Biochemistry Commons^™

Correlation Between Salivary Levels And Tissue Expression Status Of Her2 In Breast Cancer Patients - A Cross-Sectional Study, Arthi Sri A.S, Massillamani F, Vinothkumar Thilla Sekar

Annual Research Symposium

The study aims to investigate if soluble salivary human epidermal growth factor receptor-2 (HER2) would play a role in the diagnosis of breast cancer patients and also to find out the influence of demographic and hormonal factors on the salivary HER2 levels in breast cancer.

Historical Analysis Of Urban Dust Generated By The Great Salt Lake Playa, Callum Flowerday, Jaron C. Hansen, Rebekah Stanley, Kaitlyn Brewster

ScholarsArchive Data

Historical PM10 filters, provided by the Utah Division of Air Quality, were analyzed for elemental composition of various metals. This was done using ICP-MS.

Also included, EPA PM10 historical data and bathymetry data provided by the Utah USGS.

An Observational Framework For Constructing Ozone Isopleths From Long-Term Monitoring Data: Demonstration In Salt Lake City, Utah, Callum Flowerday, Isaac Sudweeks, Brad Adams, Jaron C. Hansen

ScholarsArchive Data

EPA quality assured data, collected by the Utah Division of Air Quality, was used for this analysis.

Unimer Suppression Enables Supersaturated Homopolymer Swollen Micelles With Long-Term Stability After Glassy Entrapment, Eric R. Williams, Christian X. Ruff, Morgan Stefik

Faculty Publications

Micelle sizes are critical for a range of applications where the simple ability to adjust and lock in specific stable sizes has remained largely elusive. While micelle swelling agents are well-known, their dynamic re-equilibration in solution implies limited stability. Here, a non-equilibrium processing sequence is studied where supersaturated homopolymer swelling is combined with glassy-core (“persistent”) micelles. This path-dependent process was found to sensitively depend on unimer concentration as revealed by DLS, SAXS, and TEM analysis. Here, lower-selectivity solvent combinations led to the formation of unimer-homopolymer aggregates and eventual precipitation, reminiscent of anomalous micellization. In contrast, higher-selectivity solvents enabled supersaturated homopolymer …

Unimer Suppression Enables Supersaturated Homopolymer Swollen Micelles With Long-Term Stability After Glassy Entrapment, Eric R. Williams, Christian X. Ruff, Morgan Stefik

Faculty Publications

Micelle sizes are critical for a range of applications where the simple ability to adjust and lock in specific stable sizes has remained largely elusive. While micelle swelling agents are well-known, their dynamic re-equilibration in solution implies limited stability. Here, a non-equilibrium processing sequence is studied where supersaturated homopolymer swelling is combined with glassy-core (“persistent”) micelles. This path-dependent process was found to sensitively depend on unimer concentration as revealed by DLS, SAXS, and TEM analysis. Here, lower-selectivity solvent combinations led to the formation of unimer-homopolymer aggregates and eventual precipitation, reminiscent of anomalous micellization. In contrast, higher-selectivity solvents enabled supersaturated homopolymer …

Mitochondrial Quality Control By Tail-Anchored Proteins, Jose M. Delgado

Dartmouth College Ph.D Dissertations

Autophagy is a lysosome-mediated pathway responsible for the degradation of unwanted cytosolic content. During autophagy, cytoplasmic components are enveloped by a newly generated vesicle (the autophagosome), trafficked to the lysosome, and degraded. The power of autophagy lies in its ability to selectively target specific substrates for degradation—a phenomenon known as selective autophagy.

