Treasures @ UT Dallas
Welcome to Treasures @ UT Dallas Institutional Repository, established in 2010. Treasures is a resource for our community to showcase, organize, share, and preserve research and scholarship in an Open Access repository.
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Recent Submissions
Metronidazole Degradation by the Gram-positive Bacterium Enterococcus Faecalis
(2022-05) Rappazzo, Jacob Matthew; Palmer, Kelli; Reitzer, Lawrence J.; De Nisco, Nicole; Spiro, Stephen
Enterococcus faecalis is a species of Gram-positive bacterium that natively inhabits the human
gastrointestinal tract. This bacterium is capable of causing sepsis and endocarditis and is
associated with the decreased effectiveness of antibiotic treatments for other bacterial infections.
One such antibiotic is metronidazole, a 5-nitroimidazole drug once used commonly in the
treatment of Clostridioides difficile infections. We hypothesize that E. faecalis reduces the
efficacy of metronidazole in treating C. difficile infections. The molecular mechanism for how E.
faecalis degrades metronidazole is unknown. In this work, we demonstrate how different strains
of E. faecalis affect levels of metronidazole in in vitro culture. Through the use of
spectrophotometry, we screened for E. faecalis transposon mutants unable to degrade
metronidazole and used DNA sequencing to determine the insertion sites of the transposons.
Screening has yielded two E. faecalis strains of interest, dubbed E. faecalis A7 and E. faecalis
H8. These strains have disruptions in genes that encode the proteins AroA and AroB,
respectively, which indicates that the chorismate synthesis pathway is crucial to E. faecalis’s
ability to degrade metronidazole. These data lead us to propose that E. faecalis utilizes extracellular electron transfer to degrade metronidazole, a process that relies on a reliable supply
of chorismate to synthesize demethylmenaquinone. This compound, alongside other membrane
proteins, is utilized in extracellular electron transfer in E. faecalis. Since the reduction of
metronidazole to a toxic form is seen in C. difficile, we theorize that E. faecalis uses extracellular
electron transfer to reduce metronidazole to a different compound that is non-toxic to bacteria. In
summary, we hypothesize that the work of demethylmenaquinone and other extracellular
electron transfer proteins is the link behind E. faecalis and metronidazole degradation due to the
nature of extracellular metronidazole reduction mechanisms that exist in Gram-positive bacteria.
Expression of Diverse Streptococcal Multiple Peptide Resistance Factors and Lipid Hydrolase in Streptococcus Mitis
(2022-05) Christensen, Priya M; Palmer, Kelli; Reitzer, Lawrence J; De Nisco, Nicole
Streptococcus agalactiae (Group B Streptococcus; GBS) is a gram-positive pathogen that
colonizes the gastrointestinal and lower genital tracts. In GBS, the multiple peptide resistance
factor (MprF) synthesizes a novel lipid, lysyl-glucosyl-diacylglycerol (Lys-Glc-DAG), and the
well-known lipid lysyl-phosphatidylglycerol (Lys-PG). Lys-PG reduces the negative charge of
the membrane, protecting bacteria from cationic antimicrobial peptides (CAMPs). Additionally,
GBS encodes a predicted alpha-beta hydrolase upstream of mprF. In Enterococcus faecium, this
hydrolase is responsible for the turnover of Lys-PG. This project has three aims: to determine
whether other streptococcal MprF proteins also synthesize Lys-Glc-DAG and/or Lys-PG; the
impact of Lys-Glc-DAG and Lys-PG production on Streptococcus mitis survival in low pH; and
whether the GBS hydrolase is responsible for the turnover of both Lys-Glc-DAG and Lys-PG. S.
mitis was chosen as a heterologous host for this study since it does not natively encode mprF and
does not natively synthesize Lys-Glc-DAG or Lys-PG. Candidate MprF proteins from other
streptococcal species (S. downei and S. ferus) with high identity to GBS MprF were identified by
BLASTp. These genes and the GBS hydrolase gene were inserted into a plasmid using Gibson
assembly and transformed into S. mitis. This study found that the expression of S. ferus mprF
and S. downei mprF in S. mitis conferred synthesis of Lys-Glc-DAG. Significantly, S. ferus
MprF synthesized Lys-Glc-DAG at a similar level to GBS MprF. Previous research found that
expression of S. salivarius mprF in S. mitis conferred synthesis of Lys-PG also at a similar level
to GBS MprF. The production of Lys-Glc-DAG and/or Lys-PG in S. mitis through the utilization
of plasmids expressing the different mprFs did not increase the survival of S. mitis in low pH.
