STUDIES OF THE MOLECULAR MECHANISMS OF CHROMOSOME ABERRATION FORMATION (DNA REPAIR, CROSSLINKS, MITOMYCIN C)

The objective of this research has been to study the molecular basis for chromosome aberration formation. Predicated on a variety of data, Mitomycin C (MMC)-induced DNA damage has been postulated to cause the formation of chromatid breaks (and gaps) by preventing the replication of regions of the genome prior to mitosis. The basic protocol for these experiments involved treating synchronized Hela cells in G(,1)-phase with a 1 (mu)g/ml dose of MMC for one hour. After removing the drug, cells were then allowed to progress to mitosis and were harvested for analysis by selective detachment. Utilizing the alkaline elution assay for DNA damage, evidence was obtained to support the conclusion that Hela cells can progress through S-phase into mitosis with intact DNA-DNA interstrand crosslinks. A higher level of crosslinking was observed in those cells remaining in interphase compared to those able to reach mitosis at the time of analysis. Dual radioisotope labeling experiments revealed that, at this dose, these crosslinks were associated to the same extent with both parental and newly replicated DNA. This finding was shown not to be the result of a two-step crosslink formation mechanism in which crosslink levels increase with time after drug treatment. It was also shown not to be an artefact of the double-labeling protocol. Using neutral CsCl density gradient ultracentrifugation of mitotic cells containing BrdU-labeled newly replicated DNA, control cells exhibited one major peak at a heavy/light density. However, MMC-treated cells had this same major peak at the heavy/light density, in addition to another minor peak at a density characteristic for light/light DNA. This was interpreted as indicating either: (1) that some parental DNA had not been replicated in the MMC treated sample or; (2) that a recombination repair mechanism was operational. To distinguish between these two possibilities, flow cytometric DNA fluorescence (i.e., DNA content) measurements of MMC-treated and control cells were made. These studies revealed that the mitotic cells that had been treated with MMC while in G(,1)-phase displayed a 10-20% lower DNA content than untreated control cells when measured under conditions that neutralize chromosome condensation effects (i.e., hypotonic treatment). These measurements were made under conditions in which the binding of the drug, MMC, was shown not to interfere with the stoichiometry of the ethidium bromide-mithramycin stain. At the chromosome level, differential staining techniques were used in an attempt to visualize unreplicated regions of the genome, but staining indicative of large unreplicated regions was not observed. These results are best explained by a recombinogenic mechanism. A model consistent with these results has been proposed.^

An intervention mapping approach: Identification of human trafficking victims by health professionals

Background. Today modern day slavery is known as human trafficking and is a growing pandemic that is a grave human rights violation. Estimates suggest that 12.3 million people are working under conditions of force, fraud or coercion. Working toward eradication is a worthy effort; it would free millions of humans from slavery, mostly women and children, as well as uphold basic human rights. One tactic to eradicating human trafficking is to increase identification of victims among those likely to encounter victims of human trafficking.^ Purpose. This study aims to develop an intervention that improves certain stakeholders' ability, in the health clinic setting, to appropriately identify and report victims of human trafficking to the National Human Trafficking Resource Center.^ Methods. The Intervention Mapping (IM) process was used by program planners to develop an intervention for health professionals. This methodology is a six step process that guides program planners to develop an intervention. Each step builds on the others through the execution of a needs assessment, and the development of matrices based on performance objectives and determinants of the targeted health behavior. The end product results in an ecological, theoretical, and evidence based intervention.^ Discussion. The IM process served as a useful protocol for program planners to take an ecological approach as well as incorporate theory and evidence into the intervention. Consultation with key informants, the planning group, adopters, implementers, and individuals responsible for institutionalization also contributed to the practicality and feasibility of the intervention. Program planners believe that this intervention fully meets recommendations set forth in the literature.^ Conclusions. The intervention mapping methodology enabled program planners to develop an intervention that is appropriate and acceptable to the implementer and the recipients.^

Effect of primary care availability and health insurance coverage on risk and cost of Preventable Hospitalizations in Harris County

