Molecular Biology Commons^™

Presence Of The Hppd Inhibitor Sensitive 1 Gene And AlsS653n Mutation In Weedy Oryza Sativa Sensitive To Benzobicyclon, Chad Brabham, Jason K. Norsworthy, Fidel Gonzalez-Torralva

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Benzobicyclon has shown varying results in controlling weedy rice, including those with imidazolinone (IMI) resistance. Tolerance to benzobicyclon in cultivated japonica rice, but not indica or aus-like cultivars, is conferred by a fully functional HPPD Inhibitor Sensitive 1 (HIS1) gene. Herein, a diagnostic Kompetitive Allele Specific PCR (KASP) assay was developed to predict the HIS1 genotype of weedy rice plants from 37 accessions and correlated to their response to benzobicyclon in the field. Two-thirds of the 693 weedy rice plants screened were tolerant to benzobicyclon (371 g ai ha⁻¹, SC formulation) at 30 days after treatment (DAT). …

Effect Of Ceratonia Siliqua And Cucurbita Pepo Seeds Extracts On Spermatogenesis In Male Mice, Nour Elakhdar, Roweida Bawab, Jamilah Borjac

BAU Journal - Health and Wellbeing

Worldwide, a percentage close to 50% of infertility cases is due to male-related problems including spermatogenesis defects, the process that determines sperm cells’ number and thus male fertility. Spermatogenesis is controlled by different hormones including the luteinizing hormone (LH), the follicle stimulation hormone (FSH), and testosterone. LH stimulates the Leydig cells to synthesize testosterone. FSH acts synergistically with testosterone. There is no current efficient treatment for spermatogenesis defects and people are reverting to natural remedies among which are the pumpkin and carob seeds. This study aims to evaluate the effects of pumpkin and carob seeds’ aqueous extracts on spermatogenesis and …

New Mechanisms That Regulate Dna Double-Strand Break-Induced Gene Silencing And Genome Integrity, Dante Francis Deascanis

USF Tampa Graduate Theses and Dissertations

Proliferating cells are constantly threatened by genotoxic stressors that can potentially lead to genomic instability. Breaks in the DNA, namely double-strand breaks, are detrimental sources of damage that must be repaired to maintain genomic integrity and prevent potential tumorigenesis. Here we discuss a gene silencing mechanism flanking damaged chromatin. Gene silencing and transcriptional repression at damaged DNA are necessary to prevent potential genomic aberrations from occurring through conflicts with the DNA repair machinery. BMI1, a core polycomb protein in the polycomb repressive complex 1 (PRC1) has been known to play a role in gene silencing at damaged chromatin. However, the …

From Regulation Of Secondary Metabolites To Increased Virulence Under Sublethal Dosage Of Antibiotics: An Unprecedented Role Of Global Regulator, Mftr, In Burkholderia Thailandensis, Sudarshan Singh Thapa

LSU Doctoral Dissertations

The rise of multi-drug resistant bacteria combined with a decreasing pool of effective antibiotics has placed an increasing need for the development of novel antibiotics. Bacterial natural products or secondary metabolites have been the greatest source for development of novel antibiotics. The genus Burkholderia has recently emerged as a source of promising compounds with antibacterial, antifungal, and anti-cancer activities. Bacterial secondary metabolites provide added advantage to bacteria under stressful environments such as during host infection, evading predators or nutrient deficient conditions. However, genes involved in synthesis of these novel compounds remain silent under normal laboratory growth, creating a hurdle in …

Fine-Tuning Of Alanyl-Trna Synthetase Quality Control Alleviates Global Dysregulation Of The Proteome, Paul Kelly, Arundhati Kavoor, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

One integral step in the transition from a nucleic acid encoded-genome to functional proteins is the aminoacylation of tRNA molecules. To perform this activity, aminoacyl-tRNA synthetases (aaRSs) activate free amino acids in the cell forming an aminoacyl-adenylate before transferring the amino acid on to its cognate tRNA. These newly formed aminoacyl-tRNA (aa-tRNA) can then be used by the ribosome during mRNA decoding. In Escherichia coli, there are twenty aaRSs encoded in the genome, each of which corresponds to one of the twenty proteinogenic amino acids used in translation. Given the shared chemicophysical properties of many amino acids, aaRSs have …

