LOCAL AND GLOBAL GENE REGULATION ANALYSIS OF THE AUTOINDUCER-2 MEDIATED QUORUM SENSING MECHANISM IN ESCHERICHIA COLI

The term `quorum sensing' (QS) is used to define a population density based communication mechanism which uses chemical signal molecules called autoinducers to trigger unique and varied changes in gene expression. Although several communication methods have been identified in bacteria that are unique to a particular species, one type of signal molecule, autoinducer-2 (AI-2) is linked to interspecies communication, indicating its potential as a universal signal for cueing a QS response among multiple bacterial types. In E. coli, AI-2 acts as an effector by binding to the QS repressor LsrR. As a result, LsrR unbinds and relieves repression of the lsr regulon, stimulating a subsequent QS gene expression cascade. In this dissertation, LsrR structure and in vitro binding activity are examined. Genomic binding and DNA microarray analyses are conducted and three novel sites putatively regulated by LsrR, yegE-udk, mppA and yihF, are revealed. Two cAMP receptor protein (CRP) binding locations in intergenic region of the lsr regulon are also confirmed. The role of each CRP site in divergent expression is qualified, indicating the lsr intergenic region to be a class III CRP-dependent promoter. Also, four specific DNA binding sites for LsrR in the lsr intergenic region are proposed, and reliance upon simultaneous binding to these various sites and the resulting effects on LsrR repression is presented. Finally, a complex model for regulation of the lsr regulon is depicted incorporating LsrR, CRP, DNA looping, and a predicted secondary layer of repression by an integration host factor (IHF)-like protein. Further understanding of this QS genetic mechanism may potentially be used for inhibiting bacterial proliferation and infection, modifying the natural genetic system to elicit alternate desired responses, or extracted and applied to a highly customizable and sensitive in vitro biosensor

A Simple Complete Search for Logic Programming

Here, we present a family of complete interleaving depth-first search strategies for embedded, domain-specific logic languages. We derive our search family from a stream-based implementation of incomplete depth-first search. The DSL\u27s programs\u27 texts induce particular strategies guaranteed to be complete

Evidence for phenotypic bistability resulting from transcriptional interference of bvgAS in Bordetella bronchiseptica: Phenotypic bistability inBordetella

Bordetella species cause respiratory infections in mammals. Their master regulatory system BvgAS controls expression of at least three distinct phenotypic phases in response to environmental cues. The Bvg+ phase is necessary and sufficient for respiratory infection while the Bvg− phase is required for survival ex vivo. We obtained large colony variants (LCVs) from the lungs of mice infected with B. bronchiseptica strain RBX9, which contains an in-frame deletion mutation in fhaB, encoding filamentous hemagglutinin. RBX9 also yielded LCVs when switched from Bvg− phase conditions to Bvg+ phase conditions in vitro. We determined that LCVs are composed of both Bvg+ and Bvg− phase bacteria and that they result from defective bvgAS positive autoregulation. The LCV phenotype was linked to the presence of a divergent promoter 5′ to bvgAS, suggesting a previously undescribed mechanism of transcriptional interference that, in this case, leads to feedback-based bistability (FBM). Our results also indicate that a small proportion of RBX9 bacteria modulates to the Bvg− phase in vivo. In addition to providing insight into transcriptional interference and FBM, our data provide an example of an in-frame deletion mutation exerting a ‘polar’ effect on nearby genes

Tribal consultation and collaborative governance: environmental and cultural justice through the lens of the National Environmental Policy Act (1969) and the National Historic Preservation Act (1966)

Presented at the Environmental justice in the Anthropocene symposium held on April 24-25, 2017 at the Lory Student Center, Colorado State University, Fort Collins Colorado. This symposium aims to bring together academics (faculty and graduate students), independent researchers, community and movement activists, and regulatory and policy practitioners from across disciplines, research areas, perspectives, and different countries. Our overarching goal is to build on several decades of EJ research and practice to address the seemingly intractable environmental and ecological problems of this unfolding era. How can we explore EJ amongst humans and between nature and humans, within and across generations, in an age when humans dominate the landscape? How can we better understand collective human dominance without obscuring continuing power differentials and inequities within and between human societies? What institutional and governance innovations can we adopt to address existing challenges and to promote just transitions and futures

