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The gastrointestinal (GI) tract is home to a complex and diverse microbial ecosystem that contributes to health or disease in many aspects. While bacterial species are the majority in the GI tract, their cohabitants, fungal species, should not be forgotten. Children with autism spectrum disorder (ASD) often suffer from GI disorders and associated symptoms, implying a role the bacterial and fungal gut microbiota play in maintaining human health. The irregularities in GI symptoms can negatively affect the overall quality of life or even worsen behavioral symptoms the children present. Even with the increase in the availability of next-generation sequencing technologies, the composition and diversities of fungal microbiotas are understudied, especially in the context of ASD. We therefore aimed to investigate the gut mycobiota of 36 neurotypical children and 38 children with ASD. We obtained stool samples from all participants, as well as autism severity and GI symptom scores to help us understand the effect the mycobiome has on these symptoms. By targeting the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA V4 regions, we obtained fungal and bacterial amplicon sequences, from which we investigated the diversities, composition, and potential link between two different ecological clades. From fungal amplicon sequencing results, we observed a significant decrease in the observed fungal OTUs in children with ASD, implying a lack of potentially beneficial fungi in ASD subjects. We performed Bray-Curtis principal coordinates analysis and observed significant differences in fungal microbiota composition between the two groups. Taxonomic analysis showed higher relative abundances of Candida , Pichia, Penicillium , and Exophiala in ASD subjects, yet due to a large dispersion of data, the differences were not statistically significant. Interestingly, we observed a bimodal distribution of Candida abundances within children with ASD. Candida's relative abundance was not significantly correlated with GI scores, but children with high Candida relative abundances presented significantly higher Autism Treatment Evaluation Checklist (ATEC) scores, suggesting a role of Candida on ASD behavioral symptoms. Regarding the bacterial gut microbiota, we found marginally lower observed OTUs and significantly lower relative abundance of Prevotella in the ASD group, which was consistent with previous studies. Taken together, we demonstrated that autism is closely linked with a distinct gut mycobiota, characterized by a loss of fungal and bacterial diversity and an altered fungal and bacterial composition.
ContributorsPatel, Jigar (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Kang, Dae Wook (Committee member) / Adams, James (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The effect of an anaerobic reductive environment produced by the oxidation of zero valent iron (ZVI) on the microbial reductive dechlorination of trichloroethylene and its applicability to in-situ bioremediation processes was investigated using microcosms and soil column studies. I learned that microbial dechlorination requires a highly reductive environment, as represented by negative values for oxidation-reduction potential (ORP), which can be maintained through the addition of reducing agents such as ZVI, or to a lesser extent, the fermentation of added substrates such as lactate. Microcosm conditions represented distance from an in-situ treatment injection well and contained different types of iron species and dechlorinating bioaugmentation cultures. Diminishing efficacy of microbial reductive dechlorination along a gradient away from the injection zone was observed, characterized by increasing ORP and decreasing pH. Results also suggested that the use of particular biostimulation substrates is key to prioritizing the dechlorination reaction against competing microbial and abiotic processes by supplying electrons needed for microbial dechlorination.
ContributorsMouti, Aatikah (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Delgado, Anca (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Hydrogen is a key indicator of microbial activity in soils/sediments and groundwater because of its role as an electron donor for reducing sulfate and nitrate and carrying out other metabolic processes. The goal of this study was to quantitatively measure the total biological hydrogen demand (TBHD) of soils and sediments in anaerobic environments. We define the total biological hydrogen demand as the sum of all electron acceptors that can be used by hydrogen-oxidizing microorganisms. Three sets of anaerobic microcosms were set up with different soils/sediments, named Carolina, Garden, and ASM. The microcosms included 25g of soil/sediment and 75 mL of anaerobic medium. 10 mL of hydrogen were pulse-fed for 100 days. Hydrogen consumption and methane production were tracked using gas chromatography. Chemical analysis of each soil was performed at the beginning of the experiment to determine the concentration of electron acceptors in the soils/sediments, including nitrate, sulfate, iron and bicarbonate. An analysis of the microbial community was done at t = 0 and at the end of the 100 days to examine changes in the microbial community due to the metabolic processes occurring as hydrogen was consumed. Carolina consumed 9810 43 mol of hydrogen and produced 19,572 2075 mol of methane. Garden consumed 4006 33 mol of hydrogen and produced 7,239 543 mol of methane. Lastly, ASM consumed 1557 84 mol of hydrogen and produced 1,325 715 mol of methane. I conclude that the concentration of bicarbonate initially present in the soil had the most influence over the hydrogen demand and microbial community enrichment. To improve this research, I recommend that future studies include a chemical analysis of final soil geochemistry conditions, as this will provide with a better idea of what pathway the hydrogen is taking in each soil.
