Open Access. Powered by Scholars. Published by Universities.®
Biochemistry, Biophysics, and Structural Biology Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Biochemistry (6982)
- Molecular Biology (4529)
- Medicine and Health Sciences (3209)
- Physical Sciences and Mathematics (2756)
- Cell and Developmental Biology (2132)
-
- Chemistry (2099)
- Biology (1787)
- Medical Sciences (1455)
- Cell Biology (1208)
- Genetics and Genomics (1105)
- Microbiology (1031)
- Medical Specialties (1011)
- Biotechnology (902)
- Biophysics (861)
- Other Biochemistry, Biophysics, and Structural Biology (792)
- Immunology and Infectious Disease (778)
- Chemicals and Drugs (603)
- Diseases (583)
- Structural Biology (582)
- Engineering (554)
- Physiology (493)
- Genetics (477)
- Bioinformatics (453)
- Cancer Biology (392)
- Plant Sciences (384)
- Veterinary Medicine (381)
- Molecular Genetics (375)
- Neuroscience and Neurobiology (362)
- Institution
-
- University of Nebraska - Lincoln (1329)
- The Texas Medical Center Library (762)
- University of Kentucky (654)
- Old Dominion University (576)
- University of Arkansas, Fayetteville (421)
-
- City University of New York (CUNY) (420)
- Brigham Young University (348)
- University of South Florida (342)
- Wayne State University (319)
- Virginia Commonwealth University (278)
- Utah State University (251)
- Technological University Dublin (213)
- University of Central Florida (198)
- University at Albany, State University of New York (193)
- Loyola University Chicago (187)
- University of South Carolina (180)
- University of Texas at El Paso (172)
- University of Nevada, Las Vegas (170)
- Purdue University (161)
- University of the Pacific (158)
- Chapman University (155)
- Dartmouth College (150)
- University of Montana (148)
- Aga Khan University (135)
- University of Nebraska Medical Center (133)
- Rowan University (130)
- Himmelfarb Health Sciences Library, The George Washington University (126)
- University of Denver (124)
- California Polytechnic State University, San Luis Obispo (115)
- Wright State University (115)
- Keyword
-
- Humans (499)
- Animals (382)
- Mice (235)
- Biochemistry (229)
- Cancer (216)
-
- RNA (158)
- Apoptosis (146)
- DNA (139)
- Female (137)
- Chemistry (131)
- Biological sciences (130)
- Metabolism (127)
- Male (119)
- Mitochondria (114)
- Bioinformatics (107)
- Genetics (104)
- Protein (99)
- Biology (98)
- Inflammation (96)
- Proteins (95)
- Pure sciences (92)
- Proteomics (88)
- Phosphorylation (83)
- Biological Sciences (82)
- Breast cancer (80)
- College of Natural Science and Mathematics (80)
- Oxidative stress (80)
- Transcription (78)
- Mutation (77)
- Gene expression (76)
- Publication Year
- Publication
-
- Theses and Dissertations (662)
- Department of Biochemistry: Faculty Publications (592)
- Faculty, Staff and Students Publications (543)
- Electronic Theses and Dissertations (487)
- School of Veterinary and Biomedical Sciences: Faculty Publications (330)
-
- USF Tampa Graduate Theses and Dissertations (278)
- Graduate Theses and Dissertations (244)
- Faculty Publications (235)
- Chemistry and Biochemistry Faculty Publications (213)
- Wayne State University Dissertations (213)
- Dissertations, Theses, and Capstone Projects (210)
- Dissertations (207)
- Dissertations and Theses (Open Access) (206)
- Molecular and Cellular Biochemistry Faculty Publications (206)
- Honors Theses (191)
- Legacy Theses & Dissertations (2009 - 2024) (178)
- Chemistry Faculty Publications (176)
- Articles (141)
- Publications and Research (130)
- Open Access Theses & Dissertations (125)
- Department of Biological & Biomedical Sciences (121)
- Chemistry & Biochemistry Theses & Dissertations (119)
- Dartmouth Scholarship (114)
- Theses & Dissertations (112)
- Vadim Gladyshev Publications (110)
- Biology, Chemistry, and Environmental Sciences Faculty Articles and Research (105)
