Macromolecular interaction studies on FF1-3 of human CA150 and STAT1-importin alpha5 using biophysical and biochemical methods

Macromolecular interactions, such as protein-protein interactions and protein-DNA interactions, play important roles in executing biological functions in cells. However the complexity of such interactions often makes it very challenging to elucidate the structural details of these subjects. In this thesis, two different research strategies were applied on two different two macromolecular systems: X-ray crystallography on three tandem FF domains of transcription regulator CA150 and electron microscopy on STAT1-importin α5 complex. The results from these studies provide novel insights into the function-structure relationships of transcription coupled RNA splicing mediated by CA150 and the nuclear import process of the JAK-STAT signaling pathway. ^ The first project aimed at the protein-protein interaction module FF domain, which often occurs as tandem repeats. Crystallographic structure of the first three FF domains of human CA150 was determined to 2.7 Å resolution. This is the only crystal structure of an FF domain and the only structure on tandem FF domains to date. It revealed a striking connectivity between an FF domain and the next. Peptide binding assay with the potential binding ligand of FF domains was performed using fluorescence polarization. Furthermore, for the first time, FF domains were found to potentially interact with DNA. DNA binding assays were also performed and the results were supportive to this newly proposed functionality of an FF domain. ^ The second project aimed at understanding the molecular mechanism of the nuclear import process of transcription factor STAT1. The first structural model of pSTAT1-importin α5 complex in solution was built from the images of negative staining electron microscopy. Two STAT1 molecules were observed to interact with one molecule of importin α5 in an asymmetric manner. This seems to imply that STAT1 interacts with importin α5 with a novel mechanism that is different from canonical importin α-cargo interactions. Further in vitro binding assays were performed to obtain more details on the pSTAT1-importin α5 interaction. ^

Structure-function analysis of human Integrator subunit-4

Structure-function analysis of human Integrator subunit 4 Anupama Sataluri Advisor: Eric. J. Wagner, Ph.D. Uridine-rich small nuclear RNAs (U snRNA) are RNA Polymerase-II (RNAPII) transcripts that are ubiquitously expressed and are known to be essential for gene expression. snRNAs play a key role in mRNA splicing and in histone mRNA expression. Inaccurate snRNA biosynthesis can lead to diseases related to defective splicing and histone mRNA expression. Although the 3′ end formation mechanism and processing machinery of other RNAPII transcripts such as mRNA has been well studied, the mechanism of snRNA 3′ end processing has remained a mystery until the recent discovery of the machinery that mediates this process. In 2005, a complex of 14 subunits (the Integrator complex) associated with RNA Polymerase-II was discovered. The 14subunits were annotated Integrator 1-14 based on their size. The subunits of this complex together were found to facilitate 3′ end processing of snRNA. Identification of the Integrator complex propelled research in the direction of understanding the events of snRNA 3’end processing. Recent studies from our lab confirmed that Integrator subunit (IntS) 9 and 11 together perform the endonucleolytic cleavage of the nascent snRNA 3′ end to generate mature snRNA. However, the role of other members of the Integrator complex remains elusive. Current research in our lab is focused on deciphering the role of each subunit within the Integrator complex This work specifically focuses on elucidating the role of human Integrator subunit 4 (IntS4) and understanding how it facilitates the overall function of the complex. IntS4 has structural similarity with a protein called “Symplekin”, which is part of the mRNA 3’end processing machinery. Symplekin has been thoroughly researched in recent years and structure-function correlation studies in the context of mRNA 3’end processing have reported a scaffold function for Symplekin due to the presence of HEAT repeat motifs in its N-terminus. Based upon the structural similarity between IntS4 and Symplekin, we hypothesized that Integrator subunit 4 may be behaving as a Symplekin-like scaffold molecule that facilitates the interaction between other members of the Integrator Complex. To answer this question, the two important goals of this study were to: 1) identify the region of IntS4, which is important for snRNA 3′ end processing and 2) determine binding partners of IntS4 which promote its function as a scaffold. IntS4 structurally consists of a highly conserved N-terminus with 8 HEAT repeats, followed by a nonconserved C- terminus. A series of siRNA resistant N and C-terminus deletion constructs as well as specific point mutants within its N-terminal HEAT repeats were generated for human IntS4 and, utilizing a snRNA transcriptional readthrough GFP-reporter assay, we tested their ability to rescue misprocessing. This assay revealed a possible scaffold like property of IntS4. To probe IntS4 for interaction partners, we performed co-immunoprecipitation on nuclear extracts of IntS4 expressing stable cell lines and identified IntS3 and IntS5 among other Integrator subunits to be binding partners which facilitate the scaffold like function of hIntS4. These findings have established a critical role for IntS4 in snRNA 3′ end processing, identified that both its N and C termini are essential for its function, and mapped putative interaction domains with other Integrator subunits.

