Texas A&M University – Corpus Christi
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Analysis of the vcgC gene in Vibrio vulnificus isolates from the Texas Coastal Bend region of the Gulf of Mexico
No full textVibrio vulnificus is a gram-negative, halophilic bacterium normally found in temperate marine and estuarine waters. The organism may enter wounds in the skin and cause sepsis or necrotizing fasciitis; the latter condition has a 50-60% mortality rate and may result in death or disfigurement within 4-6 days. Persons exposed to coastal flood waters during hurricanes may be at risk for this organism. The virulence-correlated gene, vcgC, is specific for clinical isolates of V. vulnificus, but the function of this locus remains unknown. This study used Polymerase Chain Reaction (PCR) and novel primers for vcgC not previously described to specifically identify V. vulnificus isolates from the Texas Coastal Bend region that may result in serious infections. Of the 28 isolates, four isolates could not be revived multiple times; crude lysates of the remaining 24 Vibrio vulnificus cultures were analyzed by PCR, and 19 were found to have amplicons of 428bp for vcgC. This study confirms the presence of the vcgC gene in V. vulnificus isolates from the Texas Coastal Bend region of the Gulf of Mexico.This research was funded by NIH Extramural Associates Research Development Award PAR 05-053 to G.W.B; Texas A&M University-Corpus Christi University Research Enhancement Award to G.W.B.; Texas Research Development Funds Award to G.W.B. Undergraduate researcher L.I.B. was funded by the McNair Scholars Program to Texas A&M Univ-Corpus Christi. Undergraduate researchers S.D.G. and D. S. P. were funded by the Research Experience for Undergraduates to Texas A&M Univ.-Corpus Christi. G.P.C was funded by Bridging Master’s Students to the Doctorate, NIGMS 2R25 GM071936-034 subaward from the University of Texas Medical Branch; Undergraduate researcher A.O.T. was funded by the Texas A&M System Louis Stokes Alliance for Minority Participation. The lab of G.W.B. was presented a substantial gift by an anonymous donor. We thank Suzzette Chopin for additional support; Alyssa Garcia, Louise Lyle, Valerie May, Jessica Ramirez, Tyler Vance and Emilio Vasquez for technical assistance; Cherie McCollough for helpful comments to the manuscript. This manuscript is dedicated to Dr. Joanna B. Mott, former Chair of Life Sciences, who provided initial exposure to working with Vibrio vulnificus
Assessment of the planetary boundary layer over the Northesatern Pacific Ocean: Impact of ducting and horizontal inhomogeneity on GNSS radio occultation measurements
No full textA dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Coastal and Marine Systems Science.In the northeastern Pacific Ocean, strong free tropospheric subsidence and cooler sea surface temperatures due to upwelling result in a distinctive planetary boundary layer (PBL), marked by a sharp temperature inversion and moisture gradient. This distinct subtropical eastern ocean region showcases a unique transition from a shallow stratocumulus-topped PBL near the southern California coast to a deeper trade cumulus PBL regime closer to Hawaii. The shallow PBL coupled with frequent cloudiness poses significant challenges for conventional space-based observations and simulations in weather and climate models. The Global Navigation Satellite System (GNSS) radio occultation (RO) technique excels in sensing the PBL due to its superior vertical resolution, global coverage, and all-weather observation capability. This dissertation is comprised of three major tasks aimed at assessing the potential and limitation of GNSS RO for PBL sensing over the northeastern Pacific Ocean. First, the RO refractivity data from the first Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC-I) for the years 2007 to 2012 were used to derive the PBL height (PBLH) climatology over the Northeastern Pacific Ocean. The PBL in this region is characterized by pronounced temperature inversions and moisture gradients across the PBLH, leading to dominant ducting conditions that introduce significant negative biases in RO refractivity retrievals. Consequently, the second task examines the characteristics of the elevated ducting layer along the transect between Los Angeles, California and Honolulu, Hawaii with high-resolution radiosondes from the MAGIC field campaign and ERA5 global reanalysis data. A systematic negative refractivity bias (N-bias) below the ducting layer is observed throughout the transect, peaking approximately 70 meters below the PBL height (−5.42%), and gradually decreasing towards the surface (−0.5%). Third, the noticeable horizontal inhomogeneity, especially near the PBLH along the transect, may introduce additional RO retrieval errors, warranting further investigation. Using MAGIC radiosonde observations, a 2-dimensional (2D) model of atmospheric refractivity is created which integrates key PBL parameters. An asymmetry index is introduced to measure the extent of horizontal inhomogeneity. Then multiple phase screen (MPS) simulations were carried out to assess the impact of ducting and horizontal inhomogeneity on GNSS RO soundings. Preliminary findings highlight ducting as the primary cause of negative N-bias in RO retrieval, while horizontal inhomogeneity within the PBL contributes an additional −1% near the PBL top. This research enhances understanding of RO data quality within the PBL, paving the way for improved RO data assimilation and advancing weather and climate prediction capabilities.Physical and Environmental SciencesCollege of Scienc
