Role of phosphatidylethanolamine in the function and assembly of phenylalanine-specific permease of Escherichia coli

Transmembrane segments of polytopic membrane proteins once inserted are generally considered stably oriented due to the large free energy barrier for topological reorientation of adjacent extra-membrane domains. However, proper topology and function of the polytopic membrane protein lactose permease (LacY) of Escherichia coli is dependent on the membrane phospholipid composition revealing topological dynamics of transmembrane domains (Bogdanov, M., Heacock, P. N., and Dowhan, W. (2002) EMBO J. 21, 2107–2116). The high affinity phenylalanine permease PheP shares many topological similarities with LacY. In this study, mutant E. coli cells lacking phosphatidylethanolamine (PE) as a membrane component were used to evaluate the role of PE in the function and assembly of PheP. Active transport of phenylalanine by cells lacking PE was severely inhibited (both Vmax and Km were altered), whereas the PheP protein level in membranes was unaffected. Cysteine residues were introduced into predicted periplasmic or cytoplasmic segments of cysteine-less PheP, and the topology of the protein was explored using a membrane-impermeable thiol-specific biotinylated probe. Based on the biotinylation patterns of PheP in whole cells, the N-terminus and adjoining transmembrane hairpin of PheP adopted an inverted topological orientation in PE-lacking cells. Introduction of PE following the assembly of PheP triggered a reorientation of the N-terminus and adjacent hairpin to their native orientation associated with regain of wild type transport function. These results coupled with the results for LacY support a specific role for membrane lipid composition in determining topological organization and function of membrane proteins. Several other secondary symporters are compromised for activity in PE-lacking cells suggesting that lipid-assisted topogenesis is a general property of such transporters. The reversible orientation of these secondary transport proteins in response to a change of phospholipid composition might be a result of inherent conformational flexibility necessary for transport function or during protein assembly. ^

The dynamics of calmodulin signaling revealed using optical methods

The Ca2+-binding protein calmodulin (CaM) is a key transducer of Ca2+ oscillations by virtue of its ability to bind Ca 2+ selectively and then interact specifically with a large number of downstream enzymes and proteins. It remains unclear whether Ca2+ -dependent signaling alone can activate the full range of Ca 2+/CaM regulated processes or whether other regulatory schemes in the cell exist that allow specific targeting of CaM to subsets of Ca 2+/CaM binding sites or regions of the cell. Here we investigate the possibility that alterations of the availability of CaM may serve as a potential cellular mechanism for regulating the activation of CaM-dependent targets. By utilizing sensitive optical techniques with high spatial and temporal resolution, we examine the intracellular dynamics of CaM signaling at a resolution previously unattainable. After optimizing and characterizing both the optical methods and fluorescently labeled probes for intracellular measurements, the diffusion of CaM in the cytoplasm of HEK293 cells was analyzed. It was discovered that the diffusion characteristics of CaM are similar to that of a comparably sized inert molecule. Independent manipulation of experimental parameters, including increases in total concentrations of CaM and intracellular Ca2+ levels, did not change the diffusion of CaM in the cytoplasm. However, changes in diffusion were seen when the concentration of Ca2+/CaM-binding targets was increased in conjunction with elevated Ca2+. This indicates that CaM is not normally limiting for the activation of Ca 2+/CaM-dependent enzymes in HEK293 cells but reveals that the ratio of CaM to CaM-dependent targets is a potential mechanism for changing CaM availability. Next we considered whether cellular compartmentalization may act to regulate concentrations of available Ca2+/CaM in hippocampal neurons. We discovered changes in diffusion parameters of CaM under elevated Ca2+ conditions in the soma, neurite and nucleus which suggest that either the composition of cytoplasm is different in these compartments and/or they are composed of unique families of CaM-binding proteins. Finally, we return to the HEK293 cell and for the first time directly show the intracellular binding of CaM and CaMKII, an important target for CaM critical for neuronal function and plasticity. Furthermore, we analyzed the complex binding stoichiometry of this molecular interaction in the basal, activated and autophosphorylated states of CaMKII and determined the impact of this binding on CaM availability in the cell. Overall these results demonstrate that regulation of CaM availability is a viable cellular mechanism for regulating the output of CaM-dependent processes and that this process is tuned to the specific functional needs of a particular cell type and subcellular compartment. ^

Parameterizing a Simple Potential Energy Function Appropriate for Vibrational Frequencies Using Molecular Dynamics

A Maple scheme for quickly parameterizing vibrational potential energy functions is presented. As an example, the potential energy function's parameters for the vibrational motions in H_2O_2 are obtained assuming the simplest potential energy function. This paper was originally written as a research paper, but rejected by the referees. It is therefore being edited into an ``educational'' paper for student usage.

