Digital Commons Network^™

Contribution Of Advanced Fluorescence Nano Microscopy Towards Revealing Mitotic Chromosome Structure, S W. Botchway, Safana Farooq, A Sajid, I K. Robinson, Mohammed Yousuf

Centre for Regenerative Medicine & Stem Cell Research

The organization of chromatin into higher-order structures and its condensation process represent one of the key challenges in structural biology. This is important for elucidating several disease states. To address this long-standing problem, development of advanced imaging methods has played an essential role in providing understanding into mitotic chromosome structure and compaction. Amongst these are two fast evolving fluorescence imaging technologies, specifically fluorescence lifetime imaging (FLIM) and super-resolution microscopy (SRM). FLIM in particular has been lacking in the application of chromosome research while SRM has been successfully applied although not widely. Both these techniques are capable of providing fluorescence imaging …

Office Of Research, Economic Engagement And Outreach Update, March 3, 2021, Office Of Research, Economic Engagement And Outreach

Office of Research, Economic Engagement and Outreach

No abstract provided.

Discovery And Characterization Of Bromodomain 2-Specific Inhibitors Of Brdt, Zhifeng Yu, Angela F Ku, Justin L Anglin, Rajesh Sharma, Melek Nihan Ucisik, John C Faver, Feng Li, Pranavanand Nyshadham, Nicholas Simmons, Kiran L Sharma, Sureshbabu Nagarajan, Kevin Riehle, Gundeep Kaur, Banumathi Sankaran, Marta Storl-Desmond, Stephen S Palmer, Damian W Young, Choel Kim, Martin M Matzuk

Faculty, Staff and Students Publications

Bromodomain testis (BRDT), a member of the bromodomain and extraterminal (BET) subfamily that includes the cancer targets BRD2, BRD3, and BRD4, is a validated contraceptive target. All BET subfamily members have two tandem bromodomains (BD1 and BD2). Knockout mice lacking BRDT-BD1 or both bromodomains are infertile. Treatment of mice with JQ1, a BET BD1/BD2 nonselective inhibitor with the highest affinity for BRD4, disrupts spermatogenesis and reduces sperm number and motility. To assess the contribution of each BRDT bromodomain, we screened our collection of DNA-encoded chemical libraries for BRDT-BD1 and BRDT-BD2 binders. High-enrichment hits were identified and resynthesized off-DNA and examined …

Inhibition Of Camkk2 Impairs Autophagy And Castration-Resistant Prostate Cancer Via Suppression Of Ampk-Ulk1 Signaling, Chenchu Lin, Alicia M Blessing, Thomas L Pulliam, Yan Shi, Sandi R Wilkenfeld, Jenny J Han, Mollianne M Murray, Alexander H Pham, Kevin Duong, Sonja N Brun, Reuben J Shaw, Michael M Ittmann, Daniel E Frigo

Faculty, Staff and Students Publications

Previous work has suggested androgen receptor (AR) signaling mediates prostate cancer progression in part through the modulation of autophagy. However, clinical trials testing autophagy inhibition using chloroquine derivatives in men with castration-resistant prostate cancer (CRPC) have yet to yield promising results, potentially due to the side effects of this class of compounds. We hypothesized that identification of the upstream activators of autophagy in prostate cancer could highlight alternative, context-dependent targets for blocking this important cellular process during disease progression. Here, we used molecular, genetic and pharmacological approaches to elucidate an AR-mediated autophagy cascade involving Ca2+/calmodulin-dependent protein kinase kinase 2 (CAMKK2; …

Tools For Visualizing And Analyzing Fourier Space Sampling In Cryo-Em, Philip R Baldwin, Dmitry Lyumkis

Faculty, Staff and Students Publications

A complete understanding of how an orientation distribution contributes to a cryo-EM reconstruction remains lacking. It is necessary to begin critically assessing the set of views to gain an understanding of its effect on experimental reconstructions. Toward that end, we recently suggested that the type of orientation distribution may alter resolution measures in a systematic manner. We introduced the sampling compensation factor (SCF), which incorporates how the collection geometry might change the spectral signal-to-noise ratio (SSNR), irrespective of the other experimental aspects. We show here that knowledge of the sampling restricted to spherical surfaces of sufficiently large radii in Fourier …

