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Full-Text Articles in Life Sciences
Escherichia Coli As A New Platform For The Study Of Phosphoinositides, Sergio Botero
Escherichia Coli As A New Platform For The Study Of Phosphoinositides, Sergio Botero
Student Theses and Dissertations
Phosphoinositides are membrane phospholipids involved in a wide variety of processes across the tree of life. In eukaryotic cells they function though their role as integral membrane components, anchors for proteins, membrane identity markers, and signaling molecules. Phosphoinositides are regulated through the phosphorylation and dephosphorylation of the inositol head-group at the 3rd, 4th, and 5th positions, creating a complex and very dynamic interconversion network. They can also be hydrolyzed into an inositide head-group and diacylglycerol which are in turn signaling molecules. The wide variety of functions, and redundancy in their synthesis pathways, makes the in-vivo study of phosphoinositides complex since …
Characterization Of Mechanisms That Mediate Cancer Metastatic Colonization, Alexander Huan Nguyen
Characterization Of Mechanisms That Mediate Cancer Metastatic Colonization, Alexander Huan Nguyen
Student Theses and Dissertations
Metastatic disease is the major cause of death in all solid tumor cancers. Current therapeutic strategies fail to target metastasis as the genes and mechanisms that regulate this process remain poorly understood. Metastatic colonization is the final step of the metastatic cascade whereby cancer cells form a tumor at a distant site. This final step is the culmination of clonal evolution of cancer populations that results in a highly aggressive population with enhanced metastatic capacity and often presents clinically as numerous inoperable tumor nodules that lead to mortality. Characterization of the mechanisms that govern metastatic colonization at cellular and molecular …
A Census Of Human Rna-Binding Proteins, Stefanie Gerstberger
A Census Of Human Rna-Binding Proteins, Stefanie Gerstberger
Student Theses and Dissertations
No abstract provided.
Genetic Dissection Of Neural Circuits Underlying Value Based Decision Making, Hirofumi Nakayama
Genetic Dissection Of Neural Circuits Underlying Value Based Decision Making, Hirofumi Nakayama
Student Theses and Dissertations
Decision making is the fundamental process that we utilize to accomplish objectives in everyday lives. To understand the neural substrates of this process, we developed a behavioral task for mice that required repetition of the processes of action initiation, action selection, and learning. The task is a two-option choice task with stochastic reward delivery and reversals. To map brain areas involved in this type of value-based learning, we inactivated neuronal activity in the prefrontal cortex (PFC) and the nucleus accumbens (NAc) while mice performed the task. Inactivation of the NAc resulted in altered action initiation and learning but had subtle …
Protein Regulators Of Phosphoinositides As Promoters Of Cancer Metastasis, Caitlin Anne Sengelaub
Protein Regulators Of Phosphoinositides As Promoters Of Cancer Metastasis, Caitlin Anne Sengelaub
Student Theses and Dissertations
Metastasis, the spread of cancer cells from a primary tumor to a distal organ, represents the predominant cause of mortality in patients with solid tumors. However, the molecular mechanisms underpinning this multistep progression are poorly defined. Successful metastasis requires a cancer cell to acquire multiple capabilities, including the ability to migrate, invade, and co-opt the microenvironment in the distal organ for colonization. Many of these phenotypes require the actions of a family of lipids called phosphoinositides (PIs). Although structurally small molecules and minor components of the cellular lipidome, PIs are critical mediators of many cellular processes through their localization, abundance, …
Qualitative And Quantitative Regulation Of The Leptin Gene In Vivo, Yi-Hsueh Lu
Qualitative And Quantitative Regulation Of The Leptin Gene In Vivo, Yi-Hsueh Lu
Student Theses and Dissertations
