Biochemistry, Biophysics, and Structural Biology Commons^™

Drosophila Let-7 Microrna Is Required For Remodeling Of The Neuromusculature During Metamorphosis, Nicholas S. Sokol, Peizhang Xu, Yuh-Nung Jan, Victor R. Ambros

Victor R. Ambros

The Drosophila let-7-Complex (let-7-C) is a polycistronic locus encoding three ancient microRNAs: let-7, miR-100, and fly lin-4 (miR-125). We find that the let-7-C locus is principally expressed in the pupal and adult neuromusculature. let-7-C knockout flies appear normal externally but display defects in adult behaviors (e.g., flight, motility, and fertility) as well as clear juvenile features in their neuromusculature. We find that the function of let-7-C to ensure the appropriate remodeling of the abdominal neuromusculature during the larval-to-adult transition is carried out predominantly by let-7 alone. This heterochronic role of let-7 is likely just one of the ways in which …

Effect Of Life History On Microrna Expression During C. Elegans Development, Xantha Karp, Molly Hammell, Maria C. Ow, Victor R. Ambros

Victor R. Ambros

Animals have evolved mechanisms to ensure the robustness of developmental outcomes to changing environments. MicroRNA expression may contribute to developmental robustness because microRNAs are key post-transcriptional regulators of developmental gene expression and can affect the expression of multiple target genes. Caenorhabditis elegans provides an excellent model to study developmental responses to environmental conditions. In favorable environments, C. elegans larvae develop rapidly and continuously through four larval stages. In contrast, in unfavorable conditions, larval development may be interrupted at either of two diapause stages: The L1 diapause occurs when embryos hatch in the absence of food, and the dauer diapause occurs …

Micrornas: Genetically Sensitized Worms Reveal New Secrets, Victor Ambros

Victor R. Ambros

Why do many microRNA gene mutants display no evident phenotype? Multiply mutant worms that are selectively impaired in genetic regulatory network activities have been used to uncover previously unknown functions for numerous Caenorhabditis elegans microRNAs.

In The Tradition Of Science: An Interview With Victor Ambros, Victor R. Ambros

Victor R. Ambros

No abstract provided.

Prb/Cki Pathways At The Interface Of Cell Cycle And Development, Victor Ambros

Victor R. Ambros

Comment on: The cyclin-dependent kinase inhibitors, cki-1 and cki-2, act in overlapping but distinct pathways to control cell-cycle quiescence during C. elegans development. Buck SH, et al. Cell Cycle 2009; 8:2613-20.

Mutations Of Adjacent Amino Acid Pairs Are Not Always Independent, Jyotsna Ramanan, Peter Revesz

CSE Conference and Workshop Papers

Evolutionary studies usually assume that the genetic mutations are independent of each other. This paper tests the independence hypothesis for genetic mutations with regard to protein coding regions. According to the new experimental results the independence assumption generally holds, but there are certain exceptions. In particular, the coding regions that represent two adjacent amino acids seem to change in ways that sometimes deviate significantly from the expected theoretical probability under the independence assumption.

Ionic Driven Embedment Of Hyaluronic Acid Coated Liposomes In Polyelectrolyte Multilayer Films For Local Therapeutic Delivery, Stephen L. Hayward, David M. Francis, Matthew J. Sis, Srivatsan Kidambi

Papers in Biomolecular Engineering

The ability to control the spatial distribution and temporal release of a therapeutic remains a central challenge for biomedical research. Here, we report the development and optimization of a novel substrate mediated therapeutic delivery system comprising of hyaluronic acid covalently functionalized liposomes (HALNPs) embedded into polyelectrolyte multilayer (PEM) platform via ionic stabilization. The PEM platform was constructed from sequential deposition of Poly-LLysine (PLL) and Poly(Sodium styrene sulfonate) (SPS) “(PLL/SPS)_4.5” followed by adsorption of anionic HALNPs. An adsorption affinity assay and saturation curve illustrated the preferential HALNP deposition density for precise therapeutic loading. (PLL/SPS)_2.5 capping layer on top …

Multi-Dimensional Glycan Microarrays With Glyco-Macroligands, Satya Nandana Narla, Huan Nie, Yu Li, Xue-Long Sun

Chemistry Faculty Publications

Glycan microarray has become a powerful high-throughput tool for examining binding interactions of carbohydrates with the carbohydrate binding biomolecules like proteins, enzymes, antibodies etc. It has shown great potential for biomedical research and applications, such as antibody detection and profiling, vaccine development, biomarker discovery, and drug screening. Most glycan microarrays were made with monovalent glycans immobilized directly onto the array surface via either covalent or non-covalent bond, which afford a multivalent glycans in two dimensional (2D) displaying. A variety of glyco-macroligands have been developed to mimic multivalent carbohydrate-protein interactions for studying carbohydrate-protein interactions and biomedical research and applications. Recently, a …