ContributorsLuna Aguero, Marisol (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Delgado, Anca (Committee member) / Civil, Environmental and Sustainable Engineering Programs (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
In the United States, the prevalence of pediatric obesity has increased to 17% in the general population and even more so in the Hispanic pediatric population to 22.4%. These children are at a higher risk for associated comorbidities, including cardiovascular disease and insulin resistance. The purpose of the following study is to determine the effectiveness of the Nutrition and Health Awareness curriculum at reducing childhood obesity by evaluating alterations in the gut microbial composition, diet, and overall health of the students throughout the five-week program. Nutrition and Health Awareness (NHA) is a student organization that strives to reduce the prevalence of obesity, diabetes, and cardiovascular diseases, specifically in children, by providing active nutrition education services through peer mentoring in elementary schools and community programs. This study went through ASU's Institutional Review Board process and all forms were translated into Spanish. The control group maintained their normal routines and the experimental group received the 5 week NHA program and then continued with their normal routines. Anthropometric measures (Body Mass Index, waist-to-hip ratio, and blood pressure), diet measures (Hispanic food frequency questionnaire), fecal swabs, and content surveys were collected on weeks 0, 5, and 8. Contrary to expected, alpha diversity, kilocalorie intake, and macronutrient intake decreased as the study progressed for both the control and experimental groups. Anthropometric measurements were relatively stable. Though not statistically significant, the greatest difference in time points is between weeks 1 and 8. This decrease in alpha diversity and kilocalorie intake could be due to a change in environment since the children started school on week 8. Future implications of this study are that parental involvement is necessary for an effective, sustainable change in these children. More research in different settings is necessary to determine NHA's effectiveness
ContributorsPatel, Kapila Cristina (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Whisner, Corrie (Committee member) / School of Nutrition and Health Promotion (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Microorganisms can produce metabolites in the gut including short chain fatty acids, vitamins, and amino acids. Certain metabolites produced in the gut can affect the brain through changes in neurotransmitter concentrations. Serotonin, a neurotransmitter, is associated with mood, appetite, and sleep. Up to 90% of serotonin synthesis is located in the gut, by human enterochromaffin cells. Bacteria known to biosynthesize tryptophan, precursor to serotonin, include Escherichia coli, Enterococcus and Streptococcus. Tryptophan is synthesized by bacteria with the enzyme tryptophan synthase and requires Vitamin B6 (Pyridoxal). We hypothesize that gut isolates from surgical weight loss patients can enhance tryptophan production, which relies on vitamin B6 availability. Our goal was to isolate bacteria in order to test for tryptophan production and to determine how Vitamin B6 concentrations could affect tryptophan production. We isolated gut bacteria was from successful surgical weight loss patient with selective pressures for Enterobacter isolates and Enterococcus isolates. We tested the isolates were tested to determine if they could biosynthesize tryptophan in-vitro. Bacterial cultures were enriched with yeast and enriched with serine and indole, substrates necessary for tryptophan biosynthesis. We analyzed the supernatant samples for tryptophan production using GC-FID. Bacterial isolates most closely related to E. coli and Klebsiella based on 16S rRNA gene sequences, produced tryptophan in vitro. While under serine & indole media conditions, R1, the isolate most similar to Klebsiella produced more tryptophan than R14, the isolate most similar to E. coli. We tested the R1 isolate with a gradient of vitamin B6 concentrations from 0.02 µg/mL to 0.2 µg/mL to determine its effect on tryptophan production. When less than 0.05 µg/mL of Vitamin B6 was added, tryptophan production at 6 hours was higher than tryptophan production with Vitamin B6 concentrations at 0.05 µg/mL and above. The production and consumption of tryptophan by Klebsiella under 0 µg/mL and 0.02 µg/mL concentrations of Vitamin B6 occurred at a faster rate when compared to concentrations 0.05 µg/mL or higher of Vitamin B6.
