serliana” en la Antigüedad Tardía y visión general de sus procesos de transferencia y metamorfosis. Demostración de la pervivencia de la “serliana” en la Edad Media. Análisis de la arcada triple como posible sustituto de la “serliana”. Comentario crítico de los dibujos tardomedievales y renacentistas sobre la “serliana” y su relación con el estudio contemporáneo de los monumentos antiguos. Identificación de ejemplos y comentario crítico de la situación de la “serliana” en la Italia del Quattrocento y del Cinquecento. Análisis de las confluencias de la “serliana” Italia-España y evolución del motivo en este último ámbito. Demostración de las novedades propias del ámbito hispano.

Combined use of pulsed arterial spin-labeling and susceptibility-weighted imaging in stroke at 3T

Background and Purpose: In acute stroke it is no longer sufficient to detect simply ischemia, but also to try to evaluate reperfusion/recanalization status and predict eventual hemorrhagic transformation. Arterial spin labeling (ASL) perfusion may have advantages over contrast-enhanced perfusion-weighted imaging (cePWI), and susceptibility weighted imaging (SWI) has an intrinsic sensitivity to paramagnetic effects in addition to its ability to detect small areas of bleeding and hemorrhage. We want to determine here if their combined use in acute stroke and stroke follow-up at 3T could bring new insight into the diagnosis and prognosis of stroke leading to eventual improved patient management. Methods: We prospectively examined 41 patients admitted for acute stroke (NIHSS >1). Early imaging was performed between 1 h and 2 weeks. The imaging protocol included ASL, cePWI, SWI, T2 and diffusion tensor imaging (DTI), in addition to standard stroke protocol. Results: We saw four kinds of imaging patterns based on ASL and SWI: patients with either hypoperfusion and hyperperfusion on ASL with or without changes on SWI. Hyperperfusion was observed on ASL in 12/41 cases, with hyperperfusion status that was not evident on conventional cePWI images. Signs of hemorrhage or blood-brain barrier breakdown were visible on SWI in 15/41 cases, not always resulting in poor outcome (2/15 were scored mRS = 0–6). Early SWI changes, together with hypoperfusion, were associated with the occurrence of hemorrhage. Hyperperfusion on ASL, even when associated with hemorrhage detected on SWI, resulted in good outcome. Hyperperfusion predicted a better outcome than hypoperfusion (p = 0.0148). Conclusions: ASL is able to detect acute-stage hyperperfusion corresponding to luxury perfusion previously reported by PET studies. The presence of hyperperfusion on ASL-type perfusion seems indicative of reperfusion/collateral flow that is protective of hemorrhagic transformation and a marker of favorable tissue outcome. The combination of hypoperfusion and changes on SWI seems on the other hand to predict hemorrhage and/or poor outcome.

Mining for Class-Specific Motifs in Protein Sequence Classification

Background: In protein sequence classification, identification of the sequence motifs or n-grams that can precisely discriminate between classes is a more interesting scientific question than the classification itself. A number of classification methods aim at accurate classification but fail to explain which sequence features indeed contribute to the accuracy. We hypothesize that sequences in lower denominations (n-grams) can be used to explore the sequence landscape and to identify class-specific motifs that discriminate between classes during classification. Discriminative n-grams are short peptide sequences that are highly frequent in one class but are either minimally present or absent in other classes. In this study, we present a new substitution-based scoring function for identifying discriminative n-grams that are highly specific to a class. Results: We present a scoring function based on discriminative n-grams that can effectively discriminate between classes. The scoring function, initially, harvests the entire set of 4- to 8-grams from the protein sequences of different classes in the dataset. Similar n-grams of the same size are combined to form new n-grams, where the similarity is defined by positive amino acid substitution scores in the BLOSUM62 matrix. Substitution has resulted in a large increase in the number of discriminatory n-grams harvested. Due to the unbalanced nature of the dataset, the frequencies of the n-grams are normalized using a dampening factor, which gives more weightage to the n-grams that appear in fewer classes and vice-versa. After the n-grams are normalized, the scoring function identifies discriminative 4- to 8-grams for each class that are frequent enough to be above a selection threshold. By mapping these discriminative n-grams back to the protein sequences, we obtained contiguous n-grams that represent short class-specific motifs in protein sequences. Our method fared well compared to an existing motif finding method known as Wordspy. We have validated our enriched set of class-specific motifs against the functionally important motifs obtained from the NLSdb, Prosite and ELM databases. We demonstrate that this method is very generic; thus can be widely applied to detect class-specific motifs in many protein sequence classification tasks. Conclusion: The proposed scoring function and methodology is able to identify class-specific motifs using discriminative n-grams derived from the protein sequences. The implementation of amino acid substitution scores for similarity detection, and the dampening factor to normalize the unbalanced datasets have significant effect on the performance of the scoring function. Our multipronged validation tests demonstrate that this method can detect class-specific motifs from a wide variety of protein sequence classes with a potential application to detecting proteome-specific motifs of different organisms.