- Markey Cancer Center Faculty Publications (103)
- Biochemistry and Molecular Medicine Faculty Publications (102)
- All Graduate Theses and Dissertations, Spring 1920 to Summer 2023 (101)
- Loma Linda University Electronic Theses, Dissertations & Projects (99)
- Publication Type
- File Type
Articles 211 - 240 of 13689
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Characterization Of Ru(Ii) Polypyridyl Photosensitizers Bound To Tio2 Supports Through A New Covalent Metal-Ester Bonding Motif, D. M. S. C. Dissanayake, Christopher T. Lebarron, Laura C. Maybach, Joseph J. Kuchta Iii, Seyyedamirhossein Hosseini, Aaron K. Vannucci
Characterization Of Ru(Ii) Polypyridyl Photosensitizers Bound To Tio2 Supports Through A New Covalent Metal-Ester Bonding Motif, D. M. S. C. Dissanayake, Christopher T. Lebarron, Laura C. Maybach, Joseph J. Kuchta Iii, Seyyedamirhossein Hosseini, Aaron K. Vannucci
Faculty Publications
The development of photoelectrochemical (PEC) devices involves the attachment of molecular photosensitizers onto solid supports. Particularly significant to this work are PECs that rely on ruthenium-based photosensitizers on high band gap metal oxide (MOx) supports. In this study, we have explored a new ester binding motif (MOx-ester) to covalently attach a ruthenium polypyridyl photosensitizer to TiO2. This new MOx-ester photoanode is compared to the traditional photoanodes that utilize acid/base binding groups to attach the molecular Ru sensitizers to TiO2. The new MOx-ester binding motif is characterized by cyclic voltammetry UV-Vis, solid state 13C NMR, and …
An Antioxidant Cocktail Of Tert-Butylhydroquinone And A Manganese Porphyrin Induces Toxic Levels Of Oxidative Stress In Cancer Cells, Sandra Tamarin, Hannah Jung, Joseph Lamorte, Laura Biesterveld, Gabriel Piñero, Grace Turchetta, Molly Myers, Rebecca Oberley-Deegan, Aimee Eggler
An Antioxidant Cocktail Of Tert-Butylhydroquinone And A Manganese Porphyrin Induces Toxic Levels Of Oxidative Stress In Cancer Cells, Sandra Tamarin, Hannah Jung, Joseph Lamorte, Laura Biesterveld, Gabriel Piñero, Grace Turchetta, Molly Myers, Rebecca Oberley-Deegan, Aimee Eggler
Student Papers, Posters & Projects
Despite significant advancement in cancer treatments, therapies with minimal toxicity to healthy cells are still limited. One targetable weakness of cancer cells is their sensitivity to oxidative stress. We find that the combination of two antioxidants—the common food additive tert-butylhydroquinone (tBHQ) and a manganese porphyrin in clinical trials, MnTnBuOE-2-PyP5+ (MnBuOE)—increases oxidative stress and causes apoptotic death in several cancer cell lines, but not in mouse primary fibroblasts. Investigating the mechanism of cell death, MnBuOE is observed to catalyze the oxidation of tBHQ, producing the electrophilic quinone tert-butylquinone (tBQ). A critical role for tBQ and its electrophilic character was revealed with …
Oral Streptococcus And Vitamin B12 Deficiency In E-Cigarette Users: A Microbial–Nutrient–Neurotransmitter Axis Linking To Mood Disturbances, Maryam Sabah Naser, Ali Jabbar Abd Al-Hussain Alkawaz, Ali Abbas Hashim Almusawi, Ali Jalil Obaid, Hasanain Ayed Mohammed Al-Khafaji, Reihaneh Sabbaghzadeh
Oral Streptococcus And Vitamin B12 Deficiency In E-Cigarette Users: A Microbial–Nutrient–Neurotransmitter Axis Linking To Mood Disturbances, Maryam Sabah Naser, Ali Jabbar Abd Al-Hussain Alkawaz, Ali Abbas Hashim Almusawi, Ali Jalil Obaid, Hasanain Ayed Mohammed Al-Khafaji, Reihaneh Sabbaghzadeh
Karbala International Journal of Modern Science
Background: With the rising popularity of e-cigarettes, questions have emerged regarding their broader influence on oral ecology, nutrient absorption, and psychological health. Disruptions in the oral microbiome may alter vitamin B12 dynamics. This, in turn, may indirectly influence serotonin biosynthesis and mood regulation.