Specialized proteins known as selective autophagy receptors play a crucial role in identifying and targeting autophagy cargo. Although historically overlooked as potential regulators, our understanding of autophagy receptors is evolving beyond the assumption that receptors merely bridge targets to pre-formed autophagosomal membranes. Previous insights were often based on …

Rational Design Of Peptide-Based Materials Informed By Multiscale Molecular Dynamics Simulations, Dhwanit Rahul Dave

Dissertations, Theses, and Capstone Projects

The challenge of establishing a sustainable and circular economy for materials in medicine and technology necessitates bioinspired design. Nature's intricate machinery, forged through evolution, relies on a finite set of biomolecular building blocks with through-bond and through-space interactions. Repurposing these molecular building blocks requires a seamless integration of computational modeling, design, and experimental validation. The tools and concepts developed in this thesis pioneer new directions in peptide-materials design, grounded in fundamental principles of physical chemistry. We present a synergistic approach that integrates experimental designs and computational methods, specifically molecular dynamics simulations, to gain in-depth molecular insights crucial for advancing the …

Biomolecular Crystals As Functional Materials, Fahmeed Khan Sheehan

Dissertations, Theses, and Capstone Projects

The field of supramolecular chemistry has undergone significant evolution over the last few decades, progressing from fundamental studies of self-assembling systems to the rational design of functional materials with exceptional properties. Among these materials, short peptides have emerged as a chemically simple yet highly versatile class of biomimetic compounds. Initially, short peptides were used as model systems to understand larger protein interactions. As the field progressed, short peptides were found to have exceptional functionality, and are now explored as functional nanomaterials for diverse applications. In many cases, short peptide materials have displayed properties not found in biology, in some cases …

Cold-Inducible Rna Binding Protein Impedes Breast Tumor Growth In The Pymt Murine Model For Breast Cancer, Daniel A. Lujan, Joey L. Ochoa, Ellen J. Beswick, Tamara A. Howard, Helen J. Hathaway, Nora I. Perrone-Bizzozero, Rebecca S. Hartley

Markey Cancer Center Faculty Publications

RNA binding proteins (RBPs) post-transcriptionally regulate gene expression by associating with regulatory sequences in the untranslated regions of mRNAs. Cold-inducible RBP (CIRP) is a stress-induced RBP that was recently shown to modulate inflammation in response to cellular stress, where it increases or decreases pro-tumorigenic (proinflammatory) cytokines in different contexts. CIRP expression is altered in several cancers, including breast cancer, but the effects of CIRP on inflammation in breast cancer is not known. Here, we investigate if CIRP alters growth and the inflammatory profile of breast tumors. Transgenic mice overexpressing CIRP in the mammary epithelium were crossed with the PyMT mouse …

Comparative Animal Mucomics, Antonio R. Cerullo

Dissertations, Theses, and Capstone Projects

Mucus is one of Nature’s most abundant and versatile biomaterials. These secretions are present in all animals, from the lowly garden snail to the great blue whale, and fulfill a multitude of functions, acting as antimicrobial barriers, moisturizers, adhesive glues, surface lubricants, and mineralizing agents. Despite their importance, very little is known about mucus compositions or properties. The largest challenge precluding the greater understanding of mucus function is its complexity; a single mucus contains complex mixtures of proteins, glycans, and ions that all have important roles in function. Therefore, understanding mucus function necessitates analysis that compares different mucus from one …

Studying The Genes And Conditions That Influence Root Development, Tessa Holtkamp, Hannah Ordonez Webb

Undergraduate Research Symposium

Root development in plants is essential for their survival and understanding how hormones influence their development can explain how plants grow under different circumstances. Researching how Indole-3-butyric acid (IBA), a hormone that induces root production, affects the plant model Arabidopsis thaliana helps explain the hormone's effect in agricultural crop systems. To understand root pathways, we performed assays on mutant lines of Arabidopsis by growing plants on varying concentrations of IBA. For wild-type and mutant lines, phenotyping experiments like branching of roots, lengths of stems, and root length were conducted along with PCR and restriction digest genotyping experiments to compare their …

Investigation Of Alzheimer’S Amyloid-Β Protein Aggregation With A New Fluorescent Dye., Emma Alberty

