Development and Application of a quantitative Mass spectrometry based Platform for Thermodynamic Analysis of Protein interaction Networks

<p>The identification and quantification of protein-protein interactions in large scale is critical to understanding biological processes at a systems level. Current approaches for the analysis of protein -protein interactions are generally not quantitative and largely limited to certain types of interactions such as binary and strong binding interactions. They also have high false-positive and false-negative rates. Described here is the development of and application of mass spectrometry-based proteomics metehods to detect and quantify the strength of protein-protein and protein-ligand interactions in the context of their interaction networks. Characterization of protein-protein and protein-ligand interactions can directly benefit diseased state analyses and drug discovery efforts. </p><p>The methodologies and protocols developed and applied in this work are all related to the Stability of Unpurified Proteins from Rates of amide H/D Exchange (SUPREX) and Stability of Protein from Rates of Oxidation (SPROX) techniques, which have been previously established for the thermodynamic analysis of protein folding reactions and protein-ligand binding interactions. The work in this thesis is comprised of four parts. Part I involves the development of a Histidine Slow H/D exchange protocol to facility SURPEX-like measurements on the proteomic scale. The Histidine Slow H/D exchange protocol is developed in the context of selected model protein systems and used to investigate the thermodynamic properties of proteins in a yeast cell lysate. </p><p>In Part II an isobaric mass tagging strategy is used in combination with SPROX (i.e., a so-called iTRAQ-SPROX protocol) is used to characterize the altered protein interactions networks associated with lung cancer. This work involved differential thermodynamic analyses on the proteins in two different cell lines, including ADLC-5M2 and ADLC-5M2-C2. </p><p>Parts III and IV of this thesis describe the development and application of a SPROX protocol for proteome-wide thermodynamic analyses that involves the use of Stable Isotope Labeling by Amino acid in cell Culture (SILAC) quantitation. A solution-based SILAC-SPROX protocol is described in Part III and a SILAC-SPROX protocol involving the use of cyanogen bromide and a gel-based fractionation step is described in Part IV. The SILAC-SPROX-Cyanogen bromide (SILAC-SPROX-CnBr) protocol is demonstrated to significantly improve the peptide and protein coverage in proteome-wide SPROX experiments. Both the SILAC-SPROX and SILAC-SPROX-CnBr porotocols were used to characterize the ATP binding properties of yeast proteins. Ultimately, the two protocols enabled 526 yeast proteins to be assayed for binding to AMP-PNP, an ATP mimic. A total of 140 proteins, including 37 known ATP-binding proteins, were found to have ATP binding interactions.</p>Dissertatio

Rotorcraft Research at the NASA Vertical Motion Simulator

In the 1970 s the role of the military helicopter evolved to encompass more demanding missions including low-level nap-of-the-earth flight and operation in severely degraded visual environments. The Vertical Motion Simulator (VMS) at the NASA Ames Research Center was built to provide a high-fidelity simulation capability to research new rotorcraft concepts and technologies that could satisfy these mission requirements. The VMS combines a high-fidelity large amplitude motion system with an adaptable simulation environment including interchangeable and configurable cockpits. In almost 30 years of operation, rotorcraft research on the VMS has contributed significantly to the knowledge-base on rotorcraft performance, handling qualities, flight control, and guidance and displays. These contributions have directly benefited current rotorcraft programs and flight safety. The high fidelity motion system in the VMS was also used to research simulation fidelity. This research provided a fundamental understanding of pilot cueing modalities and their effect on simulation fidelity

Assessment of seasonal winter temperature forecast errors in the regcm model over northern Vietnam

This study verified the seasonal six-month forecasts for winter temperatures for northern Vietnam in 1998–2018 using a regional climate model (RegCM4) with the boundary conditions of the climate forecast system Version 2 (CFSv2) from the National Centers for Environmental Prediction (NCEP). First, different physical schemes (land-surface process, cumulus, and radiation parameterizations) in RegCM4 were applied to generate 12 single forecasts. Second, the simple ensemble forecasts were generated through the combinations of those different physical formulations. Three subclimate regions (R1, R2, R3) of northern Vietnam were separately tested with surface observations and a reanalysis dataset (Japanese 55-year reanalysis (JRA55)). The highest sensitivity to the mean monthly temperature forecasts was shown by the land-surface parameterizations (the biosphere−atmosphere transfer scheme (BATS) and community land model version 4.5 (CLM)). The BATS forecast groups tended to provide forecasts with lower temperatures than the actual observations, while the CLM forecast groups tended to overestimate the temperatures. The forecast errors from single forecasts could be clearly reduced with ensemble mean forecasts, but ensemble spreads were less than those root-mean-square errors (RMSEs). This indicated that the ensemble forecast was underdispersed and that the direct forecast from RegCM4 needed more postprocessing

