Cell and Developmental Biology Commons^™

The Role Of Atypical Protein Kinase C In Colorectal Cancer Cells Carcinogenesis, S M Anisul Islam

USF Tampa Graduate Theses and Dissertations

Colorectal cancer (CRC) is the third most common malignancy and the fourth most common cause of cancer-related death worldwide. CRC is a life-threatening disease due to therapy-resistant cancerous cells. The exact mechanisms of cell growth, survival, metastasis and inter & intracellular signaling pathways involved in CRC are still a significant challenge. Moreover, the treatment of metastatic CRC considered palliative for many years aimed for an improved life, with little hope of a cure, highlighting the need for developing novel targeted therapy for CRC. Hence, investigating new molecular mechanism(s) that lead to colorectal carcinogenesis may give insight into the therapeutic target. …

The Democratization And Development Of Cell-Free Protein Synthesis, Max Z. Levine

Master's Theses

Cell-free protein synthesis (CFPS) using crude lysates has developed into a robust platform technology over the last 60 years to express numerous types of recombinant proteins. The open-nature, elimination of reliance on cell viability, and focus of all energy towards production of the protein of interest represent substantial advantages of CFPS over in vivo protein expression methods. CFPS has provided new opportunities across a series of research fields that include metabolic engineering, therapeutic and vaccine development, education, biosensors, and many more. In recent years, optimizations of CFPS have even allowed the platform to reach the industrial level of protein production. …

Updating Molecular Diagnostics For Detecting Methicillin- Susceptible And Methicillin-Resistant Staphylococcus Aureus Isolates In Blood Culture Bottles, Fred C. Tenover, Isabella A. Tickler, Victoria M. Le, Scott Dewell, Rodrigo E. Mendes, Richard V. Goering, Mrsa Consortium

Biology Faculty Publications

Molecular diagnostic tests can be used to provide rapid identification of staphylococcal species in blood culture bottles to help improve antimicrobial stewardship. However, alterations in the target nucleic acid sequences of the microorganisms or their antimicrobial resistance genes can lead to false-negative results. We determined the whole-genome sequences of 4 blood culture isolates of Staphylococcus aureus and 2 control organisms to understand the genetic basis of genotypephenotype discrepancies when using the Xpert MRSA/SA BC test (in vitro diagnostic medical device [IVD]). Three methicillin-resistant S. aureus (MRSA) isolates each had a different insertion of a genetic element in the staphylococcal cassette …

Dynamics Of Trophoblast Differentiation In Peri-Implantation–Stage Human Embryos, Rachel C. West, Hao Ming, Deirdre M. Logsdon, Jiangwen Sun, Sandeep K. Rajput, Rebecca A. Kile, William B. Schoolcraft, R. Michael Roberts, Rebecca L. Krisher, Zongliang Jiang, Ye Yuan

Computer Science Faculty Publications

Single-cell RNA sequencing of cells from cultured human blastocysts has enabled us to define the transcriptomic landscape of placental trophoblast (TB) that surrounds the epiblast and associated embryonic tissues during the enigmatic day 8 (D8) to D12 peri-implantation period before the villous placenta forms. We analyzed the transcriptomes of 3 early placental cell types, cytoTB (CTB), syncytioTB (STB), and migratoryTB (MTB), picked manually from cultured embryos dissociated with trypsin and were able to follow sublineages that emerged from proliferating CTB at the periphery of the conceptus. A unique form of CTB with some features of STB was detectable at D8, …

All Nuts And No Bolts: The Evolution Of Undergraduate Research At A Small State School, James Hawker

Florida Statewide Symposium: Best Practices in Undergraduate Research

In fall of 2017, students first started doing research with their biology instructor, and just a few terms later, two students have earned Portz Interdisciplinary Fellowships. In some ways, the program is going well with students participating in high numbers, but organizers still have questions about the “nuts and bolts” of establishing the program within the institution. Enthusiasm is high! However, key metrics are not being tracked and the workload needs to be distributed more evenly. The organizers will be talking with the audience about different ways to integrate UGR into the institution.

