Biology Commons^™

Discovery Of An Egfr Inhibitor For The Treatment Of Lung And Other Cancers, Jodie Meng '20

Student Publications & Research

The Epidermal Growth Factor Receptor (EGFR), a transmembrane protein involved in the regulation of signaling pathways, is frequently overexpressed in epithelial tumors. First generation EGFR TKIs, such as erlotinib and gefitinib, traditionally improved outcomes for non-small-cell lung carcinoma and pancreatic cancer patients by attaching competitively and reversibly to the ATP binding domain of EGFR. Second-generation EGFR TKIs have been developed to combat resistance among patients, despite demonstrating toxic side effects. In the present study, 1400 selective inhibitors were designed based on the molecular scaffolds of first and second generation EGFR TKIs. Results were refined by parameters outlined in Lipinski’s rule. …

Combination Of Curcumin And Luteolin Synergistically Inhibits Tnf-Α-Induced Vascular Inflammation In Human Vascular Cells And Mice, Lijuan Zhang, Xiaoyong Wang, Longyun Zhang, Carlos Virgous, Hongwei Si

Human Sciences Faculty Research

Emerging evidence shows that phytochemicals, the secondary plant metabolites present in a large variety of foods, have the potential ability in reducing the risk of cardiovascular diseases. However, the dosages of phytochemicals in the cellular and animal studies are too high to reach in humans by relevant foods or dietary supplement intake. The aims of this study were to investigate whether and how combined curcumin and luteolin synergistically inhibit tumor necrosis factor-alpha (TNF-α)-induced monocytes adhesion endothelium, a crucial step of the development of endothelial dysfunction, both in human vascular cells and mouse aortic endothelium. Our results show that combined curcumin …

Mycobiome Analysis Of Trees Selected By Black-Capped Chickadees (Poecile Atricapillus) As Nest Sites, Connor Gable

All NMU Master's Theses

Decay fungi may aid primary cavity excavators, such as woodpeckers, in nest excavation by softening wood, and in turn the excavators disperse fungi. Recent molecular techniques have allowed researchers to examine communities of fungi present in environmental samples more comprehensively than ever before. However, this association has not been examined for primary excavating songbirds (Passeriformes). In this study, I examine the communities of fungi in trees selected by black-capped chickadees (Poecile atricapillus) and compare them to communities in non-selected control trees to determine whether chickadee nest trees are associated with specific fungal taxa and communities. Overall, I identified …

Integrating Anthropogenic Factors Into Regional-Scale Species Distribution Models: A Novel Application In The Imperiled Sagebrush Biome, Juan M. Requena-Mullor, Kaitlin C. Maguire, Douglas J. Shinneman, Timothy Trevor Caughlin

Biology Faculty Publications and Presentations

Species distribution models (SDM) that rely on regional-scale environmental variables will play a key role in forecasting species occurrence in the face of climate change. However, in the Anthropocene, a number of local-scale anthropogenic variables, including wildfire history, land-use change, invasive species, and ecological restoration practices can override regional-scale variables to drive patterns of species distribution. Incorporating these human-induced factors into SDMs remains a major research challenge, in part because spatial variability in these factors occurs at fine scales, rendering prediction over regional extents problematic. Here, we used big sagebrush (Artemisia tridentata Nutt.) as a model species to …

Onramp: A Galaxy-Based Platform For Collaborative Annotation Of Eukaryotic Genomes, Yating Liu, Luke Sargent, Wilson Leung, Sarah C.R. Elgin, Jeremy Goecks

Biology Faculty Research

G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data and repeat finders. G-OnRamp can be used to visualize large genomics datasets and to perform collaborative genome annotation projects in both research and educational settings.

The Impact Of Genetic Background And Cell Lineage On The Level And Pattern Of Gene Expression In Position Effect Variegation, Sarah C.R. Elgin, Sh Wang

Biology Faculty Research

"Background: Chromatin-based transcriptional silencing is often described as a stochastic process, largely because of the mosaic expression observed in position effect variegation (PEV), where a euchromatic reporter gene is silenced in some cells as a consequence of juxtaposition with heterochromatin. High levels of variation in PEV phenotypes are commonly observed in reporter stocks. To ascertain whether background mutations are the major contributors to this variation, we asked how much of the variation is determined by genetic variants segregating in the population, examining both the level and pattern of expression using the fruit fly, Drosophila melanogaster, as the model.