Preventable Hospitalizations (PHs) are hospitalizations that can be avoided with appropriate and timely care in the ambulatory setting and hence are closely associated with primary care access in a community. Increased primary care availability and health insurance coverage may increase primary care access, and consequently may be significantly associated with risks and costs of PHs. Objective. To estimate the risk and cost of preventable hospitalizations (PHs); to determine the association of primary care availability and health insurance coverage with the risk and costs of PHs, first alone and then simultaneously; and finally, to estimate the impact of expansions in primary care availability and health insurance coverage on the burden of PHs among non-elderly adult residents of Harris County. Methods. The study population was residents of Harris County, age 18 to 64, who had at least one hospital discharge in a Texas hospital in 2008. The primary independent variables were availability of primary care physicians, availability of primary care safety net clinics and health insurance coverage. The primary dependent variables were PHs and associated hospitalization costs. The Texas Health Care Information Collection (THCIC) Inpatient Discharge data was used to obtain information on the number and costs of PHs in the study population. Risk of PHs in the study population, as well as average and total costs of PHs were calculated. Multivariable logistic regression models and two-step Heckman regression models with log-transformed costs were used to determine the association of primary care availability and health insurance coverage with the risk and costs of PHs respectively, while controlling for individual predisposing, enabling and need characteristics. Predicted PH risk and cost were used to calculate the predicted burden of PHs in the study population and the impact of expansions in primary care availability and health insurance coverage on the predicted burden. Results. In 2008, hospitalized non-elderly adults in Harris County had 11,313 PHs and a corresponding PH risk of 8.02%. Congestive heart failure was the most common PH. PHs imposed a total economic burden of $84 billion at an average of $7,449 per PH. Higher primary care safety net availability was significantly associated with the lower risk of PHs in the final risk model, but only in the uninsured. A unit increase in safety net availability led to a 23% decline in PH odds in the uninsured, compared to only a 4% decline in the insured. Higher primary care physician availability was associated with increased PH costs in the final cost model (β=0.0020; p<0.05). Lack of health insurance coverage increased the risk of PH, with the uninsured having 30% higher odds of PHs (OR=1.299; p<0.05), but reduced the cost of a PH by 7% (β=-0.0668; p<0.05). Expansions in primary care availability and health insurance coverage were associated with a reduction of about $1.6 million in PH burden at the highest level of expansion. Conclusions. Availability of primary care resources and health insurance coverage in hospitalized non-elderly adults in Harris County are significantly associated with the risk and costs of PHs. Expansions in these primary care access factors can be expected to produce significant reductions in the burden of PHs in Harris County.^

Adaptive clinical trial design for targeted therapy development

The development of targeted therapy involve many challenges. Our study will address some of the key issues involved in biomarker identification and clinical trial design. In our study, we propose two biomarker selection methods, and then apply them in two different clinical trial designs for targeted therapy development. In particular, we propose a Bayesian two-step lasso procedure for biomarker selection in the proportional hazards model in Chapter 2. In the first step of this strategy, we use the Bayesian group lasso to identify the important marker groups, wherein each group contains the main effect of a single marker and its interactions with treatments. In the second step, we zoom in to select each individual marker and the interactions between markers and treatments in order to identify prognostic or predictive markers using the Bayesian adaptive lasso. In Chapter 3, we propose a Bayesian two-stage adaptive design for targeted therapy development while implementing the variable selection method given in Chapter 2. In Chapter 4, we proposed an alternate frequentist adaptive randomization strategy for situations where a large number of biomarkers need to be incorporated in the study design. We also propose a new adaptive randomization rule, which takes into account the variations associated with the point estimates of survival times. In all of our designs, we seek to identify the key markers that are either prognostic or predictive with respect to treatment. We are going to use extensive simulation to evaluate the operating characteristics of our methods.^

Binding of the HIV-1 gp120 -V3 to cellular glycosphingolipids is necessary for CXCR4 recruitment and infection