Transcriptomic Profiling Of Fibropapillomatosis In Green Sea Turtles (Chelonia Mydas) From South Texas, Nicholas B. Blackburn, Ana C. Leandro, Nina Nahvi, Mariana A. Devlin, Marcelo Leandro, Ignacio Martinez Escobedo, Juan M. Peralta, Jeff George, Thomas W. Demaar, John Blangero, Megan Keniry, Joanne E. Curran

School of Medicine Publications

Sea turtle fibropapillomatosis (FP) is a tumor promoting disease that is one of several threats globally to endangered sea turtle populations. The prevalence of FP is highest in green sea turtle (Chelonia mydas) populations, and historically has shown considerable temporal growth. FP tumors can significantly affect the ability of turtles to forage for food and avoid predation and can grow to debilitating sizes. In the current study, based in South Texas, we have applied transcriptome sequencing to FP tumors and healthy control tissue to study the gene expression profiles of FP. By identifying differentially expressed turtle genes in …

Bone Microenvironmental Control Of Skeletal Malignancy, Chen Hao Lo

USF Tampa Graduate Theses and Dissertations

Bone is a common site of metastasis for many solid malignancies. Bone-metastatic cancers pose a significant clinical problem worldwide and is among the main causes for cancer patient morbidity and mortality. Patients with advanced bone-metastatic diseases often present with either osteolytic or osteogenic bone diseases as their cancers progress. These bone pathologies are products of the cancer co-opting the local bone remodeling stroma to yield important growth nutrients and factors. Unfortunately, skeletal metastases remain incurable and are fatal. Identifying and understanding the causal multicellular and molecular interactions underlying skeletal malignancies can yield crucial ideas for targeting and inhibiting disease progression. …

Robust Inference Of Kinase Activity Using Functional Networks, Serhan Yılmaz, Daniela M. Schlatzer, Mark R. Chance, Mehmet Koyutürk

Faculty Scholarship

Mass spectrometry enables high-throughput screening of phosphoproteins across a broad range of biological contexts. When complemented by computational algorithms, phospho-proteomic data allows the inference of kinase activity, facilitating the identification of dysregulated kinases in various diseases including cancer, Alzheimer’s disease and Parkinson’s disease. To enhance the reliability of kinase activity inference, we present a network-based framework, RoKAI, that integrates various sources of functional information to capture coordinated changes in signaling. Through computational experiments, we show that phosphorylation of sites in the functional neighborhood of a kinase are significantly predictive of its activity. The incorporation of this knowledge in RoKAI consistently …

A Composite Textual Phenomenological Approach To Cures Versus Traditional Laboratory Experiences, Amie S. Sommers, Dana Richter-Egger, Christine E. Cutucache

The Qualitative Report

Here we present unique perspectives from undergraduate students (n=3) in STEM who have taken both a traditional laboratory iteration and a Course-based Undergraduate Research Experience (CURE) iteration of the same introductory chemistry course. CUREs can be effective models for integrating research in courses and fostering student learning gains. Via phenomenological interviews, we asked students to describe the differences in their perspectives, feelings, and experiences between a traditional lab guided by a lab manual and a CURE. We found that (i.) critical thinking/problem solving, (ii.) group work/collaboration, (iii.) student-led research questions and activities, and (iv.) time management are the top four …

Transepithelial Anti-Neuroblastoma Response To Kale Among Four Vegetable Juices Using In Vitro Model Co-Culture System, John Piletz, Yuhan Mao, Debarshi Roy, Bilal Qizilbash, Eurielle Nkamssi, Enleyona Weir, Jessica Graham, Mary Emmanuel, Suwaira Iqbal, Kellie Brue, Bidisha Roy Sengupta

