Computational Methods on Study of Differentially Expressed Proteins in Maize Proteomes Associated with Resistance to Aflatoxin Accumulation

Plant breeders have focused on improving maize resistance to Aspergillus flavus infection and aflatoxin accumulation by breeding with genotypes having the desirable traits. Various maize inbred lines have been developed for the breeding of resistance. Identification of differentially expressed proteins among such maize inbred lines will facilitate the development of gene markers and expedite the breeding process. Computational biology and proteomics approaches on the investigation of differentially expressed proteins were explored in this research. The major research objectives included 1) application of computational methods in homology and comparative modeling to study 3D protein structures and identify single nucleotide polymorphisms (SNPs) involved in changes of protein structures and functions, which can in turn increase the efficiency of the development of DNA markers; 2) investigation of methods on total protein profiling including purification, separation, visualization, and computational analysis at the proteome level. Special research goals were set on the development of open source computational methods using Matlab image processing tools to quantify and compare protein expression levels visualized by 2D protein electrophoresis gel techniques

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

The pharmacological perturbation of brain zinc impairs BDNF-related signaling and the cognitive performances of young mice.

Zinc (Zn2+) is a pleiotropic modulator of the neuronal and brain activity. The disruption of intraneuronal Zn2+ levels triggers neurotoxic processes and affects neuronal functioning. In this study, we investigated how the pharmacological modulation of brain Zn2+ affects synaptic plasticity and cognition in wild-type mice. To manipulate brain Zn2+ levels, we employed the Zn2+ (and copper) chelator 5-chloro-7-iodo-8-hydroxyquinoline (clioquinol, CQ). CQ was administered for two weeks to 2.5-month-old (m.o.) mice, and effects studied on BDNF-related signaling, metalloproteinase activity as well as learning and memory performances. CQ treatment was found to negatively affect short- and long-term memory performances. The CQ-driven perturbation of brain Zn2+ was found to reduce levels of BDNF, synaptic plasticity-related proteins and dendritic spine density in vivo. Our study highlights the importance of choosing "when", "where", and "how much" in the modulation of brain Zn2+ levels. Our findings confirm the importance of targeting Zn2+ as a therapeutic approach against neurodegenerative conditions but, at the same time, underscore the potential drawbacks of reducing brain Zn2+ availability upon the early stages of development

Proteomic profiling of neuromas reveals alterations in protein composition and local protein synthesis in hyper-excitable nerves

Neuropathic pain may arise following peripheral nerve injury though the molecular mechanisms associated with this are unclear. We used proteomic profiling to examine changes in protein expression associated with the formation of hyper-excitable neuromas derived from rodent saphenous nerves. A two-dimensional difference gel electrophoresis ( 2D-DIGE) profiling strategy was employed to examine protein expression changes between developing neuromas and normal nerves in whole tissue lysates. We found around 200 proteins which displayed a > 1.75-fold change in expression between neuroma and normal nerve and identified 55 of these proteins using mass spectrometry. We also used immunoblotting to examine the expression of low-abundance ion channels Nav1.3, Nav1.8 and calcium channel alpha 2 delta-1 subunit in this model, since they have previously been implicated in neuronal hyperexcitability associated with neuropathic pain. Finally, S(35)methionine in vitro labelling of neuroma and control samples was used to demonstrate local protein synthesis of neuron-specific genes. A number of cytoskeletal proteins, enzymes and proteins associated with oxidative stress were up-regulated in neuromas, whilst overall levels of voltage-gated ion channel proteins were unaffected. We conclude that altered mRNA levels reported in the somata of damaged DRG neurons do not necessarily reflect levels of altered proteins in hyper-excitable damaged nerve endings. An altered repertoire of protein expression, local protein synthesis and topological re-arrangements of ion channels may all play important roles in neuroma hyper-excitability