Infection by human immunodeficiency virus type 1 (HIV-1) is a multi-step process, and detailed analyses of the various events critical for productive infection are necessary to clearly understanding the infection process and identifying novel targets for therapeutic interventions. Evidence from this study reveals binding of the viral envelope protein to host cell glycosphingolipids (GSLs) as a novel event necessary for the orderly progression of the host cell-entry and productive infection by HIV-1. Data obtained from co-immunoprecipitation analyses and confocal microscopy showed that the ability of viral envelope to interact with the co-receptor CXCR4 and productive infection of HIV-1 were inhibited in cells rendered GSL-deficient, while both these activities were restored after reconstitution of the cells with specific GSLs like GM3. Furthermore, evidence was obtained using peptide-inhibitors of HIV-1 infection to show that binding of a specific region within the V3-loop of the envelope protein gp120 to the host cell GSLs is the trigger necessary for the CD4-bound gp120 to recruit the CXCR4 co-receptor. Infection-inhibitory activity of the V3 peptides was compromised in GSL-deficient cells, but could be restored by reconstitution of GSLs. Based on these findings, a revised model for HIV-1 infection is proposed that accounts for the established interactions between the viral envelope and host cell receptors while enumerating the importance of the new findings that fill the gap in the current knowledge of the sequential events for the HIV-1 entry. According to this model, post-CD4 binding of the HIV-1 envelope surface protein gp120 to host cell GSLs, mediated by the gp120-V3 region, enables formation of the gp120-CD4-GSL-CXCR4 immune-complex and productive infection. The identification of cellular GSLs as an additional class of co-factors necessary for HIV-1 infection is important for enhancing the basic knowledge of the HIV-1 entry that can be exploited for developing novel antiviral therapeutic strategies. ^

Stable isotope analysis and temperature reconstruction data from DSDP Hole 94-609B and ODP Hole 162-984B

The Greenland ice sheet is accepted as a key factor controlling the Quaternary glacial scenario. However, the origin and mechanisms of major Arctic glaciation starting at 3.15 Ma and culminating at 2.74 Ma are still controversial. For this phase of intense cooling Ravelo et al. proposed a complex gradual forcing mechanism. In contrast, our new submillennial-scale paleoceanographic records from the Pliocene North Atlantic suggest a far more precise timing and forcing for the initiation of northern hemisphere glaciation (NHG), since it was linked to a 2-3 °C surface water warming during warm stages from 2.95 to 2.82 Ma. These records support previous models, claiming that the final closure of the Panama Isthmus (3.0- ~2.5 Ma induced an increased poleward salt and heat transport. Associated strengthening of North Atlantic Thermohaline Circulation and in turn, an intensified moisture supply to northern high latitudes resulted in the build-up of NHG, finally culminating in the great, irreversible climate crash at marine isotope stage G6 (2.74 Ma). In summary, there was a two-step threshold mechanism that marked the onset of NHG with glacial-to-interglacial cycles quasi-persistent until today.

Late Miocene-early Pliocene stable isotope record of benthic foraminifera from ODP Site 177-1088 in the sub-Antarctic South Atlantic

Benthic foraminiferal stable isotope records for the past 11 Myr from a recently drilled site in the sub-Antarctic South Atlantic (Site 1088, Ocean Drilling Program Leg 177, 41°S, 15°E, 2082 m water depth) provide, for the first time, a continuous long-term perspective on deep water distribution patterns and Southern Ocean climate change from the late Miocene through the early Pliocene. I have compiled published late Miocene through Pliocene stable isotope records to place the new South Atlantic record in a global framework. Carbon isotope gradients between the North Atlantic, South Atlantic, and Pacific indicate that a nutrient-depleted watermass, probably of North Atlantic origin, reached the sub-Antarctic South Atlantic after 6.6 Ma. By 6.0 Ma the relative proportion of the northern-provenance watermass was similar to today and by the early Pliocene it had increased to greater than the modern proportion suggesting that thermohaline overturn in the Atlantic was relatively strong prior to the early Pliocene interval of inferred climatic warmth. Site 1088 oxygen isotope values display a two-step increase between ~7.4 Ma and 6.9 Ma, a trend that parallels a published delta18O record of a site on the Atlantic coast of Morocco. This is perhaps best explained by a gradual cooling of watermasses that were sinking in the Southern Ocean. I speculate that relatively strong thermohaline overturn at rates comparable to the present day interglacial interval during the latest Miocene may have provided the initial conditions for early Pliocene climatic warmth. The impact of an emerging Central American Seaway on Atlantic-Pacific Ocean upper water exchange may have been felt in the North Atlantic beginning in the latest Miocene between 6.6 and 6.0 Ma, which would be ~1.5 Myr earlier than previously thought.

