Glycosylation site prediction using ensembles of Support Vector Machine classifiers

Article discussing the performance of different computational methods for prediction of glycosylation sites from amino acid sequences

Electron Tomography Reveals Posttranscriptional Binding of Pre-Mrnps to Specific Fibers in the Nucleoplasm

Using electron tomography, we have analyzed whether the Balbiani ring (BR) pre-mRNP particles in transit from the gene to the nuclear pore complex (NPC) are bound to any structure that could impair free diffusion through the nucleoplasm. We show that one-third of the BR particles are in contact with thin connecting fibers (CFs), which in some cases merge into large fibrogranular clusters. The CFs have a specific protein composition different from that of BR particles, as shown by immuno-EM. Moreover, we have identified hrp65 as one of the protein components of the CFs. The sequencing of hrp65 cDNA reveals similarities with hnRNP proteins and splicing factors. However, hrp65 is likely to have a different function because it does not bind to nascent pre-mRNA and is not part of the pre-mRNP itself. Taken together, our observations indicate that pre-mRNPs are not always freely diffusible in the nucleoplasm but interact with fibers of specific structure and composition, which implies that some of the posttranscriptional events that the pre-mRNPs undergo before reaching the NPC occur in a bound state

The hrp23 Protein in the Balbiani Ring Pre-mRNP Particles Is Released Just before or at the Binding of the Particles to the Nuclear Pore Complex

Balbiani ring (BR) pre-mRNP particles reside in the nuclei of salivary glands of the dipteran Chironomus tentans and carry the message for giant-sized salivary proteins. In the present study, we identify and characterize a new protein component in the BR ribonucleoprotein (RNP) particles, designated hrp23. The protein with a molecular mass of 20 kD has a single RNA-binding domain and a glycine-arginine-serine–rich auxiliary domain. As shown by immunoelectron microscopy, the hrp23 protein is added to the BR transcript concomitant with transcription, is still present in the BR particles in the nucleoplasm, but is absent from the BR particles that are bound to the nuclear pore complex or are translocating through the central channel of the complex. Thus, hrp23 is released just before or at the binding of the particles to the nuclear pore complex. It is noted that hrp23 behaves differently from two other BR RNP proteins earlier studied: hrp36 and hrp45. These proteins both reach the nuclear pore complex, and hrp36 even accompanies the RNA into the cytoplasm. It is concluded that each BR RNA-binding protein seems to have a specific flow pattern, probably related to the particular role of the protein in gene expression

The impact and pattern of gene and genome duplication in the history of increasing organismal complexity

The increase in phenotypic or morphological complexity in organisms may stem from a corresponding increase in the complexity of the underlying genetic architecture, driven by the process of gene duplication. Gene duplication is a mutational mechanism that can impact the genome through the gradual birth and death of individual genes or clusters of genes, and through infrequent episodic events of whole genome duplication. Functional and pleiotropic differences among genes may impact the probability of fixation of duplicated genes and the facility of gene families to record duplication events across deep history. Phylogenetic inference of the relationship among genes in multigene families has been used to reconstruct the history of duplication and subsequently to test hypotheses about the tempo and mode of these mutational mechanisms. We were unable to refute the hypothesis that one or two rounds of tetraploid evolution occurred subsequent to the origin of the lower deuterostomes and immediately preceding the origin of chordates. Our results suggest that the evolutionary history of gene families is defined by the nature of selection on individual genes. Genes embedded in highly constrained pleiotropic networks appear to have different patterns of diversification than genes subject to lesser (or different) selective constraints

Comparative mapping for positional cloning and defining homology regions between the mouse and human genomes

