A Comprehensive Study of the Enhanced Distributed Control Access (EDCA) Function

This technical report presents a comprehensive study of the Enhanced Distributed Control Access (EDCA) function defined in IEEE 802.11e. All the three factors are considered. They are: contention window size (CW), arbitration inter-frame space (AIFS), and transmission opportunity limit (TXOP). We first propose a discrete Markov chain model to describe the channel activities governed by EDCA. Then we evaluate the individual as well as joint effects of each factor on the throughput and QoS performance. We obtain several insightful observations showing that judiciously using the EDCA service differentiation mechanism is important to achieve maximum bandwidth utilization and user-specified QoS performance. Guided by our theoretical study, we devise a general QoS framework that provides QoS in an optimal way. The means of realizing the framework in a specific network is yet to be studied

Topology Control in Heterogeneous Wireless Networks: Problems and Solutions

Previous work on topology control usually assumes homogeneous wireless nodes with uniform transmission ranges. In this paper, we propose two localized topology control algorithms for heterogeneous wireless multi-hop networks with nonuniform transmission ranges: Directed Relative Neighborhood Graph (DRNG) and Directed Local Spanning Subgraph (DLSS). In both algorithms, each node selects a set of neighbors based on the locally collected information. We prove that (1) the topologies derived under DRNG and DLSS preserve the network connectivity; (2) the out degree of any node in the resulting topology by DLSS is bounded, while the out degree cannot be bounded in DRNG; and (3) the topologies generated by DRNG and DLSS preserve the network bi-directionality

Topology Control for Maintaining Network Connectivity and Maximizing Network Capacity Under the Physical Model

In this paper we study the issue of topology control under the physical Signal-to-Interference-Noise-Ratio (SINR) model, with the objective of maximizing network capacity. We show that existing graph-model-based topology control captures interference inadequately under the physical SINR model, and as a result, the interference in the topology thus induced is high and the network capacity attained is low. Towards bridging this gap, we propose a centralized approach, called Spatial Reuse Maximizer (MaxSR), that combines a power control algorithm T4P with a topology control algorithm P4T. T4P optimizes the assignment of transmit power given a fixed topology, where by optimality we mean that the transmit power is so assigned that it minimizes the average interference degree (defined as the number of interferencing nodes that may interfere with the on-going transmission on a link) in the topology. P4T, on the other hand, constructs, based on the power assignment made in T4P, a new topology by deriving a spanning tree that gives the minimal interference degree. By alternately invoking the two algorithms, the power assignment quickly converges to an operational point that maximizes the network capacity. We formally prove the convergence of MaxSR. We also show via simulation that the topology induced by MaxSR outperforms that derived from existing topology control algorithms by 50%-110% in terms of maximizing the network capacity

Initial Investigation of Analytic Hierarchy Process to Teach Creativity in Design and Engineering

This paper investigates the use of Analytic Hierarchy Process to teach design creativity and innovation in undergraduate engineering students. Examples are included to assess its effectiveness in the classroom. The purpose of this research is to investigate the suitability of the Analytic Hierarchy Process (AHP) to teach design innovation and creativity in undergraduate engineering classrooms. AHP is a very structured, multi-criteria, decision-making process and traditionally has been used to solve complex problem sets. This investigation takes a fresh look at how AHP provides the framework to engage and encourage students to think creatively and innovatively in design and engineering. This paper presents several separate case studies that incorporate the AHP technique in the classroom to teach design innovation and creativity to undergraduate engineering students, including introduction at the freshmen engineering level. These case studies include: the design of a robotic water vehicle; the design of a coffee maker; and the design of a website. These diverse case studies explore the suitability of this decision-making technique across abroad range of design problems to assess how AHP can be utilized to give students a better understanding of the design process, to foster a personal motivation towards creative and innovative thinking and to equip students with a strategy for creative problem solving theycan use through their engineering careers. Students who participated in the case studies completed questionnaires to assess the application of AHP and its effectiveness to understand the problem and to reach a creative and innovative solution. Based on the results of these student questionnaires, there is positive evidence that AHP can be utilized to remove barriers that inhibit creativity and to foster an environment for students to achieve more design creativity and innovation in engineering classrooms. This study has implications to change the pedagogical approach used to teach engineering design and provides a methodology for design creativity that students will carry with them throughout their career

