Digital Commons Network^™

A Chromosome-Level Genome Assembly Of The Parasitoid Wasp, Cotesia Glomerata (Hymenoptera: Braconidae), Brendan J. Pinto, Jerome J. Weis, Tony Gamble, Paul J. Ode, Ryan Paul, Jennifer M. Zaspel

Biological Sciences Faculty Research and Publications

Hymenopterans make up about 20% of all animal species, but most are poorly known and lack high-quality genomic resources. One group of important, yet understudied hymenopterans are parasitoid wasps in the family Braconidae. Among this understudied group is the genus Cotesia, a clade of ~1,000 species routinely used in studies of physiology, ecology, biological control, and genetics. However, our ability to understand these organisms has been hindered by a lack of genomic resources. We helped bridge this gap by generating a high-quality genome assembly for the parasitoid wasp, Cotesia glomerata (Braconidae; Microgastrinae). We generated this assembly using multiple sequencing …

Microbial Find, Inform, And Test Model For Identifying Spatially Distributed Contamination Sources: Framework Foundation And Demonstration Of Ruminant Bacteroides Abundance In River Sediments, Corinne Wiesner-Friedman, Rachelle E. Beattie, Jill R. Stewart, Krassimira R. Hristova, Marc L. Serre

Biological Sciences Faculty Research and Publications

Microbial pollution in rivers poses known ecological and health risks, yet causal and mechanistic linkages to sources remain difficult to establish. Host-associated microbial source tracking (MST) markers help to assess the microbial risks by linking hosts to contamination but do not identify the source locations. Land-use regression (LUR) models have been used to screen the source locations using spatial predictors but could be improved by characterizing transport (i.e., hauling, decay overland, and downstream). We introduce the microbial Find, Inform, and Test (FIT) framework, which expands previous LUR approaches and develops novel spatial predictor models to characterize the transported contributions. We …

Experiences Of Undergraduates And Graduate Teaching Assistants In Biology Course-Based Undergraduate Research Experiences, Emma Crystal Goodwin

Dissertations and Theses

Evidence of positive student outcomes from course-based undergraduate research experiences (CUREs) has sparked implementation of CUREs in introductory biology laboratory courses, as one approach to boosting student engagement in research. In a CURE, students collaborate with other students and instructors on a research project, where they conduct novel scientific research that has relevance to a local or scientific community. However, previous research rarely considers that graduate teaching assistants (GTAs) often teach introductory labs. The classroom role of GTAs expands in a CURE--they no longer need to simply teach a lab class, but also to serve as research mentors. GTAs, who …

Thanatechnology And The Living Dead: New Concepts In Digital Transformation And Human-Computer Interaction, Vural Özdemir, Simon Springer, Arif Ylldlrlm, Sehmus Biçer, Asllgül Kendirci, Semra Sardaş, Hakan Klllç, Nezih Hekim, Tanja Kunej, Kazlm Yalçln Arga, Kevin Dzobo, Wei Wang, Marius Geanta, Angela Brand, Mustafa Bayram

Research outputs 2014 to 2021

In a digital society, shall we be the authors of our own experience, not only during our lifetime but also after we die? We ask this question because dying and bereavement have become even harder, and much less private, in the digital age. New big data-driven digital industries and technologies are on the rise, with promises of interactive 3D avatars and storage of digital memories of the deceased, so they can continue to exist online as the "living dead"in a digital afterlife. Famous rock and roll icons like Roy Orbison, Frank Zappa, Ronnie James Dio, and Amy Winehouse have famously …

Systematics Of Eastern North American Podothrombium (Parasitengona: Podothrombiidae), Kelsey Lynn Cline

Graduate Theses and Dissertations

Velvet mites of the genus Podothrombium Berlese, 1910 are found worldwide with only two described species known from North America, both occurring on the west coast. The present study describes five new species occurring in the east, from both larval and post-larval stages. Species hypotheses are supported with morphology and analysis of mitochondrial (barcoding region of COI) and nuclear genes (D2-3 expansion regions of 28S rDNA). Specimens are incorporated from the Barcode of Life Data Systems (BOLD), allowing our dataset to span most of North America. Therefore, we were able to raise the number of Podothrombium in North America from …

Comparative Transcriptome Analysis Reveals Genetic Mechanisms Of Sugarcane Aphid Resistance In Grain Sorghum, Desalegn D. Serba, Xiaoxi Meng, James Schnable, Elfadil Bashir, J P. Michaud, P V. Vara Prasad, Ramasamy Perumal