An 'Ideal' Deconposition of Industry Dynamics: An Application to the Nationwide and State Level U.S. Banking Industry

This paper considers the aggregate performance of the banking industry, applying a modified and extended dynamic decomposition of bank return on equity. The aggregate performance of any industry depends on the underlying microeconomic dynamics within that industry --- adjustments within banks, reallocations between banks, entry of new banks, and exit of existing banks. Bailey, Hulten, and Campbell (1992) and Haltiwanger (1997) develop dynamic decompositions of industry performance. We extend those analyses to derive an ideal dynamic decomposition that includes their dynamic decomposition as one component. We also extend the decomposition, consider geography, and implement decomposition on a state-by-state basis, linking that geographic decomposition back to the national level. We then consider how deregulation of geographic restrictions on bank activity affects the components of the state-level dynamic decomposition, controlling for competition and the state of the economy within each state and employing fixed- and random-effects estimation for a panel database across the fifty states and the District of Columbia from 1976 to 2000.

Financial Liberalization and Inflationary Dynamics in the Context of a Small Open Economy

The paper develops a short-run model of a small open financially repressed economy characterized by unorganized money markets, capital good imports, capital mobility, wage indexation, and flexible exchange rates. The analysis shows that financial liberalization, in the form of an increased rate of interest on deposits and tight monetary policy, unambiguously and unconditionally causes deflation. Moreover, the results do not depend on the degree of capital mobility and structure of wage setting. The paper recommends that a small open developing economy should deregulate interest rates and tighten monetary policy if reducing inflation is a priority. The pre-requisite for such a policy, however, requires the establishment of a flexible exchange rate regime.

Computer Simulation of Crowd Dynamics and Destructive Crowd Behavior

The social processes that lead to destructive behavior in celebratory crowds can be studied through an agent-based computer simulation. Riots are an increasingly common outcome of sports celebrations, and pose the potential for harm to participants, bystanders, property, and the reputation of the groups with whom participants are associated. Rioting cannot necessarily be attributed to the negative emotions of individuals, such as anger, rage, frustration and despair. For instance, the celebratory behavior (e.g., chanting, cheering, singing) during UConn’s “Spring Weekend” and after the 2004 NCAA Championships resulted in several small fires and overturned cars. Further, not every individual in the area of a riot engages in violence, and those who do, do not do so continuously. Instead, small groups carry out the majority of violent acts in relatively short-lived episodes. Agent-based computer simulations are an ideal method for modeling complex group-level social phenomena, such as celebratory gatherings and riots, which emerge from the interaction of relatively “simple” individuals. By making simple assumptions about individuals’ decision-making and behaviors and allowing actors to affect one another, behavioral patterns emerge that cannot be predicted by the characteristics of individuals. The computer simulation developed here models celebratory riot behavior by repeatedly evaluating a single algorithm for each individual, the inputs of which are affected by the characteristics of nearby actors. Specifically, the simulation assumes that (a) actors possess 1 of 5 distinct social identities (group memberships), (b) actors will congregate with actors who possess the same identity, (c) the degree of social cohesion generated in the social context determines the stability of relationships within groups, and (d) actors’ level of aggression is affected by the aggression of other group members. Not only does this simulation provide a systematic investigation of the effects of the initial distribution of aggression, social identification, and cohesiveness on riot outcomes, but also an analytic tool others may use to investigate, visualize and predict how various individual characteristics affect emergent crowd behavior.

Asset Pricing with Heterogeneous Agents, Incomplete Markets and Trading Constraints

The consumption capital asset pricing model is the standard economic model used to capture stock market behavior. However, empirical tests have pointed out to its inability to account quantitatively for the high average rate of return and volatility of stocks over time for plausible parameter values. Recent research has suggested that the consumption of stockholders is more strongly correlated with the performance of the stock market than the consumption of non-stockholders. We model two types of agents, non-stockholders with standard preferences and stock holders with preferences that incorporate elements of the prospect theory developed by Kahneman and Tversky (1979). In addition to consumption, stockholders consider fluctuations in their financial wealth explicitly when making decisions. Data from the Panel Study of Income Dynamics are used to calibrate the labor income processes of the two types of agents. Each agent faces idiosyncratic shocks to his labor income as well as aggregate shocks to the per-share dividend but markets are incomplete and agents cannot hedge consumption risks completely. In addition, consumers face both borrowing and short-sale constraints. Our results show that in equilibrium, agents hold different portfolios. Our model is able to generate a time-varying risk premium of about 5.5% while maintaining a low risk free rate, thus suggesting a plausible explanation for the equity premium puzzle reported by Mehra and Prescott (1985).

