Dissertations / Theses on the topic 'Microbead'
To see the other types of publications on this topic, follow the link: Microbead.
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'Microbead.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
THOMAS, JENNIFER HODGES. "APPLICATIONS OF MICROBEAD-BASED ELECTROCHEMICAL IMMUNOASSAY." University of Cincinnati / OhioLINK, 2003. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1069337644.
Full text
2
Maruyama, Hisataka, Fumihito Arai, Toshio Fukuda, and 敏男 福田. "Fabrication of Functional Gel-Microbead for Local Environment Measurement in Microchip." IEEE, 2008. http://hdl.handle.net/2237/11147.
Full text
3
Albert, Keith J. "Microbead array-based artificial nose : explosives detection and simple/complex odor discrimination /." Thesis, Connect to Dissertations & Theses @ Tufts University, 2001.
Find full textAbstract:
Thesis (Ph.D.)--Tufts University, 2001.Adviser: David R. Walt. Submitted to the Dept. of Chemistry. Includes bibliographical references. Access restricted to members of the Tufts University community. Also available via the World Wide Web;
4
Conklin, Natasha Mwale. "Effect of dissolved chlorine on an MS2 bacteriophage immunoassay and tryptophan side chain." Cincinnati, Ohio : University of Cincinnati, 2009. http://rave.ohiolink.edu/etdc/view.cgi?acc_num=ucin1243362224.
Full textAbstract:
Thesis (Ph.D.)--University of Cincinnati, 2009.Advisors: H. Brian Halsall PhD (Committee Chair), William Heineman PhD (Committee Co-Chair), Patrick Limbach PhD (Committee Member), Pearl Tsang PhD (Committee Member). Title from electronic thesis title page (viewed July 25, 2009). Keywords: Chlorine; hypochlorous acid; immunoassay; tryptophan; indole acetic acid; paramagnetic microbead. Includes abstract. Includes bibliographical references.
5
Filipponi, Luisa, and n/a. "New micropatterning techniques for the spatial addressable immobilization of proteins." Swinburne University of Technology, 2006. http://adt.lib.swin.edu.au./public/adt-VSWT20060905.113858.
Full textAbstract:
Bio-microdevices are miniaturised devices based on biologically derived components
(e.g., DNA, proteins, and cells) combined or integrated with microfabricated substrates.
These devices are of interest for numerous applications, ranging from drug discovery, to
environmental monitoring, to tissue engineering. Before a bio-microdevice can be fully
developed, specific fabrication issues need to be addressed. One of the most important
is the spatial immobilization of selected biomolecules in specific micro-areas of the
device. Among the biomolecules of interest, the controlled immobilization of proteins to
surfaces is particularly challenging due to the complexity of these macromolecules and
their tendency to lose bioactivity during the immobilization step. The present Thesis
reports on three novel micropatterning techniques for the spatial immobilization of
proteins with bioactivity retention and improved read-out of the resulting micropatterns.
The technologies developed are based on three different micropatterning approaches,
namely 1) direct-writing UV laser microablation (proLAB), 2) a novel microcontact
printing method (�CPTA) and 3) a replica molding method combined with bead selfassembly
(BeadMicroArray). The first two technologies, proLAB and �CPTA, are an
implementation of existing techniques (laser ablation and �CP, respectively), whereas
the third, i.e., the BeadMicroArray, is a totally new technique and type of patterning
platform.
'ProLAB' is a technology that uses a micro-dissection tool equipped with a UV laser
(the LaserScissors�) for ablating a substrate made of a layer of ablatable material, gold,
deposited over a thin polymer layer. The latter layer is transparent to the laser but
favours protein adsorption. In the present work microchannels were chosen as the
structure of interest with the aim of arranging them in 'bar-codes', so to create an
'information-addressable' microarray. This platform was fabricated and its application
to specific antigen binding demonstrated.
The second technique that was developed is a microstamping method which exploits the
instability of a high-aspect ratio rubber stamp fabricated via soft-lithography. The
technique is denominated microcontact printing trapping air (�CPTA) since the collapsing of a rubber stamp made of an array of micro-pillars over a plane glass surface
resulted in the formation of a large air gap around the entire array. The method can be
successfully employed for printing micro-arrays of proteins, maintaining biological
activity. The technique was compared with robotic spotting and found that microarrays
obtained with the �CPTA method were more homogeneous and had a higher signal-tonoise
ratio.
The third technique developed, the BeadMicroArray, introduces a totally new platform
for the spatial addressable immobilization of proteins. It combines replica molding with
microbead self-assembling, resulting in a platform where diagnostic beads are entrapped
at the tip of micropillars arranged in a microarray format. The fabrication of the
BeadMicroArray involves depositing functional microbeads in an array of V-shaped
wells using spin coating. The deposition is totally random, and conditions were
optimised to fill about half the array during spin coating. After replica molding, the
resulting polymer mold contains pyramid-shaped posts with beads entrapped at the very
tip of the post. Thanks to the fabrication mode involved, every BeadMicroArray
fabricated contains a unique geometric code, therefore assigning a specific code to each
microarray. In the present work it was demonstrated that the functionality of the beads
after replica molding remains intact, and that proteins can be selectively immobilized on
the beads, for instance via biorecognition. The platform showed a remarkable level of
selectively which, together with an efficient blocking towards protein non-specific
adsorption, lead to a read-out characterized by a very good signal-to-noise. Also, after
recognition, a code was clearly visible, therefore showing the encoding capacity of this
unique microarray.
6
Prikockis, Michael Vito. "Physics and Applications of Interacting Magnetic Particles: Effect of Patterned Traps." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1452073910.
Full text
7
Lips, Olga [Verfasser], and Klaus [Akademischer Betreuer] Pantel. "Der Vergleich von Iodixanol-Dichtegradientenzentrifugation, dem MicroBead-basierten System MACS und CellSearch zur Isolierung von Tumorzellen aus peripherem Blut beim Mamma- und Ovarialkarzinom / Olga Lips. Betreuer: Klaus Pantel." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2015. http://d-nb.info/1079002081/34.
Full text
8
BIAGINI, CLAUDIO. "Bead Mediated Microscopy: from high resolution microscopy to nano-Raman." Doctoral thesis, Università degli studi di Genova, 2020. http://hdl.handle.net/11567/1030687.
Full textAbstract:
Solid-state physics, material science, as well as biology, need continuously more and more information from their samples. High spatial resolution information such as optical or electrical properties, chemical species identification as well as topography are important information that optical microscopy or Scanning Probe Microscopy (SPM) can provide. Although electron microscopy (SEM and TEM) certainly assumes a position of absolute importance in the field, its cost and its need to be used by highly specialised personnel still make it an instrument of limited everyday use. On the contrary, probe microscopy has now become of very high diffusion in research labs. To develop my thesis I focused myself on three main and somehow related microscopy techniques: high resolution Raman microscopy, Scanning Near-field Optical Microscopy (SNOM), and Tip Enhanced Raman Spectroscopy (TERS). All of them are state-of-the-art on surface optical analysis techniques but still present relevant limits; among others, respectively: spatial resolution, local power density, complexity and field of applicability. My approach wants to combine some aspects of these techniques to go beyond their limits.
Raman spectroscopy is a powerful optical technique, which measures the inelastic scattering of an incoming EM radiation due to the vibrational modes of the molecules present on the surface of a sample. Thanks to its high specificity, it is very powerful in identifying the chemical components of a sample. Several organic and inorganic molecules have their typical Raman spectral peaks, hence, by the Raman spectra, it’s possible to provide a qualitative and quantitative analysis of the elements of a sample. High spatial resolution Raman setups uses the combination of a confocal microscope with a spectrometer assisted by a series of long pass and band pass filters. Despite its extreme versatility, basing Raman spectroscopy on a confocal system also constrains it to acquire its limit in spatial resolution determined by the limit of diffraction.
To overcome this limit the most used techniques in SPM are Scanning Near-field Optical Microscopy (SNOM) and Tip Enhanced Raman Spectroscopy (TERS).
Both of them exploits evanescent field, which is an electric field that is created by oscillating charges and/or currents and does not propagate in the far field as a classical electromagnetic wave, but is spatially concentrated very near to its source. This confinement allows to obtain field sources definitely smaller than in confocal systems.
In SNOM technique, the excitation light is focused through an aperture smaller than the wavelength, creating an evanescent field strongly localized near the aperture itself. Scanning the sample in this near range brings the spatial resolution down to the aperture dimension.
The main disadvantage of aperture SNOM is that the overall optical efficiency of probes is very low. The excitation power cannot be too high in order to prevent any damage of the probe, hence the energy that reaches the sample is usually not enough for Raman analysis.
TERS instead is more suitable for this purpose. It basically exploits Surface Enhanced Raman Spectroscopy (SERS) principles, using a laser irradiated gold sharp tip to obtain a local enhancement at its apex. Its good efficiency permits to analyze Raman effects with a spatial super-resolution, but, on the other hand, TERS probes usually lack of reprodubility and require very skilled and specialised users.