Faculty Publications

Juicing vegetables is thought to be an anticancer treatment. Support exists for a rank order of anticancer greens (kale > dandelion > lettuce > spinach) based on degrees of bioavailability of different phytochemicals, also offset by some noxious molecules (i.e., calcium-oxalate). We developed a new in vitro transepithelial anti-neuroblastoma model system. The juices were diluted as predicted once in the small intestine. They were applied to apical Caco-2Bbe1 cells atop dividing SH-SY5Y neuroblastoma cells, and changes in transepithelial electrical resistance (TEER) and cell growth were considered with juice spectroscopies. Studied first in monoculture, kale and dandelion were the most cytostatic juices on SH-SY5Ys, …

Characterization And Localization Of Antigens For Serodiagnosis Of Human Paragonimiasis, Kurt C Curtis, Kerstin Fischer, Young-Jun Choi, Makedonka Mitreva, Gary J Weil, Peter U Fischer

2020-Current year OA Pubs

Paragonimiasis is a foodborne trematode infection that affects 23 million people, mainly in Asia. Lung fluke infections lead frequently to chronic cough with fever and hemoptysis, and are often confused with lung cancer or tuberculosis. Paragonimiasis can be efficiently treated with praziquantel, but diagnosis is often delayed, and patients are frequently treated for other conditions. To improve diagnosis, we selected five Paragonimus kellicotti proteins based on transcriptional abundance, recognition by patient sera, and conservation among trematodes and expressed them as His-fusion proteins in Escherichia coli. Sequences for these proteins have 76-99% identity with amino acid sequences for orthologs in the …

Biomedical Applications Of Vibrational Spectroscopy: Oral Cancer Diagnostics, Hugh Byrne, Isha Behl, Genecy Calado, Ola Ibrahim, M. Toner, Sheila Galvin, Claire M. Healy, Steven Flint, Fiona Lyng

Articles

Vibrational spectroscopy, based on either infrared absorption or Raman scattering, has attracted increasing attention for biomedical applications. Proof of concept explorations for diagnosis of oral potentially malignant disorders and cancer are reviewed, and recent advances critically appraised. Specific examples of applications of Raman microspectroscopy for analysis of histological, cytological and saliva samples are presented for illustrative purposes, and the future prospects, ultimately for routine, chairside in vivo screening are discussed.

Antecedents Of Borderline Personality Disorder And Antisocial Personality Disorder: An Examination Of Gene X Environment Interactions, Amy L. Medina

Dissertations, Theses, and Capstone Projects

Current thinking suggests that genotypes associated with impulse-control disorders and negative emotionality, such as monoamine oxidase-a (MAOA), interact with negative early environmental factors like childhood maltreatment and develop into the disorders know as Borderline Personality Disorder (BPD) and Antisocial Personality Disorder (ASPD). Using existing data from a prospective cohort design study of the consequences of child abuse and neglect, participants (N = 896 represent individuals with documented histories of child abuse and neglect and a matched comparison group that were followed up into adulthood and interviewed. A subsample of 631 participants gave permission for DNA extraction and analyses during …

A Timely Call To Arms: Covid-19, The Circadian Clock, And Critical Care, Jeffrey Haspel, Minjee Kim, Phyllis Zee, Tanja Schwarzmeier, Sara Montagnese, Satchidananda Panda, Adriana Albani, Martha Merrow

2020-Current year OA Pubs

We currently find ourselves in the midst of a global coronavirus disease 2019 (COVID-19) pandemic, caused by the highly infectious novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we discuss aspects of SARS-CoV-2 biology and pathology and how these might interact with the circadian clock of the host. We further focus on the severe manifestation of the illness, leading to hospitalization in an intensive care unit. The most common severe complications of COVID-19 relate to clock-regulated human physiology. We speculate on how the pandemic might be used to gain insights on the circadian clock but, more importantly, on …

Mfd Affects Global Transcription And The Physiology Of Stressed Bacillus Subtilis Cells, Holly Anne Martin, Anitha Sundararajan, Tatiana S. Ermi, Robert Heron, Jason Gonzales, Kaiden Lee, Diana Anguiano-Mendez, Faye Schilkey, Mario Pedraza-Reyes, Eduardo A. Robleto