Advanced Physical Chemistry Problems (VI), Free Energies

This is a set of P. Chem. problems posed at a slightly higher level than the normal textbook level, for students who are continuing in the study of this subject.

Molecular Dynamics and the Diatomic Molecule as Harmonic Oscillator and Rigid Rotor

The HCl molecule is simulated (using Maple) in its dynamics, for both vibrational (and implied) rotational motions. A discussion of the center of mass transformations involved is part of the total presentation.

Smoke free restaurant ordinance, compliance with the regulation to reduce exposure to environmental tobacco smoke while dining at local restaurants in San Antonio, Texas

This study is a secondary analysis of a survey developed by Dr. Jimmy Perkins and administered by San Antonio/Bexar County Metropolitan Health District. The survey was developed subsequent to the implementation of the city smoking ordinance effective January 1, 2004. The survey had a multi-purpose plan to establish the number of restaurants having smoke free status prior to and following the ordinance, determine compliance as it relates to a necessary smoking section and proper signage, and expose the rationale for restaurants to become smoke free. The data resulting from the survey was presented to the San Antonio/Bexar County Metropolitan Health District. The summary presented the types of establishments surveyed, smoking status of the establishment, reasons for the establishment becoming smoke free, compliance with smoking sections, compliance with signage requirements, awareness of ordinance, and chain status of the establishment. ^ The results of this study display the relationships among the variables previously mentioned. The following relationships have been examined and the outcomes have determined whether each is significant. After careful analysis, knowledge translates into compliance with signage regulations, which then translate into ordinance compliance. Size does matter as it relates to an establishment's number of employees and seating capacity. The smaller the establishment the more likely the establishment is to have become smoke free before the ordinance went into effect. Restaurants, rather than fast food establishments most commonly cited their reason for becoming smoke free was to comply with the ordinance and only ten percent of restaurants gave policy as the main reason for becoming smoke free. ^ This study is important for public health because the negative health effects of environmental tobacco smoke (ETS) are still an overwhelming problem in the United States (3). ETS is a Known Human Group A Carcinogen (5). The Environmental Protection Agency (EPA) has estimated that around 3,000 non-smoking Americans die every year from lung cancer caused by ETS (6). This information illustrates the importance of providing smoke free establishments, especially to non-smoking patrons. ^

Integrating sequence information in microarray data analysis by free energy modeling

Microarray technology is a high-throughput method for genotyping and gene expression profiling. Limited sensitivity and specificity are one of the essential problems for this technology. Most of existing methods of microarray data analysis have an apparent limitation for they merely deal with the numerical part of microarray data and have made little use of gene sequence information. Because it's the gene sequences that precisely define the physical objects being measured by a microarray, it is natural to make the gene sequences an essential part of the data analysis. This dissertation focused on the development of free energy models to integrate sequence information in microarray data analysis. The models were used to characterize the mechanism of hybridization on microarrays and enhance sensitivity and specificity of microarray measurements. ^ Cross-hybridization is a major obstacle factor for the sensitivity and specificity of microarray measurements. In this dissertation, we evaluated the scope of cross-hybridization problem on short-oligo microarrays. The results showed that cross hybridization on arrays is mostly caused by oligo fragments with a run of 10 to 16 nucleotides complementary to the probes. Furthermore, a free-energy based model was proposed to quantify the amount of cross-hybridization signal on each probe. This model treats cross-hybridization as an integral effect of the interactions between a probe and various off-target oligo fragments. Using public spike-in datasets, the model showed high accuracy in predicting the cross-hybridization signals on those probes whose intended targets are absent in the sample. ^ Several prospective models were proposed to improve Positional Dependent Nearest-Neighbor (PDNN) model for better quantification of gene expression and cross-hybridization. ^ The problem addressed in this dissertation is fundamental to the microarray technology. We expect that this study will help us to understand the detailed mechanism that determines sensitivity and specificity on the microarrays. Consequently, this research will have a wide impact on how microarrays are designed and how the data are interpreted. ^

Policy analysis of the Americans with Disabilities Act of 1990 and federal funding concerning barrier-free playgrounds