Classification of coral reef types in Torres Strait (GIS files in zip-archive 319 kB)

Coral reefs represent major accumulations of calcium carbonate (CaCO3). The particularly labyrinthine network of reefs in Torres Strait, north of the Great Barrier Reef (GBR), has been examined in order to estimate their gross CaCO3 productivity. The approach involved a two-step procedure, first characterising and classifying the morphology of reefs based on a classification scheme widely employed on the GBR and then estimating gross CaCO3 productivity rates across the region using a regional census-based approach. This was undertaken by independently verifying published rates of coral reef community gross production for use in Torres Strait, based on site-specific ecological and morphological data. A total of 606 reef platforms were mapped and classified using classification trees. Despite the complexity of the maze of reefs in Torres Strait, there are broad morphological similarities with reefs in the GBR. The spatial distribution and dimensions of reef types across both regions are underpinned by similar geological processes, sea-level history in the Holocene and exposure to the same wind/wave energetic regime, resulting in comparable geomorphic zonation. However, the presence of strong tidal currents flowing through Torres Strait and the relatively shallow and narrow dimensions of the shelf exert a control on local morphology and spatial distribution of the reef platforms. A total amount of 8.7 million tonnes of CaCO3 per year, at an average rate of 3.7 kg CaCO3 m-2 yr-1 (G), were estimated for the studied area. Extrapolated production rates based on detailed and regional census-based approaches for geomorphic zones across Torres Strait were comparable to those reported elsewhere, particularly values for the GBR based on alkalinity-reduction methods. However, differences in mapping methodologies and the impact of reduced calcification due to global trends in coral reef ecological decline and changing oceanic physical conditions warrant further research. The novel method proposed in this study to characterise the geomorphology of reef types based on classification trees provides an objective and repeatable data-driven approach that combined with regional census-based approaches has the potential to be adapted and transferred to different coral reef regions, depicting a more accurate picture of interactions between reef ecology and geomorphology.

Cenozoic oxygen isotopic values for benthic foraminifera from DSDP and ODP low and high latitude marine sediment cores

The climate during the Cenozoic era changed in several steps from ice-free poles and warm conditions to ice-covered poles and cold conditions. Since the 1950s, a body of information on ice volume and temperature changes has been built up predominantly on the basis of measurements of the oxygen isotopic composition of shells of benthic foraminifera collected from marine sediment cores. The statistical methodology of time series analysis has also evolved, allowing more information to be extracted from these records. Here we provide a comprehensive view of Cenozoic climate evolution by means of a coherent and systematic application of time series analytical tools to each record from a compilation spanning the interval from 4 to 61 Myr ago. We quantitatively describe several prominent features of the oxygen isotope record, taking into account the various sources of uncertainty (including measurement, proxy noise, and dating errors). The estimated transition times and amplitudes allow us to assess causal climatological-tectonic influences on the following known features of the Cenozoic oxygen isotopic record: Paleocene-Eocene Thermal Maximum, Eocene-Oligocene Transition, Oligocene-Miocene Boundary, and the Middle Miocene Climate Optimum. We further describe and causally interpret the following features: Paleocene-Eocene warming trend, the two-step, long-term Eocene cooling, and the changes within the most recent interval (Miocene-Pliocene). We review the scope and methods of constructing Cenozoic stacks of benthic oxygen isotope records and present two new latitudinal stacks, which capture besides global ice volume also bottom water temperatures at low (less than 30°) and high latitudes. This review concludes with an identification of future directions for data collection, statistical method development, and climate modeling.