Methods: An observational cross-sectional study involved 150 young adults segregated into groups of 50 each as vapers, smokers, or non-users. Streptococcus sanguinis and vitamin B12 metabolism-related variable statuses methylmalonic acid and holotranscobalamin were quantified in samples, along with inflammatory markers interleukin-6, kynurenine/tryptophan ratio, and serotonin. Statistical techniques, including ANOVA and the Kruskal-Walli’s test, correlation, and serial mediation …
Dapagliflozin Attenuates Cisplatin-Induced Nephrotoxicity In Rats Through Modulation Of Ros/Nf-Κb, Bcl2/Bax And Pink1/Parkin Signaling Pathways, Esraa K. Khallaf, Eman A. Ramadan, Mohey M. Elmazar, Marwa M. Safar
Dapagliflozin Attenuates Cisplatin-Induced Nephrotoxicity In Rats Through Modulation Of Ros/Nf-Κb, Bcl2/Bax And Pink1/Parkin Signaling Pathways, Esraa K. Khallaf, Eman A. Ramadan, Mohey M. Elmazar, Marwa M. Safar
Pharmacy
Dapagliflozin (DPG), an anti-diabetic drug, has gained attention for its renal protective effects through multiple molecular pathways, yet its impact on mitophagy in cisplatin (CIS) nephrotoxicity remains unclear. This study aimed to examine the impact of DPG against CIS-induced nephrotoxicity in rats, targeting mainly PINK1/Parkin-mediated mitophagy and inflammatory/apoptotic pathways. Male Sprague Dawley rats received DPG (10 mg/kg; p.o) daily for 14 consecutive days and AKI was induced by a single injection of CIS (7 mg/kg; i.p) on day 10. Blood glucose, serum levels of creatinine and urea nitrogen, oxidative stress, inflammatory, apoptotic, mitophagy markers, and histological changes were assessed. DPG …
Chasing Disinfection Byproducts Through The Pipes: How 66 Dbps Change Over Time In Chlorinated Vs. Chloraminated Distribution Systems, Erik Niehaves, Patrick T. Justen, Ashley A. Perkins, Alexandria L.B. Forster, Caroline O. Granger, Susan D. Richardson
Chasing Disinfection Byproducts Through The Pipes: How 66 Dbps Change Over Time In Chlorinated Vs. Chloraminated Distribution Systems, Erik Niehaves, Patrick T. Justen, Ashley A. Perkins, Alexandria L.B. Forster, Caroline O. Granger, Susan D. Richardson
Faculty Publications
While disinfection byproducts (DBPs) are typically measured at drinking water treatment plants, levels can change dramatically within the distribution system before reaching the consumer. In this study, the spatio-temporal trends of 66 DBPs across 9 different classes were examined in two drinking water distribution systems with similar source waters, but different pretreatments and residual disinfectants. One system uses residual chlorine in the distribution system, and the other uses chloramine, allowing for examination of how DBP concentrations change over time in distribution systems with different residual disinfectants. Four routes were sampled for each system with six time points over three days …
Optimized Photoemission From Organic Molecules In 2d Layered Halide Perovskites, Muhammad S. Muhammad, Dilruba A. Popy, Hamza Shoukat, John M. Lane, Neeraj Rai, Vojtěch Vaněček, Zdeněk Remeš, Romana Kučerková, Vladimir Babin, Chenjia Mi, Yitong Dong, Mark D. Smith, Novruz G. Akhmedov, Daniel T. Glatzhofer, Bayram Saparov
Optimized Photoemission From Organic Molecules In 2d Layered Halide Perovskites, Muhammad S. Muhammad, Dilruba A. Popy, Hamza Shoukat, John M. Lane, Neeraj Rai, Vojtěch Vaněček, Zdeněk Remeš, Romana Kučerková, Vladimir Babin, Chenjia Mi, Yitong Dong, Mark D. Smith, Novruz G. Akhmedov, Daniel T. Glatzhofer, Bayram Saparov
Faculty Publications
In recent years, hybrid organic–inorganic metal halides have been at the forefront of materials research. Typically, the functional (e.g., optoelectronic) properties of hybrid halides are derived from the inorganic structural part, whereas the organic structural units can add extra advantages in terms of stability, rigidity, and processability. Here, we report the design, synthesis, and characterization of two new hybrid materials in which the outstanding photophysical properties originate from the organic structural part. The new compounds, (C15H16N)2CdCl4 and((Br)C15H15N)2CdCl4, have 2D layered Ruddlesden–Popper-type perovskite structures. These hybrids are blue-white …
