Physical Sciences and Mathematics Commons^™

Assessing Ecological Relationships Among Late Triassic Vertebrates In Petrified Forest National Park, Alexandra Davis Apgar

Earth and Planetary Sciences ETDs

The complex vertebrate ecosystem of the Late Triassic has not yet been fully understood, largely due to oversimplification of hypothesized trophic hierarchies and limited preservation of direct evidence of faunal interaction. Paleocommunity reconstruction attempts can also fall victim to taphonomic biases, time-averaging inaccuracies, and non-analogue paleoecologies. Utilizing a combination of PAIRS analysis and NMDS ordination, we highlight vertebrate faunal relationships within the Adamanian and Revueltian faunachrons of Petrified Forest National Park, assess the likelihood that these patterns have ecological rather than preservational drivers, and examine how these potential interactions may have been impacted by the Adamanian-Revueltian turnover event. We are …

Toward The Yeast Surface Display Of Microviridin B, Jillian Leigh Stafford

Chemistry and Chemical Biology ETDs

Humans have turned to natural products for medicinal therapeutics for millennia. In recent years, the ribosomally synthesized and post-translationally modified peptide (RiPP) class of natural products have garnered a lot of attention due to their ability for heterologous expression, relative ease of mutation, and vast biological activates. Microviridins are a family of RiPPs that contain a tricyclic cage-like structure through the formation of two lactone rings and one lactam ring catalyzed by two ATP-grasp ligase family enzymes. Microviridins are potent inhibitors of serine proteases and mutational studies of a small number of residues indicates the potential of peptide engineering protease …

Applying Data Science And Machine Learning To Understand Health Care Transition For Adolescents And Emerging Adults With Special Health Care Needs, Lisamarie Turk

Nursing ETDs

A problem of classification places adolescents and emerging adults with special health care needs among the most at risk for poor or life-threatening health outcomes. This preliminary proof-of-concept study was conducted to determine if phenotypes of health care transition (HCT) for this vulnerable population could be established. Such phenotypes could support development of future studies that require data classifications as input. Mining of electronic health record data and cluster analysis were implemented to identify phenotypes. Subsequently, a machine learning concept model was developed for predicting acute care and medical condition severity. Three clusters were identified and described (Cluster 1, n …

Science, Technology, Engineering, And Mathematics (Stem) Project-Based Learning (Pbl) Education: A New Mexico Case Study For Equity And Inclusion, Kimberly A. Scheerer

Teacher Education, Educational Leadership & Policy ETDs

This research addresses how student participation in Science, Technology, Engineering, and Mathematics (STEM) project-based learning (PBL) education activities encourages underrepresented minority student achievement in STEM career field trajectories. Seven New Mexico high school counselors and 12 STEM organization personnel were interviewed during this study. Their responses represent the nuanced professional voices where New Mexico public education intersects with STEM student interest and cultural influence.

For students, STEM PBL can foster deep integration across educational disciplines and enhance STEM career trajectory interest and readiness. STEM education converged with PBL methodologies has the ability to leverage community support while broadening student networks. …

Relating Plant Community Structure To Carbon Dynamics In Semiarid Grasslands, Theodore D. Roper

Biology ETDs

Understanding how fine-scale changes in soil characteristics and plant community composition affect ecosystem functioning is key to predicting how biome shifts will affect regional and global carbon cycling. This is crucial in the dryland biomes of the US Southwest, projected to be one of the regions most affected by climate change. We examined fine-scale drivers of ecosystem function within two biomes – a Chihuahuan Desert grassland and Plains/Chihuahuan Desert ecotone – via long-term vegetation data, micrometeorological data, eddy covariance carbon flux measurements, and soil water and texture, finding that the ecotone site had over 30% higher soil water content, over …