The high prevalence of obesity is a major public health concern worldwide. Conventional strategies have failed to provide solid solutions, greater than 90% of individuals who lost weight by diet and exercise eventually regained the weight (Arner and Spalding, 2010a). As such, biological factors including genetic contributions have become the research focus on pathogenesis of obesity and the target of effective disease control. Central to energy homeostasis is the mechanism by which animals regulate and/or response to fluctuation in energy intake and output. Adipose tissues participate in metabolic regulation by serving as an energy store and by secreting adipokines such …
Metabolic Regulation Of Gene Expression Through Differential Histone Acylation: The Regulation And Function Of Histone Crotonylation, Benjamin R. Sabari
Metabolic Regulation Of Gene Expression Through Differential Histone Acylation: The Regulation And Function Of Histone Crotonylation, Benjamin R. Sabari
Student Theses and Dissertations
Histone lysine acetylation (Kac) plays a critical role in gene regulation by affecting the accessibility of the DNA wrapped around histones and by recruiting effector complexes. Three major classes of proteins are associated with Kac, namely “writers,” enzymes that covalently modify specific lysine residues, “readers,” protein domains that specifically bind modified residues, and “erasers,” enzymes that catalyze the removal of the modification. While histone acetylation is well characterized within this paradigm, little is known about the regulation and function of an expanding list of histone lysine acylations. Lysine propionylation, butyrylation, and crotonylation were all discovered by proteomics-based approaches as I …
Investigating The Role Of Muscleblind-Like 1 In The Suppression Of Breast Cancer Progression, Lisa Fish
Investigating The Role Of Muscleblind-Like 1 In The Suppression Of Breast Cancer Progression, Lisa Fish
Student Theses and Dissertations
Breast cancer is a prevalent disease. Metastatic disease accounts for the majority of deaths from breast cancer, as patients with distant metastatic disease have a much worse prognosis than those with localized disease. In order to better understand why some breast cancers metastasize and others do not, it is critical to identify and elucidate the determinants of breast cancer progression. Post-transcriptional control of gene expression plays a central role in modulating transcriptional output. The interactions between messenger RNA cis-regulatory elements and trans-factors control coordinated gene expression states. Posttranscriptional regulatory programs that enhance metastatic capacity are selected for during cancer progression. …
Molecular Basis Of Mechanosensitivity, Josefina Ines Del Marmol
Molecular Basis Of Mechanosensitivity, Josefina Ines Del Marmol
Student Theses and Dissertations
Mechanosensation is arguably the least understood of all senses. For most physiological processes, the first response to membrane stress is thought to be the opening or closing of mechanosensitive channels1, but the clonal nature of the first mechanotransducers is still largely unknown. The objective of my research was to identify molecules involved in mechanosensory transduction by both studying known channels as well as performing screens to identify previously uncharacterized channels. Shortly before my research began, Daniel Schmidt from the MacKinnon Lab showed that certain voltage gated potassium channels, not previously associated with mechanosensation, are in fact remarkably sensitive …
The Genetics Of Mosquito Heat-Seeking Behavior, Román A. Corfas
The Genetics Of Mosquito Heat-Seeking Behavior, Román A. Corfas
Student Theses and Dissertations
Temperature is a highly dynamic feature of the world, and one that deeply affects living things. Organisms have evolved sophisticated sensory-motor systems to detect and avoid excessive heat or cold—a behavior termed thermotaxis. In rare cases, however, animals use thermosensation not only to regulate their body temperature, but also to locate food sources in their environment. One example of such an adaptation is found in the female Aedes aegypti mosquito, which becomes attracted to the body heat of endothermic (“warm-blooded”) hosts when in pursuit of a blood meal. Mosquitoes are remarkably adept at finding hosts in their environment and have …
Dynamics Of Hiv-1 Infection And Therapy In Vivo, Joshua Abraham Horwitz
Dynamics Of Hiv-1 Infection And Therapy In Vivo, Joshua Abraham Horwitz
Student Theses and Dissertations
