41 research outputs found
A spectroscopic investigation of gallium lanthanum sulphide based glasses for optical devices
No full textThe optical communications network requires an efficient and cost effective 1.3 #mu#m optical fibre-amplifier. The Praseodynium ion (Pr"3"+) 1.3 #mu#m transition is the best candidate but requires a glass host with low phonon energy to produce a high radiative efficiency. Gallium Lanthanum Sulphide (GLS) based glasses are investigated as potential low phonon energy hosts. The work reported aims to link the spectroscopic results to the observed physical and optical properties and to the composition and atomic structure of the glasses. The Pr"3"+ doped GLS glass shows a high radiative quantum efficiency (RQE) for the 1.3 #mu#m transition and the lifetime of the transition is also long indicating a potentially useful glass dopant system. The Pr"3"+ enters the glass with a large coordination number and is sulphur coordinated. The Pr"3"+ doped GLS glass spectroscopic, optical and physical properties are found to be extremely susceptible to oxide impurities and added La_2O_3. In the Gallium Lanthanum Oxy-Sulphide (GLSO) glass the Pr"3"+ spectroscopy becomes excitation wavelength dependent. The temperature range of glass formation is increased as more oxide is added whilst the RQE and lifetime of the 1.3 #mu#m transition are strongly reduced. This is explained through new oxide coordination for the Pr"3"+, which experiences a higher energy phonon and a different nephelauxetic shift of the Stark levels. The increased temperature range for glass formation of the GLSO glass is beneficial since the range of GLS glass is small. By adding metal halides to the GLS glass it was hoped that the improved glass forming properties of the GLSO glass could be kept along with the high RQE and lifetime of the 1.3 #mu#m transition. The metal halide CsCI provided the largest increase in glass forming temperature range. The RQE was slightly reduced from the GLS value but much larger than the GLSO value. The lifetime was the longest measured. The dependence of the physical and optical properties on amount of metal halide was explained by changes in the bonding of the glass formers whilst the spectroscopic properties were most strongly influenced by bulk glass effects indicating a similar coordination for the Pr"3"+ in the GLS and CsCI GLS glasses. The doped GLS glass was not found to obey the simple multiphonon non-radiative decay formula with each rare-earth transition needing to be assessed individually. (author)SIGLEAvailable from British Library Document Supply Centre-DSC:DXN027875 / BLDSC - British Library Document Supply CentreGBUnited Kingdo
Polyphony and the anxiety of influence in the fiction of Henry James
No full textJames's fiction, especially in the Middle Phase, centres
on the figure of the artist and is characterized by, the two
interrelated aspects which previous criticism has largely
overlooked: the Bakhtinian 'polyphonic' -creation of
'author-thinkers'; and the conflict between ephebes and
precursors, for which Harold-Bloom's concept of 'the-anxiety of
influence' is the most illuminating model. Polyphony is the
narrative mode, and influence is the intra-artistic, theme.
These, as the Introduction to the thesis makes clear, are
rehearsed in James's inaugural novel, Roderick Hudson. Rowland
Mallet is an author-thinker, and his failure is caused by
authorial limitations. His monologism -is impaired by his
mistaking empathy for the authorial sympathy. Likewise,
Hudson's failure does not arise from a mercurial temperament,
but from a polyphonic shortcoming: not possessing the power of
fiction to contain the fiction of power in, his mentor. And the
relationships among the three artists - Gloriani, Hudson and
Singleton - perfectly exemplify the Bloomian-theme. It is these
two concepts, polyphony and influence, which are the major
preoccupation in the Middle Phase; as, the works chosen
demonstrate. These are a novella, a novel, and a number of
short stories all of which have been unjustifiably neglected.
Chapter One, on The Aspern Papers, argues that Tina Bordereau,
far from being, the artless victim seen by many critics,
actually challenges and defeats the narrator by the very form
of her narrative. Her 'realist' discourse undermines his
language of 'romance', and shows up its internal unstability.
Chapter Two is an extensive study of the critical reception of
The Tragic Muse. The most common areas of critical attention
have been its contemporary topicality, its relation to previous
novels on similar themes, and the possible genealogy of Gabriel
Nash. Those have all missed the core of the work. - Chapter Three
demonstrates how polyphony and the anxiety of influence make
the novel what it really is. Influence arises from the
juxtaposition of, and the wrestling between, artistic ephebes
and their precursors (Nick and Nash,, Miriam and Madame Carre).