Defining Rna Oligonucleotides That Reverse Deleterious Phase Transitions Of Rna-Binding Proteins With Prion-Like Domains., Lin Guo, Jacob Mann, Jocelyn Mauna, Katie Copley, Hejia Wang, Jack Rubien, Cristian Bergmann, Jenny Carey, Jessica Merjane, Marilyn Ngo, Jiazhen Xu, Hana Odeh, Jiabei Lin, Bo Lim Lee, Laura Ganser, Emma Robinson, Kevin Kim, Anastasia Murthy, Tapas Paul, Bede Portz, Amanda Gleixner, Zamia Diaz, Ashleigh Smirnov, George Padilla, Ellen Lavorando, Carolann Espy, Yulei Shang, Eric Huang, Alessandra Chesi, Nicolas Fawzi, Sua Myong, Christopher Donnelly, James Shorter
Defining Rna Oligonucleotides That Reverse Deleterious Phase Transitions Of Rna-Binding Proteins With Prion-Like Domains., Lin Guo, Jacob Mann, Jocelyn Mauna, Katie Copley, Hejia Wang, Jack Rubien, Cristian Bergmann, Jenny Carey, Jessica Merjane, Marilyn Ngo, Jiazhen Xu, Hana Odeh, Jiabei Lin, Bo Lim Lee, Laura Ganser, Emma Robinson, Kevin Kim, Anastasia Murthy, Tapas Paul, Bede Portz, Amanda Gleixner, Zamia Diaz, Ashleigh Smirnov, George Padilla, Ellen Lavorando, Carolann Espy, Yulei Shang, Eric Huang, Alessandra Chesi, Nicolas Fawzi, Sua Myong, Christopher Donnelly, James Shorter
Department of Biochemistry and Molecular Biology Faculty Papers
RNA-binding proteins (RBPs) with prion-like domains (PrLDs), such as FUS and TDP-43, condense into functional liquids, which can transform into pathological fibrils that underpin fatal neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD). Here, we define short RNAs that prevent FUS fibrillization by promoting liquid phases and distinct short RNAs that prevent and reverse FUS condensation and fibrillization. These activities require interactions with multiple RNA-binding domains of FUS and are encoded by RNA sequence, length, and structure. We define a short RNA that dissolves cytoplasmic FUS aggregates, restores nuclear FUS, and mitigates FUS toxicity in optogenetic models and ALS …
Structural Characterization Of Peptide Nanoaggregates At Varying Concentrations And Their Impact On Cellular Responses, Malika Rozmetova
Structural Characterization Of Peptide Nanoaggregates At Varying Concentrations And Their Impact On Cellular Responses, Malika Rozmetova
Theses and Dissertations
Peptide nano-assemblies can regulate cellular pathways in a structure-dependent manner. Here, we show that the enzyme-responsive peptide NapFFK(NBD)Yp forms distinct nanoscale assemblies at different concentrations, triggering differential ER stress and extracellular vesicle release in MDA-MB231 cells. These results highlight the importance of supramolecular organization in peptide–cell interactions.
Flux Crystal Growth Of Potassium Lanthanide Double Vanadates With Lanthanide-Dependent Coordination Number Variance, Hunter B. Tisdale, Hans Conrad Zur Loye
Flux Crystal Growth Of Potassium Lanthanide Double Vanadates With Lanthanide-Dependent Coordination Number Variance, Hunter B. Tisdale, Hans Conrad Zur Loye
Faculty Publications
A series of potassium rare earth double vanadates is presented. Single crystals of double vanadates with stoichiometry K3Ln(VO4)2 (Ln = La, Pr, Nd, and Sm) and crystallizing in the glaserite structure type were synthesized via a molten alkali chloride/fluoride flux reaction. Different structures were observed depending on the constituent rare earth: K3La(VO4)2 crystallizes in an as-of-yet unreported modification of the typical glaserite structure in the space group P21/c, likely due to its larger ionic size that results in an increase in the lanthanide coordination number …
Protocol For Stable Isotope Tracing Of Primary Human Peripheral Blood Mononuclear Cells, Samantha N. Hart, Holden C. Williams, William B. Inabnet Iii, Joshua P. Steiner, Varun Jain, Philip A. Kern, Cecily R. Wood, Barbara S. Nikolajczyk, Lance A. Johnson
Protocol For Stable Isotope Tracing Of Primary Human Peripheral Blood Mononuclear Cells, Samantha N. Hart, Holden C. Williams, William B. Inabnet Iii, Joshua P. Steiner, Varun Jain, Philip A. Kern, Cecily R. Wood, Barbara S. Nikolajczyk, Lance A. Johnson
Molecular and Cellular Biochemistry Faculty Publications
Stable isotope tracing gives direct insight into the rate of metabolic reactions occurring in cells by analyzing the incorporation of labeled carbons into metabolic pathways. Here, we present a protocol for stable isotope tracing of primary human peripheral blood mononuclear cells (PBMCs). We describe the steps for culturing and exposing PBMCs to stable isotopes U13C glucose and U13C glutamine. We then detail procedures for derivatization, metabolite purification, and tracing analysis via single-quadrupole gas chromatography-mass spectrometry (GC-MS).