Role Of Ceramide-1 Phosphate In Regulation Of Sphingolipid And Eicosanoid Metabolism In Lung Epithelial Cells, Brittany A. Dudley

USF Tampa Graduate Theses and Dissertations

Ceramide 1-Phosphate (C1P) is a sphingolipid metabolite which plays a large role in inflammation, cell survival and proliferation¹. C1P is known to have both pro- and anti-apoptotic roles in lung cancer cells, governed by ceramide kinase (CERK), upstream of precursor ceramide (Cer)². Previous work reveals C1P serves as the liaison between sphingolipid and eicosanoid synthesis, by decreasing the dissociation rate of group IVA cytosolic PLA₂ (cPLA_2α) from the Golgi membrane, C1P directly activates this phospholipase for downstream eicosanoid synthesis and subsequent inflammatory response³. CERK has been discovered to modulate eicosanoid synthesis, …

Graphene-Based Electrochemical Aptasensor For The Detection Of Salmonella Typhimurium, Shalini Muniandy

Student Works (2020-2029)

Recent foodborne outbreaks in multiple locations necessitate the continuous development of highly sensitive and specific biosensors that offer rapid and sensitive detection of foodborne pathogens. The emergence of electrochemical aptasensor which is a compact analytical device with a combination of an aptamer as the biorecognition element integrated on the transducer surface created a breakthrough in the detection of foodborne bacterial pathogens. Graphene has emerged as a promising nanomaterial for reliable detection of pathogenic bacteria due to its exceptional properties such as high electrical conductivity, large surface to volume ratio, high mechanical strength and its unique interactions with DNA bases of …

A Label-Free Assay For Aminoacylation Of Trna, Howard Gamper, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

Aminoacylation of tRNA generates an aminoacyl-tRNA (aa-tRNA) that is active for protein synthesis on the ribosome. Quantification of aminoacylation of tRNA is critical to understand the mechanism of specificity and the flux of the aa-tRNA into the protein synthesis machinery, which determines the rate of cell growth. Traditional assays for the quantification of tRNA aminoacylation involve radioactivity, either with a radioactive amino acid or with a [3'-32P]-labeled tRNA. We describe here a label-free assay that monitors aminoacylation by biotinylation-streptavidin (SA) conjugation to the α-amine or the α-imine of the aminoacyl group on the aa-tRNA. The conjugated aa-tRNA product is readily …

Two And Three-Dimensional Radiographic Imaging Of Contrast Agents In Heterogeneous Live Cell Media To Understand Contrast-Induced Toxicity, Fahaneda Hassan, Aldona Gjoni, Subhendra Sarkar

Publications and Research

Radiographic imaging was done using low and high energy radiography equipment. The test hypothesis that macromolecular aggregation changes sample noise in imaging samples for optical imaging methods. Inorganic complexes scatter radiation at the molecular level and may increase the sample noise locally. At high and low photon energies in various x-ray machines, sample and background noise were gathered and compared with those from mammography systems from mammography researchers. The samples with high macromolecular aggregates were prepared using various animal cell compositions and imaged under different conditions that produced different macromolecular dynamics within the samples and thus different image-based sample noise. …

Minimal Structural Elements Required For Midline Repulsive Signaling And Regulation Of Drosophila Robo1, Haley E. Brown, Timonthy A. Evans

Biological Sciences Faculty Publications and Presentations

The Roundabout (Robo) family of axon guidance receptors has a conserved ectodomain arrangement of five immunoglobulin-like (Ig) domains plus three fibronectin type III (Fn) repeats. Based on the strong evolutionary conservation of this domain structure among Robo receptors, as well as in vitro structural and domain-domain interaction studies of Robo family members, this ectodomain arrangement is predicted to be important for Robo receptor signaling in response to Slit ligands. Here, we define the minimal ectodomain structure required for Slit binding and midline repulsive signaling in vivo by Drosophila Robo1. We find that the majority of the Robo1 ectodomain is dispensable …

