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Articles 1 - 23 of 23
Full-Text Articles in Life Sciences
Natural Product Biosynthesis In Uncultured Bacteria, Jeffrey Kim
Natural Product Biosynthesis In Uncultured Bacteria, Jeffrey Kim
Student Theses and Dissertations
A single gram of soil can contain thousands of unique bacterial species, only a small fraction of which is regularly cultured in the laboratory.Although the fermentation of cultured microorganisms has provided access to numerous bioactive secondary metabolites, with these same methods it is not possible to characterize the natural products encoded by the uncultured majority. The heterologous expression of biosynthetic gene clusters cloned from DNA extracted directly from environmental samples (eDNA) has begun to provide access to the chemical diversity encoded in the genomes of previously uncultured bacteria. The systematic exploration of natural product biosynthesis in uncultured bacteria, however, still …
A Proteomic And Genomic Investigation Into Replication Fork Dynamics In Saccharomyces Cerevisiae, Matthew David Sekedat
A Proteomic And Genomic Investigation Into Replication Fork Dynamics In Saccharomyces Cerevisiae, Matthew David Sekedat
Student Theses and Dissertations
In eukaryotic organisms, each chromosome must be precisely replicated every time a cell divides so that the genetic material can be passed on to the cell’s progeny. The work presented here is an in-depth investigation into the dynamics of the proteins that associate with progressing replication forks in yeast. A focused proteomics approach is employed to specifically identify interactions between the replication fork-coupled GINS complex and other components of the replication machinery. The scope of this technique is extended by applying it to cells that have been synchronized within the cell cycle – revealing the cell cycle dependent interactions of …
The Role Of The Stereociliary Glycocalyx In Hair Bundle Cohesion, Adria Claire Le Boeuf
The Role Of The Stereociliary Glycocalyx In Hair Bundle Cohesion, Adria Claire Le Boeuf
Student Theses and Dissertations
The sensory hair cells of the inner ear are exquisitely sensitive machines that translate the broad dynamic range of sound intensities in our auditory landscape into the electrical language of neurons. The mechanosensitive organelle of the hair cell is the hair bundle, a cluster of linked, finger-like, membrane-ensheathed projections, stereocilia, emerging from the cellʼs apical surface. As a structure, the hair bundle is highly conserved, changing little yet performing many functions throughout the vertebrate evolutionary tree. The mechanosensitivity of the hair bundle is achieved by the tension-gating of mechanosensitive channels joined to proteinaceous tip links that connect the distal tips …
Long-Term Quantitative Microscopy: From Microbial Population Dynamics To Growth Of Plant Roots, Zak Frentz
Long-Term Quantitative Microscopy: From Microbial Population Dynamics To Growth Of Plant Roots, Zak Frentz
Student Theses and Dissertations
Quantitative optical measurements at the micron scale have been crucial to the study of multiple biological processes, including bacterial chemotaxis, eukaryotic gene expression and y development. Extending measurements to long time scales allows complete observation of processes that are otherwise studied piecemeal, such as development and evolution. This thesis describes the development of two types of microscope for making long term, quantitative measurements, and the tools for image analysis. The rst device is a digital holographic microscope for measuring microbial population dynamics. It allows three dimensional localization of hundreds of cells within a mm3 sized volume, at micron resolution and …
A Hydrodynamic Sensory Antenna Used By Killifish For Nocturnal Hunting, Jason S. Schwarz
A Hydrodynamic Sensory Antenna Used By Killifish For Nocturnal Hunting, Jason S. Schwarz
Student Theses and Dissertations
