Thesis (Ph.D.)--University of Delaware, 2007. / Principal faculty advisor: Jeremy S. Edwards, Dept. of Chemical Engineering. Includes bibliographical references.

Middle-Upper Eocene successions were studied in the Fayum Depression in order to establish depositional and paleoenvironmental models that link the ichnological and sedimentologic data to relative sea-level changes in a sequence stratigraphic framework. Five facies associations (FA1- FA5) are identified. The facies depositional models show overall progradation from quiescent open-marine bay (FA1-2: Gehannam and Birket Qarun formations) to lagoon/distributary channel/estuary sedimentary environments (FA3-5: Qasr El-Sagha Formation). The facies successions and their stratigraphic evolution are controlled by a regional, second-order cycle associated with the northward regression of the Tethys, which is overprinted by subordinate third- and higher-order cycles. Whale-bearing FA1 and FA2 are subdivided into five sedimentary facies. Seventeen ichnospecies belonging to thirteen ichnogenera, as well as rhizoliths are observed within these facies. Facies Association 1 accumulated in a low-energy fullymarine bay, whereas FA 2 represents a bay margin / supratidal paleoenvironments. Clastic point-sources are dominantly hypopycnal although eolian sand may represent an important source locally. The quiescent marine bay is a typical environment and biome for the Eocene whales. Preservation of these fossil whales must occur in association with rapid sedimentation rates, but sufficiently that bioturbation eradicates the physical sedimentary structures. Unusual, large-sized sedimentary structures are examined along the parasequence-bounding surfaces of the Birket Qarun Sandstone. Ichnological data, petrography and stable-isotope analysis are integrated to propose a bio-sedimentologic/diagenetic model, interpreting the origin of these structures as concretion growths around ichnofossils. The marine pore-water carbon was influenced by organic carbon and mixing of meteoric groundwater under eodiagenetic conditions. These conditions led to the precipitation of pervasive authigenic calcite-dominated cement in and around the burrows. More than twenty-five Glossifungites Ichnofaciesdemarcated discontinuities are examined in the study area. These surfaces are grouped into those of autocyclic and those of allocyclic origin. Occurrences of the allocyclically significant Glossifungites Ichnofacies can be classified into sequence-bounding, systems tract-bounding and parasequence-bounding surfaces. Sequence-bounding Glossifungites Ichnofacies-demarcated surfaces divide the studied successions into four third-order sequences. Systems tract-bounding and parasequence-bounding Glossifungites Ichnofacies-demarcated surfaces display higher-order cycles, overprinting the third-order cycles.

Sequence stratigraphy relates changes in vertical and lateral facies distribution to relative changes in sea level. These relative changes in carbonates effect early diagenesis, types of pores, cementation and dissolution patterns. As a result, in carbonates, relative changes in sea level significantly impact the lithology, porosity, diagenesis, bed and bounding surfaces which are all factors that control fracture patterns. This study explores these relationships by integrating stratigraphy with fracture analysis and petrophysical properties. A special focus is given to the relationship between mechanical boundaries and sequence stratigraphic boundaries in three different settings: 1) Mississippian strata in Sheep Mountain Anticline, Wyoming, 2) Mississippian limestones in St. Louis, Missouri, and 3) Pennsylvanian limestones intermixed with clastics in the Paradox Basin, Utah. The analysis of these sections demonstrate that a fracture hierarchy exists in relation to the sequence stratigraphic hierarchy. The majority of fractures (80%) terminate at genetic unit boundaries or the internal flooding surface that separates the transgressive from regressive hemicycle. Fractures (20%) that do not terminate at genetic unit boundaries or their internal flooding surface terminate at lower order sequence stratigraphic boundaries or their internal flooding surfaces. Secondly, the fracture spacing relates well to bed thickness in mechanical units no greater than 0.5m in thickness but with increasing bed thickness a scatter from the linear trend is observed. In the Paradox Basin the influence of strain on fracture density is illustrated by two sections measured in different strain regimes. The folded strata at Raplee Anticline has higher fracture densities than the flat-lying beds at the Honaker Trail. Cemented low porosity rocks in the Paradox Basin do not show a correlation between fracture pattern and porosity. However velocity and rock stiffness moduli's display a slight correlation to fracture spacing. Furthermore, bed thickness is found to be only one factor in determining fracture density but with increasing strain, internal bedforms and rock petrophysical heterogeneities influence fracture density patterns. This study illustrates how integrating sedimentologic and sequence stratigraphic interpretations with data on structural kinematics can lead to refined predictive understanding of fracture attributes.

Thesis (M.Sc.)--Memorial University of Newfoundland, 2005. / Bibliography: leaves 76-83.