Results: Using …

Single-Cell Transcriptomics Reveal A Correlation Between Genome Architecture And Gene Family Evolution In Ciliates, Ying Yan, Xyrus X. Maurer-Alcalá, Rob Knight, Sergei L.Kosakovsky Pond, Laura A. Katz

Biological Sciences: Faculty Publications

Ciliates, a eukaryotic clade that is over 1 billion years old, are defined by division of genome function between transcriptionally inactive germline micronu-clei and functional somatic macronuclei. To date, most analyses of gene family evolution have been limited to cultivable model lineages (e.g., Tetrahymena, Paramecium, Oxytricha, and Stylonychia). Here, we focus on the uncultivable Karyorelictea and its understudied sister class Heterotrichea, which represent two extremes in genome architecture. Somatic macronuclei within the Karyorelictea are described as nearly diploid, while the Heterotrichea have hyperpolyploid somatic genomes. Previous analyses indicate that genome architecture impacts ciliate gene family evolution as the most diverse …

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 …

Comparative Chromosome Mapping Of Musk Ox And The X Chromosome Among Some Bovidae Species, Anastasiya A. Proskuryakova, Anastasia I. Kulemzina, Polina L. Perelman, Dmitry V. Yudkin, Natalya A. Lemskaya, Innokentii M. Okhlopkov, Egor V. Kirillin, Marta Farré, Denis M. Larkin, M. Roelke-Parker, Stephen James O'Brien, Mitchell Bush, Alexander S. Graphodatsky

Biology Faculty Articles

Bovidae, the largest family in Pecora infraorder, are characterized by a striking variability in diploid number of chromosomes between species and among individuals within a species. The bovid X chromosome is also remarkably variable, with several morphological types in the family. Here we built a detailed chromosome map of musk ox (Ovibos moschatus), a relic species originating from Pleistocene megafauna, with dromedary and human probes using chromosome painting. We trace chromosomal rearrangements during Bovidae evolution by comparing species already studied by chromosome painting. The musk ox karyotype differs from the ancestral pecoran karyotype by six fusions, one fission, …

Understanding The Influence Of The Cancer Microenvironment On Metabolism And Metastasis, Shonagh Russell

USF Tampa Graduate Theses and Dissertations

Cancer is a complex and heterogeneous disease. Not only is there considerable variability between different cancer types, but there is enormous variability between and within patients who have the same type of cancer. Within tumors, there are multiple cell types, including cancer cells, stromal cells, and immune cells. The tumor microenvironment often induces the healthy cells to become pro-tumorigenic. Cell metabolism is exquisitely sensitive to changes in the tumor microenvironment and can be measured to infer the aggressiveness of cancer and predict response to therapy. In this dissertation, we aim to understand how the microenvironment, specifically low pH, affects the …

The Functional, Ecological, And Evolutionary Morphology Of Sea Lampreys (Petromyzon Marinus), Bradley Morgan Wood

LSU Doctoral Dissertations

Lampreys (Petromyzontiformes) are jawless vertebrates with an evolutionary history lasting at least 360 million years and are often used in comparisons with jawed vertebrates because some of their morphological aspects, such as the segmented trunk musculature with curved myosepta and a non-mineralized skeleton fibrous skeleton, are thought to resemble the condition of early vertebrates before the evolution of jaws. Although earlier authors studied the morphology of the skeleto-muscular system of the trunk of lampreys, their studies are not detailed and complete enough to allow a functional and biomechanical analysis that is needed as a basis for modeling the mechanics of …

Alternative Reproductive Tactics In Lake Michigan Populations Of Invasive Round Goby (Neogobius Melanostomus): How Fish Increase Fitness By Doing Less, Alex Florian, Steve Smit

Student Summer Scholars Manuscripts

Understanding the reproductive biology of invasive species is an important step in managing populations. Yet, little is known about the reproductive strategies of invasive round goby (Neogobius melanostomus) in Lake Michigan. For round goby, fertilization occurs externally in nests guarded by large “paternal” males. However, some males pursue alternative reproductive tactics (ARTs), where males sneak into a larger male’s nest and fertilize a portion of the eggs, these males are called “sneakers”. We investigated if the proportion of ARTs varies between sites and how that affects population dynamics of round goby. We caught 264 fish from 4 lakes along Eastern …