My PhD project has been focused to investigate and optimize an original approach to perform high resolution optical microscopy and Raman spectroscopy, well below the diffraction limit. The concept is to exploit the optical proprieties of a dielectric micro bead lens to achieve a powerful nanoscale near field confinement of light and the Scanning Probe Microscopy (SPM) technique to scan a sample to acquire optical maps. When a dielectric micro bead is hit by an Electromagnetic (EM) wave its effect is to transmit and concentrate the incident EM radiation in a specific area called nanojet, at first glance similar to that created with a standard lens. Some optical proprieties of the nanojets have been already introduced in the literature, but their application in the world of SPM, their employment in Raman microscopy and their combination with nanostructures to improve the spatial resolution are novel features whose investigation is promising. I gave to this technique the name of Beam Mediated Microscopy (BeMM).
The combination of super resolution bead mediated SPM with Raman spectroscopy opens interesting perspectives about powerful surface analysis for samples that need a versatile optical probe with a high spatial resolution and soft interaction with the sample, like soft matter substrates or biosamples.
9
Galkiewicz, Julia Parker. "Microbial Ecology and Functional Genomics of Deep-Water Coral-Associated Microbes." Scholar Commons, 2011. http://scholarcommons.usf.edu/etd/3111.
Full textAbstract:
Lophelia pertusa is a cosmopolitan cold-water coral, often found in aphotic waters (>200m). Aggregations of L. pertusa (reefs) provide important habitat to many invertebrate and fish species and act as biodiversity hotspots in the deep sea. The health and diversity of these reefs is of vital importance to deep-sea ecosystems, and the microbial consortia associated with L. pertusa form the most basic ecological level. Deciphering the diversity and function of these microbes provides insight into the roles they play in maintaining reef health. This dissertation takes microbiological techniques that are used in shallow-water coral microbial research and applies them to L. pertusa. A flaw in a primer set, which is commonly used in the molecular genetics method Polymerase Chain Reaction (PCR) to obtain data on coral-associated microbes, is discussed and an alternative approach is presented. In addition, two culture-based studies are employed to catalogue diversity and explore functional differences in strains of both bacteria and fungi. The cultured bacteria were tested for resistance against six antibiotics that affect a variety of cellular targets to elucidate strain level differences. The first cultured fungi ever described from L. pertusa were identified by molecular techniques and assayed using Biolog plates to test their metabolic capabilities. Preliminary data analysis on metagenomic libraries of the microbial-size fraction of L. pertusa is presented and discussed in the context of microbial diversity and function, bridging the gap between culture-based work on function and culture-independent work on diversity.
10
Battistelli, Elisa. "Microfluidic microbial fuel cell fabrication and rapid screening of electrochemically microbes." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amslaurea.unibo.it/7301/.
Full textAbstract:
The demand for novel renewable energy sources, together with the new findings on bacterial electron transport mechanisms and the progress in microbial fuel cell design, have raised a noticeable interest in microbial power generation.
Microbial fuel cell (MFC) is an electrochemical device that converts organic substrates into electricity via catalytic conversion by microorganism. It has represented a continuously growing research field during the past few years.
The great advantage of this device is the direct conversion of the substrate into electricity and in the future, MFC may be linked to municipal waste streams or sources of agricultural and animal waste, providing a sustainable system for waste treatment and energy production.
However, these novel green technologies have not yet been used for practical applications due to their low power outputs and challenges associated with scale-up, so in-depth studies are highly necessary to significantly improve and optimize the device working conditions. For the time being, the micro-scale MFCs show great potential in the rapid screening of electrochemically active microbes.
This thesis presents how it will be possible to optimize the properties and design of the micro-size microbial fuel cell for maximum efficiency by understanding the MFC system. So it will involve designing, building and testing a miniature microbial fuel cell using a new species of microorganisms that promises high efficiency and long lifetime. The new device offer unique advantages of fast start-up, high sensitivity and superior microfluidic control over the measured microenvironment, which makes them good candidates for rapid screening of electrode materials, bacterial strains and growth media.
It will be made in the Centre of Hybrid Biodevices (Faculty of Physical Sciences and Engineering, University of Southampton) from polymer materials like PDMS. The eventual aim is to develop a system with the optimum combination of microorganism, ion exchange membrane and growth medium. After fabricating the cell, different bacteria and plankton species will be grown in the device and the microbial fuel cell characterized for open circuit voltage and power. It will also use photo-sensitive organisms and characterize the power produced by the device in response to optical illumination.
11
Booker, Anne Elizabeth. "Halanaerobium congolense: A Transplanted Microbe that Dominates HydraulicallyFractured Well Microbial Communities." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1543356084632083.
Full text
12
Stephens, William. "Bacterial Colonization Dynamics and Ecology of the Developing Zebrafish Intestine." Thesis, University of Oregon, 2013. http://hdl.handle.net/1794/13237.
Full textAbstract:
Human intestinal microbiomes exhibit a large degree of interindividual compositional variation. Animal models, such as the zebrafish, facilitate the design of controlled and highly replicated studies that allow us to understand the normal variation in vertebrate intestinal composition and to study the rules guiding normal assembly of these complex communities. The smaller intestinal size and high fecundity of the zebrafish allow us to fully sample the intestinal contents of many animals, while the optical transparency allows direct in vivo observation of fluorescently labeled bacterial species within the intestine. The studies in this dissertation utilize these advantages to investigate the composition, colonization dynamics and functional requirements for colonization in the vertebrate intestine. We first describe the taxonomic composition and diversity of the zebrafish intestinal microbiota from wild-caught and domesticated zebrafish. In the process, we identify a set of core bacterial genera that are consistently present in zebrafish intestines. We then use species from two of these genera in subsequent studies to gain a detailed understanding of the colonization dynamics and genetic requirements of the two species. We initially describe the application of light sheet microscopy to imaging the zebrafish intestine and associated colonizing bacteria. We find that a single species, Aeromonas veronii, does not occupy the entire intestinal space and that competition within the same species appears to prevent further colonization. These results are extended to a zebrafish isolated Vibrio species as well as A. veronii by tagging bacteria with transposon insertions and tracking the changes in colonizing population sizes. These insertion libraries also identify genes in each bacterial species that are important in the process of colonization, highlighting the key role for motility and chemotaxis in this process. The descriptions and methods discussed in this dissertation advance the use of this important model organism towards the understanding of vertebrate host-microbial interactions.
This dissertation includes previously published co-authored material as well as unpublished co-authored material.10000-01-01
13
Macrae, Andrew. "Rhizobacterial ecology using 16S rRNA approaches." Thesis, University of Newcastle Upon Tyne, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.391289.
Full text
14
McDonough, Jessica Nicole. "CHARACTERIZATION AND INTERPRETATION OF THE CEPHALOPOD MARKER BED, OAKES QUARRY PARK, FAIRBORN, OHIO." Wright State University / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=wright1164641557.
Full text
15
Cobb, Christina. "A Link Between Gut Microbes & Depression: Microbial Activation of the Human Kynurenine Pathway." Scholarship @ Claremont, 2018. http://scholarship.claremont.edu/cmc_theses/1799.
Full textAbstract:
Our gut microbiota is involved in human development, nutrition, and the pathogenesis of gut disorders, but has more recently been implicated as a possible mechanism in the pathophysiology of several brain disorders, including disorders of mood and affect, such as depression. Researchers have referred to this dynamic, bidirectional signaling pathway between the gut and the brain as the “gut-brain axis.” However, most research on this axis has been limited to rodent studies, and there has been little insight into the mechanism behind it. I propose that the kynurenine pathway, where tryptophan is converted to kynurenine, is a compelling mechanism mediating the gut microbiota’s influence on depression. Kynurenine is a metabolite associated with depression, and this pathway has been shown to be manipulated through probiotic (Lactobacillus reuteri) consumption. I propose to study a probiotic intervention in humans, which would assess tryptophan metabolism along the kynurenine pathway by measuring metabolites downstream of this pathway. Urine, feces and blood samples would be collected from two groups, control and probiotic treatment, on day zero and day thirty. Colonic biopsies would be obtained on day thirty, and various analyses would be run to measure metabolite concentrations from the collected samples. The results from this study will help clarify a mechanistic connection between gut microbes and depression via the kynurenine pathway. Additionally, findings could indicate that a probiotic intervention has the ability to influence depressive behavior via a two-pronged approach originating from the kynurenine pathway.
16
Antibus, Doug E. "Molecular and Cultivation-based Characterization of Ancient Algal Mats from the McMurdo Dry Valleys, Antarctica." Kent State University / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=kent1258702723.
Full text
17
Gillis, Donald Patriq Bruce Gillis. "Assessment of a novel delivery system for microbial inoculants and the novel microbe Mitsuaria spp. H24L5A." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1461312230.
Full text
18
Zakem, Emily Juliette. "Linking microbes and climate : insights into the marine oxygen and nitrogen cycles with microbial metabolic functional types." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/112430.
Full textAbstract:
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences, 2017.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 173-193).