Finally, preliminary investigation of the GBS hydrolase and E. faecium hydrolase through a cell
lysate assay did not show turnover of Lys-Glc-DAG and/or Lys-PG, demonstrating that methods
for investigating hydrolase activity require refinement.
Role of Importin and Ran in Nuclear Import of Histones
(2022-05) Tripathi, Kiran; D'Arcy, Sheena; Meloni, Gabriele; Torabifard, Hedieh; Ahn, Jung-Mo
Histones H2A, H2B, H3, and H4 are called the core histones and two copies of H2A-H2B dimers
and a copy of (H3-H4)2 tetramer make up the histone octamer. Histone proteins are important to
compact the genomic DNA. Like most proteins, histones are transcribed in the cytoplasm and need
to be imported into the nucleoplasm where they function. Import of cargo involves Importins, and
Rans. Importins transport cargo from the cytoplasm to the nucleus. When this binary complex
reaches the nucleus, it binds with RanGTP and this causes the release of cargo. It is not precisely
known how Importins and Rans import histones. The work of Padavannil et al. (2019) suggests
that the Importin and Ran import histones in a non-canonical way into the nucleus. When nuclear
import does not function correctly, it leads to various cancers and developmental disorders,
highlighting a need to understand the nuclear transport processes. Here, we aim to study these
proteins and uncover the mechanism behind the nuclear transport of H2A-H2B using hydrogen-
deuterium exchange mass spectrometry. We find that addition of Ran destabilizes two of the H2A-
H2B-binding surfaces on Imp9 and stabilizes one interface. This indicates that the N-terminal heat
repeats and acidic loop of Imp9 are responsible for the formation of the unconventional ternary
complex containing Imp9, H2A-H2B, and Ran.
Far Infrared Detection and Photonic Components in Complimentary Metal-oxide Silicon (CMOS) Technologies
(2022-05) Pouya, Behnam; O, Kenneth K.; Gelb, Lev D.; Henderson, Rashaunda; Lee, Mark; Shichijo, Hisashi
Consumer applications of Infrared (IR) and Far Infrared (FIR) imaging are emerging. These
systems require fabrication of detectors on a membrane, heterogeneous integration with read-out
IC, and specialized packaging, which all increase cost. To lower the cost of Far Infrared imaging
circuits, this dissertation investigated feasibility of realizing the circuits using CMOS.
Implementing an electronic circuit becomes increasingly challenging in the Far infrared region of
the spectrum since the state-of the-art active solid-state devices no longer have gain.
First, this work proposed a metal-n+
silicon junction that is fabricated in a 130-nm CMOS process
without process modifications. Its cut-off frequency (fT) is expected to be greater than 5 THz and
flicker noise corner frequency is less than 10 kHz at a bias current of 100 nA. This is the highest
fT for any junctions fabricated in silicon technologies to date. The parasitic effects of metal
interconnect on the fT of junctions and diodes are explored and techniques to overcome the
challenges are demonstrated by increasing the fT of Poly-Gate-Separated Schottky Barrier Diodes
(PGS SBD) from ~2 THz to 2.7 THz.
Second, challenges for characterization of on-wafer devices with an fT of over 1 THz are
investigated and a de-embedding method (Sub-array-SHORT) for improving the measurement
reliability is proposed. The proposed technique overcomes the limitations of vector network
analyses of structures with a large ratio of imaginary and real parts (|X|/R) of their impedance.
Measurements and comparisons are performed to verify the effectiveness of the proposed method.
The %-variations of measured fT and series resistance over the measurement frequency range (50
to 55 GHz) and over the samples are reduced by ~50% compared to the measurements using a
conventional OPEN structure. Proper scaling of the estimated resistance and capacitance with the
number of device cells indicates that the proposed de-embedding technique provides estimations
of resistance, capacitance, and fT with improved accuracy.
For the first time, 20-THz electronic detection using foundry CMOS technologies is demonstrated.