Cell Type–Dependent Mechanisms For Formin-Mediated Assembly Of Filopodia, Lorna E. Young, Ernest G. Heimsath, Henry N. Higgs

Dartmouth Scholarship

Filopodia are finger-like protrusions from the plasma membrane and are of fundamental importance to cellular physiology, but the mechanisms governing their assembly are still in question. One model, called convergent elongation, proposes that filopodia arise from Arp2/3 complex-nucleated dendritic actin networks, with factors such as formins elongating these filaments into filopodia. We test this model using constitutively active constructs of two formins, FMNL3 and mDia2. Surprisingly, filopodial assembly requirements differ between suspension and adherent cells. In suspension cells, Arp2/3 complex is required for filopodial assembly through either formin. In contrast, a subset of filopodia remains after Arp2/3 complex inhibition in …

Expression And Purification Of Unlabelled And Isotopically Labelled Human Fibroblast Growth Factor-1 And Its Receptor Relevance In Cancer Research, Oluwadamilola Filani

Masters Theses & Specialist Projects

Studies show that fibroblast growth factors (FGFs) control variety of cellular activities such as mitosis, cell differentiation, survival and angiogenesis. The FGF family consists of 23 different heparin-binding proteins. One of the most intensively studied members is human FGF-1 (hFGF-1) because of its critical role in the formation of blood vessels and cell proliferation in some types of cancer. The biological activities of FGFs are primarily mediated via interactions with fibroblast growth factor receptors (FGFR) and are a potent target in cancer. In this study, we report an efficient affinity column purification of hFGF-1 and the D2 domain of FGFR-2 …

Dna Repair Deficiency In Huntington's Disease Fibroblasts And Induced Pluripotent Stem Cells, Peter Anthony Mollica

Biological Sciences Theses & Dissertations

Mutant huntingtin protein (mhtt)– the protein responsible for cellular dysfunction in Huntington’s disease (HD) –is a product of an expanded trinucleotide repeat (TNR) cytosine-adenine-guanine (CAG) sequence in exon 1 of the huntingtin (HTT) gene. The pathology of HD has been extensively researched; however, the mechanism by which the disease-causing TNR expansions occur in somatic cells remains elusive. Interestingly, HD has often been referred to a ‘DNA repair disease’, even though DNA repair dysfunction in situ has not been identified. We hypothesized that presence of the mhtt protein affects the expression of DNA repair genes used to address DNA repair, ultimately …

Ligand Frameworks For Transition-Metal Complexes That Model Metalloenzyme Active, Denan Wang

Dissertations (1934 -)

Advances in the field of biomimetic inorganic chemistry require the design of sophisticated ligand frameworks that reflect the amazing complexity of metalloenzyme active sites. For instance, most active sites feature extensive hydrogen-bonding interactions between ligands bound to the metal center (the “first” coordination sphere) and nearby units in the outer (or “second”) sphere. Since these interactions modify the structural and electronic properties of the active sites, a number of inorganic chemists have sought to design ligands that permit outer-sphere functional groups to interact with first-sphere donors. This dissertation describes our contribution to these broader efforts to model the second coordination …

Image-Charge Detection €“ Novel Instrumentation And Applications, Brandon Lee Barney

Theses and Dissertations

Image-charge detection is an analytical technique in which a highly-charged particle is detected by the magnitude of the image current that it generates in a detecting electrode. This current is represented as a voltage between the charged particle and the sensing electrode. It is a single particle detection method, ideal for the analysis of large, variable mass particles such as biological cells. Some of the physical properties of Bacillus subtilis spores were explored using different applications of image-charge detection. B. subtilis is a gram-negative spore-forming bacteria that has been shown to exhibit extremophile behavior. The particular extremophile behavior that was …

Characterization Of Inhibitors Of Fatty Acid Transport Protein-2 In Cell And Animal Models, Nipun Saini

Department of Biochemistry: Dissertations, Theses, and Student Research

Obesity is correlated with insulin resistance and elevated levels of glucose, triglycerides and free fatty acids in blood. This affects overall metabolism and leads to disease. In the obese state, fat also accumulates in non-adipose tissue including liver, muscle and pancreas, where it can lead to cellular dysfunction and death. Currently, only a limited number of drugs are available to combat obesity and it is clear that new drugs, which more narrowly target the metabolic pathways involved, are required. Fatty Acid Transport Proteins (FATPs) are bifunctional proteins involved in the uptake and activation of fatty acids by esterification with coenzyme …

