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. ^

Functional data analysis approaches for genotype-phenotype association studies from next-generation sequencing

Next-generation DNA sequencing platforms can effectively detect the entire spectrum of genomic variation and is emerging to be a major tool for systematic exploration of the universe of variants and interactions in the entire genome. However, the data produced by next-generation sequencing technologies will suffer from three basic problems: sequence errors, assembly errors, and missing data. Current statistical methods for genetic analysis are well suited for detecting the association of common variants, but are less suitable to rare variants. This raises great challenge for sequence-based genetic studies of complex diseases.^ This research dissertation utilized genome continuum model as a general principle, and stochastic calculus and functional data analysis as tools for developing novel and powerful statistical methods for next generation of association studies of both qualitative and quantitative traits in the context of sequencing data, which finally lead to shifting the paradigm of association analysis from the current locus-by-locus analysis to collectively analyzing genome regions.^ In this project, the functional principal component (FPC) methods coupled with high-dimensional data reduction techniques will be used to develop novel and powerful methods for testing the associations of the entire spectrum of genetic variation within a segment of genome or a gene regardless of whether the variants are common or rare.^ The classical quantitative genetics suffer from high type I error rates and low power for rare variants. To overcome these limitations for resequencing data, this project used functional linear models with scalar response to develop statistics for identifying quantitative trait loci (QTLs) for both common and rare variants. To illustrate their applications, the functional linear models were applied to five quantitative traits in Framingham heart studies. ^ This project proposed a novel concept of gene-gene co-association in which a gene or a genomic region is taken as a unit of association analysis and used stochastic calculus to develop a unified framework for testing the association of multiple genes or genomic regions for both common and rare alleles. The proposed methods were applied to gene-gene co-association analysis of psoriasis in two independent GWAS datasets which led to discovery of networks significantly associated with psoriasis.^

Performance tiers: Implementing comparative effectiveness analysis in the health care setting through operations research and spatial methods

This dissertation develops and tests a comparative effectiveness methodology utilizing a novel approach to the application of Data Envelopment Analysis (DEA) in health studies. The concept of performance tiers (PerT) is introduced as terminology to express a relative risk class for individuals within a peer group and the PerT calculation is implemented with operations research (DEA) and spatial algorithms. The analysis results in the discrimination of the individual data observations into a relative risk classification by the DEA-PerT methodology. The performance of two distance measures, kNN (k-nearest neighbor) and Mahalanobis, was subsequently tested to classify new entrants into the appropriate tier. The methods were applied to subject data for the 14 year old cohort in the Project HeartBeat! study.^ The concepts presented herein represent a paradigm shift in the potential for public health applications to identify and respond to individual health status. The resultant classification scheme provides descriptive, and potentially prescriptive, guidance to assess and implement treatments and strategies to improve the delivery and performance of health systems. ^

Use of short term test systems for the prediction of the hazard represented by potential chemical carcinogens

It has been hypothesized that results from the short term bioassays will ultimately provide information that will be useful for human health hazard assessment. Although toxicologic test systems have become increasingly refined, to date, no investigator has been able to provide qualitative or quantitative methods which would support the use of short term tests in this capacity.^ Historically, the validity of the short term tests have been assessed using the framework of the epidemiologic/medical screens. In this context, the results of the carcinogen (long term) bioassay is generally used as the standard. However, this approach is widely recognized as being biased and, because it employs qualitative data, cannot be used in the setting of priorities. In contrast, the goal of this research was to address the problem of evaluating the utility of the short term tests for hazard assessment using an alternative method of investigation.^ Chemical carcinogens were selected from the list of carcinogens published by the International Agency for Research on Carcinogens (IARC). Tumorigenicity and mutagenicity data on fifty-two chemicals were obtained from the Registry of Toxic Effects of Chemical Substances (RTECS) and were analyzed using a relative potency approach. The relative potency framework allows for the standardization of data "relative" to a reference compound. To avoid any bias associated with the choice of the reference compound, fourteen different compounds were used.^ The data were evaluated in a format which allowed for a comparison of the ranking of the mutagenic relative potencies of the compounds (as estimated using short term data) vs. the ranking of the tumorigenic relative potencies (as estimated from the chronic bioassays). The results were statistically significant (p $<$.05) for data standardized to thirteen of the fourteen reference compounds. Although this was a preliminary investigation, it offers evidence that the short term test systems may be of utility in ranking the hazards represented by chemicals which may be human carcinogens. ^

