Cell and Developmental Biology Commons^™

Introducing An Indigenous Non-Toxigenic Aspergillus Flavus Strain Isolated From Iraqi Corn Grains As A Bio-Control Agent To Reduce Aflatoxin Contamination In Corn Grains, Ali Almatakeez

Graduate Theses and Dissertations

Mycotoxin contamination of cereal crops, such as maize and sorghum, is a global concern because of the potential health effects on humans and animals. Although substantial research has been conducting regarding mycotoxin prevention and mitigation, little information is available about the association of mycotoxin-producing fungi with corn and sorghum grain in Iraq. Identifying and refining indigenous atoxigenic strains to reduce mycotoxin contamination of maize and sorghum has the potential to enhance the nutritional value of these grains while reducing economic losses. However, to our knowledge, this tactic has not yet been adopted by agricultural authorities and farmers in Iraq. To …

Mechanistic And Translational Studies On Skeletal Malignancies, Jeremy Mcguire

USF Tampa Graduate Theses and Dissertations

New treatment strategies are desperately needed for treating skeletal malignancy. Skeletal malignancies can be either primary cancer that originated in the bone, such as osteosarcoma, or metastatic cancer that spread from another organ to the skeleton, as in the case of breast or prostate cancer. In this thesis, I will detail two projects that focus on the discovery of new treatment strategies for both primary skeletal malignancy and metastatic skeletal malignancy.

The first project focuses on the primary skeletal malignancy, osteosarcoma, a rare cancer that is commonly diagnosed in children and young adults and metastasizes to the lungs. The survival …

Biological And Proteomic Characterization Of Cornus Officinalis On Human 1.1b4 Pancreatic Β Cells: Exploring Use For T1d Interventional Application, Arielle E. Tawfik

USF Tampa Graduate Theses and Dissertations

Type 1 diabetes (T1D) is an autoimmune disease resulting in the loss of pancreatic β cells and subsequent loss of insulin production. Exogenous insulin coupled with continuous glucose monitoring is the only treatment for T1D. Therefore, novel interventional therapies are needed that can inhibit the autoimmune destruction and increase β cell proliferation and function. Based on initial in vitro studies, traditional Chinese medicine (TCM) extract, Cornus officinalis, may be able to serve in this function. CO has been used for 2 millennia for its glucose regulating potential and has shown efficacy in animal models but rarely studied in the context …

Proteomic Identification Reveals The Role Of Ciliary Extracellular‐Like Vesicle In Cardiovascular Function, Ashraf M. Mohieldin, Rajasekharreddy Pala, Rinzhin T. Sherpa, Madhawi Alanazi, Ashwaq Alanazi, Kiumars Shamloo, Amir Ahsan, Wissam A. Aboualaiwi, James J. Moresco, John R. Yates Iii, Surya M. Nauli

Pharmacy Faculty Articles and Research

Primary cilia are shown to have membrane swelling, also known as ciliary bulbs. However, the role of these structures and their physiological relevance remains unknown. Here, it is reported that a ciliary bulb has extracellular vesicle (EV)‐like characteristics. The ciliary extracellular‐like vesicle (cELV) has a unique dynamic movement and can be released by mechanical fluid force. To better identify the cELV, differential multidimensional proteomic analyses are performed on the cELV. A database of 172 cELV proteins is generated, and all that examined are confirmed to be in the cELV. Repressing the expression of these proteins in vitro and in vivo …

Low-Cost Diagnostics: Using Paper As A Material And Pens As An Instrument, Annie Armitstead

Undergraduate Honors Theses

Lateral flow immunoassays (LFIs) are equipment-free tests that produce results quickly using small sample volumes. Colored lines appear as the test runs, indicating the presence of a biomarker. LFIs are ideal in a variety of settings. Development of these assays can be complicated for small team operations, and tests are not sufficiently adaptable for low resource settings. If robust point-of-care tests can be developed on site, they can expand the reach of global diagnostics, improving health around the world. We report a simple empowering LFI (seLFI) that only requires treated printer paper and a plastic backing card. This eliminates the …

Gocats: A Tool For Categorizing Gene Ontology Into Subgraphs Of User-Defined Concepts, Eugene Waverly Hinderer Iii, Hunter N. B. Moseley

Molecular and Cellular Biochemistry Faculty Publications

Gene Ontology is used extensively in scientific knowledgebases and repositories to organize a wealth of biological information. However, interpreting annotations derived from differential gene lists is often difficult without manually sorting into higher-order categories. To address these issues, we present GOcats, a novel tool that organizes the Gene Ontology (GO) into subgraphs representing user-defined concepts, while ensuring that all appropriate relations are congruent with respect to scoping semantics. We tested GOcats performance using subcellular location categories to mine annotations from GO-utilizing knowledgebases and evaluated their accuracy against immunohistochemistry datasets in the Human Protein Atlas (HPA). In comparison to term categorizations …

