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The Utilization Of Crispr/Cas9 In Monogenic Disorders Authors, Shauna M. Mellor

Spectra Undergraduate Research Journal

This paper is a literature review of various scientific research papers, exploring the recent scientific advancement in the field of genetic engineering. The research presented is a foundational tool, building awareness on the implications of CRISPR/ Cas9 technology. CRISPR/ Cas9 was first discovered through the study of bacterial immune systems, fighting against viral infections. Manipulation of the Cas9 protein would eventually lead to target specific, gene-altering medicines for human organisms. CRISPR/ Cas 9 technology has begun to show promise as an effective treatment for certain monogenic disorders. Despite this, time is required before its efficacy as a proven genetic treatment …

Brainless But Smart: Investigating Cognitive-Like Behaviors In The Acellular Slime Mold Physarum Polycephalum, Subash Kusum Ray

Dissertations

Evolutionary pressures to improve fitness, have enabled living systems to make adaptive decisions when faced with heterogeneous and changing environmental and physiological conditions. This dissertation investigated the mechanisms of how environmental and physiological factors affect the behaviors of non-neuronal organisms. The acellular slime mold Physarum polycephalum was used as the model organism, which is a macroscopic, unicellular organism, that self-organizes into a network of intersecting tubules. Without using neurons, P. polycephalum can solve labyrinth mazes, build efficient tubule networks, and make adaptive decisions when faced with complicated trade-offs, such as between food quality and risk, speed and accuracy, and exploration …

Flexibility Vs Consistency: Quantifying Differences In Neuromodulatory Elicited Patterns Of Activity, Elizabeth M. Cronin

Dissertations

Central pattern generating circuits underly fundamental behaviors such as respiration or locomotion and are under the influence of neuromodulators. The presence of neuromodulators is thought to confer flexibility to these circuits to generate distinct patterns of activity to meet distinct behavioral needs. Network output flexibility can be achieved by distinct classes of neuromodulators, those which have convergent cellular actions but divergent circuit actions or by those which have divergent cellular actions but convergent circuit actions.

Both classes of neuromodulator exist in the stomatogastric nervous system of the crab Cancer borealis and influence the activity of a central pattern generating circuit …

Global Variation In Nonstructural Carbohydrate Stores In Response To Climate, Meghan Blumstein, Jess T. Gersony, Jordi Martínez-Vilalta, Anna Sala

Biological Sciences: Faculty Publications

Woody plant species store nonstructural carbohydrates (NSCs) for many functions.While known to buffer against fluctuations in photosynthetic supply, such as at night, NSC stores are also thought to buffer against environmental extremes, such as drought or freezing temperatures by serving as either back-up energy reserves orosmolytes. However, a clear picture of how NSCs are shaped by climate is still lack-ing. Here, we update and leverage a unique global database of seasonal NSC storage measurements to examine whether maximum total NSC stores and the amount of soluble sugars are associated with clinal patterns in low temperatures or aridity, indicating they may …

Intracellular Hemin Is A Potent Inhibitor Of The Voltage-Gated Potassium Channel Kv10.1, Nirakar Sahoo, Kefan Yang, Alisa Bernert, Sandip M. Swain, Guido Gessner, Reinhard Kappl, Toni Kühl, Diana Imhof, Toshinori Hoshi, Roland Schönherr, Stefan H. Heinemann

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

Heme, an iron-protoporphyrin IX complex, is a cofactor bound to various hemoproteins and supports a broad range of functions, such as electron transfer, oxygen transport, signal transduction, and drug metabolism. In recent years, there has been a growing recognition of heme as a non-genomic modulator of ion channel functions. Here, we show that intracellular free heme and hemin modulate human ether à go-go (hEAG1, Kv10.1) voltage-gated potassium channels. Application of hemin to the intracellular side potently inhibits Kv10.1 channels with an IC50 of about 4 nM under ambient and 63 nM under reducing conditions in a weakly voltage-dependent manner, …

Characterizing Microbiome Variation In Wild Populations Of Mosquito Species, Jane Pascar

Theses - ALL

No abstract provided.