ContributorsYee, Emily L. (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Ilhan, Zehra (Committee member) / W. P. Carey School of Business (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Under current climate conditions northern peatlands mostly act as C sinks; however, changes in climate and environmental conditions, can change the soil carbon decomposition cascade, thus altering the sink status. Here I studied one of the most abundant northern peatland types, poor fen, situated along a climate gradient from tundra (Daring Lake, Canada) to boreal forest (Lutose, Canada) to temperate broadleaf and mixed forest (Bog Lake, MN and Chicago Bog, NY) biomes to assess patterns of microbial abundance across the climate gradient. Principal component regression analysis of the microbial community and environmental variables determined that mean annual temperature (MAT) (r2=0.85), mean annual precipitation (MAP) (r2=0.88), and soil temperature (r2=0.77), were the top significant drivers of microbial community composition (p < 0.001). Niche breadth analysis revealed the relative abundance of Intrasporangiaceae, Methanobacteriaceae and Candidatus Methanoflorentaceae fam. nov. to increase when MAT and MAP decrease. The same analysis showed Spirochaetaceae, Methanosaetaceae and Methanoregulaceae to increase in relative abundance when MAP, soil temperature and MAT increased, respectively. These findings indicated that climate variables were the strongest predictors of microbial community composition and that certain taxa, especially methanogenic families demonstrate distinct patterns across the climate gradient. To evaluate microbial production of methanogenic substrates, I carried out High Resolution-DNA-Stable Isotope Probing (HR-DNA-SIP) to evaluate the active portion of the community’s intermediary ecosystem metabolic processes. HR-DNA-SIP revealed several challenges in efficiency of labelling and statistical identification of responders, however families like Veillonellaceae, Magnetospirillaceae, Acidobacteriaceae 1, were found ubiquitously active in glucose amended incubations. Differences in metabolic byproducts from glucose amendments show distinct patterns in acetate and propionate accumulation across sites. Families like Spirochaetaceae and Sphingomonadaceae were only found to be active in select sites of propionate amended incubations. By-product analysis from propionate incubations indicate that the northernmost sites were acetate-accumulating communities.
These results indicate that microbial communities found in poor fen northern peatlands are strongly influenced by climate variables predicted to change under current climate scenarios. I have identified patterns of relative abundance and activity of select microbial taxa, indicating the potential for climate variables to influence the metabolic pathway in which carbon moves through peatland systems.
ContributorsSarno, Analissa Flores (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Childers, Daniel (Committee member) / Arizona State University (Publisher)
Created2022
Description
Traditional Reinforcement Learning (RL) assumes to learn policies with respect to reward available from the environment but sometimes learning in a complex domain requires wisdom which comes from a wide range of experience. In behavior based robotics, it is observed that a complex behavior can be described by a combination of simpler behaviors. It is tempting to apply similar idea such that simpler behaviors can be combined in a meaningful way to tailor the complex combination. Such an approach would enable faster learning and modular design of behaviors. Complex behaviors can be combined with other behaviors to create even more advanced behaviors resulting in a rich set of possibilities. Similar to RL, combined behavior can keep evolving by interacting with the environment. The requirement of this method is to specify a reasonable set of simple behaviors. In this research, I present an algorithm that aims at combining behavior such that the resulting behavior has characteristics of each individual behavior. This approach has been inspired by behavior based robotics, such as the subsumption architecture and motor schema-based design. The combination algorithm outputs n weights to combine behaviors linearly. The weights are state dependent and change dynamically at every step in an episode. This idea is tested on discrete and continuous environments like OpenAI’s “Lunar Lander” and “Biped Walker”. Results are compared with related domains like Multi-objective RL, Hierarchical RL, Transfer learning, and basic RL. It is observed that the combination of behaviors is a novel way of learning which helps the agent achieve required characteristics. A combination is learned for a given state and so the agent is able to learn faster in an efficient manner compared to other similar approaches. Agent beautifully demonstrates characteristics of multiple behaviors which helps the agent to learn and adapt to the environment. Future directions are also suggested as possible extensions to this research.
ContributorsVora, Kevin Jatin (Author) / Zhang, Yu (Thesis advisor) / Yang, Yezhou (Committee member) / Praharaj, Sarbeswar (Committee member) / Arizona State University (Publisher)
Created2021
Description
Widespread use of halogenated organic compounds for commercial and industrial purposes makes halogenated organic pollutants (HOPs) a global challenge for environmental quality. Current wastewater treatment plants (WWTPs) are successful at reducing chemical oxygen demand (COD), but the removal of HOPs often is poor. Since HOPs are xenobiotics, the biodegradation of HOPs is usually limited in the WWTPs. The current methods for HOPs treatments (e.g., chemical, photochemical, electrochemical, and biological methods) do have their limitations for practical applications. Therefore, a combination of catalytic and biological treatment methods may overcome the challenges of HOPs removal.This dissertation investigated a novel catalytic and biological synergistic platform to treat HOPs. 4-chlorophenol (4-CP) and halogenated herbicides were used as model pollutants for the HOPs removal tests. The biological part of experiments documented successful co-oxidation of HOPs and analog non-halogenated organic pollutants (OPs) (as the primary substrates) in the continuous operation of O2-based membrane biofilm reactor (O2-MBfR). In the first stage of the synergistic platform, HOPs were reductively dehalogenated to less toxic and more biodegradable OPs during continuous operation of a H2-based membrane catalytic-film reactor (H2-MCfR). The synergistic platform experiments demonstrated that OPs generated in the H2-MCfR were used as the primary substrates to support the co-oxidation of HOPs in the subsequent O2-MBfR. Once at least 90% conversation of HOPs to OPs was achieved in the H2-MCfR, the products (OPs to HOPs mole ratio >9) in the effluent could be completely mineralized through co-oxidation in O2-MBfR. By using H2 gas as the primary substrate, instead adding the analog OP, the synergistic platform greatly reduced chemical costs and carbon-dioxide emissions during HOPs co-oxidation.