Microbiota Analysis Of Chickens Raised Under Stressed Conditions, Rabindra Kumar Mandal, Tieshan Jiang, Robert Wideman Jr, Troy Lohrmann, Young Min Kwon

Poultry Science Faculty Publications and Presentations

A substantial progress has been made toward understanding stress-associated gut and extraintestinal microbiota. However, a comprehensive understanding of the extraintestinal microbiota of chickens raised under stressed conditions is lacking. In this study, chickens were raised on a wire-floor model to induce stress, and the microbiota in the gut (ceca) and extraintestinal sites (blood, femur, and tibia) were characterized at different ages (1, 17, and 56 days) using 16S rRNA gene microbiota profiling. Open reference OTU picking showed extraintestinal sites had a significantly higher number of unassigned OTUs compared to ceca across all ages of chickens. Extraintestinal sites of all ages, …

Sonoporation-Mediated Loading Of Trehalose In Cells For Cryopreservation., Charles W. Shaffer Iv, David F. Grimm, Michael A. Menze, Jonathan A. Kopechek

Undergraduate Research Events

Trehalose, a non-reducing disaccharide, is present in many microorganisms and metazoans. In these organisms, trehalose acts as a stress protectant and helps preserve lipid membranes of cells during states of desiccation and freezing. Trehalose is required on both sides of the cell membrane to achieve a significant cryoprotective effect. Specific loading methods for trehalose are required since this sugar is impermeant to mammalian cells. Trehalose loading in mammalian cells has been achieved by fluid-phase endocytosis and genetic modification for the expression of trehalose transporters, however cryoprotective outcomes are unable to compete with established methods of cryopreservation for mammalian cells. Sonoporation …

Tdp-43 Mediated Blood-Brain Barrier Permeability And Leukocyte Infiltration Promote Neurodegeneration In A Low-Grade Systemic Inflammation Mouse Model, Frank Zamudio, Anjanet R. Loon, Shayna Smeltzer, Khawla Benyamine, Nanda K. Navalpur Shanmugam, Nicholas J. F. Stewart, Daniel C. Lee, Kevin Nash, Maj-Linda B. Selenica

Sanders-Brown Center on Aging Faculty Publications

BACKGROUND: Neuronal cytoplasmic inclusions containing TAR DNA-binding protein 43 (TDP-43) are a neuropathological feature of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's Disease (AD). Emerging evidence also indicates that systemic inflammation may be a contributor to the pathology progression of these neurodegenerative diseases.

METHODS: To investigate the role of systemic inflammation in the progression of neuronal TDP-43 pathology, AAV9 particles driven by the UCHL1 promoter were delivered to the frontal cortex of wild-type aged mice via intracranial injections to overexpress TDP-43 or green fluorescent protein (GFP) in corticospinal motor neurons. Animals were then subjected …

Engineering And Application Of A Biosensor With Focused Ligand Specificity, Dennis Della Corte, Hugo L. Van Beek, Falk Syberg, Marcus Schallmey, Felix Tobola, Kai U. Cormann, Christine Schlicker, Philipp T. Baumann, Karin Krumbach, Sascha Sokolowsky, Connor J. Morris, Alexander Grünberger

Faculty Publications

Cell factories converting bio-based precursors to chemicals present an attractive avenue to a sustainable economy, yet screening of genetically diverse strain libraries to identify the best-performing whole-cell biocatalysts is a low-throughput endeavor. For this reason, transcriptional biosensors attract attention as they allow the screening of vast libraries when used in combination with fluorescence-activated cell sorting (FACS). However, broad ligand specificity of transcriptional regulators (TRs) often prohibits the development of such ultra-high-throughput screens. Here, we solve the structure of the TR LysG of Corynebacterium glutamicum, which detects all three basic amino acids. Based on this information, we follow a semi-rational engineering …

Retrieving Functional Pathways Of Biomolecules From Single-Particle Snapshots, Ali Dashti, Ghoncheh Mashayekhi, Mrinal Shekhar, Danya Ben Hail, Salah Salah, Peter Schwander, Amedee Des Georges, Abhishek Singharoy, Joachim Frank, Abbas Ourmazd