The Marine Gastropod Conomurex Luhuanus (Strombidae) Has High-Resolution Spatial Vision And Eyes With Complex Retinas, Allison R. Irwin, Suzanne T. Williams, Daniel Isaac Speiser, Nicholas W. Roberts

Faculty Publications

All species within the conch snail family Strombidae possess large camera-type eyes that are surprisingly well-developed compared with those found in most other gastropods. Although these eyes are known to be structurally complex, very little research on their visual function has been conducted. Here, we use isoluminant expanding visual stimuli to measure the spatial resolution and contrast sensitivity of a strombid, Conomurex luhuanus. Using these stimuli, we show that this species responds to objects as small as 1.06 deg in its visual field. We also show that C. luhuanus responds to Michelson contrasts of 0.07, a low contrast sensitivity …

Investigating The Role Of The Transcriptional Coregulator Cited2 In Regulating Intermediate Progenitor Proliferation And Modulating Behavior, Nikolaus R. Wagner

Dissertations - ALL

The mammalian neocortex develops from a thin layer of neuroepithelial cells into a robust mosaic of differentiated neurons organized into distinct layers and functional areas. This process requires a complex choreography of transcription factors and epigenetic regulators to be spatially and temporally activated in a precise manner. Disruptions in any aspect of this delicate process may lead to neurodevelopmental disorders like autism spectrum disorder, schizophrenia, or intellectual disability. One such transcriptional coregulator that is a crucial regulator of neocortical development is Cited2. Previous work demonstrated that forebrain-specific Cited2 loss-of-function causes a reduction in neocortical progenitor proliferation which leads to reduced …

Molecular Mechanisms That Regulate Centrosome Movement During Tissue Morphogenesis, Nikhila Krishnan

Dissertations - ALL

Coordination of cell division, cellular epithelialization and ciliogenesis is necessary for tissue development in vivo. We argue that the process of epithelialization and ciliogenesis requires positioning the centrosomes to specific cellular locales. We identified that the centrosome can be repositioned to these locales in a Rab11-dependent manner towards the cytokinetic bridge during abscission and to the apical membrane for cilia formation. Rab11 is an essential GTPase that is involved in regulating abscission, cleavage of the cytokinetic bridge and cilia formation. Here we identified the role of Rab11 endosomes in regulating centrosome positioning during these processes in vivo. To study the …

Nla28 Activator Modulates Σ54-Dependent Gene Regulation In Myxococcus Xanthus, Muqing Ma

Dissertations - ALL

The complex life cycle of Myxococcus xanthus makes it a model organism for studying multicellular developmental processes in bacteria. In response to environmental changes, M. xanthus cells collectively and dramatically adjust their morphology, physiological functions, and biosynthesis. Particularly, M. xanthus copes with starvation by producing fruiting bodies filled with dormant and stress-resistant spores. During secondary metabolism, it synthesizes polyketide (PK) and non-ribosomal peptide (NRP) natural products that are crucial sources of antibiotics. Bacteria including M. xanthus, require the alternative σ54 regulatory system to initiate the transcription of necessary genes for settling stress and completing developmental process. This dissertation introduces in …

Arabidopsis Shoot Gravitropism Requires The Mediator Coactivator Complex, Gabriella Newton

Honors Theses

Gravitropism is a plant response to gravity in directing the growth of its organs, such as the root and the stem. Gravity is sensed by statocytes, unique cells that contain starch-filled amyloplasts, which trigger gravitropic growth response by modulating the distribution of growth hormone auxin in the elongation zone of the stem and root. Despite the fact that multiple factors have been identified as key regulators of shoot negative gravitropism, how these factors are regulated at the transcriptional level is largely unknown. In this study, we explore the role of transcriptional machinery in regulating shoot gravity sensing and responses by …

Drone-Based Water Sampling And Characterization Of Three Freshwater Harmful Algal Blooms In The United States, Regina Hanlon, Stephen J. Jacquemin, Johnna A. Birbeck, Judy A. Westrick, Charbel Harb, Hope Gruszewski, Andrew P. Ault, Durelle Scott, Hosein Foroutan, Shane D. Ross, Javier González-Rocha, Craig Powers, Lowell Pratt, Harry Looney, Greg Baker, David G. Schmale