A Live Cell Biosensor Protocol For High-Resolution Screening Of Therapy-Resistant Cancer Cells, Viral D. Oza, Colin S. Williams, Jessica S. Blackburn
A Live Cell Biosensor Protocol For High-Resolution Screening Of Therapy-Resistant Cancer Cells, Viral D. Oza, Colin S. Williams, Jessica S. Blackburn
Molecular and Cellular Biochemistry Faculty Publications
The Genetically Encoded Death Indicator (GEDI) is a ratiometric, dual-fluorescence biosensor that enables real-time detection of cell death through calcium influx. Originally developed for use in neurodegeneration models, GEDI can be applied to cancer cells to quantify therapy-induced death at single-cell resolution. This protocol details how to generate GEDI-expressing cancer cell lines, empirically determine stress-induced GEDI thresholds using radiation or chemotherapeutic agents, and perform time-resolved imaging and image analysis to track cell fate. This workflow is optimized for high-throughput drug and radiation screening in heterogeneous populations and is especially useful for identifying chemo- and radio-resistant subclones. Key limitations include the …
A Phosphorylation Study Of Serine-8 And 26 In Two Fragments Of Amyloid Beta, A Peptide Involved In Alzheimer's Disease And Cancer, Colby J. Merrill
A Phosphorylation Study Of Serine-8 And 26 In Two Fragments Of Amyloid Beta, A Peptide Involved In Alzheimer's Disease And Cancer, Colby J. Merrill
Senior Honors Theses and Projects
Both cancer and Alzheimer’s disease (AD) affect many people in the United States and impact the families of patients suffering from these challenging illnesses. Recently, it has been reported that these two diseases share several key pathophysiological features, and an inverse relationship exists between them. These diseases share several biochemical modulators, most notably the amyloid-beta protein, which affects tissues in both AD and cancer by misfolding and aggregating. Phosphorylation is believed to regulate the aggregation and toxicity of amyloid-beta by altering the protein's shape and charge, thereby changing its interactions with cells. Phosphorylation can also toggle some proteins on and …
The Chemistry Of Red Lipstick: The Impact Red Lipstick Has On Society, Lilliana Weldeslassie
The Chemistry Of Red Lipstick: The Impact Red Lipstick Has On Society, Lilliana Weldeslassie
Electronic Theses & Dissertations (2024 - present)
Cosmetic chemistry is deeply embedded in everyday life, shaping the products people use from morning to night. Among these, red lipstick stands out as a formulation that blends complex chemistry with a cultural meaning. This thesis examines the scientific foundations of red lipstick through its chemical composition, pigment structure, toxicological history, analytical methods, and evolving sustainability practices. Historically, red lipsticks relied on high-risk ingredients such as lead, mercury, and other toxic metals, reflecting an era before chemical safety and regulatory oversight were incorporated.21 Modern formulations have established safer synthetic dyes, natural waxes, plant-based oils, and stabilizers created to optimize …
Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit
Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit
Electronic Theses & Dissertations (2024 - present)
The CRISPR–Cas9 system is a widely popular tool for genome engineering. There is a strong interest in developing tools for temporal control of CRISPR-Cas9 activity to address some of the challenges and to broaden the scope of potential applications. In this thesis I describe two biorthogonal based approaches to either Turn-ON and Turn-OFF CRISPR-Cas9 gene editing.
In first project work I describe a bio-orthogonal chemistry-based approach to Turn-ON Cas9 nuclease activity with temporal precision. We report a TCO-acylimidazole reagent that acylates 2′-OH groups of RNA. Poly-acylation (“cloaking”) of RNA was optimized in vitro using a model 18-nt oligonucleotide, as well …
Photo And Spatial Control Of Rna Structures And Functions: Exploring Positional Effects And Photo-Responsiveness Of Azobenzene Modified Nucleotides, Jinxi Du
Electronic Theses & Dissertations (2024 - present)
RNA molecules perform many important biological functions by forming complex three-dimensional structures stabilized by base pairing, tertiary interactions, and metal ion coordination. Because RNA function depends strongly on its structure, methods that allow reversible control of RNA conformation and activity are important for understanding RNA behavior and for potential therapeutic applications. However, achieving reversible and site-specific control of RNA structure, especially at the single-nucleotide level, remains challenging. In this dissertation, I developed and applied azobenzene-modified nucleotides as a chemical tool to enable optical and spatial control of RNA structure and function.
