BALTHMETRIC SURVEY IN THE KEWEENAW WATER WAY IN MICHIGAN, USA, MAKING 3D MODEL, AND COMPARING SONAR EQUIPMENT OF THE MODERN AUV AND THE TRADITIONAL SINGLE BEAM SONAR

This thesis represents the overview of hydrographic surveying and different types of modern and traditional surveying equipment, and data acquisition using the traditional single beam sonar system and a modern fully autonomous underwater vehicle, IVER3. During the thesis, the data sets were collected using the vehicles of the Great Lake Research Center at Michigan Technological University. This thesis also presents how to process and edit the bathymetric data on SonarWiz5. Moreover, the three dimensional models were created after importing the data sets in the same coordinate system. In these interpolated surfaces, the details and excavations can be easily seen on the surface models. In this study, the profiles are plotted on the surface models to compare the sensors and details on the seabed. It is shown that single beam sonar might miss some details, such as pipeline and quick elevation changes on the seabed when we compare to the side scan sonar of IVER3 because the single side scan sonar can acquire better resolution. However, sometimes using single beam sonar can save your project time and money because the single beam sonar is cheaper than side scan sonars and the processing might be easier than the side scan data.

PHYLOGENETIC ANALYSES, GENE DOSAGE EFFECT AND SELECTION IN MEMBERS OF THE LATERAL BOUNDARY DOMAIN (LBD) GENES TRANSCRIPTION FACTOR FAMILY

Wood formation is an economically and environmentally important process and has played a significant role in the evolution of terrestrial plants. Despite its significance, the molecular underpinnings of the process are still poorly understood. We have previously shown that four Lateral Boundary Domain (LBD) transcription factors have important roles in the regulation of wood formation with two (LBD1 and LBD4) involved in secondary phloem and ray cell development and two (LBD15 and LBD18) in secondary xylem formation. Here, we used comparative phylogenetic analyses to test potential roles of the four LBD genes in the evolution of woodiness. We studied the copy number and variation in DNA and amino acid sequences of the four LBDs in a wide range of woody and herbaceous plant taxa with fully sequenced and annotated genomes. LBD1 showed the highest gene copy number across the studied species, and LBD1 gene copy number was strongly and significantly correlated with the level of ray seriation. The lianas, cucumber and grape, with multiseriate ray cells showed the highest gene copy number (12 and 11, respectively). Because lianas’ growth habit requires significant twisting and bending, the less lignified ray parenchyma cells likely facilitate stem flexibility and maintenance of xylem conductivity. We further demonstrate conservation of amino acids in the LBD18 protein sequences that are specific to woody taxa. Neutrality tests showed evidence for strong purifying selection on these gene regions across various orders, indicating adaptive convergent evolution of LBD18. Structural modeling demonstrates that the conserved amino acids have a significant impact on the tertiary protein structure and thus are likely of significant functional importance.