Biological Sciences Faculty Publications

Freshwater harmful algal blooms (HABs), caused mostly by toxic cyanobacteria, produce a range of cyanotoxins that threaten the health of humans and domestic animals. Climate conditions and anthropogenic influences such as agricultural run-off can alter the onset and intensity of HABs. Little is known about the distribution and spread of freshwater HABs. Current sampling protocols in some lakes involve teams of researchers that collect samples by hand from a boat and/or from the shoreline. Water samples can be collected from the surface, from discrete-depth collections, and/or from depth-integrated intervals. These collections are often restricted to certain months of the year, …

Understanding The Effects Of Phthalate Exposure, Karen Orenshteyn

Graduate Student Dissertations, Theses, Capstones, and Portfolios

Phthalates are found in nearly all everyday products; therefore, human exposure is inevitable. Phthalates are groups of chemicals classified as plasticizers that help increase the durability and shelf life of whatever product they are put into. The effects of phthalates can occur prenatally and throughout adulthood. Despite phthalates being understood to be endocrine disruptors, chemicals that block hormones and certain receptors, phthalate use within plastics is increasing every year- raising concern to find different alternatives. This research analysis will aim to define and explain what phthalates are and where they are found along with the harmful effects that occur due …

Role Of Nucleobindin-2/Nesfatin-1 In The Regulation Of Energetic Status And Maternal Mouthbrooding In The Cichlid Fish, Astatotilapia Burtoni, Saachi Chugh

LSU Master's Theses

Feeding and energetics are fundamental processes in all species that must also be balanced with reproductive investment. The peptide hormone nesfatin-1 is encoded by the nucleobindin-2(nucb2) gene and has recently emerged as a key player involved in both feeding and reproduction across vertebrates. How nesfatin-1 might help regulate trade-offs between feeding and reproduction, however, are relatively unexplored. The female cichlid fish Astatotilapia burtoniis an ideal system to examine the role of nesfatin-1 in regulating metabolic and reproductive functions because this species cycles between a gravid feeding state while preparing to mate, followed by a forced starvation …

Analysis Of Sanitizer Rotation On The Susceptibility, Biofilm Forming Ability And Caco-2 Cell Adhesion And Invasion Of Listeria, Md Asfakur Rahman, Nirakar Sahoo, Veerachandra K. Yemmireddy

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

The purpose of this study was to determine the effect of sanitizer use conditions on the susceptibility, biofilm forming ability and pathogenicity of Listeria monocytogenes. Two different strains of L. monocytogenes and a non-pathogenic L. innocua were exposed to sodium hypochlorite, benzalkonium chloride and peroxyacetic acid at different concentrations (4 to 512 ppm) and treatment times (30 s to 5 min), respectively. Under the tested conditions, no significant difference (p > 0.05) in reduction was observed among the three tested sanitizers. A reduction of 1 to 8 log CFU/mL was observed depending upon the sanitizer concentration and treatment times. The survived …

Identification Of Secondary Structural Elements Contained Within The Intrinsically Disordered N-Terminal Tail Of The Bloom’S Syndrome Helicase., Vivek Somasundaram

USF Tampa Graduate Theses and Dissertations

The Bloom’s Syndrome Helicase (BLM) is one of five human RecQ helicases and is necessary for maintenance of genome stability. Whilst a crystal structure exists for the C-terminal domain of BLM, very limited structural knowledge is known about the intrinsically disordered N-terminal tail. This lack of insight exists, despite the fact that the N-terminus of BLM is essential for the overall biological activity of BLM. Here we provide an Nuclear Magnetic Resonance spectroscopy based approach that we used to identify two distinct ⍺-helices contained within the first 100 residues of BLM. In addition, we propose a mutagenesis-based approach involving rationally …

