College of Science Theses and Dissertations
Permanent URI for this collectionhttps://hdl.handle.net/1969.6/1175
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Browsing College of Science Theses and Dissertations by Author "Abdulla, Hussain"
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Item Assessing the influence of genotypic diversity on sulfur dynamics in the seagrass halodule wrightii using stable isotope analysis(2022-07-19) Girard, Allyson; Larkin, Patrick; Abdulla, Hussain; Felix, JosephCoastal development and other mounting anthropogenic pressures are threatening valuable seagrass habitats. The greatest risks posed to seagrasses are the effects of coastal eutrophication, which stimulates primary productivity and ultimately supplies abundant organic matter to marine sediments. The decomposition of this material is initially facilitated by aerobic microorganisms, depleting dissolved oxygen and generating anoxic conditions. Under these conditions, anaerobic microorganisms such as sulfate-reducing bacteria begin to dominate the degradation process, which reduce sulfate (SO42-) to sulfide (H2S) for energy production. The accumulation of H2S in marine sediments is problematic for seagrasses, as this molecule can be highly toxic. Yet, seagrasses can withstand relatively high concentrations of H2S in their environments. Stable isotope analyses have been used to investigate sulfide intrusion in seagrass meadows, as the unique isotopic signature of sediment-derived sulfur can be used to trace the uptake of H2S and its distribution throughout the plant. This technique has allowed the study of factors that may influence sulfide production and intrusion, such as reduced light availability, organic matter enrichment, and high temperatures. However, few studies have examined the biological or biochemical features that enable seagrasses to withstand relatively high sedimentary sulfide levels. One biological feature that may help confer resistance is population genetic diversity, which has been identified as an important trait in the survival and performance of seagrass meadows under environmental stress. In general, genetic diversity is thought to play an important role in population resistance to environmental disturbance, as a wider assortment of functional traits encoded at the molecular level results in a variety of phenotypes likely to possess morphological and physiological differences that are complementary. This genotypic complementarity may extend to biochemical strategies associated with tolerance to, or detoxification of, H2S. The purpose of this study was to determine whether sulfide intrusion differs between genotypes of the seagrass Halodule wrightii, a prominent species in the Gulf of Mexico. Further, as the sulfur isotopic composition of marine sediments and seagrass vegetation is known to exhibit high spatial variability, this study also sought to assess sulfide intrusion between populations from distinct sites along the Texas Gulf Coast. Stable isotope data was used to infer the proportion of sulfur in H. wrightii tissues that was derived from sedimentary sulfide, while total sulfur (TS) data was also considered to understand the extent of sulfur accumulation within the plant. H. wrightii genotypes were determined by screening each sample at a series of microsatellite loci previously identified for this species. Although no difference in sulfide intrusion was observed between genotypes, sulfide uptake and distribution was significantly different between the three study sites. The results offer important insight to the effect of local conditions on sulfide intrusion in seagrass meadows and may guide future investigations concerned with the influence of genotypic diversity on H2S metabolism in seagrasses.Item Comprehensive approach for dissolved organic matter chemical characterization using orbitrap fusion tribrid mass spectrometer coupled with ion and liquid chromatography techniques(2021-12) Bergmann, Daniela; Bergmann, Daniela; Abdulla, Hussain; Abdulla, Hussain; Coffin, Richard; Murgulet, Dorina; Coffin, Richard; Murgulet, DorinaDissolved organic matter (DOM) contains the largest active organic carbon in the global carbon cycle. Though it has been extensively studied, only <10% of DOM has been chemically characterized into individual dissolved compounds. DOM is one of the most complex mixtures in nature; it consists of thousands of compounds with various molecular compositions, functional groups, and physicochemical characteristics. This study introduced a more comprehensive DOM characterization method by coupling both Ion Chromatography and Liquid Chromatography with high accuracy mass and resolution mass spectrometer. Estuarine DOM samples were and analyzed by Orbitrap Fusion Tribrid mass spectrometer (OT-FT-MS) coupled to both Ion Chromatography (IC) in negative mode and Liquid Chromatography (LC) in positive mode. This combination allows us to cover various DOM compounds ranging from highly cationic to highly anionic molecules. On-the-fly mass calibration of the Orbitrap at every scan by utilizing the “lock mass” function in the OT-FT-MS assures high mass accuracy throughout the whole sample run by a post-column introduction of internal labeled standards. A pooled quality control sample was used to increase reproducibility by applying systematic error removal using the random forest (SERRF) technique. The on-the-fly internal calibration application was tested on standard mixes before applying to actual DOM samples. In LC, the mass accuracy for the standards was consistently below +1.0ppm, and in IC below -4.0ppm, giving the OT-FT-MS the potential of reaching the massaccuracy of the Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Once “lock mass” was established, estuarine surface water DOMsamples were analyzed in negative and positive modes. LC coupled to the OT-FT-MS for positive mode detection resulted in 915 compounds including 53 peptides and deaminated peptides that