The perception of sensory stimuli by an animal requires several steps, commencing with the capture of stimulus energy by an antenna. As the interface between the physical world and sensory transduction, the antenna modifies the stimulus in ways that enhance the animal’s perception. For example, the mammalian external ear collects sound and spectrally alters it to increase sensitivity and improve the detection of directionality. The surfacefeeding killifish Aplocheilus lineatus is able to hunt in darkness by detecting surface capillary waves with the lateral-line system atop its head. This cephalic lateral line consists of 18 stereotyped mechanosensitive neuromasts, each bordered by …
Spatial Control Of Cdc42 Activation Regulates Cell Width And Growth Zone Formation, Felice D. Kelly
Spatial Control Of Cdc42 Activation Regulates Cell Width And Growth Zone Formation, Felice D. Kelly
Student Theses and Dissertations
The fission yeast Schizosaccharomyces pombe is a rod--â€shaped cell that grows by linear extension at the cell tips, with a nearly constant width throughout the cell cycle. This simple geometry makes it a good system to study the control of cellular dimensions. Here I used the width of the cell as a model for the control of growth zone size. To identify genes that influence cell size I carried out a near--â€genome--â€widescreen for mutants wider than wild--â€type cells. I found eleven deletion mutants that were wider; seven of the deleted genes are implicated in the control of the small GTPase …
Rapid Functional Dissection Of Genetic Networks Via Rnai In Mouse Embryos, Geulah Livshits
Rapid Functional Dissection Of Genetic Networks Via Rnai In Mouse Embryos, Geulah Livshits
Student Theses and Dissertations
The development and maintenance of epithelial tissues is regulated by a complex array of signal cues from adjacent cells, the extracellular milieu and intracellular signaling cascades. In the mammalian epidermis, these cues instruct the specification and invagination of hair follicles as well as the stratification and turnover of the interfollicular epidermis. These processes rely on a coordinate balance of tissue growth, differentiation and regulation of cell-cell adhesion to maintain the integrity of the epithelium. Understanding the interplay between the various pathways controlling tissue development requires model systems that recapitulate the events that occur in vivo. Genetic studies in Drosophila and …
Regulation Of Polarized Protein Transport To Axons, Dendrites, And Sensory Cilia In Caeborhabditis Elegans Neurons, Tapan Apurva Maniar
Regulation Of Polarized Protein Transport To Axons, Dendrites, And Sensory Cilia In Caeborhabditis Elegans Neurons, Tapan Apurva Maniar
Student Theses and Dissertations
Neurons are highly polarized cells, capable of receiving, processing and transmitting information, with the help of their specialized domains, an axon and one or more dendrites. The molecular dissimilarities between these domains are critical for neuronal function, and are a result of asymmetric trafficking of a large number of cellular components including ion channels, neurotransmitter receptors, synaptic vesicles, and signaling proteins. Yet, despite the significance of asymmetric protein transport in neuronal polarity, the molecules and mechanisms that direct polarized transport to axons, dendrites and cilia in neurons are only partly understood. In this thesis, I describe my effort at understanding …
Bioorthogonal Chemical Reporters Reveal Fatty-Acylation Of Histone H3 Variants And Cholesterol Modification Of Proteins And Trafficking In Cells, John P. Wilson
Bioorthogonal Chemical Reporters Reveal Fatty-Acylation Of Histone H3 Variants And Cholesterol Modification Of Proteins And Trafficking In Cells, John P. Wilson
Student Theses and Dissertations
Lipids are essential components to all known life. They serve many functions from basic building blocks to covalent protein modification and are particularly involved in signaling. Many rare and widespread human health concerns involve lipids but despite their importance, their analysis either free or protein-bound has remained difficult for decades. Here, using bioorthogonal chemistry, we have developed a robust system to identify the proteins modified by lipids and advanced the ability to image cholesterol in cells and tissues. The unbiased proteomic analysis of fatty-acylated proteins using chemical reporters undertaken here revealed a greater diversity of lipid-modified proteins in mammalian cells …