The dialogic quality defined by Bakhtin is crucial to the
proper, and even-handed, characterization of all, the conflicts
in the novel. And since most of James's tales in the eighties
and nineties -are about 'masters - and acolytes, the anxiety of
influence remains central. Chapter Four is a study of 'The
Author of Beltraffiol' and 'The Lesson of the Master'. Again the
characters' manipulations are a crucial focus in a way that
G6rard Genette's terminology helps to illuminate. The fact that
the ephebe is the author-thinker emphasizes the inextricability
of the Bakhtinian and the Bloomian in James. Just as
polyphony offers a different focus for explicating the poetics
of James's fiction; so the ephebal conflict provides the basis
for a fresh perception of James's own artistic struggle
Zarathustra / Zoroaster
No full textThe name Zarathustra refers to a prophet or religious reformer of ancient Iran. He is believed to be the
author of the Gathas, the linguistically oldest part of the Avestan corpus. Information relating to
his life is extremely scarce: mentions in the sources are contradictory and there is no agreement among
the scholars on the time in which he lived or the place where he was active. Some scholars believe that
he was amythical figure and never really existed. Even his name is problematic froma linguistic point of
view and there is still no generally accepted etymology. He is a figure who had a deep impact both on the
Classical world (particularly ancient Greece) and in the Middle Ages and in modern and contemporary
Europe
Xylan degradation in filamentous fungi and bacteria
No full textEmbargo set by: Seth Robbins for item 98742
Lift date: 2019-03-01T17:05:02Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemBiochemical characterization of two recombinant gh10 family glycosyl hidrolases and differential expression in two model filamentous fungi
Polysaccharides from plant cell walls are the most abundant biomass on Earth and are important resource for biofuel production. The main components of plant cell walls are cellulose, hemicellulose and lignin. Hemicellulose is the second most abundant component of renewable biomass and as arabinoxylan, is mainly composed of xylose and arabinose. Filamentous fungi, such as Trichoderma reesei, produce gram-per-liter levels of glycoside hydrolases (GHs). GH enzymes are required for hydrolysis of the glycosidic bonds present in complex polysaccharides, releasing fermentable sugars. In this project, we investigated the biochemical characteristics of two endoxylanases in two model filamentous fungi, Neurospora crassa and Aspergillus nidulans. Putative endoxylanase genes from N. crassa (ncu05924) and A. nidulans (an1818) were expressed homologously and heterologously in both filamentous fungi. Here, we demonstrate that A. nidulans was able to expressed and secrete at the same levels, both the recombinant homologous (AN1818) and heterologous (NCU05924) proteins, while N. crassa expressed the recombinant homologous protein at 26-fold more than the recombinant heterologous protein. All 4 endoxylanases had similar optimal pH (~5.8) and temperature (50 to ~55°C), similar secondary structures, and comparable glycosylation patterns. High performance liquid chromatography (HPLC) was used to identify the end products released by each enzyme from xylan substrates. The specific activity of AN1818 was ~50% higher than NCU05924 on different model xylans.
