RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

<p>Abstract</p> <p>Background</p> <p>With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression.</p> <p>Results</p> <p><it>RNACompress </it>employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that <it>RNACompress </it>achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as <it>Gencompress, winrar </it>and <it>gzip</it>. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective.</p> <p>Conclusion</p> <p>A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed <it>RNACompress</it>, as a useful tool for academic users. Extensive tests have shown that <it>RNACompress </it>is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. <it>RNACompress </it>also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules.</p

On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks

Despite the computing power of emerging technolo-gies, predicting long RNA secondary structures with thermodynamics-based methods is still infeasible, espe-cially if the structures include complex motifs such as pseu-doknots. This paper presents preliminary results on rebuilding RNA secondary structures by an extensive and systematic sampling of nucleotide chunks. The rebuilding approach merges the significant motifs found in the secondary struc-tures of the single chunks. The extensive sampling and pre-diction of nucleotide chunks are supported by grid tech-nology as part of the RNAVLab functionality. Significant motifs are identified in the chunk secondary structures and merged in a single structure based on their recurrences an

Netplan: a telecommunications network planning support system.

by T.S. Chew.Thesis (M.Sc.)--Chinese University of Hong Kong, 1992.Includes bibliographical references.Chapter Chapter 1 --- IntroductionChapter Chapter 2 --- Network PlanningChapter 2.1 --- Routing PlanningChapter 2.2 --- Junction Circuit PlanningChapter 2.3 --- Signalling Network PlanningChapter Chapter 3 --- System ArchitectureChapter 3.1 --- User InterfaceChapter 3.2 --- ControlChapter 3.3 --- DesignChapter Chapter 4 --- Network CreationChapter 4.1 --- Network CompilationChapter 4.2 --- Traffic CharacteristicsChapter Chapter 5 --- Network DesignChapter 5.1 --- Routing DesignChapter 5.2 --- Junction Circuit DesignChapter 5.3 --- Signalling Network DesignChapter Chapter 6 --- Program DescriptionChapter Chapter 7 --- Design ExampleChapter Chapter 8 --- ConclusionsReferencesChapter Appendix 1 - --- Erlang B FormulaChapter Appendix 2 - --- Program Listing of NETPLANChapter Appendix 3 - --- Design Example ResultsChapter 3.1 - --- Network ObjectsChapter 3.2 - --- Network ConfigurationChapter 3.3 - --- Network Design Result with No. of Paths =

The role of Heparin-binding proteins in normal pancreas and acute pancreatitis

Acute pancreatitis (AP) is a leading cause for hospitalisation and has significant quality of life implications for the patient and cost implications for the National Health Service. Although most episodes of AP are mild and self-limiting, the severe form of the disease is associated with a high mortality. In the absence of definitive treatment, management is mainly supportive. There is an urgent need to develop more effective biomarkers and drugs to manage AP. Genome-wide studies have demonstrated that proteins that bind to heparin (HBPs) form highly interconnected networks which are functionally important in health and disease. It was hypothesized that this is true in the pancreas and in AP. Testing this hypothesis, using mRNA as a proxy for protein, it was shown that HBPs constitute an important extracellular sub-proteome within the normal pancreas and in major pancreatic diseases that is likely to provide a rich repository of potential biomarkers and drug targets. Building upon this work, a proteomic analysis of HBPs in normal pancreas (NP) and in caerulein-induced mouse AP was undertaken. This has more than doubled the number of HBPs to 883, with 460 new HBPs identified. These may represent the most interconnected set of extracellular proteins and therefore with the greatest regulatory potential. Non canonical HBPs such as NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFA9, NDUFA10, NDUFA9 and NDUFA10 were identified and found to be underexpressed in AP as compared to NP. These may have potential moonlighting roles, not previously known. By virtue of being extracellular and binding to heparin, HBPs are accessible and are potential biomarkers and drug targets in AP. In addition to identifying existing biomarkers in AP such as pancreatic amylase, a number of HBPs with biomarkers potential such as HRG, CD14 and FN1 were identified and need further investigation. HBPs such as SERPINC1, VEGFA and PIP5K1C need further evaluation in drug development. These along with modified heparins, heparin mimetics and matrix therapy in AP provide exciting areas for future research

Molecular Modelling and Functional Studies of the Biomineralising Protein Perlucin