PH effects on solid phase extractable dissolved organic matter: Expanding the analytical window
No full textA thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in ChemistryMarine dissolved organic matter (DOM) is the largest exchangeable organic carbon pool, holding comparable amounts of carbon as CO2 in the atmosphere and exceeding all biomass. DOM constituents are made up of thousands of unique organic compounds with astounding molecular diversity, featuring a wide range of hydrophobicity, size, and acidic or basic properties. Modern high resolution, high accuracy, and fast cycle time mass spectrometers can provide deep molecular insights into complex mixtures but require compatible samples. The inorganic matrix and low DOM concentrations have required organic biogeochemists to rely on Agilent Bond Elut Priority PoLutant (PPL) Solid Phase Extraction (SPE) to isolate and concentrate DOM through hydrophobic interactions. Currently, the standard SPE method has been optimized to maximize recovery? of dissolved organic carbon (DOC) through sample acidification and methanol elution. However, there is a lack of full understanding of the effect of adjusting the sample pH on the extraction efficiency of different DOM compounds. This study investigated the effects of pH modification on the SPE recoveries and the effects of various procedures on the isolated DOM. This study collected water samples from three sites to represent different marine systems (Lavaca River, Baffin Bay and Gulf of Mexico) with unique sources and signatures of DOM. Samples were acidified to pH 2, kept at natural pH, basified to pH 10 or run sequentially where the permeate was further isolated. Various modified methanol elution solvents were tested, comparing methanol, acidic methanol, basic methanol, and combinations of both. The isolated DOM was chemically characterized in positive mode separated with reverse-phase high performance liquid chromatography (RP-HPLC) and in negative mode with Anion Exchange Ion Chromatography (AEX-IC) on an Orbitrap Fusion Tribrid mass spectrometer (OT-FTMS) using data dependent acquisition (DDA). The standard SPE procedure with acidification yielded the highest recoveries but showed bias against dissolved organic nitrogen (DON). The samples that were not acidified, including natural pH or pH 10, yielded a different fraction of enigmatic DOM with a higher nitrogen percentage than the DOM isolates using the standard procedure. We found that through isolating DOM from a water sample at natural pH and pH 2, two fractions of DOM can be isolated, including hydrophobic DOM, acidic DOM, and basic DOM. These results suggest in order to better represent DOM from marine systems, collecting both fractions and analyzing in both positive and negative modes provide a more comprehensive and representative isolate of DOM.Environmental ScienceCollege of Scienc
Image analysis reveals environmental influences on the seagrass-epiphyte dynamic relationship for Thalassia testudinum in the northwestern Gulf of Mexico
No full textSpatiotemporal patterns in seagrass-epiphyte dynamics for Thalassia testudinum in the northwestern Gulf of Mexico were evaluated through biomass measurements and scanned-image based metrics to investigate the potentially harmful impact of excessive epiphyte accumulations on seagrass condition. Image analysis with Spectral Angle Mapper algorithms distinguished epiphyte and uncovered seagrass leaf pixels to generate a normalized metric of leaf area coverage (epiphyte pixels/total leaf pixels). Imaging metrics were compared to biomass based metrics seasonally, among three locations with different environmental conditions (depth, salinity, temperature and nutrient levels inferred from sediment porewater measurements) near Redfish Bay, Texas, USA. Image analysis, in conjunction with biomass measures, provides enhanced insight into the seagrass-epiphyte dynamic relationship and how it varies with environmental conditions. Compared with the biomass and morphological measures, image analysis may be more informative as an indicator of environmental changes. Variation in linear regressions of epiphyte biomass vs. epiphyte area (pixels) suggested changes in the thickness and/or density of accumulated epiphytes across environmental contexts and seasons. Two different epiphyte colonization patterns were presented based on the correlation between the normalized metrics of epiphyte load and epiphyte leaf coverage. The