An analysis of the revenue policy -making process of the Texas Legislature

The purpose of this dissertation was to develop a conceptual framework which can be used to account for policy decisions made by the House Ways and Means Committee (HW&MC) of the Texas House of Representatives. This analysis will examine the actions of the committee over a ten-year period with the goal of explaining and predicting the success of failure of certain efforts to raise revenue.^ The basis framework for modelling the revenue decision-making process includes three major components--the decision alternatives, the external factors and two competing contingency theories. The decision alternatives encompass the particular options available to increase tax revenue. The options were classified as non-innovative or innovative. The non-innovative options included the sales, franchise, property and severance taxes. The innovative options were principally the personal and corporate income taxes.^ The external factors included political and economic constraints that affected the actions of the HW&MC. Several key political constraints on committee decision-making were addressed--including public attitudes, interest groups, political party strength and tradition and precedents. The economic constraints that affected revenue decisions included court mandates, federal mandates and the fiscal condition of the nation and the state.^ The third component of the revenue decision-making framework included two alternative contingency theories. The first alternative theory postulated that the committee structure, including the individual member roles and the overall committee style, resulted in distinctive revenue decisions. This theory will be favored if evidence points to the committee acting autonomously with less concern for the policies of the Speaker of the House. The Speaker assignment theory, postulated that the assignment of committee members shaped or changed the course of committee decision-making. This theory will be favored if there was evidence that the committee was strictly a vehicle for the Speaker to institute his preferred tax policies.^ The ultimate goal of this analysis is to develop an explanation for legislative decision-making about tax policy. This explanation will be based on the linkages across various tax options, political and economic constraints, member roles and committee style and the patterns of committee assignment. ^

Identification, purification, sequencing and characterization of human lung fibroblast motility -stimulating factor for human soft tissue sarcoma cells

Paracrine motogenic factors, including motility cytokines and extracellular matrix molecules secreted by normal cells, can stimulate metastatic cell invasion. For extracellular matrix molecules, both the intact molecules and the degradative products may exhibit these activities, which in some cases are not shared by the intact molecules. We found that human peritumoral and lung fibroblasts secrete motility-stimulating activity for several recently established human sarcoma cell strains. The motility of lung metastasis-derived human SYN-1 sarcoma cells was preferentially stimulated by human lung and peritumoral fibroblast motility-stimulating factors (FMSFs). FMSFs were nondialyzable, susceptible to trypsin, and sensitive to dithiothreitol. Cycloheximide inhibited accumulation of FMSF activity in conditioned medium; however, addition of cycloheximide to the migration assay did not significantly affect motility-stimulating activity. Purified hepatocyte growth factor/scatter factor (HGF/SF), rabbit anti-hHGF, and RT-PCR analysis of peritumoral and lung fibroblast HGF/SF mRNA expression indicated that FMSF activity was unrelated to HGF/SF. Partial purification of FMSF by gel exclusion chromatography revealed several peaks of activity, suggesting multiple FMSF molecules or complexes.^ We purified the fibroblast motility-stimulating factor from human lung fibroblast-conditioned medium to apparent homogeneity by sequential heparin affinity chromatography and DEAE anion exchange chromatography. Lysylendopeptidase C digestion of FMSF and sequencing of peptides purified by reverse phase HPLC after digestion identified it as an N-terminal fragment of human fibronectin. Purified FMSF stimulated predominantly chemotaxis but chemokinesis as well of SYN-1 sarcoma cells and was chemotactic for a variety of human sarcoma cells, including fibrosarcoma, leiomyosarcoma, liposarcoma, synovial sarcoma and neurofibrosarcoma cells. The motility-stimulating activity present in HLF-CM was completely eliminated by either neutralization or immunodepletion with a rabbit anti-human-fibronectin antibody, thus further confirming that the fibronectin fragment was the FMSF responsible for the motility stimulation of human soft tissue sarcoma cells. Since human soft tissue sarcomas have a distinctive hematogenous metastatic pattern (predominantly lung), FMSF may play a role in this process. ^