Effects Of Intertidal Position On Metabolism And Behavior In The Acorn Barnacle, Balanus Glandula, Kali Horn

Master's Theses

The intertidal zone is characterized by persistent, tidally-driven fluctuations in both abiotic (e.g., temperature, [O₂], salinity) and biotic (e.g., food availability, predation) conditions, which makes this a very physiologically challenging habitat for resident organisms. The magnitude and degree of variability of these environmental stressors differs between intertidal zones, with the most extreme physiological stress often being experienced by organisms in the high intertidal. Given that many of the fluctuating conditions in this environment are primary drivers of metabolic rate (e.g., temperature, [O₂], food availability), we hypothesized that sessile conspecifics residing in different tidal zones would exhibit …

In Vitro Investigation Of The Effect Of Camel Milkproteins And Its Fractions On Insulin Receptor Function, Arshida Ashraf

Biology Theses

Camel milk (CM) has been reported to have anti-diabetic properties in many in vitro and in vivo studies but the molecular basis of such beneficial properties are still elusive. Recently, camel milk whey proteins (CWPs) have been shown to positively affect the activity of the human insulin receptor (hIR) in cell lines. In this study, we profiled crude CWPs and their hydrolysates as well as camel milk lactoferrin (CMLF) for their pharmacological and functional effects on hIR activity and its downstream signaling in both human embryonic kidney (HEK293) and hepatocarcinoma (HepG2) cell lines. For this, bioluminescence resonance energy transfer (BRET) …

Cul3 Regulates Cyclin E1 Protein Abundance Via A Degron Located Within The N-Terminal Region Of Cyclin E, Brittney Marie Davidge, Katia De Oliveira Rebola, Larry N. Agbor, Curt D. Sigmund, Jeffrey D. Singer

Biology Faculty Publications and Presentations

mammalian cells. Increased levels of cyclin E are found in some cancers. Additionally, proteolytic removal of the cyclin E N-terminus occurs in some cancers and is associated with increased cyclin E–Cdk2 activity and poor clinical prognosis. Cyclin E levels are tightly regulated and controlled in part through ubiquitin-mediated degradation initiated by one of two E3 ligases, Cul1 and Cul3. Cul1 ubiquitylates phosphorylated cyclin E, but the mechanism through which Cul3 ubiquitylates cyclin E is poorly understood. In experiments to ascertain how Cul3 mediates cyclin E destruction, we identified a degron on cyclin E that Cul3 targets for ubiquitylation. Recognition of …

Species-Specific Effects Of Passive Warming In An Antarctic Moss System, Hannah M. Prather, Angélica Casanova-Katny, Andrew F. Clements, Matthew Chmielewski, Mehmet Ali Balkan, Erin Shortlidge, Todd Rosenstiel, Sarah Eppley

Biology Faculty Publications and Presentations

Polar systems are experiencing rapid climate change and the high sensitivity of these Arctic and Antarctic ecosystems make them especially vulnerable to accelerated ecological transformation. In Antarctica, warming results in a mosaic of ice-free terrestrial habitats dominated by a diverse assemblage of cryptogamic plants (i.e. mosses and lichens). Although these plants provide key habitat for a wide array of microorganisms and invertebrates, we have little understanding of the interaction between trophic levels in this terrestrial ecosystem and whether there are functional effects of plant species on higher trophic levels that may alter with warming. Here, we used open top chambers …

Embryonic Development Of A Parthenogenetic Vertebrate, The Mourning Gecko (Lepidodactylus Lugubris), Aaron H. Griffing, Thomas J. Sanger, Juan D. Daza, Stuart V. Nielsen, Brendan J. Pinto, Edward L. Stanley, Tony Gamble

Biological Sciences Faculty Research and Publications

Background

One goal of evolutionary developmental biology is to understand the role of development in the origin of phenotypic novelty and convergent evolution. Geckos are an ideal system to study this topic, as they are species‐rich and exhibit a suite of diverse morphologies—many of which have independently evolved multiple times within geckos.