Xylan degrading enzymes from human colonic bacteroides intestinalis1
Many human diets contain arabinoxylan, and the ease of genome sequencing coupled with reduced cost have led to unraveling the arsenal of genes utilized by the colonic Bacteroidetes to depolymerize this polysaccharide. The colonic Bacteroidetes with potential to ferment arabinoxylans include Bacteroides intestinalis. In this study, we analyzed the hydrolytic activities of members of a xylan degradation cluster encoded on the genome of Bacteroides intestinalis DSM 17393. Here, it is demonstrated that a cocktail of the xylanolytic enzymes completely hydrolyze arabinoxylans found in human diets. Fascinatingly, this bacterium and other relatives have evolved and secrete a unique bifunctional endoxylanase/arabinofuranosidase in the same polypeptide. The bifunctional enzyme and other secreted enzymes attack the polysaccharides extracellularly to remove the side-chains, exposing the xylan backbone for cleavage to xylo-oligosaccharides and xylose. These end products are transported into the cell where a β-xylosidase cleaves the oligosaccharides to fermentable sugars. While our experiments focused on B. intestinalis, it is likely that the extracellular enzymes also release nutrients to members of the colonic microbial community that practice cross-feeding. The conservation of the genes characterized in this study in other colonic Bacteroidetes alludes to a conserved strategy for energy acquisition from xylans, a component of human diets.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2018-12-01The student, Gabriel Vasconcelos Pereira, accepted the attached license on 2016-12-09 at 10:19.The student, Gabriel Vasconcelos Pereira, submitted this Thesis for approval on 2016-12-09 at 15:15.This Thesis was approved for publication on 2016-12-09 at 16:58.DSpace SAF Submission Ingestion Package generated from Vireo submission #10491 on 2017-02-28 at 14:43:37Made available in DSpace on 2017-03-01T17:02:12Z (GMT). No. of bitstreams: 2
VASCONCELOSPEREIRA-THESIS-2016.pdf: 3404837 bytes, checksum: 6f660473b69a7fcb74a63542419adafb (MD5)
LICENSE.txt: 4224 bytes, checksum: 08adbaa72186ac97044b8588a6f48600 (MD5)
Previous issue date: 2016-12-09Embargo set by: Seth Robbins for item 98742
Lift date: 2019-03-01T17:02:22Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 98742
Lift date: 2019-03-01T17:03:32Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 98742
Lift date: 2019-03-01T17:06:55Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemLimited Restriction Lifted for Item 98742 on 2019-03-02T10:15:30Z
Polysaccharide utilization by the human colonic bacterium, bacteroides intestinalis DSM 17393
No full textThe human gastrointestinal microbiome has co-evolved with the host for an extended period, generating an intrinsic metabolic network capable of modulating both the microbial community and host physiology. Changes in the gut environment shape the microbial community with one of the main driving characteristics being competition for nutrients. A key aspect for nutrient acquisition in the gut is the ability of the microbes to degrade and ferment dietary fiber. These chemically diverse polysaccharides are the main components of the plant cell wall and function as the primary energy source for the microbiota. The dietary polysaccharides are largely indigestible by the digestive enzymes of the host. The phylum Bacteroidetes, one of the main colonizers of the gastrointestinal tract (GIT), has evolved one of the largest arrays of carbohydrate-associated enzymes (CAZymes) responsible for degrading polysaccharides. Furthermore, these bacteria have highly organized gene clusters, known as polysaccharide utilization loci (PUL), encoding the enzymes required for the degradation and transport of the sugar components of dietary fiber. These PULs also possess an unusual regulatory mechanism found only in Bacteroidetes, similar to the canonical two-component system encoded by organisms in all three domains of life. The two-component system is involved in signal transduction, mediated by a histidine-kinase sensor and a response regulator. Interestingly, the Bacteroidetes encode this system in a single polypeptide that can be delineated into a sensor, a Y_Y_Y, a histidine-kinase, a histidine-ATPase, and response regulator modules, respectively.
Through our work, we aim to understand the degradation of esterified arabinoxylan by diverse Bacteroides spp. and to develop a rapid approach for identifying the potential target of a vast number of uncharacterized PULs. Our findings demonstrate that some Bacteroides spp. highly express an esterase-enriched cluster during growth on esterified arabinoxylan compared to the mixture of its component monosaccharides xylose and arabinose. Biochemical analysis of the proteins encoded by the esterase-enriched cluster demonstrated diverse enzymatic activities and substrate specificities capable of working synergistically to fully depolymerize complex arabinoxylan substrates. Interestingly, the hypothetical domain encoded by BACINT_01040 demonstrated one of the most versatile feruloyl esterase activities, and the enzyme was able to cleave the ferulic acid side chain of every substrate tested in our studies. Moreover, we demonstrated that the bacteria harboring the esterase-enriched cluster do not metabolize the ferulic acid during growth on wheat bran. Thus, the plant phenolic compound accumulated in the spent medium. Furthermore, the accumulated ferulic acid was able to modulate the immune system and induce a Th1-type immune response and viral defenses in both gastrointestinal cell lines and mouse model.