Activation of c -Met contributes to growth and metastasis of human colorectal carcinoma

c-Met is the protein tyrosine kinase receptor for hepatocyte growth factor/scatter factor (HGF/SF) and mediates several normal cellular functions including proliferation, survival, and migration. Overexpression of c-Met correlates with progression and metastasis of human colorectal carcinoma (CRC). The goals of this study were to determine if overexpression of c-Met directly contributes to tumorigenicity and liver metastatic potential of colon cancer, and what are the critical pathways regulated by c-Met in this process. The studies used two colon tumor cell lines, KM12SM and KM20, which express high levels of constitutively active c-Met and are highly metastatic in nude mice. To examine the effects of c-Met overexpression, subclones of theses lines with reduced c-Met expression were obtained following transfection with a c-Met specific targeting ribozyme. Reduction of c-Met in KM12SM cells abolished liver metastases when cells were injected intrasplenically in an experimental metastasis assay. However, c-Met downregulation in theses clones was unstable. Three stable KM20 clones with a 25–35% reduction in c-Met protein levels but 60–90% reduction in basal c-Met autophosphorylation and kinase activity were obtained. While HGF increased c-Met kinase activity in the clones with reduced c-Met, the activity was less than that observed in parental or control transfected cells. Correlating with the reduction in c-Met kinase activity, subclones with reduced c-Met expression had significantly reduced in vitro growth rates, soft-agar colony forming abilities, and increased apoptosis. HGF/SF treatment did not affect anchorage-dependent growth or soft-agar colony forming abilities. Further, c-Met downregulation significantly impaired the ability of HGF/SF to induce migration. To examine the effects of reduced c-Met on tumor formation, parental and c-Met reduced KM20 cells were grown subcutaneously and intrahepatically in nude mice. c-Met downregulation delayed, but did not abolish growth at the subcutaneous site. When these cells were injected intrahepatically, both tumor incidences and size were significantly reduced. To further understand the molecular basis of c-Met in promoting tumor growth, the activation of several signaling intermediates that have been implicated in c-Met mediated growth, survival and migration were compared between KM20 parental cells and subclones with reduced c-Met expression levels. The expression and activity (as determined by phosphorylation) of AKT and Erk1/2 were unaltered. In contrast, Src kinase activity, as measured by immune complex kinase assay, was reduced 2–5 fold following c-Met downregulation. As Src has been implicated in growth, survival and migration, Src activation in c-Met overexpressing lines is likely contributing to the tumorigenic and metastatic capabilities of colon tumor cell lines that overexpress c-Met. Collectively, these results suggest that c-Met overexpression plays a causal role in the development of CRC liver metastases, and that c-Src and c-Met inhibitors may be of potential therapeutic benefit for late-stage colon cancer. ^

Case Study of Applied LIP Approach/Activities in the Philippines The Training Services Enhancement Project for Rural Life Improvement (TSEP-RLI) Experience