Equine Hoof Stratum Internum K14+Cd105+ Progenitor Cells: Culture, Characterization, And Model Of Epithelial To Mesenchymal Transition, Qingqiu Yang

LSU Doctoral Dissertations

For the potential benefit of progenitor cells to be realized in cell-based clinical therapies, it is vital to investigate the mechanism between progenitor cells and abnormal tissue formation. Laminitis is a fatal condition that is often presented by equine hoof inflammation and hoof tissue disarrangement. The persistence of abnormal tissue formation after the resolution of equine laminitis suggests there is progenitor cell compromise. So far, there is limited information about equine hoof progenitor cells and the effects of inflammation on hoof progenitor cells. To pursue a better understanding of both hoof progenitor cell and hoof growth as well as find …

Regulation Of The Microtubule Cytoskeleton And Cell Wall Development In Arabidopsis Thaliana, Christy J. Fornero

Theses and Dissertations

Regulation of the cortical microtubule cytoskeleton is critical for organized plant cell division. Arabidopsis ton1 and ton2 mutants display random cell division plane placement and lack the plant-specific cortical microtubule array that encircles the nucleus prior to mitosis. In wild type plants, this preprophase band (PPB) of cortical microtubules precisely marks the future division plane. The specific roles of TON1 and TON2 in PPB formation are not yet known. It is suspected that TON1 Recruiting Motif (TRM) proteins may be involved in TON1 and TON2 recruitment to the PPB. Here we describe results for the targeted disruption of a group …

Sperm Motility In Groups, Julie Simons

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Effect Of The Physical Micro-Environment On Cell Adhesion And Force Exertion, Mohamad Eftekharjoo

Mechanical & Aerospace Engineering Theses & Dissertations

Physical characteristics of the microenvironment, such as geometry and stiffness, influence cell adhesion and contractile forces. Here, we determined how these physical factors influenced cell force exertion and adhesion in two specific contexts that have broad relevance.

Fibroblasts are cells in connective tissues that interact with a fibrous extracellular matrix (ECM) that have a predominantly one-dimensional (1D) (fibrillar) geometry. However, it has been unclear as to how the 1D nature of the fibrillar ECM influences the forces exerted by fibroblasts. Here, we used fibroblast cells adherent on fibronectin lines on polyacrylamide (PAA) gels of stiffness 13 and 45 kPa to …

Dormant Pathogenic Cd4(+) T Cells Are Prevalent In The Peripheral Repertoire Of Healthy Mice, Anna Cebula, Michal Kuczma, Edyta Szurek, Maciej Pietrzak, Natasha Savage, Wessam R. Elhefnawy, Grzegorz Rempala, Piotr Kraj, Leszek Ignatowicz

Computer Science Faculty Publications

Thymic central tolerance eliminates most immature T cells with autoreactive T cell receptors (TCR) that recognize self MHC/peptide complexes. Regardless, an unknown number of autoreactive CD4+Foxp3⁻ T cells escape negative selection and in the periphery require continuous suppression by CD4+Foxp3⁺ regulatory cells (Tregs). Here, we compare immune repertoires of Treg-deficient and Treg-sufficient mice to find Tregs continuously constraining one-third of mature CD4⁺Foxp3⁻ cells from converting to pathogenic effectors in healthy mice. These dormant pathogenic clones frequently express TCRs activatable by ubiquitous autoantigens presented by class II MHCs on conventional dendritic cells, including selfpeptides that select …

Anti-Cancer Effects Of Oleocanthal And Extra Virgin Olive Oil, Limor Goren

Dissertations, Theses, and Capstone Projects

Oleocanthal is a phenolic compound found in varying concentrations in extra virgin olive oil. Oleocanthal has been shown to be active physiologically, benefiting several diseased states by conferring anti-inflammatory and neuroprotective benefits. Recently, we and other groups have demonstrated its specific and selective toxicity toward cancer cells; however, the mechanism leading to cancer cell death is still disputed. The current study demonstrates that oleocanthal induced damage to cancer cells’ lysosomes leading to cellular toxicity in vitro. Non-cancer cells were significantly less affected. Lysosomal membrane permeabilization following oleocanthal treatment in various cell lines was assayed via three complementary methods. Additionally, …

Hyaluronan At The Brain-Environment Interface, Donald M. Thevalingam

Dissertations, Theses, and Capstone Projects

Hyaluronan (HA; Hyaluronic Acid), a primary scaffolding component of the brain extracellular matrix, serves as an integral structural component to the brain extracellular space (ECS). The fossorial African naked mole-rat (Heterocephalus glaber; NM-R), a mammal which lives in a low-oxygen environment and is capable of tolerating hypoxia and hypercapnia, has been shown to synthesize and sustain a unique high-molecular-mass variant of hyaluronan macromolecule (HMM-HA). This body of work highlights HA’s role in mediating the interplay between brain ECM composition, ECS structure, and cell viability.