Dre-1/Fbxo11, A Conserved F Box Protein, Regulates Apoptosis In C. Elegans And Is Mutated In Human Lymphoma, Michael Chiorazzi
Dre-1/Fbxo11, A Conserved F Box Protein, Regulates Apoptosis In C. Elegans And Is Mutated In Human Lymphoma, Michael Chiorazzi
Student Theses and Dissertations
In the course of metazoan embryonic and post-embryonic development, more cells are generated than exist in the mature organism, and these cells are deleted by the process of programmed cell death. In addition, cells can be pushed toward death when they accumulate genetic errors, are virally-infected or are otherwise deemed potentially-harmful to the overall organism. Caenorhabditis elegans has proved to be an excellent model system for elucidating the genetic underpinnings of cell death, and research has shown that the core machinery, made up of the egl-1, ced-9, ced-4 and ced-3 genes, is conserved across metazoans, and their homologues are crucial …
The Long-Rage Directional Behavior Of The Nematode C. Elegans, Margherita Peliti
The Long-Rage Directional Behavior Of The Nematode C. Elegans, Margherita Peliti
Student Theses and Dissertations
Like any mobile organism, C. elegans relies on sensory cues to find food. In the absence of such cues, animals might display defined search patterns or other stereotyped behavior. The motion of C. elegans has previously been characterized as a sinusoid whose direction can be modulated by gradual steering or by sharp turns, reversals and omega bends. However, such a fine-grained behavioral description does not by itself predict the longrange features of the animals’ pattern of movement. Using large (24 cm x 24 cm) Petri dishes, we characterized the movement pattern of C. elegans in the absence of stimuli. To …
Expanding The Horizons Of Enzybiotic Identification, Jonathan Edward Schmitz
Expanding The Horizons Of Enzybiotic Identification, Jonathan Edward Schmitz
Student Theses and Dissertations
Recently, phage lytic enzymes (also known as endolysins or, simply, lysins) have received considerable attention as potential antibacterial agents. During the infective cycle of double-stranded DNA phage, these peptidoglycan hydrolases are responsible for digesting the cell wall of the host bacterium and freeing newly-assembled viral particles. At the same time, an increasing body of evidence has demonstrated that recombinantly-purified phage lysins—when added exogenously—can potently kill Gram-positive bacteria, whose peptidoglycan is accessible from the extracellular space. Consequently, lysins have been proposed as novel enzybiotic (i.e. enzyme-antibiotic) molecules that could serve as novel weapons in the fight against drug-resistant bacteria. Most lysins …
From Microarrays To Behavior: Genes Controlled By Feeding State In Mosquitoes And Flies, Shelli F. Farhadian
From Microarrays To Behavior: Genes Controlled By Feeding State In Mosquitoes And Flies, Shelli F. Farhadian
Student Theses and Dissertations
Across many species, animals carefully regulate their food intake according to their energy needs. They are able to do so through the ability to sense hunger or satiety cues. In vertebrates, these signals are released by the gastrointestinal tract and by adipose tissue, and reach feeding centers in the brain, where they stimulate the release of peptides that modulate feeding behavior (Benarroch, 2010; Berthoud, 2008). Although many of these neuronal populations have been identified in rodent models, the neural circuitry behind behavioral modification of food intake remains largely unknown. Insects like the blowfly and the locust have classically been used …
The Role Of 53bp1 In Dna Double-Strand Break Repair, Anne Helen Bothmer
The Role Of 53bp1 In Dna Double-Strand Break Repair, Anne Helen Bothmer
Student Theses and Dissertations
DNA double-strand breaks (DSBs) are dangerous insults to DNA integrity and can lead to genome instability if left unrepaired. However, the immune cell diversification reactions V(D)J recombination and Class Switch Recombination (CSR) require the formation of DSB intermediates, a process that is tightly controlled and strictly limited to developing B and T cells. CSR in B cells diversifies antibodies by joining DSBs between highly repetitive DNA elements, which are separated by 60-200 kb. Switch region DSBs are joined by a mechanism that requires an intact DNA damage response and classical or alternative non-homologous end-joining (CNHEJ and A-NHEJ). Among DNA damage …
