Cell Surface Adhesins, Exopolysaccharides and the Por (Type Ix) Secretion System of Flavobacterium Johnsoniae

Flavobacterium johnsoniae, a member of the phylum Bacteroidetes, crawls rapidly over surfaces. Cell movement is thought to result from the action of the gliding motor, composed of Gld proteins, on the cell-surface adhesin SprB. Cells lacking SprB are partially defective in motility. Transposon mutagenesis of an sprB mutant resulted in the identification of remA, which encodes a motility adhesin that is partially redundant with SprB. Cells lacking SprB and RemA had more severe motility defects than did cells lacking just SprB. RemA moves on the cell-surface with a speed of 1 to 2 micrometer per sec, similar to SprB. RemA contains a lectin domain that enables it to interact with exopolysaccharides secreted by the cells. RemA-exopolysaccharide interaction resulted in the formation of cell-aggregates. Cells lacking polysaccharide biosynthesis and transport proteins RemC, Wza and Wzc failed to form aggreagates. It appears that as cells move, they pave their own `roads\u27 with exopolysaccharide. Mobile cell-surface adhesins like RemA adhere to these `roads\u27 and help in motility of the cell. Recent results suggest that some proteins required for gliding are components of a novel protein secretion system, the Type IX Bacterial Protein Secretion System (T9SS). The T9SS was initially called the Por Secretion System. T9SSs are found in all gliding bacteroidetes, and in many nongliding bacteroidetes, such as the periodontal pathogen Porphyromonas gingivalis, but they are apparently not found outside of the phylum Bacteroidetes. GldN, SprE, and SprT were previously shown to be components of the F. johnsoniae T9SS. Here we show that GldK, GldL, GldM, and SprA, are also components of this secretion system. The F. johnsoniae T9SS is required for secretion of SprB and RemA, and is thus needed for motility. Other proteins required for F. johnsoniae gliding, such as GldA, GldF, GldG (which form an ABC transporter complex), and GldB, GldD, GldH, GldI, and GldJ, may interact with the T9SS. Mutations in the genes encoding any of these proteins resulted in apparent instability of the T9SS protein GldK, and thus loss of T9SS function. The gliding motility proteins and the T9SS of F. johnsoniae appear to be intertwined. Strains that produced truncated GldJ proteins were isolated that had normal T9SS function but were defective in motility. Further analysis of these strains may enable us to untangle gliding motility from protein secretion

Three Essays on Investor Reaction to Strategic Alliance Announcements

ABSTRACT ESSAY 1 RAPID OVER-REACTION: PERCEIVED VALUE CREATION VIA ALLIANCE ANNOUNCEMENTS The management literature has widely acknowledged the importance of studying and understanding the determinants of the market\u27s reactions to the announcements of strategic alliances. With a focus on dyadic alliances, I ask what types of information signaled to the market by the alliance announcement influence the investors\u27 perception of value. I hypothesize that the type of technical expertise, relationship expertise, and market expertise of each alliance partner, expressed as either explorative or exploitative, sends decodable signals to the investors, which in turn influences their reaction to the new alliance announcement. Using a sample of 927 alliances extracted from a unique biopharmaceutical dataset, I proxied investors\u27 reaction to the alliance announcements by calculating the cumulative abnormal return during a three-day window around the alliance announcement. I found that while technical expertise does not appear to be a signal that investors consider when valuing firms involved in a new alliance, both relationship expertise and market expertise showed a statistically significant influence on the investors\u27 perception of value. ABSTRACT ESSAY 2: REDUCING INVESTOR ANXIETY VIA ALLIANCE PARTNER SELECTION The management literature has recognized strategic alliances as an organizational form that has the potential to reduce uncertainty. One important step for alliances in order to achieve a reduction in uncertainty is selecting the right partner, one that enables the alliance to effectively address the specific type of uncertainty it faces. In this study, I specifically address the question of whether the perceived uncertainty of investors at the time of the alliance announcement is influenced by whether the skills and expertise of the two alliance partners are similar or complementary (diverse). I suggest that the level of technical expertise, expressed as either explorative or exploitative and interpreted as either similar or complementary, sends a signal to the investors, which in turn will impact their perception of uncertainty. In addition, I study whether this relationship is moderated by the level of exogenous uncertainty faced by the alliance. Using a sample of 927 alliances extracted from a unique biopharmaceutical dataset, I found that exogenous uncertainty in fact moderates the relationship between partner similarity/ complementarity and investors\u27 perception of uncertainty. ABSTRACT ESSAY 3: SPILLOVER EFFECTS IN ALLIANCE RELATIONSHIPS Entering multiple simultaneous alliances is a common practice, especially in R&D intense industries. While this strategy may enhance the possibility of success by attempting to simultaneously unlock possible synergistic effects in multiple alliances, it also exposes the alliance partners to spillover effects created by their partners\u27 alliances. In this study I will examine how one specific action of one partner, to enter a new alliance, affects the initial alliance partner. Specifically, given that firm A and firm B are in an existing alliance, how will the market react to the information that firm A has entered into a new alliance with firm C, and how will the market reaction affect firm B (the initial alliance partner)? I develop and test two sets of competing hypotheses using a unique biopharmaceutical dataset and find that the market reacts favorably to the new alliance as measured by the change in value of firm B\u27s stock price. My goal is to contribute to the literature by testing how the signals sent by the alliance to the market affect the initial alliance partner and thus if investors monitor and react to post-alliance events