This thesis posits that understanding the controls on microbially-mediated marine biogeochemical cycling requires a mechanistic description of microbial activity in biogeochemical models. In the work here, the diverse microbial community is resolved using metabolic functional types, which represent metabolisms as a function of their underlying redox chemistry and physiology. In Chapter 2, I use a simple model to predict the limiting oxygen concentration of aerobic microbial growth in an ecosystem. This limiting concentration is in the nanomolar range for much of the parameter space that describes microbial activity in marine environments, and so anticipates the recent measurements of oxygen to nanomolar concentrations or lower in anoxic zones. Anaerobic metabolisms should become favorable at this limiting concentration. The model provides a parameterization for dynamic oxygen depletion and limitation, without a prescribed critical oxygen concentration. In Chapter 3, I extend the above analysis to determine the full set of conditions required for favorable anaerobic metabolism. Resource ratio theory is used to explain the competitive exclusion of anaerobic metabolisms in oxygenated environments as well as the stable coexistence of aerobic and anaerobic metabolisms when oxygen is limiting. The onset of this coexistence is a function of the relative availability of oxygen and a mutually required substrate. Results hypothesize the likelihood of coexisting aerobic and anaerobic metabolisms at limiting oxygen concentrations, which is consistent with observations. These dynamics are demonstrated in an idealized oxygen minimum zone model. In Chapter 4, I use a mechanistic description of nitrification to explain the location and intensity of the primary nitrite maximum. First, competition with phytoplankton excludes nitrification from the sunlit layer of the ocean, resulting in peak nitrification at depth, as widely observed. Second, differences in the metabolisms of the microbial clades responsible for the two steps of nitrification explain why nitrite accumulates consistently as an intermediate. The model provides a dynamic resolution of nitrification in the ocean. It predicts that nitrification is favorable in sunlit waters where phytoplankton growth is limited by light or by a substrate other than reduced inorganic nitrogen.
by Emily Juliette Zakem.
Ph. D.
19
Deiss, Frédérique. "Développement de réseaux multiplexés de biocapteurs électrochimiques." Thesis, Bordeaux 1, 2009. http://www.theses.fr/2009BOR13883/document.
Full textAbstract:
Ce travail de thèse a porté sur le développement de réseaux de micro- et nanocapteurs opto-électrochimiques pour la bioanalyse. Ils répondent à la demande grandissante dans le domaine de la recherche et du diagnostic pour des outils permettant de réaliser de multiples analyses simultanément avec des échantillons de faibles volumes. Ces nouvelles biopuces de haute densité sont fabriquées à partir de faisceaux cohérents de fibres optiques. Une des deux faces est micro- ou nanostructurée par une attaque chimique, puis fonctionnalisée avec une sonde biologique. La première biopuce est un réseau de nanocapteurs fluorescents à ADN où les sondes ont été immobilisées grâce aux propriétés d’électropolymérisation du pyrrole. La lecture est réalisée à distance au travers du faisceau d’imagerie. En combinant la technique d’immobilisation avec des microleviers électrochimiques, plusieurs sondes différentes ont pu être adressées sur le même réseau nanostructuré. La seconde biopuce permet d’effectuer des immunodosages multiplexés en utilisant l’imagerie électrochimiluminescente résolue à l’échelle d’une microsphère. Le développement de cette technique permet de combiner les avantages de l’électrochimiluminescence avec des immunodosages multiplexés. L’élaboration de ces réseaux allie différentes techniques physico-chimiques, notamment électrochimiques, pour obtenir des biopuces avec un fort potentiel, grâce à une densité et un degré de multiplexage importantsThis work presents the development of optoelectrochemical micro- and nanosensor arrays for bioanalytical applications. These platforms respond to the growing need in research and diagnostic for tools allowing multiple and simultaneous analysis in small-volume samples. These new high density biochips are made from coherent optical fiber bundles: one face is micro- or nanostructured by chemical etching and then functionnalized with biological probes. The first biochip is a fluorescent DNA nanosensor array where probes have been immobilized by electrodeposition of a polypyrrole thin film. The detection of the hybridization is remotely performed through the imaging fiber. Different probes were succesfully addressed onto the same nanostructured array thanks to electrochemical cantilevers. The second biochip allows multiplexed sandwich immunoassays using electrochimiluminescent imaging resolved at the single bead level. In particular, the development of this new readout mechanism allows extending electrochemiluminescent detection for multiplexed immunoassays. Design and implementations of both platforms take advantages of different physical and chemical techniques, especially electrochemical, to obtain biochips with a great potential through high density and high multiplexing level
20
Majdak, Karolina. "Microbial binding of per- and polyfluorinated alkyl substances (PFASs) : - Analysis of PFASs in microbes with ultra-performance liquid chromatography – tandem mass spectrometry (UPLC-MS/MS)." Thesis, Örebro universitet, Institutionen för naturvetenskap och teknik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-69080.
Full textAbstract:
Per- and polyfluorinated alkyl substances (PFASs) belong to a large group of man-made chemicals that pollute the environment. Perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) are the most commonly found PFASs. The pollution of PFASs can be caused among others by using of aqueous fire-fighting foams (AFFFs). PFASs are persistent compounds; that can travel long distances and bioaccumulate in biota. There are several exposure routes for PFASs, but the most common are via food and drinking water. A possible way for PFASs to enter the food chain is by adsorption to microbes. In this project, binding of PFASs to three gram-negative bacteria, Eschericha coli, Acidovorax delafieldii and Pseudomonas nitroreducens, was assessed. Microbes were exposed for fluorinated compounds in environmental water samples and a PFAS-11 solution with 11 PFAS substances prepared in the laboratory. The binding seems to be preferential to the most abundant compounds, PFOS, since the second most abundant compound in the samples was PFHxS with concentrations at one third of the PFOS concentration but nonetheless PFHxS was not detected in any of the samples. The binding of mainly one PFAS was identified; PFOS was bound at highest concentrations in E. coli treated with both environmental water sample and a PFAS-11 solution. Low concentrations of FOSA and PFDoDS were identified in E. coli and PFNA in A. delafieldii. Only PFOS was detected in P. nitroreducens. The concentrations of other PFASs were below their respective method detection limits.
21
Driscoll, Timothy. "Host-Microbe Relations: A Phylogenomics-Driven Bioinformatic Approach to the Characterization of Microbial DNA from Heterogeneous Sequence Data." Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/50921.
Full textAbstract:
Plants and animals are characterized by intimate, enduring, often indispensable, and always complex associations with microbes. Therefore, it should come as no surprise that when the genome of a eukaryote is sequenced, a medley of bacterial sequences are produced as well. These sequences can be highly informative about the interactions between the eukaryote and its bacterial cohorts; unfortunately, they often comprise a vanishingly small constituent within a heterogeneous mixture of microbial and host sequences. Genomic analyses typically avoid the bacterial sequences in order to obtain a genome sequence for the host. Metagenomic analysis typically avoid the host sequences in order to analyze community composition and functional diversity of the bacterial component. This dissertation describes the development of a novel approach at the intersection of genomics and metagenomics, aimed at the extraction and characterization of bacterial sequences from heterogeneous sequence data using phylogenomic and bioinformatic tools.
To achieve this objective, three interoperable workflows were constructed as modular computational pipelines, with built-in checkpoints for periodic interpretation and refinement. The MetaMiner workflow uses 16S small subunit rDNA analysis to enable the systematic discovery and classification of bacteria associated with a host genome sequencing project. Using this information, the ReadMiner workflow comprehensively extracts, assembles, and characterizes sequences that belong to a target microbe. Finally, AssemblySifter examines the genes and scaffolds of the eukaryotic genome for sequences associated with the target microbe. The combined information from these three workflows is used to systemically characterize a bacterial target of interest, including robust estimation of its phylogeny, assessment of its signature profile, and determination of its relationship to the associated eukaryote.
This dissertation presents the development of the described methodology and its application to three eukaryotic genome projects. In the first study, the genomic sequences of a single, known endosymbiont was extracted from the genome sequencing data of its host. In the second study, a highly divergent endosymbiont was characterized from the assembled genome of its host. In the third study, genome sequences from a novel bacterium were extracted from both the raw sequencing data and assembled genome of a eukaryote that contained significant amounts of sequence from multiple competing bacteria. Taken together, these results demonstrate the usefulness of the described approach in singularly disparate situations, and strongly argue for a sophisticated, multifaceted, supervised approach to the characterization of host-associated microbes and their interactions.Ph. D.
22
Saba, Beenish. "Simultaneous Biotreatment and Power Generation in Microbial Fuel Cells." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu149233408160918.
Full text
23
Rohrscheib, Chelsie Elise. "Determining the Effect Wolbachia Pipientis has on Insect Neurological Function and Behaviour." Thesis, Griffith University, 2016. http://hdl.handle.net/10072/365366.
Full textAbstract:
Symbiotic microbes are commonly found associated in higher organisms, and often have evolved to play an important role in host biology. Researchers have been studying the effects that microbial symbionts have on host physiology, their effects on host nutrition or protection against pathogenic microbial infections, but have recently begun to examine how they influence the brain and behaviour. Wolbachia pipientis, a gram-negative alpha-proteobacteria, intracellular bacterial symbiont infects approximately 40% of all insect species, including Drosophila. The fruit fly, Drosophila melanogaster, one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, and is naturally infected by several strains of Wolbachia. While Wolbachia are known to infect numerous host tissues, including the brain, little research has focused on how Wolbachia affects the nervous system and behaviour of its host, despite the impact behaviour has on host fitness.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Natural Sciences
Science, Environment, Engineering and Technology
Full Text
24
Crosbie, Jeffrey. "Synchrotron microbeam radiation therapy." Monash University. Faculty of Science. School of Physics, 2008. http://arrow.monash.edu.au/hdl/1959.1/64948.