The Americans with Disabilities Act (ADA) of 1990 was created to prohibit discrimination against disabled persons in our society. The goal of the ADA as a comprehensive civil rights law is to "ensure equal opportunity and complete participation, independent living and economic self-sufficiency" for disabled persons (U.S. Department of Justice, 2008). As part of Title II and III of the ADA, states and local governments are required to provide people with disabilities the same chance to engage in and benefit from all programs and services including recreational facilities and activities as every other citizen. Recreational facilities and related structures must comply with accessibility standards when creating new structures or renovating existing ones. Through a systematic literature review of articles accessed through online databases, articles relating to children with disabilities, their quality of life and their experience gained through play were reviewed, analyzed and synthesized. Additionally, the ADA's Final Rule regarding accessible playgrounds was evaluated through a descriptive analysis which yielded the following five components relating the importance of barrier-free playgrounds to children with disabilities: appropriate dimensions for children, integration of the play area, variety of activity and stimulation, availability of accessible play structures to communities, and financial feasibility. These components were used as evaluation criteria to investigate the degree to which the ADA's Final Rule document met these criteria. An evaluation of two federal funding sources, the Urban Parks and Recreation Renewal Program (UPARR) and the Land and Water Conservation Fund (LWCF), was also conducted which revealed three components relating the two programs' ability to support the realization of the ADA's Final Rule which included: current budget for the program, ability of local communities to attain funds, and level of ADA compliance required to receive funding. Majority of the evaluation of the Final Rule concluded it be adequate in development of barrier-free playgrounds although there are some portions of the guidelines that would benefit from further elucidation. Both funding programs were concluded to not adequately support the development of barrier-free playgrounds and therefore it was recommended that their funding be re-instated or increased as necessary. ^

Early stage breast cancer and comorbidities: Their impact on breast cancer disease-free survival differences by ethnicity

The retrospective cohort study examined the association between the presence of comorbidities and breast cancer disease-free survival rates among racial/ethnic groups. The study population consisted of 2389 women with stage I and II invasive breast cancer who were diagnosed and treated at the M.D. Anderson Cancer Center between 1985 and 2000. It has been suggested that as the number of comorbidities increases, breast cancer mortality increases. It is known that African Americans and Hispanics are considered to be at a higher risk for comorbid conditions such as hypertension and diabetes compared to Caucasian women (23) (10). When compared to Caucasian women, African American women also have a higher breast cancer mortality rate (1). As a result, the study also examined whether comorbid conditions contribute to racial differences in breast cancer disease-free survival. Among the study population, 24% suffered from breast cancer recurrence, 6% died from breast cancer and 24% died from all causes. The mean age was 56 with 41% of the population being women between the ages of 40-55. One or more comorbidities were reported in 84 (36%) African Americans (OR 1.57; 95% CI 1.19-2.10), 58 (31%) Hispanics (OR 1.25; 95% CI 0.90-1.74) compared to the reference group of 531 (27%) Caucasians. Additionally, African American women were significantly more likely to suffer from either a breast cancer recurrence or breast cancer death (OR 1.5; 95% CI 0.70-1.41) when compared to Caucasian women. Multivariate analysis found hypertension (HR 1.22; 95% CI 0.99-1.49; p<0.05) to be statistically significant and a potential prognostic tool for disease-free survival with African American women (OR 2.96; 95% 2.25-3.90) more likely to suffer from hypertension when compared to Caucasian women. When compared to Caucasian women, Hispanics were also more likely to suffer from hypertension (OR 1.33; 95% CI 0.96-1.83). This suggests that comorbid conditions like hypertension could account for the racial disparities that exist when comparing breast cancer survival rates. Future studies should investigate this relationship further.^

Behavioral journalism newsletters to increase employee participation in a free worksite wellness center

Background. Providing an worksite fitness center for employees is an effective setting to increase an adult’s levels of physical activity, demonstrably reducing health care costs and elevating employee productivity. Increasing compliance and adherence among employees to consistently utilize an onsite facility remains a challenge.^ Purpose. To illustrate if two electronic behavioral journalism newsletters can increase employee participation in a free worksite wellness center.^ Design. A randomized control trial was implemented. ^ Setting. A large petroleum-producing corporation located in Houston, Texas Subjects.70 full or part time employees that had checked into visited the wellness center during September, October, and November 2009. ^ Intervention. Two behavioral journalism newsletters were created based on authentic community member role model interviews. Newsletters were distributed to intervention group participants via company email. Intervention and control group participant’s visits to the wellness center were monitored via a key card check in system at the facility for two weeks following the newsletter intervention.^ Analysis. Count variable statistics were used to identify rate differences between the intervention and control group wellness center visits. A binomial test for equality of proportions was used to identify differences between participants that had at least one visit to the wellness center compared with those with none.^ Results. Both intervention and control groups had a baseline of zero wellness center visits. The control group had a mean visit rate 0.441 and the intervention group had 0.857. A 0.416, almost one half more visits were found among the intervention group.^ Conclusion. This study indicates that behavioral journalism newsletters featuring a role model from within the worksite population can be a cost effective communication method to improve participation in an onsite wellness center. ^