A SYSTEMS BIOLOGY APPROACH TO STUDY THE DYNAMICS OF MEMBRANE MICRODOMAINS IN MALARIA PARASITES.

In recent years, several computational methods have been developed to predict protein-protein interactions at a genome-wide level. Among them, a Bayesian approach has been proposed to integrate \u201c-omics\u201d data from diverse sources, and reconstruct probabilistic global interactomes. In order to apply this method to Plasmodium falciparum, the most virulent agent of the human malaria, we generated novel genomic data sets and gene expression profiles. In particular, we performed a re-assessment of the phylogenetic profile method proposing a new strategy to select reference genomes and adopting a novel measure of similarity. We also produced a new set of rosetta stone data on the basis of a large number of non-redundant genomes used as a reference set. Furthermore, diverse transcriptomic data have been organized to obtain gene expression profiles covering the entire intra-erythrocytic Plasmodium life-cycle. All data were then integrated to predict a global P. falciparum protein-protein interaction network. To gain insights on function and dynamics of specialized membrane compartments (lipid rafts), during P. falciparum development, we filtered our global interactome with stage-specific lipid raft proteomic data. Functional and topological studies of the obtained stage-specific interactomes were undertaken. Our results revealed a conserved subnetwork, the lipid raft \u201cfunctional core\u201d, involved in fundamental parasite processes and dynamic clusters populated of stage-specific proteins, responsible for remodeling of lipid raft organization

IPv6-Message-Passing mit Open MPI

Zur Lösung komplexer wissenschaftlicher Simulationsprobleme kommen heutzutage ob ihres Rechenbedarfs verst¨arkt Cluster zum Einsatz, die mit Hilfe von Message-Passing-Frameworks programmiert werden. Stehen mehrere Cluster zur Verfügung, kann durch Cluster-Cluster-Kopplung oftmals eine höhere Gesamtrechenleistung erzielt werden. IPv6 bietet für den Aufbau und den Betrieb dieser Clusterverbünde konzeptionelle Vorteile, die sich für den Anwendungsprogrammierer jedoch nur mit IPv6-fähigen Message-Passing-Frameworks erschließen. Gegenstand dieser Diplomarbeit ist die Erweiterung des Message-Passing-Frameworks Open MPI um IPv6-Unterstützung. Es wird gezeigt, daß durch eine geeignete Implementierung sowohl administrationsarme als auch leistungsfähige Cluster-Cluster-Kopplung realisiert werden kann

Cost-effective resource management for distributed computing

Current distributed computing and resource management infrastructures (e.g., Cluster and Grid) suffer from a wide variety of problems related to resource management, which include scalability bottleneck, resource allocation delay, limited quality-of-service (QoS) support, and lack of cost-aware and service level agreement (SLA) mechanisms. This thesis addresses these issues by presenting a cost-effective resource management solution which introduces the possibility of managing geographically distributed resources in resource units that are under the control of a Virtual Authority (VA). A VA is a collection of resources controlled, but not necessarily owned, by a group of users or an authority representing a group of users. It leverages the fact that different resources in disparate locations will have varying usage levels. By creating smaller divisions of resources called VAs, users would be given the opportunity to choose between a variety of cost models, and each VA could rent resources from resource providers when necessary, or could potentially rent out its own resources when underloaded. The resource management is simplified since the user and owner of a resource recognize only the VA because all permissions and charges are associated directly with the VA. The VA is controlled by a ’rental’ policy which is supported by a pool of resources that the system may rent from external resource providers. As far as scheduling is concerned, the VA is independent from competitors and can instead concentrate on managing its own resources. As a result, the VA offers scalable resource management with minimal infrastructure and operating costs. We demonstrate the feasibility of the VA through both a practical implementation of the prototype system and an illustration of its quantitative advantages through the use of extensive simulations. First, the VA concept is demonstrated through a practical implementation of the prototype system. Further, we perform a cost-benefit analysis of current distributed resource infrastructures to demonstrate the potential cost benefit of such a VA system. We then propose a costing model for evaluating the cost effectiveness of the VA approach by using an economic approach that captures revenues generated from applications and expenses incurred from renting resources. Based on our costing methodology, we present rental policies that can potentially offer effective mechanisms for running distributed and parallel applications without a heavy upfront investment and without the cost of maintaining idle resources. By using real workload trace data, we test the effectiveness of our proposed rental approaches. Finally, we propose an extension to the VA framework that promotes long-term negotiations and rentals based on service level agreements or long-term contracts. Based on the extended framework, we present new SLA-aware policies and evaluate them using real workload traces to demonstrate their effectiveness in improving rental decisions

Gene regulatory factors that control the identities of specific neuron types in Caenorhabditis elegans