Miocene planktonic foraminifera of ODP Hole 130-806B

We document the waxing and waning of a "proto-warm pool" in the western equatorial Pacific (WEP) based on a study of multi-species planktic foraminiferal isotope ratios and census data spanning the 13.2-5.8 Ma interval at ODP Site 806. We hypothesize that the presence or absence of a proto-warm pool in the WEP, caused by the progressive tectonic constriction of the Indonesian Seaway and modulated by sea level fluctuations, created El Niño/La Niña-like alternations of hydrographic conditions across the equatorial Pacific during the late Miocene. This hypothesis is supported by the general antithetical relationship observed between carbonate productivity and preservation in the western and eastern equatorial Pacific, which we propose is caused by these alternating ocean-climate states. Warming of thermocline and surface waters, as well as a major change in planktic foraminferal assemblages record a two-step phase of proto-warm pool development ~11.6-10 Ma, which coincides with Miocene isotope events Mi5 and Mi6, and sea-level low stands. We suggest that these changes in the biota and structure of the upper water column in the WEP mark the initiation of a more modern equatorial current system, including the development of the Equatorial Undercurrent (EUC), as La Niña-like conditions became established across the tropical Pacific. This situation sustained carbonate and silica productivity in the eastern equatorial Pacific (EEP) at a time when carbonate preservation sharply declined in the Caribbean. Proto-warm pool weakening after ~10 Ma may have contributed to the nadir of a similar "carbonate crash" in the EEP. Cooling of the thermocline and increased abundances of thermocline taxa herald the decay of the proto-warm pool and higher productivity in the WEP, particularly ~ 9.0-8.8 Ma coincident with a major perturbation in tropical nannofossil assemblages. We suggest that this interval of increased productivity records El Niño-like conditions across the tropical Pacific and the initial phase of the widespread "biogenic bloom". Resurgence of a later proto-warm pool in the WEP ~6.5-6.1 Ma may have spurred renewed La Niña-like conditions, which contributed to a strong late phase of the "biogenic bloom" in the EEP.

Palynological and geochemical data of sediment core GeoB3910-2 located offshore Northeast Brazil

High resolution palynological and geochemical data of sediment core GeoB 3910-2 (located offshore Northeast Brazil) spanning the period between 19 600 and 14 500 calibrated year bp (19.6-14.5 ka) show a land-cover change in the catchment area of local rivers in two steps related to changes in precipitation associated with Heinrich Event 1 (H1 stadial). At the end of the last glacial maximum, the landscape in semi-arid Northeast Brazil was dominated by a very dry type of caatinga vegetation, mainly composed of grasslands with some herbs and shrubs. After 18 ka, considerably more humid conditions are suggested by changes in the vegetation and by Corg and C/N data indicative of fluvial erosion. The caatinga became wetter and along lakes and rivers, sedges and gallery forest expanded. The most humid period was recorded between 16.5 and 15 ka, when humid gallery (and floodplain) forest and even small patches of mountainous Atlantic rain forest occurred together with dry forest, the latter being considered as a rather lush type of caatinga vegetation. During this humid phase erosion decreased as less lithogenic material and more organic terrestrial material were deposited on the continental slope of northern Brazil. After 15 ka arid conditions returned. During the humid second phase of the H1 stadial, a rich variety of landscapes existed in Northeast Brazil and during the drier periods small pockets of forest could probably survive in favorable spots, which would have increased the resilience of the forest to climate change.

Stable oxygen isotope record and abundances of Globorotalia menardii in sediments from the tropical Atlantic Ocean

Eight box cores from the tropical Atlantic were studied in detail with regard to foraminiferal oxygen isotopes, radiocarbon, and Globorotalia menardii abundance. A standard Atlantic oxygen-isotope signal was reconstructed for the last 20,000 yr. It is quite similar to the west-equatorial Pacific signal published previously. Deglaciation is seen to occur in two steps which are separated by a pause. Onset of deglaciation is after 15,000 yr B.P. The pause is centered between 11,000 and 12,000 yr B.P., but may be correlative with the Younger Dryas (10,500 yr B.P.) if allowance is made for a scale shift due to mixing processes on the sea floor. Step 2 is centered near 10,000 yr B.P. and is followed by a brief excursion toward light oxygen values. This excursion (the M event) may correlate with the Gulf of Mexico meltwater spike.