Immune pathomechanism of drug hypersensitivity reactions

Drug hypersensitivity research has progressed enormously in recent years, and a greater understanding of mechanisms has contributed to improved drug safety. Progress has been made in genetics, enabling personalized medicine for certain drugs, and in understanding drug interactions with the immune system. In a recent meeting in Rome, the clinical, chemical, pharmacologic, immunologic, and genetic aspects of drug hypersensitivity were discussed, and certain aspects are briefly summarized here. Small chemicals, including drugs, can induce immune reactions by binding as a hapten to a carrier protein. Park (Liverpool, England) demonstrated (1) that drug haptens bind to protein in patients in a highly restricted manner and (2) that irreversibly modified carrier proteins are able to stimulate CD4(+) and CD8(+) T cells from hypersensitive patients. Drug haptens might also stimulate cells of the innate immune system, in particular dendritic cells, and thus give rise to a complex and complete immune reaction. Many drugs do not have hapten-like characteristics but might gain them on metabolism (so-called prohaptens). The group of Naisbitt found that the stimulation of dendritic cells and T cells can occur as a consequence of the transformation of a prohapten to a hapten in antigen-presenting cells and as such explain the immune-stimulatory capacity of prohaptens. The striking association between HLA-B alleles and the development of certain drug reactions was discussed in detail. Mallal (Perth, Australia) elegantly described a highly restricted HLA-B∗5701-specific T-cell response in abacavir-hypersensitive patients and healthy volunteers expressing HLA-B∗5701 but not closely related alleles. Expression of HLA-B∗1502 is a marker known to be necessary but not sufficient to predict carbamazepine-induced Stevens-Johnson syndrome/toxic epidermal necrolysis in Han Chinese. The group of Chen and Hong (Taiwan) described the possible "missing link" because they showed that the presence of certain T-cell receptor (TCR) clonotypes was necessary to elicit T-cell responses to carbamazepine. The role of TCRs in drug binding was also emphasized by Pichler (Bern, Switzerland). Following up on their "pharmacological interactions of drugs with immune receptors" concept (p-i concept), namely that drugs can bind directly to TCRs, MHC molecules, or both and thereby stimulate T cells, they looked for drug-binding sites for the drug sulfamethoxazole in drug-specific TCRs: modeling revealed up to 7 binding sites on the CDR3 and CDR2 regions of TCR Vα and Vβ. Among many other presentations, the important role of regulatory T cells in drug hypersensitivity was addressed.