The Shifting Importance of Competition and Facilitation Along Diversity, Environmental Severity, and Plant Ontogenetic Gradients

Ecological theory and empirical studies have focused heavily on the importance of competition in plant communities. Competition can help explain species coexistence, the maintenance of species diversity, and biological invasions. Competition for resources appears to be ubiquitous among coexisting organisms. This overwhelming focus on competition over the past one hundred years may have overshadowed the importance of positive interactions (facilitation). Growing near your neighbors involves competition for resources, but it also involves alteration of a shared microclimate. Neighboring plants have the capacity to increase shade, decrease air temperatures, increase humidity, and increase shallow soil moisture in their local environment. In severe environments - tundra, deserts, salt marshes - facilitation can outweigh the effects of competition. In periods of environmental severity, these benefits can prove essential. In this dissertation, I explore the importance of both competitive and facilitative interactions across gradients of environment severity, plant ontogeny, and productivity. I use an experimental manipulation of herbaceous plant diversity to manipulate the magnitude of competition and facilitation in a series of experiments in central Minnesota. I show that woody encroachment into grasslands is influenced by both competitive and facilitative interactions related to decreasing local species diversity and increasing atmospheric CO2 (Chapter 1). I show that diversity can ameliorate the microclimate to create local conditions that are cooler and more humid, and these effects can facilitate seedling growth and survival. I show that competition appears to increase as seedlings grow in size, but this size-structured change may be due more to decreasing facilitation rather than increasing competition (Chapter 2). Finally, plants may compete strongly for resources much of the time, but this can be outweighed by strong facilitation, and the interaction between the two processes can change on a day-to-day basis (Chapter 3). Finally, I use a modified Lotka-Volterra model to show how competition and facilitation may change as a function of environmental severity and productivity, and the implications of these relationships on individual plant performance and long-term community dynamics (Chapter 4). Nutrient availability, CO2 concentrations, seasonal temperatures and precipitation will likely change independently in future climate change scenarios. It is therefore essential that we have a comprehensive understanding of the positive and negative components that underlie plant interactions, to better predict how plant communities will change in the future