TSEP-RLI was a technical cooperation project jointly conducted by GOP thru DA-Agricultural Training Institute (ATI) and GOJ thru JICA aimed at institutionalizing the training program for Rural Life Improvement (RLI) at the (ATI). As expected, farmers, fisherfolk, women, youth and extension agents were provided with efficient and effective training services from ATI leading to the improvement of quality of life in the rural areas through efforts of human resource development. The ATI- Bohol was chosen as the model center where participatory trials and various activities of the project were undertaken for five years. These activities were participatory surveys and data collection of on-farm and off-farm productive activities; planning workshop for RLI; feedbacking of survey results and action plans to the community and the Local Government Units (LGUs), and signing of Memorandum of Agreement between the Project and participating LGUs. The above activities were done to facilitate the planning and development of most effective and necessary rural life improvement activities, to confirm the willingness of the people to support and participate and to formalize the partnership between the Project and the LGUs. Since the concept of rural life covers a vast range of activities, a consensus had been reached that the total aspects of rural life be grasped in three spheres, namely, Production & Livelihood (P/L), Rural Living Condition (RLC) and Community Environment (C/E). The RLI for Ubi (Yam) Growers was one of the pilot activities undertaken in two pilot barangays and the target beneficiaries were members of the Rural Improvement Club (RIC- a group of organized women) with the LGU of the Municipality of Corella as the implementing partner. During the planning workshop, the barangay residents articulated their desire to promote production and processing of ubi (sphere on P/L - as the entry point), lack of nutritious food was one of the identified problem (sphere on RLC- expansion point) and environmental degradation such as deforestation, and soil erosion was another problem articulated by the community people (sphere on C/E- expansion point). Major activities that were undertaken namely, Ubi cooking contest, cooking/processing seminar, training courses on entrepreneurial development, ubi production and storage technology, packaging and product design, human resource development and simplified bookkeeping motivated the beneficiaries as well as developed and enhanced their skills & capabilities while strengthening their associations. Their participation to the 5 ubi festivals and other related activities had brought some impacts on their economic and rural life improvement activities. The seven principles of TSEP-RLI include the participatory process, holistic approach, dialogical approach, bottom -up training needs assessment, demand-driven approach, cost sharing approach and collaborative implementation with other agencies including LGUs and the community.

Forestry Sector Reform and Distributional Change of Natural Resource Rent in Indonesia

After the collapse of the centralized Soeharto regime, deforestation caused by over-logging accelerated. To tackle this problem, an IMF/World Bank-led forestry sector reform program adopted a market-friendly approach involving the resumption of round wood exports and raising of the resource rent fee, with the aim to stop rent accumulation by plywood companies, which had enjoyed a supply of round wood at privileged prices. The Indonesian government, for its part, decentralized the forest concession management system to provide incentives for local governments and communities to carry out sustainable forest management. However, neither policy reform worked effectively. The round wood export ban was reimposed and the forest management system centralized again with cooperation from a newly funded industry-led institution. In the midst of the confusion surrounding the policy reversal, the gap between the price of round wood in international and domestic markets failed to contract, although rent allocations to plywood industries were reduced during 1998-2003. The rents were not collected properly by the government, but accumulated unexpectedly in the hands of players in the black market for round wood.

Usability Planner: A Tool to Support the Process of Selecting Usability Methods

There is increasing pressure on developers to produce usable systems, which requires the use of appropriate methods to support user centred design during development. There is currently no consistent advice on which methods are appropriate in which circumstances, so the selection of methods relies on individual experience and expertise. Considerable effort is required to collate information from various sources and to understand the applicability of each method in a particular situation. Usability Planner is a tool aimed to support the selection of the most appropriate methods depending on project and organizational constraints. Many of the rules employed are derived from ISO standards, complemented with rules from the authors’ experience.

Secure access control by means of human stress detection

This paper proposes a stress detection system based on fuzzy logic and the physiological signals heart rate and galvanic skin response. The main contribution of this method relies on the creation of a stress template, collecting the behaviour of previous signals under situations with a different level of stress in each individual. The creation of this template provides an accuracy of 99.5% in stress detection, improving the results obtained by current pattern recognition techniques like GMM, k-NN, SVM or Fisher Linear Discriminant. In addition, this system can be embedded in security systems to detect critical situations in accesses as cross-border control. Furthermore, its applications can be extended to other fields as vehicle driver state-of-mind management, medicine or sport training.

