Cold-Inducible Rna Binding Protein Impedes Breast Tumor Growth In The Pymt Murine Model For Breast Cancer,
2024
University of New Mexico School of Medicine
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,
2024
CUNY Graduate Center
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,
2024
University of Missouri-St. Louis
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.,
2024
University of Missouri, St. Louis
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,
2024
Huazhong Agricultural University
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,
2024
Chalmers University of Technology
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,
2024
Augusta University
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,
2024
Brno University of Technology, University of Nebraska-Lincoln
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,
2024
Coastal Carolina University
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),
2024
University of Nebraska-Lincoln
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,
2024
Thomas Jefferson University
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,
2024
Faculty of Allied Health Sciences
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,
2024
University of Central Florida
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,
2024
Wayne State University
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,
2024
University of Texas at Arlington
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,
2024
University of Central Florida
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,
2024
Eastern Michigan University
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,
2024
University of Mary Washington
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,
2024
University of Kentucky
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,
2024
Georgia Southern University
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 …