Publications and Research

A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the …

Current Scenario Of Covid-19 With Epidemiological And Phylogenetic Analysis Of Pakistani Coronavirus: A Review, Asma Altaf, Wafa Iqbal, Sidra Younis, Farah Deeba

Journal of Bioresource Management

A novel corona virus named as 2019 n-CoV was identified to be the actual cause of an outbreak of respiratory illness in Wuhan, China beginning in late December 2019. This respiratory disease was named as COVID-19 by WHO. There are many countries affected by COVID-19 including Pakistan. In this review we have provided a brief introduction of COVID-19 and discussed epidemiological and phylogenetic analysis of Pakistani novel corona virus strain. Our epidemiological analysis of data till 16^th May 2020 showed rapidly increasing number of new cases, while at the same time a higher recovery rate than number of deaths …

Electronic-Cigarette Vehicles And Flavoring Affect Lung Function And Immune Responses In A Murine Model, Brittany N. Szafran, Rakeysha Pinkston, Zakia Perveen, Matthew K. Ross, Timothy Morgan, Daniel B. Paulsen, Arthur L. Penn, Barbara L. F. Kaplan, Alexandra Noel

Faculty Publications

The use of electronic nicotine delivery systems (ENDS), also known as electronic-cigarettes (e-cigs), has raised serious public health concerns, especially in light of the 2019 outbreak of e-cig or vaping product use-associated acute lung injury (EVALI). While these cases have mostly been linked to ENDS that contain vitamin E acetate, there is limited research that has focused on the chronic pulmonary effects of the delivery vehicles (i.e., without nicotine and flavoring). Thus, we investigated lung function and immune responses in a mouse model following exposure to the nearly ubiquitous e-cig delivery vehicles, vegetable glycerin (VG) and propylene glycol (PG), used …

Pollen-Mediated Gene Flow And Transfer Of Resistance Alleles From Herbicide-Resistant Broadleaf Weeds, Amit J. Jhala, Jason K. Norsworthy, Zahoor A. Ganie, Lynn M. Sosnoskie, Hugh J. Beckie, Carol A. Mallory-Smith, Jun Liu, Wei Wei, Junming Wang, David E. Stoltenberg

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Pollen-mediated gene flow (PMGF) refers to the transfer of genetic information (alleles) from one plant to another compatible plant. With the evolution of herbicide-resistant (HR) weeds, PMGF plays an important role in the transfer of resistance alleles from HR to susceptible weeds; however, little attention is given to this topic. The objective of this work was to review reproductive biology, PMGF studies, and interspecific hybridization, as well as potential for herbicide resistance alleles to transfer in the economically important broadleaf weeds including common lambsquarters, giant ragweed, horseweed, kochia, Palmer amaranth, and waterhemp. The PMGF studies involving these species reveal that …

Mesenchymal Stem Cells And Their Extracellular Vesicles: A Potential Game Changer For The Covid-19 Crisis, Dina H. Kassem, Mohamed M. Kamal

Pharmacy

Corona virus disease 2019 (COVID-19) is a global public health crisis. The high infectivity of the disease even from non-symptomatic infected patients, together with the lack of a definitive cure or preventive measures are all responsible for disease outbreak. The severity of COVID-19 seems to be mostly dependent on the patients’ own immune response. The over-activation of the immune system in an attempt to kill the virus, can cause a “cytokine storm” which in turn can induce acute respiratory distress syndrome (ARDS), as well as multi-organ damage, and ultimately may lead to death. Thus, harnessing the immunomodulatory properties of mesenchymal …

Defining Relictual Biodiversity: Conservation Units In Speckled Dace (Leuciscidae: Rhinichthys Osculus) Of The Greater Death Valley Ecosystem, Steven M. Mussmann, Marlis R. Douglas, David D. Oakey, Michael E. Douglas

Biological Sciences Faculty Publications and Presentations

The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species–population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units-Canada); MUs (management units); SSP (subspecies); ESUs (Evolutionarily Significant Units); and UIEUs (uniquely identified evolutionary units)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates …