Biochemistry, Biophysics, and Structural Biology Commons^™

Detection And Capture Of Nitrogen Fixing Bacteria From Soil And Roots Using Plant Specific Lectins, Alana Horton

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Diazotrophs increase plant productivity by providing ammonia directly to plants in the rhizosphere or through association with the roots (Sun et al., 2021). Leveraging diazotrophs can aid in the reduction or application of harmful synthetic nitrogen fertilizers. This thesis aims to use plant root proteins, or lectins, to more rapidly recover viable diazotrophs that are likely to associate with crops. In this study, lectins, are used to recover bacteria from bulk soil by taking advantage of the binding relationship between lectins and bacterial cell surface polysaccharides. When commercially-available lectins were used with a magnetic pulldown to separate the lectin, bacterial …

Dpc29 Promotes Post-Initiation Mitochondrial Translation In Saccharomyces Cerevisiae, Kyle A. Hubble, Michael F. Henry

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Mitochondrial ribosomes synthesize essential components of the oxidative phosphorylation (OXPHOS) system in a tightly regulated process. In the yeast Saccharomyces cerevisiae, mitochondrial mRNAs require specific translational activators, which orchestrate protein synthesis by recognition of their target gene's 5'-untranslated region (UTR). Most of these yeast genes lack orthologues in mammals, and only one such gene-specific translational activator has been proposed in humans-TACO1. The mechanism by which TACO1 acts is unclear because mammalian mitochondrial mRNAs do not have significant 5'-UTRs, and therefore must promote translation by alternative mechanisms. In this study, we examined the role of the TACO1 orthologue in yeast. We …

Effects Of Post-Translational Histone Modifications On Transcription Rate, Aaron Bohn

Annual Research Symposium

No abstract provided.

Preparation And Characterization Of Salvia Triloba Extract And Evaluation Of Its Cytotoxic Effect On Bone Cancer Cell Line, Basma Hossam Abdelmonem

Theses and Dissertations

Background: Osteosarcoma is a tumor of mesenchymal origin characterized by uncontrolled production of immature osteoid tissue. It is more common in children and adults over the age of 65. Many studies reported the cytotoxic effect of many plant extracts, including Salvia triloba, on different cancer cell lines when used alone or in combination with other chemotherapeutic agents.

Methods: In our study, the methanolic extract obtained from the air-dried leaves of Salvia triloba leaves from Palestine was screened for its total phenolic and flavonoid contents. The major components of phenolics and flavonoids were detected using LC-QToF-MS technique. The two phenolics …

Probing Amyloid-Beta Protein Structure And Dynamics With A Selective Antibody, Shikha Grover

Dissertations

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder. The AD brain is characterized by significant neuronal loss and accumulation of insoluble fibrillar amyloid-β protein (Aβ) plaques and tau protein neurofibrillary tangles in the brain. However, over the last decade, many studies have shown that the neurodegenerative effect of Aβ may in fact be caused by various soluble oligomeric forms as opposed to the insoluble fibrils. Furthermore, the data suggest that a pre-fibrillar aggregated form, termed protofibrils, mediates direct neurotoxicity, and triggers a robust neuroinflammatory response.

Antibodies targeting the various conformation of Aβ are important therapeutic agents to prevent the progression …

Gasdermin D Deficiency In Vascular Smooth Muscle Cells Ameliorates Abdominal Aortic Aneurysm Through Reducing Putrescine Synthesis, Jianing Gao, Yanghui Chen, Huiqing Wang, Xin Li, Ke Li, Yangkai Xu, Xianwei Xie, Yansong Guo, Nana Yang, Xinhua Zhang, Dong Ma, Hong S. Lu, Ying H. Shen, Yong Liu, Jifeng Zhang, Y. Eugene Chen, Alan Daugherty, Dao Wen Wang, Lemin Zheng