Nacre is a biogenic composite material. One protein from the organic fraction of the nacreous layers of Haliotis laevigata is perlucin. It is supposed to be involved in nacre formation. This thesis presents a molecular model of the C-type lectin-like domain (CTLD) of perlucin. The model was calculated by means of comparative modelling and tested with molecular dynamic simulations. One computational study with the newly available perlucin structures is presented in this thesis. A rigid docking analysis of several structures of the CTLD of perlucin led to the proposal of several residues that could be involved in homodimer formation. The experimental part of this thesis consists of size-exclusion chromatography (SEC) experiments performed with nacre proteins. A suitable buffer solution composition - near neutral pH value of 7.3 and 1 M NaCl - is given that can serve as a basis for future SEC experiments with perlucin. Current SEC results could point to a dimerization of perlucin

Investigation of the role of sulfurtransferases in the metabolism of higher plants

[no abstract

Develoment and Application of Chemical Strategies to Study Protein Fatty-Acylation in Eukaryotes

Reversible S-palmitoylation confers spatiotemporal control of protein function by modulating protein stability, trafficking and activity as well as protein-protein and membrane-protein associations. While it is evident that palmitoylation is regulated in vivo, mechanisms that mediate cellular stimuli-driven changes of the lipid modification are not understood. Furthermore, the requirement for substrate specificity among the highly redundant palmitoyl acyltransferases (PATs) remains unresolved. To study the regulation of PATs and palmitoylomes, I developed bioorthogonal chemical strategies for improved analysis of dynamic palmitoylation in mammalian cells. I showed that alkyne-functionalized fatty acids, in conjunction with azido-fluorophores, provide the most sensitive detection of acylated proteins following CuI-catalyzed azidealkyne cycloaddition. Linkage-specific hydrolysis, mutagenesis and inhibitor studies reveal that these alkynyl-fatty acids are incorporated into proteins by endogenous fattyacylation machinery via native linkages at specific amino acid residues. In addition, shorter and longer chain fatty acids label myristoylated and palmitoylated proteins respectively. Since myristoylation is co-translational and constitutive, I employed both palmitoylation and myristoylation chemical reporters with orthogonal fluorophores to simultaneously monitor palmitate and protein turnover. Dual pulse-chase analysis of Lck, a tyrosine kinase required for T-cell signaling, revealed accelerated palmitate cycling upon T-cell activation. Pharmacological perturbation of Lck palmitate turnover suggests yet uncharacterized serine hydrolases contribute to dynamic palmitoylation in cells. These significant improvements allow rapid and robust biochemical analysis of palmitoylated proteins without overexpression, facilitating the functional characterization of cellular factors and drugs that modulate protein palmitoylation. Taking advantage of the sensitive bioorthogonal detection of protein palmitoylation and the simple PAT network in the fission yeast Schizosaccharomyces pombe, I provided evidence for regulation of PATs and palmitoylomes in vivo at physiological enzyme and substrate concentrations. I showed that the Erf2-Erf4 PAT modulates sexual differentiation, and that upregulation of its expression is required to establish the meiotic palmitoylome. Importantly, I demonstrated that changes in Erf2- Erf4 levels within the physiological range control PAT specificity and result in the differential palmitoylation of its substrates in vegetative and meiotic cells. Underscoring the biological significance of controlling PAT levels, Erf2-Erf4 overproduction in proliferating cells alters the palmitoylome and the subcellular distribution of Rho3, a major meiotic target, stimulating sexual differentiation in the absence of normal physiological cues. From this study, I conclude that PAT substrate specificity depends on enzyme levels and propose the rheostatic control of PAT activity as a mechanism by which cells shape stimuli-induced palmitoylomes. Future questions stemming from this work are also discussed

Characterizing Excluded Strand DNA Interactions with Hexameric Helicases and Determining Roles in Unwinding Mechanisms

DNA replication is an essential process for all living organisms, and errors in this process can lead to genetic mutations and disease. An assembly of protein machinery, termed the replisome, coordinates enzymatic activities at the replication fork. The DNA helicase is the heart of the replisome unwinding double-strand DNA at the head of the progressing replisome and providing single-strand templates for DNA polymerases. Replicative helicases are composed of six subunits, and arranged in a ring-like structure where ATP hydrolysis events provide the energy to translocate upon and unwind the DNA. The mechanism of helicase unwinding has been widely studied, but there are still many aspects that remain unknown. It is generally thought that these helicases encircle one strand of DNA while the other is excluded from the central channel of the helicase. Our lab has previously identified an interaction between the excluded strand and the helicase exterior that was important for unwinding in the archaeal MCM helicase. The steric exclusion model of replicative helicase unwinding was expanded to include the excluded strand interactions in this newly proposed steric exclusion and wrapping (SEW) model. Here, we present work that expands on the SEW model by revealing that the bacterial DnaB and mitochondrial Twinkle replicative helicases also interact with the excluded strand. We have also developed a new single-molecule FRET analysis program to characterize these excluded strand interactions. Although the excluded strand interaction is seen in multiple replicative helicases, we propose distinct roles for the interaction based on functional assays and known differences in replisome architecture across the various organisms. We have also begun to characterize the helicase-excluded strand wrapping interaction in the presence of other replisome components, namely the single-strand binding (SSB) protein. We further characterized the archaeal SSB protein from Sulfolobus solfataricus and provide evidence for a novel DNA-helicase-SSB ternary complex. Overall, this thesis makes significant contributions to the understanding of replicative helicase unwinding mechanisms by expanding upon the current steric exclusion and wrapping model and introduces a novel single-molecule FRET analysis program that we anticipate will be adopted and utilized by others in the field