<p>The architecture, distribution and facies of sandstone bodies in the Gog Group of the southern Rocky Mountains of western Canada record the dynamics of sand movement on the broad continental shelf of West Laurentia during the Early Cambrian phase of worldwide transgression. This study focuses on the stratigraphy, sedimentology and ichnology in the Bow Valley region, specifically the sector from Mount Assiniboine northwest to the North Saskatchewan River. The objectives of this project were several-fold: (1) revise the existing stratigraphic nomenclature; (2) document the sedimentary facies; (3) identify facies assemblages and interpret them in terms of sedimentary processes and environments; (4) characterize sandstone body geometries; (5) develop a sequence-stratigraphic framework; (6) document trace-fossil occurrences; and (7) characterize different trace-fossil assemblages in terms of colonization trends and prevailing paleoenvironmental conditions.</p> <p>The Gog Group in this area has historically comprised four units, the Fort Mountain, Lake Louise, St. Piran and Peyto formations. North of Bow Pass an additional unit, the Jasper Formation, occurs below the Fort Mountain Formation and is related to accommodation created by active rift-faulting during the latest Neoproterozoic. In the Lake Louise and Lake O'Hara area, four new formal subdivisions within the St. Piran Formation are proposed: Lake O'Hara, Lake Oesa, Lake Moraine and Wiwaxy Peaks members.</p> <p>The sequence stratigraphy of tide-dominated setting has yet not been fully explored. The stratal architecture of the Lake O'Hara and Lake Oesa members reveals a new mechanism for the formation of the regressive surface of marine erosion landward of the lever point of balance between sedimentation and erosion in the subtidal environment. As the shoreline is forced to regress with falling sea level, the laterally continuous tidal flats advance and the preexisting shallow-subtidal compound dunes are scoured by strong tidal currents that carve gradually a new equilibrium profile. We argue that the accretion of intertidal flats on top of subtidal sands is an overlooked yet predictable component of falling-stage systems tracts in tide-dominated settings.</p> <p>The Gog Group also offers an opportunity to explore animal-sediment relationships in a high-energy setting, during the early phase of Phanerozoic diversification. The presence of constrasting ichnofabrics within a single Early Cambrian sand-sheet complex illuminates how the colonisation trends of suspension and detritus feeders were controlled by factors specific to the various subenvironments.<p> <p>The variety of sandbody types in the Gog Group reflects varying sediment supply and location on the inner continental shelf. Five types of compound cross-stratified sandstone are distinguished based on foreset geometry, sedimentary structures and internal heterogeneity. These represent five broad categories of subtidal sandbodies: (1) compound-dune fields; (2) sand sheets; (3) sand ridges; and (4) patchy dunes. Trace-fossil distribution in these tide-dominated sand bodies and adjacent sediments is mostly controlled by an interplay of substrate mobility, grain size, turbidity, water-column productivity, and sediment organic matter. Salinity is a critical factor in marginal-marine locations but played no role in this region of the shelf.</p>

Sequence alignment has become one of the most common tasks in bioinformatics. Most of the existing sequence alignment methods use general scoring schemes. But these alignments are sometimes not completely relevant because they do not necessarily provide the desired information. It would be extremely difficult, if not impossible, to include any possible objective into an algorithm. Our goal is to allow a working biologist to augment a given alignment with additional information based on their knowledge and objectives.<p></p>In this thesis, we will formally define constraints and compatible constraint sets for an alignment which require some positions of the sequences to be aligned together. Using this approach, one can align some specific segments such as domains within protein sequences by inputting constraints (the positions of the segments on the sequences), and the algorithm will automatically find an optimal alignment in which the segments are aligned together.<p></p>A necessary prerequisite of calculating an alignment is that the constraints inputted be compatible with each other, and we will develop algorithms to check this condition for both pairwise and multiple sequence alignments. The algorithms are based on a depth-first search on a graph that is converted from the constraints and the alignment. We then develop algorithms to perform pairwise and multiple sequence alignments satisfying these compatible constraints.<p></p>Using straightforward dynamic programming for pairwise sequence alignment satisfying a compatible constraint set, an optimal alignment corresponds to a path going through the dynamic programming matrix, and as we are only using single-position constraints, a constraint can be represented as a point on the matrix, so a compatible constraint set is a set of points. We try to determine a new path, rather than the original path, that achieves the highest score which goes through all the compatible constraint set points. The path is a concatenation of sub-paths, so that only the scores in the sub-matrices need to be calculated. This means the time required to get the new path decreases as the number of constraints increases, and it also varies as the positions of the points change. It can be further reduced by using the information from the original alignment, which can offer a significant speed gain.<p></p>We then use exact and progressive algorithms to find multiple sequence alignments satisfying a compatible constraint set, which are extensions of pairwise sequence alignments. With exact algorithms for three sequences, where constraints are represented as lines, we discuss a method to force the optimal path to cross the constraint lines. And with progressive algorithms, we use a set of pairwise alignments satisfying compatible constraints to construct multiple sequence alignments progressively. Because they are more complex, we leave some extensions as future work.