Saha Cardiovascular Research Center Faculty Publications

Abdominal aortic aneurysm (AAA) is a common vascular disease associated with significant phenotypic alterations in vascular smooth muscle cells (VSMCs). Gasdermin D (GSDMD) is a pore-forming effector of pyroptosis. In this study, the role of VSMC-specific GSDMD in the phenotypic alteration of VSMCs and AAA formation is determined. Single-cell transcriptome analyses reveal Gsdmd upregulation in aortic VSMCs in angiotensin (Ang) II-induced AAA. VSMC-specific Gsdmd deletion ameliorates Ang II-induced AAA in apolipoprotein E (ApoE)−/− mice. Using untargeted metabolomic analysis, it is found that putrescine is significantly reduced in the plasma and aortic tissues of VSMC-specific GSDMD deficient mice. High putrescine levels …

Genetic Determinants Involved In Acquisition Of Iron In The Opportunistic Pathogen Mycobacterium Abscessus, Manal F. Farhat

Dissertations, Theses, and Capstone Projects

The opportunistic pathogen Mycobacterium abscessus subsp. abscessus (Mab) has become an emerging public health threat due to the increasing number of Mab-associated chronic pulmonary disease cases. Infection cure rates are only 50% due to the complex resistance of Mab to most antimicrobial drugs and chemotherapy.

Deeper knowledge of Mab biology is needed to illuminate potential candidates for development of improved therapeutics against Mab infections. The ESX-3 type VII protein secretion system of Mab plays an important role in host inflammatory and pathological responses during infection.

In this study, we demonstrate a functional link between the ESX-3 secretion …

Bilirubin Nanoparticle Treatment In Obese Mice Inhibits Hepatic Ceramide Production And Remodels Liver Fat Content, Zachary A. Kipp, Genesee J. Martinez, Evelyn A. Bates, Agil B. Maharramov, Robert M. Flight, Hunter N. B. Moseley, Andrew J. Morris, David E. Stec, Terry D. Hinds Jr.

Markey Cancer Center Faculty Publications

Studies have indicated that increasing plasma bilirubin levels might be useful for preventing and treating hepatic lipid accumulation that occurs with metabolic diseases such as obesity and diabetes. We have previously demonstrated that mice with hyperbilirubinemia had significantly less lipid accumulation in a diet-induced non-alcoholic fatty liver disease (NAFLD) model. However, bilirubin’s effects on individual lipid species are currently unknown. Therefore, we used liquid chromatography-mass spectroscopy (LC-MS) to determine the hepatic lipid composition of obese mice with NAFLD treated with bilirubin nanoparticles or vehicle control. We placed the mice on a high-fat diet (HFD) for 24 weeks and then treated …

Clic And Membrane Wound Repair Pathways Enable Pandemic Norovirus Entry And Infection, B. Vijayalakshmi Ayyar, Khalil Ettayebi, Wilhelm Salmen, Umesh C. Karandikar, Frederick H. Neill, Victoria R. Tenge, Sue E. Crawford, Erhard Bieberich, B. V. Venkataram Prasad, Robert L. Atmar, Mary K. Estes

Markey Cancer Center Faculty Publications

Globally, most cases of gastroenteritis are caused by pandemic GII.4 human norovirus (HuNoV) strains with no approved therapies or vaccines available. The cellular pathways that these strains exploit for cell entry and internalization are unknown. Here, using nontransformed human jejunal enteroids (HIEs) that recapitulate the physiology of the gastrointestinal tract, we show that infectious GII.4 virions and virus-like particles are endocytosed using a unique combination of endosomal acidification-dependent clathrin-independent carriers (CLIC), acid sphingomyelinase (ASM)-mediated lysosomal exocytosis, and membrane wound repair pathways. We found that besides the known interaction of the viral capsid Protruding (P) domain with host glycans, the Shell …

Critical Role Of The Sulfiredoxin-Peroxiredoxin Iv Axis In Urethane-Induced Non-Small Cell Lung Cancer, Yanning Hao, Hong Jiang, Pratik Thapa, Na Ding, Aziza Alshahrani, Junichi Fujii, Michel B. Toledano, Qiou Wei

Markey Cancer Center Faculty Publications

Non-small cell lung cancer (NSCLC), the most common type of lung cancer, etiologically associates with tobacco smoking which mechanistically contributes to oxidative stress to facilitate the occurrence of mutations, oncogenic transformation and aberrantly activated signaling pathways. Our previous reports suggested an essential role of Sulfiredoxin (Srx) in promoting the development of lung cancer in humans, and was causally related to Peroxiredoxin IV (Prx4), the major downstream substrate and mediator of Srx-enhanced signaling. To further explore the role of the Srx-Prx4 axis in de novo lung tumorigenesis, we established Prx4−/− and Srx−/−/Prx4−/− mice in pure FVB/N background. Together with wild-type litter …