Human immunodeficiency virus type 1 (HIV-1) is the causative agent of acquired immune deficiency syndrome (AIDS), a disease responsible for extensive morbidity and mortality worldwide. Despite more than thirty years of research since the discovery of HIV-1, no cure or vaccine yet exists. HIV-1 infection, while treatable with suppressive antiretroviral therapy drugs (ART), establishes lifelong persistence in the infected host as a natural consequence of the viral life cycle and the dynamic properties of the human immune cells in which HIV-1 propagates. This persistence is driven by populations of rare, long-lived HIV-1-infected cells, termed latently infected cells (LICs), that are …
Studies Towards The Discovery Of Novel Natural Products Through Functional Analysis Of Environmental Dna-Encoded Type Ii Polyketide Synthases, Debjani Chakraborty
Studies Towards The Discovery Of Novel Natural Products Through Functional Analysis Of Environmental Dna-Encoded Type Ii Polyketide Synthases, Debjani Chakraborty
Student Theses and Dissertations
Natural products have historically served as a major source for most of the therapeutically relevant compounds. A significant fraction of these natural product-based drugs and leads are derived from microorganisms. Although the traditional culture-based strategy has proven very successful over the course of more than a century of investigation, it excludes a significant portion of the molecules present in environmental samples because majority of the bacteria are not readily amenable to culture-based strategies. This uncultured majority is believed to represent 99% of bacterial species in the environment. Therefore, it has remained a significant challenge to access the chemical diversity present …
Regulatory Architecture Of Non-Apoptotic Cell Death Program In C. Elegans, Maxime Jeremie Kinet
Regulatory Architecture Of Non-Apoptotic Cell Death Program In C. Elegans, Maxime Jeremie Kinet
Student Theses and Dissertations
Cell death is prevalent in animal development, homeostasis, and disease. While apoptotic cell death has been extensively studied, many dying cells in development do not exhibit apoptotic morphology, and mice lacking core apoptotic regulators have mostly normal rates of developmental programmed cell death. However, little is known about how alternative death programs are set in motion. In the nematode Caenorhabditis elegans, most cells fated to die by apoptosis are eliminated as young, undifferentiated cells, for no obvious functional reasons. The male nematode’s linker cell, in contrast, dies as an older, differentiated cell, whose life and death subserve precise and important …
Characterization Of Skin Immune Reactions Induced By The Contact Sensitizer Diphencyprone In Healthy Volunteers And Metastatic Melanoma Patients, Nicholas Gulati
Characterization Of Skin Immune Reactions Induced By The Contact Sensitizer Diphencyprone In Healthy Volunteers And Metastatic Melanoma Patients, Nicholas Gulati
Student Theses and Dissertations
Melanoma is a life-threatening malignant disease, of which the standard of care treatment is rapidly becoming immunologically driven, due to favorable recent clinical trials using immune checkpoint inhibitors. Diphencyprone (DPCP), a topically applied contact sensitizer, has been used with an 84% success rate to treat cutaneous melanoma metastases, but the immune mechanisms underlying its efficacy are largely unknown. This thesis characterizes skin immune reactions induced by DPCP, both in healthy volunteers and patients with metastatic melanoma. In healthy volunteers, DPCP led to upgregulation of many immune molecules that may be anti-neoplastic effectors, including IFNγ, IL-24, and IL-9. We also examined …
Natural Products From Functional Screening Of Soil Metagenomic Libraries, Hala Iqbal
Natural Products From Functional Screening Of Soil Metagenomic Libraries, Hala Iqbal
Student Theses and Dissertations
Bacteria are a prolific source of therapeutically and industrially relevant natural products. Traditional routes of natural product discovery focus on cultured bacteria, a strategy that eludes 99% of the microbiome. Metagenomics offers a route to study uncultured bacteria by extracting DNA present in environmental samples and cloning this eDNA into a vector to make metagenomic libraries. Libraries can then be screened in various ways to find natural products with desired characteristics and activities. Functional screening uses phenotypically identifiable traits such as changes in color or antibiotic activity to discover clones of interest in a metagenomic library. This mode of screening …