One: but not the same

Ordinary judgments about personal identity are complicated by the fact that phrases like “same person” and “different person” have multiple uses in ordinary English. This complication calls into question the significance of recent experimental work on this topic. For example, Tobia (2015) found that judgments of personal identity were significantly affected by whether the moral change described in a vignette was for the better or for the worse, while Strohminger and Nichols (2014) found that loss of moral conscience had more of an effect on identity judgments than loss of biographical memory. In each case, however, there are grounds for questioning whether the judgments elicited in these experiments engaged a concept of numerical personal identity at all (cf. Berniūnas and Dranseika 2016; Dranseika 2017; Starmans and Bloom 2018). In two pre-registered studies we validate this criticism while also showing a way to address it: instead of attempting to engage the concept of numerical identity through specialized language or the terms of an imaginary philosophical debate, we should consider instead how the identity of a person is described through the connected use of proper names, definite descriptions, and the personal pronouns “I”, “you”, “he”, and “she”. When the experiments above are revisited in this way, there is no evidence that the differences in question had an effect on ordinary identity judgments

Barriers to HIV Care for Women of Color Living in the Southeastern US Are Associated with Physical Symptoms, Social Environment, and Self-Determination

HIV-infected women of color (WOC) face particular barriers to accessing HIV medical care. To understand the impact of physical symptoms, social support, and self-determination on barriers to care, we interviewed HIV-infected women of color. HIV-infected WOC (N=141), attending an academic infectious disease clinic for HIV care in North Carolina, completed the Barriers to Care scale and were categorized as reporting a history of low (less than four of eleven barriers) or high (five or more) barriers to care. Binomial regression was used to estimate prevalence ratios and risk differences of reported barriers to care and its correlates such as depression, anxiety, illness-severity, psychological abuse, social support, treatment-specific social support, and self-determination (autonomy, relatedness, competency). A lower risk of reporting five or more barriers to care was associated with higher levels of autonomy (PR=0.93, 95% CI: 0.89, 0.96), relatedness (PR=0.92, 95% CI: 0.89, 0.94), competency (PR=0.93, 95% CI: 0.87, 0.98), and social support (PR=0.24, 95% CI: 0.81, 0.81). Depression, illness severity, and psychological abuse were associated with a greater risk of having five or more barriers to care. There are multiple social and psychological factors that contribute to perceived barriers to HIV care among WOC in the southeastern USA. Interventions that promote social support and increase individual self-determination have the potential to improve access to HIV care for WOC

Implementing NASA's Capability-Driven Approach: Insight into NASA's Processes for Maturing Exploration Systems

NASA is engaged in transforming human spaceflight. The Agency is shifting from an exploration-based program with human activities focused on low Earth orbit (LEO) and targeted robotic missions in deep space to a more sustainable and integrated pioneering approach. Through pioneering, NASA seeks to address national goals to develop the capacity for people to work, learn, operate, live, and thrive safely beyond the Earth for extended periods of time. However, pioneering space involves more than the daunting technical challenges of transportation, maintaining health, and enabling crew productivity for long durations in remote, hostile, and alien environments. This shift also requires a change in operating processes for NASA. The Agency can no longer afford to engineer systems for specific missions and destinations and instead must focus on common capabilities that enable a range of destinations and missions. NASA has codified a capability driven approach, which provides flexible guidance for the development and maturation of common capabilities necessary for human pioneers beyond LEO. This approach has been included in NASA policy and is captured in the Agency's strategic goals. It is currently being implemented across NASA's centers and programs. Throughout 2014, NASA engaged in an Agency-wide process to define and refine exploration-related capabilities and associated gaps, focusing only on those that are critical for human exploration beyond LEO. NASA identified 12 common capabilities ranging from Environmental Control and Life Support Systems to Robotics, and established Agency-wide teams or working groups comprised of subject matter experts that are responsible for the maturation of these exploration capabilities. These teams, called the System Maturation Teams (SMTs) help formulate, guide and resolve performance gaps associated with the identified exploration capabilities. The SMTs are defining performance parameters and goals for each of the 12 capabilities, developing maturation plans and roadmaps for the identified performance gaps, specifying the interfaces between the various capabilities, and ensuring that the capabilities mature and integrate to enable future pioneering missions. By managing system development through the SMTs instead of traditional NASA programs and projects, the Agency is shifting from mission-driven development to a more flexible, capability-driven development. The process NASA uses to establish, integrate, prioritize, and manage the SMTs and associated capabilities is iterative. NASA relies on the Human Exploration and Operation Mission Directorate's SMT Integration Team within Advanced Exploration Systems to coordinate and facilitate the SMT process. The SMT Integration team conducts regular reviews and coordination meetings among the SMTs and has developed a number of tools to help the Agency implement capability driven processes. The SMT Integration team is uniquely positioned to help the Agency coordinate the SMTs and other processes that are making the capability-driven approach a reality. This paper will introduce the SMTs and the 12 key capabilities they represent. The role of the SMTs will be discussed with respect to Agency-wide processes to shift from mission-focused exploration to a capability-driven pioneering approach. Specific examples will be given to highlight systems development and testing within the SMTs. These examples will also show how NASA is using current investments in the International Space Station and future investments to develop and demonstrate capabilities. The paper will conclude by describing next steps and a process for soliciting feedback from the space exploration community to refine NASA's process for developing common exploration capabilities