Improving the capacity of software acquisition management: An Alternative methodology

The acquisition of the information system technologies using the services of an external supplier could be the the best options to reduce the implementation and maintenance cost of software solutions, and allows a company to improve the efficient use of its resources. The focus of this paper is to outline a methodology structure for the software acquisition management. The methodology proposed in this paper is the result of the study and the convergence of the weakness and strengths of some models (CMMI, SA-CMM, ISO/IEC TR 15504, COBIT, and ITIL) that include the software acquisition process.

Sistema de recomendación semántico para la movilidad en el entorno AFRICA BUILD Portal

La Gestión de Recursos Humanos a través de Internet es un problema latente y presente actualmente en cualquier sitio web dedicado a la búsqueda de empleo. Este problema también está presente en AFRICA BUILD Portal. AFRICA BUILD Portal es una emergente red socio-profesional nacida con el ánimo de crear comunidades virtuales que fomenten la educación e investigación en el área de la salud en países africanos. Uno de los métodos para fomentar la educación e investigación es mediante la movilidad de estudiantes e investigadores entre instituciones, apareciendo así, el citado problema de la gestión de recursos humanos. Por tanto, este trabajo se centra en solventar el problema de la gestión de recursos humanos en el entorno específico de AFRICA BUILD Portal. Para solventar este problema, el objetivo es desarrollar un sistema de recomendación que ayude en la gestión de recursos humanos en lo que concierne a la selección de las mejores ofertas y demandas de movilidad. Caracterizando al sistema de recomendación como un sistema semántico el cual ofrecerá las recomendaciones basándose en las reglas y restricciones impuestas por el dominio. La aproximación propuesta se basa en seguir el enfoque de los sistemas de Matchmaking semánticos. Siguiendo este enfoque, por un lado, se ha empleado un razonador de lógica descriptiva que ofrece inferencias útiles en el cálculo de las recomendaciones y por otro lado, herramientas de procesamiento de lenguaje natural para dar soporte al proceso de recomendación. Finalmente para la integración del sistema de recomendación con AFRICA BUILD Portal se han empleado diversas tecnologías web. Los resultados del sistema basados en la comparación de recomendaciones creadas por el sistema y por usuarios reales han mostrado un funcionamiento y rendimiento aceptable. Empleando medidas de evaluación de sistemas de recuperación de información se ha obtenido una precisión media del sistema de un 52%, cifra satisfactoria tratándose de un sistema semántico. Pudiendo concluir que con la solución implementada se ha construido un sistema estable y modular posibilitando: por un lado, una fácil evolución que debería ir encaminada a lograr un rendimiento mayor, incrementando su precisión y por otro lado, dejando abiertas nuevas vías de crecimiento orientadas a la explotación del potencial de AFRICA BUILD Portal mediante la Web 3.0. ---ABSTRACT---The Human Resource Management through Internet is currently a latent problem shown in any employment website. This problem has also appeared in AFRICA BUILD Portal. AFRICA BUILD Portal is an emerging socio-professional network with the objective of creating virtual communities to foster the capacity for health research and education in African countries. One way to foster this capacity of research and education is through the mobility of students and researches between institutions, thus appearing the Human Resource Management problem. Therefore, this dissertation focuses on solving the Human Resource Management problem in the specific environment of AFRICA BUILD Portal. To solve this problem, the objective is to develop a recommender system which assists the management of Human Resources with respect to the selection of the best mobility supplies and demands. The recommender system is a semantic system which will provide the recommendations according to the domain rules and restrictions. The proposed approach is based on semantic matchmaking solutions. So, this approach on the one hand uses a Description Logics reasoning engine which provides useful inferences to the recommendation process and on the other hand uses Natural Language Processing techniques to support the recommendation process. Finally, Web technologies are used in order to integrate the recommendation system into AFRICA BUILD Portal. The results of evaluating the system are based on the comparison between recommendations created by the system and by real users. These results have shown an acceptable behavior and performance. The average precision of the system has been obtained by evaluation measures for information retrieval systems, so the average precision of the system is at 52% which may be considered as a satisfactory result taking into account that the system is a semantic system. To conclude, it could be stated that the implemented system is stable and modular. This fact on the one hand allows an easy evolution that should aim to achieve a higher performance by increasing its average precision and on the other hand keeps open new ways to increase the functionality of the system oriented to exploit the potential of AFRICA BUILD Portal through Web 3.0.