Due to the vast number of uncharacterized PULs encoded in the microbiome, it is important to develop a rapid means to assign function to these gene clusters. Our current hypothesis relies on the observation of a potential endo-acting enzyme near the susC/susD-like genes. We hypothesized that these enzymes “scout” the environment for their associated target polysaccharides. In this work, we biochemically characterized the activity of two “scouting enzymes” on arabinoxylan and arabinan, thus showing that a PUL-associated hybrid two-component system (HTCS) sensor domain is able to bind and sense the products of its associated scouting enzyme. This hypothesis was further corroborated by transcriptomic analysis of B. intestinalis grown on each polysaccharide compared to its monomeric components. Thus, the results demonstrated in this study may advance the understanding of polysaccharide utilization by Bacteroidetes species by rapidly assigning function to uncharacterized PULs. Further studies may also allow us to identify a polysaccharide-degrading signature by the Bacteroidetes species, which may be used for personalized dietary interventions and modulation of the gut community.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2020-12-01The student, Gabriel Vasconcelos Pereira, accepted the attached license on 2018-07-20 at 17:19.The student, Gabriel Vasconcelos Pereira, submitted this Dissertation for approval on 2018-07-20 at 17:24.This Dissertation was approved for publication on 2018-07-23 at 15:03.DSpace SAF Submission Ingestion Package generated from Vireo submission #12958 on 2019-02-08 at 11:37:27Made available in DSpace on 2019-02-08T18:39:36Z (GMT). No. of bitstreams: 2
VASCONCELOSPEREIRA-DISSERTATION-2018.pdf: 7720876 bytes, checksum: 89bae44ef35ed9160574d4789b234ad1 (MD5)
LICENSE.txt: 4224 bytes, checksum: 48587a2b45d2fc713e59ba8b7ccd2989 (MD5)
Previous issue date: 2018-07-23Embargo set by: Seth Robbins for item 109903
Lift date: 2021-02-08T18:40:00Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 109903
Lift date: 2021-02-08T18:42:23Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 109903
Lift date: 2021-02-08T18:43:54Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 109903
Lift date: 2021-02-08T18:44:50Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemLimited Restriction Lifted for Item 109903 on 2021-02-09T10:15:41Z
Analysis of the ammonium assimilation pathways of the human colonic bacterium, bacteroides thetaiotaomicron
No full textIn ruminants, efficient rumen function and proper host metabolism is dependent on the nitrogen supply in the feed. Assimilated ammonium accounts for up to 70% of the microbial protein production, which satisfies up to 85% of the host protein requirements. Similar numbers for the human colon have not been determined. However, colonic bacteria are responsible for the production of ammonium, derived from host-secreted urea and endogenous and dietary proteins, that provides the preferred nitrogen source for microbial growth. Bacteroides thetaiotaomicron, a model organism for human gut Bacteroidetes, encodes genes for the capture of ammonium through the two primary pathways, the glutamate dehydrogenase (GDH) pathway and the glutamine synthetase/glutamate synthase (GS/GOGAT) pathway.
To gain insight into the genomic features underlying ammonium uptake and assimilation in this bacterium, comparative transcriptomic analysis using RNA-Seq was employed on cultures growing under excess or limiting ammonium concentrations. A single genomic locus, encoding for the GS/GOGAT pathway, was identified with highly increased transcription when the organism grows under limiting ammonium concentration. The relative contribution of each gene to ammonium assimilation was assessed through construction of genomic deletion strains for each of the three GS, one GOGAT, and two GDH genes. The deletion of two genes, the NADPH-dependent glutamate dehydrogenase (gdhA) and the glutamine synthetase type 3 (glnN2) significantly impeded growth of the organisms under both nitrogen conditions. Taken together, the results demonstrate the importance of the GDH pathway for constitutive ammonium assimilation, and GlnN2 for glutamine biosynthesis. However, when the organism grows under nitrogen limitation, the GS/GOGAT pathway, including glnN1, is highly induced. To extrapolate the significance of the findings, a comparative bioinformatic analysis, using all of the available sequenced Bacteroides genomes, revealed high conservation of the critical genomic loci in gut species. Understanding of nitrogen metabolism in gut microbes is essential for a complete depiction of their ecological implications on the host´s metabolism in health and disease.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2019-12-01The student, Michael Iakiviak, accepted the attached license on 2017-12-04 at 19:05.The student, Michael Iakiviak, submitted this Dissertation for approval on 2017-12-04 at 19:10.This Dissertation was approved for publication on 2017-12-06 at 09:00.DSpace SAF Submission Ingestion Package generated from Vireo submission #11843 on 2018-03-13 at 10:37:36Made available in DSpace on 2018-03-13T17:35:48Z (GMT). No. of bitstreams: 2
IAKIVIAK-DISSERTATION-2017.pdf: 7060740 bytes, checksum: 570aa357eedb4fc1230573a895140477 (MD5)
LICENSE.txt: 4213 bytes, checksum: 6bc082b7a4126182df41c02d2980deb4 (MD5)
Previous issue date: 2017-12-06Embargo set by: Seth Robbins for item 105480
Lift date: 2020-03-13T17:36:05Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemLimited Restriction Lifted for Item 105480 on 2020-03-14T09:15:12Z
Charity and Favoritism in the Field: Are Female Economists Nicer (to Each Other)?