Tracking The In Vivo Dynamics Of Antigenic Variation In The African Trypanosome, Monica R. Mugnier
Tracking The In Vivo Dynamics Of Antigenic Variation In The African Trypanosome, Monica R. Mugnier
Student Theses and Dissertations
Trypanosoma brucei, a causative agent of African sleeping sickness in humans and nagana in animals, constantly changes its dense variant surface glycoprotein (VSG) coat to avoid elimination by the immune system of its mammalian host, using an extensive repertoire of dedicated genes. Although this process, referred to as antigenic variation, is the major mechanism of pathogenesis for T. brucei, the dynamics of VSG expression in T. brucei during an infection are poorly understood. In this thesis, I describe the development of VSG-seq, a method for quantitatively examining the diversity of expressed VSGs in any population of trypanosomes. Using VSG-seq, I …
Paleovirological Analyses Of Endogenous Retroviruses And Host Innate Immune Effectors, Daniel Blanco Melo
Paleovirological Analyses Of Endogenous Retroviruses And Host Innate Immune Effectors, Daniel Blanco Melo
Student Theses and Dissertations
About 8 and 10 percent of the human and mouse genomes, respectively, are comprised of sequences of retroviral origin. Occasional infection of germ line can lead to integrated retroviral genomes being vertically inherited as host alleles. During thousands to millions of years, some of these sequences acquired inactivating mutations and were fixed in ancestral populations by genetic drift, while others became fixed by providing an evolutionary advantage to the host. Those inherited proviruses are termed endogenous retroviruses (ERVs) and have been identified in a variety of animal species representing an extensive viral “fossil” record of past retroviral infections. With the …
Extracellular Metabolic Energetics Can Promote Cancer Progression, Jia Min Loo
Extracellular Metabolic Energetics Can Promote Cancer Progression, Jia Min Loo
Student Theses and Dissertations
Colon cancer progression is characterized by growth of the primary tumor in the colon followed by metastasis to distant organs. The metastatic cascade involves invasion of cells from the primary tumor into the surrounding tissue, entering into and survival of cancer cells in the circulation, arrival at the end organ and finally colonization of the end organ. The liver is the primary site of colon cancer metastatic colonization, with over 70% of colon cancer patients experiencing liver metastases. Despite current standard-of-care surgical intervention and broad spectra cytotoxic chemotherapeutics, the survival rate of patients with metastatic disease is less then 5%. …
Plasticity Of The Nuclear Pore Complex Revealed With Proteomics, Zhanna Hakhverdyan
Plasticity Of The Nuclear Pore Complex Revealed With Proteomics, Zhanna Hakhverdyan
Student Theses and Dissertations
Cellular functions are performed by the concerted action of macromolecular assemblies. These protein machines rarely have permanent, invariable structures. Instead, the subunits forming the macromolecular assemblies exchange between free and bound states, changing the composition, conformation and function of the assembly. Characterizing the function of macromolecular assemblies, therefore, requires the study of their dynamics. I have developed a strategy for in vivo assessment of macromolecular plasticity and have successfully applied it to the yeast nuclear pore complex (NPC), one of the largest and most elaborate protein machines in the cell. NPC is a massive protein assembly situated in the nuclear …
Aversive Olfactory Imprinting In Caenorhabditis Elegans, Xin Jin
Aversive Olfactory Imprinting In Caenorhabditis Elegans, Xin Jin
Student Theses and Dissertations
Early memories are especially robust and enduring, among which the most evocative example is imprinting. Imprinting was first described in newly hatched geese that form a lasting attachment to the first moving object they see. As observed in many animal species, imprinting is a process in which a sensory cue presented early in animal’s life – a critical period – subsequently gains unique access to ecologically relevant behaviors. Little is known about the molecular and neural underpinnings of imprinting. I have used C. elegans as a model organism to study imprinting because of its compact and well characterized nervous system, …