Structure-Function Analysis Of Insect Olfactory Receptors, Maurizio Pellegrino
Structure-Function Analysis Of Insect Olfactory Receptors, Maurizio Pellegrino
Student Theses and Dissertations
Organisms use their senses to transform external stimuli into an internal representation of the world. Insects employ their keen sense of smell for a variety of tasks including location of food sources, which can vary from yeast growing on ripe fruits for the vinegar fly Drosophila melanogaster to mammals for blood-feeding insects such as the mosquito Anopheles gambiae. The first informational relay between the external environment and the organism is the olfactory sensory neuron (OSN), whose activation translates the intensity, quality, and temporal features of volatile chemicals into spike trains. This dissertation focuses on understanding how the insect olfactory system …
Studies Of The Kinetics Of Cell Cycle Processes In S. Cerevisiae: The Molecular Basis Of Start Irreversibility And Cyclin-Cdk Ordering Of Mitotic Events, Catherine Oikonomou
Studies Of The Kinetics Of Cell Cycle Processes In S. Cerevisiae: The Molecular Basis Of Start Irreversibility And Cyclin-Cdk Ordering Of Mitotic Events, Catherine Oikonomou
Student Theses and Dissertations
The cell cycle machinery of Saccharomyces cerevisiae consists of a central negative feedback oscillator comprising cyclin-CDK and its antagonist, APCCdc20. This oscillator is stabilized and tuned by positive feedback loops, and its frequency is modulated by checkpoint controls. Either by directly triggering events, or by entraining independent oscillators controlling events, the cyclin-CDK oscillator regulates the key events of the cell cycle. These events have an established order and timing within the overall cycle. The work I describe in this thesis concerns two fundamental questions: how is the order and timing of cell cycle events controlled, and what sets the intrinsic …
Cell-Type Specific Translational Profiling In Huntington's Disease Mouse Models, Robert J. Fenster
Cell-Type Specific Translational Profiling In Huntington's Disease Mouse Models, Robert J. Fenster
Student Theses and Dissertations
Medium spiny neurons (MSNs) are among the most vulnerable cell populations in Huntington’s Disease (HD). Within this population, striatopallidal MSNs are more vulnerable than striatonigral MSNs, which may explain the typical progression in HD of chorea to hypokinesis. The biological basis for this differential vulnerability is unknown, although differences in transcriptional dysfunction caused by mutant huntingtin (mhtt) have been proposed as a possible mechanism. In order to determine the differences in gene expression caused by mhtt in these two populations, we selectively isolated translated mRNAs from striatopallidal and striatonigral MSNs in the R6-2 and YAC128 HD mouse models at pre- …
Assessing The Phylogenetic And Cultural Content Of Learned Song, Nicole Creanza
Assessing The Phylogenetic And Cultural Content Of Learned Song, Nicole Creanza
Student Theses and Dissertations
In the oscine songbirds, song is learned by a juvenile from a tutor of the same species, in a pattern that is analogous to human language, and likewise has the potential to change over time by cultural evolution. The similarities between human languages have been studied for centuries, but historically the relationships between the songs of birds of different species have been seen as too divergent to be useful. Using a computational analysis of song databases coupled with genetic phylogenies, I have shown that there is indeed a significant correlation between genetic distance and song similarity in the oscines. For …
Defining Gene Expression In Normal Human Epidermal Keratinocytes And Melanocytes: A Prerequisite For Understanding Hyperplastic And Neoplastic Pathology, Erika De Wyllie Billick
Defining Gene Expression In Normal Human Epidermal Keratinocytes And Melanocytes: A Prerequisite For Understanding Hyperplastic And Neoplastic Pathology, Erika De Wyllie Billick
Student Theses and Dissertations