Life Sciences Faculty Research

© Copyright © 2021 Martin, Sundararajan, Ermi, Heron, Gonzales, Lee, Anguiano-Mendez, Schilkey, Pedraza-Reyes and Robleto. For several decades, Mfd has been studied as the bacterial transcription-coupled repair factor. However, recent observations indicate that this factor influences cell functions beyond DNA repair. Our lab recently described a role for Mfd in disulfide stress that was independent of its function in nucleotide excision repair and base excision repair. Because reports showed that Mfd influenced transcription of single genes, we investigated the global differences in transcription in wild-type and mfd mutant growth-limited cells in the presence and absence of diamide. Surprisingly, we found …

Identification And Robust Estimation Of Swapped Direct And Indirect Effects: Mediation Analysis With Unmeasured Mediator–Outcome Confounding And Intermediate Confounding, An-Shun Tai, Sheng-Hsuan Lin

Harvard University Biostatistics Working Paper Series

Counterfactual-model-based mediation analysis can yield substantial insight into the causal mechanism through the assessment of natural direct effects (NDEs) and natural indirect effects (NIEs). However, the assumptions regarding unmeasured mediator–outcome confounding and intermediate mediator–outcome confounding that are required for the determination of NDEs and NIEs present practical challenges. To address this problem, we introduce an instrumental blocker, a novel quasi-instrumental variable, to relax both of these assumptions, and we define a swapped direct effect (SDE) and a swapped indirect effect (SIE) to assess the mediation. We show that the SDE and SIE are identical to the NDE and NIE, respectively, …

A Peek Inside The Machines Of Bacterial Nucleotide Excision Repair, Thanyalak Kraithong, Silas Hartley, David Jeruzalmi, Danaya Pakotiprapha

Publications and Research

Double stranded DNA (dsDNA), the repository of genetic information in bacteria, archaea and eukaryotes, exhibits a surprising instability in the intracellular environment; this fragility is exacerbated by exogenous agents, such as ultraviolet radiation. To protect themselves against the severe consequences of DNA damage, cells have evolved at least six distinct DNA repair pathways. Here, we review recent key findings of studies aimed at understanding one of these pathways: bacterial nucleotide excision repair (NER). This pathway operates in two modes: a global genome repair (GGR) pathway and a pathway that closely interfaces with transcription by RNA polymerase called transcription-coupled repair (TCR). …

Developing Methods For Diversifying Molecular Scaffolds Directly On A Microelectrode Array, Nai-Hua Yeh

Arts & Sciences Graduate Student Theses and Dissertations

Microelectrode arrays contain collections of spatially isolated electrodes that can be individually addressed. Thus, the arrays have the potential to support synthesis of molecular libraries if unique members of the library can be located next to unique electrodes in the array. The result would be an intriguing platform for screening the molecules in the library against biological receptors in order to identify high-affinity ligands for those targets, especially since the arrays themselves can be directly used in the signaling studies. To expand the capabilities of the arrays, the goal of this thesis is to develop the new array chemistry needed …

Differentiating Human Embryonic Stem Cells In Micropatterns To Study Cell Fate Specification And Morphogenetic Events During Gastrulation, Kyaw Thu Minn

McKelvey School of Engineering Graduate Student Theses & Dissertations

During mammalian embryogenesis, the first major lineage segregation occurs when embryonic epiblast, and extraembryonic trophectoderm and hypoblast arise in the blastocyst. In the next fundamental and conserved phase of animal embryogenesis known as gastrulation, extraembryonic cells provide signals to epiblast to instruct embryonic patterning, and epiblast gives rise to germ layers ectoderm, mesoderm, and endoderm, that will establish all embryonic tissues. Proper specification and morphogenesis of germ layers during gastrulation is vital for correct embryonic development. Due to ethical and legal restrictions limiting human embryo studies, human gastrulation is poorly understood. Our knowledge of human gastrulation has largely been derived …

The Roles Of Plasmepsins Ix And X In Malaria Parasite Biology, Armiyaw Sebastian Nasamu