Production And Characterization Of Monoclonal Antibodies To Xenopus Proteins, Brett Horr, Ryan Kurtz, Ankit Pandey, Benjamin G. Hoffstrom, Elizabeth Schock, Carole Labonne, Dominique Alfandari

Markey Cancer Center Faculty Publications

Monoclonal antibodies are powerful and versatile tools that enable the study of proteins in diverse contexts. They are often utilized to assist with identification of subcellular localization and characterization of the function of target proteins of interest. However, because there can be considerable sequence diversity between orthologous proteins in Xenopus and mammals, antibodies produced against mouse or human proteins often do not recognize Xenopus counterparts. To address this issue, we refined existing mouse monoclonal antibody production protocols to generate antibodies against Xenopus proteins of interest. Here, we describe several approaches for the generation of useful mouse anti-Xenopus antibodies to multiple …

Change And Stasis Of Distinct Sediment Microbiomes Across Port Everglades Inlet (Pei) And The Adjacent Coral Reefs, Lauren E. Krausfeldt, Jose V. Lopez, Catherine Bilodeau, Hyo Won Lee, Shelby L. Casali

Biology Faculty Articles

Deep water ports are human built coastal structures that by definition welcome ship traffic and disturbance. Evidence is accumulating that enhanced port activities such as dredging or deepening have negatively affected nearby natural habitats. Port Everglades Inlet (PEI) is a large active South Florida cargo port for over two million people and lies adjacent to coral reefs, dwindling mangroves, and recreational beaches. In this study, the microbial communities of PEI and adjacent reef sediments were characterized to serve as indicators for change due to dredging and assess anthropogenic influence on these sensitive ecosystems by sequencing the V4 region of 16S …

Temperature Effects On Conductivity Of Phospholipid Bilayers, Dylan Mount, Sebastian Grabill, Loren Haarsma

Summer Research

Phospholipids molecules contain a fatty acid tail and a head made of a phosphate group (Fig.1) and serve as the building blocks of cellular membranes. The tails are hydrophobic, meaning they are weakly attracted to water, while the head group is hydrophilic, which is strongly attracted to water. Lipids in water will spontaneously form into bilayers with the tails towards the center (Fig.2) and the heads pointing towards the water on either side. This is how the lipid bilayers are formed to separate a cell's interior from exterior. Biological cells contain mixtures of many lipids and other molecules. In our …

Molecular Regulation Of The Salicylic Acid Hormone Pathway In Plants Under Changing Environmental Conditions, Christina A. M. Rossi, Eric J. R. Marchetta, Jong Hum Kim, Christian Castroverde

Biology Faculty Publications

Salicylic acid (SA) is a central plant hormone mediating immunity, growth, and development. Recently, studies have highlighted the sensitivity of the SA pathway to changing climatic factors and the plant microbiome. Here we summarize organizing principles and themes in the regulation of SA biosynthesis, signaling, and metabolism by changing abiotic/biotic environments, focusing on molecular nodes governing SA pathway vulnerability or resilience. We especially highlight advances in the thermosensitive mechanisms underpinning SA-mediated immunity, including differential regulation of key transcription factors (e.g., CAMTAs, CBP60g, SARD1, bHLH059), selective protein–protein interactions of the SA receptor NPR1, and dynamic phase separation of the recently identified …

Developing Red Fluorescent Zn2+ Sensors And Characterizing Zn2+ Homeostasis In Mucolipidosis Type Iv Disease, Anna M. Dischler

Electronic Theses and Dissertations

Zinc (Zn²⁺) is a divalent, redox-inert metal that plays a vital role in many cellular processes either by acting as a catalytic cofactor or a labile signaling molecule in the cytoplasm. Cytosolic Zn²⁺ levels are tightly regulated to stay within a narrow window of concentrations, but fluctuations in Zn²⁺ signals have been detected in a variety of cells. We developed a genetically encoded, single red fluorescent protein (RFP) based Zn²⁺ sensor, RZnP1, that can be used alongside green-wavelength sensors for the simultaneous detection of different signaling molecules within the same cells or among different subcellular …