were identified through an in-house mass list comparison. IC coupled to the OT-FT-MS for negative mode detection resulted in 1432 extra compounds and including 361 deaminated peptides. Comparing the number of compounds detected shows the importance of analyzing both detection modes and the promising results of using IC in negative mode. A random forest-based normalization termed SERRF was compared to the traditional way of data normalization constant sum technique. Although constant sum provides already meaningful PCA data, SERRF assured a tight cluster of all Quality Control (QC). In IC mode, the relative standard deviation of QC samples was as high as 34.1% and corrected to 4.4% with SERRF, and in LC, the relative standard deviation was corrected from 28.1% to 3.9%. A combination of IC, LC, “lock mass”, and SERRF with the OT-FT-MS provides reliable and comprehensive approaches for DOM molecular characterization.Item Distribution of pesticides in groundwater and surface water flood-impacted unconnected communities in South Texas following Hurricane Hanna(2022-08) Matarrita Rodríguez, Jessie; Abdulla, Hussain; Conkle, Jeremy L.; Murgulet, DorinaPesticides are a vital farming input as they help protect crops from pests and diseases for quality yields and high productivity. However, pesticides' high production, extensive use, and persistence are a potential risk for human health and ecosystems due to their leaching or runoff into the surface water (SW) and groundwater (GW). Over the years, there has been an increasing concern regarding the water quality of SW and GW next to farming areas, specifically after spills or industrial discharges, heavy rainfall, and intense storms. In the case of hurricanes, these cause deposition of contaminants from the atmosphere, disturbance and transport of the sediments in surface water bodies, surface run-off, and penetration of floodwaters to GW. In addition, pesticide degradation in the environment due to different biotic and abiotic transformation processes produces transformation products (TPs), sometimes even more toxic than the original compound. In July 2020, Hurricane Hanna severely damaged infrastructure and agriculture in many counties across the Rio Grande Valley. This area has the largest colonias in South Texas, predominantly Hispanic low-income semirural communities near the Texas-Mexico border that mainly rely on GW as a drinking water source. As part of this study, surface water and groundwater samples were collected from colonias in South Texas communities after hurricane Hanna for one year. The analytical approach involved solid-phase extraction (SPE) followed by suspect and target screening of pesticides using ultrahigh-pressure liquid chromatography (UPLC) coupled to a high-resolution Orbitrap Fusion Tribrid mass spectrometer system (OT-FTMS). The advantages of the state-of-the-art high resolution mass spectrometry allowed the accurate identification and quantification of pesticides using an in-house compound database of 308 pesticides for target screening. This is one of the most extensive studies that has screened and quantified over 200 pesticides in a single sample in the United States and, to my knowledge, is one of the largest in Texas. The results of eight monitoring sampling campaigns revealed the occurrence of 21 pesticides with minimum instrumental limit of detection (LOD) of 0.05 ng/mL and limit of quantification (LOQ) of 0.10 ng/mL. Six herbicides were the most detected compounds, followed by insecticides (5), fungicides (4), TPs (3), and a plant growth regulator (1). The most frequently detected compounds were atrazine, clothianidin, cycluron, DEA, dinotefuran, and norflurazon and those with the highest concentrations were clothianidin (211 ng/L), DEET (13,885 ng/L), and norflurazon (952 ng/L). In general, more compounds were detected in GW than in SW, except for atrazine and DEA. Atrazine in SW showed higher detections frequency (67%) than GW (15%) as well as DEA (GW = 6%, SW = 8%). DEET was the compound detected at the highest frequency in GW (74%) while atrazine was detected at the highest frequency in SW (67%). The leaching of pesticides to GW is a complex process and depends on the pesticide's chemical properties, characteristics of the soil, volatilization, climatic conditions of the site, plant uptake, and pesticide management practices. Mainly, pesticides with high leaching potential are more likely to be transported in groundwater beyond application area. In this study, clothianidin and norflurazon with high leaching potential showed significant concentrations in GW. This is one of the few studies able to survey more than 200 pesticides in the United States in general and in Texas specifically, using high resolution mass spectrometry. This work provides a baseline of the water quality for those communities that rely on GW as the primary source of drinking water supply. The occurrence of pesticides in GW demonstrates the vulnerability of the area and the need to continue monitoring the water quality in this region.Item Metabolomic profiling of human embryo during pre-implantation in vitro fertilization non-invasive approach(2021-05) Al Shaikh, Maryam; Abdulla, Hussain; Billiot, Fereshteh; Gonzales, Xavier FonzIn vitro fertilization (IVF) is a standard protocol used to treat infertility. However, the probability of successful embryo implantation during IVF is very low. Most of the IVF clinics depend on morphological scoring by embryologists to select high-quality embryos capable of implantation. But morphological scoring has only around 30% successful pregnancy rate. In this study, I investigated the potential of a new embryo scoring method based on measuring the change in culture media's metabolomic profiles. I analyzed 71 culture media samples with known pregnancy outcomes from two different culture media by ultraperformance liquid chromatography (UPLC) coupled with ultrahigh-resolution and accuracy mass spectrometer. I used a