Reconstitution And Mechanistic Studies On The Staphylococcal Agr Quorum Sensing Circuit, Boyuan Wang
Reconstitution And Mechanistic Studies On The Staphylococcal Agr Quorum Sensing Circuit, Boyuan Wang
Student Theses and Dissertations
Quorum sensing (QS) plays a central role in virulence induction in the commensal pathogen, Staphylococcus aureus. This bacterium secretes an auto-inducer peptide (AIP), a small, cyclic peptide containing a thiolactone linkage as an indicator of its population density, and up-regulates virulence gene expression in response to high extracellular AIP levels. We have investigated two key biochemical events in S. aureus QS and revealed several underlying regulatory mechanisms. The first such event, formation of the high energy thiolactone in AIP, is unusual in that it occurs directly through proteolysis of the precursor peptide, AgrD, without free-energy input from ATP hydrolysis. We …
Analysis Of Hepatocyte Secretion Pathways: A Case Study On Hepatic Apolipoproteins, Serum Albumin, And Hepatitis C Virus, Constantin N. Takacs
Analysis Of Hepatocyte Secretion Pathways: A Case Study On Hepatic Apolipoproteins, Serum Albumin, And Hepatitis C Virus, Constantin N. Takacs
Student Theses and Dissertations
The hepatocyte is one of the major secretory cell types in the body. It fulfills many of the liver's essential functions in protein secretion, lipid storage and transport, and excretion. Some of these functions are carried out via polarized secretion of simple protein cargo, such as serum albumin, or large macromolecular lipid-protein complexes, the lipoproteins. The hepatocyte is also the site of infection of several hepatotropic viruses. Of these, hepatitis C virus (HCV) is peculiar due to its close structural and functional association with the hepatic lipoproteins. All these cargoes are transported from the endoplasmic reticulum (ER) to the cell …
Retrograde Activation Of A Somatic Transcriptional Program Regulates Distal Axon Degeneration, Jason Pitts
Retrograde Activation Of A Somatic Transcriptional Program Regulates Distal Axon Degeneration, Jason Pitts
Student Theses and Dissertations
During development of the peripheral nervous system, sensory axons extend to the periphery in excess where they compete for limiting target-derived neurotrophic support. Local neurotrophin insufficiency triggers axon degeneration, resulting in the pruning of over half of all sensory axons during development. Although axon degeneration facilitates the essential sculpting of the developing nervous system, its improper activation may underlie several neurodegenerative disorders. This process can be modeled in vitro by culturing sensory neurons from mouse dorsal root ganglia in the presence of nerve growth factor either as explant cultures or in compartmented chambers that allow independent manipulation of cell bodies …
Selection Dynamics In The Germinal Center During Antibody Affinity Maturation, Alexander Gitlin
Selection Dynamics In The Germinal Center During Antibody Affinity Maturation, Alexander Gitlin
Student Theses and Dissertations
The maturation of antibody affinity during the immune response, discovered as a serological phenomenon in 1964, is critical to the development of high affinity humoral immunity. This process takes place in germinal centers (GCs), which are microanatomical structures composed of antigen-specific B lymphocytes that form in secondary lymphoid organs upon infection or immunization. High affinity B cells are selectively expanded in the GC by iterative rounds of migration between a zone of hypermutation and proliferation (the dark zone, or DZ) and a zone of selection (the light zone, or LZ). The mechanism whereby somatic antibody mutants are selected on the …
Regulation Of The Anaphase-Promoting Complex Examined At The Single Cell Level, Andrej Ondracka
Regulation Of The Anaphase-Promoting Complex Examined At The Single Cell Level, Andrej Ondracka
Student Theses and Dissertations