Klf4 transcription factor is expressed in the cytoplasm of prostate cancer cells

BACKGROUND: Cancer initiation and progression might be driven by small populations of cells endowed with stem cell-like properties. Here we comparatively addressed the expression of genes encoding putative stemness regulators including c-Myc, Klf4, Nanog, Oct4A and Sox2 genes in benign prostatic hyperplasia (BPH) and prostate cancer (PCA). METHODS: Fifty-eight PCA and thirty-nine BPH tissues samples were used for gene expression analysis, as evaluated by quantitative real-time polymerase chain reaction (qRT-PCR). The expression of specific Klf4 isoforms was tested by conventional PCR. Klf4 specific antibodies were used for protein detection in a tissue microarray including 404 prostate samples. RESULTS: Nanog, Oct4A and Sox2 genes were comparably expressed in BPH and PCA samples, whereas c-Myc and Klf4 genes were expressed to significantly higher extents in PCA than in BPH specimens. Immunohistochemical studies revealed that Klf4 protein is detectable in a large majority of epithelial prostatic cells, irrespective of malignant transformation. However, in PCA, a predominantly cytoplasmic location was observed, consistent with the expression of a differentially spliced Klf4α isoform. CONCLUSION: Klf4 is highly expressed at gene and protein level in BPH and PCA tissues but a cytoplasmic location of the specific gene product is predominantly detectable in malignant cells. Klf4 location might be of critical relevance to steer its functions during oncogenesis.

Talents in Migration Processes in the Conditions of the Czech Republic of the Nineties

The transformation of the 1990s has had a bearing on the academic and scientific world, as is becoming increasingly obvious with the changing numbers of foreign students wishing to study in the Czech Republic and of Czech students wishing to study abroad, the virtual collapse of doctoral studies, and the rapidly increasing age of Czech academics (placed at 48 by official sources and at rather more by this research). At the same time there is an apparent lack of interest in analysing and understanding these trends, which Mr. Cermak terms an ostrich policy, although his research showed that academics are in fact both aware and concerned about them. The mid-1990s migration of talent to and from R+D in the Czech Republic is also reflected in the number of talented Czech students studying abroad, who represent the largest and most interesting group of actual and potential migrants. Mr. Cermak's study took the form of a Delphi enquiry participated in by 44 specialists, including experts in the problems of higher education and science policy from the Presidium of the Higher Education Council (n = 23), members of the Council's Science and Research Commission (n = 14), former and current managers of higher education authorities (n = 4) and selected participants of the longitudinal talent research (n = 3). Questions considered included the influence of continuing talent migration from domestic R+D on the efficiency of domestic higher education, the diversification of forms of the brain drain and their impact on other processes in society, the possibility of positive influence on the brain drain processes to minimise the risks it presents, and the use of the knowledge obtained about the brain drain. The study revealed a clear drop of interest in brain drain problems in higher education in the mid-1990s, which is probably related to the collapsed of Czech R+D in the field of talent education. The effects on this segment of the labour market appeared earlier, with a major migration wave in 1991-1993 which significantly "cleared" the area of scientific talent. In addition, prospective talents from the ranks of younger students have not been integrated into domestic R+D, leading to the increasing average age of those working in this field. "Talent scouting" tended to be oriented towards much younger individuals, even in some cases towards undergraduate students. The R+D institutions deprived of human resources considered as basic in a functional R+D system have lost much of their dynamism and so no longer attract not only domestic talent but also talent from other regions. As a result the public, including the mass media and political structures, have stopped regarding the support of domestic science as a priority. This is clear both among the young people who are important for the future development of R+D (support for the education of talented children has dropped), from the drop in the prestige of this area as a profession among university students, and from the lack of explicit support for R+D by any of the political parties. On the basis of his findings Mr. Cermak concludes that there is no basis for the belief that the brain drain will represent a positive force in stimulating the development of the open society. Migration data shows that the outflow of talent from the Czech Republic far exceeds the inflow, and that the latter is largely short-term. Not only has the number of returning Czech professors dropped to half of its level at the beginning of the 1990s, but they also tend to take up only short-term contracts and retain their foreign positions. Recruitment of scientific talent from other countries, including the Slovak Republic, is limited. Furthermore internal contacts between those already involved in R+D have been badly hit by economic pressures and institutional co-operation has dropped to a minimum. There have been few moves to counteract this situation, the only notable one being the Program 250, launched in 1996 with government support to try and attract younger (i.e. under 40) talent into R+D. Its resources are however limited and its effects have not so far been evaluated. The deficit of academic and scientific talent in the Czech Republic is increasing and two major directions of academic work are emerging. Classic higher education science based on the teaching process is declining, largely due to economic factors, while there is an increasing emphasis on special; ad hoc projects which cannot be related directly to teaching but are often interesting to specialists outside the Czech Republic. This is shown clearly by the increase in publishing and in participation in domestic and foreign grant projects, which often serve to supplement the otherwise low salaries in the higher education sector. This tend was also accelerated by the collapse of applied R+D in individual sectors of the national economy and by substantial cutbacks in the Czech Academy of Sciences, which formerly fostered such research. Some part of the output of this research can be used in the education system and its financial contribution does significantly affect the stability of the present staff, but Mr. Cermak sees it as generally unfavourable for the development of talent education. In addition, it has led to a certain resignation on the question of integration into international structures, due to the emphasis on short-term targets, commercial advantages and individualism rather than team work. At the same time, he admits that these developments reflect those in other areas of the transformation in the Czech Republic.