Here we employ the NM-R as a unique animal model to observe the role of the …

Towards A Mathematical Model Of Motility Using Dictyostelium Discoideum: Proteins And Geometric Features That Regulate Bleb-Based Motility, Zully Santiago

Dissertations, Theses, and Capstone Projects

A variety of biological functions depend on actin organization. The organization of actin is tightly regulated by a plethora of extracellular and intracellular signaling, scaffolding, and actin-binding proteins. Dysfunctions in this regulation lead to immune diseases, increased susceptibility to pathogens, neurodegenerative diseases, developmental disorders, and cancer metastasis. A variety of actin-dependent processes, including cell motility, are regulated by several proteins of interest: Paxillin, a scaffolding protein; WASP, an actin nucleating protein; SCAR/WAVE, another WASP family actin nucleating protein; Talin, a cortex-to-membrane binding protein; Myosin II, an F-actin contracting motor protein; and Protein Kinase C, a protein kinase. D. discoideum cells …

Inhibition Of Mitochondrial Permeability Transition By Deletion Of The Ant Family And Cypd, Jason Karch, Michael J. Bround, Hadi Khalil, Michelle A. Sargent, Nadina Latchman, Naohiro Terada, Pablo M. Peixoto, Jeffery D. Molkentin

Publications and Research

The mitochondrial permeability transition pore (MPTP) has resisted molecular identification. The original model of the MPTP that proposed the adenine nucleotide translocator (ANT) as the inner membrane pore-forming component was challenged when mitochondria from Ant1/2 double null mouse liver still had MPTP activity. Because mice express three Ant genes, we reinvestigated whether the ANTs comprise the MPTP. Liver mitochondria from Ant1, Ant2, and Ant4 deficient mice were highly refractory to Ca2+-induced MPTP formation, and when also given cyclosporine A (CsA), the MPTP was completely inhibited. Moreover, liver mitochondria from mice with quadruple deletion of Ant1, Ant2, Ant4, and Ppif (cyclophilin …

Total Rna Extraction From Transgenic Flies Misexpressing Foreign Genes To Perform Next Generation Rna Sequencing, Abijeet Singh Mehta, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, Amit Singh

Biology Faculty Publications

Due to absence of transgenic approaches in Notopthalmus Viridescens (newt), and conservation of genetic machinery across species, we generated transgenic Drosophila melanogaster to misexpress unique genes from newt. Novel newt genes cloned, and inserted at attP site in Drosophila were misexpressed ubiquitously using tubulin Gal-4. Sample (total RNA) for RNA sequencing was collected at 3rd instar larval stage during which major developmental events takes place in Drosophila. Total RNA was extracted, and purified using RNA clean and ConcentratorTM. RNA quality was quantitated by calculating absorbance at 260 nm (A260) and 280 nm (A280) wavelengths using Nanodrop 2000 spectrophotometer. Good quality …

Histology Atlas: Basic Mammalian Tissue Types (Biol 105), Joshua Barnes, Daniel J. Yakubov, Corinna Singleman, Nathalia G. Holtzman

Open Educational Resources

This book is a guide to the basic histology lab conducted as a part of the Queens College, CUNY Biology Department Bio105 General Biology: Physiology and Cell Biology course. This course is the first half our two-part series for biology majors. The actives are designed to be conducted over a single 3-hour lab periods which focus on the relationship of form and function of the cellular and organ level anatomy and physiology. Step by step instructions for each slide set are provided for all the key organs.

In addition to the full text of the book, we also provide a …

Fetal Pig Dissection Manual (Biol 105), Nathalia G. Holtzman, Daniel J. Yakubov

Open Educational Resources

This book is a guide to the basic fetal pig dissection conducted as a part of the Queens College, CUNY Biology Department Bio105 General Biology: Physiology and Cell Biology course. This course is the first half our two-part series for biology majors. The actives are designed to be conducted over a three- 3-hour lab periods which focus on the relationship of form and function of the pig anatomy and physiology. Step by step instructions for the dissection are provided along with some microscopy tasks to look at the histology of key organs.

In addition to the full text of the …

Comparative Transcriptomic Analysis And Structure Prediction Of Novel Newt Proteins, Abijeet Singh Mehta, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, Amit Singh

Biology Faculty Publications

Notophthalmus viridescens (Red-spotted Newt) possess amazing capabilities to regenerate their organs and other tissues. Previously, using a de novo assembly of the newt transcriptome combined with proteomic validation, our group identified a novel family of five protein members expressed in adult tissues during regeneration in Notophthalmus viridescens. The presence of a putative signal peptide suggests that all these proteins are secretory in nature. Here we employed iterative threading assembly refinement (I-TASSER) server to generate three-dimensional structure of these novel Newt proteins and predicted their function. Our data suggests that these proteins could act as ion transporters, and be involved …

Mechanosensitive Epithelial Cell Scattering And Migration On Layered Matrices, Christopher Michael Walter