Cell cycle transitions are driven by oscillations of cyclin-cyclin dependent kinase (CDK) activity and associated cyclin degradation, mediated by ubiquitylation by the anaphase-promoting complex (APC). In this work, I analyzed the regulation of the APC by its activator Cdh1 in budding yeast in single cells. Inactivation of APC-Cdh1 is an important regulatory transition leading to mitotic entry. I developed and characterized a fluorescent biosensor to measure the dynamics of APC-Cdh1 activity in single cells by quantitative time-lapse microscopy. I found that APC-Cdh1 is inactivated with very reliable timing, in contrast with other cell cycle events that occur with considerable variability …
Cpispr-Cas: From A Prokaryotic Immune System To A Gene Editing Tool, Wenyan Jiang
Cpispr-Cas: From A Prokaryotic Immune System To A Gene Editing Tool, Wenyan Jiang
Student Theses and Dissertations
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and their associated genes (cas) encode an adaptive, small-RNA-based immune system that protects prokaryotes from infectious phages and plasmids. CRISPR-Cas systems can be classified into three types based on their cas gene content. My thesis work focused on two parts. First, I investigated the mechanism and function of RNA cleavage in type III CRISPR-Cas immunity. Secondly, I developed a tool to manipulate prokaryotic genomes and gene expression by using an engineered type II CRISPR-Cas system. To date, all three types of CRISPR-Cas systems target DNA. Type III CRISPR-Cas immunity displays an elaborate targeting …
Chemical Tools For Exploring Ifitm3 S-Palmitoylation And Mechanism, Xiaoqiu Yuan
Chemical Tools For Exploring Ifitm3 S-Palmitoylation And Mechanism, Xiaoqiu Yuan
Student Theses and Dissertations
Protein S-palmitoylation is a reversible post-translational lipid modification that regulates the trafficking, stability, and activity of proteins in eukaryotes. The detection of fatty-acylated proteins has been challenging but recent advances in chemical labeling methods have enabled more sensitive detection and proteomic analyses, which I summarize in Chapter 1. The proteomic analysis of S-palmitoylated proteins in dendritic cells and macrophages by our laboratory revealed that the interferon-induced transmembrane proteins (IFITMs) are S-fatty-acylated at conserved cysteine (Cys) residues. IFITMs are unique interferon-induced proteins that restrict the infection of multiple pathogenic viruses. Initial studies by our laboratory showed that S-fatty-acylation on three conserved …
Nanobody-Based Interactomic Studies Of Single Transcripts During Mrna Maturation, Peter C. Fridy
Nanobody-Based Interactomic Studies Of Single Transcripts During Mrna Maturation, Peter C. Fridy
Student Theses and Dissertations
During and after transcription in the nucleus, messenger RNAs (mRNAs) undergo a variety of processing events before being exported to the cytoplasm through the nuclear pore complex. mRNA processing and nuclear export require a wide range of protein factors, which interact with maturing transcripts and each other to form dynamic mRNP complexes. While there are many core, essential mRNP factors, the pathways governing mRNA maturation are not uniform, and different transcripts can be associated with mRNP complexes of dramatically different composition or kinetics. To date though, it has been difficult to study RNP complexes specific to any single mRNA species, …
Structural And Functional Characterization Of Spoa Domains In Salmonella Typhimurium Type Iii Secretion Systems, Ryan Q. Notti
Structural And Functional Characterization Of Spoa Domains In Salmonella Typhimurium Type Iii Secretion Systems, Ryan Q. Notti
Student Theses and Dissertations
Once optimistically believed to be a relic of the pre-antibiotic era, bacterial pathogens remain a substantial threat to human health, and the growing epidemic of antibiotic resistance has raised concerns for the long term prospects of antimicrobial therapy. By understanding the mechanisms used by bacteria to manipulate their host and cause disease, it is hypothesized that we might more rationally approach anti-infective therapeutic design. Type III secretion systems (T3SS) are employed by some gram-negative human pathogens to manipulate the host environment. One T3SS subtype, known as the “injectisome,” delivers virulence factors directly into host cells. The other T3SS subtype secretes …