Profiling The Circulating Mrna Transcriptome In Human Liver Disease, Aejaz Sayeed, Brielle E Dalvano, David E Kaplan, Usha Viswanathan, John Kulp, Alhaji H Janneh, Lu-Yu Hwang, Adam Ertel, Cataldo Doria, Timothy Block

Department of Cancer Biology Faculty Papers

The human circulation contains cell-free DNA and non-coding microRNA (miRNA). Less is known about the presence of messenger RNA (mRNA). This report profiles the human circulating mRNA transcriptome in people with liver cirrhosis (LC) and hepatocellular carcinoma (HCC) to determine whether mRNA analytes can be used as biomarkers of liver disease. Using RNAseq and RT-qPCR, we investigate circulating mRNA in plasma from HCC and LC patients and demonstrate detection of transcripts representing more than 19,000 different protein coding genes. Remarkably, the circulating mRNA expression levels were similar from person to person over the 21 individuals whose samples were analyzed by …

Metabolic Network Analysis Of Filamentous Cyanobacteria, Daniel Alexis Norena-Caro

LSU Doctoral Dissertations

Cyanobacteria were the first organisms to use oxygenic photosynthesis, converting CO₂ into useful organic chemicals. However, the chemical industry has historically relied on fossil raw materials to produce organic precursors, which has contributed to global warming. Thus, cyanobacteria have emerged as sustainable stakeholders for biotechnological production. The filamentous cyanobacterium Anabaena sp. UTEX 2576 can metabolize multiple sources of Nitrogen and was studied as a platform for biotechnological production of high-value chemicals (i.e., pigments, antioxidants, vitamins and secondary metabolites). From a Chemical engineering perspective, the biomass generation in this organism was thoroughly studied by interpreting the cell as a microbial …

Molecular And Ultrastructure Study Of Tight Junction During Experimental Entamoeba Spp. Infection, Athraa A. Al-Hilfi Dr, Maha Khalil Al-Malak, Shereen Jawad Al-Ali, Muslim Abd-Ulrahman Al-Tomah

Karbala International Journal of Modern Science

Entamoeba spp. in particular E.histolytica is the main reason of human amoebiasis. The molecular mechanism of its pathogenicity is poorly understood, therefore the aim this study is to investigate these mechanism on both molecular and ultrastructure levels. Tight junction (TJ) genes Claudin-1 (Cldn1) and Occludin (Ocln) were investigated by real time PCR and the pathological changes by scanning electron microscopy (SEM) and transmission electron microscope (TEM), the result showed that the gene expression levels of TJ genes were significantly high in rats infected with E. histolytica E. dispar and E. moshkovskii after 28, 14, 7 days in compare with healthy …

Insights Into Desiccation Tolerance: Properties Of Late Embryogenesis Abundant Proteins From Embryos Of Artemia Franciscana, Blase Matthew Leblanc

LSU Doctoral Dissertations

LEA proteins are a family of intrinsically disordered proteins that are expressed in various life stages of anhydrobiotic organisms and have been strongly associated with survival during water stress. The brine shrimp Artemia franciscana is the only known anhydrobiotic animal that expresses LEA proteins from Groups 1, 3, and 6. Here, I report that AfrLEA6, a novel Group 6 LEA protein, is most highly expressed in embryos during diapause and decreases throughout pre-emergence development. Notably, there is an acute drop in expression upon termination of the diapause state and the titer of AfrLEA6 during diapause is 10-fold lower than values …

Deploying Big Data To Crack The Genotype To Phenotype Code, E. L. Westerman, S. E. J. Bowman, Bradley Justin Davidson , '91, M. C. Davis, E. R. Larson, C. Sanford

Biology Faculty Works

Mechanistically connecting genotypes to phenotypes is a longstanding and central mission of biology. Deciphering these connections will unite questions and datasets across all scales from molecules to ecosystems. Although high-throughput sequencing has provided a rich platform on which to launch this effort, tools for deciphering mechanisms further along the genome to phenome pipeline remain limited. Machine learning approaches and other emerging computational tools hold the promise of augmenting human efforts to overcome these obstacles. This vision paper is the result of a Reintegrating Biology Workshop, bringing together the perspectives of integrative and comparative biologists to survey challenges and opportunities in …