No full textUsing a very large sample of matched author-referee pairs, we examine how the gender of referees and authors affects the former’s recommendations. Relying on changing matches of authors and referees, we find no evidence of gender differences among referees in charitableness toward authors; nor do we find any effect of the interaction between the referees’ and authors’ gender. With substantial research showing gender differences in fairness, the results suggest that an ethos of objectivity can overcome tendencies toward same-group favoritism/opposite-group discrimination.
Comparative whole genome transcriptional responses of Ruminococcus albus strain 7 and 8: a case for specialization and niche differentiation
No full textRuminococcus albus strains are one of dominant fibrolytic bacteria in the rumen that contribute to plant biomass as well as vitamin utilization in host nutrition. To better understanding of host-microbe interactions, it is relevant to establish the model for fiber degradation and vitamin metabolism of the dominant fibrolytic bacteria and investigate their roles in the gut ecosystem. However, the fibrolytic mechanism and vitamin metabolism of Ruminococcus albus remain largely unknown. In the current study, comparative genomic and transcriptomic analyses of two different strains 7 and 8 of R. albus for plant fiber and folate utilization were used to investigate the conserved and differential mechanism between the two R. albus strains.
Through comparative transcriptomic analyses of both strains grown on alkaline peroxide hydrogen treated corn stalk (AHPCS), phosphoric acid swollen cellulose (PASC) and wheat arabinoxylan (WAX), this research demonstrated that the top 5 highly expressed glycoside hydrolase (GH) families, including the versatile GH5, GH9 (Cel9B), GH10, GH11, and GH48 (Cel48A), are the primary GH enzymes employed by both strains of R. albus for the hydrolysis of plant cell wall. In addition, the co-expression of these endoglucanases and endoxylanases in response to cellulose and hemicellulose was observed. The previously known adhering mechanism of R. albus were transcriptionally analyzed and verified in this research. The genes encoding Pil-like protein or a family 37 carbohydrate binding module (CBM37) domain were highly expressed in both strains during growth on different polysaccharides. Especially, the significant role of CBM37 in the fiber utilization of R. albus was highlighted based on the prevalence of CBM37 domain on the highly expressed GH genes as well as hypothetical genes.
It is notable that distinct strategies between two strains for plant cell wall utilization were proposed in this research. Based on phenotypic, genomic, and transcriptomic evidence, wild type of R. albus 8 in rumen appears to preferentially utilize hemicellulose rather than cellulose embedded in the plant cell wall, while R. albus 7 prefers to utilize cellulose over hemicellulose. To support this conclusion, R. albus 8 utilized more hemicellosic sugars derived from the hydrolysis of AHPCS than R. albus 7. More CAZyme genes of R. albus 8 responded to WAX than PASC, while those genes of R. albus 7 responded to more PASC than WAX. When hemicellulose in AHPCS started to decrease in the culture, R. albus 8 down-regulated the expression of genes for sugar transporters and intracellular GH. In contrast, R. albus 7 exhibited a sequential expression of sugar transporters and intracellular GH genes, as preferred cellulosic sugars were released from AHPCS after removal of hemicellulose. Notably, we found the putative genes belonging to c-di-GMP regulatory and the accessory gene regulator quorum sensing (Agr QS) systems in R. albus 7 and 8. The transcriptional pattern of these genes were in accordance with differential transcriptional pattern of GH genes between both strains and the preferred planktonic growth of strain 8 on AHPCS as opposed to the substrate adherent growth of R. albus 7. These results suggest that c-di-GMP and Agr QS systems are implicated not only in biofilm formation of pathogenic bacteria, but also in the fibrolytic systems of commensal bacteria. Supported by the fermentation profile and the growth rate on beechwood xylan together with genomic and transcriptomic evidence, R. albus 8 was found to possess a predicted unique phosphoketolase (PK) pathway, which likely enables R. albus 8 to catabolize pentose rapidly as well as conserve energy and costs for enzyme synthesis required for the lower glycolytic sequence. With our proposal for the differential strategies between strains, the co-culture experiment demonstrated that despite a similar fibrolytic mechanism, R. albus 7 and 8 could co-exist on complex substrate containing cellulose and hemicellulose.