Climate Warming Amplifies The Frequency Of Fish Mass Mortality Events Across North Temperate Lakes, Simon P. Tye, Adam M. Siepielski, Andrew Bray, Andrew L. Rypel, Nicholas B.D. Phelps, Samuel B. Fey

Biological Sciences Faculty Publications and Presentations

Recent increases of animal mass mortality events have coincided with substantial changes in global climate. Yet, tractable approaches that predict how climate change will accentuate occurrences of these ecological catastrophes remain nascent. We compiled one of the most comprehensive datasets of lentic fish mortality events, thermal tolerances of affected families, and 1.2 million air and water temperature profiles across 8891 north temperate lakes in North America. Temperature extremes within and across lakes were strongly associated with the three most frequent cause types (infectious agents, summerkills, winterkills). Thermal tolerances mediated the lethality of direct thermal stress, but mortalities of warm- and …

Niche Partitioning Of Food Resources By Freshwater Mussels In A Multispecies Mussel Bed In The Sabine River, Marissa Netti

Biology Theses

Freshwater mussels (Unionids) are a very diverse group of bivalves, with about 300 species in the United States. Although freshwater mussels are very diverse, they are also critically endangered and are declining at extremely high rates. In fact, the U.S. Fish and Wildlife Service proposed excluding eight freshwater mussel species from the Endangered Species Act (ESA) in 2021 because they went extinct. Mussels play a key role in keeping our water systems healthy because of their filter feeding method. Filter feeding influences the rest of the ecosystem through the transfer of energy, cycling of nutrients, and purification of the surrounding …

Energy Drink Usage By Students Attending An Online University, Jodi Lynn Hutak, Ali Boolani, Lauri O. Byerley

School of Medicine Faculty Publications

Objective: This study determined the frequency, reasons for, and side effects of energy drinks (ED) consumption among online students. Participants: Students attending an online university. Methods: Participants were recruited by email and completed a 59-question survey about their prior months ED practices using a combination of validated surveys previously published examining similar constructs in on-campus students. Results: 307 students (age = 32.4 ± 6.5yrs) completed the survey, and 88% reported consuming EDs. Students’ reasons for consuming ED included school (p < .001), work (p < .001), an event/competition (p < .001), pick me up (p < .001), lack of rest (p < .001), more energy (p < .001), and staying awake while driving (p < .001). Only individuals who consumed > 10 ED/month reported side effects of headaches (p = .01) and speeding (p=.01). Conclusions: In our sample, a majority of …

Nup211 Plays An Important Role In Regulating Mrna Export And Stress Response, Ayana Ikenouchi

Theses and Dissertations

Nup211 is a nuclear pore basket component in Schizosaccharomyces pombe and roles in the gating functions of NPCs. Using RT-qPCR, I found that in nup211-shutoff cells, the transcript levels of genes in mRNA export and stress-response pathways were significantly changed, suggesting nup211 is involved in regulating stress response pathways.

Associations Of Rare Caddisflies With The Western Dwarf Salamander Eurycea Paludicola, Lillie Hawkins

Biology Theses

There is limited information on the three species of caddisflies Philopotamidae Chimarra holzenthali, Hydropsychidae Cheumatopsyche morsei, Hydroptilidae Hydroptila ouachita and the western dwarf salamander Eurycea paludicola. In particular, there is a lack of any habitat associations between these caddisflies and the western dwarf salamander. Museum specimens of the caddisflies are scarce; however, the literature suggests they are spring dwelling like the western dwarf salamander. The goal of this project was to sample previously known and new habitats where these organisms might be found and report overall quality of the habitats and whether the caddisflies were associated with …

Snapping Shrimp Have Helmets That Protect Their Brains By Dampening Shock Waves, Alexandra C.N. Kingston, Sarah A. Woodin, David S. Wethey, Daniel Isaac Speiser

Faculty Publications

Shock waves are supersonic high-amplitude pressure waves that cause barotrauma when they transfer kinetic energy to the tissues of animals.1, 2, 3, 4 Snapping shrimp (Alpheidae) produce shock waves and are exposed to them frequently, so we asked if these animals have evolved mechanisms of physical protection against them. Snapping shrimp generate shock waves by closing their snapping claws rapidly enough to form cavitation bubbles that release energy as an audible “snap” and a shock wave when they collapse.5, 6, 7, 8 We tested if snapping shrimp are protected from shock waves by a helmet-like extension of their exoskeleton termed …