McKelvey School of Engineering Graduate Student Theses & Dissertations

Epithelial cells form multi-layered tissue scaffolding that makes up every organ in the body. Along with epithelial cells, the basement membrane (BM) and connective tissue are composed of various proteins that sculpt the organs and protect them from foreign macromolecules. Epithelial cells respond to various cues, both chemical and mechanical, from their surrounding matrices to aid in maintenance and repair of these layers through degradation and deposition of extracellular matrix (ECM) proteins. In cancer progression, epithelial cells lose their normal function of supporting tissue structure and instead adopt more aggressive behaviors through an epithelial-to-mesenchymal transition (EMT) of their cellular traits. …

A Novel Role Of Hrr25 In Cell Wall Integrity Maintenance And Functional Analysis Of Hrr25 Domains, Amita Bhattarai

LSU New Orleans Theses and Dissertations

Hrr25 is a highly conserved serine/threonine protein kinase with diverse functions and it localizes to a number of intracellular sites. Hrr25 possesses an N-terminal kinase domain, a middle region, and a C-terminal proline/glutamine rich domain. In this thesis, we systematically characterized the roles of these three domains of Hrr25 on cell growth, cell morphology, and its cellular localizations. Additionally, we identified a novel target of Hrr25, Pin4. We show that Hrr25-dependent phosphorylation of Pin4 is required for cell wall integrity maintenance. We found that that Hrr25 and Pin4 physically interact in vivo and that the C-terminal domain of Hrr25 is …

Natural Autoantibodies: Origin, Function And Utility For Diagnosis Of Disease, Abhirup Sarkar

Graduate School of Biomedical Sciences Theses and Dissertations

Autoantibodies (aAbs) by the simplest definitions have been described as antibodies against self-antigens and were exclusively associated with autoimmune diseases. Eventually, studies demonstrated that they are abundant in the blood of all human sera, regardless of age, gender, or the presence or absence of disease, and were thus named as ‘natural autoantibodies’. The underlying reason for their ubiquity has remained elusive, but we have hypothesized that they are responsible for clearing blood-borne cell and tissue debris generated under conditions of health and disease. To test this, we chose to use two widely different disease model systems, namely neurodegenerative diseases and …

Sensory Primary Cilium Is A Distinct Signaling Compartment, Rinzhin Tshering Sherpa

Pharmaceutical Sciences (PhD) Dissertations

The primary cilium is a solitary cellular organelle that protrudes from the apical cell membrane. Findings on cilia-dependent mechanosenstation have shown that the primary cilium acts as a transducer of fluid-shear stress into intracellular signaling. Over recent years, studies in primary cilia have intensified after determining a causal relationship between dysfunctional primary cilia and cystic diseases. Along with its mechanosensory function, the primary cilium houses a variety of receptors, ion channels and transporter proteins. Studies in cilia biology have shown that primary cilia are coordinators of signaling pathways such as Hedgehog (Hh), Wnt, and platelet-derived growth factor (PDGF) pathways during …

The Influence Of Mir-322 On Skeletal Muscle Differentiation, Miles Alexander Soyer

Legacy Theses & Dissertations (2009 - 2024)

Skeletal muscle plays a crucial role in coordinating voluntary movement and accounts for nearly 50% of total body mass. Dysregulation in skeletal muscle development is known to cause muscle degenerative diseases including the devastating Duchenne Muscular Dystrophy (DMD). The majority of the biological studies investigating muscle development were based on myogenic transcription factors and signaling molecules including: Pax7, Myf5, MyoD, WNT, TGF-β and BMP. After the discovery of non-coding RNAs including microRNAs, it was postulated that these molecules could regulate gene expression and thus affect differentiation and development. MicroRNAs are small non-coding RNAs (~17-25 nucleotides) that regulate gene expression negatively …

The Functional And Structural Analysis Of Drosophila Robo2 In Axon Guidance, Lafreda Janae Howard

Graduate Theses and Dissertations

In animals with complex nervous systems such as mammals and insects, signaling pathways are responsible for guiding axons to their appropriate synaptic targets. Importantly, when this process is not successful during the development of an organism, outcomes include catastrophes such as human neurological diseases and disorders. It is vital to determine the underlying causes of such diseases by understanding the development of the nervous system. There are many pathways that have been identified to play a role in this, however, we lack an understanding of how these pathways can promote such diverse outcomes in different populations of neurons. These pathways …