Efficiency of human activity on information spreading on Twitter

In this work we study Twitter data to understand influence dynamics in social networks. We define user efficiency on Twitter, as the ratio between the emergent spreading process and the activity employed by the user. We characterize this property by means of a quantitative analysis of the structural and dynamical patterns emergent from human interactions, and show it to be universal across several Twitter conversations.

Generation of human computational models with machine learning

Services in smart environments pursue to increase the quality of people?s lives. The most important issues when developing this kind of environments is testing and validating such services. These tasks usually imply high costs and annoying or unfeasible real-world testing. In such cases, artificial societies may be used to simulate the smart environment (i.e. physical environment, equipment and humans). With this aim, the CHROMUBE methodology guides test engineers when modeling human beings. Such models reproduce behaviors which are highly similar to the real ones. Originally, these models are based on automata whose transitions are governed by random variables. Automaton?s structure and the probability distribution functions of each random variable are determined by a manual test and error process. In this paper, it is presented an alternative extension of this methodology which avoids the said manual process. It is based on learning human behavior patterns automatically from sensor data by using machine learning techniques. The presented approach has been tested on a real scenario, where this extension has given highly accurate human behavior models,

Diseño de un instrumento de evaluación de la gestión de recursos humanos. Aplicación en pymes industriales

El punto de partida para que una empresa mejore su competitividad es la evaluación de su gestión; para ello, es necesario contar con instrumentos que de manera objetiva, evalúen la gestión y proporcionen una guía para la mejora continua de los procesos. Este trabajo de investigación presenta el diseño y aplicación de un instrumento para evaluar la gestión de recursos humanos en las pymes industriales. Es un instrumento adaptado a la cultura, mercado, características y especificidades propias de las pymes del sector industrial del Estado Bolívar, Venezuela. Los items de evaluación fueron divididos en cuatro bloques de acuerdo al ciclo Planificar, Hacer, Verificar, Actuar y su validación estadística fue realizada mediante la técnica de análisis multivariante. Una vez validada, se aplicó la herramienta a trescientos setenta y cinco individuos del área de Recursos Humanos en ciento veinticinco Pymes industriales. Los resultados indican que los aspectos de tipo funcional son los que conducen la gestión en lugar de las razones estratégicas de la empresa, y en general, no existe plan de carrera ni sistema de evaluación de desempeño. La caracterización aportada por este estudio permite a las empresas evaluadas conocer cuales son los factores a mejorar en su gestión.The starting point for a company to improve its competitiveness is the evaluation of their management; for this it is necessary to have instruments that objectively evaluate and provide management guidance for continuous process improvement. This research paper presents the design and implementation of a tool to assess the human resource management in industrial SMEs. It is an instrument adapted to the culture, market characteristics and needs of SMEs in the Bolivar State, Venezuela. The evaluation items were divided into four blocks according to the Plan, Do, Check, Act cycle and its statistical validation was performed using the technique of multivariate analysis. Once validated, the tool was applied to hundred seventy five individuals of Human Resources belonging to hundred twenty five industrial SMEs. The results indicate that aspects of functional type are the leading management rather than strategic reasons, and in general, there is no career plan and system performance evaluation. The characterization provided by this study evaluated allows companies to know what factors to improve their management.