Sensitivity Analysis Method to Address User Disparities in the Analytic Hierarchy Process

Decision makers often face complex problems, which can seldom be addressed well without the use of structured analytical models. Mathematical models have been developed to streamline and facilitate decision making activities, and among these, the Analytic Hierarchy Process (AHP) constitutes one of the most utilized multi-criteria decision analysis methods. While AHP has been thoroughly researched and applied, the method still shows limitations in terms of addressing user profile disparities. A novel sensitivity analysis method based on local partial derivatives is presented here to address these limitations. This new methodology informs AHP users of which pairwise comparisons most impact the derived weights and the ranking of alternatives. The method can also be applied to decision processes that require the aggregation of results obtained by several users, as it highlights which individuals most critically impact the aggregated group results while also enabling to focus on inputs that drive the final ordering of alternatives. An aerospace design and engineering example that requires group decision making is presented to demonstrate and validate the proposed methodology

Mechanisms underlying polyene macrolide mediated rescue of growth in ion channel deficient yeast

Human diseases caused by missing or dysfunctional protein ion channels, known as channelopathies, affect several organs and systems of the body including that of the heart, lungs, kidneys, and nervous system. Channelopathies can result in devastating and potentially life-threatening diseases. To date, more than 30 human channelopathies are incurable. Although significant advances have been made in both gene therapy and protein replacement therapies, there is still a major need for new treatment strategies. We questioned whether an imperfect small molecule mimic of a missing protein ion channel could be sufficient to restore physiology in protein-deficient systems. Small molecules possess many qualities as potential therapeutics including that they are orally bio-available, cell permeable, and minimally immunogenic. Specifically for small molecule inhibitors, their primary mechanism of action is to bind to and block over-active proteins. However, in the case of unexpressed or degraded proteins where no target is available, this approach is futile. We hypothesized that through functionally interfacing with inherent networks of protein ion pumps and transporters, an imperfect small molecule ion channel could be enough to rescue physiology. Amphotericin B (AmB) is a prime example of an ion channel forming small molecule. Clinically for more than 60 years, medical providers have utilized AmB to treat patients suffering from invasive, systemic fungal infections. Previously, AmB’s mode of cell killing was thought to be through ion channel formation. However, The Burke Group at The University of Illinois at Urbana-Champaign showed that AmB kills yeast through sterol extraction. Moreover, we found that AmB only caused cell death when the ratio of AmB exceeded that of sterols; therefore, pre-complexation of AmB with sterols serves as a strategy to ameliorate toxicity. Alternatively, to harness AmB’s ion channel forming activity, we employed this small molecule at low concentrations. Further characterization showed that AmB small molecule ion channels are unselective, wherein they conduct potassium (K+), sodium (Na+), chloride (Cl-), and bicarbonate (HCO3-) ions. We employed Saccharomyces cerevisiae (S.cerevisiae) as an outstanding model organism because this unicellular eukaryote is genetically tractable, well-annotated, and amenable to genetic deletion. Furthermore, yeast have been widely utilized to elucidate several, fundamental biological processes including cell cycle regulation, telomere maintenance, and vesicle trafficking, and to characterize the pathophysiology of human disease. Yeast express two primary K+ transporters, Trk1 and Trk2 that are localized to the plasma membrane. Proton (H+)-ATPases Pma1 and V-ATPase utilize the energy from ATP hydrolysis to drive H+ out of cells or into vacuoles respectively, thereby producing favorable electrochemical gradients. These gradients promote K+ flow through Trk1 and Trk2 passive transporters into cells, to achieve cytosolic concentrations around 200-300 mM and cation storage into vacuoles. For cellular physiology, K+ is crucial for retaining intracellular pH, sustaining plasma membrane potential, and promoting enzyme activity. Deficiencies of these integral K+ transporters result in a loss of cell growth under standard laboratory conditions (10-15 mM K+). We found that an imperfect small molecule mimic of a missing protein ion channel, a.k.a. molecular prosthetic is sufficient to restore physiology in a protein-deficient model organism. We demonstrated that AmB both vigorously and sustainably restored physiology in K+ transporter deficient yeast (trk1Δtrk2Δ). Furthermore, we showed that AmB mediated rescue is ion channel dependent. Contributing to the lab’s molecular prostheses program, this thesis work has made four major contributions. First, we predicted that small molecule mediated rescue is generalizable. Initially, we reconfirmed literature reports and demonstrated that Nystatin A1, Candicidin, and Mepartricin permeabilize yeast. Then to test our