Comparative Molecular Transporter Properties Of Cyclic Peptides Containing Tryptophan And Arginine Residues Formed Through Disulfide Cyclization, Eman H. M. Mohammed, Dindyal Mandal, Saghar Mozaffari, Magdy Abdel-Hamied Zahran, Amany Mostafa Osman, Rakesh Kumar Tiwari, Keykavous Parang

Pharmacy Faculty Articles and Research

We have previously reported cyclic cell-penetrating peptides [WR]₅ and [WR]₄ as molecular transporters. To optimize further the utility of our developed peptides for targeted therapy in cancer cells using the redox condition, we designed a new generation of peptides and evaluated their cytotoxicity as well as uptake behavior against different cancer cell lines. Thus, cyclic [C(WR)_xC] and linear counterparts (C(WR)_xC), where x = 4–5, were synthesized using Fmoc/tBu solid-phase peptide synthesis, purified, and characterized. The compounds did not show any significant cytotoxicity (at 25 µM) against ovarian (SK-OV-3), leukemia (CCRF-CEM), gastric adenocarcinoma (CRL-1739), breast …

Recombinant Human Proteoglycan-4 Mediates Interleukin-6 Response In Both Human And Mouse Endothelial Cells Induced Into A Sepsis Phenotype, Holly A. Richendrfer, Mitchell M. Levy, Khaled A. Elsaid, Tannin A. Schmidt, Ling Zhang, Ralph Cabezas, Gregory D. Jay

Pharmacy Faculty Articles and Research

Objectives:

Sepsis is a leading cause of death in the United States. Putative targets to prevent systemic inflammatory response syndrome include antagonism of toll-like receptors 2 and 4 and CD44 receptors in vascular endothelial cells. Proteoglycan-4 is a mucinous glycoprotein that interacts with CD44 and toll-like receptor 4 resulting in a blockade of the NOD-like receptor pyrin domain-containing-3 pathway. We hypothesized that endothelial cells induced into a sepsis phenotype would have less interleukin-6 expression after recombinant human proteoglycan 4 treatment in vitro.

Design:

Enzyme-linked immunosorbent assay and reverse transcriptase-quantitative polymerase chain reaction to measure interleukin-6 protein and gene expression.

Setting: …

Thymosin Β4 Dynamics During Chicken Enteroid Development, Mohan Acharya, Rohana Liyanage, Anamika Gupta, Komala Arsi, Ann M. Donoghue, Jackson O. Lay Jr., Narayan Rath

Poultry Science Faculty Publications and Presentations

The sheared avian intestinal villus-crypts exhibit high tendency to self-repair and develop enteroids in culture. Presuming that this transition process involves differential biomolecular changes, we employed matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF–MS) to find whether there were differences in the spectral profiles of sheared villi versus the enteroids, assessed in the mass range of 2–18 kDa. The results showed substantial differences in the intensities of the spectral peaks, one particularly corresponding to the mass of 4963 Da, which was significantly low in the sheared villus-crypts compared with the enteroids. Based on our previous results with other avian …

Putative Flagellar Channel-Lining Residues And Their Role In Filament Synthesis, Morphology And Stability, Troy Burtchett

Masters Theses

Bacterial flagella are comprised of ~20,000 repeating subunits called flagellin and are synthesized by transporting unfolded flagellin monomers through the central channel of the flagellar filament to the distal end where they are folded and incorporated into the growing structure. The transport mechanism is predicted to be facilitated by a hydrophilic coating of amino acid side chains on the inside wall of the central channel that repels the mostly hydrophobic surface of the unfolded flagellin monomer. The lack of interaction between the flagellin monomer and the central channel wall is thought to allow for the passive diffusion of protein monomers. …

Gene Regulation And Cell Fate Choice In The Developing Vertebrate Retina, Sruti Patoori

Dissertations, Theses, and Capstone Projects

The diverse neuronal cell types in the vertebrate retina all originate from multipotent retinal progenitor cells (RPCs). These undergo a series of molecular changes driven by developmental gene regulatory networks (GRNs) as they divide to generate RPCs which are more restricted in their potential fates. It is crucial to understand these GRNs and changes to gene expression in order to understand how cell identity is established during retinal development. In particular, the GRN that promotes the development of cone photoreceptors and horizontal cells is not well-defined. This work focuses on two approaches to further elucidate the components of this regulatory …

Probing The Limits Of Singular Gene Expression Through The Activity Of High Representation Odorant Receptor Transgenes, Eugene Lempert