The Diversity Landscape of <i>Plasmodium falciparum var</i> Genes

Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) is an important group of cytoadhesive multi-domain Plasmodium falciparum surface antigens that are inserted onto the surface of infected erythrocytes and are encoded by the var multi-gene family. PfEMP1 antigens are thought to be important targets of naturally acquired immunity to malaria. This thesis describes nucleotide variation in DBLα sequence tags, a semi-conserved region within the DBLα domain that can be PCR amplified using universal primers. PfEMP1 can be classified using a number of approaches some of which are associated with particular expression patterns in severe, non-severe and asymptomatic malaria. This work compared the classification approaches with an aim of understanding the extent of overlap or discordance between them. To explore non-random distribution of variation in respect to var’s functional specialization, a clustering approach was developed and applied in exploring patterns of nucleotide variation among var subsets from different geographical locations in addition to distribution of predicted B and T-cell epitopes among the var subsets. In summary the sequences showed distinct patterns of nucleotide substitution that suggests that var sequences are under both diversifying and purifying selection

Sequence analysis of enzymes of the shikimate pathway: Development of a novel multiple sequence alignment algorithm

The possibility of homology modelling the shikimate pathway enzymes, 3-dehydroquinate synthase (el), 3-dehydroquinase (e2), shikimate dehydrogenase (e3), shikimate kinase (e4) and 5-enolpyruvylshikimate 3 -phosphate (EPSP) synthase (e5) is investigated. The sequences of these enzymes are analysed and the results found indicate that for four of these proteins, el, e2, e3, and e5, no structural homologues exist. Developing a model structure by homology modelling is therefore not possible. For shikimate kinase, statistically significant alignments are found to two proteins with known structures, adenylate kinase and H-ras p21 protein. These are also judged to be biologically significant alignments. However, the alignments obtained show too little sequence identity to permit homology modelling based on primary sequence data alone. An ab initio based methodology is next applied, with the initial step being careful evaluation of multiple sequence alignments of the shikimate pathway enzymes. Altering the parameters of the available multiple sequence alignment algorithms, produces a large range of differing alignments, with no objective way to choose a single alignment or construct a composite from the many produced for each shikimate pathway enzyme. This problem with obtaining a reliable alignment for the shikimate pathway enzyme will occur in other low sequence identity protein families, and is addressed by the development of a novel multiple sequence alignment method, Mix'n'Match. Mix'n'Match is based on finding alternating Strongly Conserved Regions (SCRs) and Loosely Conserved Regions (LCRs) in the protein sequences. The SCRs are used as 'anchors' in the alignment and are calculated from analysis of several different multiple alignments, made using varying criteria. After divided the sequences into Strongly Conserved Regions (SCRs) and Loosely Conserved Regions (LCRs), the 'best' alignment for each LCR is chosen, independently of the other LCRs, from a selection of possibilities in the multiple alignments. To help make this choice for each LCR, the secondary structure is predicted and sliown alongside each different possible alignment. One advantage of this method over automatic, non-interactive, methods, is that the final alignment is not dependent on the choice of a single set of scoring parameters. Another is that, by allowing interactive choice and by taking account of secondary structural information, the final alignment is based more on biological, rather than mathematical factors. This method can produce better alignments than any of the initial automatic multiple alignment methods used. The SCRs identified by Mix'n'Match, are found to show good correlation with the actual secondary structural elements present in the enzyme families used to test the method. Analysis of the Mix'n'Match alignment and consensus secondary structure predictions for shikimate kinase, suggest a closer match with the actual secondary structure of adenylate kinase, than is found between their amino acid sequences. These proteins appear to share functional, sequence and secondary structural homology. The proposal is made that a model structure of shikimate kinase, based on the structure of adenylate kinase, could be constructed using homology modelling techniques