Undergraduate Research Symposium

Alzheimer’s Disease (AD) is the most common form of dementia characterized by the impairment of at least two brain functions such as memory loss and judgement. AD is a progressive illness that can last as many as 20 years. AD is largely considered to be caused by the formation of extracellular amyloid plaques and intracellular neurofibrillary tangles. A better understanding of the structure and function of these plaques may lead to clearer understanding of the disease. To analyze amyloid plaques, aggregation assays are often used. During these assays we begin with monomer and place the sample in biological conditions to …

Chromosome‑Level Assembly And Analysis Of Camelina Neglecta: A Novel Diploid Model For Camelina Biotechnology Research, Shuo Wang, Rostislav Y. Blume, Zhi‑Wei Zhou, Shaoping Lu, Tara J. Nazarenus, Yaroslav B. Blume, Weibo Xie, Edgar B. Cahoon, Ling‑Ling Chen, Liang Guo

Department of Biochemistry: Faculty Publications

Camelina neglecta is a new diploid Brassicaceae species, which has great research value because of its close relationship with the hexaploid oilseed crop Camelina sativa. Here, we report a chromosome-level assembly of C. neglecta with a total length of 210 Mb. By adopting PacBio sequencing and Hi-C technology, the C. neglecta genome was assembled into 6 chromosomes with scaffold N50 of 29.62 Mb. C. neglecta has undergone the whole-genome triplication (γ) shared among eudicots and two whole-genome duplications (α and β) shared by crucifers, but it has not undergone a specific whole-genome duplication event. By synteny analysis …

Metabolic Collaboration Between Cells In The Tumor Microenvironment Has A Negligible Effect On Tumor Growth, Johan Gustafsson, Fariba Roshanzamir, Anders Hagnestål, Sagar M. Patel, Oseeyi I. Daudu, Donald F. Becker, Jonathan L. Robinson, Jens Nielsen

Department of Biochemistry: Faculty Publications

The tumor microenvironment is composed of a complex mixture of different cell types interacting under conditions of nutrient deprivation, but the metabolism therein is not fully understood due to difficulties in measuring metabolic fluxes and exchange of metabolites between different cell types in vivo. Genome-scale metabolic modeling enables estimation of such exchange fluxes as well as an opportunity to gain insight into the metabolic behavior of individual cell types. Here, we estimated the availability of nutrients and oxygen within the tumor microenvironment using concentration measurements from blood together with a metabolite diffusion model. In addition, we developed an approach …

Emerging Roles Of Cullin-Ring Ubiquitin Ligases In Cardiac Development, Josue Zambrano-Carrasco, Jianqiu Zou, Wenjuan Wang, Xinghui Sun, Jie Li, Huabo Su

Department of Biochemistry: Faculty Publications

Heart development is a spatiotemporally regulated process that extends from the embryonic phase to postnatal stages. Disruption of this highly orchestrated process can lead to congenital heart disease or predispose the heart to cardiomyopathy or heart failure. Consequently, gaining an in-depth understanding of the molecular mechanisms governing cardiac development holds considerable promise for the development of innovative therapies for various cardiac ailments. While significant progress in uncovering novel transcriptional and epigenetic regulators of heart development has been made, the exploration of post-translational mechanisms that influence this process has lagged. Culling-RING E3 ubiquitin ligases (CRLs), the largest family of ubiquitin ligases, …

Augusta: From Rna-Seq To Gene Regulatory Networks And Boolean Models, Jana Musilova, Zdenek Vafek, Bhanwar Lal Puniya, Ralf Zimmer, Tomáš Helikar, Karel Sedlar

Department of Biochemistry: Faculty Publications

Computational models of gene regulations help to understand regulatory mechanisms and are extensively used in a wide range of areas, e.g., biotechnology or medicine, with significant benefits. Unfortunately, there are only a few computational gene regulatory models of whole genomes allowing static and dynamic analysis due to the lack of sophisticated tools for their reconstruction. Here, we describe Augusta, an open-source Python package for Gene Regulatory Network (GRN) and Boolean Network (BN) inference from the high-throughput gene expression data. Augusta can reconstruct genome-wide models suitable for static and dynamic analyses. Augusta uses a unique approach where the first estimation of …