Dissertations, Theses, and Capstone Projects

Singular gene expression is a common phenomenon in biology, making its appearance in immunoglobulin selection, protocadherin expression, X chromosome-inactivation, random monoallelic expression, and olfactory receptor choice. Singularity involves an activation and a feedback step. The mechanisms of singular gene choice have some capacity to integrate additional member genes while still maintaining singularity, but will activate an additional member if an earlier choice was incapable of triggering the feedback step. Odorant Receptor (OR) genes are substantially divergent from each other in terms of coding sequence, promoter structure, and genomic locus, all of which plays a role in how many Olfactory Sensory …

Dictyostelium Discoideum Protein Kinase C-Orthologue Pkca Regulates The Actin Cytoskeleton Through Interaction With Phospholipase D And P21-Activated Kinase, Sean Singh

Dissertations, Theses, and Capstone Projects

Proper regulation of the actin cytoskeleton is crucial to many cellular processes. Many of these processes are regulated by extracellular signaling cues, which direct changes in the actin cytoskeleton, resulting in changes to cellular morphology, and directed motility. The social amoeba, Dictyostelium discoideum, is used as a simple model system to study the translation of extracellular signals to the actin cytoskeleton. When starved, these unicellular amoebae undergo a multicellular developmental process characterized by a tightly regulated sequence of signaling events. This results in chemotaxis and formation of a multicellular aggregate, and ultimately cell differentiation and the formation of a fruiting …

Development Of Ligand Guided Selection (Ligs) To Identify Specific Dna Aptamers Against Cell Surface Proteins, Hasan Ekrem Zumrut

Dissertations, Theses, and Capstone Projects

Oligonucleotide aptamers (nucleic acid-based affinity reagents) are an emerging class of synthetic molecules that display high affinity and specificity towards their targets. Aptamer molecules for a target of interest are obtained using a combinatorial chemistry-based method termed systematic evolution of ligands by exponential enrichment (SELEX). SELEX is an in vitro selection process in which a random oligonucleotide library is subjected to repeated cycles of target incubation, separation, and amplification until target-specific evolved sequences become prevalent in the library. Typically, SELEX is used against target molecules such as small molecules and proteins, in their purified state. However, aptamers selected against purified …

Epithelial-Mesenchymal Status Predics Tumor Agressivenss, Chemoresistance And Invasiveness In High Grade Serous Ovarian Cancer, Linda Sanderman

Electronic Theses, Projects, and Dissertations

High Grade Serous Ovarian Cancer (HGSOC) is one of the deadliest gynecological diseases in the United States ranking fifth in cancer deaths among women. Approximately 22 thousand new cases are expected to occur in the year 2020, and unfortunately, it is estimated that 14 thousand women will succumb to the disease; the incidence to death ratio, 64%, remains high despite current research. Current treatment includes debulking surgery followed by combinatorial chemotherapeutics with platinum-based and taxol-based compounds. But despite aggressive surgery and standard-of-care chemotherapeutics, 80% of patients will experience a recurrence and only 15-30% of those with recurring disease will respond …

Protonic Capacitor: Elucidating The Biological Significance Of Mitochondrial Cristae Formation, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

For decades, it was not entirely clear why mitochondria develop cristae? The work employing the transmembrane-electrostatic proton localization theory reported here has now provided a clear answer to this fundamental question. Surprisingly, the transmembrane-electrostatically localized proton concentration at a curved mitochondrial crista tip can be significantly higher than that at the relatively flat membrane plane regions where the proton-pumping respiratory supercomplexes are situated. The biological significance for mitochondrial cristae has now, for the first time, been elucidated at a protonic bioenergetics level: 1) The formation of cristae creates more mitochondrial inner membrane surface area and thus more protonic capacitance for …

Protein Phosphatase 2a Suppresses Spindle Elongation In Saccharomyces Cerevisiae, Shoily P. Khondker

Dissertations, Theses, and Capstone Projects

Eukaryotic cell division is an essential process that is carried out by the cell cycle, a tightly controlled process that has been extensively studied in the budding yeast Saccharomyces cerevisiae. The cell cycle is driven by Cyclin Dependent Kinase (Cdk1) activity. Protein phosphatase 2A-Cdc55 (PP2A^Cdc55) reverses Cdk1 phosphorylation events during late stages of the cell cycle to ensure the correct order of events. This thesis presents evidence that the anaphase inhibitor Pds1 is a PP2A^Cdc55 target. Pds1 binds to and inhibits separase (Esp1). Esp1 triggers sister chromatid segregation by cleaving the cohesin complex that holds the …

Pegylated Block Copolymer For Cancer Imaging And Treatment, Sweety Singh

Dissertations

Gene theranostics have emerged as an important tool for the treatment of cancer as well as other diseases. Among the challenges in this field is the lack of effective vectors to chaperone plasmids into cells while the vector itself exhibits minimal toxicity. Herein, the synthesis, cellular uptake, and gene delivery using a biocompatible norbornene-based block copolymer is reported. This block copolymer, bearing polyethylene glycol moieties along with primary amines is functionalized with both a boron dipyrromethene (BODIPY) fluorophore for fluorescence tracking and a folic acid derivative for cancer cell targeting.

