Biocomputational prediction of small non-coding RNAs in Streptomyces

<p>Abstract</p> <p>Background</p> <p>The first systematic study of small non-coding RNAs (sRNA, ncRNA) in <it>Streptomyces </it>is presented. Except for a few exceptions, the <it>Streptomyces </it>sRNAs, as well as the sRNAs in other genera of the <it>Actinomyces </it>group, have remained unstudied. This study was based on sequence conservation in intergenic regions of <it>Streptomyces</it>, localization of transcription termination factors, and genomic arrangement of genes flanking the predicted sRNAs.</p> <p>Results</p> <p>Thirty-two potential sRNAs in <it>Streptomyces </it>were predicted. Of these, expression of 20 was detected by microarrays and RT-PCR. The prediction was validated by a structure based computational approach. Two predicted sRNAs were found to be terminated by transcription termination factors different from the Rho-independent terminators. One predicted sRNA was identified computationally with high probability as a <it>Streptomyces </it>6S RNA. Out of the 32 predicted sRNAs, 24 were found to be structurally dissimilar from known sRNAs.</p> <p>Conclusion</p> <p><it>Streptomyces </it>is the largest genus of <it>Actinomyces</it>, whose sRNAs have not been studied. The <it>Actinomyces </it>is a group of bacterial species with unique genomes and phenotypes. Therefore, in <it>Actinomyces</it>, new unique bacterial sRNAs may be identified. The sequence and structural dissimilarity of the predicted <it>Streptomyces </it>sRNAs demonstrated by this study serve as the first evidence of the uniqueness of <it>Actinomyces </it>sRNAs.</p

Translation Reinitiation Relies on the Interaction between eIF3a/TIF32 and Progressively Folded cis-Acting mRNA Elements Preceding Short uORFs

Reinitiation is a gene-specific translational control mechanism characterized by the ability of some short upstream uORFs to retain post-termination 40S subunits on mRNA. Its efficiency depends on surrounding cis-acting sequences, uORF elongation rates, various initiation factors, and the intercistronic distance. To unravel effects of cis-acting sequences, we investigated previously unconsidered structural properties of one such a cis-enhancer in the mRNA leader of GCN4 using yeast genetics and biochemistry. This leader contains four uORFs but only uORF1, flanked by two transferrable 5′ and 3′ cis-acting sequences, and allows efficient reinitiation. Recently we showed that the 5′ cis-acting sequences stimulate reinitiation by interacting with the N-terminal domain (NTD) of the eIF3a/TIF32 subunit of the initiation factor eIF3 to stabilize post-termination 40S subunits on uORF1 to resume scanning downstream. Here we identify four discernible reinitiation-promoting elements (RPEs) within the 5′ sequences making up the 5′ enhancer. Genetic epistasis experiments revealed that two of these RPEs operate in the eIF3a/TIF32-dependent manner. Likewise, two separate regions in the eIF3a/TIF32-NTD were identified that stimulate reinitiation in concert with the 5′ enhancer. Computational modeling supported by experimental data suggests that, in order to act, the 5′ enhancer must progressively fold into a specific secondary structure while the ribosome scans through it prior uORF1 translation. Finally, we demonstrate that the 5′ enhancer's stimulatory activity is strictly dependent on and thus follows the 3′ enhancer's activity. These findings allow us to propose for the first time a model of events required for efficient post-termination resumption of scanning. Strikingly, structurally similar RPE was predicted and identified also in the 5′ leader of reinitiation-permissive uORF of yeast YAP1. The fact that it likewise operates in the eIF3a/TIF32-dependent manner strongly suggests that at least in yeasts the underlying mechanism of reinitiation on short uORFs is conserved

Utilization of European Union funds in Prague during programming period 2007 – 2013

Cílem bakalářské práce "Využití evropských fondů v Praze v programovém období 2007 -- 2013" je zjistit alokaci, zaměření a dopady schválených projektů. Bakalářská práce se zaměřuje na dva operační programy -- Operační program Adaptabilita a Operační program Konkurenceschopnost. Práce je rozdělena na teoretickou a praktickou část. V teoretické části je popsána politika EU a její přístup k regionálnímu rozvoji a jsou zde rozebrány struktury evropských fondů. Praktická část se již zaměřuje na hl. Praha. V jednotlivých operačních programech je popsána finanční alokace, skutečný průběh a stav čerpání evropských finančních prostředků a jsou zde uvedeny příklady typických úspěšných projektů.The goal of thesis "Utilization of European Union funds in Prague during programming period 2007 -- 2013" is to expore the allocation, focus and effects of authorized projects. The thesis focuses in two operational programmes -- Operational Programme Adaptability and Operational Programe Competitiveness. Thesis is diveded int theoretical and practival part. The theoretical part is concerned with describing EU policies and its aproach to regional development and the structure of EU funds is analyzed. The practical part is focused on the capital city Prague. Within individual operational programmes there and financial allocation, actual proces and state of fund drawing depicted and examples of typical succesful projects are mentioned