The goal of this dissertation project was to utilize genetic and physical mapping methods as a means to define genomic homology between human and mouse genomes, as well as to use this information to define functional relationships between the two species. The Comparative mapping studies were designed to expand upon the current knowledge of comparative mapping and homology regions between mouse and man, and to begin to study the homology region borders. Positional cloning research was initiated to localize the translocation breakpoints in a mutant mouse associated with a neurological defect as a first step toward isolation of genes that could be involved in the phenotype of this animal.Comparative mapping of human chromosome 19 and related regions of the mouse genome represents one major focus of this research. Human chromosome 19 was a good target for comparative studies due to the extensive physical mapping of the chromosome,and availability of conserved, mapped gene markers to use for these studies. Comparative Studies involved both the 19q- and 19p-arms of the chromosome, and helped lay the foundation of a chromosome-wide comparative map. One region, 19pl3.1, was investigated in detail. This region is shown to be prone to rearrangements during evolution, as indicated by the homology groups associated within both the mouse and human genomes. These studies revealed the need for more fine mapping of the genome for both species, demonstrating that examination of specific homology groups at a higher resolution reveals that both similarities and surprising differences between related mouse and human regions. These studies provided data suggesting that repeated sequences are associated with at least some homology region borders, a concept that may serve as a guide for future comparative mapping between human, mouse, and other species.One application of comparative mapping is its ability to link functional information derived from mouse mutations to specific genes and disease within the human genome. As part of this effort, research focused upon localizing and physical mapping a region surrounding the breakpoint in IGso, a mouse mutation associated with a reciprocal translocation. Homozygosity for the translocation causes developmental lethality. Animals That are heterozygous display neurological defects including the inability to swim and abnormal startle responses. A genetic map of the region surrounding one of the translocation breakpoints was established on mouse chromosome 2. Fluorescence in situ hybridization (FISH) techniques were used to localize translocation breakpoints to a small interval less than IcM in length. This region shows remarkable linkage conservation with a well-characterized region of human chromosome lip 13, which harbors genes responsible for the WAGR syndrome (Wilms tumor, aniridia, genitourinary malformations, and mental retardation). Comparative mapping information was used to narrow down the translocation interval, and establish a contig consisting of yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), and Pl-derived artificial chromosomes (PACs), which covered approximately 600 kb throughout the breakpoint region. This allowed the breakpoint to be isolated within a single PAC clone of 150 kb in length.Together these studies have set the stage for future investigations of genes located on chromosome 19, and for the cloning of gene(s) associated with the IGso phenotype in mice

A cooperative framework for molecular biology database integration using image object selection.

The theme and the concept of 'Molecular Biology Database Integration’ and the problems associated with this concept initiated the idea for this Ph.D research. The available technologies facilitate to analyse the data independently and discretely but it fails to integrate the data resources for more meaningful information. This along with the integration issues created the scope for this Ph.D research. The research has reviewed the 'database interoperability' problems and it has suggested a framework for integrating the molecular biology databases. The framework has proposed to develop a cooperative environment to share information on the basis of common purpose for the molecular biology databases. The research has also reviewed other implementation and interoperability issues for laboratory based, dedicated and target specific database. The research has addressed the following issues: - diversity of molecular biology databases schemas, schema constructs and schema implementation -multi-database query using image object keying -database integration technologies using context graph - automated navigation among these databases This thesis has introduced a new approach for database implementation. It has introduced an interoperable component database concept to initiate multidatabase query on gene mutation data. A number of data models have been proposed for gene mutation data which is the basis for integrating the target specific component database to be integrated with the federated information system. The proposed data models are: data models for genetic trait analysis, classification of gene mutation data, pathological lesion data and laboratory data. The main feature of this component database is non-overlapping attributes and it will follow non-redundant integration approach as explained in the thesis. This will be achieved by storing attributes which will not have the union or intersection of any attributes that exist in public domain molecular biology databases. Unlike data warehousing technique, this feature is quite unique and novel. The component database will be integrated with other biological data sources for sharing information in a cooperative environment. This/involves developing new tools. The thesis explains the role of these new tools which are: meta data extractor, mapping linker, query generator and result interpreter. These tools are used for a transparent integration without creating any global schema of the participating databases. The thesis has also established the concept of image object keying for multidatabase query and it has proposed a relevant algorithm for matching protein spot in gel electrophoresis image. An object spot in gel electrophoresis image will initiate the query when it is selected by the user. It matches the selected spot with other similar spots in other resource databases. This image object keying method is an alternative to conventional multidatabase query which requires writing complex SQL scripts. This method also resolve the semantic conflicts that exist among molecular biology databases. The research has proposed a new framework based on the context of the web data for interactions with different biological data resources. A formal description of the resource context is described in the thesis. The implementation of the context into Resource Document Framework (RDF) will be able to increase the interoperability by providing the description of the resources and the navigation plan for accessing the web based databases. A higher level construct is developed (has, provide and access) to implement the context into RDF for web interactions. The interactions within the resources are achieved by utilising an integration domain to extract the required information with a single instance and without writing any query scripts. The integration domain allows to navigate and to execute the query plan within the resource databases. An extractor module collects elements from different target webs and unify them as a whole object in a single page. The proposed framework is tested to find specific information e.g., information on Alzheimer's disease, from public domain biology resources, such as, Protein Data Bank, Genome Data Bank, Online Mendalian Inheritance in Man and local database. Finally, the thesis proposes further propositions and plans for future work