Continuum Modeling with Functional Lennard-Jones Parameters for DNA-Graphene Interactions

OnlinePublCarbon nanostructures are of particular interest as platforms for molecular storage and adsorption. In this paper, the adsorption of a single stranded DNA molecule onto a graphene sheet is considered. Even though DNA molecules are complicated heterogeneous structures comprising several types of atoms, it is found that the repeated patterns within the DNA molecules enable the use of a continuum approach to model the DNA-graphene sheet interaction. Here, a model is proposed such that the heterogeneity across the DNA molecule is captured by interaction functions, which are used to replace the attractive and repulsive constants in the Lennard-Jones potential. Result from this new model shows better agreement to molecular dynamics simulations compared to the traditional continuum approach where atoms on the DNA are averaged evenly across the molecule. Finally, the paper comments on the model, its parameters, and suggests ways for improvement.Kyle Stevens, Ngamta Thamwattana, and Thien Tran-Du

Evaluating the impacts of rice-based protection dykes on floodwater dynamics in the vietnamese mekong delta using geographical impact factor (Gif)

This study aims at evaluating the geographical influences of rice-based protection dykes on floodwater regimes along the main rivers, namely the Mekong and the Bassac, in the Vietnamese Mekong Delta (VMD). Specifically, numerous low dykes and high dykes have been constructed particularly in the upper delta’s floodplains to protect the double and triple rice cropping against the annual flooding. For the whole deltaic domain, a 1D-quasi-2D hydrodynamic model setup was used to simulate seventy-two (72) scenarios of dyke construction development in the context of low, medium, and high floods that occurred in the VMD to examine the effects of different flood magnitudes on a certain dyke construction area. Based on the model simulation results, we established an evaluation indicator, the so-called Geographical Impact Factor (GIF), to evaluate the impacts of zone-based dyke compartments on the floodwater regimes along the main rivers for different kinds of floods. Our findings revealed different rates of influences on the floodwater levels along the Mekong and Bassac Rivers under different scenarios of zone-based high-dyke developments. GIF is a useful index for scientists and decision-makers in land use planning, especially in rice intensification, in conjunction with flood management for the VMD and for similar deltas worldwide

CW Interference Effects on High Data Rate Transmission Through the ACTS Wideband Channel

Satellite communications channels are susceptible to various sources of interference. Wideband channels have a proportionally greater probability of receiving interference than narrowband channels. NASA's Advanced Communications Technology Satellite (ACTS) includes a 900 MHz bandwidth hardlimiting transponder which has provided an opportunity for the study of interference effects of wideband channels. A series of interference tests using two independent ACTS ground terminals measured the effects of continuous-wave (CW) uplink interference on the bit-error rate of a 220 Mbps digitally modulated carrier. These results indicate the susceptibility of high data rate transmissions to CW interference and are compared to results obtained with a laboratory hardware-based system simulation and a computer simulation

Acute Kidney Injury After Percutaneous Coronary Intervention Guided by Intravascular Ultrasound

Purpose We investigated the impact of intravascular ultrasound guidance on reducing the incidence of contrast-induced acute kidney injury (CI-AKI) in patients undergoing percutaneous coronary intervention (PCI). Methods Ninety-nine patients were enrolled in this prospective cohort who were not randomly assigned to angiography-guided percutaneous coronary intervention or intravascular ultrasound-guided percutaneous coronary intervention. The patients were hospitalized at the Vietnam National Heart Institute - Bach Mai Hospital between 2019 and 2020. Acute kidney injury incidence during hospitalization was the primary endpoint. Results A total of 99 patients were divided into two groups: the intravascular ultrasound-guided group (33 participants) and the angiography-guided group (66 participants). The mean ± SD contrast volume of each group was 95.2 ± 37.1 mL and 133.0 ± 36.0 mL for the ultrasound-guided and angiography-guided groups, with P \u3c 0.0001. Intravascular imaging-guided percutaneous coronary intervention (IVUS-guided PCI) was associated with reduced acute kidney injury incidence during hospitalization: 0.0% vs. 12.12% and P = 0.049. Conclusions Intravascular ultrasound is a safe imaging tool that guides percutaneous coronary intervention and significantly reduces the rate of acute kidney injury compared to angiography alone. Patients who have a high chance of experiencing acute kidney injury benefit from using intravascular ultrasound