Experimental Progress in Computation by Self-Assembly of DNA Tilings

Approaches to DNA-based computing by self-assembly require the use of D. T A nanostructures, called tiles, that have efficient chemistries, expressive computational power: and convenient input and output (I/O) mechanisms. We have designed two new classes of DNA tiles: TAO and TAE, both of which contain three double-helices linked by strand exchange. Structural analysis of a TAO molecule has shown that the molecule assembles efficiently from its four component strands. Here we demonstrate a novel method for I/O whereby multiple tiles assemble around a single-stranded (input) scaffold strand. Computation by tiling theoretically results in the formation of structures that contain single-stranded (output) reported strands, which can then be isolated for subsequent steps of computation if necessary. We illustrate the advantages of TAO and TAE designs by detailing two examples of massively parallel arithmetic: construction of complete XOR and addition tables by linear assemblies of DNA tiles. The three helix structures provide flexibility for topological routing of strands in the computation: allowing the implementation of string tile models

Cardiac protein changes in ischaemic and dilated cardiomyopathy: A proteomic study of human left ventricular tissue

The development of heart failure (HF) is characterized by progressive alteration of left ventricle structure and function. Previous works on proteomic analysis in cardiac tissue from patients with HF remain scant. The purpose of our study was to use a proteomic approach to investigate variations in protein expression of left ventricle tissue from patients with ischaemic (ICM) and dilated cardiomyopathy (DCM). Twenty-four explanted human hearts, 12 from patients with ICM and 12 with DCM undergoing cardiac transplantation and six non-diseased donor hearts (CNT) were analysed by 2DE. Proteins of interest were identified by mass spectrometry and validated by Western blotting and immunofluorescence. We encountered 35 differentially regulated spots in the comparison CNT versus ICM, 33 in CNT versus DCM, and 34 in ICM versus DCM. We identified glyceraldehyde 3-phophate dehydrogenase up-regulation in both ICM and DCM, and alpha-crystallin B down-regulation in both ICM and DCM. Heat shock 70 protein 1 was up-regulated only in ICM. Ten of the eleven differentially regulated proteins common to both aetiologies are interconnected as a part of a same network. In summary, we have shown by proteomics analysis that HF is associated with changes in proteins involved in the cellular stress response, respiratory chain and cardiac metabolism. Although we found altered expression of eleven proteins common to both ischaemic and dilated aetiology, we also observed different proteins altered in both groups. Furthermore, we obtained that seven of these eleven proteins are involved in cell death and apoptosis processes, and therefore in HF progression

MOLECULAR MECHANISMS OF OLFACTORY NEURODEGENERATION

Olfactory sensory decline has been associated with normal aging as well as neurodegenerative disorders, yet the underlying mechanisms are unclear. The overall aim of this dissertation was to investigate the fundamental molecular and cellular mechanisms associated with olfactory neurodegeneration. This investigation uses an integrative approach, combining proteomics and gene expression analyses with cellular and tissuelevel characterization. Using these approaches, two model systems were investigated: 1) normally aging C57BL/6 mice of ages 1.5-, 6- and 20-months; and 2) a mouse model of elevated endogenous oxidative stress-associated neurodegeneration, namely, the Harlequin mutant mouse. The first specific aim was to test the hypothesis that oxidative stress is associated with aging of the olfactory system. Using proteomics, I demonstrated that olfactory aging was accompanied primarily by increased oxidative stress-, mitochondrial metabolism- and synaptic/transport-associated changes. The second specific aim was to test the hypothesis that the olfactory system accumulates oxidative stress-mediated macromolecular damage over time, predisposing it to neurodegeneration. Two types of protein oxidation, namely, carbonylation and nitration, accumulated with aging in the olfactory system. Protein and cellular targets of oxidative stress-associated damage were identified using redox proteomics coupled with immunohistochemical localization. The third specific aim was to test the hypothesis that elevated oxidative stress in the olfactory system results in apoptosis/neurodegeneration. The Harlequin mutant mouse was critically selected and validated as a model for studies of oxidative stress-associated olfactory neurodegeneration at both the cellular and molecular levels. The Harlequin mouse had decreased levels and altered distribution of apoptosis inducing factor protein in mature olfactory sensory neurons, increased oxidative DNA damage and apoptosis in the olfactory epithelium, and pronounced cytoskeletal disorganization. The molecular studies confirmed and extended our cellular data and identified several significantly regulated genes associated with elevated oxidative stress and apoptosis. This novel study, by combining contemporary proteomics and genomics with cellular and tissue-level analyses, has provided a road map for understanding fundamental molecular mechanisms of olfactory degeneration