Arts & Sciences Graduate Student Theses and Dissertations

Proteases of the malaria parasite Plasmodium falciparum have been targeted for drug discovery for decades. The P. falciparum genome encodes ten aspartic proteases called plasmepsins, which are involved in diverse cellular processes. In this work we address the roles of two of these plasmepsins, plasmepsins IX and X (PM IX and X), the two least studied aspartic proteases in blood stage malaria parasites till date. We explore the essentiality of these proteases in parasite development, attempt to identify their substrates and the ability to drug them. We show that PM IX is essential for erythrocyte invasion, acting on rhoptry secretory …

Performance Evaluation And Enhancement Of Medical Imaging Using Plasmonic Gold Nanostars., Kholoud Abdelhady, Hossam El-Din Moustafa, Bedir B. Yousif

Mansoura Engineering Journal

This paper gives insights about examinations of plasmonic nanoparticles (NPs) and particularly gold nanostar as sign enhancer and contrast agent for clinical imaging and the optical properties of (NPs) of different volume and morphology and the encompassing medium were stood out from affirm that the gold nanostars are the best shape that can scatter the light, thusly obtaining better and all the clearest clinical imaging. Stars formed gold nanoparticles have a greater surface comparative with its volume and contact surface cross section than spherical and rods shaped nanoparticles, and accordingly act even more firmly as a radiation enhancer. At that …

Why Are Glycines 31, 33, And 35 Highly Conserved In All Fluorescent Proteins?, Justin Nwafor

Chemistry Honors Papers

Since the discovery of the Green Fluorescent Protein (GFP), fluorescent proteins (FPs) have been used as biomarkers to monitor biological phenomena across many scientific disciplines. All naturally-occurring FPs consist of an 11-stranded β-barrel with a non-canonical α-helix, which contains the chromophore, running through the central axis of the protein. Glycines 31, 33, and 35 are highly conserved across the fluorescent proteins found in the PDB. These three residues are of interest due to them all being located in the second strand of the β-barrel, but having no direct involvement in chromophore formation. This led to a presumption that the glycines …

Interspecific And Intraspecific Size And Shape Variation In Skull Of Two Closely Relatedspecies Bufo Bufo (Linnaeus, 1758) And Bufo Verrucosissimus (Pallas, 1814) From Turkey, Nazan Üzüm, Nurhayat Özdemi̇r, Canteki̇n Dursun, Bi̇lal Kutrup, Serkan Gül

Turkish Journal of Zoology

Anurans are the most suitable vertebrate group to see the development and also evolution in the skull, compared to other terrestrial vertebrates as they show highly derived morphology. For this reason, the cranium of anurans has been widely used for analyzing e.g., development and integration, evolutionary history, phylogenetic relationships, sexual dimorphism; and for taxon determination. We applied geometric morphometric techniques and then multivariate statistical analyses to see the skull size and shape variations in closely related Bufo species (B. bufo and B. verrucosissimus) inhabiting Turkey. Females have larger skull than males for both species. Ventral skull size of males differed …

Isolation Of Catechins From Cycas Armstrongii Miq. Of An Egyptian Origin, Ahmed Ismail, Mohamed M. Radwan, Hossam M. Hassan, Abeer S. Moawad

Faculty and Student Publications

The phytochemical investigation of Cycas armstrongii Miq. leaves and twigs using different chromatographic techniques led to the isolation of three catechin monomers; catechin (1), epicatechin (2), and epigallocatechin-3-gallate (3), for the first time from this species. The chemotaxonomic significance of the isolated compounds is discussed in the rest of this article.