Identifying The Role Of Phospholipase D1 And Phosphatidic Acid In Exocytosis, Broderick L. Bills

Electronic Theses and Dissertations

Exocytosis is an essential process for intercellular communication in eukaryotic cells. This process involves significant changes in membrane curvature, and lipids and curvature-sensing proteins can assist these processes. One protein in particular, phospholipase D1 (PLD1), and its product, the lipid phosphatidic acid (PA), are involved in multiple exocytic processes. However, PLD1 and PA’s role in this process has remained unclear. In this work, PLD1 and the production of PA were visualized during exocytosis, and PA localization to regions of membrane curvature was established. Together, these results support the hypothesis that PLD1 production of PA stabilizes negative curvature during membrane fusion. …

Investigating The Binding Of G-Quadruplex Dna To Lispro And Bovine Insulin, Sarah E. Bultje, Luke D. Witvliet, Kumar Sinniah

Summer Research

Type 1 Diabetes (T1D) is a disease characterized by the inability to produce insulin. Susceptibility to T1D is complex, involving both genetic and environmental factors. o One of the genetic components involved in insulin gene expression, and suspected T1D susceptibility, is the insulin-linked polymorphic region (ILPR). The ILPR element is located on chromosome 11p15 in the proximal promoter region, 363 base pairs upstream from the gene transcription site. o Other researchers (using fluorescence spectroscopy) and we (using ITC) have demonstrated that insulin binds to G-Quadruplex DNA with µM affinity. Since the DNA sequences in the ILPR form G-Quadruplexes and are …

Interferon Gamma Signaling In Ovarian Cancer Cells, Bijaya Gaire

Theses and Dissertations

Interferon gamma (IFNγ) is a pleiotropic cytokine that can have, depending on the cellular and molecular context, both anti-tumor and pro-tumorigenic functions. IFNγ expression can be induced in cancer cells in response to radiation therapy or immune checkpoint blockade used in cancer treatment. We have previously shown that IFNγ induces expression of the Bcl3 proto-oncogene in ovarian cancer (OC) cells, resulting in their increased proliferation and migration, but the mechanisms are unknown. Here, I demonstrate that the IFNγ-induced Bcl3 expression is dependent on JAK1 and STAT1 signaling, and on p65 NFkB. Furthermore, my data show that the IFNγ-induced Bcl3 expression …

Role Of Integrins In Hiv Infection Of Resting Cd4+ T Cells Stimulated By Intestinal Endothelial Cells, Anding Shen, Sarah Logan, Tim Kim, Zihan Zhang

Summer Research

Eradicating HIV remains a formidable challenge due to the persistence of latent reservoirs within resting CD4+ T cells. Intestinal endothelial cells (IECs) have been shown to promote HIV infection and latent reservoir formation in resting CD4+ T cells. Our research investigates the role of integrins and their ligands, specifically ICAM, VCAM, and MAdCAM, in resting T cells and their impact on productive and latent HIV infection. Findings reveal that VCAM stimulation was the most effective in promoting productive HIV infection. MAdCAM and ICAM had minimal effect. Cytokine IL-6 consistently displayed synergy with all CAMs, amplifying effects on productive HIV infection. …

Regulation Of P53 By Trpm6 And Trpm7, Thomas Whitbread

Theses and Dissertations

TRPM6 and TRPM7 are two divalent metal cation channels that also possess a serine/threonine kinase domain. They both play critical roles in cellular and organismal metal homeostasis, and are necessary for proper embryonic development and human health. They may function independently in homomeric units, or act together as heterotetramers that display unique characteristics compared to the homomeric channels. These channel-kinases have increasingly been linked to cancer, displaying altered expression levels in a variety of human cancers and contributing to disease progression. Prior work has shown that TRPM6 and TRPM7 can participate in cancer-related signaling pathways. Here, the potential for TRPM6 …