prediction, we employed two assays: the disc diffusion and micro-broth dilution assay. We observed no rescue of growth with a Natamycin control (does not form ion channels). In contrast, we observed restored cell growth for Nystatin A1 (optimal at 1 μM), Candicidin (8 nM), and Mepartricin (8 nM). These findings suggest the versatility of trk1Δtrk2Δ homeostatic mechanisms to functionally interface with different imperfect small molecule mimics, and thereby rescue physiology. Second, we elucidated a mechanism by which imperfect small molecule ion channels rescue physiology in yeast. We hypothesized that small molecule mimics harness favorable electrochemical gradients to drive K+ into cells and back to physiological levels, thereby restoring cell growth in trk1Δtrk2Δ yeast. We have obtained evidence in support of each of these steps. Consistent with prior reports, trk1Δtrk2Δ yeast are hyperpolarized compared to that of WT. These gradients drive K+ into cells as demonstrated by radioactive rubidium (86Rb+, surrogate tracer for K+) influx assays. Next, we showed that through working together with the cell’s endogenous network of protein ion pumps, small molecule ion channels significantly restored total cellular K+ levels in trk1Δtrk2Δ back to that found in WT, in both a dose- and time-dependent manner. In contrast, Natamycin did not restore total cellular K+ content nor cell growth. Furthermore, chemical inhibition of H+-ATPases abrogated restoration of total cellular K+ content and growth. Thus, these results provide mechanistic evidence for how small molecule ion channels rescue physiology. Third, our findings suggest that imperfect small molecule mediated rescue of physiology is possible through functional collaboration with the cell’s inherent network of protein ion pumps and transporters. AmB and other polyene macrolide ion channels are unregulated, unrectified, unselective, and passive. However, we hypothesized that through working together with H+-ATPases (drivers) and transporters (correctors) that imperfect small molecule ion channels are sufficient to restore physiology. V-ATPase and Pma1 generate favorable electrochemical gradients. These gradients promote K+ flux through Trk1 and Trk2 and into vacuoles. We predicted that inhibiting V-ATPase or Pma1 would abrogate small molecule mediated rescue of trk1Δtrk2Δ. To test our hypothesis, we employed three chemical inhibitors: Nocodazole (impedes microtubule dynamics), Bafilomycin (blocks V-ATPase), and Ebselen (inhibits Pma1) against small molecule ion channel treated WT and trk1Δtrk2Δ. We observed exceptional sensitivity in small molecule rescued trk1Δtrk2Δ cells to Bafilomycin and to Ebselen blockage compared to that observed in WT. In contrast, minor differences were observed between these two treatment groups, to Nocodazole inhibition. Therefore, these results suggest that cells require active V-ATPase and Pma1, possibly to drive K+ through small molecule ion channels, for rescue of trk1Δtrk2Δ cell growth. Next, we hypothesized that endogenous protein transporters are crucial for correcting the lack of ion selectivity of small molecule ion channels. Yeast express plasma membrane localized voltage gated K+ efflux pump Tok1, Na+(K+)/H+ antiporter Nha1, and Na+-ATPase Ena1-5 that extrude excess K+ and Na+. We acquired a series of isogenic yeast mutants and conducted the liquid broth rescue assay. We observed that small molecule mimics did not recover growth in trk1Δtrk2Δnha1Δ yeast for any concentrations screened. Importantly, the nha1Δ mutant showed similar growth to that of WT. In contrast, deletion of either Tok1 (trk1Δtrk2Δtok1Δ) or Ena1-5 (trk1Δtrk2Δena1-5Δ) did not hamper small molecule mediated rescue. Thus, these findings suggest that Nha1 is important for expelling excess Na+ and/or K+ from small molecule treated trk1Δtrk2Δ. Last, in collaboration with The Mitchell Group, we have identified several potential and uncharacterized small molecule polyene macrolides through biosynthetic gene cluster analysis. We hypothesized through interrogating the gene clusters of several, highly conserved domains including the aminotransferase, ketosynthase, etc. that we can identify novel producing organisms of polyene macrolides. Through utilizing a moderate throughput yeast screening platform, we have found several organisms that produce extracts that may contain novel polyene macrolides. In summary, this thesis work culminates into four major findings: first, small molecule mediated rescue is generalizable to other polyene macrolide family members; second, a primary mechanism by which small molecule ion channels rescue cell growth in trk1Δtrk2Δ yeast is through restored cellular K+ content; third, small molecule mimics work in conjunction with the cell’s inherent network of protein ion pumps and transporters to restore physiology; and last, we have identified several potential and uncharacterized polyene macrolides through biosynthetic gene cluster analysis. In conclusion, these results demonstrate the potential for imperfect small molecule mimics to provide function in the case of protein ion channel deficiencies. Furthermore, these findings showcase an in-depth mechanistic pathway for how imperfect small molecule mimics restore cellular physiology in protein-deficient yeast. Intriguingly, the same protein characters responsible for restoring physiology in yeast may also be at play in other eukaryotic systems