Full textAbstract:
This thesis presents interdisciplinary, collaborative research in the field of synchrotron microbeam radiation therapy (MRT). Synchrotron MRT is an experimental radiotherapy technique under consideration for clinical use, following demonstration of efficacy in tumour-bearing rodent models with remarkable sparing of normal tissue. A high flux, X-ray beam from a synchrotron is segmented into micro-planar arrays of narrow beams, typically 25 μm wide and with peak-to-peak separations of 200 μm. The radiobiological effect of MRT and the underlying cellular mechanisms are poorly understood. The ratio between dose in the ‘peaks’of the microbeams to the dose in the ‘valleys’, between the microbeams, has strong biological significance. However, there are difficulties in accurately measuring the dose distribution for MRT. The aim of this thesis is to address elements of both the dosimetric and radiobiological gaps that exist in the field of synchrotron MRT. A method of film dosimetry and microdensitometry was adapted in order to measure the peak-to-valley dose ratios for synchrotron MRT. Two types of radiochromic film were irradiated in a phantom and also flush against a microbeam collimator on beamline BL28B2 at the SPring-8 synchrotron. The HD-810 and EBT varieties of radiochromic film were used to record peak dose and valley dose respectively. In other experiments, a dose build-up effect was investigated and the half value layer of the beam with and without the microbeam collimator was measured to investigate the effect of the collimator on the beam quality. The valley dose obtained for films placed flush against the collimator was approximately 0.25% of the peak dose. Within the water phantom, the valley dose had increased to between 0.7–1.8% of the peak dose, depending on the depth in the phantom. We also demonstrated, experimentally and by Monte Carlo simulation, that the dose is not maximal on the surface and that there is a dose build-up effect. The microbeam collimator did not make an appreciable difference to the beam quality. The measured values of peak-to-valley dose ratio were higher than those predicted by previously published Monte Carlo simulation papers. For the radiobiological studies, planar (560 Gy) or cross-planar (2 x 280 Gy or 2 x 560 Gy) irradiations were delivered to mice inoculated with mammary tumours in their leg, on beamline BL28B2 at the SPring-8 synchrotron. Immunohistochemical staining for DNA double strand breaks, proliferation and apoptosis was performed on irradiated tissue sections. The MRT response was compared to conventional radiotherapy at 11, 22 or 44 Gy. The results of the study provides the first evidence for a differential tissue response at a cellular level between normal and tumour tissues following synchrotron MRT. Within 24 hours of MRT to tumour, obvious cell migration had occurred into and out of irradiated zones. MRT-irradiated tumours showed significantly less proliferative capacity by 24 hours post-irradiation (P = 0.002). Median survival times for EMT-6.5 and 67NR tumour-bearing mice following MRT (2 x 560 Gy) and conventional radiotherapy (22 Gy) increased significantly compared to unirradiated controls (P < 0.0005). However, there was markedly less normal tissue damage from MRT than from conventional radiotherapy. MRT-treated normal skin mounts a more coordinated repair response than tumours. Cell-cell communication of death signals from directly irradiated, migrating cells, may explain why tumours are less resistant to high dose MRT than normal tissue.
25
Slabbert, Etienne. "Microbial communities of riparian ecotone invaded by non-indigenous Acacias." Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/20367.
Full text
26
Lam, Kin-San, University of Western Sydney, and School of Science. "Biodegradation of xanthate by microbes isolated from a tailings lagoon and a potential role for biofilm and plant/microbe associations." THESIS_XXXX_SS_Lam_K.xml, 1999. http://handle.uws.edu.au:8081/1959.7/441.
Full textAbstract:
Xanthates, key compounds used in the mining industry for the separation of metals from ores, may have a significant impact on the ecosystems once discarded into the tailings. The aims of this study were to : characterize chemical and microbiological conditions in a tailings lagoon (Brown Creek gold mine); examine the feasability of using indigenous bacteria to degrade xanthate under laboratory conditions; and, optimize the biodegradation process by employing biofilm technology and plant-microbe associations. To achieve these, a simple but accurate HPLC method was developed. The chemical and biological constitution of the tailings lagoon was monitored over a 2 year period from March 1995 to February 1997. Xanthate degradative performance was improved by Phragmites australis and its root associated bacterial community. Cumulative amounts of xanthate degraded by this plant-microbe association were significantly higher than any other treatment, specifically glass-attached and free-living bacterial populations. An increased bacterial number in the extensively developed root, the presence of extracellular layer as revealed from scanning electron microscope and significance of plant removal via uptake were thought to be the possible explanations for the enhanced biodegradation activity observed. In view of the above, use of glass-attached bacteria and plant-microbe associations might provide a feasible solution to degrade xanthate in the tailings lagoon. The results obtained from this study suggest that the plant-microbe associations could provide a cost effective method to degrade/remove xanthate from the tailings lagoon runoff. This approach offers several ecological advantages. Firstly, it offers the advantage of a solar-powered treatment system that is aesthetically pleasing. Secondly, bioremediation can be done on site, thereby eliminating waste transportation costs. Finally, it has the added attraction of a higher potential for public acceptanceDoctor of Philosophy (PhD)
27
Lam, Kin-San. "Biodegradation of xanthate by microbes isolated from a tailings lagoon and a potential role for biofilm and plant/microbe associations." Thesis, View thesis, 1999. http://handle.uws.edu.au:8081/1959.7/441.
Full textAbstract:
Xanthates, key compounds used in the mining industry for the separation of metals from ores, may have a significant impact on the ecosystems once discarded into the tailings. The aims of this study were to : characterize chemical and microbiological conditions in a tailings lagoon (Brown Creek gold mine); examine the feasability of using indigenous bacteria to degrade xanthate under laboratory conditions; and, optimize the biodegradation process by employing biofilm technology and plant-microbe associations. To achieve these, a simple but accurate HPLC method was developed. The chemical and biological constitution of the tailings lagoon was monitored over a 2 year period from March 1995 to February 1997. Xanthate degradative performance was improved by Phragmites australis and its root associated bacterial community. Cumulative amounts of xanthate degraded by this plant-microbe association were significantly higher than any other treatment, specifically glass-attached and free-living bacterial populations. An increased bacterial number in the extensively developed root, the presence of extracellular layer as revealed from scanning electron microscope and significance of plant removal via uptake were thought to be the possible explanations for the enhanced biodegradation activity observed. In view of the above, use of glass-attached bacteria and plant-microbe associations might provide a feasible solution to degrade xanthate in the tailings lagoon. The results obtained from this study suggest that the plant-microbe associations could provide a cost effective method to degrade/remove xanthate from the tailings lagoon runoff. This approach offers several ecological advantages. Firstly, it offers the advantage of a solar-powered treatment system that is aesthetically pleasing. Secondly, bioremediation can be done on site, thereby eliminating waste transportation costs. Finally, it has the added attraction of a higher potential for public acceptance
28
Lam, Kin-San. "Biodegradation of xanthate by microbes isolated from a tailings lagoon and a potential role for biofilm and plant/microbe associations /." View thesis, 1999. http://library.uws.edu.au/adt-NUWS/public/adt-NUWS20030828.084802/index.html.
Full text
29
Schmidt, David A. "Paleontology and sedimentology of calcifying microbes in the Silurian of the Ohio-Indiana region an expanded role of carbonate-forming microbial communities /." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1142964356.
Full text
30
Hollis, Kevin John. "Microbeam design in radiobiological research." Thesis, Brunel University, 1995. http://bura.brunel.ac.uk/handle/2438/4824.