SOCIO-ENVIRONMENTAL FACTORS ASSOCIATED WITH THE DISTRIBUTION OF DRACUNCULUS MEDINENSIS (GUINEA WORM DISEASE) AND SUGGESTED METHODS FOR CONTROL, IBARAPA, NIGERIA, 1982 (AFRICA)

A population-based cross-sectional survey of socio-environmental factors associated with the prevalence of Dracunculus medinensis (guinea worm disease) was conducted in Idere, a rural agricultural community in Ibarapa, Oyo state, Nigeria, during 1982.^ The epidemiologic data were collected by household interview of all 501 households. The environmental data were collected by analysis of water samples collected from all domestic water sources and rainfall records.^ The specific objectives of this research were to: (a) Describe the prevalence of guinea worm disease in Idere during 1982 by age, sex, area of residence, drinking water source, religion and weekly amount of money spent by the household to collect potable drinking water. (b) Compare the characteristics of cases with non-cases of guinea worm in order to identify factors associated with high risk of infection. (c) Investigate domestic water sources for the distribution of Cyclops. (d) Determine the extent of potable water shortage with a view to identifying factors responsible for such shortage in the community. (e) Describe the effects of guinea worm on school attendance during 1980/1982 school years by class and location of school from piped water supply.^ The findings of this research indicate that during 1982, 31.8 percent of Idere's 6,527 residents experienced guinea worm infection, with higher prevalence of infection recorded in males in their most productive years and females in their teenage years. The role of sex and age to risk of higher infection rate was explained in the context of water related exposure and water intake due to dehydration from physical occupational actitives of subgroups.^ Potable water available to residents was considerably below the minimum recommended by WHO for tropical climates, with sixty-eight percent of water needs of the residents coming from unprotected surface water which harbour Cyclops, the obligatory intermediate host of Dracunculus medinensis. An association was found between periods of relative high density of Cyclops in domestic water and rainfall.^ Impact of guinea worm infection on educational activities was considerable and its implications were discussed, including the implications of the research findings in relation to control of guinea worm disease in Ibarapa. ^

Future pandemic influenza control (FPIC) related strategic management plan based on the 2009 H1N1 pandemic influenza review of health policy decisions, their practice and implications

This cross-sectional study is based on the qualitative and quantitative research design to review health policy decisions, their practice and implications during 2009 H1N1 influenza pandemic in the United States and globally. The “Future Pandemic Influenza Control (FPIC) related Strategic Management Plan” was developed based on the incorporation of the “National Strategy for Pandemic Influenza (2005)” for the United States from the U.S. Homeland Security Council and “The Canadian Pandemic Influenza Plan for the Health Sector (2006)” from the Canadian Pandemic Influenza Committee for use by the public health agencies in the United States as well as globally. The “global influenza experts’ survey” was primarily designed and administered via email through the “Survey Monkey” system to the 2009 H1N1 influenza pandemic experts as the study respondents. The effectiveness of this plan was confirmed and the approach of the study questionnaire was validated to be convenient and the excellent quality of the questions provided an efficient opportunity to the study respondents to evaluate the effectiveness of predefined strategies/interventions for future pandemic influenza control.^ The quantitative analysis of the responses to the Likert-scale based questions in the survey about predefined strategies/interventions, addressing five strategic issues to control future pandemic influenza. The effectiveness of strategies defined as pertinent interventions in this plan was evaluated by targeting five strategic issues regarding pandemic influenza control. For the first strategic issue pertaining influenza prevention and pre pandemic planning; the confirmed effectiveness (agreement) for strategy (1a) 87.5%, strategy (1b) 91.7% and strategy (1c) 83.3%. The assessment of the priority level for strategies to address the strategic issue no. (1); (1b (High Priority) > 1a (Medium Priority) > 1c (Low Priority) based on the available resources of the developing and developed countries. For the second Strategic Issue encompassing the preparedness and communication regarding pandemic influenza control; the confirmed effectiveness (agreement) for the strategy (2a) 95.6%, strategy (2b) 82.6%, strategy (2c) 91.3% and Strategy (2d) 87.0%. The assessment of the priority level for these strategies to address the strategic issue no. (2); (2a (highest priority) > 2c (high priority) >2d (medium priority) > 2b (low priority). For the third strategic issue encompassing the surveillance and detection of pandemic influenza; the confirmed effectiveness (agreement) for the strategy (3a) 90.9% and strategy (3b) 77.3%. The assessment of the priority level for theses strategies to address the strategic Issue No. (3) (3a (high priority) > 3b (medium/low priority). For the fourth strategic issue pertaining the response and containment of pandemic influenza; the confirmed effectiveness (agreement) for the strategy (4a) 63.6%, strategy (4b) 81.8%, strategy (4c) 86.3%, and strategy (4d) 86.4%. The assessment of the priority level for these strategies to address the strategic issue no. (4); (4d (highest priority) > 4c (high priority) > 4b (medium priority) > 4a (low priority). The fifth strategic issue about recovery from influenza and post pandemic planning; the confirmed effectiveness (agreement) for the strategy (5a) 68.2%, strategy (5b) 36.3% and strategy (5c) 40.9%. The assessment of the priority level for strategies to address the strategic issue no. (5); (5a (high priority) > 5c (medium priority) > 5b (low priority).^ The qualitative analysis of responses to the open-ended questions in the study questionnaire was performed by means of thematic content analysis. The following recurrent or common “themes” were determined for the future implementation of various predefined strategies to address five strategic issues from the “FPIC related Strategic Management Plan” to control future influenza pandemics. (1) Pre Pandemic Influenza Prevention, (2) Seasonal Influenza Control, (3) Cost Effectiveness of Non Pharmaceutical Interventions (NPI), (4) Raising Global Public Awareness, (5) Global Influenza Vaccination Campaigns, (6)Priority for High Risk Population, (7) Prompt Accessibility and Distribution of Influenza Vaccines and Antiviral Drugs, (8) The Vital Role of Private Sector, (9) School Based Influenza Containment, (10) Efficient Global Risk Communication, (11) Global Research Collaboration, (12) The Critical Role of Global Public Health Organizations, (13) Global Syndromic Surveillance and Surge Capacity and (14) Post Pandemic Recovery and Lessons Learned. The future implementation of these strategies with confirmed effectiveness to primarily “reduce the overall response time’ in the process of ‘early detection’, ‘strategies (interventions) formulation’ and their ‘implementation’ to eventually ensure the following health outcomes: (a) reduced influenza transmission, (b) prompt and effective influenza treatment and control, (c) reduced influenza related morbidity and mortality.^

Development and Characterization of an in vitro Four-species Anaerobic Dental Biofilm Model

Dental caries is the most common chronic disease worldwide. It is characterized by the demineralization of tooth enamel caused by acid produced by cariogenic dental bacteria growing on tooth surfaces, termed bacterial biofilms. Cariogenesis is a complex biological process that is influence by multiple factors and is not attributed to a sole causative agent. Instead, caries is associated with multispecies microbial biofilm communities composed of some bacterial species that directly influence the development of a caries lesion and other species that are seemingly benign but must contribute to the community in an uncharacterized way. Clinical analysis of dental caries and its microbial populations is challenging due to many factors including low sensitivity of clinical measurement tools, variability in saliva chemistry, and variation in the microbiota. Our laboratory has developed an in vitro anaerobic biofilm model for dental carries to facilitate both clinical and basic research-based analyses of the multispecies dynamics and individual factors that contribute to cariogenicity. The rational for development of this system was to improve upon the current models that lack key elements. This model places an emphasis on physiological relevance and ease of maintenance and reproducibility. The uniqueness of the model is based on integrating four critical elements: 1) a biofilm community composed of four distinct and representative species typically associated with dental caries, 2) a semi-defined synthetic growth medium designed to mimic saliva, 3) physiologically relevant biofilm growth substrates, and 4) a novel biofilm reactor device designed to facilitate the maintenance and analysis. Specifically, human tooth sections or hydroxyapatite discs embedded into poly(methyl methacrylate) (PMMA) discs are incubated for an initial 24 hr in a static inverted removable substrate (SIRS) biofilm reactor at 37°C under anaerobic conditions in artificial saliva (CAMM) without sucrose in the presence of 1 X 106 cells/ml of each Actinomyces odontolyticus, Fusobacterium nucleatum, Streptococcus mutans, and Veillonella dispar. During days 2 and 3 the samples are maintained continually in CAMM with various exposures to 0.2% sucrose; all of the discs are transferred into fresh medium every 24 hr. To validate that this model is an appropriate in vitro representation of a caries-associated multispecies biofilm, research aims were designed to test the following overarching hypothesis: an in vitro anaerobic biofilm composed of four species (S. mutans, V. dispar, A. odontolyticus, and F. nucleatum) will form a stable biofilm with a community profile that changes in response to environmental conditions and exhibits a cariogenic potential. For these experiments the biofilms as described above were exposed on days 2 and 3 to either CAMM lacking sucrose (no sucrose), CAMM with 0.2% sucrose (constant sucrose), or were transferred twice a day for 1 hr each time into 0.2% sucrose (intermittent sucrose). Four types of analysis were performed: 1) fluorescence microscopy of biofilms stained with Syto 9 and hexidium idodine to determine the biofilm architecture, 2) quantitative PCR (qPCR) to determine the cell number of each species per cm2, 3) vertical scanning interferometry (VSI) to determine the cariogenic potential of the biofilms, and 4) tomographic pH imaging using radiometric fluorescence microscopy after exposure to pH sensitive nanoparticles to measure the micro-environmental pH. The qualitative and quantitative results reveal the expected dynamics of the community profile when exposed to different sucrose conditions and the cariogenic potential of this in vitro four-species anaerobic biofilm model, thus confirming its usefulness for future analysis of primary and secondary dental caries.

Phosphorus and Potassium Rates and Placement Methods for Corn and Soybean Managed with No-till or Tillage

No-till management for corn and soybean results in little or no incorporation of crop residues and fertilizer with soil. Subsurface banding phosphorus (P) and potassium (K) fertilizers with planter attachments could be more effective than broadcast fertilization, because in no-till with broadcast fertilizer, both nutrients accumulate at or near the soil surface. A long-term study was initiated in 1994 at the ISU Northwest Research Farm to evaluate P and K fertilizer placement for corn and soybean managed with no-till and chiselplow tillage.

Particle flux measurements from moorings and surface sediment studies of sediment cores in the SE Pacific Ocean

Flux of siliceous plankton and taxonomic composition of diatom and silicoflagellate assemblages were determined from sediment trap samples collected in coastal upwelling-influenced waters off northern Chile (30°S, CH site) under "normal" or non-El Niño (1993-94) and El Niño conditions (1997-98). In addition, concentration of biogenic opal and siliceous plankton, and diatom and silicoflagellate assemblages preserved in surface sediments are provided for a wide area between 27° and 43°S off Chile. Regardless of the year, winter upwelling determines the maximum production pattern of siliceous microorganisms, with diatoms numerically dominating the biogenic opal flux. During the El Niño year the export is markedly lower: on an annual basis, total mass flux diminished by 60%, and diatom and silicoflagellate export by 75%. Major components of the diatom flora maintain much of their regular seasonal cycle of flux maxima and minima during both sampling periods. Neritic resting spores (RS) of Chaetoceros dominate the diatom flux, mirroring the influence of coastal-upwelled waters at the CH trap site. Occurrence of pelagic diatoms species Fragilariopsis doliolus, members of the Rhizosoleniaceae, Azpeitia spp. and Nitzschia interruptestriata, secondary components of the assemblage, reflects the intermingling of warmer waters of the Subtropical Gyre. Dictyocha messanensis dominates the silicoflagellate association almost year-around, but Distephanus pulchra delivers ca. 60% of its annual production in less than three weeks during the winter peak. The siliceous thanatocoenosis is largely dominated by diatoms, whose assemblage shows significant qualitative and quantitative variations from north to south. Between 27° and 35°S, the dominance of RS Chaetoceros, Thalassionema nitzschioides var. nitzschioides and Skeletonema costatum reflects strong export production associated with occurrence of coastal upwelling. Both highest biogenic opal content and diatom concentration at 35° and 41°-43°S coincide with highest pigment concentrations along the Chilean coast. Predominance of the diatom species Thalassiosira pacifica and T. poro-irregulata, and higher relative contribution of the silicoflagellate Distephanus speculum at 41°-43°S suggest the influence of more nutrient-rich waters and low sea surface temperatures, probably associated with the Antarctic Circumpolar Water.