The effects of thermal and electronic detections are separated noting that the output from thermal
and electronic detections can have opposite signs. A 20-THz PGS SBD detector using a 110-nm
CMOS process without process modifications is integrated with an on-chip Lock-In Amplifier.
Detectors with larger aperture sizes for FIR detection are implemented. It occupies an area of 82
µm2
. The peak optical responsivity of 29.8 V/W and shot noise limited NEP of 2.2 nW/√Hz are
achieved. Additionally, a 20-THz detector using the proposed unsilicided metal-n
+
junction is
fabricated using a standard 130-nm CMOS technology once again without any process
modifications. The pixel area is 8.6 µm2
. This is significantly smaller than other detectors reported
in the literature which makes it a good potential candidate for large detector arrays. The
measurements show that its output is higher at low bias conditions at which noise is smaller
compared to the PGS SBD detectors. The performance is better than other previously reported state-of-the-art and commercially available FIR detectors. Finally, the frequency responses of the
antennas are verified by measurements using an FTIR.
To characterize the detectors, a computer controlled low-cost wideband imaging setup is
constructed. A blackbody light source is utilized along with a wideband pyroelectric thermal
detector that is combined with an automatic 3-axis stage.
Aesthetics and Politics: Community-Based Art in Brazil
(2022-05) Stout, Patricia Jean; Terranova, Charissa N.; Hatfield, Charles; Stewart, Whitney; Gu, Ming Dong; Warren, Shilyh
This dissertation analyzes large-scale and multifaceted artworks created in 2008 by the Dutch
artists Jeroen Koolhaas and Dre Urhahn (Haas & Hahn), the French street artist JR, and the
Brazilian mixed-media artist Vik Muniz. Each of these artists were drawn specifically to Brazil’s
second largest city, Rio de Janeiro, and decided to create large-scale works of art in informal
housing settlements known as favelas with the help of local community members. In August
2008, photographs of women’s faces and eyes from Rio de Janeiro’s oldest favela, Morro da
Providência, were enlarged and pasted on building façades and rooftops in the community,
creating a hillside of women staring out at Brazil’s Marvelous City. Two months later, Haas &
Hahn completed a nine-month-long project entitled Rio Cruzeiro, which resulted in a 2,000
square meter mural of Japanese-style carp fighting the current of a roaring river rushing down
the hillside in the favela of Vila Cruzeiro. Around this same time, Vik Muniz constructed seven
large-scale assemblages on the ground from discarded materials with the help of catadores
(pickers of recyclable materials) from the Jardim Gramacho landfill and neighboring favela,
which he photographed and entitled Pictures of Garbage.
Although the works by Haas & Hahn, JR, and Muniz I study are often understood within existing
frameworks for community-based art, I argue that this framework does not fully account for
what these works are trying to achieve in both political and aesthetic terms. Specifically, I argue
that in the community-based artworks by Haas & Hahn, JR, and Muniz in Rio de Janeiro, we see
an investment in the aesthetic and political potential of commitments not usually associated with
socially engaged art in Brazil, such as to completedness, unity, intentional meaning, and beauty.
At the same time, the works of Haas & Hahn, JR, and Muniz include in varying degrees an
element of viewer experience, ultimately defining who participates in the work and who sees the
work, as they toe the line between formalism and spectatorship. Some of the strategies seen in
the community-based artworks of Haas & Hahn, JR, and Muniz can be traced to the Concrete
and Neo-Concrete art movements in Brazil from the 1950s and 1960s. By situating these
artworks, which have been created in marginalized working-class communities in Rio de Janeiro,
in dialogue with the work of Brazilian Neoconcretists in the early 1960s, such as Lygia Clark,
Hélio Oiticica, and Lygia Pape, I reveal how they constitute a deep and continued connection
between Brazilian art and the favela. Artworks by Haas & Hahn, JR, and Vik Muniz have
incorporated aspects of the art-making process employed by Clark, Oiticica, and Pape; however,
this process yields works of art that metaphorically represent the city in which they were created.
I conclude that community-based art’s aesthetic shift from viewer experience to visual
representation in Brazil is not a departure from the social and political issues of the city, but
rather a continuation of aesthetic dialogue aimed at promoting social change in Rio de Janeiro.