Identification Of Regulatory Elements In The Untranslated Regions Of Streptolysin S Associated Gene A Messenger Rna From Group A Streptococcus, Cameron R. Carroll, Sara G. Nibar, Alexis S. Brown, Lauren R. Angello, Gabriela C. Pérez-Alvarado, Brian M. Lee

Journal of the South Carolina Academy of Science

Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a human pathogen associated with a variety of diseases such as strep throat, scarlet fever, toxic shock syndrome, and necrotizing fasciitis. One of the virulence factors released by GAS during an invasive infection is a cytotoxic peptide, streptolysin S (SLS), which inhibits the immune response to necrotizing fasciitis. The streptolysin S associated gene A product, SagA, is modified to produce SLS. Thesag operon includes sagA and the genes required for enzyme-mediated post-translational modifications of SagA and the export of SLS. The sagA gene is contained within the pleiotropic …

Course Portfolio For Biochemistry 1: Structure And Metabolism (Bioc431), Didier Mena

UNL Faculty Course Portfolios

This benchmark portfolio encapsulates a comprehensive exploration aimed at enhancing the educational landscape of the BIOC431 course, a part of the general biochemistry course series (431 and 432). These courses are designed to offer a general introduction to the structure and function of cells in the body, along with their chemical reactions. Specifically, BIOC431 focuses on the structure, function, and metabolism of proteins, lipids, carbohydrates, and other major metabolic pathways. The three primary objectives addressed in this portfolio were the reevaluation of learning objectives, reassessment of assessment methods, and documentation of effective classroom strategies. Through background design, the learning objectives …

Tail-Tape-Fused Virion And Non-Virion Rna Polymerases Of A Thermophilic Virus With An Extremely Long Tail, Anastasiia Chaban, Leonid Minakhin, Ekaterina Goldobina, Brain Bae, Yue Hao, Sergei Borukhov, Leena Putzeys, Maarten Boon, Florian Kabinger, Rob Lavigne, Kira Makarova, Eugene V Koonin, Satish Nair, Shunsuke Tagami, Konstantin Severinov, Maria Sokolova

Department of Biochemistry and Molecular Biology Faculty Papers

Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of …

The Role Of Ferroptosis In Cholangiocarcinoma, Apiwit Sae-Fung

Chulalongkorn University Theses and Dissertations (Chula ETD)

Cholangiocarcinoma (CCA) is a highly heterogeneous and aggressive malignancy of the bile ducts, characterized by a poor prognosis and high mortality rate. Despite advancements in treatment, effective targeted therapies and reliable prognostic biomarkers remain limited. Ferroptosis, a regulated form of cell death, has emerged as a potential therapeutic target in various cancers. However, its role in CCA remains poorly understood. In this study, we conducted a comprehensive analysis of ferroptosis-related genes (FRGs) to predict the prognosis of CCA and identify potential therapeutic targets. Using the least absolute shrinkage and selection operator (LASSO) Cox regression analysis on a training dataset, followed …

Climate Change And Coastal Development Impacts On Oyster Abundances In Mosquito Lagoon, Fl, Emily Suchonic

Graduate Thesis and Dissertation 2023-2024

Live eastern oyster (Crassostrea virginica) reefs have declined by 62.6% in Mosquito Lagoon (ML) along the eastern Florida coast since 1943. While this species creates reefs by successive generations of oysters recruiting to conspecific shells, C. virginica can also attach to non-reef substrates including mangrove roots and armoring (e.g., seawalls), which may help counteract reef habitat loss. In recent decades, warmer winters have enabled red (Rhizophora mangle) and black (Avicennia germinans) mangrove expansion in subtropical salt marshes and temperate estuaries where oyster reefs occur. Additionally, 11.8% of ML's shorelines have been armored as of …

