Doctor of Philosophy

dissertationA diverse array of insect species harbor maternally transmitted mutualistic bacterial endosymbionts that perform a variety of functions within their hosts. Many of these associations are obligate in nature with the insect relying on the bacterial symbiont to provide nutrients that are lacking in the insect\u27s natural diet. These obligate endosymbionts often show a highly reduced genome size and maintain only a small fraction of the gene inventory of free-living bacteria. Some of the smallest known bacterial genomes are from obligate endosymbionts that have been associated with their insect hosts for long periods of time. In addition to their small size, the genomes of ancient obligate symbionts also show an increased rate of DNA and polypeptide sequence evolution as well as a nucleotide composition bias that results in an increased ratio of adenine and thymine residues. Despite extensive study of these ancient endosymbionts, little is known about their origins. To address this issue and to better understand the forces shaping genomes in the early stages of an endosymbiotic association, this work focuses on two bacteria: strain HS, a recently characterized free-living bacterium that likely served as a progenitor to the Sodalis-allied clade of bacterial endosymbionts, and the Sitophilus oryzae primary endosymbiont (SOPE), a very recent established maternally transmitted obligate endosymbiont of the rice weevil. The complete genome sequencing of these two bacteria along with comparative genomic analyses revealed that SOPE has undergone a very rapid degeneration of its genome, losing nearly half of its coding capacity, a massive expansion of insertion sequence (IS) elements and numerous intragenomic rearrangements facilitated by the IS elements. Surprisingly, these changes have happened very recently since strain HS and SOPE shared a common ancestor approximately 28,000 years ago

A Novel Setup For High-pressure Raman Spectroscopy Under A Microscope

Functional properties of biological molecules and cells are affected by environmental parameters such as temperature and pressure. While Raman spectroscopy provides an intrinsic probe of molecular structural changes, the incorporation of a microscope enables studies of minuscule amounts of biological compounds with spatial resolution on a micron scale. We have developed a novel setup which combines a Raman microscope and a high pressure cell. A micro-capillary made out of fused silica simultaneously serves as the supporting body and the optical window of the pressure cell. The cell has been tested over the pressure range from 0.1 to 4 kbar. Raman spectra of less than 100 nanoliter amount of amino acid and protein solutions have been measured in the micro-capillary high pressure cell. It is also demonstrated that the setup is well suited for spectrally resolved fluorescence measurements at variable pressure

Unique North American isolates of severe metastatic hypervirulent Klebsiella pneumoniae strain infections with hepatic abscesses seen in young patients within Texas.

RationaleHypervirulent Klebsiella pneumoniae (hvKp) infections have principally been identified in Asia. Within a two-month period, two patients between the ages of 30 to 50 years old presented to a tertiary referral hospital in Texas with septic shock, hepatic abscess, and septic thrombophlebitis. Blood cultures were positive for Klebsiella pneumoniae (isolates 2020CK-00441 and 2021CK-00720 respectively). The first patient survived after a prolonged hospital course while the second patient expired.ObjectivesDescribe the clinical presentation of these two patients. Perform whole genome sequencing and bioinformatic analysis to evaluate potential outbreak of specific hvKp bacteria isolates.MethodsWhole genome sequencing was performed using both paired-end Illumina MiSeq and nanopore sequencing to obtain a Completed genome for both isolates.Main results2020CK-00441 belonged to ST23 type while 2021CK-00720 was a ST65 type isolate. Kleborate analyses predicted with high confidence both isolates were hvKp. Phylogenetic analyses showed the two strains are not closely related to each other nor to any known hvKp isolates reported. Both isolates had yersiniabactin, colibactin, aerobactin and salmochelin producing loci which likely confer these isolates hvKp phenotype. 2020CK-00441 and 2021CK-00720 had a unique pK2044 like plasmid.ConclusionsHvKp strains capable of causing devastating metastatic septic infections have emerged in Texas. These isolates are unique compared to other hvKp strains globally. Country-wide surveillance and whole genome sequencing of these strains is essential to prevent a major public health emergency in the USA

Quorum Sensing Primes the Oxidative Stress Response in the Insect Endosymbiont, Sodalis glossinidius

quorum sensing system relies on the function of two regulatory proteins; SogI (a LuxI homolog) synthesizes a signaling molecule, characterized as N-(3-oxohexanoyl) homoserine lactone (OHHL), and SogR1 (a LuxR homolog) interacts with OHHL to modulate transcription of specific target genes. and SOPE. and SOPE indicates the potential for neofunctionalization to occur during the process of genome degeneration

Breeding on the leading edge of a northward range expansion: differences in morphology and the stress response in the arctic Gambel's white-crowned sparrow

Individuals at the forefront of a range shift are likely to exhibit phenotypic traits that distinguish them from the population breeding within the historic range. Recent studies have examined morphological, physiological and behavioral phenotypes of individuals at the edge of their range. Several studies have found differences in the hypothalamic-pituitary-adrenal (HPA) axis activity in response to acute restraint stress in individuals at the range limits. HPA axis activation leads to elevations in glucocorticoids that regulate physiology and behavior. Here we compare the hormonal profiles and morphometrics from Gambel's white-crowned sparrows (Zonotrichia leucophrys gambelii) breeding at the northern limit of the population's range to those birds breeding within the historic population range. Birds breeding at the northern limit experienced a harsher environment with colder temperatures; however, we found no differences in arthropod prey biomass between the northern limit and more southern (historic) sites. Males at the northern limit had higher body condition scores (mass corrected for body size) compared to individuals within the historic range, but no differences were found in beak and tarsus lengths, wing chord, muscle profile or fat stores. In males during the pre-parental stage, before breeding commenced, HPA axis activity was elevated in birds at the northern limit of the range, but no differences were found during the parental or molt stages. Females showed no differences in HPA axis activity during the parental stage. This study suggests that "pioneering" individuals at the limits of their breeding range exhibit physiology and morphology that are distinct from individuals within the historic range

Autism/SPiN/Prosocial Study

Study exploring autism, speech perception in noise, and prosocial orientatio

Broken and Expelled Sand of a Delta of Lake Bonneville: A Record of Ancient Earthquakes?

The research was conducted on an outcrop of deltaic sand deposited during the rise of Lake Bonneville, about 23,000 to 17,000 years ago. The outcrop, located near the mouth of Green Canyon, Cache Co., Utah, houses world-class examples of sedimentary deformation and slump structures; however the precise origin of these structures is uncertain. It is possible that these structures were earthquake-induced. The objective of the research was to ultimately broaden the understanding of the processes involved with the formation of the deformation and slump structures and thereby test if tectonic activity was indeed pertinent to the said structures. Data collected from on site analyses, combined with an analysis of aerial imagery and an analysis of part of the outcrop with photo mosaics revealed that there are 4 different ages of liquefied deposits. There are also three listric slumps, two of which dip west and one that dips east. The central slump was active twice. Some of the slumps produced scarps on the sea floor of Lake Bonneville; the scarps are overlapped by un-deformed sediment. All the sediment is lacustrine and dated from the transgression of Lake Bonneville to its high stand. Other features discovered include clay localized in the slip surfaces of the slumps and deformation structures that are brittle and some others that are ductile. It is interesting to note that an earthquake in Hansel Valley, in 1936, produced similar features. Data collected so far seem to indicate that the complex deformation is probably due to cluster of earthquakes on the East Cache fault during the highstand of Lake Bonneville