Heterogeneity Of Gene Trees, Jonathan Nenye Odumegwu Unm

Mathematics & Statistics ETDs

Multilocus phylogenetic studies often show a high degree of gene tree heterogeneity —gene trees that have different topologies from each other as well as from the species tree topology. In some cases, this can lead to studies with hundreds of loci having distinct gene tree topologies. The degree of heterogeneity is expected to increase when there is a high degree of incomplete lineage sorting due to short branches (as measured in coalescent units) in the species tree. Other potential sources of heterogeneity include other biological processes such as introgression, recombination within genes, ancestral population structure, gene duplication and loss, and …

Ontogenetic Niche Shift As A Driver Of Community Structure And Diversity In Non-Avian Dinosaurs, Katlin Schroeder

Biology ETDs

As some of the most charismatic megafauna to ever walk the earth, the physiology, morphology, growth and evolution of non-avian theropods has been studied exhaustively, yet little is understood about their roles in ecosystems as juveniles. For carnivorous megatheropods, which exceed 1,000kg in mass yet hatched from eggs of limited size, the likelihood of utilizing different prey through ontogeny was high, simply by proxy of the immense difference in size between adults and juveniles. We found these ontogenetic niche shifts, evidenced by significantly different dental microwear in Tyrannosaurids, to have excluded dinosaurian mesocarnivores from Mesozoic communities. The few dinosaurian mesocarnivores …

Effects Of Environmental Change On Ancestral Pueblo Fishing In The Middle Rio Grande, Jonathan W. Dombrosky Dr.

Anthropology ETDs

It has long been assumed that fishes were unimportant in the diet of past Pueblo people in the U.S. Southwest. Yet, small numbers of fish remains are consistently recovered from Late pre-Hispanic/Early Historic archaeological sites in the Middle Rio Grande of New Mexico. The end of drought conditions may have impacted food choice and fishing decisions during this time. I use behavioral ecology to understand how fishing could have been an optimal food-getting strategy for Ancestral Pueblo farmers. Stable isotope analysis offers a way to account for environmental change. I provide a refined ¹³C Suess correction model to support …

Studies Of The Rectification Behavior Of The Pdt Ligand And The Active Site Of Msrp, Laura J. Ingersol

Chemistry and Chemical Biology ETDs

Molybdenum (Mo) is an essential element that plays an important role in global nitrogen, carbon, and sulfur cycles with a critical role in human metabolism and ecological balance. It becomes catalytically active when complexed with the pyranopterin dithiolene ligand (PDT), forming the nearly ubiquitous molybdenum cofactor (Moco). The complex biosynthetic pathway of Moco, its presence in all three domains of life, and its role as a constituent cofactor in the last universal common ancestor (LUCA) all point toward the importance of the PDT in the development of life on Earth. Molybdoenzymes catalyze the two-electron oxidation or reduction of substrates that …

Maximum Likelihood Estimation Of Species Trees And Anomaly Zone Detection Using Ranked Gene Trees, Anastasiia Kim

Mathematics & Statistics ETDs

A phylogenetic tree represents the evolutionary relationships among a set of organisms. Gene trees can be used to reconstruct phylogenetic trees. The methods in this dissertation focus on the gene tree topologies with emphasis on ranked gene tree topologies. A ranked tree depicts the order in which nodes appear in the tree together with topological relationships among gene lineages. One challenge that arises during phylogenetic inference is the existence of the anomaly zones, the regions of branch-length space in the species tree that can produce gene trees that have topologies differing from the species tree topology but are more probable …

A Landscape On The Threshold Of Change: Patterns Of Soil Microbial Ecology Along Dynamic Geomorphic And Hydrologic Features In A Polar Desert, Kelli L. Feeser, David J. Van Horn, Heather N. Buelow, Daniel R. Colman, Theresa A. Mchugh, Jordan G. Okie, Egbert Schwartz, Cristina D. Takacs-Vesbach, Becky A. Ball, Andrew G. Fountain, Michael N. Gooseff, Joseph S. Levy, Maciej K. Obryk