Department of Agronomy and Horticulture: Faculty Publications

The sugarcane aphid, Melanaphis sacchari (Zehntner) (Hemiptera: Aphididae) (SCA), has become a major pest of grain sorghum since its appearance in the USA. Several grain sorghum parental lines are moderately resistant to the SCA. However, the molecular and genetic mechanisms underlying this resistance are poorly understood, which has constrained breeding for improved resistance. RNA-Seq was used to conduct transcriptomics analysis on a moderately resistant genotype (TAM428) and a susceptible genotype (Tx2737) to elucidate the molecular mechanisms underlying resistance. Differential expression analysis revealed differences in transcriptomic profile between the two genotypes at multiple time points after infestation by SCA. Six gene …

Spatial Ecology And Stable Isotope Composition Of Cetaceans In The Bohol Sea, Edna Sabater

Theses and Dissertations

Studies on Philippine cetaceans (i.e., whales and dolphins) began in the early 1980s, and have resulted in the location and identification of species in Philippine waters. However, the population estimates of most of the cetacean species are uncertain, which is important in evaluating whether the populations are stable, decreasing, or increasing in relation to potential threats and conservation measures. I conducted line-transect surveys between 2010 and 2019 in the Bohol Sea, Philippines. A total of 2009.5 km survey efforts were made, which covered an area of 8041 km2 throughout the 5-year survey period. Distance sampling methods estimated the total abundance …

Contemporary Challenges And Opportunities For The Management Of Bird Damage At Field Crop Establishment, Christophe Sausse, Alice Baux, Michel Bertrand, Elsa Bonnaud, Sonia Canavelli, Alexandra Destrez, Page E. Klug, Lourdes Olivera, Ethel Rodriguez, Guilllermo Tellechea, Sebastian Zuil

United States Department of Agriculture Wildlife Services: Staff Publications

Bird damage, from sowing to crop establishment, is an important issue for farmers in many parts of the world. However, reliable and cost-effective solutions remain elusive because management tools and research on the subject are limited. The spatial variability of damage across landscapes and the adaptative behaviour of birds create further challenges. Additionally, the issue must be tackled at the landscape scale and involve a variety of stakeholders with conflicting interests and objectives. We summarize some of the challenges and opportunities identified to face these difficulties and address four major research directions for operational solutions including 1) crop damage assessment, …

Biological Control And Integrated Rangeland Weed Management, Linda M. Wilson

IGC Proceedings (1977-2023)

No abstract provided.

Evaluation Of Somatic Mutations In Solid Metastatic Pan-Cancer Patients, Moom Roosan, Isa Mambetsariev, Rebecca Pharaon, Jeremy Fricke, Angel R. Baroz, Joseph Chao, Chen Chen, Mohd W. Nasser, Ramakanth Chirravuri-Venkata, Maneesh Jain, Lynette Smith, Susan E. Yost, Karen L. Reckamp, Raju Pillai, Leonidas Arvanitis, Michelle Afkhami, Edward W. Wang, Vincent Chung, Mihaela Cristea, Marwan Fakih, Marianna Koczywas, Erminia Massarelli, Joanne Mortimer, Yuan Yuan, Surinder K. Batra, Sumanta Pal, Ravi Salgia

Pharmacy Faculty Articles and Research

Metastasis continues to be the primary cause of all cancer-related deaths despite the recent advancements in cancer treatments. To evaluate the role of mutations in overall survival (OS) and treatment outcomes, we analyzed 957 metastatic patients with seven major cancer types who had available molecular testing results with a FoundationOne CDx^® panel. The most prevalent genes with somatic mutations were TP53, KRAS, APC, and LRP1B. In this analysis, these genes had mutation frequencies higher than in publicly available datasets. We identified that the somatic mutations were seven mutually exclusive gene pairs and an additional fifty-two co-occurring gene pairs. Mutations …

Development Of A Split Green Fluorescent Protein Reporting System For Angiogenin, Phan QuỳNh ChâU Lê

Lawrence University Honors Projects

Angiogenin (ANG) is a secreted protein that holds important implications in the growth and survival for a variety of cell types—from healthy endothelial or neuronal cells, to diseased cancer cells. Currently, we lack a complete understanding of ANG’s mechanism of action. Our work aims to develop a functional fluorescence-based reporting system to study ANG internalization activity in cancer cells. Specifically, we utilize a split green fluorescent protein (split GFP) system, in which the 11th strand of the GFP molecule (GFP11) is attached to ANG, while the remaining non-fluorescent GFP1-10 fragment is expressed in our target HeLaGFP1-10 cell line. The reconstitution …