epiphyte load was highest at low temperatures and locations with elevated DIN:P ratio in sediment porewater. Conversely, the mean leaf coverage by epiphytes stayed relatively constant (±10%) across seasons but differed by location (25% ~55% in this case), suggesting that leaf growth in this study is regulated to maintain the proportion of uncolonized leaf surface and that epiphyte coverage plays a role in its regulation.The image analysis development and seagrass sampling were supported by a Texas A&M University-Corpus Christi Research Enhancement Award to KC. Funding for the nutrient measurement and the stable isotope analyses were from the Millicent Quammen Memorial Research Award, Texas A&M University-Corpus Christi to CH, and the Research and Innovation Award, Texas A&M University-Corpus Christi to CH. The open access publication fee was paid by the Open Access Publication Fund administered by the Mary and Jeff Bell Library at Texas A&M University-Corpus Christi
Whole genome sequencing century-old ethanol-preserved Philippine fishes
No full textA thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Fisheries and MaricultureThe genomes of organisms stored in museums hold a wealth of information that is challenging to access. Recent success in sequencing desiccated museum insects involved using Whole Genome Amplification (WGA) and enzymatic repair of deoxyribose nucleic acid (DNA) damage. However, these techniques have not been tested on fishes preserved in ethanol for over a century. Here, I tested for the effects of WGA, repair, and the amount of template DNA on whole genome sequencing of historical (1908-09) and contemporary (2017-19) Philippine reef fishes. I attempted to construct 178 shotgun libraries (Illumina 2 x 150bp, 92 contemporary, 86 historical) using commercial kits and successfully produced 130 libraries (86 contemporary, 44 historical). Contrary to expectation, WGA had a negative effect on success of libraries, and repair had a small number of minor positive effects. A greater proportion of historical libraries treated with WGA failed than those that were not (37% +WGA, 65% -WGA, p=0.007). While the -WGA, historical libraries that succeeded produced less reads per unit effort than contemporary libraries (p=1.60E-07), this can be addressed by increasing the amount of DNA from historical specimens in the sequencing library. Increasing the template DNA mass was one of the best ways to improve library success, except when WGA was employed. However, only a limited amount of DNA can be obtained from historical samples using a standard commercial kit, and it would be useful to explore alternative protocols. Overall, I found the basic library preparation protocol without WGA or repair to be the best alternative for sequencing historical ethanol-preserved fish. This methodology is relatively cost-effective and can unlock the genomes of historical, ethanol-preserved fishes stored on the shelves of museums.Fisheries and MaricultureCollege of Scienc
Crew members and guests on the international airways
No full textCrew members with guests on standing byside and outside of the international airways plan
Determining If 'Orientation Against the Current' Is a Dolphin Foraging Tactic
Get PDFCollege of Science, Department of Life Science, Honors Program; Faculty Mentor: Dara OrbachCommon bottlenose dolphins (Tursiops truncatus) off Port Aransas, Texas, have been observed engaging in an unusual behavior termed “orienting against the current” (OAC). OAC, last described in 1990, consists of dolphins swimming in the opposite direction of the current, remaining relatively stationary in spatial positioning. To test the hypothesis that OAC is a foraging tactic, environmental conditions were assessed when dolphins engaged in OAC compared to traditional foraging off Port Aransas. Data were collected using a survey’s theodolite positioned at the convergence of the Corpus Christi Ship Channel, Lydia Ann Channel, and Aransas Channel. Dolphins were tracked from June 2021 to October 2022. Season, time of day, current speed, group size, and OAC occurrence were recorded. OAC occurred most frequently between fall (September – December) and spring (March – June) with the highest peak during winter, in the morning (7am – 11 am) and evening (5:01pm – 8pm), in fast current speeds (2.01 – 3 knots), and in large group sizes (11+ individuals). Previous studies found that dolphin foraging off Port Aransas was most prevalent during fall to spring, in the morning and evening, in fast current speeds, and in small group sizes, both supporting and contradicting the OAC foraging tactic hypothesis. Video footage of dolphins engaged in OAC showed behaviors typical of foraging such as tossing fish, tight circling, and high arching dives as well as dolphins actively catching fish. Identification of environmental conditions when OAC occurs most prevalently may aid efforts to find dolphins engaged in this foraging tactic at other locations and augment understandings of the dynamics of dolphins within their ecosystems