A Comparative Study of Two Semantic Systems: Body Russian and Russian Phraseology

Grigorij Kreidlin (Russia). A Comparative Study of Two Semantic Systems: Body Russian and Russian Phraseology. Mr. Kreidlin teaches in the Department of Theoretical and Applied Linguistics of the State University of Humanities in Moscow and worked on this project from August 1996 to July 1998. The classical approach to non-verbal and verbal oral communication is based on a traditional separation of body and mind. Linguists studied words and phrasemes, the products of mind activities, while gestures, facial expressions, postures and other forms of body language were left to anthropologists, psychologists, physiologists, and indeed to anyone but linguists. Only recently have linguists begun to turn their attention to gestures and semiotic and cognitive paradigms are now appearing that raise the question of designing an integral model for the unified description of non-verbal and verbal communicative behaviour. This project attempted to elaborate lexical and semantic fragments of such a model, producing a co-ordinated semantic description of the main Russian gestures (including gestures proper, postures and facial expressions) and their natural language analogues. The concept of emblematic gestures and gestural phrasemes and of their semantic links permitted an appropriate description of the transformation of a body as a purely physical substance into a body as a carrier of essential attributes of Russian culture - the semiotic process called the culturalisation of the human body. Here the human body embodies a system of cultural values and displays them in a text within the area of phraseology and some other important language domains. The goal of this research was to develop a theory that would account for the fundamental peculiarities of the process. The model proposed is based on the unified lexicographic representation of verbal and non-verbal units in the Dictionary of Russian Gestures, which the Mr. Kreidlin had earlier complied in collaboration with a group of his students. The Dictionary was originally oriented only towards reflecting how the lexical competence of Russian body language is represented in the Russian mind. Now a special type of phraseological zone has been designed to reflect explicitly semantic relationships between the gestures in the entries and phrasemes and to provide the necessary information for a detailed description of these. All the definitions, rules of usage and the established correlations are written in a semantic meta-language. Several classes of Russian gestural phrasemes were identified, including those phrasemes and idioms with semantic definitions close to those of the corresponding gestures, those phraseological units that have lost touch with the related gestures (although etymologically they are derived from gestures that have gone out of use), and phrasemes and idioms which have semantic traces or reflexes inherited from the meaning of the related gestures. The basic assumptions and practical considerations underlying the work were as follows. (1) To compare meanings one has to be able to state them. To state the meaning of a gesture or a phraseological expression, one needs a formal semantic meta-language of propositional character that represents the cognitive and mental aspects of the codes. (2) The semantic contrastive analysis of any semiotic codes used in person-to-person communication also requires a single semantic meta-language, i.e. a formal semantic language of description,. This language must be as linguistically and culturally independent as possible and yet must be open to interpretation through any culture and code. Another possible method of conducting comparative verbal-non-verbal semantic research is to work with different semantic meta-languages and semantic nets and to learn how to combine them, translate from one to another, etc. in order to reach a common basis for the subsequent comparison of units. (3) The practical work in defining phraseological units and organising the phraseological zone in the Dictionary of Russian Gestures unexpectedly showed that semantic links between gestures and gestural phrasemes are reflected not only in common semantic elements and syntactic structure of semantic propositions, but also in general and partial cognitive operations that are made over semantic definitions. (4) In comparative semantic analysis one should take into account different values and roles of inner form and image components in the semantic representation of non-verbal and verbal units. (5) For the most part, gestural phrasemes are direct semantic derivatives of gestures. The cognitive and formal techniques can be regarded as typological features for the future functional-semantic classification of gestural phrasemes: two phrasemes whose meaning can be obtained by the same cognitive or purely syntactic operations (or types of operations) over the meanings of the corresponding gestures, belong by definition to one and the same class. The nature of many cognitive operations has not been studied well so far, but the first steps towards its comprehension and description have been taken. The research identified 25 logically possible classes of relationships between a gesture and a gestural phraseme. The calculation is based on theoretically possible formal (set-theory) correlations between signifiers and signified of the non-verbal and verbal units. However, in order to examine which of them are realised in practice a complete semantic and lexicographic description of all (not only central) everyday emblems and gestural phrasemes is required and this unfortunately does not yet exist. Mr. Kreidlin suggests that the results of the comparative analysis of verbal and non-verbal units could also be used in other research areas such as the lexicography of emotions.