newly developed on-the-fly dynamic data acquisition technique to increase the percentage of metabolite compounds with MS2 fragmentation spectra. To identify potential metabolomic pregnancy biomarkers, we used a combination of statistical analysis techniques like principal component analysis (PCA), differential analysis (volcano plots), and trend charts. We used Molecular Formula Calculator software, ChemSpider, and mzCloud databases to assign the molecule formula and chemical structure for the detected significant biomarkers. Also, we applied in-silico fragmentation and FISh scoring to validate the chemical structures of the identified biomarkers. Using PCA, we did not find any apparent clustering for pregnant or non-pregnant samples, but we could locate a few outliers' spectra. However, with volcano plots, we were able to identify a set of up-regulated biomarkers that are associated with non-pregnancy and down-regulated biomarkers that are associated with pregnancy in both media. Utilizing the KEGG and Metabolika databases, we recognized two possible metabolomics pathways. This study can improve selecting viable embryos, which will lead to an increase in the success rate of IVF. It will also provide a better understanding of human embryos' metabolomic biochemical pathways during the preimplantation stage.Item Molecular networking with network analysis(2021-12) Cross, Breeanna; Abdulla, Hussain; Guardiola, José; Felix, Joseph D.Network analysis is the analysis of a collection of elements and their relationships based on graph theory. Graph theory has become essential for identifying and understanding the relationships between compounds in mass spectrometry (MS). A molecular network is the visual display of the chemical space in MS experiments. The advancements in coupling different chromatography techniques with high resolution and mass accuracy mass spectrometer have increased the ability to produce better quality tandem mass spectrometry (MS/MS) of individual compounds in a single run. With these advancements, compounds within complex mixtures were be analyzed and detected more thoroughly using both the targeted and untargeted approaches. Further, the structures of these compounds might be able to be identified with higher confidence. Using the generated MS/MS spectra, molecular networks were developed based on the similarities of molecular structures. However, the traditional 2-dimensional network analysis is static and could not show how these compounds change with depth, time, or distance. In this study, I have created a three-dimensional (3-D) molecular network analysis software to examine how dissolved organic matter (DOM) transforms with depth, with time, or with distance to have fully understood, for example, the accumulation and reactivity of DOM in the marine ecosystem. As a proof-of-concept example, I have used 3D molecular network analysis to understand abiotic sulfurization mechanisms in marine sediments better. The abiotic sulfurization enhances organic matter preservation and proto kerogen formation at low temperatures within marine sediments. The molecular networking method presented here supports the evidence of abiotic nucleophilic addition reactions involving bisulfide (HS−) and polysulfide (HSx−) in Santa Barbara Basin sediment porewater. This 3D-molecular Network analysis technique has a great potential to reveal different transformation and degradation pathways of dissolved organic matter by various biotic and abiotic environmental perturbations.Item Quantification and transformation of water soluble organic nitrogen in a coastal urban airshed(2021-05) Apacible, Scilyn; Apacible, Scilyn; Felix, Joseph; Felix, Joseph; Coffin, Richard; Abdulla, Hussain; Coffin, Richard; Abdulla, HussainAtmospheric organic nitrogen (ON) is poorly quantified due to its complexity, measurement difficulty and historical consensus that it was less significant than inorganic nitrogen. Studies that have measured ON are not evenly spread across various environments or geographic regions further contributing to a general lack of knowledge about global atmospheric ON deposition and transformations. In this study, PM2.5 and PM10 samples were collected in an urban coastal airshed, Corpus Christi, TX, USA between November 2019, and October 2020. The organic and inorganic forms of nitrogen were analyzed and the factors controlling their concentrations were examined. The mean concentrations of water soluble organic nitrogen (WSON) in PM2.5 and PM10 were 0.081 ± 0.12 and 0.12 ± 0.11 µg m-3, respectively. The observed WSON concentrations were similar to those observed in remote and marine sites. The WSON concentrations showed significant correlation with NO3⁻ and NH4⁺ during spring season in PM10 indicating that marine source (e.g., sea salt) and biogenic emission are contributing factor for NO3⁻, while agricultural sources are contributing factor for NH4⁺. On average, ON contributed 15% and 10% to total nitrogen in PM2.5 and PM10 at the coastal urban airshed. The average annual dry deposition fluxes for PM2.5 NO3⁻, NH4⁺, and WSON were 0.217, 0.027, and 0.68 kg ha−1 y −1, respectively. The annual dry deposition fluxes for PM10 NO3⁻, NH4⁺, and WSON were 0.55, 0.031, and 2.48 kg ha−1 y −1. The EPA CASTNET network’s closet monitoring site reports annual dry N deposition flux of 3.67 kg ha−1 y −1 , but does not account for ON thus potentially overlooking ~40% of N deposition. Furthermore, the photochemical transformation of ON into IN was investigated and results from these experiments revealed alternating photoproduction and degradation of IN (NO3⁻, NH4⁺). These WSON photochemical transformation will contribute to the increase or decrease of nitrogen bioavailability after deposition in this coastal region. This study highlights the significance of the ON component of atmospheric deposition in this northern Gulf of Mexico region and the need to for ON inclusion when determining coastal N loading and N mitigation strategies.