The nervous system is the most complex and diverse system of the human body. And so it is in the round worm Caenorhabditis elegans. The easy manipulation, maintenance and visualization features of the worm have made it one of the most understood metazoans for linking genetics, anatomy, development and behavior. This thesis work focuses on two aspects during neural development in C. elegans: neuronal asymmetry in the ASEL/R gustatory neurons and terminal fate determination of the AIA interneuron as well as the NSM neurosecretory motor neuron. I have cloned and characterized LSY-27, a C2H2 zinc finger transcription factor, which is essential in assisting the onset of the LIM homeodomain transcription factor-6 to repress ASER expressed genes in ASEL. I have also took part in characterizing LSY-12, a MYST family histone acetyltransferase, and LSY-13, a previously uncharacterized PHD finger protein, which cooperate with the bromodomain containing protein LIN-49 and form the MYST complex to both initiate and maintain the ASEL fate. I have also studied the fate determination of several distinct neuronal cell types. I dissected the cis-regulatory information of AIA expressed genes and identified that the LIM homeodomain transcription factor TTX-3 is required for AIA fate, possibly together with another yet unknown transcription factor. TTX-3 also acts synergistically with the POU-domain transcription factor UNC-86 as master regulators for NSM. TTX-3 may also act as the terminal selector for ASK. This work provides extra evidence for the terminal selector concept and further demonstrates that individual neurons use unique and combinatorial codes of transcription factors to achieve their terminal identities, and that the same regulatory factor can be reused as a terminal selector in distinct cell types through cooperation with different cofactors

Marine Glycomics

Marine creatures are rich sources of glycoconjugate-containing glycans and have diversified structures. The advance of genomics has provided a valuable clue for their production and developments. This information will encourage breeding and engineering functional polysaccharides with slime ingredients in algae. These glycans will have the potential for applications to antioxidant, anticancer, and antimicrobial drugs in addition to health supplements and cosmetics. The combination of both biochemical and transcriptome approaches of marine creatures will lead to the opportunity to discover new activities of proteins such as glycan-relating enzymes and lectins. These proteins will also be used for experimental and medical purposes, such as diagnostics and trial studies. The topic of marine glycomics is also focusing on understanding the physiological properties of marine creatures, such as body defense against pathogens and cancers. In the competitions for natural selection, living creatures have evolved both their glycans and their recognition. They have primitive systems of immunity, and few of their mechanisms are closely related to glycans. If we are able to describe the accumulation of data of glycans of creatures living in the seashore and the oceans, we may be able to anticipate a time when we can talk about the ecosystem with glycans. That knowledge will be useful for the development of drugs that cure our diseases and for an understanding of living systems in addition to the preservation of living environments

[Research activities in applied mathematics, fluid mechanics, and computer science]

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, fluid mechanics, and computer science during the period April 1, 1995 through September 30, 1995

Identification and functional characterization of the GBF1-controlled network of host proteins supporting enterovirus replication

The genus Enterovirus of the Picornaviridae family contains many established and emerging pathogens. However, licensed vaccines are currently available only against poliovirus and enterovirus A71. No therapeutics have been officially approved to treat any enterovirus infections, although some are being developed. To find suitable targets for antivirals and control the infections, we need to understand the virus's life cycle better and identify the cellular factors involved in virus infection. Enterovirus genome replication occurs on the unique membranes known as replication organelles (ROs). A Golgi resident protein, GBF1, is recruited to the ROs by a viral protein 3A. GBF1 activates small GTPases Arf, which are critical regulators of the cellular secretory pathway. Here, we investigated the mechanistic details of GBF1-dependent Arf activation during enterovirus replication and characterized the proteome of the ROs in the vicinity of GBF1. We showed that Arf1 appeared to be the first to associate with the ROs, followed by other Arfs. Once activated and recruited to the ROs, all Arfs except Arf3 were no longer sensitive to inhibition of GBF1, suggesting that they do not actively cycle between GTP- and GDP-bound states in infected cells. siRNA depletion studies demonstrated an increased sensitivity of polio replication to inhibition of GBF1 in Arf1-, and to a lesser extent, Arf6-depleted cells, indicating the importance of GBF1-mediated activation of these Arfs for the viral replication. Taking advantage of the GBF1 recruitment to the ROs and GBF1’s essential role in enterovirus replication, we used a GBF1 construct fused to APEX2 peroxidase to explore the proteome of the ROs by proximity biotinylation. Among the proteins biotinylated in infected cells were the known cellular factors recruited to the ROs, including PI4KIII, OSBP, and ACBD3, indicating that these proteins are localized close to GBF1. Among the viral proteins, the intermediate products of the polyprotein processing were overrepresented, suggesting that GBF1 is localized close to the sites of active polyprotein processing. About 85% of the proteins identified by MS have not been previously associated with enterovirus infection. Gene ontology analysis revealed a significant enrichment of RNA binding and mRNA metabolic processes, suggesting a close localization of GBF1 to the RNA replication complexes. siRNA knockdown functional analysis of the selected proteins showed the recruitment of both proviral and antiviral factors to the ROs. Collectively, our work revealed important details about the involvement of Arfs in the replication process, introduced a highly efficient system to investigate the proteome of the enterovirus ROs, and provided novel data about the protein composition of the GBF1-enriched environment in the replication sites