Full textAbstract:
Recent work using low-doses of ionising radiations, both in vitro and in ViVO, has suggested that the responses of biological systems in the region of less than 1 Gray may not be predicted by simple extrapolation from the responses at higher doses. Additional experiments, using high-LET radiations at doses of much less than one alpha particle traversal per cell nucleus, have shown responses in a greater number of cells than have received a radiation dose. These findings, and increased concern over the effects of the exposure of the general population to low-levels of background radiation, for example due to radon daughters in the lungs, have stimulated the investigation of the response of mammalian cells to ionising radiations in the extreme low-dose region. In all broad field exposures to particulate radiations at low-dose levels an inherent dose uncertainty exists due to random counting statistics. This dose variation produces a range of values for the measured biological effect within the irradiated population, therefore making the elucidation of the dose-effect relationship extremely difficult. The use of the microbeam irradiation technique will allow the delivery of a controlled number of particles to specific targets within an individual cell with a high degree of accuracy. This approach will considerably reduce the level of variation of biological effect within the irradiated cell population and will allow low-dose responses of cellular systems to be determined. In addition, the proposed high spatial resolution of the microbeam developed will allow the investigation of the distribution of radiation sensitivity within the cell, to provide a better understanding of the mechanisms of radiation action. The target parameters for the microbeam at the Gray Laboratory are a spatial resolution of less than 1 urn and a detection efficiency of better than 99 %. The work of this thesis was to develop a method of collimation, in order to produce a microbeam of 3.5 MeV protons, and to develop a detector to be used in conjunction with the collimation system. In order to determine the optimum design of collimator necessary to produce a proton microbeam, a computer simulation based upon a Monte-Carlo simulation code, written by Dr S J Watts, was developed. This programme was then used to determine the optimum collimator length and the effects of misalignment and divergence of the incident proton beam upon the quality of the collimated beam produced. Designs for silicon collimators were produced, based upon the results of these simulations, and collimators were subsequently produced for us using techniques of micro-manufacturing developed in the semiconductor industry. Other collimator designs were also produced both in-house and commercially, using a range of materials. These collimators were tested to determine both the energy and spatial resolutions of the transmitted proton beam produced. The best results were obtained using 1.6 mm lengths of 1.5 µm diameter bore fused silica tubing. This system produced a collimated beam having a spatial resolution with 90 % of the transmitted beam lying within a diameter of 2.3 ± 0.9 µm and with an energy spectrum having 75 % of the transmitted protons within a Gaussian fit to the full-energy peak. Detection of the transmitted protons was achieved by the use of a scintillation transmission detector mounted over the exit aperture of the collimator. An approximately 10 urn thick ZnS(Ag) crystal was mounted between two 30 urn diameter optical fibres and the light emitted from the crystal transmitted along the fibres to two photomultiplier tubes. The signals from the tubes were analyzed, using coincidence counting techniques, by means of electronics designed by Dr B Vojnovic. The lowest counting inefficiencies obtained using this approach were a false positive count level of 0.8 ± 0.1 % and an uncounted proton level of 0.9 ± 0.3 %. The elements of collimation and detection were then combined in a rugged microbeam assembly, using a fused silica collimator having a bore diameter of 5 urn and a scintillator crystal having a thickness of - 15 µm. The microbeam produced by this initial assembly had a spatial resolution with 90 % of the transmitted protons lying within a diameter of 5.8 ± 1.6 µm, and counting inefficiencies of 0.27 ± 0.22 % and 1.7 ± 0.4 % for the levels of false positive and missed counts respectively. The detector system in this assembly achieves the design parameter of 99 % efficiency, however, the spatial resolution of the beam is not at the desired I urn level. The diameter of the microbeam beam produced is less than the nuclear diameter of many cell lines and so the beam may be used to good effect in the low-dose irradiation of single cells. In order to investigate the variation in sensitivity within a cell the spatial resolution of the beam would require improvement. Proposed methods by which this may be achieved are described.
31
Mui, Peter Hon-Fung. "Synthesis of ion microbeam column." Diss., The University of Arizona, 1995. http://hdl.handle.net/10150/187061.
Full textAbstract:
Electrostatic lenses have traditionally been designed by analyzing and combining different electrode configurations. Computational complexity typically limits such systems to a few geometrically simple elements, where the component interactions are neglected and not exploited to combat the various aberrations. Recently, Szilagyi and Szep have demonstrated that an axially symmetric column of circular plates, with the electrode potentials optimized for focusing, can surpass the typical conventional designs by many times in performance. Following the footsteps of pioneers like Burfoot and Hawkes, we partition the plates in order to transcend the limitations set by Scherzer's theorem on the chromatic and spherical aberrations of axially symmetric structures. Two algorithms, one based upon integral asymptotics and one upon the Levinson algorithm. for Toeplitz matrix inversion, are developed to complement the charge-density method in analyzing the new column structures. Various optimization schemes are combined to avoid shallow minima at a reasonable computational cost. With each plate partitioned into four sectors, we show that the interactions between the monopole and the quadrupole components can increase the output current density by more than 400% over the axially symmetric structure. By adjusting the sector potentials, we can realize systems capable of both focusing and deflecting the beam. In comparison to some existing designs, our systems excel in both performance and compactness, sometimes by many hundred percents. We then further partition the plates to generate the "octupole" deflectors and correctors. We show that the "octupole" deflectors can drastically slow down the beam degradation with deflection distance and that the correctors can further increase the output current density by more than 300%. Finally, we apply linear system theories to the study of the first-order properties of optical systems with different symmetries. We showed, without resorting to perturbational mathematics, that the higher multipole components, with more than 2 folds of rotational symmetry, can induce no first-order influences. We also find that there are systems with other symmetries that can replace an axially symmetric structure in the first-order approximation. This latter study is the beginning of our investigation for the optimum system geometry.
32
Smith, D. C. "Microbial halogenation." Thesis, University of Kent, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.383890.
Full text
33
Xue, Peipei. "Soil Microbial Diversity: Relating Microbial Distributions to Soil Functions." Thesis, The University of Sydney, 2022. https://hdl.handle.net/2123/28830.
Full textAbstract:
Soil microbial biodiversity is an essential component of the natural ecosystem. Soil microbes work as decomposers contributing to soil nutrient cycling, primary production, and climate regulation. The heterogeneous edaphic properties lead to the diversity of microbial community structuring and functioning. This thesis investigates microbial community distributions and functions through vertical soil profiles, at the landscape level, and along regional transects. Vertically, soil microbial communities were depicted in soil profiles to a depth of 1 m using the concept of genosoils (soil formed and still under natural vegetation) and phenosoils (the same type of soil that has undergone cultivation). Bacteria community distribution in soil profiles differed by soil types but altered by soil forms. At the local scale, factors of land use and soil types on the microbial communities were evaluated in three soil depth layers through a survey across the Hunter Valley area in NSW, Australia. Topsoil microbial communities were generally regulated by land use, while the subsoil microbial communities were shaped by soil type. Additionally, microbial interactions reveal that soil protists regulate the bacterial and fungal diversity. At the regional scale, microbial functions were investigated across two ~1000 km transects which traversed significant temperature and/or rainfall gradients in NSW. Temperature and rainfall were important drivers of soil microbial functional groups. Paired (genosoils and phenosoils) samples showed that agriculture practices led to a significant shift in microbial functional groups related to particulate organic carbon (POC) degradation. Collectively, this thesis studied the factors of depth, soil type, land use, and environment for the underground microbial community, and demonstrated the significant role of soil biodiversity in the soil ecosystem, especially for soil carbon cycling.
34
Gilliam, Lucy. "Impact of anti-microbial GM plants on soil microbial populations." Thesis, University of Reading, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485401.
Full textAbstract:
The environmental risk assessment of GM plants is a fast moving area of science. Much research has focused on developing methods to evaluate potential effects on a range of organisms. Microorganisms play an essential role in many soil processes, with the rhizosphere as the prominent site of microbial activity. There is a general need for protocols to assess the effect of anthropogenic influences, the use of different crops and crop rotation an.d as well as GM plants, on the microbial community within the soil. The rhizosp~eres of three crop plants Brassica napus (Oilseed rape), Triticum aestivum (Wheat) and Solanum tuberosum (Potato) were compared using both genetic and functional diversity methods. The rhizospheres of four cultivars of potato were compared; GM potato (variety Kardal) modified with an anti-fungal transgene, GM potato (variety Kardal) with no transgene inserted (empty vector), parental .- line of potato (variety Kardal) and a different cultivar (variety Russet-Burbank). Genetic diversity of bacterial populations isolated from the rhizosphere were compared using PCR amplified DNA of 168 rRNA with denaturing gradient gel electrophoresis (DGGE) to obtain community fingerprints. Activity of the microbial populations was assessed using Biolog G.N MicroPlate™ community substrate utilisation and enzyme activity using a microplate method based on substrates linked to the fluorescent compounds methylumbelliferone (MUB) and 7-amino-4-methyl coumarin (AMC). By comparing the ~M plants to non-GM plants and other crops, observed differences are placed in context. This work shows that the GM line examined.appears to have little effect on soil microbial populations. Detected effects of1he GM potato line were minor compared with other sources of variation observed between plants cultivar or crop species, management practices and sampling time. To date, there has been little evidence that cultivation of GM plants leads to significant changes in microbial popUlations.
35
Chew, Yi Vee. "Host and microbial factors influencing the gut microbial community structure." Thesis, The University of Sydney, 2013. http://hdl.handle.net/2123/10031.
Full textAbstract:
Gut microbial colonization begins at birth and dynamic ecological succession occurs before establishment of a stable, resilient adult community structure. Colonization outcomes in early life have long-term effects on host health. Understanding factors governing neonatal gut community structure development and adult structure modulation will allow therapeutic manipulation of the gut community for disease prevention/treatment. Submetagenomic analysis was done to identify microbial factors potentially triggering community stability in neonate piglets. Piglet faecal microbiota was fractionated before and after key points in community development using suppression subtractive hybridization. Analysis of immunoglobulin A bound to gut microbes showed that distinct groups are bound, potentially influencing colonization outcomes. Comparisons using pyrosequencing showed that colon and cecum microbiota of mice on a standard diet were similar at higher taxonomic levels, with minor differences at finer scale reflecting spatial location. Changes in host nutrient intake were found to generically drive community shift in 2 independent mouse genotypes - low energy density (LED) diet samples showed significantly higher relative abundances of mucin-degrading Verrucomicrobiae and Bacteroidia. Ability to use host secretions as an alternative energy source is predicted to confer selective advantage under reduced host nutrient intake. To track host secretion uptake, mice were intravenously injected with 13C and 15N-labeled threonine. Isotope incorporation by bacteria was tracked with nanoscale secondary ion mass spectrometry. Greater uptake was seen in LED diet mice, indicating increased importance of host secretions to bacterial nutrition relative to host-ingested nutrients. Different populations showed differential uptake, suggesting varied ability to utilise host secretions. This is expected to influence population fitness and drive community shift under host nutrient intake limitation.
36
Brauer-Krisch, E. "Experimental dosimetry for Microbeam Radiation Therapy." Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1357933/.