ContributorsLuo, Yihao (Author) / Rittmann, Bruce (Thesis advisor) / Krajmalnik-Brown, Rosa (Committee member) / Torres, Cesar (Committee member) / Arizona State University (Publisher)
Created2022
Description
The imaging and detection of specific cell types deep in biological tissue is critical for the diagnosis of cancer and the study of biological phenomena. Current high-resolution optical imaging techniques are depth limited due to the high degree of optical scattering that occurs in tissues. To address these limitations, photoacoustic (PA) techniques have emerged as noninvasive methods for the imaging and detection of specific biological structures at extended depths in vivo. In addition, near-infrared (NIR) contrast agents have further increased the depth at which PA imaging can be achieved in biological tissues. The goal of this research is to combine novel PA imaging and NIR labeling strategies for the diagnosis of disease and for the detection of neuronal subtypes. Central Hypothesis: Utilizing custom-designed PA systems and NIR labeling techniques will enable the detection of specific cell types in vitro and in mammalian brain slices. Work presented in this dissertation addresses the following: (Chapter 2): The custom photoacoustic flow cytometry system combined with NIR absorbing copper sulfide nanoparticles for the detection of ovarian circulating tumor cells (CTCs) at physiologically relevant concentrations. Results obtained from this Chapter provide a unique tool for the future detection of ovarian CTCs in patient samples at the point of care. (Chapter 3): The custom photoacoustic microscopy (PAM) system can detect genetically encoded near-infrared fluorescent proteins (iRFPs) in cells in vitro. Results obtained from this Chapter can significantly increase the depth at which neurons and cellular processes can be targeted and imaged in vitro. (Chapter 4): Utilizing the Cre/lox recombination system with AAV vectors will enable selective tagging of dopaminergic neurons with iRFP for detection in brain slices using PAM. Thus, providing a new means of increasing the depth at which neuronal subtypes can be imaged and detected in the mammalian brain. Significance: Knowledge gained from this research could have significant impacts on the PA detection of ovarian cancer and extend the depth at which neuronal subtypes are imaged in the mammalian brain.
ContributorsLusk, Joel F. (Author) / Smith, Barbara S. (Thesis advisor) / Halden, Rolf (Committee member) / Anderson, Trent (Committee member) / Arizona State University (Publisher)
Created2022
Description
Electroactive bacteria connect biology to electricity, acting as livingelectrochemical catalysts. In nature, these bacteria can respire insoluble compounds like
iron oxides, and in the laboratory, they are able to respire an electrode and produce an
electrical current. This document investigates two of these electroactive bacteria:
Geobacter sulfurreducens and Thermincola ferriacetica. G. sulfurreducens is a Gramnegative iron-reducing soil bacterium, and T. ferriacetica is a thermophilic, Grampositive bacterium that can reduce iron minerals and several other electron acceptors.
Respiring insoluble electron acceptors like metal oxides presents challenges to a
bacterium. The organism must extend its electron transport chain from the inner
membrane outside the cell and across a significant distance to the surface of the electron
acceptor. G. sulfurreducens is one of the most-studied electroactive bacteria, and despite
this there are many gaps in knowledge about its mechanisms for transporting electrons
extracellularly. Research in this area is complicated by the presence of multiple pathways
that may be concurrently expressed. I used cyclic voltammetry to determine which
pathways are present in electroactive biofilms of G. sulfurreducens grown under different
conditions and correlated this information with gene expression data from the same
conditions. This correlation presented several genes that may be components of specific
pathways not just at the inner membrane but along the entire respiratory pathway, and I
propose an updated model of the pathways in this organism. I also characterized the
composition of G. sulfurreducens and found that it has high iron and lipid content
independent of growth condition, and the high iron content is explained by the large
abundance of multiheme cytochrome expression that I observed. I used multiple
microscopy techniques to examine extracellular respiration in G. sulfurreducens, and in
the process discovered a novel organelle: the intracytoplasmic membrane. I show 3D
reconstructions of the organelle in G. sulfurreducens and discuss its implications for the
cell’s metabolism. Finally, I discuss gene expression in T. ferriacetica in RNA samples
collected from an anode-respiring culture and highlight the most abundantly expressed
genes related to anode-respiring metabolism.
ContributorsHowley, Ethan Thomas (Author) / Torres, César I (Thesis advisor) / Krajmalnik-Brown, Rosa (Thesis advisor) / Nannenga, Brent (Committee member) / Arizona State University (Publisher)
Created2022