Insights into the role and mechanism of the AAA+ adaptor Clps

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. 134-141).Protein degradation is a vital process in cells for quality control and participation in regulatory pathways. Intracellular ATP-dependent proteases are responsible for regulated degradation and are highly controlled in their function, especially with respect to substrate selectivity. Adaptor proteins that can associate with the proteases add an additional layer of control to substrate selection. Thus, understanding the mechanism and role of adaptor proteins is a critical component to understanding how proteases choose their substrates. In this thesis, I examine the role of the intracellular protease ClpAP and its adaptor ClpS in Escherichia coli. ClpS binds to the N-terminal domain of ClpA and plays dual roles in ClpAP substrate selectivity: ClpS inhibits the degradation of some substrates such as ssrA-tagged proteins and enhances the degradation of other substrates such as N-end-rule proteins. We wished to elucidate how ClpS influences ClpAP substrate selection, and found that the stoichiometry of ClpS binding to ClpA is one level of regulation. Furthermore, we demonstrated that the N-terminal extension of ClpS is vital for the adaptor's role in delivering N-end-rule substrates to ClpAP for degradation, but this extension is not required for inhibition of ssrA-tagged proteins. Truncation studies of the ClpS N-terminal extension showed a dramatic length-dependence on N-end-rule protein delivery, and the chemical composition of this portion of ClpS also affected the ability to degrade N-degron-bearing substrates.(cont.) Evidence suggests that ClpS allosterically affects the ClpA enzyme, causing a modulation in substrate specificity, and preliminary studies localized the point of contact by the ClpS N-terminal extension to the ClpA pore region. ClpS therefore represents a new type of adaptor protein that modulates substrate selection allosterically, rather than simply recruiting and tethering substrates to the protease. To further understand the role of ClpS and ClpAP in the cell, we conducted a proteomic-based search for ClpS-dependent ClpAP substrates. A list of putative substrates was generated from these experiments, and we believe that ClpAP plays a key role in quality control, perhaps through the degradation of N-end-rule substrates. Combined with mechanistic studies, these physiological studies aid in the understanding of how ClpS influences substrate recognition by ClpAP.by Jennifer Yuan Hou.Ph.D