Uracil Landscape Of Mouse B Cell Genome Undergoing Class-Switch Recombination, Fathima Rukshana Mohamad Ramshan

Wayne State University Dissertations

Activation-induced cytosine deaminase (AID) is required for both somatic hypermutation (SHM) and class switch recombination (CSR) within mammalian antibody genes. Uracils created by AID in the Ig loci are recognized and processed by base-excision and mismatch repair pathways leading to antibody diversification. This involves a hypermutation process restricted to the V(D)J segments of the immunoglobulin genes, SHM, and an error-prone end-joining process that causes isotype switching, CSR, but the molecular details of these processes have remained obscure for the past 20+ years. Most studies of SHM and CSR have used AID-promoted mutations as a proxy for the uracils, but their …

A New Model For Polar Growth In Mycobacteria: The Role Of Wag31 And Mmpl3 In Cell Wall Synthesis, Neda Habibi Arejan

Biology Dissertations - Archive

The disease Tuberculosis (TB) is caused by the pathogen Mycobacterium tuberculosis and was the cause of over one million deaths worldwide in 2023 (World Health Organization, 2023). TB treatment is difficult due to antibiotic tolerance and emerging resistance in Mtb strains. Mycobacterial cells have different regulatory mechanisms that allow them to adjust to myriad environmental stressors: these responses often lead to antibiotic tolerance. Therefore, studying responses to stress will lead to insights about antibiotic tolerance and treatment failure. Here, we specifically study two essential mycobacterial proteins, Wag31 and MmpL3, involved in cell wall metabolism. We show that Wag31 has distinct …

Rhizophora Mangle (Red Mangrove) Seedling Success In Different Habitats In Mosquito Lagoon, Florida, Usa, Mekail N. Negash

Graduate Thesis and Dissertation 2023-2024

Mangroves provide many ecosystem services in coastal environments around the world. These include water quality improvement, creating habitats for terrestrial and aquatic species, and stabilizing shorelines. In central Florida, the red mangrove Rhizophora mangle is a common species in coastal wetlands, and recently the number of individuals successfully recruiting to intertidal oyster reefs has greatly increased, possibly because biogeochemical hot spots are present on oyster reefs due to nutrient-rich biodeposits from the live oysters. To understand how well R. mangle responds in terms of survival and growth to the suite of variables associated within these two unique habitats, I tracked …

Synthesis Of Dihydro-Β-Carbolines By Tandem C-H Activation And Aza-Michael Reaction In The Presence Of Rh(Ii)/Squaramide Catalysis: Investigation Of The Mechanism Via Computational Methods, Syed Wasiuddin

Senior Honors Theses and Projects

N-heterocycles are the major component of various bioactive natural products, pharmaceuticals, and their precursors. In particularly, β-carbolines are examples of substituted indole and its derivatives that serve as the basic structures of diverse, therapeutically important molecules with broad pharmacological properties. Rajasekar and Anbarasan have suggested a novel one-pot synthesis for dihydro-β-carbolines involving more than one catalytic system: a rhodium acetate dimer for C-H insertion on the indole and a basic organo-catalyst for the subsequent aza-Michael addition. The product can be obtained enantioselectively by using a chiral squaramide as the organo-catalyst. Since the mechanism of this reaction, including the rate determining …

Malate Dehydrogenase In Parasitic Protozoans: Roles In Metabolism And Potential Therapeutic Applications, Amy L. Springer, Swati Agrawal, Eric P. Chang

Biological Sciences Research

The role of malate dehydrogenase (MDH) in the metabolism of various medically significant protozoan parasites is reviewed. MDH is an NADH-dependent oxidoreductase that catalyzes interconversion between oxaloacetate and malate, provides metabolic intermediates for both catabolic and anabolic pathways, and can contribute to NAD+/NADH balance in multiple cellular compartments. MDH is present in nearly all organisms; isoforms of MDH from apicomplexans (Plasmodium falciparum, Toxoplasma gondii, Cryptosporidium spp.), trypanosomatids (Trypanosoma brucei, T. cruzi) and anaerobic protozoans (Trichomonas vaginalis, Giardia duodenalis) are presented here. Many parasitic species have complex life cycles and depend on the environment …