The first part of this dissertation focuses on establishing …
Generating A Gfp Reporter Via Crispr To Visualize Ssa4 Export, Aara Khairollahi, Rebecca Adams
Generating A Gfp Reporter Via Crispr To Visualize Ssa4 Export, Aara Khairollahi, Rebecca Adams
SPARK Symposium Presentations
In eukaryotic cells, the transport of mRNA from the nucleus to the cytoplasm is a very regulated process controlled by nuclear pore complexes (NPCs). During stress conditions, such as heat shock, most mRNA export is inhibited in Saccharomyces cerevisiae, yet the transcript for SSA4, a gene responsible for refolding denatured essential proteins, is exported. The mechanism behind this selective export remains unknown. To investigate this, we used CRISPR-Cas9 to generate a reporter strain in which the SSA4 open reading frame was replaced or inserted with green fluorescent protein (GFP). This reporter is designed to produce GFP only under conditions that …
Advancing Lipidomics Through Fluoroalcohol-Induced Multiphase Fractionation And Orthogonal Lc×Lc–Ms Detection, Md Al Amin
Chemistry & Biochemistry Dissertations
Comprehensive characterization of the lipidome remains a significant analytical challenge due to the immense structural diversity, wide dynamic range, and complex physicochemical continuum of lipid species. Conventional extraction methods, such as those by Bligh–Dyer and Folch, and one-dimensional liquid chromatography (1D-LC) often fail to resolve this complexity, leading to chromatographic overlap, severe ion suppression, and limited coverage of low-abundance or highly hydrophobic species. This dissertation addresses these bottlenecks by establishing a separation-driven analytical framework that integrates novel fluoroalcohol-induced multiphase systems (FAiTPS) with orthogonal multidimensional liquid chromatography–mass spectrometry (LC×LC–MS).
The core of this research is the development and physicochemical characterization of …
Crispr Transgenic Clytia Hemisphaerica As A Vector For Toxin Delivery In A Zebrafish Melanoma Model, Theodore G. Paz
Crispr Transgenic Clytia Hemisphaerica As A Vector For Toxin Delivery In A Zebrafish Melanoma Model, Theodore G. Paz
Theses, Dissertations and Culminating Projects
The jellyfish Clytia hemisphaerica has the potential to be used in cancer therapies with the discovery of potential active toxin target regions to be modified for use. The program Venomix is a Uniprot-based database that was utilized in this experiment to generate likely flagged hit regions using Clytia hemisphaerica CDS files run against its database of terrestrial toxins (Furuno et al., 2003; Macrander et al., 2018). By themselves they are indeterminate as to whether they are active toxin region hits (Macrander et al., 2018). With further analysis such as toxin homology in closely related, annotated marine taxa and accounting for …
Interest, Self-Efficacy, And Belonging In Classroom Learning, K. Ann Renninger, Lux K. Barton , '21, Gia Bautista , '23, Mary Garcia-Barrios , '24, Iyinoluwa Ogunyinka , '24, Kathryn R. Riley
Interest, Self-Efficacy, And Belonging In Classroom Learning, K. Ann Renninger, Lux K. Barton , '21, Gia Bautista , '23, Mary Garcia-Barrios , '24, Iyinoluwa Ogunyinka , '24, Kathryn R. Riley
Educational Studies Faculty Works
Students’ interest, self-efficacy, and belonging are considered essential for classroom learning, as each has been shown to promote sustained engagement and school achievement. However, our review of the literature suggested that research on interest, self-efficacy, and belonging is largely siloed. To address practitioner questions about supporting classroom learning by working with the three variables, we added a mixed-method pilot study to the review process. Pilot participants were Black, middle-school-age youth living in a low-income community, who were enrolled in a five-week, inquiry-informed science workshop facilitated by a Black professor. Findings showed that during learning, interest, self-efficacy, and belonging were increasingly …