Walking Velocity And Estimated Distance Of The Armored Scale Crawler Rhizaspidiotus Donacis, A Biological Control Agent For Arundo Donax, Joshua A. Villarreal, Alexis Racelis, John A. Goolsby

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

Arundo scale, Rhizaspidiotus donacis (Leonardi) (Hemiptera: Diaspididae), is an armored scale biological control agent established on the invasive weed, Arundo donax L. (Poaceae; Arundinoideae) at several locations along the Rio Grande in Texas (Goolsby et. al. 2009, Moran and Goolsby 2010, Goolsby et al. 2011, Villarreal et al. 2016). The arundo scale is having significant impact on the target weed in areas where it established (Goolsby and Moran 2019), and no non-target plant use was observed (Goolsby et al. 2020). Armored scale crawlers usually live for less than a day and …

Modeling And Analysis Of Intracellular Signaling Networks And Cellular Decisions, Mustafa Ozen

Dissertations

Developing molecular network analysis methods is important due to their applications on complex biological systems such as target discovery, development of drugs, discovering drug effects, and finding treatments for many complex diseases, e.g., cancer, autoimmune, and mental disorders. An example of analysis techniques is the fault diagnosis analysis, in which the purpose is to quantify how much vulnerable the entire network is to dysfunction of one or multiple molecules. Such analysis can be done after proper network models are implemented, trained, and tested against the experimental data. In this dissertation, a Boolean modeling framework is implemented and methods to train …

Antioxidant And Antibacterial Activities Of Different Polar Parts From Manilkara Zapota Leaves, Ma Fei-Yue, Zhang Ming, Li Ya, Du Li-Qing, Shuai Xi-Xiang

Food and Machinery

In order to investigate the antioxidant and antibacterial activity of different polar parts (petroleum ether part, ethyl acetate part, n-butanol part and water part) from Manilkara zapota leaves. The DPPH radical-scavenging assay, ABTS radical-scavenging assay and FRAP antioxidant capacity assay were carried out. And the antibacterial effects of different polar parts from Manilkara zapota leaves against Bacilus subtillis, Escherichia coli and Staphylococcus aureus were studied. The results showed that the extracts obtained from ethyl acetate extraction had the highest antioxidant activities; the IC₅₀ of the DPPH radical-scavenging and ABTS radical-scavenging were (0.019±0.010) mg/mL, and the Trolox Equivalent Antioxidant Capacity …

Advancing The Preclinical Development Of Secondary Metabolites From Cacospongia Mycofijiensis For The Treatment Of Cancer, Joseph Morris

Natural Sciences and Mathematics | Biological Sciences Master's Theses

The marine sponge Cacospongia mycofijiensis from the Indo-Pacific has proven to be a source of structurally diverse secondary metabolites that are biologically active against a variety of distinct targets. Current interest in the secondary metabolites of C. mycofijiensis largely stems from a) their potent and preferential cytotoxicity for cancer cell lines versus normal cells, making many of them promising leads as cancer therapeutics and b) the novel mechanisms of action responsible for their impressive cytotoxicity. However, limited compound availability has resulted in a paucity of studies aimed at advancing the preclinical development of these secondary metabolites from C. mycofijiensis for …

Vitamin B12 Deficiency Does Not Stimulate Amyloid-Beta Toxicity In A Ceanorhabditis Elegans Model Of Alzheimer’S Disease, Opeyemi F. Showemimo

Electronic Theses and Dissertations

Alzheimer’s disease (AD) is symptomized by amyloid-beta plaques in the brain and accounts for more than 65 percent of dementia cases. Vitamin B12 (cobalamin) deficiency can result in similar cognitive impairment and roughly 15% of the elderly are vitamin B12 deficient. Vitamin B12 deficiency results in the accumulation of toxic methylmalonic acid and homocysteine. Hyperhomocysteinemia is a strong risk factor for AD. To test if vitamin B12 deficiency stimulates amyloid-beta toxicity, Caenorhabditis elegans expressing amyloid-beta in muscle were fed either vitamin B12-deficient OP50-1 or vitamin B12-rich HT115(DE3) E. coli bacteria. Increased amyloid-beta toxicity was found in worms fed the …

Machine Learning Models For Deciphering Regulatory Mechanisms And Morphological Variations In Cancer, Saman Farahmand