The Effects of Privatization of State-Owned Enterprises in Poland and East Germany

The main goal of this project was to propose appropriate methods of analysing the effects of the privatisation of state-owned enterprises, methods which were then tested on a limited sample of 16 Polish and 8 German enterprises privatised in 1992. A considerable amount of information was collected relating to the six-year period 1989-1994 relating to most aspects of the companies' activities. The effects of privatisation were taken to be those changes within the enterprises which were the result of privatisation, in such areas as production, the productivity of labour and fixed assets, investments and innovations, employment and wages, economic incentives (especially for top managers), financing (internal and external sources), bad debts and economic effects (financial analysis). A second important goal was to identify the main factors which represent methodological obstacles in surveys of the effects of privatisation during a period of fundamental transformation of the entire economic system. The list of enterprises for the research was compiled in such a way as to allow for the differentiation of ownership structures of privatised firms and to permit (at least to a certain extent) the empirical verification of some hypotheses regarding the privatisation process. The enterprises selected were divided into the following three groups representing (as far as possible) various types of ownership structures or types of control: (1) enterprises control by strategic investors (domestic or foreign), (2) enterprises controlled by employees (employee-owned companies), (3) enterprises controlled by managers. Formal methods such as econometric models with varying parameters were used to separate pure privatisation effects from other factors which influence various aspects of an enterprise's working, including policies on the productivity of labour and capital, average wages, the remuneration of top managers, etc. While the group admits that their findings and conclusions cannot be treated as representative of all privatised enterprises in Poland and Germany, they found considerable convergence with their findings and those of other surveys conducted on a wider scale. The main hypotheses that were confirmed included that privatisation (especially in companies controlled by large investors and managers) leads to a significant increase in the effectiveness of these production process, growing pay differentials between different employee groups (e.g. between executives and rank-and-file employees) and between different jobs and positions within particular professional groups. They also confirmed the growing importance in incentives to top executives of incentives linked with the company's economic effects (particularly profit-related incentives), long-term incentives and the capital market.

Central Europe in the Process of European Integration. A Comparative Study of the Strategies of the Czech Republic, Hungary, Poland and Slovakia towards the Deepening and Widening of the European Union

Membership of the European Union U is usually seen as a strategic goal of the associated states of central and eastern Europe. At the beginning of the 1990s central European countries, where the economic and political transformation was relatively advanced, received preferential treatment from the European Community, which was starting to evolve a policy of differentiation. Podraza studied the strategies of four central European countries towards changes under way in the European Union, analysing several aspects for each case: (1) the process of political transformation (2) decision-making structures in the field of foreign policy and European integration (3) integration strategies: (a) main foreign policy priorities (b) application for membership of the European Union (c) the Commission option on each country (d) accession partnership, including a National Programme for the Adoption of the Acquis (NPAA) (e) regular Commission reports (f) accession negotiations