Revolutionizing Our Understanding Of Specific Platelet-Pathogen Interactions, Hammodah Rawhi Hammodah Alfar

Theses and Dissertations--Molecular and Cellular Biochemistry

Aside from their classical role in maintaining hemostasis, platelets are considered first-line vascular guardians that influence both the innate and adaptive immune systems. This is mediated by either direct interactions with immune cells or through the release of pre-stored cytokines and chemokines upon interacting with pathogens such as viruses. While this establishes platelets as potential players in the response to pathogens, it remains unclear what platelets can do with pathogens and how important that is to immune responses, especially against viruses. Most systemic viremias, such as HIV-1, present with mild thrombocytopenia, which is mediated through several mechanisms such as a …

Characterization And Evolutionary Analysis Of Poly(Aspartic Acid) Degrading Enzymes: Exploring Enzymes-Dna Interactions And Expanding The Enzyme Family, Thi Ho

College of Graduate Studies: Theses & Dissertations

Poly(aspartic acid) (PAA) has emerged as a biodegradable and environmentally friendly alternative to non- biodegradable polycarboxylates. This thesis aims to further advance the understanding of PAA degradation by exploring multiple facets focusing on PAA-DNA interactions, particularly those involving the enzyme PahZ1 from Pedobacter sp. KP-2, and to investigate their physiological relevance and potential role in the evolution of PAA biodegradation enzymes. Additionally, the research characterizes PahZ1 homologs from various bacterial species, including Brevifollis gellanilyticus, Erythrobacter insulae, Sphingomonadales, and Sphingopyxis sp. Root 1497. These efforts have identified four novel homologs capable of degrading PAA. Synthetic oligopeptides were employed to identify potential …

The Multifunctional Catalytic Hemoglobin Fromamphitrite Ornata: Protocols On Isolation, Taxonomic Identification, Protein Extraction, Purification, And Characterization, Anna L. Husted, Lauren A. Presnar, R. Kevin Blackburn, Joseph L. Staton, Stephen A. Borgiani, Edward L. D'Antonio

Natural Sciences Faculty Publications

The multifunctional catalytic hemoglobin from the terebellid polychaete Amphitrite ornata, also named dehaloperoxidase (AoDHP), utilizes the typical oxygen transport function in addition to four observed activities involved in substrate oxidation. The multifunctional ability of AoDHP is presently a rare observation, and there exists a limitation for how novel dehaloperoxidases can be identified from macrobenthic infauna. In order to discover more infaunal DHP-bearing candidates, we have devised a facilitated method for an accurate taxonomic identification that places visual and molecular taxonomic approaches in parallel. Traditional visual taxonomic species identification by the non-specialist, at least for A. ornata or even for other …

Heterogeneity Of Nitrogen Fixation In The Mesopelagic Zone Of The South China Sea, Siqi Wu, Xianhui Sean Wan, Moge Du, Xirong Chen, Corday R. Selden, Mar Benavides, Sophie Bonnet, Carolin R. Löscher, M. Robert Hamersley, Margaret R. Mulholland, Xiuli Yan, Shuh-Ji Kao

OES Faculty Publications

Biological dinitrogen (N₂) fixation, the energetically expensive conversion of N₂ gas to ammonia, plays an essential role in balancing the nitrogen budget in the ocean. Accumulating studies show detectable N₂ fixation rates below the euphotic zone in various marine systems, revealing new insights of marine N₂ fixation. However, the reported rates are highly variable and frequently fall close to detection limits, raising the question of the ubiquity and significance of N₂ fixation in the global dark ocean. Using highly sensitive isotopic labeling incubation including a set of control incubations, we confirm the occurrence of mesopelagic N₂ fixation in the South …