Systemic analysis of microarray data sets towards identifying genes regulating root development

Nitrogen and water are essential for plant growth and development. In this study, we designed experiments to produce gene expression data of poplar roots under nitrogen starvation and water deprivation conditions. We found low concentration of nitrogen led first to increased root elongation followed by lateral root proliferation and eventually increased root biomass. To identify genes regulating root growth and development under nitrogen starvation and water deprivation, we designed a series of data analysis procedures, through which, we have successfully identified biologically important genes. Differentially Expressed Genes (DEGs) analysis identified the genes that are differentially expressed under nitrogen starvation or drought. Protein domain enrichment analysis identified enriched themes (in same domains) that are highly interactive during the treatment. Gene Ontology (GO) enrichment analysis allowed us to identify biological process changed during nitrogen starvation. Based on the above analyses, we examined the local Gene Regulatory Network (GRN) and identified a number of transcription factors. After testing, one of them is a high hierarchically ranked transcription factor that affects root growth under nitrogen starvation. It is very tedious and time-consuming to analyze gene expression data. To avoid doing analysis manually, we attempt to automate a computational pipeline that now can be used for identification of DEGs and protein domain analysis in a single run. It is implemented in scripts of Perl and R.

Engineering design motivations : a qualitative and quantitative analysis of university students

What motivates students to perform and pursue engineering design tasks? This study examines this question by way of three Learning Through Service (LTS) programs: 1) an on-going longitudinal study examining the impacts of service on engineering students, 2) an on-going analysis of an international senior design capstone program, and 3) an on-going evaluation of an international graduate-level research program. The evaluation of these programs incorporates both qualitative and quantitative methods, utilizing surveys, questionnaires, and interviews, which help to provide insight on what motivates students to do engineering design work. The quantitative methods were utilized in analyzing various instruments including: a Readiness assessment inventory, Intercultural Development Inventory, Sustainable Engineering through Service Learning survey, the Impacts of Service on Engineering Students’ survey, Motivational narratives, as well as some analysis for interview text. The results of these instruments help to provide some much needed insight on how prepared students are to participate in engineering programs. Additional qualitative methods include: Word clouds, Motivational narratives, as well as interview analysis. This thesis focused on how these instruments help to determine what motivates engineering students to pursue engineering design tasks. These instruments aim to collect some more in-depth information than the quantitative instruments will allow. Preliminary results suggest that of the 120 interviews analyzed Interest/Enjoyment, Application of knowledge and skills, as well as gaining knowledge are key motivating factors regardless of gender or academic level. Together these findings begin to shed light on what motivates students to perform engineering design tasks, which can be applied for better recruitment and retention in university programs.

COMPUTATIONAL ANALYSIS OF THE AEROELASTIC DYNAMICS OF A WIND TURBINE BLADE WITH VARIABLE-SPEED STALL CONTROL

The accuracy of simulating the aerodynamics and structural properties of the blades is crucial in the wind-turbine technology. Hence the models used to implement these features need to be very precise and their level of detailing needs to be high. With the variety of blade designs being developed the models should be versatile enough to adapt to the changes required by every design. We are going to implement a combination of numerical models which are associated with the structural and the aerodynamic part of the simulation using the computational power of a parallel HPC cluster. The structural part models the heterogeneous internal structure of the beam based on a novel implementation of the Generalized Timoshenko Beam Model Technique.. Using this technique the 3-D structure of the blade is reduced into a 1-D beam which is asymptotically equivalent. This reduces the computational cost of the model without compromising its accuracy. This structural model interacts with the Flow model which is a modified version of the Blade Element Momentum Theory. The modified version of the BEM accounts for the large deflections of the blade and also considers the pre-defined structure of the blade. The coning, sweeping of the blade, tilt of the nacelle and the twist of the sections along the blade length are all computed by the model which aren’t considered in the classical BEM theory. Each of these two models provides feedback to the other and the interactive computations lead to more accurate outputs. We successfully implemented the computational models to analyze and simulate the structural and aerodynamic aspects of the blades. The interactive nature of these models and their ability to recompute data using the feedback from each other makes this code more efficient than the commercial codes available. In this thesis we start off with the verification of these models by testing it on the well-known benchmark blade for the NREL-5MW Reference Wind Turbine, an alternative fixed-speed stall-controlled blade design proposed by Delft University, and a novel alternative design that we proposed for a variable-speed stall-controlled turbine, which offers the potential for more uniform power control and improved annual energy production.. To optimize the power output of the stall-controlled blade we modify the existing designs and study their behavior using the aforementioned aero elastic model.

SLOPE STABILITY ANALYSIS OF MOUNT MEAGER, SOUTH-WESTERN BRITISH COLUMBIA, CANADA

The Mount Meager Volcanic Complex (MMVC) in south-western British Columbia is a potentially active, hydrothermally altered massif comprising a series of steep, glaciated peaks. Climatic conditions and glacial retreat has led to the further weathering, exposure and de-buttressing of steep slopes composed of weak, unconsolidated material. This has resulted in an increased frequency of landslide events over the past few decades, many of which have dammed the rivers bordering the Complex. The breach of these debris dams presents a risk of flooding to the downstream communities. Preliminary mapping showed there are numerous sites around the Complex where future failure could occur. Some of these areas are currently undergoing progressive slope movement and display features to support this such as anti-scarps and tension cracks. The effect of water infiltration on stability was modelled using the Rocscience program Slide 6.0. The main site of focus was Mount Meager in the south- east of the Complex where the most recent landslide took place. Two profiles through Mount Meager were analysed along with one other location in the northern section of the MMVC, where instability had been detected. The lowest Factor of Safety (FOS) for each profile was displayed and an estimate of the volume which could be generated was deduced. A hazard map showing the inundation zones for various volumes of debris flows was created from simulations using LAHARZ. Results showed the massif is unstable, even before infiltration. Varying the amount of infiltration appears to have no significant impact on the FOS annually implying that small changes of any kind could also trigger failure. Further modelling could be done to assess the impact of infiltration over shorter time scales. The Slide models show the volume of material that could be delivered to the Lillooet River Valley to be of the order of 109 m3 which, based on the LAHARZ simulations, would completely inundate the valley and communities downstream. A major hazard of this is that the removal of such a large amount of material has the potential to trigger an explosive eruption of the geothermal system and renew volcanic activity. Although events of this size are infrequent, there is a significant risk to the communities downstream of the complex.