Functional Characterization of Burkholderia pseudomallei Trimeric Autotransporters

ABSTRACT Burkholderia pseudomallei is a tier 1 select agent and the causative agent of melioidosis, a severe and often fatal disease with symptoms ranging from acute pneumonia and septic shock to a chronic infection characterized by abscess formation in the lungs, liver, and spleen. Autotransporters (ATs) are exoproteins belonging to the type V secretion system family, with many playing roles in pathogenesis. The genome of B. pseudomallei strain 1026b encodes nine putative trimeric AT proteins, of which only four have been described. Using a bioinformatic approach, we annotated putative domains within each trimeric AT protein, excluding the well-studied BimA protein, and found short repeated sequences unique to Burkholderia species, as well as an unexpectedly large proportion of ATs with extended signal peptide regions (ESPRs). To characterize the role of trimeric ATs in pathogenesis, we constructed disruption or deletion mutations in each of eight AT-encoding genes and evaluated the resulting strains for adherence to, invasion of, and plaque formation in A549 cells. The majority of the ATs (and/or the proteins encoded downstream) contributed to adherence to and efficient invasion of A549 cells. Using a BALB/c mouse model of infection, we determined the contributions of each AT to bacterial burdens in the lungs, liver, and spleen. At 48 h postinoculation, only one strain, Bp340::pD bpaC , demonstrated a defect in dissemination and/or survival in the liver, indicating that BpaC is required for wild-type virulence in this model

Select Metal and Metalloid Surveillance of Free-ranging Eastern Box Turtles from Illinois and Tennessee

The Eastern box turtle has been proposed as a biomonitor because it is long lived, relies on the environment for food and water, and has a small home range. To establish this designation, ISTC partnered with the Illinois Natural History Survey, the College of Veterinary Medicine at the University of Illinois, and the Clinch River Environmental Studies Organization. Plasma samples from 273 free-range box turtles were collected in 2011 and 2012 in Tennessee and Illinois. Full results reported in Allender, Matthew C., et al (2015). "Select metal and metalloid surveillance of free-ranging Eastern box turtles from Illinois and Tennessee (Terrapene carolina carolina)." Ecotoxicology 24, 1269–1278. https://doi.org/10.1007/s10646-015-1498-5Ope

Comparison of Image Registration Based Measures of Regional Lung Ventilation from Dynamic Spiral CT with Xe-CT

Purpose: Regional lung volume change as a function of lung inflation serves as an index of parenchymal and airway status as well as an index of regional ventilation and can be used to detect pathologic changes over time. In this article, we propose a new regional measure of lung mechanics --- the specific air volume change by corrected Jacobian. Methods: 4DCT and Xe-CT data sets from four adult sheep are used in this study. Nonlinear, 3D image registration is applied to register an image acquired near end inspiration to an image acquired near end expiration. Approximately 200 annotated anatomical points are used as landmarks to evaluate registration accuracy. Three different registration-based measures of regional lung mechanics are derived and compared: the specific air volume change calculated from the Jacobian (SAJ); the specific air volume change calculated by the corrected Jacobian (SACJ); and the specific air volume change by intensity change (SAI). Results: After registration, the mean registration error is on the order of 1 mm. For cubical ROIs in cubes with size 20 mm $\times$ 20 mm $\times$ 20 mm, the SAJ and SACJ measures show significantly higher correlation (linear regression, average $r^2=0.75$ and $r^2=0.82$) with the Xe-CT based measure of specific ventilation (sV) than the SAI measure. For ROIs in slabs along the ventral-dorsal vertical direction with size of 150 mm $\times$ 8 mm $\times$ 40 mm, the SAJ, SACJ, and SAI all show high correlation (linear regression, average $r^2=0.88$, $r^2=0.92$ and $r^2=0.87$) with the Xe-CT based sV without significant differences when comparing between the three methods. Conclusion: Given a deformation field by an image registration algorithm, significant differences between the SAJ, SACJ, and SAI measures were found at a regional level compared to the Xe-CT sV in four sheep that were studied