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Burkholderia fungorum strain Rifle

Descriptive

TitleInfo
Title
Burkholderia fungorum strain Rifle
SubTitle
growth on and interaction with uranium
Name (type = personal)
NamePart (type = family)
Koribanics
NamePart (type = given)
Nicole Michele
NamePart (type = date)
1986-
DisplayForm
Nicole Michele Koribanics
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Kerkhof
NamePart (type = given)
Lee
DisplayForm
Lee Kerkhof
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
chair
Name (type = personal)
NamePart (type = family)
Bromberg
NamePart (type = given)
Yana
DisplayForm
Yana Bromberg
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Haggblom
NamePart (type = given)
Max
DisplayForm
Max Haggblom
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Yee
NamePart (type = given)
Nathan
DisplayForm
Nathan Yee
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
outside member
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
School of Graduate Studies
Role
RoleTerm (authority = RULIB)
school
TypeOfResource
Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (qualifier = exact)
2017
DateOther (qualifier = exact); (type = degree)
2017-10
CopyrightDate (encoding = w3cdtf); (qualifier = exact)
2017
Place
PlaceTerm (type = code)
xx
Language
LanguageTerm (authority = ISO639-2b); (type = code)
eng
Abstract (type = abstract)
A novel strain of Burkholderia fungorum was isolated from the Department of Energy’s Rifle Integrated Field-Scale Subsurface Research Challenge Site in Rifle Colorado which can utilize uranium as a terminal electron acceptor under anaerobic conditions. The Rifle strain demonstrated growth with uranyl acetate as the terminal electron acceptor (1-10 μM) in a dose-dependent manner concomitant with decreases in soluble uranium. Each 1 μM increase of uranium initiated an increase of ~ 0.5 x 106 + 1.3 x 105 cells/ml, concurrent with a shift in uranium solubility from 90% soluble to 70-97% insoluble at the end of the time course. Cultures exposed to 5-10 μM uranium did not grow, but exhibited significantly decreased levels of soluble uranium at time point zero (78-18%), indicating either an additional cellular precipitation/detoxification mechanism in response to increased uranium concentrations or a media solubility threshold. To identify the capability of Burkholderia fungorum strain Rifle to precipitate elevated levels uranium, cultures were grown aerobically in the absence and presence of uranium (0-200 μM). Cultures grown in the presence of uranium exhibited variable lag phases, indicating a toxic response to uranium. However, the fraction of uranium which remained within the soluble fraction exhibited no difference over the course of growth, excluding bio-precipitation as mechanism of toxicity resistance under aerobic conditions. To identify possible genes of interest in regards to the anaerobic reduction of uranium or the overall toxicity resistance mechanism, the genome of Burkholderia fungorum strain Rifle was sequenced. The draft genome was assembled and annotated for prospective gene functions. A subset of seven genes sharing homology with genes of known uranium reducing species was earmarked for redox reaction capabilities. Additionally, genes associated with heavy metal toxic response were tested for up-regulation by transcription analysis using cultures shifted from uranium (-) to uranium (+) conditions. Reverse Transcriptase-PCR analysis demonstrated no variation in transcriptional level from day 0 of uranium transition to day 3 compared to the expression levels of the maleate isomerase indicating that while all select genes chosen were constitutively expressed. The nucleotide sequencing reads for these strains were also submitted for functional annotation of sequencing reads via mifaser to generate an enzymatic enrichment profile for these strains. This profile revealed that the Rifle strain exhibited enrichment for c-class cytochrome and P-type ATPase functions. An in silico proteome was also generated to identify genes of functionally similar phenotype, including a number which belong to a different genus, using Fusion phenotypic classification. Comparisons for proteins of similar function identified 42 proteins shared across genus, most with clearly defined functions but including 4 hypothetical proteins of interest. However, no gene was identified which was up-regulated by exposure to uranium. Further study of the remaining hypothetical proteins is warranted to identifying the genes involved with uranium respiration/detoxification in B. fungorum Rifle.
Subject (authority = RUETD)
Topic
Microbiology and Molecular Genetics
Subject (authority = ETD-LCSH)
Topic
Uranium
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
ETD_8497
PhysicalDescription
Form (authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
1 online resource (xiv, 126 p. : ill.)
Note (type = degree)
Ph.D.
Note (type = bibliography)
Includes bibliographical references
Note (type = statement of responsibility)
by Nicole Michele Koribanics
RelatedItem (type = host)
TitleInfo
Title
School of Graduate Studies Electronic Theses and Dissertations
Identifier (type = local)
rucore10001600001
Location
PhysicalLocation (authority = marcorg); (displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier (type = doi)
doi:10.7282/T3CZ3B9G
Genre (authority = ExL-Esploro)
ETD doctoral
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Rights

RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Koribanics
GivenName
Nicole
MiddleName
Michele
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2017-10-03 01:05:08
AssociatedEntity
Name
Nicole Koribanics
Role
Copyright holder
Affiliation
Rutgers University. School of Graduate Studies
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
RightsEvent
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2017-10-31
DateTime (encoding = w3cdtf); (qualifier = exact); (point = end)
2019-10-31
Type
Embargo
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after October 31st, 2019.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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Technical

RULTechMD (ID = TECHNICAL1)
ContentModel
ETD
OperatingSystem (VERSION = 5.1)
windows xp
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2018-01-29T10:54:47
CreatingApplication
Version
1.5
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