Biophysical Properties Of Cellular Membranes In Gram-Positive Bacterial Pathogens And Their Impact On Major Physiological Attributes And Virulence Determinants, Suranjana Sen

Theses and Dissertations

The cytoplasmic membrane of bacterial cells, forming an essential barrier from the surroundings, is a critical component of cellular physiology ensuring proper survival and maintenance of major cellular functions. The integrity of the membrane is an important feature that plays an essential role in the transport of solutes and nutrients through active and passive pathways, functions of membrane-associated proteins, electron transport and ATP synthesis, maintaining turgor pressure and combating environmental stresses, and thus is a crucial factor of a majority of cellular adaptations. The various biophysical properties affecting the integrity of this membrane are mainly determined by the composition and …

Biophysical Characterization Of A De Novo Elastin, Kelly Nicole Greenland

Dissertations, Theses, and Capstone Projects

Natural human elastin is found in tissue such as the lungs, arteries, and skin. This protein is formed at birth with no mechanism present to repair or supplement the initial quantity formed. As a result, the functionality and durability of elastin's elasticity is critically important. To date, the mechanics of this ability to stretch and recoil is not fully understood. This study utilizes de novo protein design to create a small library of simplistic versions of elastin-like proteins, demonstrate the elastin-like proteins, maintain elastin's functionality, and inquire into its structure using solution nuclear magnetic resonance (NMR).

Elastin is formed from …

Regulation Of The Vacuolar Atpase Activity, Paulina Konarzewska

Dissertations, Theses, and Capstone Projects

In eukaryotes, V-ATPases play an essential role in cellular pH homeostasis as they transport hydrogen ions into the vacuoles. This assures an acidic vacuolar interior and normal physiological processes associated with this organelle. Studies show that mutations in any of the VMA genes encoding for subunits of the V-ATPase pump result in growth inhibition in the absence of inositol, suggesting that V-ATPases may play an important role in phospholipid biosynthesis or vice versa. It is not clear how VMA genes affect phospholipid biosynthesis and how the regulators of phospholipid biosynthetic genes may affect ATPase activity. Here, we employ biochemical and …

The Role Of Atp And Cleavage Factor Phosphorylation In Pre-Mrna 3' Cleavage Reaction, Asya Khleborodova

Dissertations, Theses, and Capstone Projects

The 3' end cleavage/polyadenylation (3' processing) is important in generating a functional messenger RNA (mRNA) transcript. It is long-known that ATP can significantly stimulate the in vitro cleavage of adenovirus type 2 L3 (Ad2L3) RNA substrate. Here, we used ATP analogs in structure-activity assays to show that the structural features of ATP and its analogs determine in vitro 3' cleavage efficiency. More specifically, we demonstrate that the structure of the nitrogenous base, the nucleotide sugar and the triphosphate group contribute to the efficiency of the nucleotide-stimulated in vitro 3' cleavage reaction.

It was found that AppNp, an analog of ATP …

Exploiting Cancer Cell Signaling And Metabolism: Implications For Therapeutic Approach, Suman Mukhopadhyay

Dissertations, Theses, and Capstone Projects

Over the last decade, metabolic dysregulation in cancer cells has stimulated a significant amount of interest in basic research. It has been established that cancer cells increase glucose uptake and alter the fate of glycolytic and tricarboxylic acid (TCA) cycle intermediates for the synthesis of biological molecules to accommodate high rates of cellular growth and proliferation. Moreover, it is more prominent that some metabolic dysregulations are specific to particular oncogenes. Exploiting the dysregulated metabolic dependency of cancer cells with therapeutic means could represent a novel approach for clinical aspect.

To meet the need of increased anabolic metabolism cancer cells engage …

Exploring Chromatin-Bound Mdm2 Functions In Compromised Transcriptional Regulation Of P53 Target Genes, Melissa Rosso

Dissertations, Theses, and Capstone Projects

MDM2 overexpression is a common occurrence in many types of cancer. A single nucleotide polymorphism (T to G) near the mdm2 promoter, termed mdm2 SNP309, leads to MDM2 overexpression. This polymorphism is associated with accelerated tumor formation, decreased sensitivity to DNA damage treatment and compromised p53 transcriptional activity. Two G/G SNP309 cancer cell lines MANCA and A875, a Burkitts' lymphoma and melanoma respectively, express a stable wild-type p53 protein. We previously reported these cells have DNA damage resistant MDM2-p53 chromatin complexes and hypothesized that MDM2 is the contributing factor for the compromised p53 transcriptional activity. We created constitutive mdm2 shRNA …