Full textAbstract:
The thesis gives an overview on the preclinical results in Microbeam Radiation Therapy (MRT), a novel radiation therapy using microscopically small beams. In the first chapter preclinical results and biological observations after Microbeam Radiation Therapy are presented, in particular the normal tissue tolerance is highlighted. A chapter based on theoretical Monte Carlo dose calculations is summarizing a set of data on peak to valley dose ratios (PVDR) and relative dose distributions for various parameter settings, providing some guideline for preclinical studies. The main part of the thesis is focusing on the experimental dosimetry, on one side to measure the high dose rate in the homogenous field proposing the necessary corrections to be applied for absolute dose measurements and on the other side, to measure peak and valley dose. For the high resolution dose measurements of the spatially fractionated beam, results using several types of detectors are presented and discussed. Various results using Gafchromic film dosimetry in combination with a microdensitometer show slightly higher (~10-15 %) valley dose than the MC calculated values. Results of theoretical calculations of output factors and their experimental verification are in very good agreement. The great potential of interlaced Microbeams in an anthropomorphic phantom with one single high dose delivery is discussed, including the technical challenges to be mastered in the future.
37
Bailey, Jennifer Diane. "Vertical Distribution of Wetland Plant Roots and Their Associated Bacteria in Groundwater-fed Wetlands." Wright State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=wright1452708738.
Full text
38
Samuels, Toby Stephen. "Microbial weathering of shale rock in natural and historic industrial environments." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31041.
Full textAbstract:
The weathering of shales is a globally important process affecting both natural and built environments. Shales form roughly 70 % of worldwide sedimentary rock deposits and therefore the weathering of these rocks has substantial effects on the geochemical cycling of elements such as carbon, iron and sulfur. Microbes have been shown to play a key role in weathering shales, primarily through the oxidation of the iron and sulfur of embedded pyrite and the resultant production of sulfuric acid. Despite significant interest in the microbial weathering of shales within industrial sectors such as biohydrometallurgy and civil engineering, comparatively few studies have investigated microbial shale weathering in natural environments. Furthermore, the role of microbes in natural shale weathering processes beyond iron oxidation has largely remained unexplored. In this thesis, the weathering capabilities of microbial communities from natural weathered shale was investigated. The North Yorkshire coastline was used as a study location, due to the abundance and diversity of natural cliffs and historic, disused industrial sites. Cliff erosion and recession on the North Yorkshire coastline is a major concern for local authorities and is the focus of current research. The aim of this work has been to evaluate microbial shale weathering processes within these environments, and hypothesise the possible contribution they may have to erosive processes. Phenotypic plate assays inoculated with weathered shale material were used to obtain rock weathering bacterial isolates that tested positive for a specific weathering phenotype, such as iron oxidation or siderophore production. Subsequent 16S rRNA sequencing enabled genera level identification, revealing 15 genera with rock weathering capabilities with several being associated with multiple weathering phenotypes including Aeromonas sp., Pseudomonas sp. and Streptomyces sp. Shale enrichment liquid cultures were incubated with shale rock chips to simulate natural biological weathering conditions, and the concentration of rock-leached elements in the fluid measured. No evidence of microbially-enhanced leaching was found consistently for any element, however the significant reduction in leachate iron concentration under biological conditions indicates that iron precipitation occurred via microbial iron oxidation. Enrichment cultures inoculated with weathered shale and containing organic matter (OM) rich rocks in water or M9 medium, both liquids lacking an organic carbon source, were grown over several months. The cultures yielded microbial isolates that could utilise rock bound OM sources and one bacterial isolate, Variovorax paradoxus, was taken forward for ecophysiological study. The shale rock that the organism was isolated from, along with other OM rich rocks (mudstones and coals), elicited complex responses from V. paradoxus including enhanced growth and motility. Finally, mineral microcosms in vitro and mesocosms in situ investigated microbial colonization and weathering of shale-comprising minerals (albite, calcite, muscovite, pyrite and quartz). Microcosms were established using iron oxidizing enrichment cultures, as based on the results of the simulated rock weathering experiments, while the in situ mesocosms were buried within weathered shale scree within a disused mine level. Levels of colonization significantly varied between minerals within the microcosms (pyrite > albite, muscovite > quartz > calcite). Although differences in mineral colonization were seen in the mesocosms, they did not match those in the microcosms and were not statistically significant. Pyrite incubated in the microcosms became significantly weathered, with extensive pit formation across the mineral surface that is consistent with microbial iron oxidation. In the mesocosms, pit formation was not identified on pyrite surfaces but dark etchings into the pyrite surface were found underneath fungi hyphal growth. The results of this thesis highlights that a range of microbial rock weathering mechanisms are abundant across weathered shale environments. Microbial iron oxidizing activity was a dominant biogeochemical process that altered rock-fluid geochemistry and weathered pyrite surfaces. However, the impact on rock or mineral weathering of other microbial mechanisms was not elucidated by this work. Given the known capabilities of these mechanisms, the conditions under which they are active may not have been met within the experimental setup used. Microbial iron oxidation in shale and shale-derived materials has previously been demonstrated to weaken rock structure through acid production and secondary mineral formation. From the results of this thesis, it is clear that microbial iron oxidation is an active process within some of the weathered shale environments studied, including cliff surfaces. Therefore, it can be hypothesised that microbial activity could play a role in structurally weakening shale rock within cliffs and accelerate their erosion. Future work should attempt to quantify the rate and extent of microbial iron oxidizing activity within shale cliff environments and investigate its contribution to erosive processes.
39
Thomas, D. J. "Microbial cellulase systems." Thesis, Swansea University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.639202.
Full textAbstract:
The work presented studies the cellulolytic system of Trichoderma koningii with particular reference to its ability to produce "short fibres" in the early stages of cellulose degradation. The culture filtrate of this organism was shown to produce short fibres from both filter paper (Whatman No.1) and cotton (Texas, non-dewaxed). The optimum conditions for production were identified and an assay system developed to measure this activity. Assay using filter paper was rapid and sensitive in determining short fibre producing activity, all results were subsequently confirmed on the more resistant substrate (cotton). The cellulase system was separated using an ion exchanger with a non-carbohydrate matrix and affinity chromatography on cellulose. Initial separation on ion exchange yielded the main cellobiohydrolase (CBH 1). Another fraction from this column separated on cellulose columns gave purified fractions of β-glucosidase, CM-cellulase and the short fibres forming activity (D2Cc). Only this latter fraction produced short fibres and synergised with CM-cellulase and β-glucosidase to increase short fibre production. Short fibres produced by D2Cc were more susceptible to subsequent hydrolysis by culture filtrate or CBH 1, degraded (bacterial) cellulose showed no physical changes on action of D2Cc but subsequent hydrolysis by CBH 1 or culture filtrate was increased. The main product of D2Cc was cellobiose but some cellotriose was detected from filter paper. D2Cc was inactive against cellobiose and cellotriose, both were potent inhibitors of D2Cc activity. Cellobiose was also an inhibitor of CBH 1 but cellotriose was not. D2Cc was shown to reduce the DP of bacterial cellulose. D2Cc and CBH 1 synergised in hydrolysing degraded cellulose, filter paper and cotton. The suggested role for this enzyme component is that it produces short fibres in concert with CM-cellulase which are then attacked by CBH 1 to produce cellobiose which is utilized by the organism.
40
Brain, Stephen. "Monitoring microbial biofilms." Thesis, London South Bank University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.337401.
Full text
41
Lafis, S. "Rapid microbial detection." Thesis, Cranfield University, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.357505.
Full text
42
Hart, Murray. "Effects of pesticides on the soil microbial biomass and microbial activity." Thesis, University of Nottingham, 1995. http://eprints.nottingham.ac.uk/11542/.
Full textAbstract:
This thesis describes research investigating the side-effects of pesticides on soil microbial biomass and microbial activity, with particular reference to two recently developed pesticides, a fungicide, epoxiconazole, and a herbicide, quinmerac. In a dose-responsee xperiment,a pplication of thesep esticidest o a sandy loam soil, at up to 10 and 20 times field rate, had no significant effect on soil microbial biomass C or ninhydrin-reactive N, over 84 days incubation. There was also no effect on soil respiration, except for the higher rate quinmerac-treated soil, which evolved 13% lessC02-Cthan the control. The rate of mineralisation of epoxiconazole and quinmerac, and their long-term effect on soil respiration, were measured in three contrasting soils: a sandy loam, a silty clay loam, and a clay soil, using 14C -labelled active ingredients. The kinetics of the pesticides' mineralisation were quite different, epoxiconazole being hyperbolic, while quinmerac was sigmoidal. The maximum amount of mineralisation of both pesticides occurred in the silty clay loam soil, which had the lowest microbial biomass content. The mineralisation of the pesticides was increased by the addition of ryegrass, with the greatest effect in the silty clay loam soil, probably because of the large ryegrass C: biomass C ratio. The mineralisation of epoxiconazole was affected by the ryegrass amendment much more than quinmerac. Further additions of the pesticides had no significant effect on soil respiration or pesticide mineralisation. The mineralisation of epoxiconazole and quimnerac was further investigated in the silty clay loam soil, using samples with different crop management histories, and the effects of ryegrass and glucose amendment. Pesticide mineralisation was shown to be related to the amount of soil microbial biomass, indicating that the difference in mineralisation rate between the three soil types above was not due to differences in their crop management, but innate differences in soil chemistry and microbiology. Ryegrass addition stimulated the mineralisation of epoxiconazole more than quinmerac, while the reverse was true for glucose, indicating that the pesticides were being degraded by two distinct fractions of the microbial biomass. The effects of long-term cumulative field application of the pesticides benomyl, chlorfenvinphos, aldicarb, triadimefon and glyphosate, on soil microbial biomass and mineralisation of soil organic matter were investigated. The addition of aldicarb consistently increased the microbial biomass, due to its beneficial effect on crop growth, but this effect was not reflected in the rate of organic matter mineralisation. However, in general, the continued application of these pesticides for up to 19 years, at slightly higher than the recommended rates, had very little effect on the soil microbial population. The effects of epoxiconazole and triadimefon on soil ergosterol content and microbial biomass C were compared in a sandy loam soil. Both pesticides temporarily reduced soil ergosterol by about 30%, while biomass C remained largely unaffected. However, when straw was added to the soils, the inhibition of ergosterol was still evident, as was an inhibitory effect on biomass C. The measurement of soil ergosterol was more sensitive to the pesticide effects than biomass C, and could be a useful test in determining changes in fungal populations.