Graduate Doctoral Dissertations

The exponential growth of multi-omics biological datasets is resulting in an emerging paradigm shift in fundamental biological research. In recent years, imaging and transcriptomics datasets are increasingly incorporated into biological studies, pushing biology further into the domain of data-intensive-sciences. New approaches and tools from statistics, computer science, and data engineering are profoundly influencing biological research. Harnessing this ever-growing deluge of multi-omics biological data requires the development of novel and creative computational approaches. In parallel, fundamental research in data sciences and Artificial Intelligence (AI) has advanced tremendously, allowing the scientific community to generate a massive amount of knowledge from data. Advances …

Analyzing The Effects Of E-Hook Peptides On Kinesin-1, Ashton Ward Murrah, Baylee Hope Howard

Honors Theses

Cancer is the second leading cause of death in the United States. Cancerous growth is a result of oncogenes, or mutated genes that increase the rate of cell division in an uncontrolled manner. Cell division, which consists of mitosis and cytokinesis phases, is dependent upon the active movement of kinesin motor proteins along microtubules to rearrange the cytoskeleton for equitable distribution of genetic material to daughter cells. As kinesins are vital to this process, if we could prevent kinesin from binding to the microtubules, cell division would cease.

The goal of this study is to develop a method to prevent …

Total Synthesis And Biological Evaluation Of Siderophores: Key To Develop Iron Chelators And Tackle Antibiotic Delivery To Gram-Negative Bacteria, .Pratibha Desman

Research Symposium

Siderophores are molecules that act as iron carriers in bacteria. As they sequester iron from the environment and penetrate bacterial cells through active transporters, they can bypass the porin-mediated transportation in Gram-negative bacteria. Therefore, conjugating antibiotics that lacks the ability to pass through porins to siderophores and forming “sideromycins” has been proven as a way to battle antibiotic resistance in Gram-negative bacteria. My research will focus on synthesizing two siderophores, catenulobactin B and talarazine A as well as their analogs and exploring their potential to synthesize sideromycins. These molecules will be synthesized in a modular way and their cytotoxicity, ability …

Herbal Extracts As Neuroprotective Agents In An In-Vitro Model Of Aluminum Neurotoxicity, Nada Ezzelarab

Theses and Dissertations

Background: Aluminum toxicity due to environmental or industrial exposure, medical applications, or from cooking utensils is a serious medical problem. The current study aims to investigate three herbal extracts: pomegranate peel extract, Achillea fragrantissima extract, and papaya fruit extract to combat this neurotoxicity.

Methods: Chemical characterization of the three extracts were evaluated using HPLC MS while their neuroprotective activity was assayed using MTT assay on SHSY5Y cells and nitric oxide levels.

Results: Using HPLC-MS chromatography, we have identified twenty-one compounds in the hydro-alcoholic Achillea fragrantissima, seventeen were determined in the pomegranate peel, eleven were assessed in the Carica papaya …

Classification Of Molecular Subtypes Of High-Grade Serous Ovarian Cancer By Maldi-Imaging., Wanja Kassuhn, Oliver Klein, Silvia Darb-Esfahani, Hedwig Lammert, Sylwia Handzik, Eliane T Taube, Wolfgang D Schmitt, Carlotta Keunecke, David Horst, Felix Dreher, Joshy George, David D Bowtell, Oliver Dorigo, Michael Hummel, Jalid Sehouli, Nils Blüthgen, Hagen Kulbe, Elena I Braicu

Faculty Research 2021

Despite the correlation of clinical outcome and molecular subtypes of high-grade serous ovarian cancer (HGSOC), contemporary gene expression signatures have not been implemented in clinical practice to stratify patients for targeted therapy. Hence, we aimed to examine the potential of unsupervised matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) to stratify patients who might benefit from targeted therapeutic strategies. Molecular subtyping of paraffin-embedded tissue samples from 279 HGSOC patients was performed by NanoString analysis (ground truth labeling). Next, we applied MALDI-IMS paired with machine-learning algorithms to identify distinct mass profiles on the same paraffin-embedded tissue sections and distinguish HGSOC subtypes by …

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

Centre for Regenerative Medicine & Stem Cell Research

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

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

School of Medicine Publications

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

Bone Microenvironmental Control Of Skeletal Malignancy, Chen Hao Lo

USF Tampa Graduate Theses and Dissertations

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

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

Life Sciences Faculty Research

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

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

Publications and Research

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

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

McKelvey School of Engineering Graduate Student Theses & Dissertations

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

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

Arts & Sciences Graduate Student Theses and Dissertations

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

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

Turkish Journal of Zoology

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

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

Electronic Theses and Dissertations

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