Perdurance and Personhood: A Reply to Burge

This essay is a response to the attack on reductionist and perdurantist views of persons which Tyler Burge presents in a paper entitled Memory and Perons . Burge\u27s arguments appeal to a specific form of egocentric indexing called de se form, which he suggests is involved in the individuation conditions of the mental states entailed in the exercise of the core psychological competencies of personhood (i.e. intentional agency, perception with use, inference). Burge argues that the preservation of states with de se form requires the possession of a veridical de se memory competency, which in turn requires transtemporal agent identity. Burge suggests that perdurantist views which convey the persistence of individual persons through time in terms of causal continuity between momentary selves cannot be made compatible with this view of the relation between memory and the core competencies, and that reductionist accounts which attempt to explain personal identity in terms of psychological continuity cannot avoid falling into explanatory circularity in any attempt to account for the core psychological competencies. My response comprises three major parts. First, I argue that Burge\u27s apparently endurantist interpretation of the transtemporal agent identity condition entailed in memory is indefensible, and that a perdurantist interpretation is available which is amenable to reductionist views. Second, I present an exploratory discussion which attempts to ascertain the extent to which egocentric indexing and its relation to memory are relevant to one of the core psychological competencies, intentional agency. I find that while some form of egocentric indexing is apparently necessary to adequately accounting for the exercise of intentional agency, it is not apparent - contrary to Burge\u27s claims - that such indexing need be considered to be partly individuated in terms of an endurantist conception of transtemporal agent identity. Finally, I present arguments from Sydney Shoemaker\u27s response to Burge which I suggest provide a way out of the difficulties occasioned for the reductionists by Burge\u27s arguments. Following Shoemaker, I conclude that Burge\u27s attack on reductionism fails because alternate forms of egocentric indexing are available to the reductionists which they may utilize to account for the core psychological competencies in a non-circular manner. I further suggest that the considerations adduced in favor of perdurantism provide support to the reductionist side of the anti-reductionst versus reductionist debate regarding persons

Investigating the Impact of Formal Reflective Activities on Skill Adaptation in a Work-Related Instrumental Learning Setting

In work-related, instrumental learning contexts the role of reflective activities is unclear. Kolb\u27s (1985) experiential learning theory and Mezirow\u27s transformative learning theory (2000) predict skill-adaptation as a possible outcome. This prediction was experimentally explored by manipulating reflective activities and assessing participants\u27 response and error rates when an instrumentally learned skill is applied in a novel way (skill-adaptation). Participants were randomly assigned to three conditions (interference, reflection, or critical reflection) using three blocking variables: (a) gender, (b) age, and (c) reflective propensity. Participants then completed a behavioral skills training program with embedded reflective activities. Afterwards, participants were asked to complete a novel application task. ANOVAs neither revealed: differences in response or error rates between reflective activity groups, even when accounting for reflective propensity, nor a significant interaction between reflective activity and reflective propensity on response rate. A significant interaction, however, was found between reflective activity and reflective propensity on error rate. In the critical reflection condition, non-reflective learners had higher error rates than reflective learners. Four conclusions based on these findings are offered, along with implications for teaching, practice, and research

Constructing Orthogonal Arrays on Non-abelian Groups

For an orthogonal array (or fractional factorial design) on k factors, Xu and Wu (2001) define the array\u27s generalized wordlength pattern (A1, ..., Ak), by relating a cyclic group to each factor. They prove the property that the array has strength t if and only if A1 = ... = At = 0. In their 2012 paper, Beder and Beder show that this result is independent of the group structure used. Non-abelian groups can be used if the assumption is made that the groups Gi are chosen so that the counting function O of the array is a class function on G. The aim of this thesis is to construct examples of orthogonal arrays on G = G1 x ... x Gk, where G is non-abelian, having two properties: given strength, and counting function O that is constant on the conjugacy classes of G

Evaluation of Vdr-coactivator Inhibitors Using Biochemical and Cell-based Assays

ABSTRACT EVALUATION OF VDR–COACTIVATOR INHIBITORS USING BIOCHEMICAL AND CELL–BASED ASSAYS by Athena Baranowski The University of Wisconsin–Milwaukee, 2013 Under the Supervision of Dr. Alexander Arnold The vitamin D receptor (VDR) is a ligand–dependent transcription factor, which belongs to the nuclear receptor superfamily. VDR–mediated gene regulation is governed by coregulators (coactivators and corepressors). VDR coregulator binding inhibitors (CBIs), which were discovered using high throughput screening (HTS), were evaluated using cell–based assays and biochemical assays to determine their ability to inhibit the interaction between VDR and steroid receptor coactivator–2 (SRC–2). Determining their ability to inhibit the VDR–SRC–2 interaction can lead to the development of novel and safer pharmaceutical treatments for VDR–related disorders, such as cancer, autoimmune diseases, and cardiovascular disease; therefore, the study of transcription, toxicity, and protein–protein interactions are critical to the development of pharmaceutical treatments. The methods used to study CBIs include a cell–based transcription assay, which was based on the formation of β–lactamase in the Hek 293T cell line. The readout of this assay was fluorescence resonance energy transfer (FRET) of a cell–permeable substrate in the event of transcription inhibition, and a blue fluorescent signal in the event of transcription activation. Active CBIs, such as compound WL052410G (31b), exhibit a reduced blue to green fluorescent ratio. A luciferase–based viability assay, which detected ATP levels from metabolically active Hek 293T cells, was used to determine the toxicity of the CBIs, in hopes of detecting partial toxicity for pharmaceutical targets of VDR, such as compound WL052410G (31b). Different co–immunoprecipitation pull–down assays were developed to precipitate and isolate target proteins, such as VDR, SRC–2, and SRC–2–3, using affinity–based tagging, in order to determine the ability of CBIs to disrupt the protein–protein interaction between VDR and SRC–2 coactivator. The VDR–SRC–2 interaction was visualized using a fluorescently tagged antibody, which was realized using a laser imager. The most active compounds for all the assays performed belong to a series of 3–indolyl–methanamines and include a highly selective and active compound, WL052410G (31b)