43
Korin, Tetyana Olegivna. "Microbial ecology of anaerobic biodegradation of benzoate : microbial communities and processes." Thesis, University of Newcastle upon Tyne, 2018. http://hdl.handle.net/10443/4138.
Full textAbstract:
Microbial conversion of hydrocarbons and other aromatic compounds has been studied extensively under various electron accepting conditions, by investigating cultured microorganisms and by using samples collected directly from diverse environments. However, the functions of the principal microbial organisms taking part in the biodegradation process are not fully understood, especially when the organisms comprise complex microbial communities. The focus of the research reported here is the identification of a microbial community enriched during methanogenic benzoate degradation using inocula from two contrasting environments, river sediment and oil sands. Benzoate is a monoaromatic compound used extensively as a model compound in studies of hydrocarbons and other aromatics. The microorganisms which were most abundant and which had been shown by earlier work to take part in syntrophic benzoate degradation were investigated. Their functional potential was also investigated using metagenomic approaches. It was found that enrichments from different environments contained different microbial communities, different members of which were thought to take part in the syntrophic degradation of benzoate. In benzoate enrichments with Tyne sediment, two types of methanogen were enriched: hydrogenotrophic Methanofollis and acetoclastic Methanosaeta. In contrast, in oil sands enrichments with benzoate, the most abundant methanogens were metabolically versatile Methanosarcina spp. The primary benzoate degrader in enrichments with Tyne sediment was Syntrophus, most likely Syntrophus aciditrophicus as was suggested by 99% sequence identity. In oil sands enrichments the supposed primary benzoate degrader was an unknown species of Desulfotomaculum. Syntrophic acetate oxidisers (e.g. Syntrophomonas) were not found in abundance in Tyne sediment cocultures with benzoate. Instead, the conversion of acetate into hydrogen and carbon dioxide appeared to be mediated by acetoclastic methanogenesis, which utilised acetate directly as has been evidenced by the enrichment of acetoclastic methanogens Methanosaeta and Methanosarcina. In the oil sands, syntrophic acetate oxidation was likely to have been carried out by the known acetoclastic methanogen Methanosarcina. However, it was conjectured that unclassified Sphingobacteriales clone WCHB1.69 could have taken part in the acetate utilisation. Regardless of the observed differences between the microbial communities, investigation of the metabolic potential showed the presence of the same pathways, key genes and enzymes that are known to take part in the degradation of benzoate iv and the production of methane. The same four pathways were found in both sets of methanogenic enrichments, namely the benzoate degradation pathway and hydrogenotrophic, acetoclastic and methylotrophic methanogenesis pathways. The same key genes that take part in benzoate degradation, namely dienoyl-CoA hydratase (dch), β-hydroxyacyl-CoA dehydrogenase (had) and β-oxoacyl-CoA hydrolase (oah) were found in high abundance in both enrichment cultures. The same key genes coding for essential proteins involved in methanogenesis were also found in high abundance in all the methanogenic archaea tested in both Tyne sediment and oil sands methanogenic enrichment cultures with benzoate, namely tetrahydromethanopterin S-methyltransferase (mtrA), methyl-coenzyme M reductase A (mcrA) and heterodisulfide reductase subunit A (hdrA). Other genes found in high abundance were methanogenic pathway specific genes, namely formylmethanofuran dehydrogenase, subunit A (fmdA) involved in hydrogenotrophic methanogenesis, phosphate acetyltransferase (pta), acetate kinase (ackA) and acetyl-CoA synthetase (ACSS) involved in acetoclastic methanogenesis and coenzyme M methyltransferase (mtaA) involved in methylotrophic methanogenesis. These results suggest that the functional capabilities of the microorganisms in different environments remain constant but the communities might vary from one environment to another. In addition, a comparison was made between two sequencing platforms, Illumina MiSeq and Ion Torrent PGM. The result suggested that, overall, the two sequencers concurred. The sequencers found the same most abundant taxa, but there were instances where both sequencers detected some microorganisms which were not detected by the other sequencer. Syntrophic degradation of many different types of compound such as alcohols, saturated and unsaturated fatty acids, hydrocarbons and aromatic compounds has been identified in methanogenic environments, suggesting the global importance of this process and of the microorganisms involved. Further work on the syntrophic processes, including methanogenesis, would clarify which microorganisms take part in syntrophy, in which environments syntrophy occurs, what substrates can be utilised, which members of the microbial community participate and how. Such knowledge would be useful in understanding the processes that attenuate the contamination of industrial land and the development of strategies for bioremediation. A quantitative model of syntrophic biodegradation could also assist in understanding the processes that release greenhouse gases. There is also a likelihood that microbial degradation could find a use in the development of sustainable and environmentally innocuous sources of energy.
44
Yan, Shuangchun. "Using the Bacterial Plant Pathogen Pseudomonas syringae pv. tomato as a Model to Study the Evolution and Mechanisms of Host Range and Virulence." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/77293.
Full textAbstract:
Most plant pathogens are specialists where only few plant species are susceptible, while all other plants are resistant. Unraveling the mechanisms behind this can thus provide valuable information for breeding or engineering crops with durable disease resistance. A group of Pseudomonas syringae strains with different host ranges while still closely related were thus chosen for comparative study. We confirmed their close phylogenetic relationship. We found evidence supporting that these strains recombined during evolution. The Arabidopsis thaliana and tomato pathogen P. syringae pv. tomato (Pto) DC3000 was found to be an atypical tomato strain, distinct from the typical Pto strains commonly isolated in the field that do not cause disease in A. thaliana, such as Pto T1. Comparing A. thaliana defense responses to DC3000 and T1, we found that T1 is eliciting stronger responses than DC3000. T1 is likely lacking Type III effector genes necessary to suppress plant defense. To test this, we sequenced the genomes of strains that cause and do not cause disease in A. thaliana. Comparative genomics revealed candidate effector genes responsible for this host range difference. Effector genes conserved in strains pathogenic in A. thaliana were expressed in T1 to test whether they would allow T1 to growth better in A. thaliana. Surprisingly, most of them reduced T1 growth. One of the effectors, HopM1, was of particular interest because it is disrupted in typical Pto strains. Although HopM1 has known virulence function in A. thaliana, HopM1 reduced T1 growth in both A. thaliana and tomato. HopM1 also increased the number of bacterial specks but reduced their average size in tomato. Our data suggest that HopM1 can trigger defenses in these plants. Additionally, transgenic detritivore Pseudomonas fluorescens that can secrete HopM1 shows dramatically increased growth in planta. The importance of genetic background of the pathogen for the functions of individual effectors is discussed. T1 cannot be manipulated to become an A. thaliana pathogen by deleting or adding individual genes. We now have a list of genes that can be studied in the future for the molecular basis of host range determination.Ph. D.
45
Carder, Phyllis. "Microbial Communities of Spinach at Various Stages of Plant Growth From Seed to Maturity." Thesis, Virginia Tech, 2010. http://hdl.handle.net/10919/34104.
Full textAbstract:
Little is known about how the leaf bacterial community is affected by the seed microbiota at different stages of plant development. The bacterial populations of spinach seed and leaves after germination were compared using DGGE, to assess bacterial community richness, and real-time PCR to compare the abundance of select phyla (total bacteria, Actinobacteria, Bacteroidetes, Firmicutes, α-Proteobacteria and β- Proteobacteria). To determine the effect of environment, the plants were grown in the field and growth chambers. Vertical transmission of bacterial community members was evident; the developmental stage of the plant affected the richness and abundance of select bacterial phyla. The bacterial richness of plants grown in the two environments was not affected. However, overall numbers of bacteria increased in field grown samples in comparison to those produced in growth chambers during development. A statistically significant interaction was seen between growth stage and environment with each of the selected phyla. Populations on cotyledons were smaller than mature leaves, but were not significantly different than the 3-4 leaf stage plants. The culturable populations of bacteria on seeds (~5 log CFU/g) were significantly smaller than determined using real time PCR (~7 log copies). Of these bacteria cultured from spinach seeds, isolates belonging to the genera Pantoea were found to inhibit growth of E. coli O157:H7 in vitro. This study highlights the importance of vertical transmission on the bacterial community of plants and suggests the importance of developing strategies to influence these communities on seed to control human and plant pathogens on the leaf surface.