Biology ETDs

The McMurdo Dry Valleys (MDV) of Antarctica are on the threshold of widespread landscape scale change due to increasing temperature and solar radiation and altered hydrology: buried ice is melting, the soil active layer is thickening, thermokarst features are developing along streams, water tracks are expanding, and lake levels are rising. These changes will impact the microbial communities found in each of the affected habitats. The purpose of this work is to first, understand the spatial distribution of soil bacteria in the MDV, specifically investigating the scale-dependent effects of environmental heterogeneity, and second, to perform surveys and coupled experiments to …

Reconstructing Energy Flow Through Modern And Historical Marine Communities: Insights From Amino Acid Isotope Analysis, Emma A. Elliott Smith

Biology ETDs

The fundamental currency of life is energy. Organisms need energy to grow, to survive and to reproduce. Understanding the acquisition of energy by consumers is thus a foundational aspect of biological research. This is especially important in the modern era, as impacts of ongoing anthropogenic effects will be mediated or amplified through food webs. Here, I explore how isotopic analysis of individual amino acids – a technique new to ecological studies – can be used to trace energy flow through animal communities in modern and ancient time periods. In particular, I focus on kelp forest food webs, which are nearshore …

Eutherian Biogeography During The Puercan North American Land Mammal Age (Paleocene, Earliest Danian): Problems And Potential Solutions, Jason Sterling Silviria

Earth and Planetary Sciences ETDs

The Puercan North American Land Mammal Age (NALMA) is the earliest major North American terrestrial biochron of the Cenozoic era, spanning roughly the first one million years of the Paleogene period (Paleocene epoch, Danian stage; ~66.04-65.12 Ma). It is typified by the explosive ecomorphological diversification of the mammalian clade Eutheria (particularly our subclade, Placentalia), following the annihilation of non-avian dinosaurs and “archaic” mammal groups during the Cretaceous/Paleogene (K-Pg) mass extinction event. The spatiotemporal mode and tempo of Puercan eutherian diversification has long been the subject of debate, with disagreements over biogeographic zonation. The traditional model – based largely on well-sampled, …

Multi-Resolution Analysis Of Large Molecular Structures And Interactions, Kasra Manavi

Computer Science ETDs

Simulation of large molecular structures and their interactions has become a major component of modern biomolecular research. Methods to simulate these type of molecules span a wide array of resolutions, from all atom molecular dynamics to model interaction energetics to systems of linear equations to evaluate population kinetics. In recent years, there has been an acceleration of molecular structural information production, primarily from x-ray crystallography and electron microscopy. This data has provided modelers the ability to produce better representations of these molecular structures. The purpose of this research is to take advantage of this information to develop multi-resolution models for …

Assessment Of Vegetation Response To Wildfire At Bandelier National Monument, New Mexico: Case Study Of The Las Conchas Fire, Gladys Valentin-Gonzalez

Geography ETDs

In the past couple of decades, there has been an increase in the occurrence of wildfire events in the United States. The U.S. Forest Service estimates that over 73,000 wildfires on average occur annually in the U.S., burning about 7.3 million acres of land. Bandelier National Monument, in northern New Mexico, has been affected by several wildfires in the past 40 years, one of the most recent being the Las Conchas Fire in 2011, which burned over 60,700 hectaresin Bandelier National Monument and Valles Caldera National Preserve. This research explores a remote-sensing based assessment of vegetation response to and recovery …

An Integrated Bioinformatic/Experimental Approach For Discovering Novel Type Ii Polyketides Encoded In Actinobacterial Genomes, Wubin Gao

Chemistry and Chemical Biology ETDs

Discovery of new natural products (NPs) is critical both for diseases treatment and crops protection. Numerous NP biosynthetic gene clusters (BGCs) in sequenced microbial genomes allow identification of new NPs through genome mining. Developing an integrated bioinformatic/experimental approach for discovering novel type II polyketides (PK-IIs) facilitates investigation of this family of NPs in an efficient, systematic way. Here, we developed an approach to analyze ketosynthase α/β (KSα/β) gene sequences to predict PK-II core structures, allowing us to target novel PK-II BGCs either from isolated genomic DNA or genomes from the NCBI databank, and to isolate novel PK-IIs produced by these …