To define pathologic alterations, a reference of "normal" cells is needed in order to interpret genomic methods that study gene expression of melanocytes and keratinocytes in growth-activated or neoplastic skin diseases. Historically, mRNAs isolated from cultured epidermal keratinocytes or melanocytes are used to define normal gene expression patterns. In this study, we profiled global gene expression in human epidermal keratinocytes on Affymetrix U133 plus 2.0 arrays from three different "normal" sources: 1) cultured keratinocytes, 2) FACS keratinocytes from dispase-separated epidermis, and 3) laser-capture microdissected (LCM) epidermis. For melanocytes, the precursor cell of melanoma, the attempt was made to isolate a …
Net Addition And Long-Term Survival Of Adult-Born Neurons In The Zebra Finch Hvc: Why Replace When You Can Keep Them All?, Clare Walton
Net Addition And Long-Term Survival Of Adult-Born Neurons In The Zebra Finch Hvc: Why Replace When You Can Keep Them All?, Clare Walton
Student Theses and Dissertations
The study of neurogenesis in adult songbirds focused initially on the canary, a species that learns new song elements each year. Many neurons in the canary song control nucleus, HVC, are discarded every year, with cell loss peaking at the end of the breeding season. New neurons numerically replace those that have died and this replacement process occurs at a time when vocal output is most plastic, suggesting adult neurogenesis may have a role in the learning process. It is not known, however, whether spontaneous neuronal replacement accompanies recruitment of new HVC neurons in the adult zebra finch, a species …
Sensory Organ Morphogenesis In Caenorhabditis Elegans, Grigorios Oikonomou
Sensory Organ Morphogenesis In Caenorhabditis Elegans, Grigorios Oikonomou
Student Theses and Dissertations
Sensory organs are the gates through which information flows into the nervous system. In most animals, such organs consist of sensory neurons, which can transform stimuli into changes in their membrane potential, and glial cells, which establish a niche important for the morphogenesis and function of the neurons. Although similar glial compartments are seen throughout the nervous system, their morphogenesis is poorly understood. In the work presented here, I use the main sensory organ of Caenorhabditis elegans, the amphid, as a model system for understanding how glia form these compartments. First, by the interpretation of electron microscopy reconstructions of the …
Mitotic Exit: Thresholds And Targets, Andrea Geoghegan Procko
Mitotic Exit: Thresholds And Targets, Andrea Geoghegan Procko
Student Theses and Dissertations
Cyclin dependent kinases (CDKs) are at the heart of the cell cycle. Throughout the cycle, these complexes modify many proteins, changing various aspects of their regulation (stability, localization, etc.). As cells exit mitosis, the CDK that has driven many of the cell cycle processes is inhibited and degraded, allowing many of the kinase substrates to return to their unphosphorylated state. This assures that each subsequent cell cycle is begun in the same naïve state, again ready for CDK-dependent regulation. The studies in this thesis focus on two mechanisms by which this restoration is accomplished in the budding yeast, Saccharomyces cerevisiae: …
Antigen Presentation : Influence Of Cell Type And Route Of Antigen Uptake, Alice O. Kamphorst
Antigen Presentation : Influence Of Cell Type And Route Of Antigen Uptake, Alice O. Kamphorst
Student Theses and Dissertations
"Dendritic cells (DCs), which maintain tolerance and orchestrate T cell immune responses, comprise a heterogeneous group of cells. For example, in the steady state, murine spleen contains pre-DC-derived CD8+DEC-205+ and CD8-DCIR2+ conventional DCs. To examine antigen processing and presentation in vivo, antigens were specifically targeted to CD8+ and CD8- DCs using chimeric monoclonal antibodies. We find that CD8- DCs are better than CD8- DCs for presentation of exogenous antigens onto major histocompatibility complex (MHC) class II molecules due to cell intrinsic differences. DCs are responsible for initiating T cell responses. However, during inflammation, monocytes become activated and acquire some DC-like …