Comparing The Performance Of A Targeted Pull-Down Assay To Shotgun Sequencing For Improving Respiratory Infectious Disease Surveillance, Monica R. Christian

Browse all Theses and Dissertations

Current surveillance focuses on well characterized pathogens such as influenza. Since 2000, there have been multiple outbreaks of respiratory disease. These outbreaks have demonstrated the need for robust and collaborative global efforts to identify, monitor, and contain novel respiratory viruses. This study aims to improve the ability of public health agencies to monitor and respond to respiratory disease outbreaks. Using five respiratory pathogens, this study compares a molecular capture technology from Twist Biosciences to the shotgun sequencing approach of whole transcriptome amplification (WTA, Qiagen) with the goal of determining which method is most effective using cost, usability, and sequencing quality …

Trichloroethylene (Tce) And Metabolite S-(1,2-Dichlorovinyl)-L-Cysteine (Dcvc) Alters Pregnancy Mediators In Rat Amniotic Fluid And Thp-1 Cells, Audrey Luce, Lyric Johnson, Karena Moleakunnel, Eleanor Scheeres, Emily Schellenboom, Sean Harris, Erica Boldenow

Summer Research

• Proinflammatory cytokines, such as TNF-α recruit immune cells to help fight infection and aid in cervical ripening (i.e. dilation).

• Matrix metalloproteinases (MMPs) such as MMP-9 help with rupture of the gestational membranes (i.e. breaking of the water).

• Prostaglandins, such as PGE2 contribute to myometrial contractions and labor induction.

• Working pregnant women are exposed to both toxicants and pathogens which can contribute to adverse birth outcomes such as preterm birth.

Molecular And Systemic Epigenetic Inheritance: Integrating Development, Genetics, And Evolution, Robert Lickliter, David S. Moore

Pitzer Faculty Publications and Research

Currently, a central problem for theoretical biology is the integration of development with genetics and evolutionary theory. Through the late 20^th century, biologists held that animals resemble their ancestors strictly because of the transgenerational transmission of DNA. This view effectively wrote development out of evolutionary biology. However, many molecular and developmental biologists now understand that phenotypes—anatomical, physiological, and behavioral traits—are not determined by genes (i.e., DNA segments) alone; instead, they emerge epigenetically from developmental processes involving co-acting genetic factors, environmental factors, molecular epigenetic factors, and other non-genetic factors within organisms’ bodies. This insight forces a rethinking of biological inheritance. …

Effect Of Molecular Crowders On The Activation Of Cholera Toxin By Protein Disulfide Isomerase, Niral Shah

Honors Undergraduate Theses

Cholera toxin (CT) is a classic A-B type protein toxin that has an A subunit (A1 + A2) and a pentameric B subunit. The catalytic A1 domain is linked to the A2 domain via a disulfide linkage. CTA1 must be dissociated from the rest of the toxin to cause a cytopathic effect. Protein disulfide isomerase (PDI) can reduce the CTA1/CTA2 disulfide bond, but disassembly of the reduced toxin requires the partial unfolding of PDI that occurs when it binds to CTA1. This unfolding event allows PDI to push CTA1 away from the rest of the toxin.

My research question is …

Dcaf14 Regulates Cdt2 To Promote Set8-Dependent Replication Fork Protection, Neysha Tirado-Class, Caitlin Hathaway, Anthony Nelligan, Huzefa Dungrawala

Molecular Biosciences Faculty Publications

DDB1- and CUL4-associated factors (DCAFs) CDT2 and DCAF14 are substrate receptors for Cullin4–RING E3 ubiquitin ligase (CRL4) complexes. CDT2 is responsible for PCNA-coupled proteolysis of substrates CDT1, p21, and SET8 during S-phase of cell cycle. DCAF14 functions at stalled replication forks to promote genome stability, but the mechanism is unknown. We find that DCAF14 mediates replication fork protection by regulating CRL4CDT2 activity. Absence of DCAF14 causes increased proteasomal degradation of CDT2 substrates. When forks are challenged with replication stress, increased CDT2 function causes stalled fork collapse and impairs fork recovery in DCAF14-deficient conditions. We further show that stalled fork protection …