Developing A Targeted Ultrasound-Responsive Nanobubble-Based Gene Delivery System For Osteoporosis Treatment, Angela Shar

Honors Undergraduate Theses

The overall goal of this project was to develop, optimize, and test an ultrasound-responsive targeted nanobubble for delivering osteoporosis-related silencing genes such as Cathepsin K small interfering RNA (CTSK siRNA) for osteoporosis treatment. The nanobubbles were synthesized using an in situ sonochemical method. The nanobubble (NB) is composed of a gas core made from perfluorocarbon, stabilized with albumin, encapsulated with CTSK siRNA, and embedded with alendronate (AL) for bone targeting (CTSK siRNA-NB-AL). Following its development, the responsiveness of CTSK siRNA-NB-AL to a therapeutic ultrasound probe was examined. The results of biocompatibility tests with human bone marrow-derived mesenchymal stem cells proved …

Synthesis And Biological Evaluations Of Oleanolic Acid Indole Derivatives As Hyaluronidase Inhibitors With Enhanced Skin Permeability, Hao He, Huifang Li, Toyosi Akanji, Shengli Niu, Zhujun Luo, Dongli Li, Navindra P. Seeram, Panpan Wu, Hang Ma

Biomedical and Pharmaceutical Sciences Faculty Publications

Oleanolic acid (OA) is a natural cosmeceutical compound with various skin beneficial activities including inhibitory effect on hyaluronidase but the anti-hyaluronidase activity and mechanisms of action of its synthetic analogues remain unclear. Herein, a series of OA derivatives were synthesised and evaluated for their inhibitory effects on hyaluronidase. Compared to OA, an induction of fluorinated (6c) and chlorinated (6g) indole moieties led to enhanced anti-hyaluronidase activity (IC50 = 80.3 vs. 9.97 and 9.57 µg/mL, respectively). Furthermore, spectroscopic and computational studies revealed that 6c and 6g can bind to hyaluronidase protein and alter its secondary structure leading …

Photoassisted Synthesis Of Complex Polyheterocycles Via Rational Design Of Tailored Photoprecursors, Tina Alanna Holt

Electronic Theses and Dissertations

Natural products remain the most common source for drug leads, although diversity-oriented synthesis of unnatural complex molecules is gaining momentum. Our lab has been developing experimentally simple and straightforward approaches to complex molecular architectures via photochemical reactions involving a minimal number of experimental steps. In order to achieve this, photoprecursors were assembled via high yielding reactions. Next, we deployed photoinduced cycloadditions to create complex 3-dimentional structures. Lastly, with this obtained primary photoproduct, post-photochemical transformations were used to further grow its scaffold complexity.

One method to increase scaffold complexity is the [4+2] intramolecular cycloadditions of azaxylylenes, which are developed through standard …

A Biophysical Investigation Of Hiv-1 Envelope Cytoplasmic-Tail Mediated Retention In The Gag Lattice, Nicholas Scott Groves

Electronic Theses and Dissertations

The infectivity of Human Immunodeficiency Virus is critically dependent on successful incorporation of the trimeric viral envelope glycoprotein, Envelope (Env), into Gag lattice assembly sites on the host-cell plasma membrane during virus biogenesis. The mechanistic nature of interaction between Gag, the structural protein, and Env, the viral spike, are dependent on the Gag matrix (MA) and Env cytoplasmic tail (CT) domains. Env laterally diffuses on the host cell plasma membrane until encountering a budding Gag lattice, where it is retained until particle scission and release. The mechanism of Env entry and retention in the lattice remains elusive and enigmatic. Here …

Reframing A Curative To Preventative Culture, Gabriella Dacosta

Student Research Poster Presentations 2021

No abstract provided.

Optimized Microbial Recombinant Production Of Hiv-1 Anti-Envelope Antibody Fragments With Applications To Single Particle Tracking Of Virus Assembly, Merissa Michelle Bruns

Electronic Theses and Dissertations

In my findings, I have established a set series of protocols to recombinantly produce, purify and apply various fluorescent probes in vitro for the fluorescent labeling and study of the human immunodeficiency virus type 1 (HIV-1) envelope (Env) protein during HIV viral assembly. There remains insufficient knowledge about the molecular dynamics and interactions of HIV-1 Env protein with its counterpart, Gag, on the inner host cell surface during assembly of a mature virus particle. There also remains an insufficient amount of data for the understanding and clarification of the mechanism of action of a known host cell HIV-1 restriction factor, …