The Global Spread Of Misinformation On Spiders, Stefano Mammola, Jagoba Malumbres-Olarte, Valeria Arabesky, Diego Alejandro Barrales-Alcalá, Aimee Lynn Barrion-Dupo, Marco Antonio Benamú, Tharina L. Bird, Maria Bogomolova, Pedro Cardoso, Maria Chatzaki, Ren Chung Cheng, Tien Ai Chu, Leticia M. Classen-Rodríguez, Iva Čupić, Naufal Urfi Dhiya'ulhaq, André Philippe Drapeau Picard, Hisham K. El-Hennawy, Mert Elverici, Caroline S. Fukushima, Zeana Ganem, Efrat Gavish-Regev, Naledi T. Gonnye, Axel Hacala, Charles R. Haddad, Thomas Hesselberg, Tammy Ai Tian Ho, Thanakorn Into, Marco Isaia, Dharmaraj Jayaraman, Nanguei Karuaera, Rajashree Khalap, Kiran Khalap, Dongyoung Kim, Tuuli Korhonen, Laura Segura-Hernández, Et Al.

School of Biological Sciences: Faculty Publications

In the internet era, the digital architecture that keeps us connected and informed may also amplify the spread of misinformation. This problem is gaining global attention, as evidence accumulates that misinformation may interfere with democratic processes and undermine collective responses to environmental and health crises1,2. In an increasingly polluted information ecosystem, understanding the factors underlying the generation and spread of misinformation is becoming a pressing scientific and societal challenge3. Here, we studied the global spread of (mis-)information on spiders using a high-resolution global database of online newspaper articles on spider–human interactions, covering stories of spider–human encounters and biting events published …

Assessing Changes In Freshwater And Marine Food Web Connections Following Restoration On The Penobscot River, Maine, Using Stable Isotope Analysis, Matthew Brewer Ms

Student Scholarship

Oiadromous fish provide ecological subsidies to freshwater and marine food

webs, connecting both ecosystems. A main goal of the Penobscot River Restoration

Project was to increase connectivity between food webs by removing two mainstem

dams, improving fish passage, and reintroducing river herring through stocking.

Oiadromous fish now reach historic spawning habitat that was not accessible for

centuries. As a result, river herring runs in the Penobscot River increased from

2,336 fish in 2009 to over 3 million fish by 2018. To assess food web connectivity in

the Penobscot watershed, I analyzed stable isotopes from samples collected before

(2009-2010) and after …

Niche Overlap In Sympatric Rocio (Teleostei: Cichlidae) Of Guatemala, Cesar Estuardo Fuentes Montejo

College of Science and Health Theses and Dissertations

Rocio is a small genus of Neotropical freshwater fishes that is distributed in Atlantic drainages of northern Middle America. Two species in the genus exhibit sympatry in the Río Dulce basin (in Izabal, Guatemala), where one species is endemic (R. spinosissima), while the other only includes this area as part of a larger geographic range (R. octofasciata). Unfortunately, the ecology of these species has been poorly studied. This study sought to determine the ecological and morphological differences between these two closely related sympatric freshwater fishes. We hypothesized that R. octofasciata would exhibit greater ecological and morphological …

Temperature Effects On The Development Of The Axial Skeleton And Body Shape In Astyanax Mexicanus (Teleostei: Characidae), Joseph David Forberg

College of Science and Health Theses and Dissertations

Humans are causing large-scale changes in environmental conditions across the planet including in temperature. Changes in the environmental conditions can lead to phenotypic changes in ectotherms that affect adaptively important traits like body shape and the axial skeleton. Previous studies have shown that temperature changes during development significantly affects body shape and vertebral number in the Mexican tetra Astyanax mexicanus. How these changes arise early in development is not clear. In this study, I examine how changes in developmental temperature affect body shape in larval and juvenile fish, the order of ossification of elements of the axial skeleton, the size …