Impacts Of Long-Term Precipitation Manipulation On Hydraulic Architecture, Xylem Function, And Canopy Status In A Piñon-Juniper Woodland, Patrick J. Hudson

Biology ETDs

The Southwestern US is predicted to become hotter and drier, as global climate change forces increasing temperatures and variability in timing and size of precipitation inputs. Drought stress has become more frequent in recent decades, and resulted in massive forest mortality in piñon-juniper woodlands. During recent severe droughts (2000-2003, 2009-2012), piñon pine (Pinus edulis Englem.) suffered disproportionately high mortality compared to co-occurring one-seed juniper (Juniperus monosperma [Engelm.] Sarg.). A large-scale precipitation manipulation experiment was established in a piñon-juniper woodland in central New Mexico to test hypotheses regarding tree survival and mortality with respect to altered water regimes. Our …

Development Of In Vivo Systems For Detecting And Studying Ribosome Inhibition By Small Molecules, Shijie Huang

Chemistry and Chemical Biology ETDs

The ribosome is the quintessential antibacterial drug target, with many structurally and mechanistically distinct classes of antibacterial agents acting by inhibiting ribosome function. Detecting and quantifying ribosome inhibition by small molecules and investigating their binding modes and mechanisms of action are critical to antibacterial drug discovery and development efforts. To develop a ribosome inhibition assay that is operationally simple, yet provides direct information on the drug target and the mechanism of action, we have developed engineered E. coli strains harboring an orthogonal ribosome controlled green fluorescent protein reporter that produce fluorescent signal when the O-ribosome is inhibited. As a proof …

Network Inference Driven Drug Discovery, Gergely Zahoránszky-Kőhalmi, Tudor I. Oprea Md, Phd, Cristian G. Bologa Phd, Subramani Mani Md, Phd, Oleg Ursu Phd

Biomedical Sciences ETDs

The application of rational drug design principles in the era of network-pharmacology requires the investigation of drug-target and target-target interactions in order to design new drugs. The presented research was aimed at developing novel computational methods that enable the efficient analysis of complex biomedical data and to promote the hypothesis generation in the context of translational research. The three chapters of the Dissertation relate to various segments of drug discovery and development process.

The first chapter introduces the integrated predictive drug discovery platform „SmartGraph”. The novel collaborative-filtering based algorithm „Target Based Recommender (TBR)” was developed in the framework of this …

Engineering Small Molecule Based Dimerization To Induce Translation And Provide Optogenetic Control, Catherine Wright

Chemistry and Chemical Biology ETDs

We wanted to develop a system that combines the spatial control of photoactivation and control of translation to build a tool to spatially control translation in neurons. This kind of tool could be used to investigate the role of spatially controlled translation of any protein in neural behavior. In this way the development and growth of neural processes could be studied to elucidate the mechanisms for spatially sensitive events such as pathfinding, repair, or long-term potentiation.

Chemically induced dimerization was used to install a switch into the activation of translation for specific genes. An abscisic acid (ABA) dependent dimerization of …

Towards Deeper Understanding In Neuroimaging, Rex Devon Hjelm

Computer Science ETDs

Neuroimaging is a growing domain of research, with advances in machine learning having tremendous potential to expand understanding in neuroscience and improve public health. Deep neural networks have recently and rapidly achieved historic success in numerous domains, and as a consequence have completely redefined the landscape of automated learners, giving promise of significant advances in numerous domains of research. Despite recent advances and advantages over traditional machine learning methods, deep neural networks have yet to have permeated significantly into neuroscience studies, particularly as a tool for discovery. This dissertation presents well-established and novel tools for unsupervised learning which aid in …