Development and Validation of a Mathematical Model for Predicting the Performance of Rotary Hammer Drills

Rotary hammer drills are specialized drills used by plumbers, electricians, and other construction trades to drill holes in concrete. This type of tool employs a mechanism driven by an electric motor to compress a column of air, generating an impact on a drill bit to break the concrete work piece. Rotary hammer development requires the ability to accurately predict tool performance to minimize the number of prototype iterations required during the design phase and ensure the tool delivers a satisfactory level of performance. In order to predict the performance of a rotary hammer drill, a mathematical model was developed to simulate the response of the tool under load, from the time the tool is activated until it achieves steady state. Inputs for this model were taken from physical tool dimensions, motor performance data, and FEA simulation of component impact events. Validation of the model was carried out by simulating the performance of a Milwaukee Electric Tool model 5262-20 rotary hammer and comparing the model outputs to actual performance data, measured following the European Power Tool Association test procedure 05/2009 - Measurement of single impact energy of rotary hammers and breakers

Extraction and Classification of Drug-Drug Interaction from Biomedical Text Using a Two-Stage Classifier

One of the critical causes of medical errors is Drug-Drug interaction (DDI), which occurs when one drug increases or decreases the effect of another drug. We propose a machine learning system to extract and classify drug-drug interactions from the biomedical literature, using the annotated corpus from the DDIExtraction-2013 shared task challenge. Our approach applies a two-stage classifier to handle the highly unbalanced class distribution in the corpus. The first stage is designed for binary classification of drug pairs as interacting or non-interacting, and the second stage for further classification of interacting pairs into one of four interacting types: advise, effect, mechanism, and int. To find the set of best features for classification, we explored many features, including stemmed words, bigrams, part of speech tags, verb lists, parse tree information, mutual information, and similarity measures, among others. As the system faced two different classification tasks, binary and multi-class, we also explored various classifiers in each stage. Our results show that the best performing classifier in both stages was Support Vector Machines, and the best performing features were 1000 top informative words and part of speech tags between two main drugs. We obtained an F-Measure of 0.64, showing a 12% improvement over our submitted system to the DDIExtraction 2013 competition

Nonresidential Parenting: Parental Roles and Parent/child Relationships

Nonresidential parents are defined as parents who do not live with one or more of their biological children all or most of the time. Using symbolic interactionism as a theoretical framework, this study considers nonresidential parenting from a communication perspective. 40 nonresidential parents (20 mothers and 20 fathers) were interviewed in order to explore how nonresidential parents conceptualize their parent roles, how these parents report enacting their parenting, and the communication challenges they experience within their relationships with their children. Inductive analysis resulted in the identification of eight nonresidential parent roles (limited role, active participant, nurturer, provider - tangible, teacher, sole parent, co-parent, and disciplinarian), 11 parenting behaviors (school involvement, spending time together, keeping in touch, assurances, providing - tangible, showing physical affection, supporting - emotional, disciplining, teaching, physical well-being - involvement, and co-parenting), and four main communication challenges (the residential parent, difficult topics, the children\u27s refusal to communicate, and limits of mediated communication). These results are described within the context of the pre-existing literature on nonresidential parenting and connections between categories and research questions are presented