Protein Structure Analysis, Agnieszka Szarecka, Chris Dobson

Peer Reviewed Articles

We describe a series of engaging exercises in which students emulate the process that researchers use to efficiently develop new pharmaceutical drugs, that of rational drug design. The activities are taken from a three- to four-hour workshop regularly conducted with first-year college students and presented here to take place over three to four class periods. Although targeted at college students, these activities may be appropriate at the high school level as well, particularly in an AP Biology course. The exercises introduce students to the topics of bioinformatics and computer modeling, in the context of rational drug design, using free online …

Assessing The Efficacy Of Seedling Planting As A Forest Restoration Technique In Temperate Hardwood Forests Impacted By Invasive Species, Michaela J. Woods, Meredith Cobb, Katie Hickle

Biology Faculty Publications

The emerald ash borer (Agrilus planipennis Fairmaire; EAB) is an invasive insect that causes mortality of trees in the genus Fraxinus, creating canopy gaps that may facilitate invasion by exotic plants. Planting native tree seedlings under EAB-infested Fraxinus may accelerate succession and preclude invasive plant expansion; however, the effectiveness of this approach has not been experimentally tested. We assessed understory seedling planting of Quercus rubra, Carya laciniosa, and Juglans cinerea in EAB-infested forests, where the invasive shrub Lonicera maackii (Amur honeysuckle) was removed. We tested whether the use of plastic tree shelters (“tree tubes”) or planting season (fall versus spring) …

Ipsc Based Gene Correction And Disease Model Of A New Class Of Lgmd Due To Poglut1 Mutation, Jose Ortiz-Vitali

Dissertations and Theses (Open Access)

Recently, a novel class of muscular dystrophy has been discovered in a family due to autosomal recessive missense mutation in POGLUT1. Mutation of this enzyme leads to decreased O-glucosyltransferase activity and impaired Notch signaling, the pathways important for skeletal muscle stem cell (satellite cells) quiescence and activation. We hypothesize that reduced POGLUT1 activity and impaired Notch signaling is causative of this limb girdle muscular dystrophy through dysfunction of muscle stem cells and myogenic progenitors.

To test this, we have used iPSCs for disease modeling and rescue experiments. Using a CRISPR based gene targeting method, we aimed to correct the point …

The Gsk-3Β-Fbxl21 Axis Regulates Tcap Via Ubiquitin-Mediated Proteasomal Pathway In The Cytoplasm, Jiah Yang

Dissertations and Theses (Open Access)

Protein turnover is one of the most essential mechanisms controlling circadian rhythms. F-Box and Leucine Rich Repeat Protein21 (FBXL21) is a circadian E3 ligase which shows oscillatory mRNA transcripts and protein levels. It was previously found to perform subcellular compartment-specific E3 ligase activities targeting the core clock proteins CRYPTOCHROME(CRY)1/2. Here we identified a new sarcomeric target substrate, Telethonin(TCAP), which also shows circadian oscillation in its mRNA transcript and protein expression and, importantly, interaction with FBXL21 in an anti-phasic manner. Via computational and pharmacological tests, we identified Glycogen Synthase Kinase-3β(GSK-3β) as a regulator of FBXL21. Biochemical and molecular characterizations demonstrated that …

The Distinct Expressions Of Integrins Αdβ2 And Αmβ2 Differently Regulate Macrophage Migration In 3d Matrix In Vitro And In Tissue During Inflammation, Kui Cui

Electronic Theses and Dissertations

Chronic inflammation is an essential mechanism during the development of cardiovascular and metabolic diseases. The outcome of diseases depends on the balance between the migration and accumulation of macrophages in damaged tissues. Macrophage motility is highly regulated by adhesive receptors, integrins. Namely, intermediate expression of integrin supports macrophage migration, while a high integrin density inhibits it. Our studies are focused on evaluation of the contribution of related integrins α_Dβ₂ and α_Mβ₂ to macrophage migration and development of chronic inflammation.

We found that integrin α_Dβ₂ is upregulated on M1-macrophages in vitro and …

Modeling Cancer Using Li-Fraumeni Syndrome Patient-Derived Induced Pluripotent Stem Cells, Ruoji Zhou

Dissertations and Theses (Open Access)

Li-Fraumeni syndrome (LFS) is an autosomal dominant disease caused by germline mutations in the gene TP53, which predispose individuals to a wide range of malignancies, including osteosarcoma and breast cancer. In the previous study, our group developed a novel disease model platform by reprograming LFS patients' fibroblasts to induced pluripotent stem cells (iPSCs), and further differentiate these iPSCs into mesenchymal stem cells (MSCs) then to osteoblasts (OBs), the cells from which osteosarcomas originate. Interestingly, LFS iPSC-derived osteoblasts recapitulated the osteosarcoma phenotype, creating “a bone tumor in a dish”. This “tumor in a dish” platform proved that LFS is an …