This research on folate metabolism in R. albus 7 and 8 provided genomic evidence for three folate utilization pathways (either de novo synthesis, salvage, or both pathways) conserved in the Firmicutes including R. albus strains. Through the growth experiments in the presence or absence of folate and para-aminobenzoate (pABA), it was shown that R. albus strains 7 and 8 rely on different folate metabolic pathways, de novo synthesis or salvage pathway, respectively. In addition, the results of transcriptomic analysis suggest that the folate autotrophic strain, R. albus 7, also has an alternative pathway for pABA synthesis and likewise other Ruminococcus species lacking the canonical pABA synthetic pathway are likely autotrophs and not auxotrophs.
Notably, the potential long non-coding RNA (lncRNA) loci was identified in the genomes of R. albus strains. The putative lncRNA loci consisted of four sequence components; lncRNA, DUF1292 gene, putative 6S RNA, and alcohol dehydrogenase. Based on their transcriptional profiles assessed by RNA-seq and northern blot analyses, it seems likely that the lncRNA loci are involved in the regulatory system related to the stationary phase of cells.
This study provides molecular insight in conserved and differentiated fibrolytic system and folate metabolism between R. albus 7 and 8. In addition, the presence of novel lncRNA loci was identified, providing more information on the regulatory mechanism in Gram-positive Firmicutes.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2018-05-01The student, Inhyuk Kwon, accepted the attached license on 2016-03-23 at 18:58.The student, Inhyuk Kwon, submitted this Dissertation for approval on 2016-03-23 at 19:08.This Dissertation was approved for publication on 2016-03-28 at 11:20.DSpace SAF Submission Ingestion Package generated from Vireo submission #9116 on 2016-07-07 at 13:48:38Made available in DSpace on 2016-07-07T20:27:00Z (GMT). No. of bitstreams: 3
KWON-DISSERTATION-2016.pdf: 10610438 bytes, checksum: 22e24f42dc9ec7a99dce325ab32a9786 (MD5)
LICENSE.txt: 4208 bytes, checksum: b68a69b0e48b5907ca334357e846c741 (MD5)
PROQUEST_LICENSE.txt: 4554 bytes, checksum: f9497955d19c91789f0bba3946fafd47 (MD5)
Previous issue date: 2016-03-28Embargo set by: Seth Robbins for item 93083
Lift date: 2018-07-07T20:28:14Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 93083
Lift date: 2018-07-07T20:35:34Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemU of I Only Restriction Lifted for Item 93083 on 2018-07-08T09:15:09Z
Microbial pathways of sulfur metabolism and colorectal cancer risk
No full textColorectal cancer (CRC) is the third leading cause of cancer, and the second leading cause of cancer death in the United States (US). Recent evidence links consumption of a diet high in animal protein and fat as an environmental risk factor for CRC development, and the intestinal microbiota modulates the tumor promoting or protective effects of diet. Hydrogen sulfide (H2S), produced by resident sulfidogenic bacteria, triggers hyper-proliferation and pro-inflammatory pathways, and is genotoxic. In the US, there is a higher incidence of CRC in African Americans (AAs) compared to non-Hispanic whites (NHWs). We hypothesized that sulfidogenic bacterial abundance in colonic mucosa may be an environmental CRC risk factor that distinguishes AAs and NHWs, and may be correlated with differences in dietary composition. Colonic biopsies from uninvolved or healthy mucosa from CRC cases and controls were collected from five medical centers through the Chicago Colorectal Cancer Consortium. Using quantitative PCR, sulfidogenic bacterial abundance was measured in uninvolved colonic mucosa of 97 AA and 56 NHW CRC cases, and 100 AA and 76 NHW