Master of Science in Life Sciences
46
Fischer, Caleb Nathaniel. "Microbe-microbe interactions in the Drosophila melanogaster microbiome." Thesis, Yale University, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10584945.
Full textAbstract:
Microbiologists have traditionally focused on understanding the lethal consequences instigated by a handful of microorganisms. Nonetheless, the symbiotic nature of microorganisms was evident at the dawn of microbiology when Anton Van Leeuwenhoek discovered thousands of microorganisms inside the human oral cavity. Over the last century, the realization that microorganisms benefit animals has eroded the ossified perspective that microorganisms are primarily harmful. Instead, microorganisms are regarded as fundamental to animal biology.
A central goal in microbiology is to understand the molecular mechanisms by which symbiotic microorganisms associate with their hosts. The mechanisms underpinning microbial community function depend on a complex suite of metabolic interactions between microorganisms. In this dissertation, the model system Drosophila melanogaster and its simple microbiome will be used to deconstruct the mechanisms underlying microbe-microbe interactions and their consequences on host biology.
CHAPTER 1: Greater than the sum of the parts: microbe-microbe interactions in gut microbiomes. In this introductory chapter, progress in understanding microbe-microbe interactions in host-associated microbial communities will be discussed. This chapter will organize attempts at understanding microbe-microbe interactions within hosts into top-down and bottom-up approaches. The two approaches are complementary and rest on starting with pairwise interactions (bottom-up) versus modeling all interactions (top-down). Drosophila melanogaster is an attractive model system in which both approaches can be used due to the simplicity of its microbiome.
CHAPTER 2: Frequent replenishment sustains the beneficial microbiome of Drosophila melanogaster. The characterization of several ecological properties of the Drosophila microbiome, including its assembly and maintenance, will be discussed. The study also sheds light on a microbe-microbe interaction and its consequence for host infectious disease.
CHAPTER 3: Metabolite exchange within the microbiome produces compounds that influence Drosophila behavior. Drosophila olfactory behavior toward microbiome members, individually and in communities, will be assessed. The work presented in this chapter supports a model whereby Drosophila identifies interacting microbial communities via their production of specific metabolites. The molecular differences by which Drosophila discriminates a co-culture from the same two microorganisms growing separately are identified. The behavior corresponds with Drosophila egg-laying preference and adult survival. The results are discussed in light of the potential role of the observed behavior in microbiome assembly and maintenance.
CHAPTER 4: Conclusions and future directions. In this chapter the major findings of the dissertation will be placed into context of their potential ecological significance. Future research questions that emanate from the findings of the dissertation will be discussed. APPENDIX I: Microbe-microbe interactions and their impact on Drosophila egg-laying behavior.
APPENDIX I: Microbe-microbe interactions and their impact on Drosophila egg-laying behavior.Appendix I identifies in vitro microbe-microbe interactions between Drosophila microbiome members and their consequence for Drosophila egg-laying behavior.
APPENDIX II: Invasion of the Drosophila gut microbiome by human fecal bacteria. Results that characterized the Drosophila microbiome following invasion from a single microorganism (Enterococcus faecalis) and a complex community (fecal microbiome) are discussed.
APPENDIX III: Drosophila feeding behavior toward microbiome members. The adaptation of the capillary feeding (CAFE) to interrogate Drosophila behavior toward microbiome members will be discussed.
APPENDIX IV: Costs of the Drosophila bacterial microbiome. Consumption and survival costs of the bacterial microbiome in Drosophila will be highlighted.
47
Neri, E. "BMMIB-BEHIND MICROBE-MICROBE INTRACTIONS IN BLUE CHEESE." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/541171.
Full textAbstract:
Gorgonzola is a blue-veined, mould-ripened cheese, made from pasteurized cow’s milk inoculated with starter cultures (Streptococcus thermophilus and Lactobacillus delbrueckii), along with Saccharomyces cerevisiae and Penicillium roqueforti, the main responsible of the aroma and flavour of the cheese at the end of ripening. For this reason, monitoring the fungal growth and unravel the microbial dynamics during the ripening process is crucial. Traditional methods based on colony forming unit (CFU) along with alternatives (ergosterol, dry weight, spores counting) are not suitable for hyphal filaments quantification in the cheese matrix. Here we monitored and compared the P. roqueforti development between two Gorgonzola productions from two different years and the same plant, by means of a qPCR assay, mass spectrometry-based chemical analysis and an assay with a glutamate-sensitive luminescent biosensor for the evaluation of proteolysis. qPCR assay was based on a species-specific primer set targeted on ari1 gene. This assay allowed the monitoring of P. roqueforti development during cheese ripening. The lipolysis and proteolysis cheese profiles obtained by mass-spectrometry and luminometric analysis were in good agreement with the qPCR data, revealing that the most relevant blooming of the mould occurs after 20 days of ripening, and that the most recent production had a lower amount of fungal mycelium produced and a lower enzymatic activity, thus affecting the final product quality. The metabolic analysis on sugars consumption revealed the importance of galactose degradation on the final product quality. The analytical methods here described are useful for a rapid evaluation of the maturation process and the quality of blue-cheeses.
48
Barberán, Torrents Albert. "Microbial Macroecology understanding microbial community pattems using phylogenetic and multivariate statistical tools." Doctoral thesis, Universitat de Barcelona, 2012. http://hdl.handle.net/10803/101511.
Full textAbstract:
El estudio de los microorganismos en cultivo puro ha propiciado el desarrollo de la genética, la bioquímica y la biotecnología. Sin embargo, la ecología ha permanecido reticente a incorporar a los microorganismos en su acervo teórico y experimental, principalmente debido a las dificultades metodológicas para observar a los microbios en la naturaleza, y como resultado de los caminos divergentes que han trazado las disciplinas de la microbiología y la ecología general. Esta tesis trata de demostrar que los patrones ecológicos de comunidades microbianas son susceptibles de ser analizados mediante la combinación de técnicas filogenéticas y herramientas de estadística multivariante. El uso de técnicas filogenéticas permite solventar, o al menos paliar, el hecho de la no independencia de los organismos vivos debido a la ascendencia común. Con la información ambiental adicional (como reflejo del determinismo abiótico) y la información espacial (como amalgama de eventos históricos y de dispersión), es posible explorar los posibles mecanismos que subyacen a la estructura y a la diversidad de las comunidades microbianas.The study of microorganisms in pure laboratory culture has delivered fruitful insights into genetics, biochemistry and biotechnology. However, ecology has remained reluctant to incorporate microorganisms in its experimental and theoretical underpinnings mainly due to methodological difficulties in observing microorganisms in nature, and as a result of the different paths followed by the disciplines of microbiology and general ecology. In this dissertation, I argue that novel insights into microbial community patterns arise when phylogenetic relatedness are used in conjunction with multivariate statistical techniques in the context of broad scales of description.
49
Shi, Yanmei Ph D. Massachusetts Institute of Technology. "Microbial metatranscriptomics : towards understanding microbial gene expression and regulation in natural habitats." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/64570.
Full textAbstract:
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2011.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 195-212).
Metagenomic research has paved the way for a comprehensive understanding of the microbial gene parts list in nature, but a full understanding of microbial gene expression, regulation, and ecology remains a challenge. In this thesis, I present the methodological foundations and applications of deep sequencing-based metatranscriptomics, for profiling community transcriptomes on spatial and temporal scales. Several findings and relevant hypotheses have emerged from this work. I show that transcripts of house-keeping genes necessary for the maintenance of basic cellular machinery are abundant and readily detectable. Habitat-specific transcripts are also discernible when comparing community transcriptomes along distinct geochemical conditions. Normalization of detected transcripts to their corresponding gene abundance suggests that numerically less abundant microorganisms may nevertheless contribute actively to ecologically relevant processes. Along the same lines, it is a recurrent observation that many transcripts are of unknown function or phylogenetic origin, and have not been detected in genomic/metagenomic data sets. These novel sequences may be derived from less abundant species or variable genomic regions that are not represented in sequenced genomes. Furthermore, I applied metatranscriptomics in a microcosm experiment, where a deep water mixing event was simulated and community transcriptomes were monitored over the course of 27 hours. Relative to the control, the treatment sample showed signals of stimulated photosynthesis and carbon fixation by phytoplankton cells, enhanced chemotactic, motility, and growth responses of heterotrophic bacteria, as well as possibly altered phage-host interactions. Such experimental metatranscriptomic studies are well suited to reveal how microorganisms respond during the early stages of environmental perturbations. Finally, I show that metatranscriptomic data sets contain a wealth of highly expressed small RNAs (sRNAs), transcripts that are not translated to proteins but instead function as regulators. I propose a bioinformatics pipeline for identifying these sRNA elements, characterizing their structures and genomic contexts, and predicting possible regulatory targets. The extraordinary abundance of some of the identified sRNAs raises questions about their ecological function, which warrants further biochemical and genetic studies. Overall, this work has extended our knowledge of functional potentials and in situ gene expression of natural microbial communities.
by Yanmei Shi.
Ph.D.
50
Gregory, Jarod. "Microbial Detection in Surface Waters: Creating a Remote-Controlled Mobile Microbial Biosensor." University of Cincinnati / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439301079.
Full text