Stoichiometry control afforded residual unreacted amine functional groups available to …

Spatiotemporal Characterization Of Anterior Segment Mesenchyme Heterogeneity During Zebrafish Ocular Anterior Segment Development, Kristyn L. Van Der Meulen, Oliver Vöcking, Megan L. Weaver, Nishita N. Meshram, Jakub K. Famulski

Biology Faculty Publications

Assembly of the ocular anterior segment (AS) is a critical event during development of the vertebrate visual system. Failure in this process leads to anterior segment dysgenesis (ASD), which is characterized by congenital blindness and predisposition to glaucoma. The anterior segment is largely formed via a neural crest-derived population, the Periocular Mesenchyme (POM). In this study, we aimed to characterize POM behaviors and transcriptional identities during early establishment of the zebrafish AS. Two-color fluorescent in situ hybridization suggested that early AS associated POM comprise of a heterogenous population. In vivo and time-course imaging analysis of POM distribution and migratory dynamics …

Rapamycin Treatment Correlates Changes In Primary Cilia Expression With Cell Cycle Regulation In Epithelial Cells, Maha Jamal, Ane C.F. Nunes, Nosratola D. Vaziri, Ramani Ramchandran, Robert L. Bacallao, Andromeda M. Nauli, Surya M. Nauli

Pharmacy Faculty Articles and Research

Primary cilia are sensory organelles that regulate cell cycle and signaling pathways. In addition to its association with cancer, dysfunction of primary cilia is responsible for the pathogenesis of polycystic kidney disease (PKD) and other ciliopathies. Because the association between cilia formation or length and cell cycle or division is poorly understood, we here evaluated their correlation in this study. Using Spectral Karyotyping (SKY) technique, we showed that PKD and the cancer/tumorigenic epithelial cells PC3, DU145, and NL20-TA were associated with abnormal ploidy. We also showed that PKD and the cancer epithelia were highly proliferative. Importantly, the cancer epithelial cells …

Determining The Genetic Control Of Neural Tube Malformation Through Genetic Interactions With Idgf3, Elli N. Fox

Honors Projects

Genetic mutations disrupting human neural tube formation can lead to birth defects such as spina bifida and anencephaly. Defects can result in lack of neural tube closure in either the caudal (spina bifida) or cranial (anencephaly) regions. Little is known about the genes that cause these malformations. Researchers have been using the model organism Drosophila melanogaster in an attempt to determine genes responsible for neural tube malformations. Recently, an ortholog of human chitin-like protein, imaginal disc growth factor 3 (Idgf3), has been identified as important in the proper formation of Drosophila egg dorsal appendages. However, the molecular mechanism responsible for …

Developmental Programming Effects Of Maternal Obesity, Carolle J. Kassab

University Honors Theses

Population studies within the United States indicate increasing rates of obesity, considerably prominent for women within reproductive age. Maternal obesity is associated with the offspring’s hyperlipidemia, diabetes, and cardiovascular disease, which have chronic consequences. Obesity in pregnancy causes metabolic and epigenetic perturbations within the fetal environment, disrupting future health of offspring. This phenomenon is known as developmental programming. Although the relationship between maternal undernutrition and developmental programming has been demonstrated, its relationship to maternal obesity remains understudied.

Mutagenesis Of The Btea Gene Encoding A Bordetella Virulence Protein, Xiaolei Mao

2020 Symposium Posters

Bordetella Type III Secretion System Effector A (BteA) is a virulence protein found in members of the genus Bordetella which include important pathogens of humans and other mammals. Bordetella pertussis is a causative agent of the whooping cough, a highly contagious respiratory disease that is especially dangerous, and sometimes deadly, for infants. The BteA protein appears to be an important factor in the ability of these pathogens to cause disease, as it leads to rapid killing of a wide range of mammalian cells. The aim of this project is to determine which regions of the DNA are important for mediating …

Science, But Not Fiction: Colby Researchers Consider How "Extreme-Ophiles" Survive And Thrive In The World's Toughest Places, Gerry Boyle

Colby Magazine

"We're exploring how the cell makes the decision to do this," said Assistant Professor of Biology Ron Peck.

Good Works: Giving Back After Cancer, Gerry Boyle

Colby Magazine

David Pulver '63 turns his experience into a primer for patients