A Thymine Dimer Stalls A High-Fidelity Dna Polymerase By Providing No Template Information In The Same Manner As An Abasic Site, Amanda R. Walsh, Hye Rhee Kim, Lorena S. Beese, Eugene Y. Wu
A Thymine Dimer Stalls A High-Fidelity Dna Polymerase By Providing No Template Information In The Same Manner As An Abasic Site, Amanda R. Walsh, Hye Rhee Kim, Lorena S. Beese, Eugene Y. Wu
Biology Faculty Publications
Cyclobutane pyrimidine dimers are photolesions that form when UV-B irradiation causes adjacent thymine or cytosine bases to covalently bond and can arrest DNA synthesis by replicative polymerases. To gain insight into the effects of cis-syn cyclobutane thymine dimers (T=T) on DNA replication in a model polymerase, we conducted solution and crystallographic studies of the Bacillus DNA polymerase I large fragment (BF) in complex with a T=T-containing template and an incoming dNTP. A thymine dimer lesion blocked nucleotide addition by BF in solution. The crystal structure of the BF-T=T-dATP complex indicated that the thymine dimer is too large to enter the …
Soil Nutrient Sufficiency Versus Plant Nutrient Status In Compost-Amended Soils: Plant Tissue Analysis As A Diagnostic Tool, Chandralekha Joga Miss
Soil Nutrient Sufficiency Versus Plant Nutrient Status In Compost-Amended Soils: Plant Tissue Analysis As A Diagnostic Tool, Chandralekha Joga Miss
Murray State Theses and Dissertations
This study evaluated whether Mehlich III soil nutrient sufficiency ratings reliably predict plant nutrient status and chlorophyll response across contrasting compost application histories. A greenhouse pot experiment was conducted with Chijimisai (Brassica rapa) planted in three treatment soils that had no compost (T1), moderate compost history (T2), and long-term hog manure compost application (T3). Plant performance was assessed through weekly shoot length and chlorophyll content (SPAD) measurements, leaf number at maturity, and leaf tissue nutrient analysis conducted at harvest. Soil test results indicated adequate to high nutrient levels across all three treatments. Leaf tissue analysis, however, revealed substantial …
Generating Concentrated Ring Polymers Through Supercoiled And Open Circle Pdna Isoform Separation, Kelsey E. Hodsdon
Generating Concentrated Ring Polymers Through Supercoiled And Open Circle Pdna Isoform Separation, Kelsey E. Hodsdon
Honors Theses and Capstones
DNA can serve as a model polymer due to its high uniformity compared to synthetic polymers. Plasmid DNA (pDNA) in particular offers a well-defined, low-dispersity model for studying topologically uniform systems of a cyclic nature. pDNA has unique isoforms known as open circle (OC) and supercoiled (SC). Using fast protein liquid chromatography (FPLC), specifically anion exchange chromatography (AEX), these OC and SC isoforms can be separated in order to access their unique material properties. Our lab was able to yield the pure SC isoform. However, OC isoform separation has been more challenging. Various difficulties arose during this process, including imaging …
Fgf Signaling Is Necessary For Newt Lens Regeneration, Leo Alexander Napoleon
Fgf Signaling Is Necessary For Newt Lens Regeneration, Leo Alexander Napoleon
Honors Theses and Capstones
The Iberian ribbed newt Pleurodeles waltl can regenerate the lens by transdifferentiating iris pigmented epithelial (IPE) cells into lens epithelial cells (LECs), but the mechanism by which this occurs remains largely uncharacterized. We aim to mechanistically show an early and critical role for FGF signaling by using small molecules to inhibit FGF receptors and observe the histological and intracellular effects. Two inhibitors were found to completely stall lens regeneration. Cell cycle analysis revealed decreased DNA synthesis and uniformly low but unchanged entry to mitosis under signaling inhibition by staining for EdU incorporation and phospho-histone H3 (pH3), respectively. Western blot revealed …
Bpa: Effects Of The "Plastic Era", Bianca G. Pietrangeli
Bpa: Effects Of The "Plastic Era", Bianca G. Pietrangeli
Student Work
Infographic review of sources of BPA and its impacts on human health with a focus on osteoporosis.