Characterization Of A Stenotrophomonas Maltophilia Bacteriophage, Edward Eshoo

College of Science and Health Theses and Dissertations

Stenotrophomonas maltophilia is a ubiquitous Gram-negative, multidrug resistant, opportunistic bacterial pathogen that causes various infections in humans. Recently, the use of bacteriophages as therapeutic agents, has gained interest as an alternative to traditional antibiotics. This thesis describes the isolation, purification, and characterization of S. maltophilia bacteriophage Bfi2 and discusses its activity against related, and often co-isolated, bacterial pathogens. Amplification of the phage resulted in clear, well-defined plaques and a titer of 1.73 ± 0.38 x 1011 PFU/ml. Bfi2 demonstrated the ability to lyse 55% of the S. maltophilia strains tested, suggesting that it has a moderate host range. However, the …

The Transcriptional Regulator Ctra Controls Gene Expression In Alphaproteobacteria Phages: Evidence For A Lytic Deferment Pathway, Elia Mascolo, Satish Adhikari, Steven M. Caruso, Tagide Decarvalho, Anna Folch Salvador, Joan Serra-Sagristà, Ry Young, Ivan Erill, Patrick D. Curtis

Faculty and Student Publications

Pilitropic and flagellotropic phages adsorb to bacterial pili and flagella. These phages have long been used to investigate multiple aspects of bacterial physiology, such as the cell cycle control in the Caulobacterales. Targeting cellular appendages for adsorption effectively constrains the population of infectable hosts, suggesting that phages may have developed strategies to maximize their infective yield. Brevundimonas phage vB_BsubS-Delta is a recently characterized pilitropic phage infecting the Alphaproteobacterium Brevundimonas subvibrioides. Like other Caulobacterales, B. subvibrioides divides asymmetrically and its cell cycle is governed by multiple transcriptional regulators, including the master regulator CtrA. Genomic characterization of phage vB_BsubS-Delta identified the presence …

Mechanisms Of Carbapenemase-Mediated Resistance Among High-Risk Pseudomonas Aeruginosa Lineages In Peru, Isabella A. Tickler, Juan Carlos Gomez De La Torre, Luis Alvarado, Anne E. Obradovich, Fred C. Tenover

Biology Faculty Publications

Objectives: Pseudomonas aeruginosa is one of the leading causes of healthcare-associated infections globally. High-risk carbapenemase-encoding P. aeruginosa clones are disseminating in many regions. The aim of this study was to learn more about the lineages and mechanisms of resistance of P. aeruginosa circulating in Peru.

Methods: A total of 141 carbapenemase-producing isolates recovered from hospitalized and ambulatory patients in Lima were sequenced and analyzed to infer their lineages through whole-genome sequence typing (wgST) and to identify their antimicrobial resistance genes.

Results: wgST identified nine sequence types (STs); ST111 and ST357 were the most frequently encountered (44.0% and 38.3%, respectively), followed …

Intermediates In Sars-Cov-2 Spike–Mediated Cell Entry, Tara C. Marcink, Thomas Kicmal, Emily Armbruster, Zhening Zhang, Gillian Zipursky, Kate L. Golub, Mohab Idris, Jonathan Khao, Jennifer Drew-Bear, Gael Mcgill, Tom Gallagher, Matteo Porotto, Amédée Des Georges, Anne Moscona

Advanced Science Research Center

SARS-CoV-2 cell entry is completed after viral spike (S) protein–mediated membrane fusion between viral and host cell membranes. Stable prefusion and postfusion S structures have been resolved by cryo–electron microscopy and cryo–electron tomography, but the refolding intermediates on the fusion pathway are transient and have not been examined. We used an antiviral lipopeptide entry inhibitor to arrest S protein refolding and thereby capture intermediates as S proteins interact with hACE2 and fusion-activating proteases on cell-derived target membranes. Cryo–electron tomography imaged both extended and partially folded intermediate states of S2, as well as a novel late-stage conformation on the pathway to …