controls. In addition, 16S rRNA sequencing was performed in AA cases and AA controls. A Block Brief 2000 Food Frequency Questionnaire was collected from a subset of subjects of 50 AA and 31 NHW CRC cases and 30 AA and 24 NHW controls. Differences were examined among bacterial targets, race, disease status, and dietary intake. African Americans harbored a greater abundance (p<0.001) of sulfidogenic bacteria compared to NHWs regardless of disease status, including the functional gene for H2S production in sulfate-reducing bacteria (SRB), dissimilatory sulfate reductase (pan-dsrA), Bilophila wadsworthia-specific dsrA, and 16S rRNA genes for Desulfobacter spp., Desulfovibrio spp., and Desulfotomaculum spp.. Bilophila wadsworthia-specific dsrA was more abundant in AA cases compared to AA controls (p<0.001). Linear discriminant analysis of 16S rRNA gene sequences highlighted the sulfidogenic Bilophila, Lactococcus, Odoribacter, Porphyromonas and Pyramidobacter genera as features that characterize AA CRC. Fat intake and daily servings of meat were higher (p<0.01) in AAs compared with NHWs, and dietary fat intake correlated positively with pan-dsrA abundance (p=0.011). Additionally, dairy and calcium intake were lower (p<0.001) in AA, and servings of dairy correlated negatively with pan-dsrA abundance (p=0.007). Together, these results implicate sulfidogenic bacteria as an environmental risk factor contributing to CRC development in AAs.
Sulfidogenic bacteria metabolize organic and inorganic sulfur in order to produce H2S. We observed that microbes that metabolize organic sulfur distinguished AA CRC from NHW CRC subjects and AA controls. We hypothesize that SRB, (inorganic sulfur metabolizers), may impart beneficial functions, such as hydrogen disposal and barrier protection through antimicrobial effects of sulfide. Increased abundance of bacteria that utilize organic sources of sulfur may increase sulfide concentrations to levels that are proinflammatory and genotoxic. Bilophila wadsworthia produces H2S through metabolism of taurine, a sulfur amino acid available in the colon by diet and taurine conjugated bile acids. While studies have demonstrated preference for taurine as a terminal electron acceptor by B. wadworthia in vitro, none have determined the in vivo metobolic ‘lifestyle’ in a defined mixed community. Thus, as it was one of the most significant markers distinguishing AA CRC, we aimed to observe the baseline metabolic activity of this bacterium in vivo in mice fed a standard chow diet. Six gnotobiotic mice were colonized with a synthetic microbial community previously validated to be capable of metabolizing the taurine conjugated bile acid taurocholate (TCA), and were housed at the Mayo Clinic Gnotobiotic Facility for 30 days. A transcriptome analysis of cecal content revealed 4099 transcripts expressed by B. wadsworthia. Transcripts were observed for all three enzymes involved in taurine metabolism: taurine:pyruvate aminotransferase (tpa), sulfoacetaldehyde sulfolyase, and dissimilatory sulfite reductase A (dsrA). Taurine metabolism was the most abundant metabolic pathway expressed by the microbe, and dsrA an upstream enzyme to tpa were among the most abundant genes transcribed. Community analysis revealed expression of genes involved in liberating taurine from the bile acid taurocholate. Additionally, genes for D-cysteine and nitrogen metabolism were highly expressed, indicating that alternate forms of metabolism may be important for pathogenesis and microbial fitness. These results indicate that B. wadsworthia is likely producing H2S in the colonic environment from taurine and D-cysteine metabolism, and that taurine from TCA metabolism is an available substrate for this microbe.