Multidisciplinary cooperation of the body for social and legal protection of children seated in Tachov with other selected authorities in the field of children at risk

The thesis focuses on the multidisciplinary cooperation in the area of the social and legal protection of children at risk. At the beginning, the theoretical notion of the child and the child at risk are defined as the concepts essentials in terms of the focus group of this thesis. The next chapter describes the existing social and legal protection of children, including its legislative definition, who is being protected, which subjects can provide these welfare services as well as the application of social work in social and legal protection of children. The second part examines three forms of multidisciplinary collaboration: a project of system early intervention, rehabilitation of families and case conferences. Individual types are primarily defined in theory, followed by a description of their functionality on the example of the Tachov town. The Annex section presents nine case reports, including their evaluation, that describe multidisciplinary collaboration through case conferences implemented by the authority for social and legal protection of children in Tachov

Utilization of European Union funds in Prague during programming period 2007 – 2013

The goal of thesis "Utilization of European Union funds in Prague during programming period 2007 -- 2013" is to expore the allocation, focus and effects of authorized projects. The thesis focuses in two operational programmes -- Operational Programme Adaptability and Operational Programe Competitiveness. Thesis is diveded int theoretical and practival part. The theoretical part is concerned with describing EU policies and its aproach to regional development and the structure of EU funds is analyzed. The practical part is focused on the capital city Prague. Within individual operational programmes there and financial allocation, actual proces and state of fund drawing depicted and examples of typical succesful projects are mentioned

An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences

While understanding the structure of RNA molecules is vital for deciphering their functions, determining RNA structures experimentally is exceptionally hard. At the same time, extant approaches to computational RNA structure prediction have limited applicability and reliability. In this paper we provide a method to solve a simpler yet still biologically relevant problem: prediction of secondary RNA structure using structure of different molecules as a template. Our method identifies conserved and unconserved subsequences within an RNA molecule. For conserved subsequences, the template structure is directly transferred into the generated structure and combined with de-novo predicted structure for the unconserved subsequences with low evolutionary conservation. The method also determines, when the generated structure is unreliable. The method is validated using experimentally identified structures. The accuracy of the method exceeds that of classical prediction algorithms and constrained prediction methods. This is demonstrated by comparison using large number of heterogeneous RNAs. The presented method is fast and robust, and useful for various applications requiring knowledge of secondary structures of individual RNA sequences

Does eIF3 promote reinitiation after translation of short upstream ORFs also in mammalian cells?

<p>Reinitiation after translation of short upstream ORFs (uORFs) represents one of the means of regulation of gene expression on the mRNA-specific level in response to changing environmental conditions. Over the years it has been shown-mainly in budding yeast-that its efficiency depends on <i>cis</i>-acting features occurring in sequences flanking reinitiation-permissive uORFs, the nature of their coding sequences, as well as protein factors acting <i>in trans</i>. We earlier demonstrated that the first two uORFs from the reinitiation-regulated yeast <i>GCN4</i> mRNA leader carry specific structural elements in their 5′ sequences that interact with the translation initiation factor eIF3 to prevent full ribosomal recycling post their translation. Actually, this interaction turned out to be instrumental in stabilizing the mRNA·40S post-termination complex, which is thus capable to eventually resume scanning and reinitiate on the next AUG start site downstream. Recently, we also provided important <i>in vivo</i> evidence strongly supporting the long-standing idea that to stimulate reinitiation, eIF3 has to remain bound to ribosomes elongating these uORFs until their stop codon has been reached. Here we examined the importance of eIF3 and sequences flanking uORF1 of the human functional homolog of yeast <i>GCN4, ATF4</i>, in stimulation of efficient reinitiation. We revealed that the molecular basis of the reinitiation mechanism is conserved between yeasts and humans.</p