Toxic Torts Are In Your Blood: An Examination Of Pfas And Tort Liability, Aiden M. Holden
Toxic Torts Are In Your Blood: An Examination Of Pfas And Tort Liability, Aiden M. Holden
Undergraduate Theses, Professional Papers, and Capstone Artifacts
Abstract
Per- and polyfluoroalkyl substances (PFAS), are a group of chemicals widely manufactured for industrial and commercial applications in the past decade due to their remarkable stability. Despite the “useful” nature of PFAS in various applications, they represent one of the most profound environmental and public health crises of the modern era. The chemical stability of PFAS has made them almost completely resistant to natural degradation, earning them the moniker “forever chemicals.” PFAS forever haunt our plant, contaminating the soil, water, and the blood of approximately 95% of the United States population. As the scale of corporate malfeasance by chemical …
Psr Impacts Chromatin Condensation During Spermatogenesis In Nasonia Vitripennis, Jacqueline R. Solomon
Psr Impacts Chromatin Condensation During Spermatogenesis In Nasonia Vitripennis, Jacqueline R. Solomon
CMC Senior Theses
Paternal Sex Ratio (PSR) is a supernumerary, selfish B chromosome found in the jewel wasp (Nasonia vitripennis). PSR is transmitted strictly paternally to progeny, and when present, it causes paternal genome elimination (PGE) just after fertilization. Due to the haplo-diploid reproduction of N. vitripennis, this PGE event results in all-male broods of progeny, ~90% of which carry and transmit PSR. Thus, PGE is beneficial for PSR’s transmission. A previous study showed that PSR induces PGE by expressing a gene called haploidizer during spermatogenesis. Although how haploidizer functions in PGE is unknown, this finding suggests two basic models: that (i) the …
Mxene-Enabled Wearable Biosensors: A Design Framework For Autonomous Biosensing, Jegan Rajendran, Gymama Slaughter
Mxene-Enabled Wearable Biosensors: A Design Framework For Autonomous Biosensing, Jegan Rajendran, Gymama Slaughter
Center for Bioelectronics Publications
MXenes, a rapidly expanding family of two-dimensional transition metal carbides and nitrides, have emerged as leading materials for wearable bioelectronics due to their metallic conductivity, termination-rich surfaces, mechanical compliance, and tunable interlayer structures. However, wearable biosensor performance does not arise from conductivity alone, but from coupled interactions among surface termination chemistry, heterointerface engineering, hierarchical architecture, and device integration under dynamic physiological conditions. This review establishes a predictive structure-interface-device framework linking MXene chemistry to system-level performance across electrochemical, mechanical, gas, optical, and energy-storage modalities. We analyze how termination-controlled adsorption governs charge transfer and selectivity, how heterojunction formation modulates carrier density and …
Potential Environmental Triggers Of Goodpasture's Disease And The Role Of The Sulfimine Crosslink, Colton S. Miller, Andrea Florian, Elena Pokidysheva
Potential Environmental Triggers Of Goodpasture's Disease And The Role Of The Sulfimine Crosslink, Colton S. Miller, Andrea Florian, Elena Pokidysheva
SPARK Symposium Presentations
Goodpasture’s syndrome (GP) is an autoimmune disorder that primarily affects kidneys and lungs. The main issue for patients with Goodpasture's syndrome is the binding of autoantibodies to the glomerular basement membrane (GBM), which hinders the filtration of blood. A key characteristic of Goodpasture's syndrome is the presence of autoantibodies that target the NC1 domain of the α345 isoform of type IV collagen, a crucial component of the GBM that provides structural support and is critical for filtration function. Sulfilimine bonds crosslink the collagen IV NC1 hexamers, contributing to the stabilization of these structures. A recent clinical case of recurring Goodpasture's …
Comparing The Differences Of Hsp90Α And Hsp90Β In Native Protein Complex Incorporation, Daryna Serediuk
Comparing The Differences Of Hsp90Α And Hsp90Β In Native Protein Complex Incorporation, Daryna Serediuk
Honors Theses and Capstones
Epichaperomes are long-lasting, stable assemblies of chaperones, co-chaperones, and associated factors that facilitate cell survival in maladaptive cellular states. Their inhibition has emerged as an attractive therapeutic strategy for the treatment of cancer and neurodegenerative diseases (Rodina et al., 2016). Epichaperomes are hallmarks of robust proliferation in cancer cell populations across many cancer types and are abundantly present in several stem cell varieties, including induced pluripotent stem cells, human embryonic kidney cells, and cancer stem cells (Kishinevsky et al., 2018).
The core protein of the eukaryotic heat shock protein machinery, Heat Shock Protein 90 (Hsp90), is a central chaperone that …
Perinatal Inflammation And Oxidative Stress Alter Adult Rat (Rattus Norvegicus) Motor Behavior, Alexander Young
Perinatal Inflammation And Oxidative Stress Alter Adult Rat (Rattus Norvegicus) Motor Behavior, Alexander Young
Honors College Theses
Recent evidence in comparative animal models suggests that early life exposure to elevated inflammation (via LPS exposure) and oxidative stress (via acetaminophen exposure) may synergistically interact to alter typical neurodevelopmental trajectories, resulting in lasting effects on both behavior and gut-brain neurochemistry. The current study observed emotional and motor behaviors and collected fecal-boli to measure Tyrosine (TE) levels in male and female Long-Evans (Rattus norvegicus) rats. Subjects were either treated with [1] saline [2] lipopolysaccharide (LPS) to introduce an inflammatory state, [3] acetaminophen (APAP) to introduce oxidative stress, or [4] a dual-hit of both LPS + APAP on postnatal day (PD) …