Otud5 Limits Replication Fork Instability By Organizing Chromatin Remodelers, Angelo De Vivo, Hongseon Song, Yujin Lee, Neysha Tirado-Class, Anthony Sanchez, Sandy D. Westerheide, Huzefa Dungrawala, Younghoon Kee

Molecular Biosciences Faculty Publications

Proper regulation of replication fork progression is important for genomic maintenance. Subverting the transcription-induced conflicts is crucial in preserving the integrity of replication forks. Various chromatin remodelers, such as histone chaperone and histone deacetylases are known to modulate replication stress, but how these factors are organized or collaborate are not well understood. Here we found a new role of the OTUD5 deubiquitinase in limiting replication stress. We found that OTUD5 is recruited to replication forks, and its depletion causes replication fork stress. Through its C-terminal disordered tail, OTUD5 assembles a complex containing FACT, HDAC1 and HDAC2 at replication forks. A …

The Identification Of Two M20b Family Peptidases Required For Full Virulence In Staphylococcus Aureus, Nathanial James Torres, Devon Rizzo, Maria A. Reinberg, Mary-Elizabeth Jobson, Brendan C. Totzke, Jessica K. Jackson, Wenqi Yu, Lindsey Neil Shaw

Molecular Biosciences Faculty Publications

We have previously demonstrated that deletion of an intracellular leucine aminopeptidase results in attenuated virulence of S. aureus. Herein we explore the role of 10 other aminopeptidases in S. aureus pathogenesis. Using a human blood survival assay we identified mutations in two enzymes from the M20B family (PepT1 and PepT2) as having markedly decreased survival compared to the parent. We further reveal that pepT1, pepT2 and pepT1/2 mutant strains are impaired in their ability to resist phagocytosis by, and engender survival within, human macrophages. Using a co-infection model of murine sepsis, we demonstrate impairment of dissemination and survival …

Establishing A Biochemical System For The Purification And Atpase Activity Of Gst-Dbp5, Sarah Utley, Rachel E. Rigsby Phd, Rebecca L. Adams Phd

Science University Research Symposium (SURS)

The export of mRNA out of the nucleus is a crucial step for eukaryotic gene expression. The export of mRNA transcripts is aided by Mex67, which allows export through the nuclear pore complex doorways in the nuclear envelope. Once out of the nucleus, a protein known as Dbp5, bound to ATP, Gle1, and Nup42 aids in the directionality of mRNA export by helping remove Mex67 from the mRNA strand. Following interaction with RNA, Dbp5 then hydrolyzes ATP so that it unbinds the mRNA, allowing for enzyme recycling. The goal of this study is to explore the ATPase activity of Saccharomyces …

Detecting Linc Complex Mps3 And Nuclear Pore Complex Ndj1 Protein Interactions On Yeast Nuclear Membrane S Through Fluorescence Microscopy, Dean Boecher, Rebecca Adams

Science University Research Symposium (SURS)

Though cancer cells have been shown to have abnormal nuclear morphologies and responses to mechanical forces, the mechanisms of how mechanical stress is translated into cellular action and structural reorganization within the nuclear envelope are largely unexplored. The Linker of Nucleoskeleton and Cytoskeleton (LINC) complex is a transmembrane protein complex that connects the actin cytoskeleton to the lamin nucleoskeleton, enabling mechanical forces to be translated between the cytoplasm and the nucleus. In cells exposed to physical stress, nuclear pore complexes (NPCs) –which control the exchange of biochemical signals and macromolecules in and out of the nucleus through mRNA export –have …

Analyzing Mex67 Interaction With The Ssa4 Transcript For Selective Export, Gretchen E. Stalnaker, Rebecca Adams

Science University Research Symposium (SURS)

In eukaryotic cells, such as the budding yeast Saccharomyces cerevisiae, mRNA export is the essential process in which mature mRNA is transported from its site of production, the nucleus, through the nuclear pore complex (NPC) to the cytoplasm, where it can then be translated into protein. This is accomplished when a transcript interacts with the mRNA export protein Mex67, which shuttles the message across the NPC. When the cell is under conditions of stress, such as heat shock, most mRNA export is prohibited, allowing for selective gene expression that prioritizes cell recovery. Specifically, SSA4, which encodes a protein that …