In addition to B. wadsworthia, our recent study revealed Odoribacter spp. as a feature that distinguished AA CRC. Therefore, we aimed to verify that members of this genus do produce sulfide, and to determine the mechanism of their sulfur metabolism. The microbial species Odoribacter splanchnicus served as a surrogate for this analysis. Culture of O. splanchnicus in Sulfide Indole and Motility Medium revealed the microbe does indeed produce H2S. A genome search revealed a bifunctional tryptophanase/cysteine desulfhydrase (tnaA). The gene tnaA from O. splanchnicus was amplified by PCR, ligated into the expression vector pET-28a, transformed into Eschericia coli strain BL21, and overexpressed at 16°C for 16 hours. Functional analysis of the recombinant enzyme revealed positive cysteine desulfhydrase and tryptophanase activity. Cysteine desulfhydrase activity resulted in the consumption of cysteine and production of H2S and pyruvate. This implicates tnaA as an important functional enzyme in future analyses of the microbiome in CRC.
Given that our analyses revealed microbial organic sulfur metabolism as a significant indicator of CRC, and identified two additional sulfidogenic enzymes to be considered in evaluations of sulfur metabolism in the human gut, an examination of the sulfidogenic capacity of the human microbiome was performed. A survey of genomes published from the Human Microbiome Project (HMP) revealed that over a third of microbial species harbored genes for sulfur metabolism. Genes for cysteine metabolism were the most abundant sulfidogenic genes, revealing that it may be a more important driver of sulfidogenesis than inorganic sulfate metabolism in the human gut. In addition, a retroactive analysis revealed several species that were significantly correlated with CRC harbored genes for sulfur metabolism. These findings suggest that sulfur metabolism is more wide-spread in the human gut than previously understood, and that H2S production from organic sulfur metabolism may be an environmental trigger of CRC.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2020-12-01The student, Patricia Wolf, accepted the attached license on 2018-12-06 at 13:18.The student, Patricia Wolf, submitted this Dissertation for approval on 2018-12-06 at 13:44.This Dissertation was approved for publication on 2018-12-06 at 16:27.DSpace SAF Submission Ingestion Package generated from Vireo submission #13240 on 2019-02-07 at 14:23:02Made available in DSpace on 2019-02-07T20:44:26Z (GMT). No. of bitstreams: 6
WOLF-DISSERTATION-2018.pdf: 4859508 bytes, checksum: 343c474eea8d5e7066da84dfb5231e7b (MD5)
Dissertation draft_PGW_120618.docx: 8850789 bytes, checksum: 2af2f8ca657ce73ae14662e8036b5977 (MD5)
LICENSE.txt: 4210 bytes, checksum: 115d647afa2917b695ac5be63743f120 (MD5)
PROQUEST_LICENSE.txt: 4556 bytes, checksum: b5adb770b036a1481834a14cb3249492 (MD5)
RightsLink Printable License-2.html: 776 bytes, checksum: e46c4ed85b2307df3e01b2a01c82f45b (MD5)
RightsLink Printable License.html: 772 bytes, checksum: 9cd35136733c5a4c6fdaa048318085f5 (MD5)
Previous issue date: 2018-12-06Embargo set by: Seth Robbins for item 109872
Lift date: 2021-02-07T20:44:35Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemU of I Only Restriction Lifted for Item 109872 on 2021-02-08T10:15:39Z
Incorporating Indigenous voices: the struggle for increased representation in Jasper National Park
No full textThis thesis focuses on the lack of Indigenous representation in Jasper National Park (JNP) and the negative impacts it has on Indigenous communities and their relationship with JNP management. These representational issues foster the formation and dissemination of problematic Indigenous stereotypes and reinforce pan-Indigenous notions in Jasper and Canada. Relying on Indigenous Methodologies, I conducted semi-structured interviews with members of the Jasper Indigenous Forum (JIF) and JNP management which helped address a gap in knowledge as there are so few scholarly works on this issue, particularly in national parks. The findings from this research clearly indicated that while JNP management and the JIF have some overlapping priorities, they have different levels of understandings about the obstacles each group faces. Unequal power dynamics became evident in this research, which suggests a desire among JNP management to maintain the status quo. The research participants identified several areas of concern: Indigenous histories and cultures presented from non-Indigenous perspectives; a lack of cultural awareness training for JNP staff; the presence of culturally insensitive structures in JNP; inadequate time to meet on issues; and a lack of consultation. These key issues are examined in great detail in an effort to increase culturally appropriate representation in JNP and offer some viable solutions to help reconcile the past and move forward to address some of the concerns of Indigenous peoples in Jasper.IndigenousRepresentationJasperJIFJNPStereotypesInterpretationReconciliationHistoryTraditiona