A cooperative framework for molecular biology database integration using image object selection

The theme and the concept of 'Molecular Biology Database Integration' and the problems associated with this concept initiated the idea for this Ph.D research. The available technologies facilitate to analyse the data independently and discretely but it fails to integrate the data resources for more meaningful information. This along with the integration issues created the scope for this Ph.D research. The research has reviewed the 'database interoperability' problems and it has suggested a framework for integrating the molecular biology databases. The framework has proposed to develop a cooperative environment to share information on the basis of common purpose for the molecular biology databases. The research has also reviewed other implementation and interoperability issues for laboratory based, dedicated and target specific database. The research has addressed the following issues: diversity of molecular biology databases schemas, schema constructs and schema implementation multi-database query using image object keying, database integration technologies using context graph, automated navigation among these databases. This thesis has introduced a new approach for database implementation. It has introduced an interoperable component database concept to initiate multidatabase query on gene mutation data. A number of data models have been proposed for gene mutation data which is the basis for integrating the target specific component database to be integrated with the federated information system. The proposed data models are: data models for genetic trait analysis, classification of gene mutation data, pathological lesion data and laboratory data. The main feature of this component database is non-overlapping attributes and it will follow non-redundant integration approach as explained in the thesis. This will be achieved by storing attributes which will not have the union or intersection of any attributes that exist in public domain molecular biology databases. Unlike data warehousing technique, this feature is quite unique and novel. The component database will be integrated with other biological data sources for sharing information in a cooperative environment. This involves developing new tools. The thesis explains the role of these new tools which are: meta data extractor, mapping linker, query generator and result interpreter. These tools are used for a transparent integration without creating any global schema of the participating databases. The thesis has also established the concept of image object keying for multidatabase query and it has proposed a relevant algorithm for matching protein spot in gel electrophoresis image. An object spot in gel electrophoresis image will initiate the query when it is selected by the user. It matches the selected spot with other similar spots in other resource databases. This image object keying method is an alternative to conventional multidatabase query which requires writing complex SQL scripts. This method also resolve the semantic conflicts that exist among molecular biology databases. The research has proposed a new framework based on the context of the web data for interactions with different biological data resources. A formal description of the resource context is described in the thesis. The implementation of the context into Resource Document Framework (RDF) will be able to increase the interoperability by providing the description of the resources and the navigation plan for accessing the web based databases. A higher level construct is developed (has, provide and access) to implement the context into RDF for web interactions. The interactions within the resources are achieved by utilising an integration domain to extract the required information with a single instance and without writing any query scripts. The integration domain allows to navigate and to execute the query plan within the resource databases. An extractor module collects elements from different target webs and unify them as a whole object in a single page. The proposed framework is tested to find specific information e.g., information on Alzheimer's disease, from public domain biology resources, such as, Protein Data Bank, Genome Data Bank, Online Mendalian Inheritance in Man and local database. Finally, the thesis proposes further propositions and plans for future work