Miocene to Quaternary paleoenvironments and uplift history on the mid Norwegian shelf

Based on benthic and planktic foraminifera, Bolboforma, oxygen isotope measurements and seismic data, major changes in Miocene, Pliocene and Pleistocene paleoenvironments on the mid Norwegian shelf are discussed and a possible scenario of the late Cenozoic uplift history is given. The dating of the Neogene sequence has been done using foraminifera and Bolboforma. Four main assemblage zones have been identified with nine distinct subzones. Most of the Miocene sequence is preserved. The lower Miocene sediments contain only siliceous microfossils. A period of high fertility and upwelling in the study area prevailed. The early Miocene-early mid Miocene (15 Ma?) change from a siliceous to a calcareous rich microfauna, dominated by Nonion barleeanum, can be related to increased surface-water circulation due to overflow across the Iceland-Faeroe ridge. During the Miocene the temperature decreased in the study area. Evidence of increased amounts of coarser sediments may suggest that an uplift of the mainland areas occurred during the mid-late Miocene. Lower Pliocene sediments contain a foraminiferal fauna that seems to occur in slightly colder conditions than the late Miocene fauna suggesting a further cooling. Possibly, Arctic waters entered the study area in the early Pliocene. A very marked change in lithology (from compacted claystone to unconsolidated diamicton), fauna (from deep dwelling to shallow dwelling species) and seismic signature (from flat lying reflectors to prograding clinoforms) occurs during the mid?-late Pliocene. A two step cooling trend is indicated by the microfauna of these prograding wedges. (1) The first wedge buildups might have been associated with an uplift of the mainland during the early late Pliocene (mid Pliocene, ca. 4 Ma). However, the age determination is somewhat uncertain and may very well be of late Pliocene age. (2) The second step of wedge buildup is associated with a glacial phase where the dominating microfauna exists of arctic species. Large continental ice sheets might have occurred at this time reaching coastal areas and that possibly many of the geomorphological features such as the strandflat were made during this episode. The Pleistocene epoch is represented by an increased percentage of boreal foraminifera intermingled with high arctic species which indicates that interglacial-glacial cycles prevailed and the dynamics of the glacier system changed.

Foraminiferal Mg/Ca and Mn/Ca ratios across the Eocene-Oligocene transition

Constraining the magnitude of high-latitude temperature change across the Eocene-Oligocene transition (EOT) is essential for quantifying the magnitude of Antarctic ice-sheet expansion and understanding regional climate response to this event. To this end, we constructed high-resolution stable oxygen isotope (d18O) and magnesium/calcium (Mg/Ca) records from planktic and benthic foraminifera at four Ocean Drilling Program (ODP) sites in the Southern Ocean. Planktic foraminiferal Mg/Ca records from the Kerguelen Plateau (ODP Sites 738, 744, and 748) show a consistent pattern of temperature change, indicating 2-3 °C cooling in direct conjunction with the first step of a two-step increase in benthic and planktic foraminiferal d18O values across the EOT. In contrast, benthic Mg/Ca records from Maud Rise (ODP Site 689) and the Kerguelen Plateau (ODP Site 748) do not exhibit significant temperature change. The contrasting temperature histories derived from the planktic and benthic Mg/Ca records are not reconcilable, since vertical d18O gradients remained nearly constant at all sites between 35.0 and 32.5 Ma. Based on the coherency of the planktic Mg/Ca records from the Kerguelen Plateau sites and complications with benthic Mg/Ca paleothermometry at low temperatures, the planktic Mg/Ca records are deemed the most reliable measure of Southern Ocean temperature change. We therefore interpret a uniform cooling of 2-3 °C in both deep surface (thermocline) waters and intermediate deep waters of the Southern Ocean across the EOT. Cooling of Southern Ocean surface waters across the EOT was likely propagated to the deep ocean, since deep waters were primarily sourced on the Antarctic margin throughout this time interval. Removal of the temperature component from the observed foraminiferal d18O shift indicates that seawater d18O values increased by 0.6 ± 0.15 per mil across the EOT interval, corresponding to an increase in global ice volume to a level equivalent with 60-130% modern East Antarctic ice sheet volume.