Results

We characterized and discretized the embryonic development of Lepidodactylus lugubris—an all‐female, parthenogenetic gecko species. We also used soft‐tissue μCT to characterize the development of the brain and central nervous system, which is difficult to visualize using traditional microscopy techniques. Additionally, we sequenced and assembled a de …

Ubiquity Or Not Ubiquity: That Is The Question, Robin S. Sleith, Laura A. Katz

Biological Sciences: Faculty Publications

The nature of population structure in eukaryotic microbes has been the subject of intense debate, but until recently the tools to test these hypotheses were either problematic (e.g., allozymes that cannot detect all genetic changes) or beyond financial and technological limits of most laboratories (e.g., high throughput sequencing). In a recent issue of Molecular Ecology, Craig et al. (2019) use a genomic approach to investigate the population structure of a model alga, the chlorophyte Chlamydomonas reinhardtii (Figure 1). Using high throughput sequencing, read mapping, and variant calling, they detected strong signals of differentiation at a continental scale, while local patterns …

Culturing Embryonic Cells From The Parthenogenetic Clonal Marble Crayfish Marmorkrebs Procambarus Virginalis Lyko, 2017 (Decapoda: Astacidea: Cambaridae), Heriberto Deleon Iii, Juan Garcia Jr., Dionn Carlo Silva, Oscar Quintanilla, Zen Faulkes, John M. Thomas Iii

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

The parthenogenetic marbled crayfish, or Marmorkrebs (Procambarus virginalis Lyko 2017), is an emerging model organism. We describe a method to isolate cells from early-stage embryos and culture them in vitro. The identity of the cells was confirmed by sequencing the cytochrome c oxidase subunit I (COI) gene. This technique can be applied for use in the manipulation of embryonic parthenogenetic crayfish cells.

Harbor Branch Oceanographic Institute Summer Intern Program, Nicolas Vitari

Trick to the Treat of Internships and Research

No abstract provided.

Md Anderson University Outreach Summer Program, Melanie Fraidenburg

Trick to the Treat of Internships and Research

No abstract provided.

University Of Miami Summer Undergraduate Research Fellowship (Surf), Elizabeth Feldman

Trick to the Treat of Internships and Research

No abstract provided.

Clear Vision Optometry Clinic Internship, Taylor Veneza

Trick to the Treat of Internships and Research

No abstract provided.

Love & Angels Care Internship, Kristin Addison

Trick to the Treat of Internships and Research

No abstract provided.

Clear Vision Optometry Clinic Internship, Howard Ho

Trick to the Treat of Internships and Research

No abstract provided.

Medical University Of Graz, Austria Internship, Vanessa Cruise

Trick to the Treat of Internships and Research

No abstract provided.

Biology Practicum Course, Jose Garcia

Trick to the Treat of Internships and Research

No abstract provided.

Atlantis Fellowship - Spain / Italy Summer Internship, Cassidy Campanella

Trick to the Treat of Internships and Research

No abstract provided.

Chlorophyll A And Primary Productivity Dynamics In Kentucky Lake Mainstem And Embayment Habitats., Morgan Franklin

Scholars Week

Chlorophyll α (Chl α) has been used as a proxy for phytoplankton biomass, while primary productivity (PP), the rate at which carbon is fixed into phytoplankton cells, is an indicator of how quickly carbon is turned over within the phytoplankton community. The purpose of this research was to examine the spatial distribution of and the relationship between Chl α and PP seasonally in the main channel of Kentucky Lake reservoir and two embayments of contrasting land use. Correlation coefficients (r) for Chl α versus PP were 0.45 in Ledbetter embayment, 0.55 in Panther embayment, and 0.57 in the main …

Spatial And Temporal Variation Of Offshore Wind Power And Its Values Along The Central California Coast, Yi-Hui Wang, Ryan K. Walter, Crow White, Matthew D. Kehrli, Stephen F. Hamilton, Patrick H. Soper, Benjamin I. Ruttenberg

Physics

The analysis of the spatiotemporal variability of wind power remains limited during the planning stage of an offshore wind farm. This study provides a framework to investigate how offshore wind power varies along the Central California Coast over diurnal and seasonal time scales, which is critical for reliability and functionality of the grid system. We find that offshore wind power in this region peaks during evening hours across all seasons and maximizes in spring and summer. The timing of peak offshore wind power production better aligns with that of peak demand across California than solar and land-based wind power production, …