The New Electoral Geography of Central Europe

Zarycki studied the political map of Central Europe today on the basis of results of recent parliamentary and/or presidential elections in the Czech Republic, Hungary, L8ithuania, Poland, Slovakia and Ukraine. He identified first the structure of regional political cleavages, then the spatial patterns emerging in different countries. He also considered the significance and eventual regional differentiation of various possible influences on these patterns, including urbanisation, historical heritage, ethnic factors, population movements, economic differentiation, the effects of the transformation, demographic factors, education and religion. Virtually all the countries showed a cleavage between more traditional, anti (or non-) communist regions and secular areas with higher post-communist support. Except in Ukraine and the Czech Republic, the post-communist party is dominated by the direct heirs of the former communist parties transformed into moderate left parties. The second major class of cleavages was typical of the Visegrad countries, i.e. the conflict between liberal, mostly metropolitan, regions and a different periphery, usually with a strong populist or anti-liberal appeal. This usually depends on the existence of a sizeable well-educated class, usually pro-market and pro-Western, and on the resolution of the conflict between post and anti-Communists. The third type of cleavage is based on ethnic factors and is clearest in Lithuania and Slovakia, where there are large ethnic minorities. Of factors influencing political behaviour, the two major ones identified were the historical heritage and urbanisation.

Differential expression of TGFbeta-stimulated clone 22 in normal prostate and prostate cancer

The transforming growth factor-beta (TGFbeta) superfamily and its downstream effector genes are key regulators of epithelial homeostasis. Altered expression of these genes may be associated with malignant transformation of the prostate gland. The cDNA array analysis of differential expression of the TGFbeta superfamily and functionally related genes between patient-matched noncancerous prostate (NP) and prostate cancer (PC) bulk tissue specimens highlighted two genes, namely TGFbeta-stimulated clone-22 (TSC-22) and Id4. Verification of their mRNA expression by real-time PCR in patient-matched NP and PC bulk tissue, in laser-captured pure epithelial and cancer cells and in NP and PC cell lines confirmed TSC-22 underexpression, but not Id4 overexpression, in PC and in human PC cell lines. Immunohistochemical analysis showed that TSC-22 protein expression in NP is restricted to the basal cells and colocalizes with the basal cell marker cytokeratin 5. In contrast, all matched PC samples lack TSC-22 immunoreactivity. Likewise, PC cell lines do not show detectable TSC-22 protein expression as shown by immunoblotting. TSC-22 should be considered as a novel basal cell marker, potentially useful for studying lineage determination within the epithelial compartment of the prostate. Conversely, lack of TSC-22 seems to be a hallmark of malignant transformation of the prostate epithelium. Accordingly, TSC-22 immunohistochemistry may prove to be a diagnostic tool for discriminating benign lesions from malignant ones of the prostate. The suggested tumour suppressor function of TSC-22 warrants further investigation on its role in prostate carcinogenesis and on the TSC-22 pathway as a candidate therapeutic target in PC.

Conformational analysis of a potent SSTR3-selective somatostatin analogue by NMR in water solution

The three-dimensional structure of a potent SSTR3-selective analogue of somatostatin, cyclo(3-14)H-Cys(3)-Phe(6)-Tyr(7)-D-Agl(8)(N(beta) Me, 2-naphthoyl)-Lys(9)-Thr(10)-Phe(11)-Cys(14)-OH (des-AA(1, 2, 4, 5, 12, 13)[Tyr(7), D-Agl(8)(N(beta) Me, 2-naphthoyl)]-SRIF) (peptide 1) has been determined by (1)H NMR in water and molecular dynamics (MD) simulations. The peptide exists in two conformational isomers differing mainly by the cis/trans isomerization of the side chain in residue 8. The structure of 1 is compared with the consensus structural motifs of other somatostatin analogues that bind predominantly to SSTR1, SSTR2/SSTR5 and SSTR4 receptors, and to the 3D structure of a non-selective SRIF analogue, cyclo(3-14)H-Cys(3)-Phe(6)-Tyr(7)-D-2Nal(8)-Lys(9)-Thr(10)-Phe(11)-Cys(14)-OH (des-AA(1, 2, 4, 5, 12, 13)[Tyr(7), D-2Nal(8)]-SRIF) (peptide 2). The structural determinant factors that could explain selectivity of peptide 1 for SSTR3 receptors are discussed.