Hidden realities: What women do when they want to terminate an unwanted pregnancy in Bolivia

OBJECTIVE: To explore women's experience of unwanted pregnancy and induced abortion in Bolivia, where nearly all induced abortions are carried out in clandestine, unregulated, and unsafe conditions. METHODS: Qualitative and quantitative research methods, including focus group discussions, in-depth interviews and a structured survey of women of reproductive age, were used to explore the experience of unwanted pregnancy and induced abortion in poor urban areas of 5 Bolivian cities. RESULTS: Of the 1175 sexually experienced women surveyed, 13% reported having had an induced abortion. The methods they tried included surgical abortion, taking misoprostol, drinking herbal and chemical preparations, and inflicting physical trauma on themselves. Many women made multiple attempts before successfully terminating a pregnancy. Lack of knowledge and confusion about how to use misoprostol may have contributed to the complications that resulted in seeking postabortion care. CONCLUSION: Increased access to accurate information and counseling about abortion options are paramount if women are to make informed decisions and minimize health risks.

Finely dispersed fraction of particulate organic matter and primary production in sea water of the Equatorial East Pacific

Qualitative and quantitative evaluation of the finely dispersed fraction of particulate organic matter in sea water is given. It is demonstrated that in the euphotic zone of high productivity waters this fraction constitutes 86%, in waters with low productivity 61%, and in deep waters (>200 m) 53% of the organic carbon in particulate matter. Formation of the finely dispersed fraction and its role in distribution of energy in the detrital food chain of the ecosystem are discussed.

(Table 2) Characteristics of influence of cyclonic and anticyclonic activity of water masses on hydrophysical, hydrochemical, and hydrobiological parameters in the southern part of the Black Sea in September 1996

Characteristics of the spatial structure of vertical synoptic currents were calculated from data of the density field surveys in order to estimate their influence on distribution of chlorophyll a concentration. Comparisons of chlorophyll concentration and vertical currents were implemented for two multidisciplinary surveys in the Black Sea carried out in summer, 1991 and in winter, 1994. The results showed qualitative and quantitative indications of coincidence of characteristics cited and, in particular, significant positive values of the correlation coefficient (0.65 for the summer survey and 0.83 for the winter one).

Biostratigraphy of benthic and planktonic foraminifera in Paleocene samples of DSDP HOle 93-605

Paleocene benthic and planktonic foraminifers occur throughout a long interval of the sedimentary succession cored at Site 605. A biostratigraphic zonation based on planktonic foraminifers is proposed for this Paleocene section. Zones identified are Subbotina pseudobulloides Zone, Morozovella trinidadensis Zone, M. uncinata Zone, M. pusilla pusilla Zone, Planorotalites pseudomenardii Zone, and M. velascoensis Zone. Fluctuations in the sedimentation rate occurred at Site 605. Rates of deposition were high during the M. pusilla pusilla and P. pseudomenardii zones, and a depositional hiatus may occur at the base of the M. velascoensis Zone. Qualitative and quantitative analysis of benthic foraminiferal assemblages suggests that the Paleocene sediments of Site 605 were deposited near the upper limit of Nuttallides truempyi, that is, approximately in the middle bathyal zone (600 m or more).

Los desafíos del uso combinado de un cuestionario estructurado y un calendario de historia de vida para el estudio de trayectorias laborales

El presente artículo se enmarca en un proyecto de investigación más amplio, realizado en la localidad de Ministro Rivadavia en el Partido de Alte. Brown. La investigación tiene como objetivo evaluar los procesos de movilidad, estancamiento y marginalización social en el período 1994-2008, para una población con elevados índices de pobreza e inserciones laborales precarias e informales. En este estudio nos proponemos reflexionar sobre los desafíos que implicó la articulación entre un cuestionario estructurado y un calendario de historia de vida para el análisis de trayectorias laborales. El trabajo presenta las características de la metodología empleada, discute sus antecedentes teórico-metodológicos y especifica dónde se inscribe la articulación metodológica propuesta en el mapa posible de estrategias de investigación sociológica. A lo largo del artículo, retomamos los debates y propuestas en torno al manejo de la dimensión temporal y presentamos distintos esquemas de análisis centrados en la consideración del tiempo en sus múltiples manifestaciones micro y macrosociales. El artículo contribuye al debate sobre la integración de estrategias de investigación cualitativas y cuantitativas, y evidencia las potencialidades del instrumento propuesto para captar la temporalidad en su carácter plural y multidimensional