Comparing protein sequences is an essential procedure that has many applications in the field of bioinformatics. The recent advances in computational capabilities and algorithm design, simplified the comparison procedure of protein sequences from several databases. Various algorithms have emerged using state of the art approaches to match protein sequences based on structural and functional properties of the amino acids. The matching involves structural alignment, and this alignment may be global; comprising of the whole length of the protein, or local; comprising of the sub-sequences of the proteins. Families of related proteins are found by clustering sequence alignments. The frequency distributions of the amino acids within these different clusters define the sequence profile. The best alignment algorithm uses these profiles. In this thesis, we have studied different profile alignment algorithms where the cost function for comparing two profiles is changed. These are compared to the FFAS3 (Fold and Function Assignment) algorithm.

Elastin is an essential extracellular protein that is a key component of elastic fibres, providing elasticity to cardiac, dermal, and arterial tissues. During the development of the human cardiovascular system, elastin self-assembles before being integrated into fibres, undergoing no significant turnover during the human lifetime. Abnormalities in elastin can adversely affect its self-assembly, and may lead to malformed elastic fibres. Due to the longevity required of these fibres, even minor abnormalities may have a large cumulative effect over the course of a lifetime, leading to late-onset vascular diseases. This thesis project has identified important, over-represented repetitive elements in elastin which are believed to be important for the self-assembly and elastomeric properties of elastin. Initial studies of single nucleotide polymorphisms (SNPs) from the HapMap project and dbSNP resulted in a set of genetic variation sites in the elastin gene. Based on these studies, glycine to serine and lysine to arginine substitutions were introduced in elastin-like polypeptides. The self-assembly properties of the resulting elastin-like polypeptides were observed under microscope and measured using absorbance at 440nm. Assembled polypeptides were also cross-linked to form thin membranes whose mechanical and physical properties were measured and compared. These mutations resulted in markedly different behavior than wild-type elastin-like proteins, suggesting that mutations in the repetitive elements of the elastin sequence can lead to adverse changes in the physical and functional properties of the resulting protein. Using next-generation sequencing, patients with thoracic aortic aneurysms are being genotyped to discover polymorphisms which may adversely affect the self-assembly properties of elastin, providing a link between genetic variation in elastin and cardiovascular disease.

Elastin is an essential extracellular protein that is a key component of elastic fibres, providing elasticity to cardiac, dermal, and arterial tissues. During the development of the human cardiovascular system, elastin self-assembles before being integrated into fibres, undergoing no significant turnover during the human lifetime. Abnormalities in elastin can adversely affect its self-assembly, and may lead to malformed elastic fibres. Due to the longevity required of these fibres, even minor abnormalities may have a large cumulative effect over the course of a lifetime, leading to late-onset vascular diseases. This thesis project has identified important, over-represented repetitive elements in elastin which are believed to be important for the self-assembly and elastomeric properties of elastin. Initial studies of single nucleotide polymorphisms (SNPs) from the HapMap project and dbSNP resulted in a set of genetic variation sites in the elastin gene. Based on these studies, glycine to serine and lysine to arginine substitutions were introduced in elastin-like polypeptides. The self-assembly properties of the resulting elastin-like polypeptides were observed under microscope and measured using absorbance at 440nm. Assembled polypeptides were also cross-linked to form thin membranes whose mechanical and physical properties were measured and compared. These mutations resulted in markedly different behavior than wild-type elastin-like proteins, suggesting that mutations in the repetitive elements of the elastin sequence can lead to adverse changes in the physical and functional properties of the resulting protein. Using next-generation sequencing, patients with thoracic aortic aneurysms are being genotyped to discover polymorphisms which may adversely affect the self-assembly properties of elastin, providing a link between genetic variation in elastin and cardiovascular disease.

The sequence stratigraphy of the middle Eocene-Pliocene of the Pannonian Basin permits to differentiate fifty-nine depositional sequences. An earlier compressional Paleogene basin in the central and eastern Pannonian Basin is unconformably overlain by a Neogene extensional basin. Tectonic regimes interacted with transgressive-regressive facies cycles. The boundaries of these cycles coincide with regional stage boundaries. Unconformities separating these cycles mark the episodic closure of connections between the Pannonian Basin and the European epicontinental seas from Oligocene through middle Miocene time. The unconformities are the result of short-term glacio-eustatic falls, sometimes enhanced by tectonic events. Within the limits of biostratigraphic resolution during the Eocene-middle Miocene, many of the sequences of the Pannonian Basin correlate well with the sequences proposed by Haq et al. (1987). However, eight sequences, i.e. one in the Lutetian, three in the Bartonian, one in the Priabonian, one in the Rupelian and two in the Burdigalian, were not identified by Haq et al. (1987). The sequences and their boundaries are directly correlated with global oxygen isotope events. Glacioeustasy generates sequence boundaries beginning as early as the middle Eocene. Within the lacustrine setting of the Pannonian Basin (late Miocene- Pliocene time) relative lake level changes appear to control the overall sequence development. However, other minor variables, the sediment supply and the topography of the initial depositional surface were additional controlling factors. Thus differences in the physiography of the basin lead to totally different sequence types that all reflect to lake level fluctuations. In lateral direction, during a short time period, these lacustrine sequences are more sensitive to changes in the initial depositional profile and sediment supply. / pages 390 and 396 are missing from text.